Publications of Weitao Yang    :chronological  alphabetical  combined listing:

%% Books   
@book{fds24489,
   Author = {W. Yang},
   Title = {Special issue: Symposium on density functional and
             applications (Part I of II)},
   Journal = {Int. J. Quantum Chem.},
   Volume = {69},
   Year = {1998},
   Key = {fds24489}
}

@book{fds24404,
   Author = {R.G. Parr and W. Yang},
   Title = {Density-Functional Theory of Atoms and Molecules},
   Publisher = {Oxford University Press, New York},
   Year = {1989},
   Key = {fds24404}
}


%% Papers Accepted   
@article{fds235067,
   Author = {Ke, S-H and Baranger, HU and Yang, W},
   Title = {Molecular conductance: chemical trends of anchoring
             groups.},
   Journal = {Journal of the American Chemical Society},
   Volume = {126},
   Number = {48},
   Pages = {15897-15904},
   Year = {2004},
   Month = {December},
   ISSN = {0002-7863},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15571415},
   Abstract = {Combining density functional theory calculations for
             molecular electronic structure with a Green function method
             for electron transport, we calculate from first principles
             the molecular conductance of benzene connected to two Au
             leads through different anchoring atoms-S, Se, and Te. The
             relaxed atomic structure of the contact, different lead
             orientations, and different adsorption sites are fully
             considered. We find that the molecule-lead coupling,
             electron transfer, and conductance all depend strongly on
             the adsorption site, lead orientation, and local contact
             atomic configuration. For flat contacts the conductance
             decreases as the atomic number of the anchoring atom
             increases, regardless of the adsorption site, lead
             orientation, or bias. For small bias this chemical trend is,
             however, dependent on the contact atomic configuration: an
             additional Au atom at the contact with the (111) lead
             changes the best anchoring atom from S to Se, although for
             large bias the original chemical trend is
             recovered.},
   Doi = {10.1021/ja047367e},
   Key = {fds235067}
}

@article{fds235064,
   Author = {Cohen, AJ and Wu, Q and Yang, W},
   Title = {Calculation of nuclear magnetic resonance shielding
             constants using potential-based methods},
   Journal = {Chemical Physics Letters},
   Volume = {399},
   Number = {1-3},
   Pages = {84-88},
   Year = {2004},
   ISSN = {0009-2614},
   url = {http://dx.doi.org/10.1016/j.cplett.2004.09.112},
   Abstract = {We present the calculation of nuclear magnetic resonance
             shielding constants using a range of different methods. In
             particular we examine two new methods proposed by Yang and
             Wu which are based on the Kohn-Sham potential. The first is
             a method which reproduces an accurate input density (WY) and
             the second is an implementation of the optimised effective
             potential method. We find that these methods give results
             which are very similar to each other and when the methods
             are applied to a hybrid functional (e.g. B3LYP) we obtain
             good agreement with experiment. © 2004 Elsevier B.V. All
             rights reserved.},
   Doi = {10.1016/j.cplett.2004.09.112},
   Key = {fds235064}
}


%% Preprints   
@article{fds318096,
   Author = {Scholl, ZN and Li, Q and Yang, W and Marszalek, P},
   Title = {Single-Molecule Force-Spectroscopy Reveals the Calcium
             Dependency of Folding Intermediates in the Multidomain
             Protein S},
   Journal = {Biophysical Journal},
   Volume = {110},
   Number = {3},
   Pages = {393A-393A},
   Year = {2016},
   Month = {February},
   Key = {fds318096}
}

@article{fds313235,
   Author = {Wang, W and Li, Z and Yang, W},
   Title = {Angular momentum dependent field emission energy
             distribution},
   Journal = {IVNC 2015 - Technical Digest: 28th International Vacuum
             Nanoelectronics Conference},
   Pages = {30-31},
   Year = {2015},
   Month = {August},
   ISBN = {9781467393577},
   url = {http://dx.doi.org/10.1109/IVNC.2015.7225519},
   Abstract = {© 2015 IEEE. We developed a multi-scale time dependent
             density functional method to simulate electrons in
             semi-infinite long nano structures emitting into vacuum via
             the apex of nano structures. A relation between the field
             emission energy distribution and the angular momentum inside
             the single wall carbon nanotube is shown.},
   Doi = {10.1109/IVNC.2015.7225519},
   Key = {fds313235}
}

@article{fds318097,
   Author = {Scholl, ZN and Yang, W and Marszalek, P},
   Title = {N-terminal Domain Of Luciferase Controls Misfolding
             Avoidance},
   Journal = {Protein Science},
   Volume = {23},
   Pages = {249-249},
   Year = {2014},
   Month = {July},
   Key = {fds318097}
}

@article{fds318098,
   Author = {Yang, W},
   Title = {Mechanism of catalytic reactions and redox processes for
             solar fuel with multiscale QM/MM simulation},
   Journal = {ACS National Meeting Book of Abstracts},
   Volume = {246},
   Year = {2013},
   Month = {September},
   Key = {fds318098}
}

@article{fds318099,
   Author = {Yang, W},
   Title = {Progress in exchange-correlation energy functionals},
   Journal = {ACS National Meeting Book of Abstracts},
   Volume = {242},
   Year = {2011},
   Month = {August},
   Key = {fds318099}
}

@article{fds318101,
   Author = {Rinderspacher, BC and Beratan, DN and Yang, W},
   Title = {CINF 71-Inverse design of host-guest complexes in
             competitive binding problems},
   Journal = {ACS National Meeting Book of Abstracts},
   Volume = {236},
   Year = {2008},
   Month = {August},
   Key = {fds318101}
}

@article{fds324282,
   Author = {Cohen, AJ and Mori-Sanchez, P and Heaton-Burgess, T and Bulat, FA and Yang, W},
   Title = {COMP 436-Accurate density functionals addressing the
             self-interaction error and potential functional
             formalism},
   Journal = {ACS National Meeting Book of Abstracts},
   Volume = {234},
   Year = {2007},
   Month = {August},
   Key = {fds324282}
}

@article{fds313876,
   Author = {Yang, WT and Lu, ZY and Wang, ML},
   Title = {Reaction path potential for simulation of chemical reactions
             in enzymes derived from ab initio QM/MM calculations},
   Journal = {ACS National Meeting Book of Abstracts},
   Volume = {228},
   Pages = {U247-U247},
   Year = {2004},
   Month = {August},
   ISSN = {0065-7727},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000223713801267&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds313876}
}


%% Journal Articles   
@article{fds318090,
   Author = {Zhang, D and Yang, W},
   Title = {Accurate and efficient calculation of excitation energies
             with the active-space particle-particle random phase
             approximation.},
   Journal = {Journal of Chemical Physics},
   Volume = {145},
   Number = {14},
   Pages = {144105},
   Year = {2016},
   Month = {October},
   url = {http://dx.doi.org/10.1063/1.4964501},
   Abstract = {An efficient method for calculating excitation energies
             based on the particle-particle random phase approximation
             (ppRPA) is presented. Neglecting the contributions from the
             high-lying virtual states and the low-lying core states
             leads to the significantly smaller active-space ppRPA matrix
             while keeping the error to within 0.05 eV from the
             corresponding full ppRPA excitation energies. The resulting
             computational cost is significantly reduced and becomes less
             than the construction of the non-local Fock exchange
             potential matrix in the self-consistent-field (SCF)
             procedure. With only a modest number of active orbitals, the
             original ppRPA singlet-triplet (ST) gaps as well as the
             low-lying single and double excitation energies can be
             accurately reproduced at much reduced computational costs,
             up to 100 times faster than the iterative Davidson
             diagonalization of the original full ppRPA matrix. For
             high-lying Rydberg excitations where the Davidson algorithm
             fails, the computational savings of active-space ppRPA with
             respect to the direct diagonalization is even more dramatic.
             The virtues of the underlying full ppRPA combined with the
             significantly lower computational cost of the active-space
             approach will significantly expand the applicability of the
             ppRPA method to calculate excitation energies at a cost of
             O(K4), with a prefactor much smaller than a single SCF
             Hartree-Fock (HF)/hybrid functional calculation, thus
             opening up new possibilities for the quantum mechanical
             study of excited state electronic structure of large
             systems.},
   Doi = {10.1063/1.4964501},
   Key = {fds318090}
}

@article{fds318091,
   Author = {Shen, L and Wu, J and Yang, W},
   Title = {Multiscale Quantum Mechanics/Molecular Mechanics Simulations
             with Neural Networks.},
   Journal = {Journal of Chemical Theory and Computation},
   Year = {2016},
   Month = {September},
   Abstract = {Molecular dynamics simulation with multiscale quantum
             mechanics/molecular mechanics (QM/MM) methods is a very
             powerful tool for understanding the mechanism of chemical
             and biological processes in solution or enzymes. However,
             its computational cost can be too high for many biochemical
             systems because of the large number of ab initio QM
             calculations. Semiempirical QM/MM simulations have much
             higher efficiency. Its accuracy can be improved with a
             correction to reach the ab initio QM/MM level. The
             computational cost on the ab initio calculation for the
             correction determines the efficiency. In this paper we
             developed a neural network method for QM/MM calculation as
             an extension of the neural-network representation reported
             by Behler and Parrinello. With this approach, the potential
             energy of any configuration along the reaction path for a
             given QM/MM system can be predicted at the ab initio QM/MM
             level based on the semiempirical QM/MM simulations. We
             further applied this method to three reactions in water to
             calculate the free energy changes. The free-energy profile
             obtained from the semiempirical QM/MM simulation is
             corrected to the ab initio QM/MM level with the potential
             energies predicted with the constructed neural network. The
             results are in excellent accordance with the reference data
             that are obtained from the ab initio QM/MM molecular
             dynamics simulation or corrected with direct ab initio QM/MM
             potential energies. Compared with the correction using
             direct ab initio QM/MM potential energies, our method shows
             a speed-up of 1 or 2 orders of magnitude. It demonstrates
             that the neural network method combined with the
             semiempirical QM/MM calculation can be an efficient and
             reliable strategy for chemical reaction simulations.},
   Key = {fds318091}
}

@article{fds318092,
   Author = {Yang, Y and Davidson, ER and Yang, W},
   Title = {Nature of ground and electronic excited states of higher
             acenes.},
   Journal = {Proceedings of the National Academy of Sciences of
             USA},
   Volume = {113},
   Number = {35},
   Pages = {E5098-E5107},
   Year = {2016},
   Month = {August},
   url = {http://dx.doi.org/10.1073/pnas.1606021113},
   Abstract = {Higher acenes have drawn much attention as promising organic
             semiconductors with versatile electronic properties.
             However, the nature of their ground state and electronic
             excited states is still not fully clear. Their unusual
             chemical reactivity and instability are the main obstacles
             for experimental studies, and the potentially prominent
             diradical character, which might require a multireference
             description in such large systems, hinders theoretical
             investigations. Here, we provide a detailed answer with the
             particle-particle random-phase approximation calculation.
             The (1)Ag ground states of acenes up to decacene are on the
             closed-shell side of the diradical continuum, whereas the
             ground state of undecacene and dodecacene tilts more to the
             open-shell side with a growing polyradical character. The
             ground state of all acenes has covalent nature with respect
             to both short and long axes. The lowest triplet state (3)B2u
             is always above the singlet ground state even though the
             energy gap could be vanishingly small in the polyacene
             limit. The bright singlet excited state (1)B2u is a
             zwitterionic state to the short axis. The excited (1)Ag
             state gradually switches from a double-excitation state to
             another zwitterionic state to the short axis, but always
             keeps its covalent nature to the long axis. An energy
             crossing between the (1)B2u and excited (1)Ag states happens
             between hexacene and heptacene. Further energetic
             consideration suggests that higher acenes are likely to
             undergo singlet fission with a low photovoltaic efficiency;
             however, the efficiency might be improved if a singlet
             fission into multiple triplets could be achieved.},
   Doi = {10.1073/pnas.1606021113},
   Key = {fds318092}
}

@article{fds318093,
   Author = {Scholl, ZN and Li, Q and Yang, W and Marszalek, PE},
   Title = {Single-molecule Force Spectroscopy Reveals the Calcium
             Dependence of the Alternative Conformations in the Native
             State of a βγ-Crystallin Protein.},
   Journal = {The Journal of biological chemistry},
   Volume = {291},
   Number = {35},
   Pages = {18263-18275},
   Year = {2016},
   Month = {August},
   url = {http://dx.doi.org/10.1074/jbc.m116.729525},
   Abstract = {Although multidomain proteins predominate the proteome of
             all organisms and are expected to display complex folding
             behaviors and significantly greater structural dynamics as
             compared with single-domain proteins, their conformational
             heterogeneity and its impact on their interaction with
             ligands are poorly understood due to a lack of experimental
             techniques. The multidomain calcium-binding βγ-crystallin
             proteins are particularly important because their
             deterioration and misfolding/aggregation are associated with
             melanoma tumors and cataracts. Here we investigate the
             mechanical stability and conformational dynamics of a model
             calcium-binding βγ-crystallin protein, Protein S, and
             elaborate on its interactions with calcium. We ask whether
             domain interactions and calcium binding affect Protein S
             folding and potential structural heterogeneity. Our results
             from single-molecule force spectroscopy show that the
             N-terminal (but not the C-terminal) domain is in equilibrium
             with an alternative conformation in the absence of Ca(2+),
             which is mechanically stable in contrast to other proteins
             that were observed to sample a molten globule under similar
             conditions. Mutagenesis experiments and computer simulations
             reveal that the alternative conformation of the N-terminal
             domain is caused by structural instability produced by the
             high charge density of a calcium binding site. We find that
             this alternative conformation in the N-terminal domain is
             diminished in the presence of calcium and can also be
             partially eliminated with a hitherto unrecognized
             compensatory mechanism that uses the interaction of the
             C-terminal domain to neutralize the electronegative site. We
             find that up to 1% of all identified multidomain
             calcium-binding proteins contain a similarly highly charged
             site and therefore may exploit a similar compensatory
             mechanism to prevent structural instability in the absence
             of ligand.},
   Doi = {10.1074/jbc.m116.729525},
   Key = {fds318093}
}

@article{fds318094,
   Author = {Yang, Y and Shen, L and Zhang, D and Yang, W},
   Title = {Conical Intersections from Particle-Particle Random Phase
             and Tamm-Dancoff Approximations.},
   Journal = {Journal of Physical Chemistry Letters},
   Volume = {7},
   Number = {13},
   Pages = {2407-2411},
   Year = {2016},
   Month = {July},
   url = {http://dx.doi.org/10.1021/acs.jpclett.6b00936},
   Abstract = {The particle-particle random phase approximation (pp-RPA)
             and the particle-particle Tamm-Dancoff approximation
             (pp-TDA) are applied to the challenging conical intersection
             problem. Because they describe the ground and excited states
             on the same footing and naturally take into account the
             interstate interaction, these particle-particle methods,
             especially the pp-TDA, can correctly predict the
             dimensionality of the conical intersection seam as well as
             describe the potential energy surface in the vicinity of
             conical intersections. Though the bond length of conical
             intersections is slightly underestimated compared with the
             complete-active-space self-consistent field (CASSCF) theory,
             the efficient particle-particle methods are promising for
             conical intersections and nonadiabatic dynamics.},
   Doi = {10.1021/acs.jpclett.6b00936},
   Key = {fds318094}
}

@article{fds318095,
   Author = {Wang, H and Yang, W},
   Title = {Determining polarizable force fields with electrostatic
             potentials from quantum mechanical linear response
             theory.},
   Journal = {Journal of Chemical Physics},
   Volume = {144},
   Number = {22},
   Pages = {224107},
   Year = {2016},
   Month = {June},
   url = {http://dx.doi.org/10.1063/1.4953558},
   Abstract = {We developed a new method to calculate the atomic
             polarizabilities by fitting to the electrostatic potentials
             (ESPs) obtained from quantum mechanical (QM) calculations
             within the linear response theory. This parallels the
             conventional approach of fitting atomic charges based on
             electrostatic potentials from the electron density. Our ESP
             fitting is combined with the induced dipole model under the
             perturbation of uniform external electric fields of all
             orientations. QM calculations for the linear response to the
             external electric fields are used as input, fully consistent
             with the induced dipole model, which itself is a linear
             response model. The orientation of the uniform external
             electric fields is integrated in all directions. The
             integration of orientation and QM linear response
             calculations together makes the fitting results independent
             of the orientations and magnitudes of the uniform external
             electric fields applied. Another advantage of our method is
             that QM calculation is only needed once, in contrast to the
             conventional approach, where many QM calculations are needed
             for many different applied electric fields. The molecular
             polarizabilities obtained from our method show comparable
             accuracy with those from fitting directly to the
             experimental or theoretical molecular polarizabilities.
             Since ESP is directly fitted, atomic polarizabilities
             obtained from our method are expected to reproduce the
             electrostatic interactions better. Our method was used to
             calculate both transferable atomic polarizabilities for
             polarizable molecular mechanics' force fields and
             nontransferable molecule-specific atomic
             polarizabilities.},
   Doi = {10.1063/1.4953558},
   Key = {fds318095}
}

@article{fds328034,
   Author = {Yang, Y and Burke, K and Yang, W},
   Title = {Accurate atomic quantum defects from particle–particle
             random phase approximation},
   Journal = {Molecular Physics},
   Volume = {114},
   Number = {7-8},
   Pages = {1189-1198},
   Year = {2016},
   Month = {April},
   url = {http://dx.doi.org/10.1080/00268976.2015.1123316},
   Doi = {10.1080/00268976.2015.1123316},
   Key = {fds328034}
}

@article{fds315418,
   Author = {Rupakheti, C and Al-Saadon, R and Zhang, Y and Virshup, AM and Zhang, P and Yang, W and Beratan, DN},
   Title = {Diverse Optimal Molecular Libraries for Organic
             Light-Emitting Diodes.},
   Journal = {Journal of Chemical Theory and Computation},
   Volume = {12},
   Number = {4},
   Pages = {1942-1952},
   Year = {2016},
   Month = {April},
   ISSN = {1549-9618},
   url = {http://dx.doi.org/10.1021/acs.jctc.5b00829},
   Abstract = {Organic light-emitting diodes (OLEDs) have wide-ranging
             applications, from lighting to device displays. However, the
             repertoire of organic molecules with efficient blue emission
             is limited. To address this limitation, we have developed a
             strategy to design property-optimized, diversity-oriented
             libraries of structures with favorable fluorescence
             properties. This approach identifies novel diverse candidate
             organic molecules for blue emission with strong oscillator
             strengths and low singlet-triplet energy gaps that favor
             thermally activated delayed fluorescence (TADF)
             emission.},
   Doi = {10.1021/acs.jctc.5b00829},
   Key = {fds315418}
}

@article{fds315417,
   Author = {Shen, L and Yang, W},
   Title = {Quantum Mechanics/Molecular Mechanics Method Combined with
             Hybrid All-Atom and Coarse-Grained Model: Theory and
             Application on Redox Potential Calculations.},
   Journal = {Journal of Chemical Theory and Computation},
   Volume = {12},
   Number = {4},
   Pages = {2017-2027},
   Year = {2016},
   Month = {April},
   ISSN = {1549-9618},
   url = {http://dx.doi.org/10.1021/acs.jctc.5b01107},
   Abstract = {We developed a new multiresolution method that spans three
             levels of resolution with quantum mechanical, atomistic
             molecular mechanical, and coarse-grained models. The
             resolution-adapted all-atom and coarse-grained water model,
             in which an all-atom structural description of the entire
             system is maintained during the simulations, is combined
             with the ab initio quantum mechanics and molecular mechanics
             method. We apply this model to calculate the redox
             potentials of the aqueous ruthenium and iron complexes by
             using the fractional number of electrons approach and
             thermodynamic integration simulations. The redox potentials
             are recovered in excellent accordance with the experimental
             data. The speed-up of the hybrid all-atom and coarse-grained
             water model renders it computationally more attractive. The
             accuracy depends on the hybrid all-atom and coarse-grained
             water model used in the combined quantum mechanical and
             molecular mechanical method. We have used another
             multiresolution model, in which an atomic-level layer of
             water molecules around redox center is solvated in
             supramolecular coarse-grained waters for the redox potential
             calculations. Compared with the experimental data, this
             alternative multilayer model leads to less accurate results
             when used with the coarse-grained polarizable MARTINI water
             or big multipole water model for the coarse-grained
             layer.},
   Doi = {10.1021/acs.jctc.5b01107},
   Key = {fds315417}
}

@article{fds313236,
   Author = {Li, C and Lu, J and Yang, W},
   Title = {Gentlest ascent dynamics for calculating first excited state
             and exploring energy landscape of Kohn-Sham density
             functionals.},
   Journal = {Journal of Chemical Physics},
   Volume = {143},
   Number = {22},
   Pages = {224110},
   Year = {2015},
   Month = {December},
   ISSN = {0021-9606},
   url = {http://dx.doi.org/10.1063/1.4936411},
   Abstract = {We develop the gentlest ascent dynamics for Kohn-Sham
             density functional theory to search for the index-1 saddle
             points on the energy landscape of the Kohn-Sham density
             functionals. These stationary solutions correspond to
             excited states in the ground state functionals. As shown by
             various examples, the first excited states of many chemical
             systems are given by these index-1 saddle points. Our novel
             approach provides an alternative, more robust way to obtain
             these excited states, compared with the widely used ΔSCF
             approach. The method can be easily generalized to target
             higher index saddle points. Our results also reveal the
             physical interest and relevance of studying the Kohn-Sham
             energy landscape.},
   Doi = {10.1063/1.4936411},
   Key = {fds313236}
}

@article{fds320121,
   Author = {Zheng, X and Li, C and Zhang, D and Yang, W},
   Title = {Scaling correction approaches for reducing delocalization
             error in density functional approximations},
   Journal = {Science China Chemistry},
   Volume = {58},
   Number = {12},
   Pages = {1825-1844},
   Year = {2015},
   Month = {December},
   url = {http://dx.doi.org/10.1007/s11426-015-5501-z},
   Doi = {10.1007/s11426-015-5501-z},
   Key = {fds320121}
}

@article{fds234850,
   Author = {Yang, Y and Peng, D and Davidson, ER and Yang, W},
   Title = {Singlet-triplet energy gaps for diradicals from
             particle-particle random phase approximation.},
   Journal = {The Journal of Physical Chemistry Part A: Molecules,
             Spectroscopy, Kinetics, Environment and General
             Theory},
   Volume = {119},
   Number = {20},
   Pages = {4923-4932},
   Year = {2015},
   Month = {May},
   ISSN = {1089-5639},
   url = {http://dx.doi.org/10.1021/jp512727a},
   Abstract = {The particle-particle random phase approximation (pp-RPA)
             for calculating excitation energies has been applied to
             diradical systems. With pp-RPA, the two nonbonding electrons
             are treated in a subspace configuration interaction fashion
             while the remaining part is described by density functional
             theory (DFT). The vertical or adiabatic singlet-triplet
             energy gaps for a variety of categories of diradicals,
             including diatomic diradicals, carbene-like diradicals,
             disjoint diradicals, four-π-electron diradicals, and
             benzynes are calculated. Except for some excitations in
             four-π-electron diradicals, where four-electron correlation
             may play an important role, the singlet-triplet gaps are
             generally well predicted by pp-RPA. With a relatively low
             O(r(4)) scaling, the pp-RPA with DFT references outperforms
             spin-flip configuration interaction singles. It is similar
             to or better than the (variational) fractional-spin method.
             For small diradicals such as diatomic and carbene-like ones,
             the error of pp-RPA is slightly larger than noncollinear
             spin-flip time-dependent density functional theory
             (NC-SF-TDDFT) with LDA or PBE functional. However, for
             disjoint diradicals and benzynes, the pp-RPA performs much
             better and is comparable to NC-SF-TDDFT with long-range
             corrected ωPBEh functional and spin-flip configuration
             interaction singles with perturbative doubles (SF-CIS(D)).
             In particular, with a correct asymptotic behavior and being
             almost free from static correlation error, the pp-RPA with
             DFT references can well describe the challenging ground
             state and charge transfer excitations of disjoint diradicals
             in which almost all other DFT-based methods fail. Therefore,
             the pp-RPA could be a promising theoretical method for
             general diradical problems.},
   Doi = {10.1021/jp512727a},
   Key = {fds234850}
}

@article{fds234851,
   Author = {Zhang, D and Zheng, X and Li, C and Yang, W},
   Title = {Orbital relaxation effects on Kohn-Sham frontier orbital
             energies in density functional theory.},
   Journal = {Journal of Chemical Physics},
   Volume = {142},
   Number = {15},
   Pages = {154113},
   Year = {2015},
   Month = {April},
   ISSN = {0021-9606},
   url = {http://dx.doi.org/10.1063/1.4918347},
   Abstract = {We explore effects of orbital relaxation on Kohn-Sham
             frontier orbital energies in density functional theory by
             using a nonempirical scaling correction approach developed
             in Zheng et al. [J. Chem. Phys. 138, 174105 (2013)].
             Relaxation of Kohn-Sham orbitals upon addition/removal of a
             fractional number of electrons to/from a finite system is
             determined by a systematic perturbative treatment. The
             information of orbital relaxation is then used to improve
             the accuracy of predicted Kohn-Sham frontier orbital
             energies by Hartree-Fock, local density approximation, and
             generalized gradient approximation methods. The results
             clearly highlight the significance of capturing the orbital
             relaxation effects. Moreover, the proposed scaling
             correction approach provides a useful way of computing
             derivative gaps and Fukui quantities of N-electron finite
             systems (N is an integer), without the need to perform
             self-consistent-field calculations for (N ± 1)-electron
             systems.},
   Doi = {10.1063/1.4918347},
   Key = {fds234851}
}

@article{fds234852,
   Author = {Li, S and Hu, L and Peng, L and Yang, W and Gu, FL},
   Title = {Coupled-Perturbed SCF Approach for Calculating Static
             Polarizabilities and Hyperpolarizabilities with
             Nonorthogonal Localized Molecular Orbitals.},
   Journal = {Journal of Chemical Theory and Computation},
   Volume = {11},
   Number = {3},
   Pages = {923-931},
   Year = {2015},
   Month = {March},
   ISSN = {1549-9618},
   url = {http://dx.doi.org/10.1021/ct500889k},
   Abstract = {Coupled-perturbed self-consistent-field (CPSCF) approach has
             been broadly used for polarizabilities and
             hyperpolarizabilities computation. To extend this
             application to large systems, we have reformulated the CPSCF
             equations with nonorthogonal localized molecular orbitals
             (NOLMOs). NOLMOs are the most localized representation of
             electronic degrees of freedom. Methods based on NOLMOs are
             potentially ideal for investigating large systems. In atomic
             orbital representation, with a static external electric
             field added, the wave function and SCF operator of
             unperturbed NOLMO-SCF wave function/orbitals are expanded to
             different orders of perturbations. We have derived the
             corresponding equations up to the third order, which are
             significantly different from those of a conventional CPSCF
             method because of the release of the orthogonal restrictions
             on MOs. The solution to these equations has been
             implemented. Several chemical systems are used to verify our
             method. This work represents the first step toward efficient
             calculations of molecular response and excitation properties
             with NOLMOs.},
   Doi = {10.1021/ct500889k},
   Key = {fds234852}
}

@article{fds234853,
   Author = {Rupakheti, C and Virshup, A and Yang, W and Beratan,
             DN},
   Title = {Strategy to discover diverse optimal molecules in the small
             molecule universe.},
   Journal = {Journal of Chemical Information and Modeling},
   Volume = {55},
   Number = {3},
   Pages = {529-537},
   Year = {2015},
   Month = {March},
   ISSN = {1549-9596},
   url = {http://dx.doi.org/10.1021/ci500749q},
   Abstract = {The small molecule universe (SMU) is defined as a set of
             over 10(60) synthetically feasible organic molecules with
             molecular weight less than ∼500 Da. Exhaustive
             enumerations and evaluation of all SMU molecules for the
             purpose of discovering favorable structures is impossible.
             We take a stochastic approach and extend the ACSESS
             framework ( Virshup et al. J. Am. Chem. Soc. 2013 , 135 ,
             7296 - 7303 ) to develop diversity oriented molecular
             libraries that can generate a set of compounds that is
             representative of the small molecule universe and that also
             biases the library toward favorable physical property
             values. We show that the approach is efficient compared to
             exhaustive enumeration and to existing evolutionary
             algorithms for generating such libraries by testing in the
             NKp fitness landscape model and in the fully enumerated
             GDB-9 chemical universe containing 3 × 10(5)
             molecules.},
   Doi = {10.1021/ci500749q},
   Key = {fds234853}
}

@article{fds234854,
   Author = {Scholl, ZN and Yang, W and Marszalek, PE},
   Title = {Direct observation of multimer stabilization in the
             mechanical unfolding pathway of a protein undergoing
             oligomerization.},
   Journal = {ACS Nano},
   Volume = {9},
   Number = {2},
   Pages = {1189-1197},
   Year = {2015},
   Month = {February},
   ISSN = {1936-0851},
   url = {http://dx.doi.org/10.1021/nn504686f},
   Abstract = {Understanding how protein oligomerization affects the
             stability of monomers in self-assembled structures is
             crucial to the development of new protein-based
             nanomaterials and protein cages for drug delivery. Here, we
             use single-molecule force spectroscopy (AFM-SMFS), protein
             engineering, and computer simulations to evaluate how
             dimerization and tetramerization affects the stability of
             the monomer of Streptavidin, a model homotetrameric protein.
             The unfolding force directly relates to the folding
             stability, and we find that monomer of Streptavidin is
             mechanically stabilized by 40% upon dimerization, and that
             it is stabilized an additional 24% upon tetramerization. We
             also find that biotin binding increases stability by another
             50% as compared to the apo-tetrameric form. We used the
             distribution of unfolding forces to extract properties of
             the underlying energy landscape and found that the distance
             to the transition state is decreased and the barrier height
             is increased upon multimerization. Finally, we investigated
             the origin of the strengthening by ligand binding. We found
             that, rather than being strengthened through intramolecular
             contacts, it is strengthened due to the contacts provided by
             the biotin-binding loop that crosses the interface between
             the dimers.},
   Doi = {10.1021/nn504686f},
   Key = {fds234854}
}

@article{fds234855,
   Author = {Li, C and Zheng, X and Cohen, AJ and Mori-Sánchez, P and Yang,
             W},
   Title = {Local scaling correction for reducing delocalization error
             in density functional approximations.},
   Journal = {Physical Review Letters},
   Volume = {114},
   Number = {5},
   Pages = {053001},
   Year = {2015},
   Month = {February},
   ISSN = {0031-9007},
   url = {http://dx.doi.org/10.1103/physrevlett.114.053001},
   Abstract = {Delocalization error is one of the most fundamental and
             dominant errors that plagues presently used density
             functional approximations. It is responsible for a large
             class of problems in the density functional theory
             calculations. For an effective and universal alleviation of
             the delocalization error, we develop a local scaling
             correction scheme by imposing the Perdew-Parr-Levy- Balduz
             linearity condition to local regions of a system. Our novel
             scheme is applicable to various mainstream density
             functional approximations. It substantially reduces the
             delocalization error, as exemplified by the significantly
             improved description of dissociating molecules,
             transition-state species, and charge-transfer systems. The
             usefulness of our novel scheme affirms that the explicit
             treatment of fractional electron distributions is
             essentially important for reducing the intrinsic
             delocalization error associated with approximate density
             functionals.},
   Doi = {10.1103/physrevlett.114.053001},
   Key = {fds234855}
}

@article{fds234849,
   Author = {Scholl, ZN and Yang, W and Marszalek, PE},
   Title = {Chaperones rescue luciferase folding by separating its
             domains.},
   Journal = {The Journal of biological chemistry},
   Volume = {290},
   Number = {2},
   Pages = {883-883},
   Year = {2015},
   Month = {January},
   ISSN = {0021-9258},
   url = {http://dx.doi.org/10.1074/jbc.A114.582049},
   Doi = {10.1074/jbc.A114.582049},
   Key = {fds234849}
}

@article{fds234857,
   Author = {Zhang, D and Peng, D and Zhang, P and Yang, W},
   Title = {Analytic gradients, geometry optimization and excited state
             potential energy surfaces from the particle-particle random
             phase approximation.},
   Journal = {Physical Chemistry Chemical Physics},
   Volume = {17},
   Number = {2},
   Pages = {1025-1038},
   Year = {2015},
   Month = {January},
   ISSN = {1463-9076},
   url = {http://dx.doi.org/10.1039/c4cp04109g},
   Abstract = {The energy gradient for electronic excited states is of
             immense interest not only for spectroscopy but also for the
             theoretical study of photochemical reactions. We present the
             analytic excited state energy gradient of the
             particle-particle random phase approximation (pp-RPA). The
             analytic gradient formula is developed from an approach
             similar to that of time-dependent density-functional theory
             (TDDFT). The formula is verified for both the Hartree-Fock
             and (Generalized) Kohn-Sham reference states via comparison
             with finite difference results. The excited state potential
             energy surfaces and optimized geometries of some small
             molecules are investigated, yielding results of similar or
             better quality compared to adiabatic TDDFT. The
             singlet-to-triplet instability in TDDFT resulting in
             underestimated energies of the lowest triplet states is
             eliminated by pp-RPA. Charge transfer excitations and double
             excitations, which are challenging for most adiabatic TDDFT
             methods, can be reasonably well captured by pp-RPA. Within
             this framework, ground state potential energy surfaces of
             stretched single bonds can also be described
             well.},
   Doi = {10.1039/c4cp04109g},
   Key = {fds234857}
}

@article{fds234856,
   Author = {Peng, D and Yang, Y and Zhang, P and Yang, W},
   Title = {Restricted second random phase approximations and
             Tamm-Dancoff approximations for electronic excitation energy
             calculations.},
   Journal = {Journal of Chemical Physics},
   Volume = {141},
   Number = {21},
   Pages = {214102},
   Year = {2014},
   Month = {December},
   ISSN = {0021-9606},
   url = {http://dx.doi.org/10.1063/1.4901716},
   Abstract = {In this article, we develop systematically second random
             phase approximations (RPA) and Tamm-Dancoff approximations
             (TDA) of particle-hole and particle-particle channels for
             calculating molecular excitation energies. The second
             particle-hole RPA/TDA can capture double excitations missed
             by the particle-hole RPA/TDA and time-dependent
             density-functional theory (TDDFT), while the second
             particle-particle RPA/TDA recovers non-highest-occupied-molecular-orbital
             excitations missed by the particle-particle RPA/TDA. With
             proper orbital restrictions, these restricted second RPAs
             and TDAs have a formal scaling of only O(N(4)). The
             restricted versions of second RPAs and TDAs are tested with
             various small molecules to show some positive results. Data
             suggest that the restricted second particle-hole TDA
             (r2ph-TDA) has the best overall performance with a
             correlation coefficient similar to TDDFT, but with a larger
             negative bias. The negative bias of the r2ph-TDA may be
             induced by the unaccounted ground state correlation energy
             to be investigated further. Overall, the r2ph-TDA is
             recommended to study systems with both single and some
             low-lying double excitations with a moderate accuracy. Some
             expressions on excited state property evaluations, such as
             ⟨Ŝ(2)⟩ are also developed and tested.},
   Doi = {10.1063/1.4901716},
   Key = {fds234856}
}

@article{fds324281,
   Author = {Guo, H and Xie, D and Yang, W},
   Title = {A tribute to Guosen Yan},
   Journal = {Theoretical Chemistry Accounts},
   Volume = {133},
   Number = {12},
   Year = {2014},
   Month = {December},
   url = {http://dx.doi.org/10.1007/s00214-014-1581-7},
   Doi = {10.1007/s00214-014-1581-7},
   Key = {fds324281}
}

@article{fds234858,
   Author = {Su, NQ and Yang, W and Mori-Sánchez, P and Xu, X},
   Title = {Fractional charge behavior and band gap predictions with the
             XYG3 type of doubly hybrid density functionals.},
   Journal = {The Journal of Physical Chemistry Part A: Molecules,
             Spectroscopy, Kinetics, Environment and General
             Theory},
   Volume = {118},
   Number = {39},
   Pages = {9201-9211},
   Year = {2014},
   Month = {October},
   ISSN = {1089-5639},
   url = {http://dx.doi.org/10.1021/jp5029992},
   Abstract = {In this work, we examine the fractional charge behaviors of
             doubly hybrid (DH) functionals. By plotting the ground-state
             energies E and energy derivatives for atoms and molecules
             with fractional electron numbers N, we directly quantify the
             delocalization errors of some representative DH functionals
             such as B2PLYP, XYG3, and XYGJ-OS. Numerical assessments on
             ionization potentials (IPs), electron affinities (EAs), and
             fundamental gaps, from either integer number calculations or
             energy derivative calculations, are provided. It is shown
             that the XYG3 type of DH functionals gives good agreement
             between their energy derivatives and the experimental IPs,
             EAs, and gaps, as expected from their nearly straight line
             fractional charge behaviors.},
   Doi = {10.1021/jp5029992},
   Key = {fds234858}
}

@article{fds234860,
   Author = {Scholl, ZN and Yang, W and Marszalek, PE},
   Title = {Chaperones rescue luciferase folding by separating its
             domains.},
   Journal = {The Journal of biological chemistry},
   Volume = {289},
   Number = {41},
   Pages = {28607-28618},
   Year = {2014},
   Month = {October},
   ISSN = {0021-9258},
   url = {http://dx.doi.org/10.1074/jbc.m114.582049},
   Abstract = {Over the last 50 years, significant progress has been made
             toward understanding how small single-domain proteins fold.
             However, very little is known about folding mechanisms of
             medium and large multidomain proteins that predominate the
             proteomes of all forms of life. Large proteins frequently
             fold cotranslationally and/or require chaperones. Firefly
             (Photinus pyralis) luciferase (Luciferase, 550 residues) has
             been a model of a cotranslationally folding protein whose
             extremely slow refolding (approximately days) is catalyzed
             by chaperones. However, the mechanism by which Luciferase
             misfolds and how chaperones assist Luciferase refolding
             remains unknown. Here we combine single-molecule force
             spectroscopy (atomic force microscopy (AFM)/single-molecule
             force spectroscopy) with steered molecular dynamic computer
             simulations to unravel the mechanism of chaperone-assisted
             Luciferase refolding. Our AFM and steered molecular dynamic
             results show that partially unfolded Luciferase, with the
             N-terminal domain remaining folded, can refold robustly
             without chaperones. Complete unfolding causes Luciferase to
             get trapped in very stable non-native configurations
             involving interactions between N- and C-terminal residues.
             However, chaperones allow the completely unfolded Luciferase
             to refold quickly in AFM experiments, strongly suggesting
             that chaperones are able to sequester non-natively
             contacting residues. More generally, we suggest that many
             chaperones, rather than actively promoting the folding,
             mimic the ribosomal exit tunnel and physically separate
             protein domains, allowing them to fold in a
             cotranslational-like sequential process.},
   Doi = {10.1074/jbc.m114.582049},
   Key = {fds234860}
}

@article{fds234859,
   Author = {Yang, Y and Peng, D and Lu, J and Yang, W},
   Title = {Excitation energies from particle-particle random phase
             approximation: Davidson algorithm and benchmark
             studies.},
   Journal = {Journal of Chemical Physics},
   Volume = {141},
   Number = {12},
   Pages = {124104},
   Year = {2014},
   Month = {September},
   ISSN = {0021-9606},
   url = {http://dx.doi.org/10.1063/1.4895792},
   Abstract = {The particle-particle random phase approximation (pp-RPA)
             has been used to investigate excitation problems in our
             recent paper [Y. Yang, H. van Aggelen, and W. Yang, J. Chem.
             Phys. 139, 224105 (2013)]. It has been shown to be capable
             of describing double, Rydberg, and charge transfer
             excitations, which are challenging for conventional
             time-dependent density functional theory (TDDFT). However,
             its performance on larger molecules is unknown as a result
             of its expensive O(N(6)) scaling. In this article, we derive
             and implement a Davidson iterative algorithm for the pp-RPA
             to calculate the lowest few excitations for large systems.
             The formal scaling is reduced to O(N(4)), which is
             comparable with the commonly used configuration interaction
             singles (CIS) and TDDFT methods. With this iterative
             algorithm, we carried out benchmark tests on molecules that
             are significantly larger than the molecules in our previous
             paper with a reasonably large basis set. Despite some
             self-consistent field convergence problems with ground state
             calculations of (N - 2)-electron systems, we are able to
             accurately capture lowest few excitations for systems with
             converged calculations. Compared to CIS and TDDFT, there is
             no systematic bias for the pp-RPA with the mean signed error
             close to zero. The mean absolute error of pp-RPA with B3LYP
             or PBE references is similar to that of TDDFT, which
             suggests that the pp-RPA is a comparable method to TDDFT for
             large molecules. Moreover, excitations with relatively large
             non-HOMO excitation contributions are also well described in
             terms of excitation energies, as long as there is also a
             relatively large HOMO excitation contribution. These
             findings, in conjunction with the capability of pp-RPA for
             describing challenging excitations shown earlier, further
             demonstrate the potential of pp-RPA as a reliable and
             general method to describe excitations, and to be a good
             alternative to TDDFT methods.},
   Doi = {10.1063/1.4895792},
   Key = {fds234859}
}

@article{fds234861,
   Author = {Li, Y and Nese, A and Hu, X and Lebedeva, NV and LaJoie, TW and Burdyńska,
             J and Stefan, MC and You, W and Yang, W and Matyjaszewski, K and Sheiko,
             SS},
   Title = {Shifting Electronic Structure by Inherent Tension in
             Molecular Bottlebrushes with Polythiophene
             Backbones},
   Journal = {ACS Macro Letters},
   Volume = {3},
   Number = {8},
   Pages = {738-742},
   Year = {2014},
   Month = {August},
   ISSN = {2161-1653},
   url = {http://dx.doi.org/10.1021/mz5003323},
   Doi = {10.1021/mz5003323},
   Key = {fds234861}
}

@article{fds234862,
   Author = {Shenvi, N and van Aggelen, H and Yang, Y and Yang,
             W},
   Title = {Tensor hypercontracted ppRPA: reducing the cost of the
             particle-particle random phase approximation from O(r(6)) to
             O(r(4)).},
   Journal = {Journal of Chemical Physics},
   Volume = {141},
   Number = {2},
   Pages = {024119},
   Year = {2014},
   Month = {July},
   ISSN = {0021-9606},
   url = {http://dx.doi.org/10.1063/1.4886584},
   Abstract = {In recent years, interest in the random-phase approximation
             (RPA) has grown rapidly. At the same time, tensor
             hypercontraction has emerged as an intriguing method to
             reduce the computational cost of electronic structure
             algorithms. In this paper, we combine the particle-particle
             random phase approximation with tensor hypercontraction to
             produce the tensor-hypercontracted particle-particle RPA
             (THC-ppRPA) algorithm. Unlike previous implementations of
             ppRPA which scale as O(r(6)), the THC-ppRPA algorithm scales
             asymptotically as only O(r(4)), albeit with a much larger
             prefactor than the traditional algorithm. We apply THC-ppRPA
             to several model systems and show that it yields the same
             results as traditional ppRPA to within mH accuracy. Our
             method opens the door to the development of post-Kohn Sham
             functionals based on ppRPA without the excessive asymptotic
             cost of traditional ppRPA implementations.},
   Doi = {10.1063/1.4886584},
   Key = {fds234862}
}

@article{fds234869,
   Author = {Yang, W},
   Title = {Preface: Special topic on advances in density functional
             theory.},
   Journal = {Journal of Chemical Physics},
   Volume = {140},
   Number = {18},
   Pages = {18A101},
   Year = {2014},
   Month = {May},
   ISSN = {0021-9606},
   url = {http://dx.doi.org/10.1063/1.4872309},
   Abstract = {This Special Topic Issue on the Advances in Density
             Functional Theory, published as a celebration of the fifty
             years of density functional theory, contains a retrospective
             article, a perspective article, and a collection of original
             research articles that showcase recent theoretical advances
             in the field. It provides a timely discussion reflecting a
             cross section of our understanding, and the theoretical and
             computational developments, which have significant
             implications in broad areas of sciences and
             engineering.},
   Doi = {10.1063/1.4872309},
   Key = {fds234869}
}

@article{fds234870,
   Author = {van Aggelen, H and Yang, Y and Yang, W},
   Title = {Exchange-correlation energy from pairing matrix fluctuation
             and the particle-particle random phase approximation.},
   Journal = {Journal of Chemical Physics},
   Volume = {140},
   Number = {18},
   Pages = {18A511},
   Year = {2014},
   Month = {May},
   ISSN = {0021-9606},
   url = {http://dx.doi.org/10.1063/1.4865816},
   Abstract = {Despite their unmatched success for many applications,
             commonly used local, semi-local, and hybrid density
             functionals still face challenges when it comes to
             describing long-range interactions, static correlation, and
             electron delocalization. Density functionals of both the
             occupied and virtual orbitals are able to address these
             problems. The particle-hole (ph-) Random Phase Approximation
             (RPA), a functional of occupied and virtual orbitals, has
             recently known a revival within the density functional
             theory community. Following up on an idea introduced in our
             recent communication [H. van Aggelen, Y. Yang, and W. Yang,
             Phys. Rev. A 88, 030501 (2013)], we formulate more general
             adiabatic connections for the correlation energy in terms of
             pairing matrix fluctuations described by the
             particle-particle (pp-) propagator. With numerical examples
             of the pp-RPA, the lowest-order approximation to the
             pp-propagator, we illustrate the potential of density
             functional approximations based on pairing matrix
             fluctuations. The pp-RPA is size-extensive, self-interaction
             free, fully anti-symmetric, describes the strong static
             correlation limit in H2, and eliminates delocalization
             errors in H2(+) and other single-bond systems. It gives
             surprisingly good non-bonded interaction
             energies--competitive with the ph-RPA--with the correct
             R(-6) asymptotic decay as a function of the separation R,
             which we argue is mainly attributable to its correct
             second-order energy term. While the pp-RPA tends to
             underestimate absolute correlation energies, it gives good
             relative energies: much better atomization energies than the
             ph-RPA, as it has no tendency to underbind, and reaction
             energies of similar quality. The adiabatic connection in
             terms of pairing matrix fluctuation paves the way for
             promising new density functional approximations.},
   Doi = {10.1063/1.4865816},
   Key = {fds234870}
}

@article{fds234871,
   Author = {Peng, D and van Aggelen, H and Yang, Y and Yang, W},
   Title = {Linear-response time-dependent density-functional theory
             with pairing fields.},
   Journal = {Journal of Chemical Physics},
   Volume = {140},
   Number = {18},
   Pages = {18A522},
   Year = {2014},
   Month = {May},
   ISSN = {0021-9606},
   url = {http://dx.doi.org/10.1063/1.4867540},
   Abstract = {Recent development in particle-particle random phase
             approximation (pp-RPA) broadens the perspective on ground
             state correlation energies [H. van Aggelen, Y. Yang, and W.
             Yang, Phys. Rev. A 88, 030501 (2013), Y. Yang, H. van
             Aggelen, S. N. Steinmann, D. Peng, and W. Yang, J. Chem.
             Phys. 139, 174110 (2013); D. Peng, S. N. Steinmann, H. van
             Aggelen, and W. Yang, J. Chem. Phys. 139, 104112 (2013)] and
             N ± 2 excitation energies [Y. Yang, H. van Aggelen, and W.
             Yang, J. Chem. Phys. 139, 224105 (2013)]. So far
             Hartree-Fock and approximated density-functional orbitals
             have been utilized to evaluate the pp-RPA equation. In this
             paper, to further explore the fundamentals and the potential
             use of pairing matrix dependent functionals, we present the
             linear-response time-dependent density-functional theory
             with pairing fields with both adiabatic and
             frequency-dependent kernels. This theory is related to the
             density-functional theory and time-dependent
             density-functional theory for superconductors, but is
             applied to normal non-superconducting systems for our
             purpose. Due to the lack of the proof of the one-to-one
             mapping between the pairing matrix and the pairing field for
             time-dependent systems, the linear-response theory is
             established based on the representability assumption of the
             pairing matrix. The linear response theory justifies the use
             of approximated density-functionals in the pp-RPA equation.
             This work sets the fundamentals for future
             density-functional development to enhance the description of
             ground state correlation energies and N ± 2 excitation
             energies.},
   Doi = {10.1063/1.4867540},
   Key = {fds234871}
}

@article{fds234872,
   Author = {Chaudret, R and Contreras-Garcia, J and Delcey, M and Parisel, O and Yang, W and Piquemal, J-P},
   Title = {Revisiting H2O Nucleation around Au(+) and Hg(2+): The
             Peculiar "Pseudo-Soft" Character of the Gold
             Cation.},
   Journal = {Journal of Chemical Theory and Computation},
   Volume = {10},
   Number = {5},
   Pages = {1900-1909},
   Year = {2014},
   Month = {May},
   ISSN = {1549-9618},
   url = {http://dx.doi.org/10.1021/ct4006135},
   Abstract = {In this contribution, we propose a deeper understanding of
             the electronic effects affecting the nucleation of water
             around the Au(+) and Hg(2+) metal cations using quantum
             chemistry. To do so, and in order to go beyond usual
             energetical studies, we make extensive use of state of the
             art quantum interpretative techniques combining
             ELF/NCI/QTAIM/EDA computations to capture all ranges of
             interactions stabilizing the well characterized
             microhydrated structures. The Electron Localization Function
             (ELF) topological analysis reveals the peculiar role of the
             Au+ outer-shell core electrons (subvalence) that appear
             already spatially preorganized once the addition of the
             first water molecule occurs. Thus, despite the addition of
             other water molecules, the electronic structure of
             Au(H2O)(+) appears frozen due to relativistic effects
             leading to a maximal acceptation of only two waters in
             gold's first hydration shell. As the values of the QTAIM
             (Quantum Theory of Atoms in Molecules) cations's charge is
             discussed, the Non Covalent Interactions (NCI) analysis
             showed that Au(+) appears still able to interact through
             longer range van der Waals interaction with the third or
             fourth hydration shell water molecules. As these types of
             interaction are not characteristic of either a hard or soft
             metal cation, we introduced the concept of a "pseudo-soft"
             cation to define Au(+) behavior. Then, extending the study,
             we performed the same computations replacing Au(+) with
             Hg(2+), an isoelectronic cation. If Hg(2+) behaves like
             Au(+) for small water clusters, a topological, geometrical,
             and energetical transition appears when the number of water
             molecules increases. Regarding the HSAB theory, this
             transition is characteristic of a shift of Hg(2+) from a
             pseudosoft form to a soft ion and appears to be due to a
             competition between the relativistic and correlation
             effects. Indeed, if relativistic effects are predominant,
             then mercury will behave like gold and have a similar
             subvalence/geometry; otherwise when correlation effects are
             predominant, Hg(2+) behaves like a soft cation.},
   Doi = {10.1021/ct4006135},
   Key = {fds234872}
}

@article{fds234873,
   Author = {Yu, Y and Huang, S-Y and Li, Y and Steinmann, SN and Yang, W and Cao,
             L},
   Title = {Layer-Dependent Electrocatalysis of MoS 2 for Hydrogen
             Evolution},
   Journal = {Nano Letters},
   Volume = {14},
   Number = {2},
   Pages = {553-558},
   Year = {2014},
   Month = {February},
   ISSN = {1530-6984},
   url = {http://dx.doi.org/10.1021/nl403620g},
   Doi = {10.1021/nl403620g},
   Key = {fds234873}
}

@article{fds234874,
   Author = {Franks, AT and Peng, D and Yang, W and Franz, KJ},
   Title = {Characterization of a photoswitching chelator with
             light-modulated geometric, electronic, and metal-binding
             properties.},
   Journal = {Inorganic Chemistry},
   Volume = {53},
   Number = {3},
   Pages = {1397-1405},
   Year = {2014},
   Month = {February},
   ISSN = {0020-1669},
   url = {http://dx.doi.org/10.1021/ic402221x},
   Abstract = {Photoswitching molecules are utilized for a variety of
             applications where the rapid manipulation of the molecules'
             chemical properties and spatial orientations allows for new
             spatiotemporal control over molecular-scale interactions and
             processes. Here, we present a hydrazone-containing
             transition metal chelator, HAPI ((E)-N'-[1-(2-hydroxyphenyl)ethyliden]isonicotinoylhydrazide),
             that displays dual-wavelength photoswitching behavior.
             Several of its metal complexes, however, are inert to
             photoreaction and thereby add another layer of control over
             the photoswitch system. The light-induced twist in HAPI
             structure is accompanied by a dramatic change in electronic
             properties as well as chelator strength. This work
             introduces HAPI as the prototype for a class of molecules
             with properties that may be optimized for a variety of
             experimental applications that take advantage of
             phototriggered molecular changes.},
   Doi = {10.1021/ic402221x},
   Key = {fds234874}
}

@article{fds234868,
   Author = {Yang, Y and Van Aggelen and H and Yang, W},
   Title = {Double, Rydberg and charge transfer excitations from pairing
             matrix fluctuation and particle-particle random phase
             approximation},
   Journal = {Journal of Chemical Physics},
   Volume = {139},
   Number = {22},
   Year = {2013},
   Month = {December},
   ISSN = {0021-9606},
   url = {http://dx.doi.org/10.1063/1.4834875},
   Abstract = {Double, Rydberg, and charge transfer (CT) excitations have
             been great challenges for time-dependent density functional
             theory (TDDFT). Starting from an (N ± 2)-electron
             single-determinant reference, we investigate excitations for
             the N-electron system through the pairing matrix
             fluctuation, which contains information on two-electron
             addition/removal processes. We adopt the particle-particle
             random phase approximation (pp-RPA) and the
             particle-particle Tamm-Dancoff approximation (pp-TDA) to
             approximate the pairing matrix fluctuation and then
             determine excitation energies by the differences of
             two-electron addition/removal energies. This approach
             captures all types of interesting excitations: single and
             double excitations are described accurately, Rydberg
             excitations are in good agreement with experimental data and
             CT excitations display correct 1/R dependence. Furthermore,
             the pp-RPA and the pp-TDA have a computational cost similar
             to TDDFT and consequently are promising for practical
             calculations. © 2013 AIP Publishing LLC.},
   Doi = {10.1063/1.4834875},
   Key = {fds234868}
}

@article{fds234875,
   Author = {Yang, Y and van Aggelen, H and Yang, W},
   Title = {Double, Rydberg and charge transfer excitations from pairing
             matrix fluctuation and particle-particle random phase
             approximation.},
   Journal = {Journal of Chemical Physics},
   Volume = {139},
   Number = {22},
   Pages = {224105},
   Year = {2013},
   Month = {December},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/24329054},
   Abstract = {Double, Rydberg, and charge transfer (CT) excitations have
             been great challenges for time-dependent density functional
             theory (TDDFT). Starting from an (N ± 2)-electron
             single-determinant reference, we investigate excitations for
             the N-electron system through the pairing matrix
             fluctuation, which contains information on two-electron
             addition/removal processes. We adopt the particle-particle
             random phase approximation (pp-RPA) and the
             particle-particle Tamm-Dancoff approximation (pp-TDA) to
             approximate the pairing matrix fluctuation and then
             determine excitation energies by the differences of
             two-electron addition/removal energies. This approach
             captures all types of interesting excitations: single and
             double excitations are described accurately, Rydberg
             excitations are in good agreement with experimental data and
             CT excitations display correct 1/R dependence. Furthermore,
             the pp-RPA and the pp-TDA have a computational cost similar
             to TDDFT and consequently are promising for practical
             calculations.},
   Doi = {10.1063/1.4834875},
   Key = {fds234875}
}

@article{fds234876,
   Author = {Yang, Y and van Aggelen, H and Steinmann, SN and Peng, D and Yang,
             W},
   Title = {Benchmark tests and spin adaptation for the
             particle-particle random phase approximation.},
   Journal = {Journal of Chemical Physics},
   Volume = {139},
   Number = {17},
   Pages = {174110},
   Year = {2013},
   Month = {November},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/24206290},
   Abstract = {The particle-particle random phase approximation (pp-RPA)
             provides an approximation to the correlation energy in
             density functional theory via the adiabatic connection [H.
             van Aggelen, Y. Yang, and W. Yang, Phys. Rev. A 88, 030501
             (2013)]. It has virtually no delocalization error nor static
             correlation error for single-bond systems. However, with its
             formal O(N(6)) scaling, the pp-RPA is computationally
             expensive. In this paper, we implement a spin-separated and
             spin-adapted pp-RPA algorithm, which reduces the
             computational cost by a substantial factor. We then perform
             benchmark tests on the G2/97 enthalpies of formation
             database, DBH24 reaction barrier database, and four test
             sets for non-bonded interactions (HB6/04, CT7/04, DI6/04,
             and WI9/04). For the G2/97 database, the pp-RPA gives a
             significantly smaller mean absolute error (8.3 kcal/mol)
             than the direct particle-hole RPA (ph-RPA) (22.7 kcal/mol).
             Furthermore, the error in the pp-RPA is nearly constant with
             the number of atoms in a molecule, while the error in the
             ph-RPA increases. For chemical reactions involving typical
             organic closed-shell molecules, pp- and ph-RPA both give
             accurate reaction energies. Similarly, both RPAs perform
             well for reaction barriers and nonbonded interactions. These
             results suggest that the pp-RPA gives reliable energies in
             chemical applications. The adiabatic connection formalism
             based on pairing matrix fluctuation is therefore expected to
             lead to widely applicable and accurate density
             functionals.},
   Doi = {10.1063/1.4828728},
   Key = {fds234876}
}

@article{fds234879,
   Author = {Zhang, D and Steinmann, SN and Yang, W},
   Title = {Dynamical second-order Bethe-Salpeter equation kernel: a
             method for electronic excitation beyond the adiabatic
             approximation.},
   Journal = {Journal of Chemical Physics},
   Volume = {139},
   Number = {15},
   Pages = {154109},
   Year = {2013},
   Month = {October},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/24160502},
   Abstract = {We present a dynamical second-order kernel for the
             Bethe-Salpeter equation to calculate electronic excitation
             energies. The derivation takes explicitly the functional
             derivative of the exact second-order self energy with
             respect to the one-particle Green's function. It includes
             naturally a frequency dependence, going beyond the adiabatic
             approximation. Perturbative calculations under the
             Tamm-Dancoff approximation, using the configuration
             interaction singles (CIS) eigenvectors, reveal an
             appreciable improvement over CIS, time-dependent
             Hartree-Fock, and adiabatic time-dependent density
             functional theory results. The perturbative results also
             compare well with equation-of-motion coupled-cluster and
             experimental results.},
   Doi = {10.1063/1.4824907},
   Key = {fds234879}
}

@article{fds234881,
   Author = {Peng, D and Steinmann, SN and van Aggelen, H and Yang,
             W},
   Title = {Equivalence of particle-particle random phase approximation
             correlation energy and ladder-coupled-cluster
             doubles.},
   Journal = {Journal of Chemical Physics},
   Volume = {139},
   Number = {10},
   Pages = {104112},
   Year = {2013},
   Month = {September},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/24050333},
   Abstract = {The recent proposal to determine the (exact) correlation
             energy based on pairing matrix fluctuations by van Aggelen
             et al. ["Exchange-correlation energy from pairing matrix
             fluctuation and the particle-particle random phase
             approximation," preprint arXiv:1306.4957 (2013)] revived the
             interest in the simplest approximation along this path: the
             particle-particle random phase approximation (pp-RPA). In
             this paper, we present an analytical connection and
             numerical demonstrations of the equivalence of the
             correlation energy from pp-RPA and ladder-coupled-cluster
             doubles. These two theories reduce to identical algebraic
             matrix equations and correlation energy expressions. The
             numerical examples illustrate that the correlation energy
             missed by pp-RPA in comparison with coupled-cluster singles
             and doubles is largely canceled out when considering
             reaction energies. This theoretical connection will be
             beneficial to design density functionals with strong ties to
             coupled-cluster theories and to study molecular properties
             at the pp-RPA level relying on well established coupled
             cluster techniques.},
   Doi = {10.1063/1.4820556},
   Key = {fds234881}
}

@article{fds234882,
   Author = {Yang, W and Mori-Sánchez, P and Cohen, AJ},
   Title = {Extension of many-body theory and approximate density
             functionals to fractional charges and fractional
             spins.},
   Journal = {Journal of Chemical Physics},
   Volume = {139},
   Number = {10},
   Pages = {104114},
   Year = {2013},
   Month = {September},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/24050335},
   Abstract = {The exact conditions for density functionals and density
             matrix functionals in terms of fractional charges and
             fractional spins are known, and their violation in commonly
             used functionals has been shown to be the root of many major
             failures in practical applications. However, approximate
             functionals are designed for physical systems with integer
             charges and spins, not in terms of the fractional variables.
             Here we develop a general framework for extending
             approximate density functionals and many-electron theory to
             fractional-charge and fractional-spin systems. Our
             development allows for the fractional extension of any
             approximate theory that is a functional of G(0), the
             one-electron Green's function of the non-interacting
             reference system. The extension to fractional charge and
             fractional spin systems is based on the ensemble average of
             the basic variable, G(0). We demonstrate the fractional
             extension for the following theories: (1) any explicit
             functional of the one-electron density, such as the local
             density approximation and generalized gradient
             approximations; (2) any explicit functional of the
             one-electron density matrix of the non-interacting reference
             system, such as the exact exchange functional (or
             Hartree-Fock theory) and hybrid functionals; (3) many-body
             perturbation theory; and (4) random-phase approximations. A
             general rule for such an extension has also been derived
             through scaling the orbitals and should be useful for
             functionals where the link to the Green's function is not
             obvious. The development thus enables the examination of
             approximate theories against known exact conditions on the
             fractional variables and the analysis of their failures in
             chemical and physical applications in terms of violations of
             exact conditions of the energy functionals. The present work
             should facilitate the calculation of chemical potentials and
             fundamental bandgaps with approximate functionals and
             many-electron theories through the energy derivatives with
             respect to the fractional charge. It should play an
             important role in developing accurate approximate density
             functionals and many-body theory.},
   Doi = {10.1063/1.4817183},
   Key = {fds234882}
}

@article{fds234884,
   Author = {Steinmann, SN and Yang, W},
   Title = {Wave function methods for fractional electrons.},
   Journal = {Journal of Chemical Physics},
   Volume = {139},
   Number = {7},
   Pages = {074107},
   Year = {2013},
   Month = {August},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23968072},
   Abstract = {Determining accurate chemical potentials is of considerable
             interest in various chemical and physical contexts: from
             small molecular charge-transfer complexes to bandgap in bulk
             materials such as semi-conductors. Chemical potentials are
             typically evaluated either by density functional theory, or,
             alternatively, by computationally more intensive Greens
             function based GW computations. To calculate chemical
             potentials, the ground state energy needs to be defined for
             fractional charges. We thus explore an extension of wave
             function theories to fractional charges, and investigate the
             ionization potential and electron affinity as the
             derivatives of the energy with respect to the electron
             number. The ultimate aim is to access the chemical potential
             of correlated wave function methods without the need of
             explicitly changing the numbers of electrons, making the
             approach readily applicable to bulk materials. We find that
             even though second order perturbation theory reduces the
             fractional charge error considerably compared to
             Hartree-Fock and standard density functionals, higher order
             perturbation theory is more accurate and coupled-cluster
             approaches are even more robust, provided the electrons are
             bound at the Hartree-Fock level. The success of post-HF
             approaches to improve over HF relies on two equally
             important aspects: the integer values are more accurate and
             the Coulomb correlation between the fractionally occupied
             orbital and all others improves the straight line behavior
             significantly as identified by a correction to Hartree-Fock.
             Our description of fractional electrons is also applicable
             to fractional spins, illustrating the ability of
             coupled-cluster singles and doubles to deal with two
             degenerate fractionally occupied orbitals, but its
             inadequacy for three and more fractional spins, which occur,
             for instance, for spherical atoms and when dissociating
             double bonds. Our approach explores the realm of typical
             wave function methods that are applied mostly in molecular
             chemistry, but become available to the solid state community
             and offer the advantage of an integrated approach:
             fundamental gap, relative energies, and optimal geometries
             can be obtained at the same level.},
   Doi = {10.1063/1.4817849},
   Key = {fds234884}
}

@article{fds234885,
   Author = {Wang, J and Yang, W},
   Title = {Concerted proton transfer mechanism of Clostridium
             thermocellum ribose-5-phosphate isomerase.},
   Journal = {The Journal of Physical Chemistry Part B: Condensed Matter,
             Materials, Surfaces, Interfaces and Biophysical},
   Volume = {117},
   Number = {32},
   Pages = {9354-9361},
   Year = {2013},
   Month = {August},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23875675},
   Abstract = {Ribose-5-phosphate isomerase (Rpi) catalyzes the
             interconversion of D-ribose-5-phosphate and
             D-ribulose-5-phosphate and plays an essential role in the
             pentose phosphate pathway and the Calvin cycle of
             photosynthesis. RpiB, one of the two isoforms of Rpi, is
             also a potential drug target for some pathogenic bacteria.
             Clostridium thermocellum ribose-5-phosphate isomerase
             (CtRpi), belonging to the RpiB family, has recently been
             employed in the industrial production of rare sugars because
             of its fast reaction kinetics and narrow substrate
             specificity. It is known that this enzyme adopts a proton
             transfer mechanism. It was suggested that the deprotonated
             Cys65 attracts the proton at C2 of the substrate to initiate
             the isomerization reaction, and this step is the
             rate-limiting step. However the elaborate catalytic
             mechanism is still unclear. We have performed quantum
             mechanical/molecular mechanical simulations of this
             rate-limiting step of the reaction catalyzed by CtRpi with
             the substrate D-ribose. Our results demonstrate that the
             deprotonated Cys65 is not a stable reactant. Instead, our
             calculations revealed a concerted proton-transfer mechanism:
             Asp8, a highly conserved residue in the RpiB family,
             performs as the base to abstract the proton at Cys65 and
             Cys65 in turn abstracting the proton of the D-ribose
             simultaneously. Moreover, we found Thr67 cannot catalyze the
             proton transfer from O2 to O1 of the D-ribose alone. Water
             molecule(s) may assist this proton transfer with Thr67. Our
             findings lead to a clear understanding of the catalysis
             mechanism of the RpiB family and should guide experiments to
             increase the catalysis efficiency. This study also
             highlights the importance of initial protonation states of
             cysteines.},
   Doi = {10.1021/jp404948c},
   Key = {fds234885}
}

@article{fds234886,
   Author = {Shenvi, N and van Aggelen, H and Yang, Y and Yang, W and Schwerdtfeger,
             C and Mazziotti, D},
   Title = {The tensor hypercontracted parametric reduced density matrix
             algorithm: coupled-cluster accuracy with O(r(4))
             scaling.},
   Journal = {Journal of Chemical Physics},
   Volume = {139},
   Number = {5},
   Pages = {054110},
   Year = {2013},
   Month = {August},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23927246},
   Abstract = {Tensor hypercontraction is a method that allows the
             representation of a high-rank tensor as a product of
             lower-rank tensors. In this paper, we show how tensor
             hypercontraction can be applied to both the electron
             repulsion integral tensor and the two-particle excitation
             amplitudes used in the parametric 2-electron reduced density
             matrix (p2RDM) algorithm. Because only O(r) auxiliary
             functions are needed in both of these approximations, our
             overall algorithm can be shown to scale as O(r(4)), where r
             is the number of single-particle basis functions. We apply
             our algorithm to several small molecules, hydrogen chains,
             and alkanes to demonstrate its low formal scaling and
             practical utility. Provided we use enough auxiliary
             functions, we obtain accuracy similar to that of the
             standard p2RDM algorithm, somewhere between that of CCSD and
             CCSD(T).},
   Doi = {10.1063/1.4817184},
   Key = {fds234886}
}

@article{fds234889,
   Author = {Virshup, AM and Contreras-García, J and Wipf, P and Yang, W and Beratan, DN},
   Title = {Stochastic voyages into uncharted chemical space produce a
             representative library of all possible drug-like
             compounds.},
   Journal = {Journal of the American Chemical Society},
   Volume = {135},
   Number = {19},
   Pages = {7296-7303},
   Year = {2013},
   Month = {May},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23548177},
   Abstract = {The "small molecule universe" (SMU), the set of all
             synthetically feasible organic molecules of 500 Da molecular
             weight or less, is estimated to contain over 10(60)
             structures, making exhaustive searches for structures of
             interest impractical. Here, we describe the construction of
             a "representative universal library" spanning the SMU that
             samples the full extent of feasible small molecule
             chemistries. This library was generated using the newly
             developed Algorithm for Chemical Space Exploration with
             Stochastic Search (ACSESS). ACSESS makes two important
             contributions to chemical space exploration: it allows the
             systematic search of the unexplored regions of the small
             molecule universe, and it facilitates the mining of chemical
             libraries that do not yet exist, providing a near-infinite
             source of diverse novel compounds.},
   Doi = {10.1021/ja401184g},
   Key = {fds234889}
}

@article{fds234891,
   Author = {Peng, D and Yang, W},
   Title = {Fukui function and response function for nonlocal and
             fractional systems.},
   Journal = {Journal of Chemical Physics},
   Volume = {138},
   Number = {18},
   Pages = {184108},
   Year = {2013},
   Month = {May},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23676030},
   Abstract = {We present extensions to our previous work on Fukui
             functions and linear-response functions [W. Yang, A. J.
             Cohen, F. D. Proft, and P. Geerlings, J. Chem. Phys. 136,
             144110 (2012)]. Viewed as energy derivatives with respect to
             the number of electrons and the external potential, all
             second-order derivatives (the linear-response function, the
             Fukui function, and the chemical hardness) are extended to
             fractional systems, and all third-order derivatives (the
             second-order response function, the Fukui response function,
             the dual descriptor, and the hyperhardness) for integer
             systems are also obtained. These analytical derivatives are
             verified by finite difference numerical derivatives. In the
             context of the exact linearity condition and the constancy
             condition, these analytical derivatives enrich greatly the
             information of the exact conditions on the energy functional
             through establishing real-space dependency. The introduction
             of an external nonlocal potential defines the nonlocal Fukui
             function and the nonlocal linear-response function. The
             nonlocal linear-response function so defined also provides
             the precise meaning for the time-dependent linear-response
             density-functional theory calculations with generalized
             Kohn-Sham functionals. These extensions will be useful to
             conceptual density-functional theory and density functional
             development.},
   Doi = {10.1063/1.4803101},
   Key = {fds234891}
}

@article{fds313879,
   Author = {Scholl, ZN and Yang, W and Marszalek, PE},
   Title = {Improving Single Molecule Force Spectroscopy through
             Automated Real-Time Data Collection and Quantification of
             Experimental Conditions},
   Journal = {Biophysical Journal},
   Volume = {104},
   Number = {2},
   Pages = {512A-512A},
   Year = {2013},
   Month = {January},
   ISSN = {0006-3495},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000316074305106&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds313879}
}

@article{fds234893,
   Author = {Chaudret, R and Parks, JM and Yang, W},
   Title = {Pseudobond parameters for QM/MM studies involving
             nucleosides, nucleotides, and their analogs.},
   Journal = {Journal of Chemical Physics},
   Volume = {138},
   Number = {4},
   Pages = {045102},
   Year = {2013},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23387624},
   Abstract = {In biological systems involving nucleosides, nucleotides, or
             their respective analogs, the ribose sugar moiety is the
             most common reaction site, for example, during DNA
             replication and repair. However, nucleic bases, which
             comprise a sizable portion of nucleotide molecules, are
             usually unreactive during such processes. In quantum
             mechanical∕molecular simulations of nucleic acid
             reactivity, it may therefore be advantageous to describe
             specific ribosyl or ribosyl phosphate groups quantum
             mechanically and their respective nucleic bases with a
             molecular mechanics potential function. Here, we have
             extended the pseudobond approach to enable quantum
             mechanical∕molecular mechanical simulations involving
             nucleotides, nucleosides, and their analogs in which the
             interface between the two subsystems is located between the
             sugar and the base, namely, the C(sp(3))-N(sp(2)) bond. The
             pseudobond parameters were optimized on a training set of 10
             molecules representing several nucleotide and nucleoside
             bases and analogs, and they were then tested on a larger
             test set of 20 diverse molecules. Particular emphasis was
             placed on providing accurate geometries and electrostatic
             properties, including electrostatic potential, natural bond
             orbital (NBO) and atoms in molecules (AIM) charges and AIM
             first moments. We also tested the optimized parameters on
             five nucleotide and nucleoside analogues of pharmaceutical
             relevance and a small polypeptide (triglycine). Accuracy was
             maintained for these systems, which highlights the
             generality and transferability of the pseudobond
             approach.},
   Doi = {10.1063/1.4772182},
   Key = {fds234893}
}

@article{fds234877,
   Author = {Aggelen, HV and Yang, Y and Yang, W},
   Title = {Exchange-correlation energy from pairing matrix fluctuation
             and the particle-particle random-phase approximation},
   Journal = {Physical Review A - Atomic, Molecular, and Optical
             Physics},
   Volume = {88},
   Number = {3},
   Pages = {030501},
   Year = {2013},
   ISSN = {1050-2947},
   url = {http://dx.doi.org/10.1103/PhysRevA.88.030501},
   Abstract = {We formulate an adiabatic connection for the
             exchange-correlation energy in terms of pairing matrix
             fluctuation. This connection opens new channels for density
             functional approximations based on pairing interactions.
             Even the simplest approximation to the pairing matrix
             fluctuation, the particle-particle random phase
             approximation (pp-RPA), has some highly desirable
             properties. It has no delocalization error with a nearly
             linear energy behavior for systems with fractional charges,
             describes van der Waals interactions similarly and
             thermodynamic properties significantly better than
             particle-hole RPA, and eliminates static correlation error
             for single-bond systems. Most significantly, the pp-RPA is
             the first known functional that has an explicit and
             closed-form dependence on the occupied and unoccupied
             orbitals and captures the energy derivative discontinuity in
             strongly correlated systems. These findings illustrate the
             potential of including pairing interactions within a density
             functional framework. © 2013 American Physical
             Society.},
   Doi = {10.1103/PhysRevA.88.030501},
   Key = {fds234877}
}

@article{fds234880,
   Author = {Peng, L and Gu, FL and Yang, W},
   Title = {Effective preconditioning for ab initio ground state energy
             minimization with non-orthogonal localized molecular
             orbitals},
   Journal = {Physical Chemistry Chemical Physics},
   Volume = {15},
   Number = {37},
   Pages = {15518-15527},
   Year = {2013},
   ISSN = {1463-9076},
   url = {http://dx.doi.org/10.1039/c3cp52989d},
   Abstract = {The non-orthogonal localized molecular orbital (NOLMO) is
             the most localized representation of electronic degrees of
             freedom. As such, NOLMOs are thus potentially the most
             efficient for linear-scaling calculations of electronic
             structures for large systems. However, direct ab initio
             calculations with NOLMO have not been fully implemented and
             widely used, partly because of the slow convergence issue in
             the optimization of NOLMO. Towards realizing the potential
             of NOLMO for large systems, we applied an energy minimum
             variational principle for carrying out ab initio
             self-consistent-field (SCF) calculations with NOLMOs. We
             developed an effective preconditioning approach using the
             diagonal part of the second order derivatives and show that
             the convergence of the energy optimization is significantly
             improved. The speed of convergence of the energy and density
             are comparable with that of the conventional SCF approach,
             thus paving the way for the optimization of NOLMO in linear
             scaling calculations for large systems. This journal is ©
             2013 the Owner Societies.},
   Doi = {10.1039/c3cp52989d},
   Key = {fds234880}
}

@article{fds234883,
   Author = {Jin, Y and Johnson, ER and Hu, X and Yang, W and Hu,
             H},
   Title = {Contributions of Pauli repulsions to the energetics and
             physical properties computed in QM/MM methods},
   Journal = {Journal of Computational Chemistry},
   Volume = {34},
   Number = {27},
   Pages = {2380-2388},
   Year = {2013},
   ISSN = {0192-8651},
   url = {http://dx.doi.org/10.1002/jcc.23401},
   Abstract = {Conventional combined quantum mechanical/molecular
             mechanical (QM/MM) methods lack explicit treatment of Pauli
             repulsions between the quantum-mechanical and
             molecular-mechanical subsystems. Instead, classical
             Lennard-Jones (LJ) potentials between QM and MM nuclei are
             used to model electronic Pauli repulsion and long-range
             London dispersion, despite the fact that the latter two are
             inherently of quantum nature. Use of the simple LJ potential
             in QM/MM methods can reproduce minimal geometries and
             energies of many molecular clusters reasonably well, as
             compared to full QM calculations. However, we show here that
             the LJ potential cannot correctly describe subtle details of
             the electron density of the QM subsystem because of the
             neglect of Pauli repulsions between the QM and MM
             subsystems. The inaccurate electron density subsequently
             affects the calculation of electronic and magnetic
             properties of the QM subsystem. To explicitly consider Pauli
             interactions with QM/MM methods, we propose a method to use
             empirical effective potentials on the MM atoms. The test
             case of the binding energy and magnetic properties of a
             water dimer shows promising results for the general
             application of effective potentials to mimic Pauli
             repulsions in QM/MM calculations. © 2013 Wiley Periodicals,
             Inc.},
   Doi = {10.1002/jcc.23401},
   Key = {fds234883}
}

@article{fds234887,
   Author = {Zheng, X and Zhou, T and Yang, W},
   Title = {A nonempirical scaling correction approach for density
             functional methods involving substantial amount of
             Hartree-Fock exchange},
   Journal = {Journal of Chemical Physics},
   Volume = {138},
   Number = {17},
   Pages = {174105},
   Year = {2013},
   ISSN = {0021-9606},
   url = {http://dx.doi.org/10.1063/1.4801922},
   Abstract = {A nonempirical scaling correction (SC) approach has been
             developed for improving bandgap prediction in density
             functional theory [X. Zheng, A. J. Cohen, P. Mori-Sánchez,
             X. Hu, and W. Yang, Phys. Rev. Lett. 107, 026403
             (2011)10.1103/PhysRevLett.107.026403]. For finite systems
             such as atoms and molecules, the SC approach restores the
             Perdew-Parr-Levy-Balduz condition [Phys. Rev. Lett. 49, 1691
             (1982)10.1103/PhysRevLett.49.1691] that the total electronic
             energy should scale linearly with number of electrons
             between integers. Although the original SC approach is
             applicable to a variety of mainstream density functional
             approximations, it gives zero correction to the Hartree-Fock
             method. This is because the relaxation of orbitals with the
             change in electron number is completely neglected. In this
             work, with an iterative scheme for the evaluation of Fukui
             function, the orbital relaxation effects are accounted for
             explicitly via a perturbative treatment. In doing so, the SC
             approach is extended to density functionals involving
             substantial amount of Hartree-Fock exchange. Our new SC
             approach is demonstrated to improve systematically the
             predicted Kohn-Sham frontier orbital energies, and alleviate
             significantly the mismatch between fundamental and
             derivative gaps. © 2013 AIP Publishing LLC.},
   Doi = {10.1063/1.4801922},
   Key = {fds234887}
}

@article{fds234888,
   Author = {Wu, P and Chaudret, R and Hu, X and Yang, W},
   Title = {Noncovalent interaction analysis in fluctuating
             environments},
   Journal = {Journal of Chemical Theory and Computation},
   Volume = {9},
   Number = {5},
   Pages = {2226-2234},
   Year = {2013},
   ISSN = {1549-9618},
   url = {http://dx.doi.org/10.1021/ct4001087},
   Abstract = {Noncovalent interactions play a central role in many
             chemical and biological systems. In a previous study,
             Johnson et al. developed a noncovalent interaction (NCI)
             index to characterize and visualize different types of weak
             interactions. To apply the NCI analysis to fluctuating
             environments as in the solution phase, we here developed a
             new averaged noncovalent interaction (i.e., aNCI) index
             along with a fluctuation index to characterize the magnitude
             of interactions and fluctuations. We applied aNCI for
             various systems including solute-solvent and ligand-protein
             noncovalent interactions. For water and benzene molecules in
             aqueous solution, solvation structures and the specific
             hydrogen bond patterns were visualized clearly. For the Cl-
             + CH 3Cl SN2 reaction in aqueous solution, charge
             reorganization influences over solvation structure along SN2
             reaction were revealed. For ligand-protein systems, aNCI can
             recover several key fluctuating hydrogen bond patterns that
             have potential applications for drug design. Therefore,
             aNCI, as a complementary approach to the original NCI
             method, can extract and visualize noncovalent interactions
             from thermal noise in fluctuating environments. © 2013
             American Chemical Society.},
   Doi = {10.1021/ct4001087},
   Key = {fds234888}
}

@article{fds234890,
   Author = {Vleeschouwer, FD and Chankisjijev, A and Yang, W and Geerlings, P and Proft, FD},
   Title = {Pushing the boundaries of intrinsically stable radicals:
             Inverse design using the thiadiazinyl radical as a
             template},
   Journal = {The Journal of Organic Chemistry},
   Volume = {78},
   Number = {7},
   Pages = {3151-3158},
   Year = {2013},
   ISSN = {0022-3263},
   url = {http://dx.doi.org/10.1021/jo400101d},
   Abstract = {In this study, for the first time inverse design was applied
             to search for the intrinsically most stable radical system
             in a predefined chemical space of enormous size by scanning
             in a rational way that entire chemical space. The focus was
             predominantly on thermodynamic stabilization effects, such
             as stabilization through resonance. Two different properties
             were optimized: a newly introduced descriptor called the
             radical delocalization value and the intrinsic stability via
             a previously established bond dissociation enthalpy model.
             The thiadiazinyl radical was chosen as case study of this
             new approach of inverse design in stable radical chemistry.
             The resulting optimal structure is found to be highly
             stable, intrinsically more so than other well-known stable
             radicals, such as verdazyls and N,N-diphenyl-N′-picrylhydrazyl,
             and even rivaling the intrinsic stability of nitrogen
             monoxide. © 2013 American Chemical Society.},
   Doi = {10.1021/jo400101d},
   Key = {fds234890}
}

@article{fds234942,
   Author = {Shenvi, N and Yang, W},
   Title = {Achieving partial decoherence in surface hopping through
             phase correction.},
   Journal = {Journal of Chemical Physics},
   Volume = {137},
   Number = {22},
   Pages = {22A528},
   Year = {2012},
   Month = {December},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23249065},
   Abstract = {Fewest-switches surface hopping is one of the simplest and
             most popular methods for the computational study of
             nonadiabatic processes. Recently, a very simple phase
             correction was introduced to the traditional surface hopping
             algorithm, substantially improving its accuracy with
             essentially no associated computational cost [N. Shenvi, J.
             E. Subotnik, and W. Yang, J. Chem. Phys. 135, 024101
             (2011)]. In this paper, we show that we can modify our
             phase-corrected algorithm slightly such that it takes into
             account one type of decoherence, again with no additional
             computational cost. We apply our algorithm to two existing
             model problems, demonstrating that it can indeed capture one
             particular type of decoherence without any of the
             sophisticated machinery of alternative algorithms.},
   Doi = {10.1063/1.4746407},
   Key = {fds234942}
}

@article{fds234955,
   Author = {De Vleeschouwer and F and Yang, W and Beratan, DN and Geerlings, P and De
             Proft, F},
   Title = {Inverse design of molecules with optimal reactivity
             properties: acidity of 2-naphthol derivatives.},
   Journal = {Physical Chemistry Chemical Physics},
   Volume = {14},
   Number = {46},
   Pages = {16002-16013},
   Year = {2012},
   Month = {December},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23089917},
   Abstract = {The design of molecules with optimal properties is an
             important challenge in chemistry because of the
             astronomically large number of possible stable structures
             that is accessible in chemical space. This obstacle can be
             overcome through inverse molecular design. In inverse
             design, one uses the computation of certain indices to
             design molecules with an optimal target property. In this
             study, for the first time, inverse design was used to
             optimize reactivity properties of molecules. Specifically,
             we optimized the acidity of substituted 2-naphthols, both in
             the ground and the excited state. Substituted 2-naphthols
             belong to the class of photoacids, showing enhanced acidity
             when excited from the singlet ground state to the first
             singlet excited state. The focus of this work is the ground
             state. As a measure of acidity, three different properties
             are optimized: the charge on the hydroxyl hydrogen atom of
             the acid, the charge on the negatively charged oxygen atom
             of the conjugate base and the energy difference between acid
             and conjugate base. Both the practical use of the
             methodology and the results for ground and excited states
             are discussed.},
   Doi = {10.1039/c2cp42623d},
   Key = {fds234955}
}

@article{fds234937,
   Author = {Peng, D and Hu, X and Devarajan, D and Ess, DH and Johnson, ER and Yang,
             W},
   Title = {Variational fractional-spin density-functional theory for
             diradicals.},
   Journal = {Journal of Chemical Physics},
   Volume = {137},
   Number = {11},
   Pages = {114112},
   Year = {2012},
   Month = {September},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22998254},
   Abstract = {Accurate computation of singlet-triplet energy gaps of
             diradicals remains a challenging problem in
             density-functional theory (DFT). In this work, we propose a
             variational extension of our previous work [D. H. Ess, E. R.
             Johnson, X. Q. Hu, and W. T. Yang, J. Phys. Chem. A 115, 76
             (2011)], which applied fractional-spin density-functional
             theory (FS-DFT) to diradicals. The original FS-DFT approach
             assumed equal spin-orbital occupancies of 0.5 α-spin and
             0.5 β-spin for the two degenerate, or nearly degenerate,
             frontier orbitals. In contrast, the variational approach
             (VFS-DFT) optimizes the total energy of a singlet diradical
             with respect to the frontier-orbital occupation numbers,
             based on a full configuration-interaction picture. It is
             found that the optimal occupation numbers are exactly 0.5
             α-spin and 0.5 β-spin for diradicals such as O(2), where
             the frontier orbitals belong to the same multidimensional
             irreducible representation, and VFS-DFT reduces to FS-DFT
             for these cases. However, for diradicals where the frontier
             orbitals do not belong to the same irreducible
             representation, the optimal occupation numbers can vary
             between 0 and 1. Furthermore, analysis of CH(2) by VFS-DFT
             and FS-DFT captures the (1)A(1) and (1)B(1) states,
             respectively. Finally, because of the static correlation
             error in commonly used density functional approximations,
             both VFS-DFT and FS-DFT calculations significantly
             overestimate the singlet-triplet energy gaps for disjoint
             diradicals, such as cyclobutadiene, in which the frontier
             orbitals are confined to separate atomic
             centers.},
   Doi = {10.1063/1.4749242},
   Key = {fds234937}
}

@article{fds234934,
   Author = {Wu, P and Cisneros, GA and Hu, H and Chaudret, R and Hu, X and Yang,
             W},
   Title = {Catalytic mechanism of 4-oxalocrotonate tautomerase:
             significances of protein-protein interactions on proton
             transfer pathways.},
   Journal = {The Journal of Physical Chemistry Part B: Condensed Matter,
             Materials, Surfaces, Interfaces and Biophysical},
   Volume = {116},
   Number = {23},
   Pages = {6889-6897},
   Year = {2012},
   Month = {June},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22417185},
   Abstract = {4-Oxalocrotonate tautomerase (4-OT), a member of tautomerase
             superfamily, is an essential enzyme in the degradative
             metabolism pathway occurring in the Krebs cycle. The proton
             transfer process catalyzed by 4-OT has been explored
             previously using both experimental and theoretical methods;
             however, the elaborate catalytic mechanism of 4-OT still
             remains unsettled. By combining classical molecular
             mechanics with quantum mechanics, our results demonstrate
             that the native hexametric 4-OT enzyme, including six
             protein monomers, must be employed to simulate the proton
             transfer process in 4-OT due to protein-protein steric and
             electrostatic interactions. As a consequence, only three out
             of the six active sites in the 4-OT hexamer are observed to
             be occupied by three 2-oxo-4-hexenedioates (2o4hex), i.e.,
             half-of-the-sites occupation. This agrees with experimental
             observations on negative cooperative effect between two
             adjacent substrates. Two sequential proton transfers occur:
             one proton from the C3 position of 2o4hex is initially
             transferred to the nitrogen atom of the general base, Pro1.
             Subsequently, the same proton is shuttled back to the
             position C5 of 2o4hex to complete the proton transfer
             process in 4-OT. During the catalytic reaction,
             conformational changes (i.e., 1-carboxyl group rotation) of
             2o4hex may occur in the 4-OT dimer model but cannot proceed
             in the hexametric structure. We further explained that the
             docking process of 2o4hex can influence the specific
             reactant conformations and an alternative substrate
             (2-hydroxymuconate) may serve as reactant under a different
             reaction mechanism than 2o4hex.},
   Doi = {10.1021/jp212643j},
   Key = {fds234934}
}

@article{fds234932,
   Author = {Hu, X and Jin, Y and Zeng, X and Hu, H and Yang, W},
   Title = {Liquid water simulations with the density fragment
             interaction approach.},
   Journal = {Physical Chemistry Chemical Physics},
   Volume = {14},
   Number = {21},
   Pages = {7700-7709},
   Year = {2012},
   Month = {June},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22466097},
   Abstract = {We reformulate the density fragment interaction (DFI)
             approach [Fujimoto and Yang, J. Chem. Phys., 2008, 129,
             054102.] to achieve linear-scaling quantum mechanical
             calculations for large molecular systems. Two key
             approximations are developed to improve the efficiency of
             the DFI approach and thus enable the calculations for large
             molecules: the electrostatic interactions between fragments
             are computed efficiently by means of polarizable
             electrostatic-potential-fitted atomic charges; and frozen
             fragment pseudopotentials, similar to the effective fragment
             potentials that can be fitted from interactions between
             small molecules, are employed to take into account the Pauli
             repulsion effect among fragments. Our reformulated and
             parallelized DFI method demonstrates excellent parallel
             performance based on the benchmarks for the system of 256
             water molecules. Molecular dynamics simulations for the
             structural properties of liquid water also show a
             qualitatively good agreement with experimental measurements
             including the heat capacity, binding energy per water
             molecule, and the radial distribution functions of atomic
             pairs of O-O, O-H, and H-H. With this approach, large-scale
             quantum mechanical simulations for water and other liquids
             become feasible.},
   Doi = {10.1039/c2cp23714h},
   Key = {fds234932}
}

@article{fds234933,
   Author = {Yang, W and Cohen, AJ and Mori-Sánchez, P},
   Title = {Derivative discontinuity, bandgap and lowest unoccupied
             molecular orbital in density functional theory.},
   Journal = {Journal of Chemical Physics},
   Volume = {136},
   Number = {20},
   Pages = {204111},
   Year = {2012},
   Month = {May},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22667544},
   Abstract = {The conventional analysis of Perdew and Levy, and Sham and
             Schlüter shows that the functional derivative
             discontinuity of the exchange-correlation density functional
             plays a critical role in the correct prediction of bandgaps,
             or the chemical hardness. In a recent work by the present
             authors, explicit expressions for bandgap prediction with
             all common types of exchange-correlation functionals have
             been derived without invoking the concept of
             exchange-correlation energy functional derivative
             discontinuity at all. We here analyze the two approaches and
             establish their connection and difference. The present
             analysis further leads to several important results: (1) The
             lowest unoccupied molecular orbital (LUMO) in DFT has as
             much meaning in describing electron addition as the highest
             occupied molecular orbital (HOMO) in describing electron
             removal. (2) Every term in the total energy functional
             contributes to the energy gap because of the discontinuity
             of the derivative of the density (or density matrix) with
             respect to the number of electrons, ((∂ρ(s)(r('),r))/∂N)(v(s)
             ), at integers. (3) Consistent with the Perdew-Levy-Sham-Schlüter
             conclusion that the exact Kohn-Sham energy gap differs from
             the fundamental bandgap by a finite correction due to the
             functional derivative discontinuity of the
             exchange-correlation energy, we show that the
             exchange-correlation functional cannot be an explicit and
             differentiable functional of the electron density, either
             local or nonlocal. The last result is further strengthened
             when we consider Mott insulators. There, the exact
             exchange-correlation functional needs to have an explicitly
             discontinuous (nondifferentiable) dependence on the density
             or the density matrix. (4) We obtain exact conditions on the
             derivatives of total energy with respect to the spin-up and
             spin-down number of electrons.},
   Doi = {10.1063/1.3702391},
   Key = {fds234933}
}

@article{fds234930,
   Author = {Yang, W and Cohen, AJ and De Proft and F and Geerlings,
             P},
   Title = {Analytical evaluation of Fukui functions and real-space
             linear response function.},
   Journal = {Journal of Chemical Physics},
   Volume = {136},
   Number = {14},
   Pages = {144110},
   Year = {2012},
   Month = {April},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22502504},
   Abstract = {Many useful concepts developed within density functional
             theory provide much insight for the understanding and
             prediction of chemical reactivity, one of the main aims in
             the field of conceptual density functional theory. While
             approximate evaluations of such concepts exist, the
             analytical and efficient evaluation is, however,
             challenging, because such concepts are usually expressed in
             terms of functional derivatives with respect to the electron
             density, or partial derivatives with respect to the number
             of electrons, complicating the connection to the
             computational variables of the Kohn-Sham one-electron
             orbitals. Only recently, the analytical expressions for the
             chemical potential, one of the key concepts, have been
             derived by Cohen, Mori-Sánchez, and Yang, based on the
             potential functional theory formalism. In the present work,
             we obtain the analytical expressions for the real-space
             linear response function using the coupled perturbed
             Kohn-Sham and generalized Kohn-Sham equations, and the Fukui
             functions using the previous analytical expressions for
             chemical potentials of Cohen, Mori-Sánchez, and Yang. The
             analytical expressions are exact within the given
             exchange-correlation functional. They are applicable to all
             commonly used approximate functionals, such as local density
             approximation (LDA), generalized gradient approximation
             (GGA), and hybrid functionals. The analytical expressions
             obtained here for Fukui function and linear response
             functions, along with that for the chemical potential by
             Cohen, Mori-Sánchez, and Yang, provide the rigorous and
             efficient evaluation of the key quantities in conceptual
             density functional theory within the computational framework
             of the Kohn-Sham and generalized Kohn-Sham approaches.
             Furthermore, the obtained analytical expressions for Fukui
             functions, in conjunction with the linearity condition of
             the ground state energy as a function of the fractional
             charges, also lead to new local conditions on the exact
             functionals, expressed in terms of the second-order
             functional derivatives. We implemented the expressions and
             demonstrate the efficacy with some atomic and molecular
             calculations, highlighting the importance of relaxation
             effects.},
   Doi = {10.1063/1.3701562},
   Key = {fds234930}
}

@article{fds234958,
   Author = {Lee, W and Zeng, X and Rotolo, K and Yang, M and Schofield, CJ and Bennett,
             V and Yang, W and Marszalek, PE},
   Title = {Mechanical anisotropy of ankyrin repeats.},
   Journal = {Biophysical Journal},
   Volume = {102},
   Number = {5},
   Pages = {1118-1126},
   Year = {2012},
   Month = {March},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22404934},
   Abstract = {Red blood cells are frequently deformed and their
             cytoskeletal proteins such as spectrin and ankyrin-R are
             repeatedly subjected to mechanical forces. While the
             mechanics of spectrin was thoroughly investigated in vitro
             and in vivo, little is known about the mechanical behavior
             of ankyrin-R. In this study, we combine coarse-grained
             steered molecular dynamics simulations and atomic force
             spectroscopy to examine the mechanical response of ankyrin
             repeats (ARs) in a model synthetic AR protein NI6C, and in
             the D34 fragment of native ankyrin-R when these proteins are
             subjected to various stretching geometry conditions. Our
             steered molecular dynamics results, supported by AFM
             measurements, reveal an unusual mechanical anisotropy of
             ARs: their mechanical stability is greater when their
             unfolding is forced to propagate from the N-terminus toward
             the C-terminus (repeats unfold at ~60 pN), as compared to
             the unfolding in the opposite direction (unfolding force ∼
             30 pN). This anisotropy is also reflected in the complex
             refolding behavior of ARs. The origin of this unfolding and
             refolding anisotropy is in the various numbers of native
             contacts that are broken and formed at the interfaces
             between neighboring repeats depending on the
             unfolding/refolding propagation directions. Finally, we
             discuss how these complex mechanical properties of ARs in
             D34 may affect its behavior in vivo.},
   Doi = {10.1016/j.bpj.2012.01.046},
   Key = {fds234958}
}

@article{fds234892,
   Author = {Yang, W and Mori-Sanchez, P and Cohen, AJ},
   Title = {Insight and progress in density functional
             theory},
   Journal = {AIP Conference Proceedings},
   Volume = {1504},
   Pages = {605-606},
   Year = {2012},
   ISSN = {0094-243X},
   url = {http://dx.doi.org/10.1063/1.4771769},
   Abstract = {Density functional theory of electronic structure is widely
             and successfully applied in simulations throughout
             engineering and sciences. However, there are spectacular
             failures for many predicted properties. The errors include
             underestimation of the barriers of chemical reactions, the
             band gaps of materials, the energies of dissociating
             molecular ions and charge transfer excitation energies.
             Typical DFT calculations also fail to describe degenerate or
             near degenerate systems, as arise in the breaking of
             chemical bonds, and strongly correlated materials. These
             errors can all be characterized and understood through the
             perspective of fractional charges and fractional spins
             introduced recently. © 2012 American Institute of
             Physics.},
   Doi = {10.1063/1.4771769},
   Key = {fds234892}
}

@article{fds234927,
   Author = {Sun, Z and Yang, W and Zhang, DH},
   Title = {Higher-order split operator schemes for solving the
             Schrödinger equation in the time-dependent wave packet
             method: Applications to triatomic reactive scattering
             calculations},
   Journal = {Physical Chemistry Chemical Physics},
   Volume = {14},
   Number = {6},
   Pages = {1827-1845},
   Year = {2012},
   ISSN = {1463-9076},
   url = {http://dx.doi.org/10.1039/c1cp22790d},
   Abstract = {The efficiency of the numerical propagators for solving the
             time-dependent Schrödinger equation in the wave packet
             approach to reactive scattering is of vital importance. In
             this Perspective, we first briefly review the propagators
             used in quantum reactive scattering calculations and their
             applications to triatomic reactions. Then we present a
             detailed comparison of about thirty higher-order split
             operator propagators for solving the Schrödinger equation
             with their applications to the wave packet evolution within
             a one-dimensional Morse potential, and the total reaction
             probability calculations for the H + HD, H + NH, H + O 2,
             and F + HD reactions. These four triatomic reactions have
             quite different dynamic characteristics and thus provide a
             comprehensive picture of the relative advantages of these
             higher-order propagation methods for describing reactive
             scattering dynamics. Our calculations reveal that the most
             often used second-order split operator method is typically
             more efficient for a direct reaction, particularly for those
             involving flat potential energy surfaces. However, the
             optimal higher-order split operator methods are more
             suitable for a reaction with resonances and intermediate
             complexes or a reaction experiencing potential energy
             surface with fluctuations of considerable amplitude. Three
             4th-order and one 6th-order split operator methods, which
             are most efficient for solving reactive scattering in
             various conditions among the tested ones, are recommended
             for general applications. In addition, a brief discussion on
             the relative performance between the Chebyshev real wave
             packet method and the split operator method is given. The
             results in this Perspective are expected to stimulate more
             applications of (high-order) split operators to the quantum
             reactive scattering calculation and other related problems.
             © 2012 the Owner Societies.},
   Doi = {10.1039/c1cp22790d},
   Key = {fds234927}
}

@article{fds234928,
   Author = {Cohen, AJ and Mori-Sánchez, P and Yang, W},
   Title = {Challenges for density functional theory},
   Journal = {Chemical Reviews},
   Volume = {112},
   Number = {1},
   Pages = {289-320},
   Year = {2012},
   ISSN = {0009-2665},
   url = {http://dx.doi.org/10.1021/cr200107z},
   Abstract = {Understanding current and future challenges for density
             functional theory (DFT) are focused. One of the main
             challenges for DFT is to keep as its cornerstone some
             element of simplicity. It also include the need to improve
             the description of reaction barriers and dispersion/van der
             waals interactions and understand the energy of two protons
             separated by infinity with one and two electrons. It is very
             difficult to determine an accurate form of the
             exchangecorrelation from first principles. A more practical
             approach is to take available experimental information to
             help determine and test the functional forms. It is
             important to address the particularly challenging problem of
             exchangecorrelation from other angles as well such as
             constructing approximate functionals and minimizing the
             total energy. The essence of self-interaction can be
             understood from the behavior of the energy of one
             electron.},
   Doi = {10.1021/cr200107z},
   Key = {fds234928}
}

@article{fds234929,
   Author = {Mori-Sánchez, P and Cohen, AJ and Yang, W},
   Title = {Failure of the random-phase-approximation correlation
             energy},
   Journal = {Physical Review A - Atomic, Molecular, and Optical
             Physics},
   Volume = {85},
   Number = {4},
   Year = {2012},
   ISSN = {1050-2947},
   url = {http://dx.doi.org/10.1103/PhysRevA.85.042507},
   Abstract = {The random phase approximation (RPA) is thought to be a
             successful method; however, basic errors have been found
             that have massive implications in the simplest molecular
             systems. The observed successes and failures are
             rationalized by examining its performance against exact
             conditions on the energy for fractional charges and
             fractional spins. Extremely simple tests reveal that the RPA
             method satisfies the constancy condition for fractional
             spins that leads to correct dissociation of closed-shell
             molecules and no static correlation error (such as in H 2
             dissociation) but massively fails for dissociation of odd
             electron systems, with an enormous delocalization error
             (such as H 2+ dissociation). Other methods related to the
             RPA, including the Hartree-Fock response (RPAE) or
             range-separated RPA, can reduce this delocalization error
             but only at the cost of increasing the static correlation
             error. None of the RPA methods have the discontinuous nature
             required to satisfy both exact conditions and the full
             unified condition (e.g., dissociation of H 2+ and H 2 at the
             same time), emphasizing the need to go beyond differentiable
             energy functionals of the orbitals and eigenvalues. © 2012
             American Physical Society.},
   Doi = {10.1103/PhysRevA.85.042507},
   Key = {fds234929}
}

@article{fds234931,
   Author = {Peng, D and Zhao, B and Cohen, AJ and Hu, X and Yang,
             W},
   Title = {Optimized effective potential for calculations with
             orbital-free potential functionals},
   Journal = {Molecular Physics},
   Volume = {110},
   Number = {9-10},
   Pages = {925-934},
   Year = {2012},
   ISSN = {0026-8976},
   url = {http://dx.doi.org/10.1080/00268976.2012.681310},
   Abstract = {Approximation of electronic kinetic energy can be naturally
             expressed in terms of the one-electron effective potential,
             namely as a potential functional. Such approximate
             functionals can lead to linear scaling orbital-free
             calculations of large systems. For calculation within
             orbital-free potential functionals, a new optimized
             effective potential (OEP) method has been developed
             presently for the direct optimization of electronic ground
             state energy. This approach parallels the development of OEP
             for the direct optimization of orbital-dependent
             exchange-correlation functionals within the Kohn-Sham
             density functional theory (DFT) framework. It uses the
             effective one-electron potential as the basic computation
             variable. This potential is further expanded as a linear
             combination of basis functions plus a fixed reference
             potential. Thus, the potential optimization is transformed
             into the optimization of linear coefficients associated with
             the basis sets. As a key quantity within the orbital-free
             potential functionals, the chemical potential controls the
             correct number of electrons and depends on the trial
             one-electron potential. The derivatives of the chemical
             potential with respect to the potential variations have been
             derived and their use leads to a very efficient
             electron-number conserving update of the trial potential.
             The calculations of several atoms and diatomic molecules
             with the simple Thomas-Fermi-Dirac approximate functional
             has been carried out to demonstrate our approach. The
             developed OEP approach should be an efficient computational
             tool for orbital-free potential functionals. © 2012 Taylor
             & Francis.},
   Doi = {10.1080/00268976.2012.681310},
   Key = {fds234931}
}

@article{fds234935,
   Author = {Johnson, ER and Contreras-García, J and Yang,
             W},
   Title = {Density-functional errors in alkanes: A real-space
             perspective},
   Journal = {Journal of Chemical Theory and Computation},
   Volume = {8},
   Number = {8},
   Pages = {2676-2681},
   Year = {2012},
   ISSN = {1549-9618},
   url = {http://dx.doi.org/10.1021/ct300412g},
   Abstract = {Density-functional theory (DFT) approximations are known to
             give systematic errors for isodesmic reaction energies of
             n-alkanes to form ethane. Several explanations have been
             proposed, involving both the exchange or correlation nature
             of the problem and its distance range (i.e., medium-range or
             long-range interactions). In this work, a new isodesmic
             reaction is defined to demonstrate that the reaction energy
             differences originate from localized interactions between
             contiguous CH 2 units in the n-alkane, i.e., from 1,3
             interactions. Furthermore, we introduce a real-space
             interpretation of the error based on changes in electron
             density, described by our recently developed Non-Covalent
             Interactions (NCI) method. The reduced density gradient has
             smaller values for noncovalent 1,3 interactions in n-alkane
             reactants compared to ethane products. The gradient
             contribution to the exchange energy is consequently reduced,
             giving a constant energy bias against each propane unit in
             an n-alkane. Differences in exchange energy for grid points
             within the NCI regions are shown to be responsible for the
             reaction-energy errors. This is also demonstrated to be the
             source of error in Diels-Alder addition barrier heights
             obtained with GGA-based hybrid functionals. © 2012 American
             Chemical Society.},
   Doi = {10.1021/ct300412g},
   Key = {fds234935}
}

@article{fds234936,
   Author = {Xu, Y and Wang, B-J and Ke, S-H and Yang, W and Alzahrani,
             AZ},
   Title = {Highly tunable spin-dependent electron transport through
             carbon atomic chains connecting two zigzag graphene
             nanoribbons},
   Journal = {Journal of Chemical Physics},
   Volume = {137},
   Number = {10},
   Year = {2012},
   ISSN = {0021-9606},
   url = {http://dx.doi.org/10.1063/1.4752197},
   Abstract = {Motivated by recent experiments of successfully carving out
             stable carbon atomic chains from graphene, we investigate a
             device structure of a carbon chain connecting two zigzag
             graphene nanoribbons with highly tunable spin-dependent
             transport properties. Our calculation based on the
             non-equilibrium Greens function approach combined with the
             density functional theory shows that the transport behavior
             is sensitive to the spin configuration of the leads and the
             bridge position in the gap. A bridge in the middle gives an
             overall good coupling except for around the Fermi energy
             where the leads with anti-parallel spins create a small
             transport gap, while the leads with parallel spins give a
             finite density of states and induce an even-odd oscillation
             in conductance in terms of the number of atoms in the carbon
             chain. On the other hand, a bridge at the edge shows a
             transport behavior associated with the spin-polarized edge
             states, presenting sharp pure α-spin and β-spin peaks
             beside the Fermi energy in the transmission function. This
             makes it possible to realize on-chip interconnects or
             spintronic devices by tuning the spin state of the leads and
             the bridge position. © 2012 American Institute of
             Physics.},
   Doi = {10.1063/1.4752197},
   Key = {fds234936}
}

@article{fds234938,
   Author = {Lin, X and Hu, X and Concepcion, JJ and Chen, Z and Liu, S and Meyer, TJ and Yang, W},
   Title = {Theoretical study of catalytic mechanism for single-site
             water oxidation process},
   Journal = {Proceedings of the National Academy of Sciences of
             USA},
   Volume = {109},
   Number = {39},
   Pages = {15669-15672},
   Year = {2012},
   ISSN = {0027-8424},
   url = {http://dx.doi.org/10.1073/pnas.1118344109},
   Abstract = {Water oxidation is a linchpin in solar fuels formation, and
             catalysis by single-site ruthenium complexes has generated
             significant interest in this area. Combining several
             theoretical tools, we have studied the entire catalytic
             cycle of water oxidation for a single-site catalyst starting
             with [Ru II(tpy)(bpm)(OH2)]2+ (i.e., [Ru II-OH2]2+; tpy is
             2,2′:6′,2″- terpyridine and bpm is
             2,2′-bypyrimidine) as a representative example of a new
             class of single-site catalysts. The redox potentials and pKa
             calculations for the first two proton-coupled electron
             transfers (PCETs) from [RuII-OH2]2+ to [RuIV = O] 2+ and the
             following electron-transfer process to [RuV = O]3+ suggest
             that these processes can proceed readily in acidic or weakly
             basic conditions. The subsequent water splitting process
             involves two water molecules, [RuV = O]3+ to generate [Ru
             III-OOH]2+, and H3O+ with a low activation barrier (∼10
             kcal/mol). After the key O-O bond forming step in the
             single-site Ru catalysis, another PECT process oxidizes [Ru
             III-OOH]2+ to [RuIV-OO]2+ when the pH is lower than 3.7. Two
             possible forms of [RuIV-OO]2+, open and closed, can exist
             and interconvert with a low activation barrier (<7
             kcal/mol) due to strong spin-orbital coupling effects. In
             Pathway 1 at pH = 1.0, oxygen release is rate-limiting with
             an activation barrier ∼12 kcal/mol while the
             electron-transfer step from [RuIV-OO]2+ to [RuV - OO]3+
             becomes rate-determining at pH = 0 (Pathway 2) with Ce(IV)
             as oxidant. The results of these theoretical studies with
             atomistic details have revealed subtle details of reaction
             mechanisms at several stages during the catalytic cycle.
             This understanding is helpful in the design of new catalysts
             for water oxidation.},
   Doi = {10.1073/pnas.1118344109},
   Key = {fds234938}
}

@article{fds234939,
   Author = {Zheng, X and Liu, M and Johnson, ER and Contreras-García, J and Yang,
             W},
   Title = {Delocalization error of density-functional approximations: A
             distinct manifestation in hydrogen molecular
             chains},
   Journal = {Journal of Chemical Physics},
   Volume = {137},
   Number = {21},
   Year = {2012},
   ISSN = {0021-9606},
   url = {http://dx.doi.org/10.1063/1.4768673},
   Abstract = {Delocalization error is one of the major sources of
             inaccuracy for mainstream density functional approximations
             and it is responsible for many of the most glaring failures.
             Quantitative identification of delocalization error in
             chemical species and analysis of its influence on calculated
             thermodynamic properties have remained scarce. In this work
             we demonstrate unambiguously the effect of delocalization
             error on a series of hydrogen molecular chains and elucidate
             the underlying relationship between the error magnitude and
             system geometry. This work stresses the necessity of
             minimizing delocalization error associated with density
             functional approximations. © 2012 American Institute of
             Physics.},
   Doi = {10.1063/1.4768673},
   Key = {fds234939}
}

@article{fds234940,
   Author = {Gillet, N and Chaudret, R and Contreras-García, J and Yang, W and Silvi, B and Piquemal, J-P},
   Title = {Coupling quantum interpretative techniques: Another look at
             chemical mechanisms in organic reactions},
   Journal = {Journal of Chemical Theory and Computation},
   Volume = {8},
   Number = {11},
   Pages = {3993-3997},
   Year = {2012},
   ISSN = {1549-9618},
   url = {http://dx.doi.org/10.1021/ct300234g},
   Abstract = {A cross ELF/NCI analysis is tested over prototypical organic
             reactions. The synergetic use of ELF and NCI enables the
             understanding of reaction mechanisms since each method can
             respectively identify regions of strong and weak electron
             pairing. Chemically intuitive results are recovered and
             enriched by the identification of new features. Noncovalent
             interactions are found to foresee the evolution of the
             reaction from the initial steps. Within NCI, no topological
             catastrophe is observed as changes are continuous to such an
             extent that future reaction steps can be predicted from the
             evolution of the initial NCI critical points. Indeed, strong
             convergences through the reaction paths between ELF and NCI
             critical points enable identification of key interactions at
             the origin of the bond formation. VMD scripts enabling the
             automatic generation of movies depicting the cross NCI/ELF
             analysis along a reaction path (or following a
             Born-Oppenheimer molecular dynamics trajectory) are provided
             as Supporting Information. © 2012 American Chemical
             Society.},
   Doi = {10.1021/ct300234g},
   Key = {fds234940}
}

@article{fds234941,
   Author = {Zeng, X and Hu, X and Yang, W},
   Title = {Fragment-based quantum mechanical/molecular mechanical
             simulations of thermodynamic and kinetic process of the
             Ru2+-Ru3+ self-exchange electron
             transfer},
   Journal = {Journal of Chemical Theory and Computation},
   Volume = {8},
   Number = {12},
   Pages = {4960-4967},
   Year = {2012},
   ISSN = {1549-9618},
   url = {http://dx.doi.org/10.1021/ct300758v},
   Abstract = {A fragment-based fractional number of electrons (FNE)
             approach is developed to study entire electron transfer (ET)
             processes from the electron donor region to the acceptor
             region in the condensed phase. Both regions are described by
             the density-fragment interaction (DFI) method, while FNE as
             an efficient ET order parameter is applied to simulate the
             electron transfer process. In association with the QM/MM
             energy expression, the DFI-FNE method is demonstrated to
             describe ET processes robustly with the Ru2+-Ru3+
             self-exchange ET as a proof-of-concept example. This method
             allows for systematic calculations of redox free energies,
             reorganization energies, electronic couplings and the
             absolute ET rate constants within the Marcus regime. © 2012
             American Chemical Society.},
   Doi = {10.1021/ct300758v},
   Key = {fds234941}
}

@article{fds234948,
   Author = {Cho, J and Lin, Q and Yang, S and Jr, JGS and Cheng, Y and Lin, E and Yang, J and Foreman, JV and Everitt, HO and Yang, W and Kim, J and Liu,
             J},
   Title = {Sulfur-doped zinc oxide (ZnO) Nanostars: Synthesis and
             simulation of growth mechanism},
   Journal = {Nano Research},
   Volume = {5},
   Number = {1},
   Pages = {20-26},
   Year = {2012},
   ISSN = {1998-0124},
   url = {http://dx.doi.org/10.1007/s12274-011-0180-3},
   Abstract = {We present a bottom-up synthesis, spectroscopic
             characterization, and ab initio simulations of star-shaped
             hexagonal zinc oxide (ZnO) nanowires. The ZnO nanostructures
             were synthesized by a low-temperature hydrothermal growth
             method. The cross-section of the ZnO nanowires transformed
             from a hexagon to a hexagram when sulfur dopants from
             thiourea [SC(NH 2) 2] were added into the growth solution,
             but no transformation occurred when urea (OC(NH 2) 2) was
             added. Comparison of the X-ray photoemission and
             photoluminescence spectra of undoped and sulfur-doped ZnO
             confirmed that sulfur is responsible for the novel
             morphology. Large-scale theoretical calculations were
             conducted to understand the role of sulfur doping in the
             growth process. The ab initio simulations demonstrated that
             the addition of sulfur causes a local change in charge
             distribution that is stronger at the vertices than at the
             edges, leading to the observed transformation from hexagon
             to hexagram nanostructures. © 2012 Tsinghua University
             Press and Springer-Verlag Berlin Heidelberg.},
   Doi = {10.1007/s12274-011-0180-3},
   Key = {fds234948}
}

@article{fds234954,
   Author = {Jiang, N and Zuber, G and Keinan, S and Nayak, A and Yang, W and Therien,
             MJ and Beratan, DN},
   Title = {Design of coupled porphyrin chromophores with unusually
             large hyperpolarizabilities},
   Journal = {The Journal of Physical Chemistry C},
   Volume = {116},
   Number = {17},
   Pages = {9724-9733},
   Year = {2012},
   ISSN = {1932-7447},
   url = {http://dx.doi.org/10.1021/jp2115065},
   Abstract = {Figure Persented: A new series of push-pull porphyrin-based
             chromophores with unusually large static first
             hyperpolarizabilities are designed on the basis of
             coupled-perturbed Hartree-Fock and density functional
             calculations. The proper combination of critical building
             blocks, including a ruthenium(II) bisterpyridine complex,
             proquinoidal thiadiazoloquinoxaline, and
             (porphinato)zinc(II) units, gives rise to considerable
             predicted enhancements of the static nonlinear optical (NLO)
             response, computed to be as large as 11 300 × 10 -30 esu, 2
             orders of magnitude larger than the benchmark
             [5-((4′-(dimethylamino)phenyl)ethynyl)-15-((4″-nitrophenyl)ethynyl)
             porphinato]zinc(II) chromophore. A two-state model was found
             to be useful for the qualitative description of the first
             hyperpolarizabilities in this class of NLO chromophores,
             which are predicted to have hyperpolarizabilities
             approaching the fundamental limit predicted to be attainable
             by empirical theoretical models. © 2012 American Chemical
             Society.},
   Doi = {10.1021/jp2115065},
   Key = {fds234954}
}

@article{fds234984,
   Author = {Zhang, J and Yang, W and Piquemal, J-P and Ren, P},
   Title = {Modeling structural coordination and ligand binding in zinc
             proteins with a polarizable potential},
   Journal = {Journal of Chemical Theory and Computation},
   Volume = {8},
   Number = {4},
   Pages = {1314-1324},
   Year = {2012},
   ISSN = {1549-9618},
   url = {http://dx.doi.org/10.1021/ct200812y},
   Abstract = {As the second most abundant cation in the human body, zinc
             is vital for the structures and functions of many proteins.
             Zinc-containing matrix metalloproteinases (MMPs) have been
             widely investigated as potential drug targets in a range of
             diseases ranging from cardiovascular disorders to cancers.
             However, it remains a challenge in theoretical studies to
             treat zinc in proteins with classical mechanics. In this
             study, we examined Zn 2+ coordination with organic compounds
             and protein side chains using a polarizable atomic
             multipole-based electrostatic model. We find that the
             polarization effect plays a determining role in Zn 2+
             coordination geometry in both matrix metalloproteinase (MMP)
             complexes and zinc-finger proteins. In addition, the
             relative binding free energies of selected inhibitors
             binding with MMP13 have been estimated and compared with
             experimental results. While not directly interacting with
             the small molecule inhibitors, the permanent and polarizing
             field of Zn 2+ exerts a strong influence on the relative
             affinities of the ligands. The simulation results also
             reveal that the polarization effect on binding is
             ligand-dependent and thus difficult to incorporate into
             fixed-charge models implicitly. © 2012 American Chemical
             Society.},
   Doi = {10.1021/ct200812y},
   Key = {fds234984}
}

@article{fds234926,
   Author = {Shenvi, N and Yang, W},
   Title = {An algebraic operator approach to electronic
             structure.},
   Journal = {Journal of Chemical Physics},
   Volume = {135},
   Number = {24},
   Pages = {244111},
   Year = {2011},
   Month = {December},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22225148},
   Abstract = {In this paper, we introduce an algebraic approach to
             electronic structure calculations. Our approach constructs a
             Jordan algebra based on the second-quantized electronic
             Hamiltonian. From the structure factor of this algebra, we
             show that we can calculate the energy of the ground
             electronic state of the Hamiltonian operator. We apply our
             method to several generalized Hubbard models and show that
             we can usually obtain a significant fraction of the
             correlation energy for low-to-moderate values of the
             electronic repulsion parameter while still retaining the
             O(L(3)) scaling of the Hartree-Fock algorithm. This
             surprising result, along with several other observations,
             suggests that our algebraic approach represents a new
             paradigm for electronic structure calculations which opens
             up many new directions for research.},
   Doi = {10.1063/1.3671388},
   Key = {fds234926}
}

@article{fds234995,
   Author = {Contreras-García, J and Yang, W and Johnson, ER},
   Title = {Analysis of hydrogen-bond interaction potentials from the
             electron density: integration of noncovalent interaction
             regions.},
   Journal = {The Journal of Physical Chemistry Part A: Molecules,
             Spectroscopy, Kinetics, Environment and General
             Theory},
   Volume = {115},
   Number = {45},
   Pages = {12983-12990},
   Year = {2011},
   Month = {November},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21786796},
   Abstract = {Hydrogen bonds are of crucial relevance to many problems in
             chemistry, biology, and materials science. The recently
             developed NCI (noncovalent interactions) index enables
             real-space visualization of both attractive (van der Waals
             and hydrogen-bonding) and repulsive (steric) interactions
             based on properties of the electron density. It is thus an
             optimal index to describe the interplay of stabilizing and
             destabilizing contributions that determine stable minima on
             hydrogen-bonding potential-energy surfaces (PESs). In the
             framework of density-functional theory, energetics are
             completely determined by the electron density. Consequently,
             NCI will be shown to allow quantitative treatment of
             hydrogen-bond energetics. The evolution of NCI regions along
             a PES follows a well-behaved pattern which, upon integration
             of the electron density, is capable of mimicking
             conventional hydrogen-bond interatomic potentials.},
   Doi = {10.1021/jp204278k},
   Key = {fds234995}
}

@article{fds234987,
   Author = {Wu, P and Hu, X and Yang, W},
   Title = {lambda-Metadynamics Approach To Compute Absolute Solvation
             Free Energy},
   Journal = {Journal of Physical Chemistry Letters},
   Volume = {2},
   Number = {17},
   Pages = {2099-2103},
   Year = {2011},
   Month = {September},
   ISSN = {1948-7185},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000294701800004&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Doi = {10.1021/jz200808x},
   Key = {fds234987}
}

@article{fds234986,
   Author = {Zheng, X and Cohen, AJ and Mori-Sanchez, P and Hu, X and Yang,
             W},
   Title = {Improving Band Gap Prediction in Density Functional Theory
             from Molecules to Solids},
   Journal = {Physical Review Letters},
   Volume = {107},
   Number = {2},
   Pages = {026403},
   Year = {2011},
   Month = {July},
   ISSN = {0031-9007},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21797627},
   Abstract = {A novel nonempirical scaling correction method is developed
             to tackle the challenge of band gap prediction in density
             functional theory. For finite systems the scaling correction
             largely restores the straight-line behavior of electronic
             energy at fractional electron numbers. The scaling
             correction can be generally applied to a variety of
             mainstream density functional approximations, leading to
             significant improvement in the band gap prediction. In
             particular, the scaled version of a modified local density
             approximation predicts band gaps with an accuracy consistent
             for systems of all sizes, ranging from atoms and molecules
             to solids. The scaled modified local density approximation
             thus provides a useful tool to quantitatively characterize
             the size-dependent effect on the energy gaps of
             nanostructures.},
   Doi = {10.1103/PhysRevLett.107.026403},
   Key = {fds234986}
}

@article{fds234990,
   Author = {Shenvi, N and Subotnik, JE and Yang, W},
   Title = {Phase-corrected surface hopping: correcting the phase
             evolution of the electronic wavefunction.},
   Journal = {Journal of Chemical Physics},
   Volume = {135},
   Number = {2},
   Pages = {024101},
   Year = {2011},
   Month = {July},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21766919},
   Abstract = {In this paper, we show that a remarkably simple correction
             can be made to the equation of motion which governs the
             evolution of the electronic wavefunction over some
             prescribed nuclear trajectory in the fewest-switches surface
             hopping algorithm. This corrected electronic equation of
             motion can then be used in conjunction with traditional or
             modified surface hopping methods to calculate nonadiabatic
             effects in large systems. Although the correction adds no
             computational cost to the algorithm, it leads to a dramatic
             improvement in scattering probabilities for all model
             problems studied thus far. We show that this correction can
             be applied to one of Tully's original one-dimensional model
             problems or to a more sophisticated two-dimensional example
             and yields substantially greater accuracy than the
             traditional approach.},
   Doi = {10.1063/1.3603447},
   Key = {fds234990}
}

@article{fds234994,
   Author = {Cui, G and Yang, W},
   Title = {Conical intersections in solution: formulation, algorithm,
             and implementation with combined quantum mechanics/molecular
             mechanics method.},
   Journal = {Journal of Chemical Physics},
   Volume = {134},
   Number = {20},
   Pages = {204115},
   Year = {2011},
   Month = {May},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21639432},
   Abstract = {The significance of conical intersections in photophysics,
             photochemistry, and photodissociation of polyatomic
             molecules in gas phase has been demonstrated by numerous
             experimental and theoretical studies. Optimization of
             conical intersections of small- and medium-size molecules in
             gas phase has currently become a routine optimization
             process, as it has been implemented in many electronic
             structure packages. However, optimization of conical
             intersections of small- and medium-size molecules in
             solution or macromolecules remains inefficient, even poorly
             defined, due to large number of degrees of freedom and
             costly evaluations of gradient difference and nonadiabatic
             coupling vectors. In this work, based on the sequential
             quantum mechanics and molecular mechanics (QM/MM) and
             QM/MM-minimum free energy path methods, we have designed two
             conical intersection optimization methods for small- and
             medium-size molecules in solution or macromolecules. The
             first one is sequential QM conical intersection optimization
             and MM minimization for potential energy surfaces; the
             second one is sequential QM conical intersection
             optimization and MM sampling for potential of mean force
             surfaces, i.e., free energy surfaces. In such methods, the
             region where electronic structures change remarkably is
             placed into the QM subsystem, while the rest of the system
             is placed into the MM subsystem; thus, dimensionalities of
             gradient difference and nonadiabatic coupling vectors are
             decreased due to the relatively small QM subsystem.
             Furthermore, in comparison with the concurrent optimization
             scheme, sequential QM conical intersection optimization and
             MM minimization or sampling reduce the number of evaluations
             of gradient difference and nonadiabatic coupling vectors
             because these vectors need to be calculated only when the QM
             subsystem moves, independent of the MM minimization or
             sampling. Taken together, costly evaluations of gradient
             difference and nonadiabatic coupling vectors in solution or
             macromolecules can be reduced significantly. Test
             optimizations of conical intersections of cyclopropanone and
             acetaldehyde in aqueous solution have been carried out
             successfully.},
   Doi = {10.1063/1.3593390},
   Key = {fds234994}
}

@article{fds234991,
   Author = {Shenvi, N and Subotnik, JE and Yang, W},
   Title = {Simultaneous-trajectory surface hopping: a parameter-free
             algorithm for implementing decoherence in nonadiabatic
             dynamics.},
   Journal = {Journal of Chemical Physics},
   Volume = {134},
   Number = {14},
   Pages = {144102},
   Year = {2011},
   Month = {April},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21495737},
   Abstract = {In this paper, we introduce a trajectory-based nonadiabatic
             dynamics algorithm which aims to correct the well-known
             overcoherence problem in Tully's popular fewest-switches
             surface hopping algorithm. Our simultaneous-trajectory
             surface hopping algorithm propagates a separate classical
             trajectory on each energetically accessible adiabatic
             surface. The divergence of these trajectories generates
             decoherence, which collapses the particle wavefunction onto
             a single adiabatic state. Decoherence is implemented without
             the need for any parameters, either empirical or adjustable.
             We apply our algorithm to several model problems and find a
             significant improvement over the traditional
             algorithm.},
   Doi = {10.1063/1.3575588},
   Key = {fds234991}
}

@article{fds234996,
   Author = {Contreras-García, J and Johnson, ER and Keinan, S and Chaudret, R and Piquemal, J-P and Beratan, DN and Yang, W},
   Title = {NCIPLOT: a program for plotting non-covalent interaction
             regions.},
   Journal = {Journal of Chemical Theory and Computation},
   Volume = {7},
   Number = {3},
   Pages = {625-632},
   Year = {2011},
   Month = {March},
   ISSN = {1549-9618},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21516178},
   Abstract = {Non-covalent interactions hold the key to understanding many
             chemical, biological, and technological problems. Describing
             these non-covalent interactions accurately, including their
             positions in real space, constitutes a first step in the
             process of decoupling the complex balance of forces that
             define non-covalent interactions. Because of the size of
             macromolecules, the most common approach has been to assign
             van der Waals interactions (vdW), steric clashes (SC), and
             hydrogen bonds (HBs) based on pairwise distances between
             atoms according to their van der Waals radii. We recently
             developed an alternative perspective, derived from the
             electronic density: the Non-Covalent Interactions (NCI)
             index [J. Am. Chem. Soc. 2010, 132, 6498]. This index has
             the dual advantages of being generally transferable to
             diverse chemical applications and being very fast to
             compute, since it can be calculated from promolecular
             densities. Thus, NCI analysis is applicable to large
             systems, including proteins and DNA, where analysis of
             non-covalent interactions is of great potential value. Here,
             we describe the NCI computational algorithms and their
             implementation for the analysis and visualization of weak
             interactions, using both self-consistent fully
             quantum-mechanical, as well as promolecular, densities. A
             wide range of options for tuning the range of interactions
             to be plotted is also presented. To demonstrate the
             capabilities of our approach, several examples are given
             from organic, inorganic, solid state, and macromolecular
             chemistry, including cases where NCI analysis gives insight
             into unconventional chemical bonding. The NCI code and its
             manual are available for download at http://www.chem.duke.edu/~yang/software.htm.},
   Doi = {10.1021/ct100641a},
   Key = {fds234996}
}

@article{fds234924,
   Author = {Sun, Z and Yang, W},
   Title = {Communication: An exact short-time solver for the
             time-dependent Schrödinger equation.},
   Journal = {Journal of Chemical Physics},
   Volume = {134},
   Number = {4},
   Pages = {041101},
   Year = {2011},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21280676},
   Abstract = {The short-time integrator for propagating the time-dependent
             Schrödinger equation, which is exact to machine's round
             off accuracy when the Hamiltonian of the system is
             time-independent, was applied to solve dynamics processes.
             This integrator has the old Cayley's form [i.e., the Padé
             (1,1) approximation], but is implemented in a spectrally
             transformed Hamiltonian which was first introduced by Chen
             and Guo. Two examples are presented for illustration,
             including calculations of the collision energy-dependent
             probability passing over a barrier, and interaction process
             between pulse laser and the I(2) diatomic
             molecule.},
   Doi = {10.1063/1.3549570},
   Key = {fds234924}
}

@article{fds234989,
   Author = {Sun, Z and Yang, W},
   Title = {An exact short-time solver for the time-dependent
             Schrodinger equation},
   Journal = {Journal of Chemical Physics},
   Volume = {134},
   Number = {4},
   Pages = {041101},
   Year = {2011},
   Month = {January},
   ISSN = {0021-9606},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000286897600001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Doi = {10.1063/1.3549570},
   Key = {fds234989}
}

@article{fds234992,
   Author = {Hu, X and Hu, H and Melvin, JA and Clancy, KW and McCafferty, DG and Yang,
             W},
   Title = {Autocatalytic intramolecular isopeptide bond formation in
             gram-positive bacterial pili: a QM/MM simulation.},
   Journal = {Journal of the American Chemical Society},
   Volume = {133},
   Number = {3},
   Pages = {478-485},
   Year = {2011},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21142157},
   Abstract = {Many gram-positive pathogens possess external pili or
             fimbriae with which they adhere to host cells during the
             infection process. Unusual dual intramolecular isopeptide
             bonds between Asn and Lys side chains within the N-terminal
             and C-terminal domains of the pilus subunits have been
             observed initially in the Streptococcus pyogenes pilin
             subunit Spy0128 and subsequently in GBS52 from Streptococcus
             agalactiae, in the BcpA major pilin of Bacillus cereus and
             in the RrgB pilin of Streptococcus pneumoniae, among others.
             Within each pilin subunit, intramolecular isopeptide bonds
             serve to stabilize the protein. These bonds provide a means
             to withstand large external mechanical forces, as well as
             possibly assisting in supporting a conformation favored for
             pilin subunit polymerization via sortase transpeptidases.
             Genome-wide analyses of pili-containing gram-positive
             bacteria are known or suspected to contain isopeptide bonds
             in pilin subunits. For the autocatalytic formation of
             isopeptide cross-links, a conservation of three amino acids
             including Asn, Lys, and a catalytically important acidic Glu
             (or Asp) residue are responsible. However, the chemical
             mechanism of how isopeptide bonds form within pilin remains
             poorly understood. Although it is possible that several
             mechanistic paths could lead to isopeptide bond formation in
             pili, the requirement of a conserved glutamate and highly
             organized positioning of residues within the hydrophobic
             environment of the active site were found in numerous pilin
             crystal structures such as Spy0128 and RrgB. This suggests a
             mechanism involving direct coupling of lysine side chain
             amine to the asparagine carboxamide mediated by critical
             acid/base or hydrogen bonding interactions with the
             catalytic glutamate residue. From this mechanistic
             perspective, we used the QM/MM minimum free-energy path
             method to examine the reaction details of forming the
             isopeptide bonds with Spy0128 as a model pilin, specifically
             focusing on the role of the glutamate in catalysis. It was
             determined that the reaction mechanism likely consists of
             two major steps: the nucleophilic attack on Cγ by nitrogen
             in the unprotonated Lys ε-amino group and, then two
             concerted proton transfers occur during the formation of the
             intramolecular isopeptide bond to subsequently release
             ammonia. More importantly, within the dual active sites of
             Spy0128, Glu(117), and Glu(258) residues function as crucial
             catalysts for each isopeptide bond formation, respectively,
             by relaying two proton transfers. This work also suggests
             that domain-domain interactions within Spy0128 may modulate
             the reactivity of residues within each active site. Our
             results may hopefully shed light on the molecular mechanisms
             of pilin biogenesis in gram-positive bacteria.},
   Doi = {10.1021/ja107513t},
   Key = {fds234992}
}

@article{fds234923,
   Author = {Lin, X and Hu, X and Concepcion, JJ and Chen, Z and Liu, S and Meyer, TJ and Yang, W},
   Title = {Catalytic mechanism for single-site water oxidation process:
             A theoretical study},
   Journal = {ACS National Meeting Book of Abstracts},
   Year = {2011},
   ISSN = {0065-7727},
   Abstract = {Water oxidation catalyzed by single-site ruthenium complexes
             has generated enormous interests related to solar fuels.
             Combining several theoretical tools, we studied the entire
             catalytic cycle of water oxidation for a single site
             catalyst starting with [RuII(OH2)(tpy)(bpm)]2+ (i.e,
             [RuII-OH2]2+) as a representative example of a new class of
             single site catalysts. The electronic spin states of
             ruthenium intermediates during the catalytic cycle are
             identified as well as the corresponding optimal geometries.
             Results about each individual step will be presented in this
             talk. Our theoretical studies with atomistic details shed
             light on the reaction mechanisms of several pivotal reaction
             steps during the entire catalytic cycle and should be
             helpful in the design new catalysts for solar
             fuels.},
   Key = {fds234923}
}

@article{fds234925,
   Author = {Wu, P and Hu, X and Yang, W},
   Title = {λ-metadynamics approach to compute absolute solvation free
             energy},
   Journal = {Journal of Physical Chemistry Letters},
   Volume = {2},
   Number = {17},
   Pages = {2099-2103},
   Year = {2011},
   ISSN = {1948-7185},
   url = {http://dx.doi.org/10.1021/jz200808x},
   Abstract = {We present a new approach to combine λ dynamics with
             metadynamics (named λ-metadynamics) to compute free energy
             surfaces with respect to λ. Particularly, the
             λ-metadynamics method extends metadynamics to a single
             virtual variable λ, i.e., the coupling parameter between
             solute and solvent, to compute absolute solvation free
             energy as an exemplary application. We demonstrate that
             λ-metadynamics simulations can recover the accurate
             potential of mean force surface with respect to λ compared
             to the benchmark results from traditional λ-dynamics with
             umbrella sampling. The solvation free energy results for
             five small organic molecules from λ-metadynamics
             simulations using the same filling scheme show that the
             statistical errors are within ±0.5 kcal/mol. The new
             λ-metadynamics method is general, and other variables such
             as order parameters to describe conformational changes can
             be easily combined with λ-metadynamics. This should allow
             for efficient samplings on high-dimension free energy
             landscapes. © 2011 American Chemical Society.},
   Doi = {10.1021/jz200808x},
   Key = {fds234925}
}

@article{fds234957,
   Author = {Lee, W and Zeng, X and Zhou, H-X and Bennett, V and Yang, W and Marszalek,
             PE},
   Title = {Full reconstruction of a vectorial protein folding pathway
             by atomic force microscopy and molecular dynamics
             simulations},
   Journal = {The Journal of biological chemistry},
   Volume = {286},
   Number = {10},
   Pages = {8708-},
   Year = {2011},
   ISSN = {0021-9258},
   url = {http://dx.doi.org/10.1074/jbc.A110.179697},
   Doi = {10.1074/jbc.A110.179697},
   Key = {fds234957}
}

@article{fds234988,
   Author = {Tam, ES and Parks, JJ and Shum, WW and Zhong, Y-W and Santiago-Berríos,
             MB and Zheng, X and Yang, W and Chan, GK-L and Abruña, HD and Ralph,
             DC},
   Title = {Single-molecule conductance of pyridine-terminated
             dithienylethene switch molecules},
   Journal = {ACS Nano},
   Volume = {5},
   Number = {6},
   Pages = {5115-5123},
   Year = {2011},
   ISSN = {1936-0851},
   url = {http://dx.doi.org/10.1021/nn201199b},
   Abstract = {We have investigated the conductance of individual optically
             switchable dithienylethene molecules in both their
             conducting closed configuration and nonconducting open
             configuration, using the technique of repeatedly formed
             break-junctions. We employed pyridine groups to link the
             molecules to gold electrodes in order to achieve relatively
             well-defined molecular contacts and stable conductance. For
             the closed form of each molecule, we observed a peak in the
             conductance histogram constructed without any data
             selection, allowing us to determine the conductance of the
             fully stretched molecules. For two different dithienylethene
             derivatives, these closed-configuration conductances were
             (3.3 ± 0.5) - 10-5G0 and (1.5 ± 0.5) - 10 -6G0, where G0
             is the conductance quantum. For the open configuration of
             the molecules, the existence of electrical conduction via
             the molecule was evident in traces of conductance versus
             junction displacement, but the conductance of the fully
             stretched molecules was less than the noise floor of our
             measurement. We can set a lower limit of 30 for the on/off
             ratio for the simplest dithienylethene derivative we have
             investigated. Density functional theory calculations predict
             an on/off ratio consistent with this result. © 2011
             American Chemical Society.},
   Doi = {10.1021/nn201199b},
   Key = {fds234988}
}

@article{fds234993,
   Author = {Ess, DH and Johnson, ER and Hu, X and Yang, W},
   Title = {Singlet-triplet energy gaps for diradicals from
             fractional-spin density-functional theory},
   Journal = {The Journal of Physical Chemistry Part A: Molecules,
             Spectroscopy, Kinetics, Environment and General
             Theory},
   Volume = {115},
   Number = {1},
   Pages = {76-83},
   Year = {2011},
   ISSN = {1089-5639},
   url = {http://dx.doi.org/10.1021/jp109280y},
   Abstract = {Open-shell singlet diradicals are difficult to model
             accurately within conventional Kohn-Sham (KS)
             density-functional theory (DFT). These methods are hampered
             by spin contamination because the KS determinant wave
             function is neither a pure spin state nor an eigenfunction
             of the S2 operator. Here we present a theoretical foray for
             using single-reference closed-shell ground states to
             describe diradicals by fractional-spin DFT (FS-DFT). This
             approach allows direct, self-consistent calculation of
             electronic properties using the electron density
             corresponding to the proper spin eigenfunction. The
             resulting FS-DFT approach is benchmarked against diradical
             singlet-triplet gaps for atoms and small molecules. We have
             also applied FS-DFT to the singlet-triplet gaps of
             hydrocarbon polyacenes. © 2010 American Chemical
             Society.},
   Doi = {10.1021/jp109280y},
   Key = {fds234993}
}

@article{fds234956,
   Author = {Lee, W and Zeng, X and Zhou, H-X and Bennett, V and Yang, W and Marszalek,
             PE},
   Title = {Full reconstruction of a vectorial protein folding pathway
             by atomic force microscopy and molecular dynamics
             simulations.},
   Journal = {The Journal of biological chemistry},
   Volume = {285},
   Number = {49},
   Pages = {38167-38172},
   Year = {2010},
   Month = {December},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20870713},
   Abstract = {During co-translational folding, the nascent polypeptide
             chain is extruded sequentially from the ribosome exit tunnel
             and is [corrected] under severe conformational constraints
             [corrected] dictated by the one-dimensional geometry of the
             tunnel. [corrected] How do such vectorial constraints impact
             the folding pathway? Here, we combine single-molecule atomic
             force spectroscopy and steered molecular dynamics
             simulations to examine protein folding in the presence of
             one-dimensional constraints that are similar to those
             imposed on the nascent polypeptide chain. The simulations
             exquisitely reproduced the experimental unfolding and
             refolding force extension relationships and led to the full
             reconstruction of the vectorial folding pathway of a large
             polypeptide, the 253-residue consensus ankyrin repeat
             protein, NI6C. We show that fully stretched and then relaxed
             NI6C starts folding by the formation of local secondary
             structures, followed by the nucleation of three N-terminal
             repeats. This rate-limiting step is then followed by the
             vectorial and sequential folding of the remaining repeats.
             However, after partial unfolding, when allowed to refold,
             the C-terminal repeats successively regain structures
             without any nucleation step by using the intact N-terminal
             repeats as a template. These results suggest a pathway for
             the co-translational folding of repeat proteins and have
             implications for mechanotransduction.},
   Doi = {10.1074/jbc.M110.179697},
   Key = {fds234956}
}

@article{fds234920,
   Author = {Cui, G and Fang, W and Yang, W},
   Title = {Efficient construction of nonorthogonal localized molecular
             orbitals in large systems.},
   Journal = {The Journal of Physical Chemistry Part A: Molecules,
             Spectroscopy, Kinetics, Environment and General
             Theory},
   Volume = {114},
   Number = {33},
   Pages = {8878-8883},
   Year = {2010},
   Month = {August},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20550205},
   Abstract = {Localized molecular orbitals (LMOs) are much more compact
             representations of electronic degrees of freedom than
             canonical molecular orbitals (CMOs). The most compact
             representation is provided by nonorthogonal localized
             molecular orbitals (NOLMOs), which are linearly independent
             but are not orthogonal. Both LMOs and NOLMOs are thus useful
             for linear-scaling calculations of electronic structures for
             large systems. Recently, NOLMOs have been successfully
             applied to linear-scaling calculations with density
             functional theory (DFT) and to reformulating time-dependent
             density functional theory (TDDFT) for calculations of
             excited states and spectroscopy. However, a challenge
             remains as NOLMO construction from CMOs is still inefficient
             for large systems. In this work, we develop an efficient
             method to accelerate the NOLMO construction by using
             predefined centroids of the NOLMO and thereby removing the
             nonlinear equality constraints in the original method ( J.
             Chem. Phys. 2004 , 120 , 9458 and J. Chem. Phys. 2000 , 112
             , 4 ). Thus, NOLMO construction becomes an unconstrained
             optimization. Its efficiency is demonstrated for the
             selected saturated and conjugated molecules. Our method for
             fast NOLMO construction should lead to efficient DFT and
             NOLMO-TDDFT applications to large systems.},
   Doi = {10.1021/jp1027838},
   Key = {fds234920}
}

@article{fds234953,
   Author = {Hu, X and Hu, H and Beratan, DN and Yang, W},
   Title = {A gradient-directed Monte Carlo approach for protein
             design.},
   Journal = {Journal of Computational Chemistry},
   Volume = {31},
   Number = {11},
   Pages = {2164-2168},
   Year = {2010},
   Month = {August},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20186860},
   Abstract = {We develop a new global optimization strategy,
             gradient-directed Monte Carlo (GDMC) sampling, to optimize
             protein sequence for a target structure using RosettaDesign.
             GDMC significantly improves the sampling of sequence space,
             compared to the classical Monte Carlo search protocol, for a
             fixed backbone conformation as well as for the simultaneous
             optimization of sequence and structure. As such, GDMC
             sampling enhances the efficiency of protein
             design.},
   Doi = {10.1002/jcc.21506},
   Key = {fds234953}
}

@article{fds234918,
   Author = {Heaton-Burgess, T and Yang, W},
   Title = {Structural manifestation of the delocalization error of
             density functional approximations: C(4N+2) rings and C(20)
             bowl, cage, and ring isomers.},
   Journal = {Journal of Chemical Physics},
   Volume = {132},
   Number = {23},
   Pages = {234113},
   Year = {2010},
   Month = {June},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20572695},
   Abstract = {The ground state structure of C(4N+2) rings is believed to
             exhibit a geometric transition from angle alternation (N <
             or = 2) to bond alternation (N > 2). All previous density
             functional theory (DFT) studies on these molecules have
             failed to reproduce this behavior by predicting either that
             the transition occurs at too large a ring size, or that the
             transition leads to a higher symmetry cumulene. Employing
             the recently proposed perspective of delocalization error
             within DFT we rationalize this failure of common density
             functional approximations (DFAs) and present calculations
             with the rCAM-B3LYP exchange-correlation functional that
             show an angle-to-bond-alternation transition between C(10)
             and C(14). The behavior exemplified here manifests itself
             more generally as the well known tendency of DFAs to bias
             toward delocalized electron distributions as favored by
             Huckel aromaticity, of which the C(4N+2) rings provide a
             quintessential example. Additional examples are the relative
             energies of the C(20) bowl, cage, and ring isomers; we show
             that the results from functionals with minimal
             delocalization error are in good agreement with CCSD(T)
             results, in contrast to other commonly used DFAs. An
             unbiased DFT treatment of electron delocalization is a key
             for reliable prediction of relative stability and hence the
             structures of complex molecules where many structure
             stabilization mechanisms exist.},
   Doi = {10.1063/1.3445266},
   Key = {fds234918}
}

@article{fds234971,
   Author = {Ke, S-H and Liu, R and Yang, W and Baranger, HU},
   Title = {Time-dependent transport through molecular
             junctions.},
   Journal = {Journal of Chemical Physics},
   Volume = {132},
   Number = {23},
   Pages = {234105},
   Year = {2010},
   Month = {June},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20572687},
   Abstract = {We investigate transport properties of molecular junctions
             under two types of bias--a short time pulse or an ac
             bias--by combining a solution for Green's functions in the
             time domain with electronic structure information coming
             from ab initio density functional calculations. We find that
             the short time response depends on lead structure, bias
             voltage, and barrier heights both at the molecule-lead
             contacts and within molecules. Under a low frequency ac
             bias, the electron flow either tracks or leads the bias
             signal (resistive or capacitive response) depending on
             whether the junction is perfectly conducting or not. For
             high frequency, the current lags the bias signal due to the
             kinetic inductance. The transition frequency is an intrinsic
             property of the junctions.},
   Doi = {10.1063/1.3435351},
   Key = {fds234971}
}

@article{fds234919,
   Author = {Johnson, ER and Keinan, S and Mori-Sánchez, P and Contreras-García,
             J and Cohen, AJ and Yang, W},
   Title = {Revealing noncovalent interactions.},
   Journal = {Journal of the American Chemical Society},
   Volume = {132},
   Number = {18},
   Pages = {6498-6506},
   Year = {2010},
   Month = {May},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20394428},
   Abstract = {Molecular structure does not easily identify the intricate
             noncovalent interactions that govern many areas of biology
             and chemistry, including design of new materials and drugs.
             We develop an approach to detect noncovalent interactions in
             real space, based on the electron density and its
             derivatives. Our approach reveals the underlying chemistry
             that compliments the covalent structure. It provides a rich
             representation of van der Waals interactions, hydrogen
             bonds, and steric repulsion in small molecules, molecular
             complexes, and solids. Most importantly, the method,
             requiring only knowledge of the atomic coordinates, is
             efficient and applicable to large systems, such as proteins
             or DNA. Across these applications, a view of nonbonded
             interactions emerges as continuous surfaces rather than
             close contacts between atom pairs, offering rich insight
             into the design of new and improved ligands.},
   Doi = {10.1021/ja100936w},
   Key = {fds234919}
}

@article{fds234915,
   Author = {Zheng, X and Ke, S-H and Yang, W},
   Title = {Conductive junctions with parallel graphene
             sheets.},
   Journal = {Journal of Chemical Physics},
   Volume = {132},
   Number = {11},
   Pages = {114703},
   Year = {2010},
   Month = {March},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20331312},
   Abstract = {The establishment of conductive graphene-molecule-graphene
             junction is investigated through first-principles electronic
             structure calculations and quantum transport calculations.
             The junction consists of a conjugated molecule connecting
             two parallel graphene sheets. The effects of molecular
             electronic states, structure relaxation, and
             molecule-graphene contact on the conductance of the junction
             are explored. A conductance as large as 0.38 conductance
             quantum is found achievable with an appropriately oriented
             dithiophene bridge. This work elucidates the designing
             principles of promising nanoelectronic devices based on
             conductive graphene-molecule-graphene junctions.},
   Doi = {10.1063/1.3357416},
   Key = {fds234915}
}

@article{fds234947,
   Author = {Zeng, X and Hu, H and Zhou, H-X and Marszalek, PE and Yang,
             W},
   Title = {Equilibrium sampling for biomolecules under mechanical
             tension.},
   Journal = {Biophysical Journal},
   Volume = {98},
   Number = {4},
   Pages = {733-740},
   Year = {2010},
   Month = {February},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20159170},
   Abstract = {In the studies of force-induced conformational transitions
             of biomolecules, the large timescale difference from
             experiments presents the challenge of obtaining convergent
             sampling for molecular dynamics simulations. To circumvent
             this fundamental problem, an approach combining the
             replica-exchange method and umbrella sampling (REM-US) was
             developed to simulate mechanical stretching of biomolecules
             under equilibrium conditions. Equilibrium properties of
             conformational transitions can be obtained directly from
             simulations without further assumptions. To test the
             performance, we carried out REM-US simulations of atomic
             force microscope (AFM) stretching and relaxing measurements
             on the polysaccharide pustulan, a (1-->6)-beta-D-glucan,
             which undergoes well-characterized rotameric transitions in
             the backbone bonds. With significantly enhanced sampling
             convergence and efficiency, the REM-US approach closely
             reproduced the equilibrium force-extension curves measured
             in AFM experiments. Consistent with the reversibility in the
             AFM measurements, the new approach generated identical
             force-extension curves in both stretching and relaxing
             simulations-an outcome not reported in previous studies,
             proving that equilibrium conditions were achieved in the
             simulations. REM-US may provide a robust approach to
             modeling of mechanical stretching on polysaccharides and
             even nucleic acids.},
   Doi = {10.1016/j.bpj.2009.11.004},
   Key = {fds234947}
}

@article{fds234914,
   Author = {Hu, X and Yang, W},
   Title = {Accelerating self-consistent field convergence with the
             augmented Roothaan-Hall energy function.},
   Journal = {Journal of Chemical Physics},
   Volume = {132},
   Number = {5},
   Pages = {054109},
   Year = {2010},
   Month = {February},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20136307},
   Abstract = {Based on Pulay's direct inversion iterative subspace (DIIS)
             approach, we present a method to accelerate self-consistent
             field (SCF) convergence. In this method, the quadratic
             augmented Roothaan-Hall (ARH) energy function, proposed
             recently by Høst and co-workers [J. Chem. Phys. 129, 124106
             (2008)], is used as the object of minimization for obtaining
             the linear coefficients of Fock matrices within DIIS. This
             differs from the traditional DIIS of Pulay, which uses an
             object function derived from the commutator of the density
             and Fock matrices. Our results show that the present
             algorithm, abbreviated ADIIS, is more robust and efficient
             than the energy-DIIS (EDIIS) approach. In particular,
             several examples demonstrate that the combination of ADIIS
             and DIIS ("ADIIS+DIIS") is highly reliable and efficient in
             accelerating SCF convergence.},
   Doi = {10.1063/1.3304922},
   Key = {fds234914}
}

@article{fds234913,
   Author = {Cui, G and Fang, W and Yang, W},
   Title = {Reformulating time-dependent density functional theory with
             non-orthogonal localized molecular orbitals.},
   Journal = {Physical Chemistry Chemical Physics},
   Volume = {12},
   Number = {2},
   Pages = {416-421},
   Year = {2010},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20023819},
   Abstract = {Time-dependent density functional theory (TDDFT) has broad
             application in the study of electronic response, excitation
             and transport. To extend such application to large and
             complex systems, we develop a reformulation of TDDFT
             equations in terms of non-orthogonal localized molecular
             orbitals (NOLMOs). NOLMO is the most localized
             representation of electronic degrees of freedom and has been
             used in ground state calculations. In atomic orbital (AO)
             representation, the sparsity of NOLMO is transferred to the
             coefficient matrix of molecular orbitals (MOs). Its novel
             use in TDDFT here leads to a very simple form of time
             propagation equations which can be solved with
             linear-scaling effort. We have tested the method for several
             long-chain saturated and conjugated molecular systems within
             the self-consistent charge density-functional tight-binding
             method (SCC-DFTB) and demonstrated its accuracy. This opens
             up pathways for TDDFT applications to large bio- and
             nano-systems.},
   Doi = {10.1039/b916688b},
   Key = {fds234913}
}

@article{fds234916,
   Author = {Hu, H and Yang, W},
   Title = {Elucidating solvent contributions to solution reactions with
             Ab initio QM/MM methods},
   Journal = {The Journal of Physical Chemistry Part B: Condensed Matter,
             Materials, Surfaces, Interfaces and Biophysical},
   Volume = {114},
   Number = {8},
   Pages = {2755-2759},
   Year = {2010},
   ISSN = {1520-6106},
   url = {http://hdl.handle.net/10161/4075 Duke open
             access},
   Abstract = {Computer simulations of reaction processes in solution in
             general rely on the definition of a reaction coordinate and
             the determination of the thermodynamic changes of the system
             along the reaction coordinate. The reaction coordinate often
             is constituted of characteristic geometrical properties of
             the reactive solute species, while the contributions of
             solvent molecules are implicitly included in the
             thermodynamics of the solute degrees of freedoms. However,
             solvent dynamics can provide the driving force for the
             reaction process, and in such cases explicit description of
             the solvent contribution in the free energy of the reaction
             process becomes necessary. We report here a method that can
             be used to analyze the solvent contributions to the reaction
             activation free energies from the combined QM/MM minimum
             free-energy path simulations. The method was applied to the
             self-exchange SN2 reaction of CH3Cl + Cl-, showing that the
             importance of solvent-solute interactions to the reaction
             process. The results were further discussed in the context
             of coupling between solvent and solute molecules in reaction
             processes. © 2010 American Chemical Society.},
   Doi = {10.1021/jp905886q},
   Key = {fds234916}
}

@article{fds234917,
   Author = {Chen, Z and Concepcion, JJ and Hu, X and Yang, W and Hoertz, PG and Meyer,
             TJ},
   Title = {Concerted O atom-proton transfer in the O - O bond forming
             step in water oxidation},
   Journal = {Proceedings of the National Academy of Sciences of
             USA},
   Volume = {107},
   Number = {16},
   Pages = {7225-7229},
   Year = {2010},
   ISSN = {0027-8424},
   url = {http://dx.doi.org/10.1073/pnas.1001132107},
   Abstract = {As the terminal step in photosystem II, and a potential
             half-reaction for artificial photosynthesis, water oxidation
             (2H2O → O2 + 4e-+ 4H+) is key, but it imposes a
             significant mechanistic challenge with requirements for both
             4e-/4H+ loss and O - O bond formation. Significant progress
             in water oxidation catalysis has been achieved recently by
             use of single-site Ru metal complex catalysts such as
             [Ru(Mebimpy)(bpy)(OH2)]2+ [Mebimpy = 2,6-bis(1-methylbenzimidazol-2-yl)pyridine;
             bpy = 2,2′-bipyridine]. When oxidized from RuII-OH22+ to
             RuV = O3+, these complexes undergo O - O bond formation by
             O-atom attack on a H2O molecule, which is often the
             rate-limiting step. Microscopic details of O - O bond
             formation have been explored by quantum mechanical/molecular
             mechanical (QM/MM) simulations the results of which provide
             detailed insight into mechanism and a strategy for enhancing
             catalytic rates. It utilizes added bases as proton acceptors
             and concerted atom-proton transfer (APT) with O-atom
             transfer to the O atom of a water molecule in concert with
             proton transfer to the base (B). Base catalyzed APT
             reactivity in water oxidation is observed both in solution
             and on the surfaces of oxide electrodes derivatized by
             attached phosphonated metal complex catalysts. These results
             have important implications for catalytic, electrocatalytic,
             and photoelectrocatalytic water oxidation.},
   Doi = {10.1073/pnas.1001132107},
   Key = {fds234917}
}

@article{fds234921,
   Author = {Cui, G and Yang, W},
   Title = {Challenges with range-separated exchange-correlation
             functionals in time-dependent density functional theory
             calculations},
   Journal = {Molecular Physics},
   Volume = {108},
   Number = {19-20},
   Pages = {2745-2750},
   Year = {2010},
   ISSN = {0026-8976},
   url = {http://dx.doi.org/10.1080/00268976.2010.523442},
   Abstract = {The conventional approximate exchange-correlation
             functionals and kernels can lead to a large error in
             time-dependent density functional theory (TDDFT)
             calculations in certain cases, such as in the descriptions
             of charge-transfer excited states, Rydberg states, and
             double excitations, which can be remedied to some degree
             with the recently developed range-separated
             exchange-correlation functionals. How do these
             range-separated functionals perform in the TDDFT
             calculations? In this work, we explored the S0(A′)→ T
             1(A′) and S0 (A′)→ S1(A′ ) transition energies of
             C2H4 and other molecules by TDDFT methods and ΔSCF
             calculations in density functional theory (DFT), with
             several regular and range-separated exchange-correlation
             functionals. We have found the following: (1) for the S0 →
             S1 transition, both range- and non-range-separated
             exchange-correlation functionals work well and consistently
             in the TDDFT calculations; (2) for the S0 → T1 transition,
             the used range-separated exchange-correlation functionals
             work on average worse than the non-separated ones in the
             TDDFT calculations; in the SCF DFT calculations, however,
             both kinds of functionals achieve a similar performance.
             Because of the common approximations used in DFT and TDDFT,
             our present computational results suggest that the adiabatic
             approximation error in the range-separated
             exchange-correlation functionals is much larger than that in
             the non-range-separated ones for the S0 → T1 transition,
             and the adiabatic approximation error for the S0 → T1
             transition - a spin-flip process - is larger than that for
             the S0 → S1 transition. These findings will be useful for
             designing better exchange-correlation functionals and
             kernels that will work well not only for excited singlet
             states, but also for excited triplet states. Furthermore,
             this study will provide insights into the drawbacks of the
             present approximate exchange-correlation functionals and
             kernels used in TDDFT calculations. © 2010 Taylor &amp;
             Francis.},
   Doi = {10.1080/00268976.2010.523442},
   Key = {fds234921}
}

@article{fds234922,
   Author = {Johnson, ER and Yang, W and Davidson, ER},
   Title = {Spin-state splittings, highest-occupied-molecular-orbital
             and lowest-unoccupied-molecular-orbital energies, and
             chemical hardness},
   Journal = {Journal of Chemical Physics},
   Volume = {133},
   Number = {16},
   Year = {2010},
   ISSN = {0021-9606},
   url = {http://hdl.handle.net/10161/3345 Duke open
             access},
   Abstract = {It is known that the exact density functional must give
             ground-state energies that are piecewise linear as a
             function of electron number. In this work we prove that this
             is also true for the lowest-energy excited states of
             different spin or spatial symmetry. This has three important
             consequences for chemical applications: the ground state of
             a molecule must correspond to the state with the maximum
             highest-occupied-molecular-orbital energy, minimum
             lowest-unoccupied-molecular-orbital energy, and maximum
             chemical hardness. The beryllium, carbon, and vanadium
             atoms, as well as the CH2 and C 3 H3 molecules are
             considered as illustrative examples. Our result also
             directly and rigorously connects the ionization potential
             and electron affinity to the stability of spin states. ©
             2010 American Institute of Physics.},
   Doi = {10.1063/1.3497190},
   Key = {fds234922}
}

@article{fds234951,
   Author = {Hu, X and Xiao, D and Keinan, S and Asselberghs, I and Therien, MJ and Clays, K and Yang, W and Beratan, DN},
   Title = {Predicting the frequency dispersion of electronic
             hyperpolarizabilities on the basis of absorption data and
             thomas-kuhn sum rules},
   Journal = {The Journal of Physical Chemistry C},
   Volume = {114},
   Number = {5},
   Pages = {2349-2359},
   Year = {2010},
   ISSN = {1932-7447},
   url = {http://hdl.handle.net/10161/4078 Duke open
             access},
   Abstract = {Successfully predicting the frequency dispersion of
             electronic hyperpolarizabilities is an unresolved challenge
             in materials science and electronic structure theory. We
             show that the generalized Thomas-Kuhn sum rules, combined
             with linear absorption data and measured hyperpolarizability
             at one or two frequencies, may be used to predict the entire
             frequency-dependent electronic hyperpolarizability spectrum.
             This treatment includes two- and three-level contributions
             that arise from the lowest two or three excited electronic
             state manifolds, enabling us to describe the unusual
             observed frequency dispersion of the dynamic
             hyperpolarizability in high oscillator strength M-PZn
             chromophores, where (porphinato)zinc(II) (PZn) and
             metal(II)polypyridyl (M) units are connected via an ethyne
             unit that aligns the high oscillator strength transition
             dipoles of these components in a head-to-tail arrangement.
             We show that some of these structures can possess very
             similar linear absorption spectra yet manifest dramatically
             different frequency dependent hyperpolarizabilities, because
             of three-level contributions that result from excited
             state-to excited state transition dipoles among charge
             polarized states. Importantly, this approach provides a
             quantitative scheme to use linear optical absorption spectra
             and very limited individual hyperpolarizability measurements
             to predict the entire frequency-dependent nonlinear optical
             response. Copyright © 2010 American Chemical
             Society.},
   Doi = {10.1021/jp911556x},
   Key = {fds234951}
}

@article{fds234952,
   Author = {Hammill, JT and Contreras-García, J and Virshup, AM and Beratan, DN and Yang, W and Wipf, P},
   Title = {Synthesis and chemical diversity analysis of
             bicyclo[3.3.1]non-3-en-2-ones},
   Journal = {Tetrahedron},
   Volume = {66},
   Number = {31},
   Pages = {5852-5862},
   Year = {2010},
   ISSN = {0040-4020},
   url = {http://dx.doi.org/10.1016/j.tet.2010.04.112},
   Abstract = {Functionalized bicyclo[3.3.1]non-3-en-2-ones are obtained
             from commercially available phenols by a hypervalent iodine
             oxidation, enone epoxidation, epoxide thiolysis, and
             intramolecular aldol reaction sequence. Reaction
             optimization studies identified room temperature as well as
             microwave-mediated procedures, providing moderate to good
             yields (57-88%) in the thiophenol-mediated epoxide opening
             and intramolecular aldol reaction. In addition, the
             isolation of a key intermediate and in situ NMR studies
             supported the mechanistic hypothesis. The bicyclic ring
             products occupy novel chemical space according to ChemGPS
             and Chemaxon chemical diversity and cheminformatics
             analyses. © 2010 Elsevier Ltd.},
   Doi = {10.1016/j.tet.2010.04.112},
   Key = {fds234952}
}

@article{fds235006,
   Author = {Hu, X and Beratan, DN and Yang, W},
   Title = {A gradient-directed Monte Carlo method for global
             optimization in a discrete space: application to protein
             sequence design and folding.},
   Journal = {Journal of Chemical Physics},
   Volume = {131},
   Number = {15},
   Pages = {154117},
   Year = {2009},
   Month = {October},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20568857},
   Abstract = {We apply the gradient-directed Monte Carlo (GDMC) method to
             select optimal members of a discrete space, the space of
             chemically viable proteins described by a model Hamiltonian.
             In contrast to conventional Monte Carlo approaches, our GDMC
             method uses local property gradients with respect to
             chemical variables that have discrete values in the actual
             systems, e.g., residue types in a protein sequence. The
             local property gradients are obtained from the interpolation
             of discrete property values, following the linear
             combination of atomic potentials scheme developed recently
             [M. Wang et al., J. Am. Chem. Soc. 128, 3228 (2006)]. The
             local property derivative information directs the search
             toward the global minima while the Metropolis criterion
             incorporated in the method overcomes barriers between local
             minima. Using the simple HP lattice model, we apply the GDMC
             method to protein sequence design and folding. The GDMC
             algorithm proves to be particularly efficient, suggesting
             that this strategy can be extended to other discrete
             optimization problems in addition to inverse molecular
             design.},
   Doi = {10.1063/1.3236834},
   Key = {fds235006}
}

@article{fds235009,
   Author = {Balabin, IA and Yang, W and Beratan, DN},
   Title = {Coarse-grained modeling of allosteric regulation in protein
             receptors.},
   Journal = {Proceedings of the National Academy of Sciences of
             USA},
   Volume = {106},
   Number = {34},
   Pages = {14253-14258},
   Year = {2009},
   Month = {August},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19706508},
   Abstract = {Allosteric regulation provides highly specific ligand
             recognition and signaling by transmembrane protein
             receptors. Unlike functions of protein molecular machines
             that rely on large-scale conformational transitions, signal
             transduction in receptors appears to be mediated by more
             subtle structural motions that are difficult to identify. We
             describe a theoretical model for allosteric regulation in
             receptors that addresses a fundamental riddle of signaling:
             What are the structural origins of the receptor agonism
             (specific signaling response to ligand binding)? The model
             suggests that different signaling pathways in bovine
             rhodopsin or human beta(2)-adrenergic receptor can be
             mediated by specific structural motions in the receptors. We
             discuss implications for understanding the receptor agonism,
             particularly the recently observed "biased agonism"
             (selected activation of specific signaling pathways), and
             for developing rational structure-based drug-design
             strategies.},
   Doi = {10.1073/pnas.0901811106},
   Key = {fds235009}
}

@article{fds313880,
   Author = {Balabin, IA and Yang, W and Beratan, DN},
   Title = {Modeling allosteric regulation in GPCRs: Toward rational
             structure-based drug design},
   Journal = {ACS National Meeting Book of Abstracts},
   Volume = {238},
   Year = {2009},
   Month = {August},
   ISSN = {0065-7727},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000207861904149&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds313880}
}

@article{fds318100,
   Author = {Yang, W},
   Title = {Free energies and mechanisms of chemical reactions in
             enzymes and in solution with QMMM minimum free energy
             path},
   Journal = {ACS National Meeting Book of Abstracts},
   Volume = {238},
   Year = {2009},
   Month = {August},
   Key = {fds318100}
}

@article{fds235003,
   Author = {Kasper, AC and Moon, EJ and Hu, X and Park, Y and Wooten, CM and Kim, H and Yang, W and Dewhirst, MW and Hong, J},
   Title = {Analysis of HIF-1 inhibition by manassantin A and analogues
             with modified tetrahydrofuran configurations.},
   Journal = {Bioorganic & Medicinal Chemistry Letters},
   Volume = {19},
   Number = {14},
   Pages = {3783-3786},
   Year = {2009},
   Month = {July},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19423348},
   Abstract = {We have shown that manassantin A downregulated the
             HIF-1alpha expression and inhibited the secretion of VEGF.
             We have also demonstrated that the 2,3-cis-3,4-trans-4,5-cis-configuration
             of the tetrahydrofuran is critical to the HIF-1 inhibition
             of manassantin A.},
   Doi = {10.1016/j.bmcl.2009.04.071},
   Key = {fds235003}
}

@article{fds235008,
   Author = {Bulat, FA and Couchman, L and Yang, W},
   Title = {Contact geometry and conductance of crossed nanotube
             junctions under pressure.},
   Journal = {Nano Letters},
   Volume = {9},
   Number = {5},
   Pages = {1759-1763},
   Year = {2009},
   Month = {May},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19331377},
   Abstract = {We explored the relative stability, structure, and
             conductance of crossed nanotube junctions with dispersion
             corrected density functional theory. We found that the most
             stable junction geometry, not studied before, displays the
             smallest conductance. While the conductance increases as
             force is applied, it levels off very rapidly. This behavior
             contrasts with a less stable junction geometry that show
             steady increase of the conductance as force is applied.
             Electromechanical sensing devices based on this effect
             should exploit the conductance changes close to
             equilibrium.},
   Doi = {10.1021/nl803388m},
   Key = {fds235008}
}

@article{fds234997,
   Author = {Zeng, X and Hu, H and Hu, X and Yang, W},
   Title = {Calculating solution redox free energies with ab initio
             quantum mechanical/molecular mechanical minimum free energy
             path method.},
   Journal = {Journal of Chemical Physics},
   Volume = {130},
   Number = {16},
   Pages = {164111},
   Year = {2009},
   Month = {April},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19405565},
   Abstract = {A quantum mechanical/molecular mechanical minimum free
             energy path (QM/MM-MFEP) method was developed to calculate
             the redox free energies of large systems in solution with
             greatly enhanced efficiency for conformation sampling. The
             QM/MM-MFEP method describes the thermodynamics of a system
             on the potential of mean force surface of the solute degrees
             of freedom. The molecular dynamics (MD) sampling is only
             carried out with the QM subsystem fixed. It thus avoids
             "on-the-fly" QM calculations and thus overcomes the high
             computational cost in the direct QM/MM MD sampling. In the
             applications to two metal complexes in aqueous solution, the
             new QM/MM-MFEP method yielded redox free energies in good
             agreement with those calculated from the direct QM/MM MD
             method. Two larger biologically important redox molecules,
             lumichrome and riboflavin, were further investigated to
             demonstrate the efficiency of the method. The enhanced
             efficiency and uncompromised accuracy are especially
             significant for biochemical systems. The QM/MM-MFEP method
             thus provides an efficient approach to free energy
             simulation of complex electron transfer reactions.},
   Doi = {10.1063/1.3120605},
   Key = {fds234997}
}

@article{fds234999,
   Author = {Parks, JM and Hu, H and Rudolph, J and Yang, W},
   Title = {Mechanism of Cdc25B phosphatase with the small molecule
             substrate p-nitrophenyl phosphate from QM/MM-MFEP
             calculations.},
   Journal = {The Journal of Physical Chemistry Part B: Condensed Matter,
             Materials, Surfaces, Interfaces and Biophysical},
   Volume = {113},
   Number = {15},
   Pages = {5217-5224},
   Year = {2009},
   Month = {April},
   ISSN = {1520-6106},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19301836},
   Abstract = {Cdc25B is a dual-specificity phosphatase that catalyzes the
             dephosphorylation of the Cdk2/CycA protein complex. This
             enzyme is an important regulator of the human cell cycle and
             has been identified as a potential anticancer target. In
             general, protein tyrosine phosphatases are thought to bind
             the dianionic form of the phosphate and employ general acid
             catalysis via the Asp residue in the highly conserved
             WPD-loop. However, the Cdc25 phosphatases form a special
             subfamily based on their distinct differences from other
             protein tyrosine phosphatases. Although Cdc25B contains the
             (H/V)CX(5)R catalytic motif present in all other protein
             tyrosine phosphatases, it lacks an analogous catalytic acid
             residue. No crystallographic data currently exist for the
             complex of Cdc25B with Cdk2/CycA, so in addition to its
             natural protein substrate, experimental and theoretical
             studies are often carried out with small molecule
             substrates. In an effort to gain understanding of the
             dephosphorylation mechanism of Cdc25B with a commonly used
             small molecule substrate, we have performed simulations of
             the rate-limiting step of the reaction catalyzed by Cdc25B
             with the substrate p-nitrophenyl phosphate using the
             recently developed QM/MM Minimum Free Energy Path method (Hu
             et al. J. Chem. Phys. 2008, 034105). We have simulated the
             first step of the reaction with both the monoanionic and the
             dianionic forms of the substrate, and our calculations favor
             a mechanism involving the monoanionic form. Thus, Cdc25 may
             employ a unique dephosphorylation mechanism among protein
             tyrosine phosphatases, at least in the case of the small
             molecule substrate p-nitrophenyl phosphate.},
   Doi = {10.1021/jp805137x},
   Key = {fds234999}
}

@article{fds235002,
   Author = {Ke, S-H and Yang, W and Curtarolo, S and Baranger,
             HU},
   Title = {Thermopower of molecular junctions: an ab initio
             study.},
   Journal = {Nano Letters},
   Volume = {9},
   Number = {3},
   Pages = {1011-1014},
   Year = {2009},
   Month = {March},
   ISSN = {1530-6984},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19203208},
   Abstract = {Molecular nanojunctions may support efficient thermoelectric
             conversion through enhanced thermopower. Recently, this
             quantity has been measured for several conjugated molecular
             nanojunctions with gold electrodes. Considering the wide
             variety of possible metal/molecule systems-almost none of
             which have been studied-it seems highly desirable to be able
             to calculate the thermopower of junctions with reasonable
             accuracy and high efficiency. To address this task, we
             demonstrate an effective approach based on the single
             particle green function (SPGF) method combined with density
             functional theory (DFT) using B3LYP and PBE0 energy
             functionals. Systematic good agreement between theory and
             experiment is obtained; indeed, much better agreement is
             found here than for comparable calculations of the
             conductance.},
   Doi = {10.1021/nl8031229},
   Key = {fds235002}
}

@article{fds235000,
   Author = {Mori-Sánchez, P and Cohen, AJ and Yang, W},
   Title = {Discontinuous nature of the exchange-correlation functional
             in strongly correlated systems.},
   Journal = {Physical Review Letters},
   Volume = {102},
   Number = {6},
   Pages = {066403},
   Year = {2009},
   Month = {February},
   ISSN = {0031-9007},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19257614},
   Abstract = {Standard approximations for the exchange-correlation
             functional have been found to give big errors for the
             linearity condition of fractional charges, leading to
             delocalization error, and the constancy condition of
             fractional spins, leading to static correlation error. These
             two conditions are now unified and extended to states with
             both fractional charge and fractional spin to give a much
             more stringent condition: the exact energy functional is a
             plane, linear along the fractional charge coordinate and
             constant along the fractional spin coordinate with a line of
             discontinuity at the integer. Violation of this condition
             underlies the failure of all known approximate functionals
             to describe the gaps in strongly correlated systems. It is
             shown that explicitly discontinuous functionals of the
             density or orbitals that go beyond these currently used
             smooth approximations is the key for the application of
             density functional theory to strongly correlated
             systems.},
   Doi = {10.1103/PhysRevLett.102.066403},
   Key = {fds235000}
}

@article{fds234998,
   Author = {Rinderspacher, BC and Andzelm, J and Rawlett, A and Dougherty, J and Beratan, DN and Yang, W},
   Title = {Discrete optimization of electronic hyperpolarizabilities in
             a chemical subspace},
   Journal = {Journal of Chemical Theory and Computation},
   Volume = {5},
   Number = {12},
   Pages = {3321-3329},
   Year = {2009},
   ISSN = {1549-9618},
   url = {http://dx.doi.org/10.1021/ct900325p},
   Abstract = {We introduce a general optimization algorithm based on an
             interpolation of property values on a hypercube. Each vertex
             of the hypercube represents a molecule, while the interior
             of the interpolation represents a virtual superposition
             ("alchemical" mutation) of molecules. The resultant
             algorithm is similar to branch-and-bound/tree-search
             methods. We apply the algorithm to the optimization of the
             first electronic hyperpolarizability for several tolane
             libraries. The search includes structural and conformational
             information. Geometries were optimized using the AM1
             Hamiltonian, and first hyperpolarizabilities were computed
             using the INDO/S method. Even for small libraries, a
             significant improvement of the hyperpolarizability, up to a
             factor of ca. 4, was achieved. The algorithm was validated
             for efficiency and reproduced known experimental results.
             The algorithm converges to a local optimum at a
             computational cost on the order of the logarithm of the
             library size, making large libraries accessible. For larger
             libraries, the improvement was accomplished by performing
             electronic structure calculations on less than 0.01% of the
             compounds in the larger libraries. Alternation of electron
             donating and accepting groups in the tolane scaffold was
             found to produce candidates with large hyperpolarizabilities
             consistently. © 2009 American Chemical Society.},
   Doi = {10.1021/ct900325p},
   Key = {fds234998}
}

@article{fds235001,
   Author = {Li, Z and Wang, C-Y and Ke, S-H and Yang, W},
   Title = {First-principles study for transport properties of defective
             carbon nanotubes with oxygen adsorption},
   Journal = {The European Physical Journal B - Condensed Matter and
             Complex Systems},
   Volume = {69},
   Number = {3},
   Pages = {375-382},
   Year = {2009},
   ISSN = {1434-6028},
   url = {http://dx.doi.org/10.1140/epjb/e2009-00179-2},
   Abstract = {Oxygen gas usually presents in carbon nanotube (CNT) based
             devices and can affect their transport properties. Here, we
             perform simulations for O 2 adsorption on a (5, 5) CNT with
             a double vacancy. We first use first-principles plane-wave
             calculation to optimize the structures and then use
             single-particle Green function method to study their
             transport properties. It is found that an O 2 can be either
             physisorbed or chemisorbed on the defective CNT. The
             physisorption has only minor effects on the transport while
             the chemisorption can improve it and the resulting
             conductance is affected by the orientation of the O 2
             bonding. © 2009 EDP Sciences, SIF, Springer-Verlag Berlin
             Heidelberg.},
   Doi = {10.1140/epjb/e2009-00179-2},
   Key = {fds235001}
}

@article{fds235004,
   Author = {Hu, X and Beratan, DN and Yang, W},
   Title = {Emergent strategies for inverse molecular
             design},
   Journal = {Science in China Series B-Chemistry},
   Volume = {52},
   Number = {11},
   Pages = {1769-1776},
   Year = {2009},
   ISSN = {1006-9291},
   url = {http://dx.doi.org/10.1007/s11426-009-0260-3},
   Abstract = {Molecular design is essential and ubiquitous in chemistry,
             physics, biology, and material science. The immense space of
             available candidate molecules requires novel optimization
             strategies and algorithms for exploring the space and
             achieving efficient and effective molecular design. This
             paper summarizes the current progress toward developing
             practical theoretical optimization schemes for molecular
             design. In particular, we emphasize emergent strategies for
             inverse molecular design. Several representative design
             examples, based on recently developed strategies, are
             described to demonstrate the principles of inverse molecular
             design. © 2009 Science in China Press and Springer Berlin
             Heidelberg.},
   Doi = {10.1007/s11426-009-0260-3},
   Key = {fds235004}
}

@article{fds235005,
   Author = {Hu, H and Yang, W},
   Title = {Development and application of ab initio QM/MM methods for
             mechanistic simulation of reactions in solution and in
             enzymes},
   Journal = {Journal of Molecular Structure: THEOCHEM},
   Volume = {898},
   Number = {1-3},
   Pages = {17-30},
   Year = {2009},
   ISSN = {0166-1280},
   url = {http://dx.doi.org/10.1016/j.theochem.2008.12.025},
   Abstract = {Determining the free energies and mechanisms of chemical
             reactions in solution and enzymes is a major challenge. For
             such complex reaction processes, combined quantum
             mechanics/molecular mechanics (QM/MM) method is the most
             effective simulation method to provide an accurate and
             efficient theoretical description of the molecular system.
             The computational costs of ab initio QM methods, however,
             have limited the application of ab initio QM/MM methods.
             Recent advances in ab initio QM/MM methods allowed accurate
             simulation of the free energies for reactions in solution
             and in enzymes and thus paved the way for broader
             applications of the ab initio QM/MM methods. We review here
             the theoretical developments and applications of the ab
             initio QM/MM methods, focusing on the determination of
             reaction path and the free energies of the reaction
             processes in solution and enzymes. © 2008 Elsevier B.V. All
             rights reserved.},
   Doi = {10.1016/j.theochem.2008.12.025},
   Key = {fds235005}
}

@article{fds235007,
   Author = {Cohen, AJ and Mori Sanchez and P and Yang, WT},
   Title = {Second-order perturbation theory with fractional charges and
             fractional spins},
   Journal = {Journal of Chemical Theory and Computation},
   Volume = {5},
   Number = {5},
   Pages = {786-792},
   Year = {2009},
   ISSN = {1549-9618},
   url = {http://dx.doi.org/10.1021/ct8005419},
   Abstract = {In this work the behavior of MP2 for fractional occupations
             is investigated. The consideration of fractional charge
             behavior gives a simple derivation of an expression for the
             chemical potential (or the derivative of energy with respect
             to the number of electrons) of MP2. A generalized optimized
             effective potential formalism (OEP) has been developed in
             which the OEP is a nonlocal potential, which can be applied
             to explicit functionals of the orbitals and eigenvalues and
             also facilitates the evaluation of the chemical potential.
             The MP2 derivative improves upon the corresponding Koopmans'
             theorem in Hartree-Fock theory for the ionization energy and
             also gives a good estimate of the electron affinity. In
             strongly correlated systems with degeneracies and fractional
             spins, MP2 diverges, and another corrected second-order
             perturbative method ameliorates this failure for the energy
             but still does not recapture the correct behavior for the
             energy derivatives that yield the gap. Overall we present a
             view of wave function based methods and their behavior for
             fractional charges and spins that offers insight into the
             application of these methods to challenging chemical
             problems. © 2009 American Chemical Society.},
   Doi = {10.1021/ct8005419},
   Key = {fds235007}
}

@article{fds304408,
   Author = {Cohen, AJ and Mori-Sánchez, P and Yang, W},
   Title = {Second-order perturbation theory with fractional charges and
             fractional spins},
   Journal = {Journal of Chemical Theory and Computation},
   Volume = {5},
   Number = {4},
   Pages = {786-792},
   Year = {2009},
   ISSN = {1549-9618},
   url = {http://dx.doi.org/10.1021/ct8005419},
   Abstract = {In this work the behavior of MP2 for fractional occupations
             is investigated. The consideration of fractional charge
             behavior gives a simple derivation of an expression for the
             chemical potential (or the derivative of energy with respect
             to the number of electrons) of MP2. A generalized optimized
             effective potential formalism (OEP) has been developed in
             which the OEP is a nonlocal potential, which can be applied
             to explicit functionals of the orbitals and eigenvalues and
             also facilitates the evaluation of the chemical potential.
             The MP2 derivative improves upon the corresponding Koopmans'
             theorem in Hartree-Fock theory for the ionization energy and
             also gives a good estimate of the electron affinity. In
             strongly correlated systems with degeneracies and fractional
             spins, MP2 diverges, and another corrected second-order
             perturbative method ameliorates this failure for the energy
             but still does not recapture the correct behavior for the
             energy derivatives that yield the gap. Overall we present a
             view of wave function based methods and their behavior for
             fractional charges and spins that offers insight into the
             application of these methods to challenging chemical
             problems. © 2009 American Chemical Society.},
   Doi = {10.1021/ct8005419},
   Key = {fds304408}
}

@article{fds235021,
   Author = {Johnson, ER and Mori-Sánchez, P and Cohen, AJ and Yang,
             W},
   Title = {Delocalization errors in density functionals and
             implications for main-group thermochemistry.},
   Journal = {Journal of Chemical Physics},
   Volume = {129},
   Number = {20},
   Pages = {204112},
   Year = {2008},
   Month = {November},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19045857},
   Abstract = {The difficulty of approximate density functionals in
             describing the energetics of Diels-Alder reactions and
             dimerization of aluminum complexes is analyzed. Both of
             these reaction classes involve formation of cyclic or
             bicyclic products, which are found to be underbound by the
             majority of functionals considered. We present a consistent
             view of these results from the perspective of delocalization
             error. This error causes approximate functionals to give too
             low energy for delocalized densities or too high energy for
             localized densities, as in the cyclic and bicyclic reaction
             products. This interpretation allows us to understand better
             a wide range of errors in main-group thermochemistry
             obtained with popular density functionals. In general,
             functionals with minimal delocalization error should be used
             for theoretical studies of reactions where there is a loss
             of extended conjugation or formation of highly branched,
             cyclic, and cagelike molecules.},
   Doi = {10.1063/1.3021474},
   Key = {fds235021}
}

@article{fds235019,
   Author = {Keinan, S and Therien, MJ and Beratan, DN and Yang,
             W},
   Title = {Molecular design of porphyrin-based nonlinear optical
             materials.},
   Journal = {The Journal of Physical Chemistry Part A: Molecules,
             Spectroscopy, Kinetics, Environment and General
             Theory},
   Volume = {112},
   Number = {47},
   Pages = {12203-12207},
   Year = {2008},
   Month = {November},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18973325},
   Abstract = {Nonlinear optical chromophores containing
             (porphyrinato)Zn(II), proquinoid, and (terpyridyl)metal(II)
             building blocks were optimized in a library containing
             approximately 10(6) structures using the linear combination
             of atomic potentials (LCAP) methodology. We report here the
             library design and molecular property optimizations. Two
             basic structural types of large beta(0) chromophores were
             examined: linear and T-shaped motifs. These T-shaped
             geometries suggest a promising NLO chromophoric architecture
             for experimental investigation and further support the value
             of performing LCAP searches in large chemical
             spaces.},
   Doi = {10.1021/jp806351d},
   Key = {fds235019}
}

@article{fds235045,
   Author = {Heaton-Burgess, T and Yang, W},
   Title = {Optimized effective potentials from arbitrary basis
             sets.},
   Journal = {Journal of Chemical Physics},
   Volume = {129},
   Number = {19},
   Pages = {194102},
   Year = {2008},
   Month = {November},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19026040},
   Abstract = {We investigate the use of a regularized optimized effective
             potential (OEP) energy functional and L-curve procedure [T.
             Heaton-Burgess, F. A. Bulat, and W. Yang, Phys. Rev. Lett.
             98, 256401 (2007)] for determining physically meaningful
             OEPs from arbitrary combinations of finite orbital and
             potential basis sets. The important issue of the manner in
             which the optimal regularization parameter is determined
             from the L-curve perspective is reconsidered with the
             introduction of a rigorous measure of the quality of the
             potential generated-that being, the extent to which the
             Ghosh-Parr exchange energy virial relation is satisfied
             along the L-curve. This approach yields nearly identical
             potentials to our previous work employing a minimum
             derivative condition, however, gives rise to slightly lower
             exact-exchange total energies. We observe that the
             ground-state energy and orbital energies obtained from this
             approach, either with balanced or unbalanced basis sets,
             yield meaningful potentials and energies which are in good
             comparison to other (a priori balanced) finite basis OEP
             calculations and experimental ionization potentials. As
             such, we believe that the regularized OEP functional
             approach provides a computationally robust method to address
             the numerical stability issues of this often ill-posed
             problem.},
   Doi = {10.1063/1.2982799},
   Key = {fds235045}
}

@article{fds235028,
   Author = {Balamurugan, D and Yang, W and Beratan, DN},
   Title = {Exploring chemical space with discrete, gradient, and hybrid
             optimization methods.},
   Journal = {Journal of Chemical Physics},
   Volume = {129},
   Number = {17},
   Pages = {174105},
   Year = {2008},
   Month = {November},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19045331},
   Abstract = {Discrete, gradient, and hybrid optimization methods are
             applied to the challenge of discovering molecules with
             optimized properties. The cost and performance of the
             approaches were studied using a tight-binding model to
             maximize the static first electronic hyperpolarizability of
             molecules. Our analysis shows that discrete branch and bound
             methods provide robust strategies for inverse chemical
             design involving diverse chemical structures. Based on the
             linear combination of atomic potentials, a hybrid
             discrete-gradient optimization strategy significantly
             improves the performance of the gradient methods. The hybrid
             method performs better than dead-end elimination and
             competes with branch and bound and genetic algorithms. The
             branch and bound methods for these model Hamiltonians are
             more cost effective than genetic algorithms for
             moderate-sized molecular optimization.},
   Doi = {10.1063/1.2987711},
   Key = {fds235028}
}

@article{fds235031,
   Author = {Hu, H and Boone, A and Yang, W},
   Title = {Mechanism of OMP decarboxylation in orotidine
             5'-monophosphate decarboxylase.},
   Journal = {Journal of the American Chemical Society},
   Volume = {130},
   Number = {44},
   Pages = {14493-14503},
   Year = {2008},
   Month = {November},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18839943},
   Abstract = {Despite extensive experimental and theoretical studies, the
             detailed catalytic mechanism of orotidine 5'-monophosphate
             decarboxylase (ODCase) remains controversial. In particular
             simulation studies using high level quantum mechanics have
             failed to reproduce experimental activation free energy. One
             common feature of many previous simulations is that there is
             a water molecule in the vicinity of the leaving CO2 group
             whose presence was only observed in the inhibitor bound
             complex of ODCase/BMP. Various roles have even been proposed
             for this water molecule from the perspective of stabilizing
             the transition state and/or intermediate state. We
             hypothesize that this water molecule is not present in the
             active ODCase/OMP complex. Based on QM/MM minimum free
             energy path simulations with accurate density functional
             methods, we show here that in the absence of this water
             molecule the enzyme functions through a simple direct
             decarboxylation mechanism. Analysis of the interactions in
             the active site indicates multiple factors contributing to
             the catalysis, including the fine-tuned electrostatic
             environment of the active site and multiple hydrogen-bonding
             interactions. To understand better the interactions between
             the enzyme and the inhibitor BMP molecule, simulations were
             also carried out to determine the binding free energy of
             this special water molecule in the ODCase/BMP complex. The
             results indicate that the water molecule in the active site
             plays a significant role in the binding of BMP by
             contributing approximately -3 kcal/mol to the binding free
             energy of the complex. Therefore, the complex of BMP plus a
             water molecule, instead of the BMP molecule alone, better
             represents the tight binding transition state analogue of
             ODCase. Our simulation results support the direct
             decarboxylation mechanism and highlight the importance of
             proper recognition of protein bound water molecules in the
             protein-ligand binding and the enzyme catalysis.},
   Doi = {10.1021/ja801202j},
   Key = {fds235031}
}

@article{fds235032,
   Author = {Heaton Burgess and T and Yang, WT},
   Title = {Optimized effective potentials from arbitrary basis
             sets},
   Journal = {Journal of Chemical Physics},
   Volume = {129},
   Pages = {194102},
   Year = {2008},
   Month = {November},
   Key = {fds235032}
}

@article{fds235014,
   Author = {Parks, JM and Hu, H and Cohen, AJ and Yang, W},
   Title = {A pseudobond parametrization for improved electrostatics in
             quantum mechanical/molecular mechanical simulations of
             enzymes.},
   Journal = {Journal of Chemical Physics},
   Volume = {129},
   Number = {15},
   Pages = {154106},
   Year = {2008},
   Month = {October},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19045175},
   Abstract = {The pseudobond method is used in quantum
             mechanical/molecular mechanical (QM/MM) simulations in which
             a covalent bond connects the quantum mechanical and
             classical subsystems. In this method, the molecular
             mechanical boundary atom is replaced by a special quantum
             mechanical atom with one free valence that forms a bond with
             the rest of the quantum mechanical subsystem. This boundary
             atom is modified through the use of a parametrized effective
             core potential and basis set. The pseudobond is designed to
             reproduce the properties of the covalent bond that it has
             replaced, while invoking as small a perturbation as possible
             on the system. Following the work of Zhang [J. Chem. Phys.
             122, 024114 (2005)], we have developed new pseudobond
             parameters for use in the simulation of enzymatic systems.
             Our parameters yield improved electrostatics and
             deprotonation energies, while at the same time maintaining
             accurate geometries. We provide parameters for
             C(ps)(sp(3))-C(sp(3)), C(ps)(sp(3))-C(sp(2),carbonyl), and
             C(ps)(sp(3))-N(sp(3)) pseudobonds, which allow the interface
             between the quantum mechanical and molecular mechanical
             subsystems to be constructed at either the C(alpha)-C(beta)
             bond of a given amino acid residue or along the peptide
             backbone. In addition, we demonstrate the efficiency of our
             parametrization method by generating residue-specific
             pseudobond parameters for a single amino acid. Such an
             approach may enable higher accuracy than general purpose
             parameters for specific QM/MM applications.},
   Doi = {10.1063/1.2994288},
   Key = {fds235014}
}

@article{fds235020,
   Author = {Ke, S-H and Yang, W and Baranger, HU},
   Title = {Quantum-interference-controlled molecular
             electronics.},
   Journal = {Nano Letters},
   Volume = {8},
   Number = {10},
   Pages = {3257-3261},
   Year = {2008},
   Month = {October},
   ISSN = {1530-6984},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18803424},
   Abstract = {Quantum interference in coherent transport through single
             molecular rings may provide a mechanism to control the
             current in molecular electronics. We investigate its
             applicability, using a single-particle Green function method
             combined with ab initio electronic structure calculations.
             We find that the quantum interference effect (QIE) is
             strongly dependent on the interaction between molecular
             pi-states and contact sigma-states. It is masked by sigma
             tunneling in small molecular rings with Au leads, such as
             benzene, due to strong pi-sigma hybridization, while it is
             preserved in large rings, such as [18]annulene, which then
             could be used to realize quantum interference effect (QIE)
             transistors.},
   Doi = {10.1021/nl8016175},
   Key = {fds235020}
}

@article{fds235025,
   Author = {Cohen, AJ and Mori-Sánchez, P and Yang, W},
   Title = {Fractional spins and static correlation error in density
             functional theory.},
   Journal = {Journal of Chemical Physics},
   Volume = {129},
   Number = {12},
   Pages = {121104},
   Year = {2008},
   Month = {September},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19044996},
   Abstract = {Electronic states with fractional spins arise in systems
             with large static correlation (strongly correlated systems).
             Such fractional-spin states are shown to be ensembles of
             degenerate ground states with normal spins. It is proven
             here that the energy of the exact functional for
             fractional-spin states is a constant, equal to the energy of
             the comprising degenerate pure-spin states. Dramatic
             deviations from this exact constancy condition exist with
             all approximate functionals, leading to large static
             correlation errors for strongly correlated systems, such as
             chemical bond dissociation and band structure of Mott
             insulators. This is demonstrated with numerical calculations
             for several molecular systems. Approximating the constancy
             behavior for fractional spins should be a major aim in
             functional constructions and should open the frontier for
             density functional theory to describe strongly correlated
             systems. The key results are also shown to apply in reduced
             density-matrix functional theory.},
   Doi = {10.1063/1.2987202},
   Key = {fds235025}
}

@article{fds235018,
   Author = {Keinan, S and Paquette, WD and Skoko, JJ and Beratan, DN and Yang, W and Shinde, S and Johnston, PA and Lazo, JS and Wipf,
             P},
   Title = {Computational design, synthesis and biological evaluation of
             para-quinone-based inhibitors for redox regulation of the
             dual-specificity phosphatase Cdc25B.},
   Journal = {Organic & Biomolecular Chemistry},
   Volume = {6},
   Number = {18},
   Pages = {3256-3263},
   Year = {2008},
   Month = {September},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18802630},
   Abstract = {Quinoid inhibitors of Cdc25B were designed based on the
             Linear Combination of Atomic Potentials (LCAP) methodology.
             In contrast to a published hypothesis, the biological
             activities and hydrogen peroxide generation in reducing
             media of three synthetic models did not correlate with the
             quinone half-wave potential, E(1/2).},
   Doi = {10.1039/b806712k},
   Key = {fds235018}
}

@article{fds235012,
   Author = {Xiao, D and Bulat, FA and Yang, W and Beratan, DN},
   Title = {A donor-nanotube paradigm for nonlinear optical
             materials.},
   Journal = {Nano Letters},
   Volume = {8},
   Number = {9},
   Pages = {2814-2818},
   Year = {2008},
   Month = {September},
   ISSN = {1530-6984},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18698728},
   Abstract = {Studies of the nonlinear electronic response of
             donor/acceptor substituted nanotubes suggest a behavior that
             is both surprising and qualitatively distinct from that in
             conventional conjugated organic species. We find that the
             carbon nanotubes serve as both electronic bridges and
             acceptors, leading to a donor-nanotube paradigm for the
             effective design of large first hyperpolarizabilities. We
             also find that tuning the donor orientation, relative to the
             nanotube, can significantly enhance the first
             hyperpolarizability.},
   Doi = {10.1021/nl801388z},
   Key = {fds235012}
}

@article{fds235022,
   Author = {Hu, X and Beratan, DN and Yang, W},
   Title = {A gradient-directed Monte Carlo approach to molecular
             design.},
   Journal = {Journal of Chemical Physics},
   Volume = {129},
   Number = {6},
   Pages = {064102},
   Year = {2008},
   Month = {August},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18715046},
   Abstract = {The recently developed linear combination of atomic
             potentials (LCAP) approach [M. Wang et al., J. Am. Chem.
             Soc. 128, 3228 (2006)] allows continuous optimization in a
             discrete chemical space, and thus is useful in the design of
             molecules for targeted properties. To address further
             challenges arising from the rugged, continuous property
             surfaces in the LCAP approach, we develop a
             gradient-directed Monte Carlo (GDMC) strategy as an
             augmentation to the original LCAP optimization method. The
             GDMC method retains the power of exploring molecular space
             by utilizing local gradient information computed from the
             LCAP approach to jump between discrete molecular structures.
             It also allows random MC moves to overcome barriers between
             local optima on property surfaces. The combined GDMC-LCAP
             approach is demonstrated here for optimizing nonlinear
             optical properties in a class of donor-acceptor substituted
             benzene and porphyrin frameworks. Specifically, one molecule
             with four nitrogen atoms in the porphyrin ring was found to
             have a larger first hyperpolarizability than structures with
             the conventional porphyrin motif.},
   Doi = {10.1063/1.2958255},
   Key = {fds235022}
}

@article{fds235024,
   Author = {Cohen, AJ and Mori-Sánchez, P and Yang, W},
   Title = {Insights into current limitations of density functional
             theory.},
   Journal = {Science},
   Volume = {321},
   Number = {5890},
   Pages = {792-794},
   Year = {2008},
   Month = {August},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18687952},
   Abstract = {Density functional theory of electronic structure is widely
             and successfully applied in simulations throughout
             engineering and sciences. However, for many predicted
             properties, there are spectacular failures that can be
             traced to the delocalization error and static correlation
             error of commonly used approximations. These errors can be
             characterized and understood through the perspective of
             fractional charges and fractional spins introduced recently.
             Reducing these errors will open new frontiers for
             applications of density functional theory.},
   Doi = {10.1126/science.1158722},
   Key = {fds235024}
}

@article{fds235023,
   Author = {Fujimoto, K and Yang, W},
   Title = {Density-fragment interaction approach for
             quantum-mechanical/molecular-mechanical calculations with
             application to the excited states of a Mg(2+)-sensitive
             dye.},
   Journal = {Journal of Chemical Physics},
   Volume = {129},
   Number = {5},
   Pages = {054102},
   Year = {2008},
   Month = {August},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18698883},
   Abstract = {A density-fragment interaction (DFI) approach for
             large-scale calculations is proposed. The DFI scheme
             describes electron density interaction between many
             quantum-mechanical (QM) fragments, which overcomes errors in
             electrostatic interactions with the fixed point-charge
             description in the conventional quantum-mechanical/molecular-mechanical
             (QM/MM) method. A self-consistent method, which is a
             mean-field treatment of the QM fragment interactions, was
             adopted to include equally the electron density interactions
             between the QM fragments. As a result, this method enables
             the evaluation of the polarization effects of the solvent
             and the protein surroundings. This method was combined with
             not only density functional theory (DFT) but also
             time-dependent DFT. In order to evaluate the solvent
             polarization effects in the DFI-QM/MM method, we have
             applied it to the excited states of the magnesium-sensitive
             dye, KMG-20. The DFI-QM/MM method succeeds in including
             solvent polarization effects and predicting accurately the
             spectral shift caused by Mg(2+) binding.},
   Doi = {10.1063/1.2958257},
   Key = {fds235023}
}

@article{fds235011,
   Author = {Xiao, D and Yang, W and Beratan, DN},
   Title = {Inverse molecular design in a tight-binding
             framework.},
   Journal = {Journal of Chemical Physics},
   Volume = {129},
   Number = {4},
   Pages = {044106},
   Year = {2008},
   Month = {July},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18681633},
   Abstract = {The number of chemical species of modest molecular weight
             that can be accessed with known synthetic methods is
             astronomical. An open challenge is to explore this space in
             a manner that will enable the discovery of molecular species
             and materials with optimized properties. Recently, an
             inverse molecular design strategy, the linear combination of
             atomic potentials (LCAP) approach [J. Am. Chem. Soc. 128,
             3228 (2006)] was developed to optimize electronic
             polarizabilities and first hyperpolarizabilities. Here,
             using a simple tight-binding (TB) approach, we show that
             continuous optimization can be carried out on the LCAP
             surface successfully to explore vast chemical libraries of
             10(2) to 10(16) extended aromatic compounds. We show that
             the TB-LCAP optimization is not only effective in locating
             globally optimal structures based on their electronic
             polarizabilities and first hyperpolarizabilities, but also
             is straightforwardly extended to optimize transition dipole
             moments and HOMO-LUMO energy gaps. This approach finds
             optimal structures among 10(4) candidates with about 40
             individual molecular property calculations. As such, for
             structurally similar molecular candidates, the TB-LCAP
             approach may provide an effective means to identify
             structures with optimal properties.},
   Doi = {10.1063/1.2955756},
   Key = {fds235011}
}

@article{fds235015,
   Author = {Mori-Sánchez, P and Cohen, AJ and Yang, W},
   Title = {Localization and delocalization errors in density functional
             theory and implications for band-gap prediction.},
   Journal = {Physical Review Letters},
   Volume = {100},
   Number = {14},
   Pages = {146401},
   Year = {2008},
   Month = {April},
   ISSN = {0031-9007},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18518055},
   Abstract = {The band-gap problem and other systematic failures of
             approximate exchange-correlation functionals are explained
             from an analysis of total energy for fractional charges. The
             deviation from the correct intrinsic linear behavior in
             finite systems leads to delocalization and localization
             errors in large and bulk systems. Functionals whose energy
             is convex for fractional charges such as the local density
             approximation display an incorrect apparent linearity in the
             bulk limit, due to the delocalization error. Concave
             functionals also have an incorrect apparent linearity in the
             bulk calculation, due to the localization error and imposed
             symmetry. This resolves an apparent paradox and identifies
             the physical nature of the error to be addressed to obtain
             accurate band gaps from density functional
             theory.},
   Doi = {10.1103/PhysRevLett.100.146401},
   Key = {fds235015}
}

@article{fds235010,
   Author = {Zeng, X and Hu, H and Hu, X and Cohen, AJ and Yang, W},
   Title = {Ab initio quantum mechanical/molecular mechanical simulation
             of electron transfer process: fractional electron
             approach.},
   Journal = {Journal of Chemical Physics},
   Volume = {128},
   Number = {12},
   Pages = {124510},
   Year = {2008},
   Month = {March},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18376946},
   Abstract = {Electron transfer (ET) reactions are one of the most
             important processes in chemistry and biology. Because of the
             quantum nature of the processes and the complicated roles of
             the solvent, theoretical study of ET processes is
             challenging. To simulate ET processes at the electronic
             level, we have developed an efficient density functional
             theory (DFT) quantum mechanical (QM)/molecular mechanical
             (MM) approach that uses the fractional number of electrons
             as the order parameter to calculate the redox free energy of
             ET reactions in solution. We applied this method to study
             the ET reactions of the aqueous metal complexes
             Fe(H(2)O)(6)(2+/3+) and Ru(H(2)O)(6)(2+/3+). The calculated
             oxidation potentials, 5.82 eV for Fe(II/III) and 5.14 eV for
             Ru(II/III), agree well with the experimental data, 5.50 and
             4.96 eV, for iron and ruthenium, respectively. Furthermore,
             we have constructed the diabatic free energy surfaces from
             histogram analysis based on the molecular dynamics
             trajectories. The resulting reorganization energy and the
             diabatic activation energy also show good agreement with
             experimental data. Our calculations show that using the
             fractional number of electrons (FNE) as the order parameter
             in the thermodynamic integration process leads to efficient
             sampling and validate the ab initio QM/MM approach in the
             calculation of redox free energies.},
   Doi = {10.1063/1.2832946},
   Key = {fds235010}
}

@article{fds235033,
   Author = {Heaton-Burgess, T and Cohen, AJ and Yang, W and Davidson,
             ER},
   Title = {Size extensivity of the direct optimized effective potential
             method.},
   Journal = {Journal of Chemical Physics},
   Volume = {128},
   Number = {11},
   Pages = {114702},
   Year = {2008},
   Month = {March},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18361596},
   Abstract = {We investigate the size extensivity of the direct optimized
             effective potential procedure of Yang and Wu [Phys. Rev.
             Lett. 89, 143002 (2002)]. The choice of reference potential
             within the finite basis construction of the local Kohn-Sham
             potential can lead to a method that is not size extensive.
             Such a situation is encountered when one employs the
             Fermi-Amaldi potential, which is often used to enforce the
             correct asymptotic behavior of the exact
             exchange-correlation potential. The size extensivity error
             with the Fermi-Amaldi reference potential is shown to behave
             linearly with the number of electrons in the limit of an
             infinite number of well separated monomers. In practice, the
             error tends to be rather small and rapidly approaches the
             limiting linear behavior. Moreover, with a flexible enough
             potential basis set, the error can be decreased
             significantly. We also consider one possible reference
             potential, constructed from the van Leeuwen-Baerends
             potential, which provides a size extensive implementation
             while also enforcing the correct asymptotic
             behavior.},
   Doi = {10.1063/1.2877129},
   Key = {fds235033}
}

@article{fds235013,
   Author = {Parks, JM and Kondru, RK and Hu, H and Beratan, DN and Yang,
             W},
   Title = {Hepatitis C virus NS5B polymerase: QM/MM calculations show
             the important role of the internal energy in ligand
             binding.},
   Journal = {The Journal of Physical Chemistry Part B: Condensed Matter,
             Materials, Surfaces, Interfaces and Biophysical},
   Volume = {112},
   Number = {10},
   Pages = {3168-3176},
   Year = {2008},
   Month = {March},
   ISSN = {1520-6106},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18271573},
   Abstract = {The inter- and intramolecular interactions that determine
             the experimentally observed binding mode of the ligand
             (2Z)-2-(benzoylamino)-3-[4-(2-bromophenoxy)phenyl]-2-propenoate
             in complex with hepatitis C virus NS5B polymerase have been
             studied using QM/MM calculations. DFT-based QM/MM
             optimizations were performed on a number of ligand
             conformers in the protein-ligand complex. Using these
             initial poses, our aim is 2-fold. First, we identify the
             minimum energy pose. Second, we dissect the energetic
             contributions to this pose using QM/MM methods. The study
             reveals the critical importance of internal energy for the
             proper energy ranking of the docked poses. Using this
             protocol, we successfully identified three poses that have
             low RMSD with respect to the crystallographic structure from
             among the top 20 initially docked poses. We show that the
             most important energetic component contributing to binding
             for this particular protein-ligand system is the
             conformational (i.e., QM internal) energy.},
   Doi = {10.1021/jp076885j},
   Key = {fds235013}
}

@article{fds235030,
   Author = {Hu, H and Lu, Z and Parks, JM and Burger, SK and Yang,
             W},
   Title = {Quantum mechanics/molecular mechanics minimum free-energy
             path for accurate reaction energetics in solution and
             enzymes: sequential sampling and optimization on the
             potential of mean force surface.},
   Journal = {Journal of Chemical Physics},
   Volume = {128},
   Number = {3},
   Pages = {034105},
   Year = {2008},
   Month = {January},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18205486},
   Abstract = {To accurately determine the reaction path and its energetics
             for enzymatic and solution-phase reactions, we present a
             sequential sampling and optimization approach that greatly
             enhances the efficiency of the ab initio quantum
             mechanics/molecular mechanics minimum free-energy path
             (QM/MM-MFEP) method. In the QM/MM-MFEP method, the
             thermodynamics of a complex reaction system is described by
             the potential of mean force (PMF) surface of the quantum
             mechanical (QM) subsystem with a small number of degrees of
             freedom, somewhat like describing a reaction process in the
             gas phase. The main computational cost of the QM/MM-MFEP
             method comes from the statistical sampling of conformations
             of the molecular mechanical (MM) subsystem required for the
             calculation of the QM PMF and its gradient. In our new
             sequential sampling and optimization approach, we aim to
             reduce the amount of MM sampling while still retaining the
             accuracy of the results by first carrying out MM phase-space
             sampling and then optimizing the QM subsystem in the
             fixed-size ensemble of MM conformations. The resulting QM
             optimized structures are then used to obtain more accurate
             sampling of the MM subsystem. This process of sequential MM
             sampling and QM optimization is iterated until convergence.
             The use of a fixed-size, finite MM conformational ensemble
             enables the precise evaluation of the QM potential of mean
             force and its gradient within the ensemble, thus
             circumventing the challenges associated with statistical
             averaging and significantly speeding up the convergence of
             the optimization process. To further improve the accuracy of
             the QM/MM-MFEP method, the reaction path potential method
             developed by Lu and Yang [Z. Lu and W. Yang, J. Chem. Phys.
             121, 89 (2004)] is employed to describe the QM/MM
             electrostatic interactions in an approximate yet accurate
             way with a computational cost that is comparable to
             classical MM simulations. The new method was successfully
             applied to two example reaction processes, the classical SN2
             reaction of Cl-+CH3Cl in solution and the second proton
             transfer step of the reaction catalyzed by the enzyme
             4-oxalocrotonate tautomerase. The activation free energies
             calculated with this new sequential sampling and
             optimization approach to the QM/MM-MFEP method agree well
             with results from other simulation approaches such as the
             umbrella sampling technique with direct QM/MM dynamics
             sampling, demonstrating the accuracy of the iterative
             QM/MM-MFEP method.},
   Doi = {10.1063/1.2816557},
   Key = {fds235030}
}

@article{fds234910,
   Author = {Li, Z and Wang, C-Y and Zhang, X and Ke, S-H and Yang,
             W},
   Title = {First-principles study for transport properties of armchair
             carbon nanotubes with a double vacancy under
             strain},
   Journal = {Journal of Applied Physics},
   Volume = {103},
   Number = {11},
   Year = {2008},
   ISSN = {0021-8979},
   url = {http://dx.doi.org/10.1063/1.2939279},
   Abstract = {Vacancies are one of the most important defects in carbon
             nanotubes (CNTs). Vacancies could affect the mechanical,
             chemical, and electronic properties of CNTs. In this study,
             we first use first-principles plane-wave calculation to
             optimize the structure of single-walled CNTs with a double
             vacancy under 0%, 3%, and 6% strains, respectively. Then, we
             use the single-particle Green function method to calculate
             their transport properties. It is found that different
             strains cause different local structures near the defect,
             which change the transmission function around the Fermi
             energy, and the conductance tends to be maximized under
             ∼3% strain. © 2008 American Institute of
             Physics.},
   Doi = {10.1063/1.2939279},
   Key = {fds234910}
}

@article{fds234911,
   Author = {Bulat, FA and Ke, S-H and Yang, W and Couchman, L},
   Title = {Lead-molecule coupling effects on the distortion-dependent
             conductance of carbon nanotubes},
   Journal = {Physical Review B - Condensed Matter and Materials
             Physics},
   Volume = {77},
   Number = {15},
   Year = {2008},
   ISSN = {1098-0121},
   url = {http://dx.doi.org/10.1103/PhysRevB.77.153401},
   Abstract = {The effect of the lead-molecule coupling on the zero-bias
             conductance of carbon nanotubes as a function of tube
             distortion is studied. It is shown that the coupling
             strength can have a dramatic effect on the electromechanical
             characteristics. Robust conductance as a function of
             distortion is realized in the strong coupling regime, while
             sharp oscillations on the conductance for small geometrical
             changes can be observed in the weak coupling regime. The
             origin of the phenomenon is traced to the combined effect of
             the coupling-induced broadening and distortion-induced
             shifts of the energy levels. © 2008 The American Physical
             Society.},
   Doi = {10.1103/PhysRevB.77.153401},
   Key = {fds234911}
}

@article{fds235016,
   Author = {Li, Z and Wang, C-Y and Zhang, X and Ke, S-H and Yang,
             W},
   Title = {Transport properties of an armchair carbon nanotube with a
             double vacancy under stretching},
   Journal = {Journal of Physics: Condensed Matter},
   Volume = {20},
   Number = {34},
   Pages = {345225},
   Year = {2008},
   ISSN = {0953-8984},
   url = {http://dx.doi.org/10.1088/0953-8984/20/34/345225},
   Abstract = {Structural properties of metallic single-walled carbon
             nanotubes with a double vacancy under stretching are studied
             by using a multiscale hybrid energy density method. Based on
             the optimized structure, the single-particle Green function
             method is then used to investigate the transport property.
             It is found that a reconstruction of the structure occurs
             with an increase of the imposed axial force, which alters
             the transmission function around the Fermi energy and will
             reduce the current. This reconstruction cannot be found by
             running a molecular dynamics simulation without a quantum
             description. © 2008 IOP Publishing Ltd.},
   Doi = {10.1088/0953-8984/20/34/345225},
   Key = {fds235016}
}

@article{fds235017,
   Author = {Lee, H and Kim, KW and Park, J and Kim, H and Kim, S and Kim, D and Hu, X and Yang, W and Hong, J},
   Title = {A general strategy for construction of both 2,6-cis- and
             2,6-trans-disubstituted tetrahydropyrans:
             Substrate-controlled asymmetric total synthesis of
             (+)-scanlonenyne},
   Journal = {Angewandte Chemie International Edition},
   Volume = {47},
   Number = {22},
   Pages = {4200-4203},
   Year = {2008},
   ISSN = {1433-7851},
   url = {http://dx.doi.org/10.1002/anie.200705663},
   Abstract = {(Chemical Equation Presented) A synthetic three-ring circus:
             The asymmetric total synthesis of (+)-scanlonenyne includes
             a sequential epimerization and intramolecular hetero-Michael
             addition for the construction of pyrano-γ-lactones (see
             scheme; DBU: 1,8-diazabicyclo[5.4.0]undec-7-ene), a highly
             efficient one-carbon homologation/bromination strategy, and
             a Weinreb ketone synthesis/cross-metathesis protocol for the
             elaboration of a sensitive side chain. © 2008 Wiley-VCH
             Verlag GmbH &amp; Co. KGaA.},
   Doi = {10.1002/anie.200705663},
   Key = {fds235017}
}

@article{fds235026,
   Author = {Cohen, AJ and Mori-Sánchez, P and Yang, W},
   Title = {Fractional charge perspective on the band gap in
             density-functional theory},
   Journal = {Physical Review B - Condensed Matter and Materials
             Physics},
   Volume = {77},
   Number = {11},
   Pages = {115123},
   Year = {2008},
   ISSN = {1098-0121},
   url = {http://dx.doi.org/10.1103/PhysRevB.77.115123},
   Abstract = {The calculation of the band gap by density-functional theory
             (DFT) is examined by considering the behavior of the energy
             as a function of number of electrons. It is explained that
             the incorrect band-gap prediction with most approximate
             functionals originates mainly from errors in describing
             systems with fractional charges. Formulas for the energy
             derivatives with respect to number of electrons are derived,
             which clarify the role of optimized effective potentials in
             prediction of the band gap. Calculations with a recent
             functional that has much improved behavior for fractional
             charges give a good prediction of the energy gap and also
             εHOMO -I for finite systems. Our results indicate that it
             is possible, within DFT, to have a functional whose
             eigenvalues or derivatives accurately predict the band gap.
             © 2008 The American Physical Society.},
   Doi = {10.1103/PhysRevB.77.115123},
   Key = {fds235026}
}

@article{fds235027,
   Author = {Burger, SK and Yang, W},
   Title = {Linear-scaling quantum calculations using non-orthogonal
             localized molecular orbitals},
   Journal = {Journal of Physics: Condensed Matter},
   Volume = {20},
   Number = {29},
   Pages = {294209},
   Year = {2008},
   ISSN = {0953-8984},
   url = {http://dx.doi.org/10.1088/0953-8984/20/29/294209},
   Abstract = {An absolute energy minimum variational principle is used for
             carrying out linear-scaling calculations with non-orthogonal
             localized orbitals. Comparing with results based on
             orthogonal localized molecular orbitals, the method is shown
             to give significantly more accurate results when the
             localized molecular orbitals are allowed to be
             non-orthogonal. This is made possible by introducing a
             second minimization for approximating the inverse overlap
             matrix. We also show how an exact line search may be used
             efficiently with the conjugate gradient method for
             minimizing the energy functional. © 2008 IOP Publishing
             Ltd.},
   Doi = {10.1088/0953-8984/20/29/294209},
   Key = {fds235027}
}

@article{fds235029,
   Author = {Hu, H and Yang, W},
   Title = {Free energies of chemical reactions in solution and in
             enzymes with ab initio quantum mechanics/molecular mechanics
             methods.},
   Journal = {Annual Review of Physical Chemistry},
   Volume = {59},
   Pages = {573-601},
   Year = {2008},
   ISSN = {0066-426X},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18393679},
   Abstract = {Combined quantum mechanics/molecular mechanics (QM/MM)
             methods provide an accurate and efficient energetic
             description of complex chemical and biological systems,
             leading to significant advances in the understanding of
             chemical reactions in solution and in enzymes. Here we
             review progress in QM/MM methodology and applications,
             focusing on ab initio QM-based approaches. Ab initio QM/MM
             methods capitalize on the accuracy and reliability of the
             associated quantum-mechanical approaches, however, at a much
             higher computational cost compared with semiempirical
             quantum-mechanical approaches. Thus reaction-path and
             activation free-energy calculations based on ab initio QM/MM
             methods encounter unique challenges in simulation timescales
             and phase-space sampling. This review features recent
             developments overcoming these challenges and enabling
             accurate free-energy determination for reaction processes in
             solution and in enzymes, along with applications.},
   Doi = {10.1146/annurev.physchem.59.032607.093618},
   Key = {fds235029}
}

@article{fds235034,
   Author = {Bulat, FA and Heaton-Burgess, T and Cohen, AJ and Yang,
             W},
   Title = {Optimized effective potentials from electron densities in
             finite basis sets.},
   Journal = {Journal of Chemical Physics},
   Volume = {127},
   Number = {17},
   Pages = {174101},
   Year = {2007},
   Month = {November},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17994801},
   Abstract = {The Wu-Yang method for determining the optimized effective
             potential (OEP) and implicit density functionals from a
             given electron density is revisited to account for its
             ill-posed nature, as recently done for the direct
             minimization method for OEP's from a given orbital
             functional [T. Heaton-Burgess, F. A. Bulat, and W. Yang,
             Phys. Rev. Lett. 98, 256401 (2007)]. To address the issues
             on the general validity and practical applicability of
             methods that determine the Kohn-Sham (local) multiplicative
             potential in a finite basis expansion, a new functional is
             introduced as a regularized version of the original work of
             Wu and Yang. It is shown that the unphysical, highly
             oscillatory potentials that can be obtained when unbalanced
             basis sets are used are the controllable manifestation of
             the ill-posed nature of the problem. The new method ensures
             that well behaved potentials are obtained for arbitrary
             basis sets.},
   Doi = {10.1063/1.2800021},
   Key = {fds235034}
}

@article{fds235049,
   Author = {Burger, SK and Yang, W},
   Title = {Sequential quadratic programming method for determining the
             minimum energy path.},
   Journal = {Journal of Chemical Physics},
   Volume = {127},
   Number = {16},
   Pages = {164107},
   Year = {2007},
   Month = {October},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17979319},
   Abstract = {A new method, referred to as the sequential quadratic
             programming method, is presented for determining minimum
             energy paths. The method is based on minimizing the points
             representing the path in the subspace perpendicular to the
             tangent of the path while using a penalty term to prevent
             kinks from forming. Rather than taking one full step, the
             minimization is divided into a number of sequential steps on
             an approximate quadratic surface. The resulting method can
             efficiently determine the reaction mechanism, from which
             transition state can be easily identified and refined with
             other methods. To improve the resolution of the path close
             to the transition state, points are clustered close to this
             region with a reparametrization scheme. The usefulness of
             the algorithm is demonstrated for the Muller-Brown
             potential, amide hydrolysis, and an 89 atom cluster taken
             from the active site of 4-oxalocrotonate tautomerase for the
             reaction which catalyzes 2-oxo-4-hexenedioate to the
             intermediate 2-hydroxy-2,4-hexadienedioate.},
   Doi = {10.1063/1.2780147},
   Key = {fds235049}
}

@article{fds235036,
   Author = {Liu, R and Ke, S-H and Yang, W and Baranger, HU},
   Title = {Cobaltocene as a spin filter.},
   Journal = {Journal of Chemical Physics},
   Volume = {127},
   Number = {14},
   Pages = {141104},
   Year = {2007},
   Month = {October},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17935378},
   Abstract = {In the context of investigating organic molecules for
             molecular electronics, doping molecular wires with
             transition metal atoms provides additional means of
             controlling their transport behavior. The incorporation of
             transition metal atoms may generate spin dependence because
             the conduction channels of only one spin component align
             with the chemical potential of the leads, resulting in a
             spin polarized electric current. The possibility to create
             such a spin polarized current is investigated here with the
             organometallic moiety cobaltocene. According to our
             calculations, cobaltocene contacted with gold electrodes
             acts as a robust spin filter: Applying a voltage less than
             0.2 V causes the current of one spin component crossing the
             molecular bridge to be two orders of magnitude larger than
             the other. We address the key issue of sensitivity to
             molecule-lead geometry by showing that a weak barrier
             generated by CH(2) groups between the cobaltocene and the
             leads is crucial in reducing the sensitivity to the contact
             geometry while only reducing the current modestly. These
             results suggest cobaltocene as a robust basic building block
             for molecular spintronics.},
   Doi = {10.1063/1.2796151},
   Key = {fds235036}
}

@article{fds235040,
   Author = {Ke, S-H and Baranger, HU and Yang, W},
   Title = {Electron transport through single conjugated organic
             molecules: basis set effects in ab initio
             calculations.},
   Journal = {Journal of Chemical Physics},
   Volume = {127},
   Number = {14},
   Pages = {144107},
   Year = {2007},
   Month = {October},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17935386},
   Abstract = {We investigate electron transport through single conjugated
             molecules--including benzenedithiol, oligophenylene
             ethynylenes of different lengths, and a ferrocene-containing
             molecule sandwiched between two gold electrodes with
             different contact structures--by using a single-particle
             Green function method combined with density functional
             theory calculation. We focus on the effect of the basis set
             in the ab initio calculation. It is shown that the position
             of the Fermi energy in the transport gap is sensitive to the
             molecule-lead charge transfer which is affected by the size
             of basis set. This can dramatically change, by orders of
             magnitude, the conductance for long molecules, though the
             effect is only minor for short ones. A resonance around the
             Fermi energy tends to pin the position of the Fermi energy
             and suppress this effect. The result is discussed in
             comparison with experimental data.},
   Doi = {10.1063/1.2770718},
   Key = {fds235040}
}

@article{fds235039,
   Author = {Ke, S-H and Baranger, HU and Yang, W},
   Title = {Contact transparency of nanotube-molecule-nanotube
             junctions.},
   Journal = {Physical Review Letters},
   Volume = {99},
   Number = {14},
   Pages = {146802},
   Year = {2007},
   Month = {October},
   ISSN = {0031-9007},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17930697},
   Abstract = {The transparency of contacts between conjugated molecules
             and metallic single-walled carbon nanotubes is investigated
             using a single-particle Green's function method which
             combines a Landauer approach with ab initio density
             functional theory. We find that the overall conjugation
             required for good contact transparency is broken by
             connecting through a six-member ring on the tube. Full
             conjugation achieved by an all-carbon contact through a
             five-member ring leads to near perfect contact transparency
             for different conjugated molecular bridges.},
   Doi = {10.1103/PhysRevLett.99.146802},
   Key = {fds235039}
}

@article{fds313878,
   Author = {Parks, JM and Hu, H and Kondru, R and Yang, W},
   Title = {COMP 244-Nature of ligand binding in HCV polymerase:
             Characterization of specific interactions from QM/MM
             calculations},
   Journal = {ACS National Meeting Book of Abstracts},
   Volume = {234},
   Year = {2007},
   Month = {August},
   ISSN = {0065-7727},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000207593906134&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds313878}
}

@article{fds318102,
   Author = {Zeng, X and Hu, H and Yang, W},
   Title = {PHYS 124-QM/MM calculation of electron transfer process:
             Fractional number of electrons approach},
   Journal = {ACS National Meeting Book of Abstracts},
   Volume = {234},
   Year = {2007},
   Month = {August},
   Key = {fds318102}
}

@article{fds318103,
   Author = {Hu, H and Yang, W},
   Title = {PHYS 301-Free energies of chemical reactions in enzyme and
             in solution},
   Journal = {ACS National Meeting Book of Abstracts},
   Volume = {234},
   Year = {2007},
   Month = {August},
   Key = {fds318103}
}

@article{fds235048,
   Author = {Cohen, AJ and Mori-Sánchez, P and Yang, W},
   Title = {Assessment and formal properties of exchange-correlation
             functionals constructed from the adiabatic
             connection.},
   Journal = {Journal of Chemical Physics},
   Volume = {127},
   Number = {3},
   Pages = {034101},
   Year = {2007},
   Month = {July},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17655425},
   Abstract = {We examine the development and investigate the performance
             of exchange-correlation functionals constructed from the
             adiabatic connection. Our method is based on a direct
             modeling of the adiabatic connection curve in the
             coupling-constant space and is very flexible in the models.
             Several different models are investigated in the
             construction of new families of exchange-correlation
             functionals. Also the performance of two of these models
             (MCY1 and MCY2) is investigated over a wider range of
             systems and properties, with comparison made to the
             performance of established functionals. Overall, the
             adiabatic functionals improve upon widely used hybrid and
             generalized gradient approximation functionals, particularly
             in correctly describing one-electron systems and reaction
             energy barriers.},
   Doi = {10.1063/1.2749510},
   Key = {fds235048}
}

@article{fds235041,
   Author = {Hu, H and Lu, Z and Elstner, M and Hermans, J and Yang,
             W},
   Title = {Simulating water with the self-consistent-charge density
             functional tight binding method: from molecular clusters to
             the liquid state.},
   Journal = {The Journal of Physical Chemistry Part A: Molecules,
             Spectroscopy, Kinetics, Environment and General
             Theory},
   Volume = {111},
   Number = {26},
   Pages = {5685-5691},
   Year = {2007},
   Month = {July},
   ISSN = {1089-5639},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17474727},
   Abstract = {The recently developed self-consistent-charge density
             functional tight binding (SCCDFTB) method provides an
             accurate and inexpensive quantum mechanical solution to many
             molecular systems of interests. To examine the performance
             of the SCCDFTB method on (liquid) water, the most
             fundamental yet indispensable molecule in biological
             systems, we report here the simulation results of water in
             sizes ranging from molecular clusters to the liquid state.
             The latter simulation was achieved through the use of the
             linear scaling divide-and-conquer approach. The results of
             liquid water simulation indicate that the SCCDFTB method can
             describe the structural and energetics of liquid water in
             qualitative agreement with experiments, and the results for
             water clusters suggest potential future improvements of the
             SCCDFTB method.},
   Doi = {10.1021/jp070308d},
   Key = {fds235041}
}

@article{fds285333,
   Author = {Heaton-Burgess, T and Bulat, FA and Yang, W},
   Title = {Optimized effective potentials in finite basis
             sets.},
   Journal = {Physical Review Letters},
   Volume = {98},
   Number = {25},
   Pages = {256401},
   Year = {2007},
   Month = {June},
   ISSN = {0031-9007},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17678039},
   Abstract = {The finite basis optimized effective potential (OEP) method
             within density functional theory is examined as an ill-posed
             problem. It is shown that the generation of nonphysical
             potentials is a controllable manifestation of the use of
             unbalanced, and thus unsuitable, basis sets. A modified
             functional incorporating a regularizing smoothness measure
             of the OEP is introduced. This provides a condition on
             balanced basis sets for the potential, as well as a method
             to determine the most appropriate OEP and energy from
             calculations performed with any finite basis
             set.},
   Doi = {10.1103/PhysRevLett.98.256401},
   Key = {fds285333}
}

@article{fds304412,
   Author = {Ke, S-H and Baranger, HU and Yang, W},
   Title = {Role of the exchange-correlation potential in ab initio
             electron transport calculations.},
   Journal = {Journal of Chemical Physics},
   Volume = {126},
   Number = {20},
   Pages = {201102},
   Year = {2007},
   Month = {May},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17552745},
   Abstract = {The effect of the exchange-correlation potential in ab
             initio electron transport calculations is investigated by
             constructing optimized effective potentials using different
             energy functionals or the electron density from second-order
             perturbation theory. The authors calculate electron
             transmission through two atomic chain systems, one with
             charge transfer and one without. Dramatic effects are caused
             by two factors: changes in the energy gap and the
             self-interaction error. The error in conductance caused by
             the former is about one order of magnitude while that caused
             by the latter ranges from several times to two orders of
             magnitude, depending on the coupling strength and charge
             transfer. The implications for accurate quantum transport
             calculations are discussed.},
   Doi = {10.1063/1.2743004},
   Key = {fds304412}
}

@article{fds235047,
   Author = {Cohen, AJ and Mori-Sánchez, P and Yang, W},
   Title = {Development of exchange-correlation functionals with minimal
             many-electron self-interaction error.},
   Journal = {Journal of Chemical Physics},
   Volume = {126},
   Number = {19},
   Pages = {191109},
   Year = {2007},
   Month = {May},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17523789},
   Abstract = {New exchange-correlation functionals that address the
             important issue of many-electron self-interaction are
             developed. This is carried out by considering the
             performance of the functional on systems with fractional
             numbers of electrons at the same time as more standard
             thermochemical tests. The inclusion of Coulomb-attenuated
             exchange in the functional is facilitated by use of the
             adiabatic connection coupled with a short-range and
             long-range splittings. The new functionals have a good
             performance on thermochemistry and a much improved
             description of the total energy versus number of electrons
             and henceforth a much smaller many-electron self-interaction
             error.},
   Doi = {10.1063/1.2741248},
   Key = {fds235047}
}

@article{fds235042,
   Author = {Hu, H and Lu, Z and Yang, W},
   Title = {QM/MM Minimum Free Energy Path: Methodology and Application
             to Triosephosphate Isomerase.},
   Journal = {Journal of Chemical Theory and Computation},
   Volume = {3},
   Number = {2},
   Pages = {390-406},
   Year = {2007},
   Month = {March},
   ISSN = {1549-9618},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19079734},
   Abstract = {Structural and energetic changes are two important
             characteristic properties of a chemical reaction process. In
             the condensed phase, studying these two properties is very
             challenging because of the great computational cost
             associated with the quantum mechanical calculations and
             phase space sampling. Although the combined quantum
             mechanics/molecular mechanics (QM/MM) approach significantly
             reduces the amount of the quantum mechanical calculations
             and facilitates the simulation of solution phase and enzyme
             catalyzed reactions, the required quantum mechanical
             calculations remain quite expensive and extensive sampling
             can be achieved routinely only with semiempirical quantum
             mechanical methods. QM/MM simulations with ab initio QM
             methods, therefore, are often restricted to narrow regions
             of the potential energy surface such as the reactant,
             product and transition state, or the minimum energy path.
             Such ab initio QM/MM calculations have previously been
             performed with the QM/MM-Free Energy (QM/MM-FE) method of
             Zhang et al.1 to generate the free energy profile along the
             reaction coordinate using free energy perturbation
             calculations at fixed structures of the QM subsystems.
             Results obtained with the QM/MM-FE method depend on the
             determination of the minimum energy reaction path, which is
             based on local conformations of the protein/solvent
             environment and can be difficult to obtain in practice. To
             overcome the difficulties associated with the QM/MM-FE
             method and to further enhance the sampling of the MM
             environment conformations, we develop here a new method to
             determine the QM/MM minimum free energy path (QM/MM-MFEP)
             for chemical reaction processes in solution and in enzymes.
             Within the QM/MM framework, we express the free energy of
             the system as a function of the QM conformation, thus
             leading to a simplified potential of mean force (PMF)
             description for the thermodynamics of the system. The free
             energy difference between two QM conformations is evaluated
             by the QM/MM free energy perturbation method. The free
             energy gradients with respect to the QM degrees of freedom
             are calculated from molecular dynamics simulations at given
             QM conformations. With the free energy and free energy
             gradients in hand, we further implement chain-of-conformation
             optimization algorithms in the search for the reaction path
             on the free energy surface without specifying a reaction
             coordinate. This method thus efficiently provides a unique
             minimum free energy path for solution and enzyme reactions,
             with structural and energetic properties being determined
             simultaneously. To further incorporate the dynamic
             contributions of the QM subsystem into the simulations, we
             develop the reaction path potential of Lu, et al.2 for the
             minimum free energy path. The combination of the methods
             developed here presents a comprehensive and accurate
             treatment for the simulation of reaction processes in
             solution and in enzymes with ab initio QM/MM methods. The
             method has been demonstrated on the first step of the
             reaction of the enzyme triosephosphate isomerase with good
             agreement with previous studies.},
   Doi = {10.1021/ct600240y},
   Key = {fds235042}
}

@article{fds235046,
   Author = {Heaton-Burgess, T and Ayers, P and Yang, W},
   Title = {Spin-potential functional formalism for current-carrying
             noncollinear magnetic systems.},
   Journal = {Physical Review Letters},
   Volume = {98},
   Number = {3},
   Pages = {036403},
   Year = {2007},
   Month = {January},
   ISSN = {0031-9007},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17358702},
   Abstract = {We develop a formalism dual to spin-current-density
             functional theory (CDFT) where minimization with respect to
             the scalar and vector spin potentials is used. In this way
             we circumvent the issues surrounding the nonuniqueness of
             the mapping between spin potentials and ground-state wave
             functions, and the v representability issue of
             current-density functionals. The approach applied within the
             Kohn-Sham formalism provides the foundations for the
             optimized effective potential method for
             CDFT.},
   Doi = {10.1103/PhysRevLett.98.036403},
   Key = {fds235046}
}

@article{fds235037,
   Author = {Keinan, S and Hu, X and Beratan, DN and Yang, W},
   Title = {Designing molecules with optimal properties using the linear
             combination of atomic potentials approach in an AM1
             semiempirical framework.},
   Journal = {The Journal of Physical Chemistry Part A: Molecules,
             Spectroscopy, Kinetics, Environment and General
             Theory},
   Volume = {111},
   Number = {1},
   Pages = {176-181},
   Year = {2007},
   Month = {January},
   ISSN = {1089-5639},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17201401},
   Abstract = {The linear combination of atomic potentials (LCAP) approach
             is implemented in the AM1 semiempirical framework and is
             used to design molecular structures with optimized
             properties. The optimization procedure uses property
             derivative information to search molecular space and thus
             avoid direct enumeration and evaluation of each molecule in
             a library. Two tests are described: the optimization of
             first hyperpolarizabilities of substituted aromatics and the
             optimization of a figure of merit for n-type organic
             semiconductors.},
   Doi = {10.1021/jp0646168},
   Key = {fds235037}
}

@article{fds235035,
   Author = {Wang, W and Qiao, J and Wang, L and Duan, L and Zhang, D and Yang, W and Qiu,
             Y},
   Title = {Synthesis, structures, and optical properties of cadmium
             iodide/phenethylamine hybrid materials with controlled
             structures and emissions},
   Journal = {Inorganic Chemistry},
   Volume = {46},
   Number = {24},
   Pages = {10252-10260},
   Year = {2007},
   ISSN = {0020-1669},
   url = {http://dx.doi.org/10.1021/ic7007304},
   Abstract = {A new type of organic-inorganic hybrid materials based on
             cadmium iodide (CdI2) and phenethylamine (PEA) has been
             synthesized and characterized. The reaction of CdI2 with PEA
             in a 1:2 molar ratio yields a four-coordinate hybrid
             material CdI2(PEA)2 (1) with extended 1D (CdI2)n chains,
             while the reaction of CdI2 with PEA in a 1:4 molar ratio
             produces a six-coordinate hybrid material CdI2(PEA)4 (2)
             with a discrete linear structure of CdI2 moiety. By
             introducing a trace amount of Na2S to the reaction for
             CdI2(PEA)2, we obtained a new compound [CdI2(PEA)2]-(CdS)0.038
             (3) with uniformly doped CdS nanoparticles. Steady and
             transient photoluminescence studies reveal that compounds 1
             and 2 exhibit bright blue (465 nm) and green (512 nm)
             fluorescent emissions in solid state at room temperature,
             respectively, while compound 3 gives a broad and complex
             emission ranging from 450 to 700 nm. Theoretical studies of
             electronic structures were carried out using density
             functional theory in order to gain a good understanding of
             the luminescent behaviors of these hybrid materials. © 2007
             American Chemical Society.},
   Doi = {10.1021/ic7007304},
   Key = {fds235035}
}

@article{fds235038,
   Author = {Ke, S-H and Baranger, HU and Yang, W},
   Title = {Role of the exchange-correlation potential in ab initio
             electron transport calculations},
   Journal = {Journal of Chemical Physics},
   Volume = {126},
   Number = {20},
   Pages = {201102/1-201102/4},
   Year = {2007},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17552745},
   Abstract = {The effect of the exchange-correlation potential in ab
             initio electron transport calculations is investigated by
             constructing optimized effective potentials using different
             energy functionals or the electron density from second-order
             perturbation theory. The authors calculate electron
             transmission through two atomic chain systems, one with
             charge transfer and one without. Dramatic effects are caused
             by two factors: changes in the energy gap and the
             self-interaction error. The error in conductance caused by
             the former is about one order of magnitude while that caused
             by the latter ranges from several times to two orders of
             magnitude, depending on the coupling strength and charge
             transfer. The implications for accurate quantum transport
             calculations are discussed.},
   Doi = {10.1063/1.2743004},
   Key = {fds235038}
}

@article{fds235043,
   Author = {Hu, H and Lu, Z and Yang, W},
   Title = {Fitting molecular electrostatic potentials from quantum
             mechanical calculations},
   Journal = {Journal of Chemical Theory and Computation},
   Volume = {3},
   Number = {3},
   Pages = {1004-1013},
   Year = {2007},
   ISSN = {1549-9618},
   url = {http://dx.doi.org/10.1021/ct600295n},
   Abstract = {We develop here a new method to fit the molecular
             electrostatic potentials obtained in quantum mechanical
             calculations to a set of classical electrostatic multipoles,
             usually point charges located at atomic positions. We define
             an object function of fitting as an integration of the
             difference of electrostatic potentials in the entire
             3-dimensional physical space. The object function is thus
             rotationally invariant with respect to the molecular
             orientation and varies smoothly with respect to molecular
             geometric fluctuations. Compared with commonly employed
             methods such as the Merz-Singh-Kollman and CHELPG schemes,
             this new method, while possessing comparable accuracy, shows
             greatly improved numerical stability with respect to the
             molecular positions and geometries. The method can be used
             in the fitting of electrostatic potentials for the molecular
             mechanics force fields and also can be applied to the
             calculation of electrostatic polarizabilites of molecular or
             atomic systems. © 2007 American Chemical
             Society.},
   Doi = {10.1021/ct600295n},
   Key = {fds235043}
}

@article{fds235044,
   Author = {Hori, T and Takahashi, H and Furukawa, S-I and Nakano, M and Yang,
             W},
   Title = {Computational study on the relative acidity of acetic acid
             by the QM/MM method combined with the theory of energy
             representation},
   Journal = {The Journal of Physical Chemistry Part B: Condensed Matter,
             Materials, Surfaces, Interfaces and Biophysical},
   Volume = {111},
   Number = {3},
   Pages = {581-588},
   Year = {2007},
   ISSN = {1520-6106},
   url = {http://dx.doi.org/10.1021/jp066334d},
   Abstract = {We have applied the quantum mechanical/molecular mechanical
             (QM/MM) method combined with the theory of energy
             representation (ER) to study the acidity of acetic acid in
             aqueous solution. We have focused our attention on the
             relative acidity ΔpKa, of the molecule with respect to
             water solvent to circumvent the ambiguity of the solvation
             free energies of the molecular species referred to as
             proton. The value of ΔpK a for the acetic acid has been
             computed as -11.5 when we adopt the free energy change in
             the gas phase obtained by the B3LYP functional, which is in
             excellent agreement with the experimental value of -11.0. It
             has been demonstrated that the QM/MM-ER approach recently
             developed gives an adequate description for the solvation
             free energies related to the acidity/basicity calculations
             of organic molecules. © 2007 American Chemical
             Society.},
   Doi = {10.1021/jp066334d},
   Key = {fds235044}
}

@article{fds234907,
   Author = {Burger, SK and Yang, W},
   Title = {Automatic integration of the reaction path using diagonally
             implicit Runge-Kutta methods.},
   Journal = {Journal of Chemical Physics},
   Volume = {125},
   Number = {24},
   Pages = {244108},
   Year = {2006},
   Month = {December},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17199341},
   Abstract = {The diagonally implicit Runge-Kutta framework is shown to be
             a general form for constructing stable, efficient steepest
             descent reaction path integrators, of any order. With this
             framework tolerance driven, adaptive step-size methods can
             be constructed by embedding methods to obtain error
             estimates of each step without additional computational
             cost. There are many embedded and nonembedded, diagonally
             implicit Runge-Kutta methods available from the numerical
             analysis literature and these are reviewed for orders two,
             three, and four. New embedded methods are also developed
             which are tailored to the application of reaction path
             following. All integrators are summarized and compared for
             three systems: the Muller-Brown [Theor. Chem. Acta 53, 75
             (1979)] potential and two gas phase chemical reactions. The
             results show that many of the methods are capable of
             integrating efficiently while reliably keeping the error
             bound within the desired tolerance. This allows the reaction
             path to be determined through automatic integration by only
             specifying the desired accuracy and transition
             state.},
   Doi = {10.1063/1.2402166},
   Key = {fds234907}
}

@article{fds234904,
   Author = {Mori-Sánchez, P and Cohen, AJ and Yang, W},
   Title = {Many-electron self-interaction error in approximate density
             functionals.},
   Journal = {Journal of Chemical Physics},
   Volume = {125},
   Number = {20},
   Pages = {201102},
   Year = {2006},
   Month = {November},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17144681},
   Abstract = {One of the most important challenges in density functional
             theory (DFT) is the proper description of fractional charge
             systems relating to the self-interaction error (SIE).
             Traditionally, the SIE has been formulated as a one-electron
             problem, which has been addressed in several recent
             functionals. However, these recent one-electron SIE-free
             functionals, while greatly improving the description of
             thermochemistry and reaction barriers in general, still
             exhibit many of the difficulties associated with SIE. Thus
             we emphasize the need to surpass this limit and shed light
             on the many-electron SIE. After identifying the sufficient
             condition for functionals to be free from SIE, we focus on
             the symptoms and investigate the performance of most popular
             functionals. We show that these functionals suffer from
             many-electron SIE. Finally, we give a SIE classification of
             density functionals.},
   Doi = {10.1063/1.2403848},
   Key = {fds234904}
}

@article{fds234945,
   Author = {Lu, Z and Hu, H and Yang, W and Marszalek, PE},
   Title = {Simulating force-induced conformational transitions in
             polysaccharides with the SMD replica exchange
             method.},
   Journal = {Biophysical Journal},
   Volume = {91},
   Number = {6},
   Pages = {L57-L59},
   Year = {2006},
   Month = {September},
   ISSN = {0006-3495},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16829559},
   Abstract = {Conventional steered molecular dynamics (SMD) simulations do
             not readily reproduce equilibrium conditions of atomic force
             microscopy (AFM) stretch and release measurements of
             polysaccharides undergoing force-induced conformational
             transitions because of the gap between the timescales of
             computer simulations ( approximately 1 mus) and AFM
             measurements ( approximately 1 s). To circumvent this
             limitation, we propose using the replica exchange method
             (REM) to enhance sampling during SMD simulations. By
             applying REM SMD to a small polysaccharide system and
             comparing the results with those from AFM stretching
             experiments, we demonstrate that REM SMD reproduces the
             experimental results not only qualitatively but
             quantitatively, approaching near equilibrium conditions of
             AFM measurements. As tested in this work, hysteresis and
             computational time of REM SMD simulations of short
             polysaccharide chains are significantly reduced as compared
             to regular SMD simulations, making REM SMD an attractive
             tool for studying forced-induced conformational transitions
             of small biopolymer systems.},
   Doi = {10.1529/biophysj.106.090324},
   Key = {fds234945}
}

@article{fds234946,
   Author = {Zhang, Q and Lu, Z and Hu, H and Yang, W and Marszalek,
             PE},
   Title = {Direct detection of the formation of V-amylose helix by
             single molecule force spectroscopy.},
   Journal = {Journal of the American Chemical Society},
   Volume = {128},
   Number = {29},
   Pages = {9387-9393},
   Year = {2006},
   Month = {July},
   ISSN = {0002-7863},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16848474},
   Abstract = {An important polysaccharide, amylose crystallizes as a
             regular single left-handed helix from a propanol, butanol,
             or iodine solution. However, its solution structure remains
             elusive because amylose does not form molecular solutions in
             these solvents, and standard spectroscopic techniques cannot
             be exploited to determine its structure. Using AFM, we
             forced individual amylose chains adsorbed to a surface to
             enter these poor solvents and carried out stretch-release
             measurements on them in solution. In this manner, we
             directly captured the formation of individual amylose
             helices induced by butanol and iodine. With an accuracy
             approaching that of X-ray diffraction on amylose crystals,
             we determined that the pitch of the helix in solution is 1.3
             angstroms/ring. We also directly measured the force driving
             the formation of the helix in solution to be 50 pN. SMD
             simulations in explicit butanol reproduced the AFM-measured
             force-extension curves and revealed that the long plateau
             feature is caused by the rupture of O(2)n-O(6)(n+6) and
             O(3)n-O(6)(n+6) hydrogen bonds and by the unwinding of the
             helix. We also found that amylose helices formed in iodine
             solution are more compliant and hysteretic as compared to
             helices in butanol, which extend/relax reversibly. In iodine
             solution, the formation of the helix is inhibited by force
             and limited by the slow kinetics of the amylose-iodine
             complex. By forcing individual molecules into poor solvents
             and performing force spectroscopy measurements in solution,
             our AFM approach uniquely supplements X-ray diffraction and
             NMR methods for investigating solution conformations of
             insoluble biopolymers.},
   Doi = {10.1021/ja057693+},
   Key = {fds234946}
}

@article{fds234982,
   Author = {Burger, SK and Yang, W},
   Title = {A combined explicit-implicit method for high accuracy
             reaction path integration.},
   Journal = {Journal of Chemical Physics},
   Volume = {124},
   Number = {22},
   Pages = {224102},
   Year = {2006},
   Month = {June},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16784258},
   Abstract = {We present the use of an optimal combined explicit-implicit
             method for following the reaction path to high accuracy.
             This is in contrast to most purely implicit reaction path
             integration algorithms, which are only efficient on stiff
             ordinary differential equations. The defining equation for
             the reaction path is considered to be stiff, however, we
             show here that the reaction path is not uniformly stiff and
             instead is only stiff near stationary points. The optimal
             algorithm developed in this work is a combination of
             explicit and implicit methods with a simple criterion to
             switch between the two. Using three different chemical
             reactions, we combine and compare three different
             integration methods: the implicit trapezoidal method, an
             explicit stabilized third order algorithm implemented in the
             code DUMKA3 and the traditional explicit fourth order
             Runge-Kutta method written in the code RKSUITE. The results
             for high accuracy show that when the implicit trapezoidal
             method is combined with either explicit method the number of
             energy and gradient calculations can potentially be reduced
             by almost a half compared with integrating either method
             alone. Finally, to explain the improvements of the combined
             method we expand on the concepts of stability and stiffness
             and relate them to the efficiency of integration
             methods.},
   Doi = {10.1063/1.2202830},
   Key = {fds234982}
}

@article{fds234981,
   Author = {Ayers, PW and Yang, W},
   Title = {Legendre-transform functionals for spin-density-functional
             theory.},
   Journal = {Journal of Chemical Physics},
   Volume = {124},
   Number = {22},
   Pages = {224108},
   Year = {2006},
   Month = {June},
   ISSN = {0021-9606},
   url = {http://dx.doi.org/10.1063/1.2200884},
   Abstract = {We provide a rigorous proof that the Hohenberg-Kohn theorem
             holds for spin densities by extending Lieb's
             Legendre-transform formulation to spin densities. The
             resulting spin-density-functional theory resolves several
             troublesome issues. Most importantly, the present paper
             provides an explicit construction for the spin potentials at
             any point along the adiabatic connection curve, thus
             providing a formal basis for the use of exchange-correlation
             functionals of the spin density in the Kohn-Sham
             density-functional theory (DFT). The practical implications
             of this result for unrestricted Kohn-Sham DFT calculations
             is considered, and the existence of holes below the Fermi
             level is discussed. We argue that an orbital's energy tends
             to increase as its occupation number increases, which
             provides the basis for a computational algorithm for
             determining the occupation numbers in Kohn-Sham DFT and
             helps explain the origin of Hund's rules and holes below the
             Fermi level.},
   Doi = {10.1063/1.2200884},
   Key = {fds234981}
}

@article{fds234969,
   Author = {Liu, R and Ke, S-H and Baranger, HU and Yang, W},
   Title = {Negative differential resistance and hysteresis through an
             organometallic molecule from molecular-level
             crossing.},
   Journal = {Journal of the American Chemical Society},
   Volume = {128},
   Number = {19},
   Pages = {6274-6275},
   Year = {2006},
   Month = {May},
   ISSN = {0002-7863},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16683765},
   Abstract = {Analogous to a quantum double-dot system, diblock structured
             molecules could also show negative differential resistance
             (NDR). Using combined density functional theory and
             nonequilibrium Green function technique, we show that
             molecular-level crossing in a molecular double-dot system
             containing cobaltocene and ferrocene leads to NDR and
             hysteresis.},
   Doi = {10.1021/ja057054z},
   Key = {fds234969}
}

@article{fds234968,
   Author = {Ke, S-H and Yang, W and Baranger, HU},
   Title = {Nanotube-metal junctions: 2- and 3-terminal electrical
             transport.},
   Journal = {Journal of Chemical Physics},
   Volume = {124},
   Number = {18},
   Pages = {181102},
   Year = {2006},
   Month = {May},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16709090},
   Abstract = {We address the quality of electrical contact between carbon
             nanotubes and metallic electrodes by performing
             first-principles calculations for the electron transmission
             through ideal 2- and 3-terminal junctions, thus revealing
             the physical limit of tube-metal conduction. The structural
             model constructed involves surrounding the tube by the metal
             atoms of the electrode as in most experiments; we consider
             metallic (5,5) and n-doped semiconducting (10,0) tubes
             surrounded by Au or Pd. In the case of metallic tubes, the
             contact conductance is shown to approach the ideal 4e2/h in
             the limit of large contact area. For three-terminals, the
             division of flux among the different transmission channels
             depends strongly on the metal material. A Pd electrode has
             nearly perfect tube-electrode transmission and therefore
             turns off the straight transport along the tube. Our results
             are in good agreement with some recent experimental reports
             and clarify a fundamental discrepancy between theory and
             experiment.},
   Doi = {10.1063/1.2200356},
   Key = {fds234968}
}

@article{fds234906,
   Author = {Wang, M and Lu, Z and Yang, W},
   Title = {Nuclear quantum effects on an enzyme-catalyzed reaction with
             reaction path potential: proton transfer in triosephosphate
             isomerase.},
   Journal = {Journal of Chemical Physics},
   Volume = {124},
   Number = {12},
   Pages = {124516},
   Year = {2006},
   Month = {March},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16599706},
   Abstract = {Nuclear quantum mechanical effects have been examined for
             the proton transfer reaction catalyzed by triosephosphate
             isomerase, with the normal mode centroid path integral
             molecular dynamics based on the potential energy surface
             from the recently developed reaction path potential method.
             In the simulation, the primary and secondary hydrogens and
             the C and O atoms involving bond forming and bond breaking
             were treated quantum mechanically, while all other atoms
             were dealt classical mechanically. The quantum mechanical
             activation free energy and the primary kinetic isotope
             effects were examined. Because of the quantum mechanical
             effects in the proton transfer, the activation free energy
             was reduced by 2.3 kcal/mol in comparison with the classical
             one, which accelerates the rate of proton transfer by a
             factor of 47.5. The primary kinetic isotope effects of kH/kD
             and kH/kT were estimated to be 4.65 and 9.97, respectively,
             which are in agreement with the experimental value of
             4+/-0.3 and 9. The corresponding Swain-Schadd exponent was
             predicted to be 3.01, less than the semiclassical limit
             value of 3.34, indicating that the quantum mechanical
             effects mainly arise from quantum vibrational motion rather
             than tunneling. The reaction path potential, in conjunction
             with the normal mode centroid molecular dynamics, is shown
             to be an efficient computational tool for investigating the
             quantum effects on enzymatic reactions involving proton
             transfer.},
   Doi = {10.1063/1.2181145},
   Key = {fds234906}
}

@article{fds234950,
   Author = {Wang, ML and Hu, XQ and Beratan, DN and Yang, WT},
   Title = {Designing molecules by optimizing potentials},
   Journal = {Journal of the American Chemical Society},
   Volume = {128},
   Number = {10},
   Pages = {3228-3232},
   Year = {2006},
   Month = {March},
   ISSN = {0002-7863},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16522103},
   Abstract = {The astronomical number of accessible discrete chemical
             structures makes rational molecular design extremely
             challenging. We formulate the design of molecules with
             specific tailored properties as performing a continuous
             optimization in the space of electron-nuclear attraction
             potentials. The optimization is facilitated by using a
             linear combination of atomic potentials (LCAP), a general
             framework that creates a continuous property landscape from
             an otherwise unlinked set of discrete molecular-property
             values. A demonstration of this approach is given for the
             optimization of molecular electronic polarizability and
             hyperpolarizability. We show that the optimal structures can
             be determined without enumerating and separately evaluating
             the characteristics of the combinatorial number of possible
             structures, a process that would be much slower. The LCAP
             approach may be used with quantum or classical Hamiltonians,
             suggesting possible applications to drug design and new
             materials discovery.},
   Doi = {10.1021/ja0572046},
   Key = {fds234950}
}

@article{fds234908,
   Author = {Mori-Sánchez, P and Cohen, AJ and Yang, W},
   Title = {Self-interaction-free exchange-correlation functional for
             thermochemistry and kinetics.},
   Journal = {Journal of Chemical Physics},
   Volume = {124},
   Number = {9},
   Pages = {91102},
   Year = {2006},
   Month = {March},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16526838},
   Abstract = {We develop a self-interaction-free exchange-correlation
             functional which is very accurate for thermochemistry and
             kinetics. This is achieved by theoretical construction of
             the functional form and nonlinear fitting. We define a
             simple interpolation of the adiabatic connection that uses
             exact exchange, generalized gradient approximation (GGA) and
             meta-GGA functionals. The performance is optimized by
             fitting a small number of empirical parameters. Overall the
             new functional improves significantly upon hybrids and
             meta-GGAs while correctly describing one-electron systems.
             The mean absolute error on a large set of reaction barriers
             is reduced to 1.99 kcal/mol.},
   Doi = {10.1063/1.2179072},
   Key = {fds234908}
}

@article{fds234979,
   Author = {Burger, SK and Yang, W},
   Title = {Quadratic string method for determining the minimum-energy
             path based on multiobjective optimization.},
   Journal = {Journal of Chemical Physics},
   Volume = {124},
   Number = {5},
   Pages = {054109},
   Year = {2006},
   Month = {February},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16468853},
   Abstract = {Based on a multiobjective optimization framework, we develop
             a new quadratic string method for finding the minimum-energy
             path. In the method, each point on the minimum-energy path
             is minimized by integration in the descent direction
             perpendicular to path. Each local integration is done on a
             quadratic surface approximated by a damped
             Broyden-Fletcher-Goldfarb-Shanno updated Hessian, allowing
             the algorithm to take many steps between energy and gradient
             calls. The integration is performed with an adaptive
             step-size solver, which is restricted in length to the trust
             radius of the approximate Hessian. The full algorithm is
             shown to be capable of practical superlinear convergence, in
             contrast to the linear convergence of other methods. The
             method also eliminates the need for predetermining such
             parameters as step size and spring constants, and is
             applicable to reactions with multiple barriers. The
             effectiveness of this method is demonstrated for the
             Muller-Brown potential, a seven-atom Lennard-Jones cluster,
             and the enolation of acetaldehyde to vinyl
             alcohol.},
   Doi = {10.1063/1.2163875},
   Key = {fds234979}
}

@article{fds234949,
   Author = {Cisneros, GA and Wang, M and Silinski, P and Fitzgerald, MC and Yang,
             W},
   Title = {Theoretical and experimental determination on two substrates
             turned over by 4-oxalocrotonate tautomerase.},
   Journal = {The Journal of Physical Chemistry Part A: Molecules,
             Spectroscopy, Kinetics, Environment and General
             Theory},
   Volume = {110},
   Number = {2},
   Pages = {700-708},
   Year = {2006},
   Month = {January},
   ISSN = {1089-5639},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16405343},
   Abstract = {Quantum mechanical/molecular mechanical (QM/MM) calculations
             and experimental kinetic studies have been performed on
             4-oxalocrotonate tautomerase (4OT) for two different
             substrates, 2-hydroxymuconate (2HM) and 2-oxo-4-hexenedioate
             (2o4hex). Potential (deltaE) and free energy (deltaG) paths
             for both steps of the reaction using both substrates were
             calculated to determine the free energy barriers and
             compared to the experimental values obtained from the
             kinetic studies via the transition state theory. In the
             first step, a proton from the hydroxyl oxygen on the second
             carbon of 2HM, or from the third carbon of 2o4hex, is
             abstracted by Pro-1. In the second step, the proton is
             transferred to the fifth carbon of the substrate to form the
             product, 2-oxo-3-hexenedioate (2o3hex). For both substrates
             we obtain a calculated deltaG of approximately 13 kcal/mol,
             in agreement with experimental determinations. The
             calculated free energy barrier difference deltaG2o4hex -
             deltaG2HM (deltadeltaG) is 0.87 kcal/mol. We obtained an
             experimental deltadeltaG of 0.85 kcal/mol. These results
             suggest that 2HM is turned over faster than 2o4hex by 4OT.
             However, these energy differences are so small that both 2HM
             and 2o4hex need to be taken into account in considering the
             mechanism of catalysis of 4OT.},
   Doi = {10.1021/jp0543328},
   Key = {fds234949}
}

@article{fds234966,
   Author = {Liu, R and Ke, S-H and Yang, W and Baranger, HU},
   Title = {Organometallic molecular rectification.},
   Journal = {Journal of Chemical Physics},
   Volume = {124},
   Number = {2},
   Pages = {024718},
   Year = {2006},
   Month = {January},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16422637},
   Abstract = {We study the rectification of current through a single
             molecule with an intrinsic spatial asymmetry. The molecule
             contains a cobaltocene moiety in order to take advantage of
             its relatively localized and high-energy d states. A
             rectifier with large voltage range, high current, and low
             threshold can be realized. The evolution of molecular
             orbitals under both forward and reverse biases is captured
             in a self-consistent nonequilibrium Green function plus
             density functional theory description. Our calculations
             demonstrate the plausibility of making excellent molecular
             diodes by using metallocenes, pointing to a fruitful class
             of molecules.},
   Doi = {10.1063/1.2141955},
   Key = {fds234966}
}

@article{fds234905,
   Author = {Champagne, B and Bulat, FA and Yang, W and Bonness, S and Kirtman,
             B},
   Title = {Density functional theory investigation of the
             polarizability and second hyperpolarizability of
             polydiacetylene and polybutatriene chains: Treatment of
             exact exchange and role of correlation},
   Journal = {Journal of Chemical Physics},
   Volume = {125},
   Number = {19},
   Year = {2006},
   ISSN = {0021-9606},
   url = {http://dx.doi.org/10.1063/1.2388262},
   Abstract = {The static polarizability and second hyperpolarizability of
             increasingly large polydiacetylene and polybutatriene (PBT)
             chains have been evaluated using the optimized effective
             potential for exact exchange (OEP-EXX) method developed by
             Yang and Wu [Phys. Rev. Lett. 89, 143002 (2002)], where the
             unknown part of the effective potential is expressed as a
             linear combination of Gaussian functions. Various
             conventional atomic orbital basis sets were employed for the
             exchange potential (X basis) as well as for the Kohn-Sham
             orbitals [molecular orbital (MO) basis]. Our results were
             compared to coupled-perturbed Hartree-Fock (CPHF)
             calculations and to ab initio correlated values obtained at
             various levels of approximation. It turns out that (a) small
             conventional basis sets are, in general, unsatisfactory for
             the X basis; (b) the performance of a given X basis depends
             on the MO basis and is generally improved when using a
             larger MO basis; (c) these effects are exaggerated for the
             second hyperpolarizability compared to the polarizability;
             (d) except for the second hyperpolarizability of PBT chains,
             using 6-311++G* for the X basis gives reasonable agreement
             with the CPHF results for all MO basis sets; (e) our results
             suggest that in the limit of a complete X basis the OEP-EXX
             values may approach the CPHF data; and (f) in general, the
             quality of a given conventional X basis degrades with the
             length of the oligomer, which correlates with the fact that
             the number of X basis functions becomes a smaller fraction
             of the number required to reproduce exactly the
             finite-basis-set Hartree-Fock energies. Linear and
             especially nonlinear electric field responses constitute a
             very stringent test for assessing the quality of functionals
             and potentials; appropriately tailored basis sets are needed
             to describe the latter. Finally, this study further
             highlights the importance of electron correlation effects on
             linear and nonlinear responses, for which correlated
             functionals with OEP are required. © 2006 American
             Institute of Physics.},
   Doi = {10.1063/1.2388262},
   Key = {fds234905}
}

@article{fds234967,
   Author = {Ke, S-H and Baranger, HU and Yang, W},
   Title = {Development of ab initio calculation for electron transport
             and the effects of lead and contact structures in molecular
             electronics},
   Journal = {Journal of computational and theoretical
             nanoscience},
   Volume = {3},
   Number = {5},
   Pages = {819-823},
   Year = {2006},
   ISSN = {1546-1955},
   url = {http://dx.doi.org/10.1166/jctn.2006.022},
   Abstract = {A fully self-consistent method combining density functional
             theory (DFT) and nonequilibrium Green function approach for
             calculating electron transport through molecular devices is
             reviewed. It uses periodic boundary conditions for DFT and
             treats the leads and molecule of a device system on the same
             footing. Also reviewed is its application for the molecular
             conductance of Au-benzenedithiol-Au systems. Two important
             issues in molecular electronics are discussed: (1) quantum
             confinement effects in thin electrodes (leads) and (2)
             effects of local atomic configuration around the contacts.
             Quantum-confinement- induced waveguide effect causes large
             oscillations in the transmission function. Single or double
             apex Au atoms at each contact lead to a significant
             conductance resonance, which is quite similar to increasing
             the molecule-lead separation. Copyright © 2006 American
             Scientific Publishers All rights reserved.},
   Doi = {10.1166/jctn.2006.022},
   Key = {fds234967}
}

@article{fds234980,
   Author = {Hori, T and Takahashi, H and Nakano, M and Nitta, T and Yang,
             W},
   Title = {A QM/MM study combined with the theory of energy
             representation: Solvation free energies for anti/syn acetic
             acids in aqueous solution},
   Journal = {Chemical Physics Letters},
   Volume = {419},
   Number = {1-3},
   Pages = {240-244},
   Year = {2006},
   ISSN = {0009-2614},
   url = {http://dx.doi.org/10.1016/j.cplett.2005.11.096},
   Abstract = {The solvation free energies for acetic acids in the anti/syn
             conformations in water solution have been computed by the
             novel QM/MM approach combined with the theory of energy
             representation (QM/MM-ER). To examine the accuracy of the
             methodology, we have compared the results with those given
             by experiments and other theoretical calculations. The
             solvation free energies computed by the QM/MM-ER approach
             are in reasonable agreement with corresponding experimental
             values. The free energy difference between the anti and syn
             conformers also agrees well with the results of AM1/TIP3P or
             RISM-SCF calculations. © 2005 Elsevier B.V. All rights
             reserved.},
   Doi = {10.1016/j.cplett.2005.11.096},
   Key = {fds234980}
}

@article{fds234983,
   Author = {Ping, L and Yang, W and Pedersen, LC and Negishi, M and Pedersen,
             LG},
   Title = {Searching for the minimum energy path in the sulfuryl
             transfer reaction catalyzed by human estrogen
             sulfotransferase: Role of enzyme dynamics},
   Journal = {International Journal of Quantum Chemistry},
   Volume = {106},
   Number = {14},
   Pages = {2981-2998},
   Year = {2006},
   ISSN = {0020-7608},
   url = {http://dx.doi.org/10.1002/qua.21123},
   Abstract = {The enzymatic transfer of a sulfuryl group from the
             ubiquitous biological source of sulfate 3′-phosphoadenosine
             5′-phosphosulfate (PAPS) to estrogen is investigated by
             the pseudo-bond quantum mechanical/molecular mechanical
             method (QM/MM) method. Calculations of the reaction path are
             performed starting with models based on two crystal
             structures, which differ in information about the cofactor
             and substrates. In addition, a subsequent relaxation of the
             enzyme was performed with the found transition state frozen,
             followed by redetermination of the path. An activation
             barrier of 22 kcal/mol is estimated. The reaction mechanism
             features a proton transfer from the estrogen to a catalytic
             histidine followed by the rate determining SO 3 transfer.
             The mechanism found is largely dissociative. © 2006 Wiley
             Periodicals, Inc.},
   Doi = {10.1002/qua.21123},
   Key = {fds234983}
}

@article{fds235050,
   Author = {Sohn, J and Parks, JM and Buhrman, G and Brown, P and Kristjánsdóttir,
             K and Safi, A and Edelsbrunner, H and Yang, W and Rudolph,
             J},
   Title = {Experimental validation of the docking orientation of Cdc25
             with its Cdk2-CycA protein substrate.},
   Journal = {Biochemistry},
   Volume = {44},
   Number = {50},
   Pages = {16563-16573},
   Year = {2005},
   Month = {December},
   ISSN = {0006-2960},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16342947},
   Abstract = {Cdc25 phosphatases are key activators of the eukaryotic cell
             cycle and compelling anticancer targets because their
             overexpression has been associated with numerous cancers.
             However, drug discovery targeting these phosphatases has
             been hampered by the lack of structural information about
             how Cdc25s interact with their native protein substrates,
             the cyclin-dependent kinases. Herein, we predict a docked
             orientation for Cdc25B with its Cdk2-pTpY-CycA protein
             substrate by a rigid-body docking method and refine the
             docked models with full-scale molecular dynamics simulations
             and minimization. We validate the stable ensemble structure
             experimentally by a variety of in vitro and in vivo
             techniques. Specifically, we compare our model with a
             crystal structure of the substrate-trapping mutant of
             Cdc25B. We identify and validate in vivo a novel hot-spot
             residue on Cdc25B (Arg492) that plays a central role in
             protein substrate recognition. We identify a hot-spot
             residue on the substrate Cdk2 (Asp206) and confirm its
             interaction with hot-spot residues on Cdc25 using hot-spot
             swapping and double mutant cycles to derive interaction
             energies. Our experimentally validated model is consistent
             with previous studies of Cdk2 and its interaction partners
             and initiates the opportunity for drug discovery of
             inhibitors that target the remote binding sites of this
             protein-protein interaction.},
   Doi = {10.1021/bi0516879},
   Key = {fds235050}
}

@article{fds235062,
   Author = {Liu, R and Ke, S-H and Baranger, HU and Yang, W},
   Title = {Organometallic spintronics: dicobaltocene
             switch.},
   Journal = {Nano Letters},
   Volume = {5},
   Number = {10},
   Pages = {1959-1962},
   Year = {2005},
   Month = {October},
   ISSN = {1530-6984},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16218717},
   Abstract = {A single-molecule spintronic switch and spin valve using two
             cobaltocene moieties is proposed. Spin-dependent transport
             through a lead-molecule-lead junction has been calculated
             using first-principles density functional and nonequilibrium
             Green function methods. We find that the antiparallel
             (singlet) configuration of the cobaltocene spins blocks
             electron transport near the Fermi energy, while the spin
             parallel (triplet) configuration enables much higher
             current. The energy difierence between the antiparallel and
             parallel states depends on the insulating spacer separating
             the two cobaltocenes, allowing switching through the
             application of a moderate magnetic field.},
   Doi = {10.1021/nl0513380},
   Key = {fds235062}
}

@article{fds304407,
   Author = {Wu, Q and Cohen, AJ and Yang, W},
   Title = {Analytic energy gradients of the optimized effective
             potential method.},
   Journal = {Journal of Chemical Physics},
   Volume = {123},
   Number = {13},
   Pages = {134111},
   Year = {2005},
   Month = {October},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16223279},
   Abstract = {The analytic energy gradients of the optimized effective
             potential (OEP) method in density-functional theory are
             developed. Their implementation in the direct optimization
             approach of Yang and Wu [Phys. Rev. Lett. 89, 143002 (2002)]
             and Wu and Yang [J. Theor. Comput. Chem. 2, 627 (2003)] are
             carried out and the validity is confirmed by comparison with
             corresponding gradients calculated via numerical finite
             difference. These gradients are then used to perform
             geometry optimizations on a test set of molecules. It is
             found that exchange-only OEP (EXX) molecular geometries are
             very close to the Hartree-Fock results and that the
             difference between the B3LYP and OEP-B3LYP results is
             negligible. When the energy is expressed in terms of a
             functional of Kohn-Sham orbitals, or in terms of a Kohn-Sham
             potential, the OEP becomes the only way to perform
             density-functional calculations and the present development
             in the OEP method should play an important role in the
             applications of orbital or potential functionals.},
   Doi = {10.1063/1.1989310},
   Key = {fds304407}
}

@article{fds235057,
   Author = {Ke, S-H and Baranger, HU and Yang, W},
   Title = {Models of electrodes and contacts in molecular
             electronics.},
   Journal = {Journal of Chemical Physics},
   Volume = {123},
   Number = {11},
   Pages = {114701},
   Year = {2005},
   Month = {September},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16392577},
   Abstract = {Bridging the difference in atomic structure between
             experiments and theoretical calculations and exploring
             quantum confinement effects in thin electrodes (leads) are
             both important issues in molecular electronics. To address
             these issues, we report here, by using Au-benzenedithiol-Au
             as a model system, systematic investigations of different
             models for the leads and the lead-molecule contacts: leads
             with different cross sections, leads consisting of infinite
             surfaces, and surface leads with a local nanowire or atomic
             chain of different lengths. The method adopted is a
             nonequilibrium Green's-function approach combined with
             density-functional theory calculations for the electronic
             structure and transport, in which the leads and molecule are
             treated on the same footing. It is shown that leads with a
             small cross section will lead to large oscillations in the
             transmission function T(E), which depend significantly on
             the lead structure (orientation) because of quantum
             waveguide effects. This oscillation slowly decays as the
             lead width increases, with the average approaching the limit
             given by infinite surface leads. Local nanowire structures
             around the contacts induce moderate fluctuations in T(E),
             while a Au atomic chain (including a single Au apex atom) at
             each contact leads to a significant conductance
             resonance.},
   Key = {fds235057}
}

@article{fds235052,
   Author = {Hu, H and Yang, W},
   Title = {Dual-topology/dual-coordinate free-energy simulation using
             QM/MM force field.},
   Journal = {Journal of Chemical Physics},
   Volume = {123},
   Number = {4},
   Pages = {041102},
   Year = {2005},
   Month = {July},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16095339},
   Abstract = {We have developed a dual-topology/dual-coordinate
             free-energy simulation method for use with a QM/MM force
             field. By combining two parallel processes into one
             alchemical process, we are able to compute the double
             free-energy difference (delta deltaF) within a single
             simulation, which eliminates half of the expensive
             quantum-mechanical simulation in general. The method has
             been tested in computing the solvation free-energy
             differences of several molecular pairs and shows close
             agreement with experimental results.},
   Doi = {10.1063/1.1990113},
   Key = {fds235052}
}

@article{fds235056,
   Author = {Cisneros, GA and Liu, H and Lu, Z and Yang, W},
   Title = {Reaction path determination for quantum mechanical/molecular
             mechanical modeling of enzyme reactions by combining first
             order and second order "chain-of-replicas"
             methods.},
   Journal = {Journal of Chemical Physics},
   Volume = {122},
   Number = {11},
   Pages = {114502},
   Year = {2005},
   Month = {March},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15836224},
   Abstract = {A two-step procedure for the determination of reaction paths
             in enzyme systems is presented. This procedure combines two
             chain-of-states methods: a quantum mechanical/molecular
             mechanical (QM/MM) implementation of the nudged elastic band
             (NEB) method and a second order parallel path optimizer
             method both recently developed in our laboratory. In the
             first step, a reaction path determination is performed with
             the NEB method, along with a restrained minimization
             procedure for the MM environment to obtain a first
             approximation to the reaction path. In the second step, the
             calculated path is refined with the parallel path optimizer
             method. By combining these two methods the reaction paths
             are determined accurately, and in addition, the number of
             path optimization iterations are significantly reduced. This
             procedure is tested by calculating both steps of the
             isomerization of 2-oxo-4-hexenedioate by 4-oxalocrotonate
             tautomerase, which have been previously determined by our
             group. The calculated paths agree with the previously
             reported results and we obtain a reduction of 45%-55% in the
             number of path optimization cycles.},
   Doi = {10.1063/1.1860560},
   Key = {fds235056}
}

@article{fds304411,
   Author = {Ke, S-H and Baranger, HU and Yang, W},
   Title = {Contact atomic structure and electron transport through
             molecules.},
   Journal = {Journal of Chemical Physics},
   Volume = {122},
   Number = {7},
   Pages = {074704},
   Year = {2005},
   Month = {February},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15743262},
   Abstract = {Using benzene sandwiched between two Au leads as a model
             system, we investigate from first principles the change in
             molecular conductance caused by different atomic structures
             around the metal-molecule contact. Our motivation is the
             variable situations that may arise in break junction
             experiments; our approach is a combined density functional
             theory and Green function technique. We focus on effects
             caused by (1) the presence of an additional Au atom at the
             contact and (2) possible changes in the molecule-lead
             separation. The effects of contact atomic relaxation and two
             different lead orientations are fully considered. We find
             that the presence of an additional Au atom at each of the
             two contacts will increase the equilibrium conductance by up
             to two orders of magnitude regardless of either the lead
             orientation or different group-VI anchoring atoms. This is
             due to a resonance peak near the Fermi energy from the
             lowest energy unoccupied molecular orbital. In the
             nonequilibrium properties, the resonance peak manifests
             itself in a negative differential conductance. We find that
             the dependence of the equilibrium conductance on the
             molecule-lead separation can be quite subtle: either very
             weak or very strong depending on the separation
             regime.},
   Doi = {10.1063/1.1851496},
   Key = {fds304411}
}

@article{fds235059,
   Author = {Liu, R and Ke, S-H and Baranger, HU and Yang, W},
   Title = {Intermolecular effect in molecular electronics.},
   Journal = {Journal of Chemical Physics},
   Volume = {122},
   Number = {4},
   Pages = {44703},
   Year = {2005},
   Month = {January},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15740279},
   Abstract = {We investigate the effects of lateral interactions on the
             conductance of two molecules connected in parallel to
             semi-infinite leads. The method we use combines a Green
             function approach to quantum transport with density
             functional theory for the electronic properties. The system,
             modeled after a self-assembled monolayer, consists of
             benzylmercaptane molecules sandwiched between gold
             electrodes. We find that the conductance increases when
             intermolecular interaction comes into play. The source of
             this increase is the indirect interaction through the gold
             substrate rather than direct molecule-molecule interaction.
             A striking resonance is produced only 0.3 eV above the Fermi
             energy.},
   Doi = {10.1063/1.1825377},
   Key = {fds235059}
}

@article{fds45273,
   Author = {Stephanie A. Getty and Chaiwat Engtrakul and Lixin Wang and Rui Liu and San-Huang Ke and Harold U. Baranger and Weitao Yang and Michal S.
             Fuhrer and Lawrence R. Sita},
   Title = {Near-perfect conduction through a ferrocence-based molecular
             wire},
   Journal = {Phys. Rev. B.},
   Volume = {71},
   Pages = {241401 (R)/1-241401(R)/4},
   Year = {2005},
   Key = {fds45273}
}

@article{fds234964,
   Author = {Ullmo, D and Jiang, H and Yang, W and Baranger, HU},
   Title = {Interactions and broken time-reversal symmetry in chaotic
             quantum dots},
   Journal = {Physical Review B - Condensed Matter and Materials
             Physics},
   Volume = {71},
   Number = {20},
   Year = {2005},
   url = {http://dx.doi.org/10.1103/PhysRevB.71.201310},
   Abstract = {When treating interactions in quantum dots within a
             random-phase- approximation (RPA)-like approach,
             time-reversal symmetry plays an important role as
             higher-order terms-the Cooper series-need to be included
             when this symmetry is present. Here we consider model
             quantum dots in a magnetic field weak enough to leave the
             dynamics of the dot chaotic, but strong enough to break
             time-reversal symmetry. The ground-state spin and addition
             energy for dots containing 120-200 electrons are found using
             local spin-density-functional theory, and we compare the
             corresponding distributions with those derived from an
             RPA-like treatment of the interactions. The agreement
             between the two approaches is very good, significantly
             better than for analogous calculations in the presence of
             time-reversal-symmetry. This demonstrates that the
             discrepancies between the two approaches in the
             time-reversal symmetric case indeed originate from the
             Cooper channel, indicating that these higher-order terms
             might not be properly taken into account in the
             spin-density-functional calculations. © 2005 The American
             Physical Society.},
   Doi = {10.1103/PhysRevB.71.201310},
   Key = {fds234964}
}

@article{fds234965,
   Author = {Jiang, H and Ullmo, D and Yang, W and Baranger, HU},
   Title = {Scrambling and gate-induced fluctuations in realistic
             quantum dots},
   Journal = {Physical Review B - Condensed Matter and Materials
             Physics},
   Volume = {71},
   Number = {8},
   Year = {2005},
   ISSN = {1098-0121},
   url = {http://dx.doi.org/10.1103/PhysRevB.71.085313},
   Abstract = {We evaluate the magnitude of two important mesoscopic
             effects using a realistic model of typical quantum dots.
             "Scrambling" and "gate effect" are defined as the change in
             the single-particle spectrum due to added electrons or
             gate-induced shape deformation, respectively. These two
             effects are investigated systematically in both the
             'self-consistent Kohn-Sham (KS) theory and a Fermi
             liquidlike Strutinsky approach. We find that the genuine
             scrambling effect is small because the potential here is
             smooth. In the KS theory, a key point is the implicit
             inclusion of residual interactions in the spectrum; these
             dominate and make scrambling appear larger. Finally, the
             gate effect is comparable in the two cases and, while small,
             is able to cause gate-induced spin transitions. ©2005 The
             American Physical Society.},
   Doi = {10.1103/PhysRevB.71.085313},
   Key = {fds234965}
}

@article{fds234976,
   Author = {Bulat, FA and Toro-Labb́, A and Champagne, B and Kirtman, B and Yang,
             W},
   Title = {Density-functional theory (hyper)polarizabilities of
             push-pull π -conjugated systems: Treatment of exact
             exchange and role of correlation},
   Journal = {Journal of Chemical Physics},
   Volume = {123},
   Number = {1},
   Year = {2005},
   ISSN = {0021-9606},
   url = {http://dx.doi.org/10.1063/1.1926275},
   Abstract = {The performance of the optimized effective potential
             procedure for exact exchange in calculating static
             electric-field response properties of push-pull π
             -conjugated systems has been studied, with an emphasis on N
             O2 - (CH=CH)n -N H2 chains. Good agreement with Hartree-Fock
             dipole moments and (hyper)polarizabilities is obtained;
             particularly noteworthy is the chain length dependence for
             Βn. Thus, the problem that conventional density-functional
             theory functionals dramatically overestimate these
             properties is largely solved, although there remains a
             significant correlation contribution that cannot be
             accounted for with current correlation functionals. © 2005
             American Institute of Physics.},
   Doi = {10.1063/1.1926275},
   Key = {fds234976}
}

@article{fds235051,
   Author = {Wu, Q and Cohen, AJ and Yang, W},
   Title = {Analytic energy gradients of the optimized effective
             potential method},
   Journal = {J. Chem. Phys.},
   Volume = {123},
   Number = {134111/1-134111/10},
   Pages = {134111},
   Year = {2005},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16223279},
   Abstract = {The analytic energy gradients of the optimized effective
             potential (OEP) method in density-functional theory are
             developed. Their implementation in the direct optimization
             approach of Yang and Wu [Phys. Rev. Lett. 89, 143002 (2002)]
             and Wu and Yang [J. Theor. Comput. Chem. 2, 627 (2003)] are
             carried out and the validity is confirmed by comparison with
             corresponding gradients calculated via numerical finite
             difference. These gradients are then used to perform
             geometry optimizations on a test set of molecules. It is
             found that exchange-only OEP (EXX) molecular geometries are
             very close to the Hartree-Fock results and that the
             difference between the B3LYP and OEP-B3LYP results is
             negligible. When the energy is expressed in terms of a
             functional of Kohn-Sham orbitals, or in terms of a Kohn-Sham
             potential, the OEP becomes the only way to perform
             density-functional calculations and the present development
             in the OEP method should play an important role in the
             applications of orbital or potential functionals.},
   Doi = {10.1063/1.1989310},
   Key = {fds235051}
}

@article{fds235053,
   Author = {Getty, SA and Engtrakul, C and Wang, L and Liu, R and Ke, S-H and Baranger,
             HU and Yang, W and Fuhrer, MS and Sita, LR},
   Title = {Near-perfect conduction through a ferrocene-based molecular
             wire},
   Journal = {Physical Review B - Condensed Matter and Materials
             Physics},
   Volume = {71},
   Number = {24},
   Year = {2005},
   ISSN = {1098-0121},
   url = {http://dx.doi.org/10.1103/PhysRevB.71.241401},
   Abstract = {Here we describe the design, single-molecule transport
             measurements, and theoretical modeling of a ferrocene-based
             organometallic molecular wire, whose bias-dependent
             conductance shows a clear Lorentzian form with magnitude
             exceeding 70% of the conductance quantum G0. We attribute
             this unprecedented level of single-molecule conductance to a
             manifestation of the low-lying molecular resonance and
             extended orbital network long predicted for a conjugated
             organic system. A similar-in-length, all-organic conjugated
             phenylethynyl oligomer molecular framework shows much lower
             conductance. © 2005 The American Physical
             Society.},
   Doi = {10.1103/PhysRevB.71.241401},
   Key = {fds235053}
}

@article{fds235054,
   Author = {Bulat, FA and Toro-Labbe, A and Champagne, B and Kirtman, B and Yang,
             W},
   Title = {Dft (hyper)polarizabilities of push-pull pi-conjugated
             systems, treatment of exact exchange and role
             correlation},
   Journal = {J. Chem. Phys.},
   Volume = {123},
   Pages = {014319/1-014319/7},
   Year = {2005},
   Key = {fds235054}
}

@article{fds235055,
   Author = {Wu, Q and Cohen, AJ and Yang, W},
   Title = {Excitation energies from time-dependent density functional
             theory with accurate exchange-correlation
             potentials},
   Journal = {Molecular Physics},
   Volume = {103},
   Number = {6-8},
   Pages = {711-717},
   Year = {2005},
   ISSN = {0026-8976},
   url = {http://dx.doi.org/10.1080/0026897051234267},
   Abstract = {We have applied two of our recently developed methods for
             calculating accurate Kohn-Sham potentials, namely direct
             optimization of non-interacting kinetic energy of a known
             electron density and the asymptotic correction of
             approximate exchange-correlation potentials, to the
             calculation of excitation energies within time-dependent
             density functional theory. Our asymptotic correction method
             is found not to be adequate in improving Rydberg state
             results, probably because the potential is still affected by
             the approximate energy functional due to the variational
             nature of the method. However, Kohn-Sham potentials
             calculated from coupled cluster singles and doubles
             densities give excellent results for the He and Be atoms,
             and consistently much improved results for molecules. ©
             2005 Taylor &amp; Francis Group Ltd.},
   Doi = {10.1080/0026897051234267},
   Key = {fds235055}
}

@article{fds235058,
   Author = {Ke, S-H and Baranger, HU and Yang, W},
   Title = {Electron transport through molecules: Gate-induced
             polarization and potential shift},
   Journal = {Physical Review B - Condensed Matter and Materials
             Physics},
   Volume = {71},
   Number = {11},
   Pages = {113401/1-113401/4},
   Year = {2005},
   ISSN = {1098-0121},
   url = {http://dx.doi.org/10.1103/PhysRevB.71.113401},
   Abstract = {We analyze the effect of a gate on the conductance of
             molecules by separately evaluating the gate-induced
             polarization and the potential shift of the molecule
             relative to the leads. The calculations use ab initio
             density functional theory combined with a Green function
             method for electron transport. For a general view, we study
             several systems: (1) atomic chains of C or Al sandwiched
             between Al electrodes, (2) a benzene molecule between Au
             leads, and (3) (9,0) and (5,5) carbon nanotubes. We find
             that the polarization effect is small because of screening,
             while the effect of the potential shift is significant,
             providing a mechanism for single-molecule transistors.
             ©2005 The American Physical Society.},
   Doi = {10.1103/PhysRevB.71.113401},
   Key = {fds235058}
}

@article{fds235060,
   Author = {Ke, S-H and Baranger, H and Yang, W},
   Title = {"Contact Atomic Structure and Electron Transport Through
             Molecules"},
   Journal = {J. Chem. Phys.},
   Volume = {122},
   Number = {7},
   Pages = {114502/1-114502/7},
   Year = {2005},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15743262},
   Abstract = {Using benzene sandwiched between two Au leads as a model
             system, we investigate from first principles the change in
             molecular conductance caused by different atomic structures
             around the metal-molecule contact. Our motivation is the
             variable situations that may arise in break junction
             experiments; our approach is a combined density functional
             theory and Green function technique. We focus on effects
             caused by (1) the presence of an additional Au atom at the
             contact and (2) possible changes in the molecule-lead
             separation. The effects of contact atomic relaxation and two
             different lead orientations are fully considered. We find
             that the presence of an additional Au atom at each of the
             two contacts will increase the equilibrium conductance by up
             to two orders of magnitude regardless of either the lead
             orientation or different group-VI anchoring atoms. This is
             due to a resonance peak near the Fermi energy from the
             lowest energy unoccupied molecular orbital. In the
             nonequilibrium properties, the resonance peak manifests
             itself in a negative differential conductance. We find that
             the dependence of the equilibrium conductance on the
             molecule-lead separation can be quite subtle: either very
             weak or very strong depending on the separation
             regime.},
   Doi = {10.1063/1.1851496},
   Key = {fds235060}
}

@article{fds235061,
   Author = {Mori-Sánchez, P and Wu, Q and Yang, W},
   Title = {Orbital-dependent correlation energy in density-functional
             theory based on a second-order perturbation approach:
             success and failure.},
   Journal = {Journal of Chemical Physics},
   Volume = {123},
   Number = {6},
   Pages = {62204-},
   Year = {2005},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16122290},
   Abstract = {We have developed a second-order perturbation theory (PT)
             energy functional within density-functional theory (DFT).
             Based on PT with the Kohn-Sham (KS) determinant as a
             reference, this new ab initio exchange-correlation
             functional includes an exact exchange (EXX) energy in the
             first order and a correlation energy including all single
             and double excitations from the KS reference in the second
             order. The explicit dependence of the exchange and
             correlation energy on the KS orbitals in the functional fits
             well into our direct minimization approach for the optimized
             effective potential, which is a very efficient method to
             perform fully self-consistent calculations for any
             orbital-dependent functionals. To investigate the quality of
             the correlation functional, we have applied the method to
             selected atoms and molecules. For two-electron atoms and
             small molecules described with small basis sets, this new
             method provides excellent results, improving both
             second-order Moller-Plesset expression and any conventional
             DFT results significantly. For larger systems, however, it
             performs poorly, converging to very low unphysical total
             energies. The failure of PT based energy functionals is
             analyzed, and its origin is traced back to near degeneracy
             problems due to the orbital- and eigenvalue-dependent
             algebraic structure of the correlation functional. The
             failure emerges in the self-consistent approach but not in
             perturbative post-EXX calculations, emphasizing the crucial
             importance of self-consistency in testing new
             orbital-dependent energy functionals.},
   Doi = {10.1063/1.1904584},
   Key = {fds235061}
}

@article{fds235063,
   Author = {Ulmo, D and Jiang, H and Yang, W and Baranger, H},
   Title = {"Landau Fermi Liquid Picture of Spin Density Functional
             Theory: Strutinsky Approach to Quantum Dots"},
   Journal = {Phys. Rev. B., Rapid Communication},
   Volume = {71},
   Number = {20},
   Pages = {201310/1-201310/4},
   Year = {2005},
   ISSN = {0163-1829},
   url = {http://dx.doi.org/10.1103/PhysRevB.70.205309},
   Abstract = {We analyze the ground-state energy and spin of quantum dots
             obtained from spin density functional theory (SDFT)
             calculations. First, we introduce a Strutinsky-type
             approximation, in which quantum interference is treated as a
             correction to a smooth Thomas-Fermi description. For large
             irregular dots, we find that the second-order Strutinsky
             expressions have an accuracy of about 5% of a mean level
             spacing compared to the full SDFT and capture all the
             qualitative features. Second, we perform a random
             matrix-theory/random-plane wave analysis of the Strutinsky
             SDFT expressions. The results are statistically similar to
             the SDFT quantum dot statistics. Finally, we note that the
             second-order Strutinsky approximation provides, in essence,
             a Landau Fermi-liquid picture of spin density functional
             theory. For instance, the leading term in the spin channel
             is simply the familiar exchange constant. A direct
             comparison between SDFT and the perturbation theory derived
             "universal Hamiltonian" is thus made possible.},
   Doi = {10.1103/PhysRevB.70.205309},
   Key = {fds235063}
}

@article{fds318104,
   Author = {Cisneros, GA and Liu, H and Lu, Z and Yang, W},
   Title = {Reaction path determination for quantum mechanical/molecular
             mechanical modeling of enzyme reactions by combining first
             order and second order "chain-of-replicas"
             methods.},
   Journal = {Journal of Chemical Physics},
   Volume = {122},
   Number = {11},
   Pages = {114502-},
   Year = {2005},
   Abstract = {A two-step procedure for the determination of reaction paths
             in enzyme systems is presented. This procedure combines two
             chain-of-states methods: a quantum mechanical/molecular
             mechanical (QM/MM) implementation of the nudged elastic band
             (NEB) method and a second order parallel path optimizer
             method both recently developed in our laboratory. In the
             first step, a reaction path determination is performed with
             the NEB method, along with a restrained minimization
             procedure for the MM environment to obtain a first
             approximation to the reaction path. In the second step, the
             calculated path is refined with the parallel path optimizer
             method. By combining these two methods the reaction paths
             are determined accurately, and in addition, the number of
             path optimization iterations are significantly reduced. This
             procedure is tested by calculating both steps of the
             isomerization of 2-oxo-4-hexenedioate by 4-oxalocrotonate
             tautomerase, which have been previously determined by our
             group. The calculated paths agree with the previously
             reported results and we obtain a reduction of 45%-55% in the
             number of path optimization cycles.},
   Key = {fds318104}
}

@article{fds235066,
   Author = {Jiang, H and Yang, W},
   Title = {Conjugate-gradient optimization method for orbital-free
             density functional calculations.},
   Journal = {Journal of Chemical Physics},
   Volume = {121},
   Number = {5},
   Pages = {2030-2036},
   Year = {2004},
   Month = {August},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15260756},
   Abstract = {Orbital-free density functional theory as an extension of
             traditional Thomas-Fermi theory has attracted a lot of
             interest in the past decade because of developments in both
             more accurate kinetic energy functionals and highly
             efficient numerical methodology. In this paper, we developed
             a conjugate-gradient method for the numerical solution of
             spin-dependent extended Thomas-Fermi equation by
             incorporating techniques previously used in Kohn-Sham
             calculations. The key ingredient of the method is an
             approximate line-search scheme and a collective treatment of
             two spin densities in the case of spin-dependent extended
             Thomas-Fermi problem. Test calculations for a quartic
             two-dimensional quantum dot system and a three-dimensional
             sodium cluster Na216 with a local pseudopotential
             demonstrate that the method is accurate and
             efficient.},
   Doi = {10.1063/1.1768163},
   Key = {fds235066}
}

@article{fds304409,
   Author = {Lu, Z and Nowak, W and Lee, G and Marszalek, PE and Yang,
             W},
   Title = {Elastic properties of single amylose chains in water: a
             quantum mechanical and AFM study.},
   Journal = {Journal of the American Chemical Society},
   Volume = {126},
   Number = {29},
   Pages = {9033-9041},
   Year = {2004},
   Month = {July},
   ISSN = {0002-7863},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15264836},
   Abstract = {Recent single-molecule atomic force microscopy (AFM)
             experiments have revealed that some polysaccharides display
             large deviations from force-extension relationships of other
             polymers which typically behave as simple entropic springs.
             However, the mechanism of these deviations has not been
             fully elucidated. Here we report the use of novel quantum
             mechanical methodologies, the divide-and-conquer linear
             scaling approach and the self-consistent charge density
             functional-based tight binding (SCC-DFTB) method, to unravel
             the mechanism of the extensibility of the polysaccharide
             amylose, which in water displays particularly large
             deviations from the simple entropic elasticity. We studied
             the deformations of maltose, a building block of amylose,
             both in a vacuum and in solution. To simulate the
             deformations in solution, the TIP3P molecular mechanical
             model is used to model the solvent water, and the SCC-DFTB
             method is used to model the solute. The interactions between
             the solute and water are treated by the combined quantum
             mechanical and molecular mechanical approach. We find that
             water significantly affects the mechanical properties of
             maltose. Furthermore, we performed two nanosecond-scale
             steered molecular dynamics simulations for single amylose
             chains composed of 10 glucopyranose rings in solution. Our
             SCC-DFTB/MM simulations reproduce the experimentally
             measured force-extension curve, and we find that the
             force-induced chair-to-boat transitions of glucopyranose
             rings are responsible for the characteristic plateau in the
             force-extension curve of amylose. In addition, we performed
             single-molecule AFM measurements on carboxymethyl amylose,
             and we found that, in contrast to the results of an earlier
             work by others, these side groups do not significantly
             affect amylose elasticity. By combining our experimental and
             modeling results, we conclude that the nonentropic elastic
             behavior of amylose is governed by the mechanics of pyranose
             rings themselves and their force-induced conformational
             transitions.},
   Doi = {10.1021/ja031940x},
   Key = {fds304409}
}

@article{fds304405,
   Author = {Lu, Z and Yang, W},
   Title = {Reaction path potential for complex systems derived from
             combined ab initio quantum mechanical and molecular
             mechanical calculations.},
   Journal = {Journal of Chemical Physics},
   Volume = {121},
   Number = {1},
   Pages = {89-100},
   Year = {2004},
   Month = {July},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15260525},
   Abstract = {Combined ab initio quantum mechanical and molecular
             mechanical calculations have been widely used for modeling
             chemical reactions in complex systems such as enzymes, with
             most applications being based on the determination of a
             minimum energy path connecting the reactant through the
             transition state to the product in the enzyme environment.
             However, statistical mechanics sampling and reaction
             dynamics calculations with a combined ab initio quantum
             mechanical (QM) and molecular mechanical (MM) potential are
             still not feasible because of the computational costs
             associated mainly with the ab initio quantum mechanical
             calculations for the QM subsystem. To address this issue, a
             reaction path potential energy surface is developed here for
             statistical mechanics and dynamics simulation of chemical
             reactions in enzymes and other complex systems. The reaction
             path potential follows the ideas from the reaction path
             Hamiltonian of Miller, Handy and Adams for gas phase
             chemical reactions but is designed specifically for large
             systems that are described with combined ab initio quantum
             mechanical and molecular mechanical methods. The reaction
             path potential is an analytical energy expression of the
             combined quantum mechanical and molecular mechanical
             potential energy along the minimum energy path. An expansion
             around the minimum energy path is made in both the nuclear
             and the electronic degrees of freedom for the QM subsystem
             internal energy, while the energy of the subsystem described
             with MM remains unchanged from that in the combined quantum
             mechanical and molecular mechanical expression and the
             electrostatic interaction between the QM and MM subsystems
             is described as the interaction of the MM charges with the
             QM charges. The QM charges are polarizable in response to
             the changes in both the MM and the QM degrees of freedom
             through a new response kernel developed in the present work.
             The input data for constructing the reaction path potential
             are energies, vibrational frequencies, and electron density
             response properties of the QM subsystem along the minimum
             energy path, all of which can be obtained from the combined
             quantum mechanical and molecular mechanical calculations.
             Once constructed, it costs much less for its evaluation.
             Thus, the reaction path potential provides a potential
             energy surface for rigorous statistical mechanics and
             reaction dynamics calculations of complex systems. As an
             example, the method is applied to the statistical mechanical
             calculations for the potential of mean force of the chemical
             reaction in triosephosphate isomerase.},
   Doi = {10.1063/1.1757436},
   Key = {fds304405}
}

@article{fds304406,
   Author = {Wang, M and Lu, Z and Yang, W},
   Title = {Transmission coefficient calculation for proton transfer in
             triosephosphate isomerase based on the reaction path
             potential method.},
   Journal = {Journal of Chemical Physics},
   Volume = {121},
   Number = {1},
   Pages = {101-107},
   Year = {2004},
   Month = {July},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15260526},
   Abstract = {A global potential energy surface has been constructed
             through interpolation of our recently developed reaction
             path potential for chemical reactions in enzymes which is
             derived from combined ab initio quantum mechanical and
             molecular mechanical calculations. It has been implemented
             for the activated molecular dynamics simulations of the
             initial proton transfer reaction catalyzed by
             triosephosphate isomerase. To examine the dynamical effects
             on the rate constants of the enzymatic reaction, the
             classical transmission coefficient kappa(t) is evaluated to
             be 0.47 with the reactive flux approach, demonstrating
             considerable deviations from transition state theory. In
             addition, the fluctuations of protein environments have
             small effects on the barrier recrossing, and the
             transmission coefficient kappa(t) strongly depends on the
             fluctuations of atoms near the active site of the
             enzyme.},
   Doi = {10.1063/1.1757437},
   Key = {fds304406}
}

@article{fds235065,
   Author = {Cisneros, GA and Wang, M and Silinski, P and Fitzgerald, MC and Yang,
             W},
   Title = {The protein backbone makes important contributions to
             4-oxalocrotonate tautomerase enzyme catalysis: understanding
             from theory and experiment.},
   Journal = {Biochemistry},
   Volume = {43},
   Number = {22},
   Pages = {6885-6892},
   Year = {2004},
   Month = {June},
   ISSN = {0006-2960},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15170325},
   Abstract = {The role of polypeptide backbone interactions in
             4-oxalocrotonate tautomerase (4OT) catalysis has been
             investigated using a combination of site-directed
             mutagenesis experiments with unnatural amino acids and
             quantum mechanical/molecular mechanical (QM/MM) calculations
             of the 4OT reaction mechanism. Energy barriers for the
             wild-type enzyme (wt-4OT) and for a 4OT analogue containing
             a backbone amide to ester bond mutation between Ile-7 and
             Leu-8 [(OL8)4OT] were determined by both theory and
             experiment. The amide to ester bond mutation in (OL8)4OT
             effectively deleted a putative hydrogen bonding interaction
             between the enzyme's polypeptide backbone and its substrate.
             Recent theoretical calculations for the 4OT reaction
             mechanism suggested that this hydrogen bonding interaction
             helps properly position the substrate in the active site
             [Cisneros, G. A., et al. (2003) J. Am. Chem. Soc. 125,
             10384-10393]. Our experimental results for (OL8)4OT reveal
             that the energy barrier for the (OL8)4OT-catalyzed reaction
             was increased 1.8 kcal/mol over that of the wild-type
             enzyme. This increase was in good agreement with the 1.0
             kcal/mol increase obtained from QM/MM calculations for this
             analogue. Our theoretical calculations further suggest the
             hydrogen bond deletion in (OL8)4OT results in a
             rearrangement of the substrate in the active site. In this
             rearrangement, an ordered water molecule loses its ability
             to stabilize the transition state (TS), and Arg-61 gains the
             ability to stabilize the TS. The predicted role of Arg-61 in
             (OL8)4OT catalysis was confirmed in kinetic experiments with
             an analogue of (OL8)4OT containing an Arg to Ala mutation at
             position 61.},
   Doi = {10.1021/bi049943p},
   Key = {fds235065}
}

@article{fds303177,
   Author = {Jiang, H and Ullmo, D and Yang, W and Baranger, HU},
   Title = {Scrambling and Gate Effects in Realistic Quantum
             Dots},
   Volume = {71},
   Pages = {085313/1-085313/6},
   Year = {2004},
   Month = {May},
   url = {http://arxiv.org/abs/cond-mat/0405262v2},
   Abstract = {We evaluate the magnitude of two important mesoscopic
             effects using a realistic model of typical quantum dots.
             ``Scrambling'' and ``gate effect'' are defined as the change
             in the single-particle spectrum due to added electrons or
             gate-induced shape deformation, respectively. These two
             effects are investigated systematically in both the
             self-consistent Kohn-Sham (KS) theory and a Fermi
             liquid-like Strutinsky approach. We find that the genuine
             scrambling effect is small because the potential here is
             smooth. In the KS theory, a key point is the implicit
             inclusion of residual interactions in the spectrum; these
             dominate and make scrambling appear larger. Finally, the
             gate effect is comparable in the two cases and, while small,
             is able to cause gate-induced spin transitions.},
   Doi = {10.1103/PhysRevB.71.085313},
   Key = {fds303177}
}

@article{fds235072,
   Author = {Yang, W and Ayers, PW and Wu, Q},
   Title = {Potential functionals: dual to density functionals and
             solution to the v-representability problem.},
   Journal = {Physical Review Letters},
   Volume = {92},
   Number = {14},
   Pages = {146404},
   Year = {2004},
   Month = {April},
   ISSN = {0031-9007},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15089563},
   Abstract = {A functional of external potentials and its variational
             principle for the ground-state energy is constructed. This
             potential functional formulation is dual to the density
             functional approach and provides a solution to the
             v-representability problem in the original Hohenberg-Kohn
             theory. A second potential functional for Kohn-Sham
             noninteracting systems establishes the foundation for the
             optimized effective potential approach and results in
             efficient approaches for ensemble Kohn-Sham
             calculations.},
   Doi = {10.1103/PhysRevLett.92.146404},
   Key = {fds235072}
}

@article{fds234899,
   Author = {Feng, H and Bian, J and Li, L and Yang, W},
   Title = {An efficient method for constructing nonorthogonal localized
             molecular orbitals},
   Journal = {Journal of Chemical Physics},
   Volume = {120},
   Number = {20},
   Pages = {9458-9466},
   Year = {2004},
   ISSN = {0021-9606},
   url = {http://dx.doi.org/10.1063/1.1691396},
   Abstract = {A method aimed at the construction of nonorthogonal
             localized molecular orbitals (NOLMO) was presented. By
             minimizing the spread functional starting from a initial set
             of canonical orthogonal molecular orbitals, a set of highly
             localized NOLMOs were obtained. The centroids of the NOLMOs
             were constrained to be those of the corresponding orthogonal
             localized molecular orbitals (OLMO), obtained with the Boys
             criterion in order to enhance the stability and efficiency.
             It was found that the centroid constraints made the
             optimization for each NOLMO independent of the others, which
             enabled its application in large systems.},
   Doi = {10.1063/1.1691396},
   Key = {fds234899}
}

@article{fds234900,
   Author = {Xie, L and Liu, H and Yang, W},
   Title = {Adapting the nudged elastic band method for determining
             minimum-energy paths of chemical reactions in
             enzymes},
   Journal = {Journal of Chemical Physics},
   Volume = {120},
   Number = {17},
   Pages = {8039-8052},
   Year = {2004},
   ISSN = {0021-9606},
   url = {http://dx.doi.org/10.1063/1.1691404},
   Abstract = {An efficient, robust and general approach, based on nudged
             elastic band reaction path optimization method, for the
             optimization of reaction paths for enzymatic systems was
             presented. The soft spectator degree of freedom were
             excluded from path definitions using only inter-atomic
             distances corresponding to forming/breaking bonds in a
             reaction. The applicability of the approach was demonstrated
             using the acylation reaction of type A β-lactamase as an
             example. Analysis shows that a continuous minimum energy
             path was obtained without any assumption on reaction
             coordinates.},
   Doi = {10.1063/1.1691404},
   Key = {fds234900}
}

@article{fds234943,
   Author = {Goj, LA and Cisneros, GA and Yang, W and Widenhoefer,
             RA},
   Title = {Erratum: "Dramatic effect of homoallylic substitution on the
             rate of palladium-catalyzed diene cycloisomerization"
             (Journal of Organometallic Chemistry (2003) vol. 687
             (498-507) 10.1016/j.jorganchem.2003.09.046)},
   Journal = {Journal of Organometallic Chemistry},
   Volume = {689},
   Number = {17},
   Pages = {2845-},
   Year = {2004},
   url = {http://dx.doi.org/10.1016/j.jorganchem.2004.06.001},
   Doi = {10.1016/j.jorganchem.2004.06.001},
   Key = {fds234943}
}

@article{fds234960,
   Author = {Jiang, H and Ullmo, D and Yang, W and Baranger, HU},
   Title = {Electron-electron interactions in isolated and realistic
             quantum dots: A density functional theory
             study},
   Journal = {Physical Review B - Condensed Matter and Materials
             Physics},
   Volume = {69},
   Number = {23},
   Pages = {235326-1-235326-10},
   Year = {2004},
   ISSN = {0163-1829},
   url = {http://dx.doi.org/10.1103/PhysRevB.69.235326},
   Abstract = {We use Kohn-Sham spin-density-functional theory to study the
             statistics of ground-state spin and the spacing between
             conductance peaks in the Coulomb blockade regime for both
             two-dimensional isolated and realistic quantum dots. We make
             a systematic investigation of the effects of
             electron-electron interaction strength and electron number
             on both the peak spacing and spin distributions. A direct
             comparison between the distributions from isolated and
             realistic dots shows that, despite the difference in the
             boundary conditions and confining potential, the statistical
             properties are qualitatively the same. Strong even/odd
             pairing in the peak spacing distribution is observed only in
             the weak e-e interaction regime and vanishes for moderate
             interactions. The probability of high spin ground states
             increases for stronger e-e interaction and seems to saturate
             around rs ∼4. The saturated value is larger than previous
             theoretical predictions. Both spin and conductance peak
             spacing distributions show substantial variation as the
             electron number increases, not saturating until N ∼150. To
             interpret our numerical results, we analyze the spin
             distribution in the even N case using a simple two-level
             model.},
   Doi = {10.1103/PhysRevB.69.235326},
   Key = {fds234960}
}

@article{fds234962,
   Author = {Ke, S-H and Baranger, HU and Yang, W},
   Title = {Electron transport through molecules: Self-consistent and
             non-self-consistent approaches},
   Journal = {Physical Review B - Condensed Matter and Materials
             Physics},
   Volume = {70},
   Number = {8},
   Pages = {085410-1-085410-12},
   Year = {2004},
   url = {http://dx.doi.org/10.1103/PhysRevB.70.085410},
   Abstract = {A self-consistent method for calculating electron transport
             through a molecular device is developed. It is based on
             density functional theory electronic structure calculations
             under periodic boundary conditions and implemented in the
             framework of the nonequilibrium Green function approach. To
             avoid the substantial computational cost in finding the I-V
             characteristic of large systems, we also develop an
             approximate but much more efficient non-self-consistent
             method. Here the change in effective potential in the device
             region caused by a bias is approximated by the main features
             of the voltage drop. As applications, the I-V curves of a
             carbon chain and an aluminum chain sandwiched between two
             aluminum electrodes are calculated-two systems in which the
             voltage drops very differently. By comparing to the
             self-consistent results, we show that this
             non-self-consistent approach works well and can give
             quantitatively good results.},
   Doi = {10.1103/PhysRevB.70.085410},
   Key = {fds234962}
}

@article{fds235068,
   Author = {Wang, M and Lu, Z and Yang, W},
   Title = {"Transmission Coefficient Calculation for Proton Transfer in
             Triosephosphate Isomerase on the Reaction Path Potential
             Generated from ab initio qm/mm Calculations"},
   Journal = {J. Chem. Phys.},
   Volume = {121},
   Number = {1},
   Pages = {101-107},
   Year = {2004},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15260526},
   Abstract = {A global potential energy surface has been constructed
             through interpolation of our recently developed reaction
             path potential for chemical reactions in enzymes which is
             derived from combined ab initio quantum mechanical and
             molecular mechanical calculations. It has been implemented
             for the activated molecular dynamics simulations of the
             initial proton transfer reaction catalyzed by
             triosephosphate isomerase. To examine the dynamical effects
             on the rate constants of the enzymatic reaction, the
             classical transmission coefficient kappa(t) is evaluated to
             be 0.47 with the reactive flux approach, demonstrating
             considerable deviations from transition state theory. In
             addition, the fluctuations of protein environments have
             small effects on the barrier recrossing, and the
             transmission coefficient kappa(t) strongly depends on the
             fluctuations of atoms near the active site of the
             enzyme.},
   Doi = {10.1063/1.1757437},
   Key = {fds235068}
}

@article{fds235069,
   Author = {Lu, Z and Yang, W},
   Title = {"Reaction Path Potential for Complex Systems Derived From ab
             initioqm/mm Calculations"},
   Journal = {J. Chem. Phys.},
   Volume = {121},
   Number = {1},
   Pages = {89-100},
   Year = {2004},
   ISSN = {0021-9606},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15260525},
   Abstract = {Combined ab initio quantum mechanical and molecular
             mechanical calculations have been widely used for modeling
             chemical reactions in complex systems such as enzymes, with
             most applications being based on the determination of a
             minimum energy path connecting the reactant through the
             transition state to the product in the enzyme environment.
             However, statistical mechanics sampling and reaction
             dynamics calculations with a combined ab initio quantum
             mechanical (QM) and molecular mechanical (MM) potential are
             still not feasible because of the computational costs
             associated mainly with the ab initio quantum mechanical
             calculations for the QM subsystem. To address this issue, a
             reaction path potential energy surface is developed here for
             statistical mechanics and dynamics simulation of chemical
             reactions in enzymes and other complex systems. The reaction
             path potential follows the ideas from the reaction path
             Hamiltonian of Miller, Handy and Adams for gas phase
             chemical reactions but is designed specifically for large
             systems that are described with combined ab initio quantum
             mechanical and molecular mechanical methods. The reaction
             path potential is an analytical energy expression of the
             combined quantum mechanical and molecular mechanical
             potential energy along the minimum energy path. An expansion
             around the minimum energy path is made in both the nuclear
             and the electronic degrees of freedom for the QM subsystem
             internal energy, while the energy of the subsystem described
             with MM remains unchanged from that in the combined quantum
             mechanical and molecular mechanical expression and the
             electrostatic interaction between the QM and MM subsystems
             is described as the interaction of the MM charges with the
             QM charges. The QM charges are polarizable in response to
             the changes in both the MM and the QM degrees of freedom
             through a new response kernel developed in the present work.
             The input data for constructing the reaction path potential
             are energies, vibrational frequencies, and electron density
             response properties of the QM subsystem along the minimum
             energy path, all of which can be obtained from the combined
             quantum mechanical and molecular mechanical calculations.
             Once constructed, it costs much less for its evaluation.
             Thus, the reaction path potential provides a potential
             energy surface for rigorous statistical mechanics and
             reaction dynamics calculations of complex systems. As an
             example, the method is applied to the statistical mechanical
             calculations for the potential of mean force of the chemical
             reaction in triosephosphate isomerase.},
   Doi = {10.1063/1.1757436},
   Key = {fds235069}
}

@article{fds235070,
   Author = {Liu, H and Lu, Z and Cisneros, GA and Yang, W},
   Title = {Parallel iterative reaction path optimization in ab initio
             quantum mechanical/molecular mechanical modeling of enzyme
             reactions},
   Journal = {Journal of Chemical Physics},
   Volume = {121},
   Number = {2},
   Pages = {697-706},
   Year = {2004},
   ISSN = {0021-9606},
   url = {http://dx.doi.org/10.1063/1.1759318},
   Abstract = {A parallel iterative reaction path optimization method,
             aimed at use in chemical reaction in enzymes was presented.
             The method was based on an adaptation of the path
             optimization procedure for small molecules in gas phase, and
             on a new metric defining the distance between different
             structures in the configuration space. For each structures,
             the atoms were partitioned into a core set that usually
             included the quantum mechanical (QM) subsystems and an
             environment set containing the molecular mechanism (MM)
             subsystem. The applicability and efficiency of the method
             was also demonstrated by testing it on triosephosphate
             isomerase and 4-oxalocrotonate tautomerase.},
   Doi = {10.1063/1.1759318},
   Key = {fds235070}
}

@article{fds235071,
   Author = {Lu, Z and Nowak, W and Lee, G and Marszalek, P and Yang,
             W},
   Title = {"Elastic Properties of Single Amylose Chains in
             Water"},
   Journal = {J. Am. Chem. Soc.},
   Volume = {126},
   Number = {29},
   Pages = {9033-9041},
   Year = {2004},
   ISSN = {0002-7863},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15264836},
   Abstract = {Recent single-molecule atomic force microscopy (AFM)
             experiments have revealed that some polysaccharides display
             large deviations from force-extension relationships of other
             polymers which typically behave as simple entropic springs.
             However, the mechanism of these deviations has not been
             fully elucidated. Here we report the use of novel quantum
             mechanical methodologies, the divide-and-conquer linear
             scaling approach and the self-consistent charge density
             functional-based tight binding (SCC-DFTB) method, to unravel
             the mechanism of the extensibility of the polysaccharide
             amylose, which in water displays particularly large
             deviations from the simple entropic elasticity. We studied
             the deformations of maltose, a building block of amylose,
             both in a vacuum and in solution. To simulate the
             deformations in solution, the TIP3P molecular mechanical
             model is used to model the solvent water, and the SCC-DFTB
             method is used to model the solute. The interactions between
             the solute and water are treated by the combined quantum
             mechanical and molecular mechanical approach. We find that
             water significantly affects the mechanical properties of
             maltose. Furthermore, we performed two nanosecond-scale
             steered molecular dynamics simulations for single amylose
             chains composed of 10 glucopyranose rings in solution. Our
             SCC-DFTB/MM simulations reproduce the experimentally
             measured force-extension curve, and we find that the
             force-induced chair-to-boat transitions of glucopyranose
             rings are responsible for the characteristic plateau in the
             force-extension curve of amylose. In addition, we performed
             single-molecule AFM measurements on carboxymethyl amylose,
             and we found that, in contrast to the results of an earlier
             work by others, these side groups do not significantly
             affect amylose elasticity. By combining our experimental and
             modeling results, we conclude that the nonentropic elastic
             behavior of amylose is governed by the mechanics of pyranose
             rings themselves and their force-induced conformational
             transitions.},
   Doi = {10.1021/ja031940x},
   Key = {fds235071}
}

@article{fds304410,
   Author = {Ullmo, D and Jiang, H and Yang, W and Baranger, HU},
   Title = {Landau Fermi-liquid picture of spin density functional
             theory: Strutinsky approach to quantum dots},
   Journal = {Physical Review B - Condensed Matter and Materials
             Physics},
   Volume = {70},
   Number = {20},
   Pages = {205309-1-205309-15},
   Year = {2004},
   ISSN = {0163-1829},
   url = {http://dx.doi.org/10.1103/PhysRevB.70.205309},
   Abstract = {We analyze the ground-state energy and spin of quantum dots
             obtained from spin density functional theory (SDFT)
             calculations. First, we introduce a Strutinsky-type
             approximation, in which quantum interference is treated as a
             correction to a smooth Thomas-Fermi description. For large
             irregular dots, we find that the second-order Strutinsky
             expressions have an accuracy of about 5% of a mean level
             spacing compared to the full SDFT and capture all the
             qualitative features. Second, we perform a random
             matrix-theory/random-plane wave analysis of the Strutinsky
             SDFT expressions. The results are statistically similar to
             the SDFT quantum dot statistics. Finally, we note that the
             second-order Strutinsky approximation provides, in essence,
             a Landau Fermi-liquid picture of spin density functional
             theory. For instance, the leading term in the spin channel
             is simply the familiar exchange constant. A direct
             comparison between SDFT and the perturbation theory derived
             "universal Hamiltonian" is thus made possible.},
   Doi = {10.1103/PhysRevB.70.205309},
   Key = {fds304410}
}

@article{fds235077,
   Author = {Wu, Q and Yang, WT},
   Title = {Algebraic equation and iterative optimization for the
             optimized effective potential in density functional
             theory},
   Journal = {Journal of Theoretical and Computational
             Chemistry},
   Volume = {2},
   Number = {4},
   Pages = {627-638},
   Year = {2003},
   Month = {December},
   ISSN = {0219-6336},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000220867400015&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Doi = {10.1142/S0219633603000690},
   Key = {fds235077}
}

@article{fds235076,
   Author = {Jiang, H and Baranger, HU and Yang, WT},
   Title = {Density-functional theory simulation of large quantum
             dots},
   Journal = {Physical Review B},
   Volume = {68},
   Number = {16},
   Pages = {1653371-1653379},
   Year = {2003},
   Month = {October},
   ISSN = {1098-0121},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000186571800068&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Abstract = {Kohn-Sham spin-density functional theory provides an
             efficient and accurate model to study electron-electron
             interaction effects in quantum dots, but its application to
             large systems is a challenge. Here an efficient method for
             the simulation of quantum dots using density-function theory
             is developed; it includes the particle-in-the-box
             representation of the Kohn-Sham orbitals, an efficient
             conjugate-gradient method to directly minimize the total
             energy, a Fourier convolution approach for the calculation
             of the Hartree potential, and a simplified multigrid
             technique to accelerate the convergence. We test the
             methodology in a two-dimensional model system and show that
             numerical studies of large quantum dots with several hundred
             electrons become computationally affordable. In the
             noninteracting limit, the classical dynamics of the system
             we study can be continuously varied from integrable to fully
             chaotic. The qualitative difference in the noninteracting
             classical dynamics has an effect on the quantum properties
             of the interacting system: integrable classical dynamics
             leads to higher-spin states and a broader distribution of
             spacing between Coulomb blockade peaks.},
   Doi = {10.1103/PhysRevB.68.165337},
   Key = {fds235076}
}

@article{fds235080,
   Author = {Ke, S-H and Baranger, HU and Yang, W},
   Title = {Addition energies of fullerenes and carbon nanotubes as
             quantum dots: the role of symmetry.},
   Journal = {Physical Review Letters},
   Volume = {91},
   Number = {11},
   Pages = {116803},
   Year = {2003},
   Month = {September},
   ISSN = {0031-9007},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/14525451},
   Abstract = {Using density-functional theory calculations, we investigate
             the addition energy (AE) of quantum dots formed of
             fullerenes or closed single-wall carbon nanotubes. We focus
             on the connection between symmetry and oscillations in the
             AE spectrum. In the highly symmetric fullerenes the
             oscillation period is large because of the large level
             degeneracy and Hund's rule. For long nanotubes, the AE
             oscillation is fourfold. Adding defects destroys the spatial
             symmetry of the tubes, leaving only spin degeneracy;
             correspondingly, the fourfold behavior is destroyed, leaving
             an even/odd behavior which is quite robust. We use our
             symmetry results to explain recent experiments.},
   Doi = {10.1103/PhysRevLett.91.116803},
   Key = {fds235080}
}

@article{fds235081,
   Author = {Cisneros, GA and Liu, H and Zhang, Y and Yang, W},
   Title = {Ab initio QM/MM study shows there is no general acid in the
             reaction catalyzed by 4-oxalocrotonate tautomerase.},
   Journal = {Journal of the American Chemical Society},
   Volume = {125},
   Number = {34},
   Pages = {10384-10393},
   Year = {2003},
   Month = {August},
   ISSN = {0002-7863},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12926963},
   Abstract = {The mechanism for the reaction catalyzed by the
             4-oxalocrotonate tautomerase (4-OT) enzyme has been studied
             using a quantum mechanical/molecular mechanical (QM/MM)
             method developed in our laboratory. Total free energy
             barriers were obtained for the two steps involved in this
             reaction. In the first step, Pro-1 acts as a general base to
             abstract a proton from the third carbon of the substrate,
             2-oxo-4-hexenedioate, creating a negative charge on the
             oxygen at C-2 of this substrate. In the second step, the
             same hydrogen abstracted by the N-terminal Pro-1 is shuttled
             back to the fifth carbon of the substrate to form the
             product, 2-oxo-3-hexenedioate. The calculated total free
             energy barriers are 14.54 and 16.45 kcal/mol for the first
             and second steps, respectively. Our calculations clearly
             show that there is no general acid in the reaction. Arg-39'
             ', which is hydrogen bonded to the carboxylate group of the
             substrate, and an ordered water, which moves closer to the
             site of the charge formed in the transition state and
             intermediate, play the main role in transition
             state/intermediate stabilization without acting as general
             acids in the reaction.},
   Doi = {10.1021/ja029672a},
   Key = {fds235081}
}

@article{fds235082,
   Author = {Jiang, H and Baranger, HU and Yang, W},
   Title = {Spin and conductance-peak-spacing distributions in large
             quantum dots: a density-functional theory
             study.},
   Journal = {Physical Review Letters},
   Volume = {90},
   Number = {2},
   Pages = {026806},
   Year = {2003},
   Month = {January},
   ISSN = {0031-9007},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12570571},
   Abstract = {We use spin-density-functional theory to study the spacing
             between conductance peaks and the ground-state spin of 2D
             model quantum dots with up to 200 electrons. Distributions
             for different ranges of electron number are obtained in both
             symmetric and asymmetric potentials. The even/odd effect is
             pronounced for small symmetric dots but vanishes for large
             asymmetric ones, suggesting substantially stronger
             interaction effects than expected. The fraction of high-spin
             ground states is remarkably large.},
   Doi = {10.1103/PhysRevLett.90.026806},
   Key = {fds235082}
}

@article{fds235074,
   Author = {Goj, LA and Cisneros, GA and Yang, W and Widenhoefer,
             RA},
   Title = {Dramatic effect of homoallylic substitution on the rate of
             palladium-catalyzed diene cycloisomerization},
   Journal = {Journal of Organometallic Chemistry},
   Volume = {687},
   Number = {2},
   Pages = {498-507},
   Year = {2003},
   url = {http://dx.doi.org/10.1016/j.jorganchem.2003.09.046},
   Abstract = {Cycloisomerization of 4,4-bis(acetoxymethyl)-1,6-heptadiene
             (5) catalyzed by [(phen)Pd(Me)CNCH3]+ [BAr4]- [Ar=3,5-C6H3
             (CF3)2] (2) to form predominantly 3,3-bis(acetoxymethyl)-1,5-dimethylcyclopentene
             (6) was ∼400 times faster than was the cycloisomerization
             of dimethyl diallylmalonate (1) under identical conditions.
             Mechanistic studies performed in conjunction with density
             functional theory calculations attribute the large rate
             acceleration of the cycloisomerization of 5 relative to the
             cycloisomerization of 1 to the formation of a stable oxo
             chelate complex as an intermediate in the cycloisomerization
             of 1, but not in the cycloisomerization of 5. © 2003
             Published by Elsevier B.V.},
   Doi = {10.1016/j.jorganchem.2003.09.046},
   Key = {fds235074}
}

@article{fds235075,
   Author = {Jiang, H and Baranger, HU and Yang, W},
   Title = {Desnity functional theory simulation of large quantum
             dots},
   Journal = {Phys. Rev. B.},
   Volume = {68},
   Pages = {165337-1-165337-9},
   Year = {2003},
   Key = {fds235075}
}

@article{fds235078,
   Author = {Mori-Sánchez, P and Wu, Q and Yang, W},
   Title = {Accurate polymer polarizabilities with exact exchange
             density-functional theory},
   Journal = {Journal of Chemical Physics},
   Volume = {119},
   Number = {21},
   Pages = {11001-11004},
   Year = {2003},
   url = {http://dx.doi.org/10.1063/1.1630011},
   Abstract = {Exact exchange DFT was used to describe the polarizability
             of polymers. This was achieved by using an accurate
             optimized effective potential that properly develops an
             ultranonlocal response component under an external electric
             field. In addition, it was found that the SIE cancellation
             embodied in the EXX approach is necessary to properly
             describe the polarization of any system. Thus, the
             long-standing problem of over-polarizations of hydrogen
             polymers was largely solved and a fresh understanding of the
             LDA weakness provided.},
   Doi = {10.1063/1.1630011},
   Key = {fds235078}
}

@article{fds235079,
   Author = {Hasegawa, J-Y and Ishida, M and Nakatsuji, H and Lu, Z and Liu, H and Yang,
             W},
   Title = {Energetics of the electron transfer from bacteriopheophytin
             to ubiquinone in the photosynthetic reaction center for
             Rhodopseudomonas viridis: Theoretical study},
   Journal = {Journal of Physical Chemistry B},
   Volume = {107},
   Number = {3},
   Pages = {838-847},
   Year = {2003},
   url = {http://dx.doi.org/10.1021/jp022334b},
   Abstract = {The energetics of electron transfer in the photosynthetic
             reaction center of Rhodopseudomonas viridis was studied
             using the density functional theory (DFT). By examining the
             basis set-dependence and the accuracy of the DFT for
             calculating adiabatic electron affinity, single-point
             calculations with 6-31+G(d) basis sets, at the geometry
             optimized with 6-31G(d) basis sets, were found to be almost
             independent of the basis set. In gas-phase calculations,
             bacteriopheophytin (H) had the greatest electron affinity
             among the three chromophores: H, menaquinone (MQ), and
             ubiquinone (UQ). However, the order of the electron affinity
             was reversed to be UQ &gt; MQ &gt; H by including residues
             that interacted with the chromophores through hydrogen
             bonding. Based on the QM/MM optimized geometries, cluster
             models for the binding sites were constructed. The computed
             reaction energy was comparable to values obtained
             experimentally. The reaction energy can be decomposed into a
             vertical electron affinity term and a relaxation energy term
             using a driving force analysis. The most important term was
             the vertical electron affinity of the chromophores. Based on
             optimization, there was little structural reorganization.
             The present results indicate that, with regard to the
             energetics of electron transfer, local interactions between
             the chromophores and proteins play a decisive role by tuning
             the electron affinity of the chromophores, whereas the
             effects of distant residues are of secondary
             importance.},
   Doi = {10.1021/jp022334b},
   Key = {fds235079}
}

@article{fds235083,
   Author = {Wu, Q and Yang, W},
   Title = {A direct optimization method for calculating density
             functionals and exchange-correlation potentials from
             electron densities},
   Journal = {Journal of Chemical Physics},
   Volume = {118},
   Number = {6},
   Pages = {2498-2509},
   Year = {2003},
   url = {http://dx.doi.org/10.1063/1.1535422},
   Abstract = {A direct optimization method for carrying out the
             computation of implicit density functionals from given
             electron densities was developed. The analytic first and
             second derivatives of the vibrational functional with
             respect to the linear basis set expansion coefficients and
             also the nonlinear parameters in the basis set were derived.
             The accuracy and the efficiency of the method were
             demonstrated in the case of the Kohn-Sham kinetic energies,
             HOMO energies, and exchange-correlation potentials.},
   Doi = {10.1063/1.1535422},
   Key = {fds235083}
}

@article{fds235084,
   Author = {Wu, Q and Ayers, PW and Yang, W},
   Title = {Density-functional theory calculations with correct
             long-range potentials},
   Journal = {Journal of Chemical Physics},
   Volume = {119},
   Number = {6},
   Pages = {2978-2990},
   Year = {2003},
   url = {http://dx.doi.org/10.1063/1.1590631},
   Abstract = {A different technique for constructing asymptotically
             correct potentials was explored. This technique was first
             developed to determine the optimized effective potential in
             density-functional theory and produced excellent results.
             This paper uses a fixed referenced potential, namely the
             Fermi-Amaldi term, to account for the long-range behavior,
             and a linear combination of basis functions whose
             coefficients are determined through energy
             optimization.},
   Doi = {10.1063/1.1590631},
   Key = {fds235084}
}

@article{fds318105,
   Author = {Jiang, H and Baranger, HU and Yang, W},
   Title = {Density-functional theory simulation of large quantum
             dots},
   Journal = {Physical Review B - Condensed Matter and Materials
             Physics},
   Volume = {68},
   Number = {16},
   Pages = {1653371-1653379},
   Year = {2003},
   Abstract = {Kohn-Sham spin-density functional theory provides an
             efficient and accurate model to study electron-electron
             interaction effects in quantum dots, but its application to
             large systems is a challenge. Here an efficient method for
             the simulation of quantum dots using density-function theory
             is developed; it includes the particle-in-the-box
             representation of the Kohn-Sham orbitals, an efficient
             conjugate-gradient method to directly minimize the total
             energy, a Fourier convolution approach for the calculation
             of the Hartree potential, and a simplified multigrid
             technique to accelerate the convergence. We test the
             methodology in a two-dimensional model system and show that
             numerical studies of large quantum dots with several hundred
             electrons become computationally affordable. In the
             noninteracting limit, the classical dynamics of the system
             we study can be continuously varied from integrable to fully
             chaotic. The qualitative difference in the noninteracting
             classical dynamics has an effect on the quantum properties
             of the interacting system: integrable classical dynamics
             leads to higher-spin states and a broader distribution of
             spacing between Coulomb blockade peaks.},
   Key = {fds318105}
}

@article{fds235085,
   Author = {Yang, W and Wu, Q},
   Title = {Direct method for optimized effective potentials in
             density-functional theory.},
   Journal = {Physical Review Letters},
   Volume = {89},
   Number = {14},
   Pages = {143002},
   Year = {2002},
   Month = {September},
   ISSN = {0031-9007},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12366042},
   Abstract = {The conventional optimized effective potential method is
             based on a difficult-to-solve integral equation. In the new
             method, this potential is constructed as a sum of a fixed
             potential and a linear combination of basis functions. The
             energy derivatives with respect to the coefficients of the
             linear combination are obtained. This enables calculations
             by optimization methods. Accurate atomic and molecular
             calculations with Gaussian basis sets are presented for
             exact exchange functionals. This efficient and accurate
             method for the optimized effective potential should play an
             important role in the development and application of density
             functionals.},
   Doi = {10.1103/PhysRevLett.89.143002},
   Key = {fds235085}
}

@article{fds26208,
   Author = {Qiang Xue and Weitao Yang},
   Title = {Distributed electronic structure calculations with
             divide-and-conquer approach},
   Journal = {Work-in-Progress Session of the PACT-02 Conference,
             Charlottesville, VA},
   Year = {2002},
   Month = {September},
   Key = {fds26208}
}

@article{fds318106,
   Author = {Lu, ZY and Liu, HY and Yang, WT},
   Title = {A QM/MM study on the structure and catalysis mechanism of
             PDE4B.},
   Journal = {ACS National Meeting Book of Abstracts},
   Volume = {223},
   Pages = {C76-C76},
   Year = {2002},
   Month = {April},
   Key = {fds318106}
}

@article{fds313874,
   Author = {Cisneros, GA and Liu, HY and Zhang, YK and Yang, WT},
   Title = {QM/MM study of the reaction mechanism of 4-oxalocrotonate
             tautomerase.},
   Journal = {ACS National Meeting Book of Abstracts},
   Volume = {223},
   Pages = {C78-C78},
   Year = {2002},
   Month = {April},
   ISSN = {0065-7727},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000176296801845&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds313874}
}

@article{fds313875,
   Author = {Yang, WT and Zhang, YK and Liu, HY},
   Title = {Developments and applications of a DFT QM/MM free energy
             method for simulation of chemical reactions in
             enzymes.},
   Journal = {ACS National Meeting Book of Abstracts},
   Volume = {223},
   Pages = {C89-C89},
   Year = {2002},
   Month = {April},
   ISSN = {0065-7727},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000176296801919&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds313875}
}

@article{fds24467,
   Author = {Qin Wu and Weitao Yang},
   Title = {An empirical correction to density functional theory for van
             der waals interactions},
   Journal = {J. Chem. Phys.},
   Volume = {116},
   Pages = {515-524},
   Year = {2002},
   Key = {fds24467}
}

@article{fds234898,
   Author = {Wu, Q and Yang, W},
   Title = {Empirical correction to density functional theory for van
             der Waals interactions},
   Journal = {Journal of Chemical Physics},
   Volume = {116},
   Number = {2},
   Pages = {515-524},
   Year = {2002},
   url = {http://dx.doi.org/10.1063/1.1424928},
   Abstract = {Accounting of the van der Waals interactions in pratical
             molecular calculations with density functional theory was
             analyzed by an empirical method. The coefficients of C6 for
             pair interactions between carbon, nitrogen, and oxygen atoms
             were developed by the least-square fitting to the molecular
             coefficients obtained from the dipole oscillator strength
             distribution method. The empirical method with the damping
             function was showed to drop to zero smoothly, and provided a
             significant correction to both of the Becke's hybrid
             functional, the PW91 exchange and correlation
             functional.},
   Doi = {10.1063/1.1424928},
   Key = {fds234898}
}

@article{fds235161,
   Author = {Wu, Q and Yang, W},
   Title = {An Empirical Correction to Density Functional Theory for van
             der Waals Interactions},
   Journal = {J. Chem. Phys.},
   Volume = {116},
   Pages = {515-524},
   Year = {2002},
   Key = {fds235161}
}

@article{fds324031,
   Author = {Yang, W and Lee, H-W and Hellinga, H and Yang, JJ},
   Title = {Structural analysis, identification, and design of
             calcium-binding sites in proteins},
   Journal = {Proteins: Structure, Function and Bioinformatics},
   Volume = {47},
   Number = {3},
   Pages = {344-356},
   Year = {2002},
   url = {http://dx.doi.org/10.1002/prot.10093},
   Abstract = {Assigning proteins with functions based on the 3-D structure
             requires high-speed techniques to make a systematic survey
             of protein structures. Calcium regulates many biological
             systems by binding numerous proteins in different biological
             environments. Despite the great diversity in the composition
             of ligand residues and bond angles and lengths of
             calcium-binding sites, our structural analysis of 11
             calcium-binding sites in different classes of proteins has
             shown that common local structural parameters can be used to
             identify and design calcium-binding proteins. Natural
             calcium-binding sites in both EF-hand proteins and
             non-EF-hand proteins can be described with the smallest
             deviation from the geometry of an ideal pentagonal
             bipyramid. Further, two different magnesium-binding sites in
             parvalbumin and calbindinD9K can also be identified using an
             octahedral geometry. Using the established method, we have
             designed de novo calcium-binding sites into the scaffold of
             noncalcium-binding proteins CD2 and Rop. Our results suggest
             that it is possible to identify calcium- and
             magnesium-binding sites in proteins and design de novo
             metal-binding sites. © 2002 Wiley-Liss,
             Inc.},
   Doi = {10.1002/prot.10093},
   Key = {fds324031}
}

@article{fds235086,
   Author = {Liu, H and Elstner, M and Kaxiras, E and Frauenheim, T and Hermans, J and Yang, W},
   Title = {Quantum mechanics simulation of protein dynamics on long
             timescale.},
   Journal = {Proteins: Structure, Function and Bioinformatics},
   Volume = {44},
   Number = {4},
   Pages = {484-489},
   Year = {2001},
   Month = {September},
   ISSN = {0887-3585},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11484226},
   Abstract = {Protein structure and dynamics are the keys to a wide range
             of problems in biology. In principle, both can be fully
             understood by using quantum mechanics as the ultimate tool
             to unveil the molecular interactions involved. Indeed,
             quantum mechanics of atoms and molecules have come to play a
             central role in chemistry and physics. In practice, however,
             direct application of quantum mechanics to protein systems
             has been prohibited by the large molecular size of proteins.
             As a consequence, there is no general quantum mechanical
             treatment that not only exceeds the accuracy of
             state-of-the-art empirical models for proteins but also
             maintains the efficiency needed for extensive sampling in
             the conformational space, a requirement mandated by the
             complexity of protein systems. Here we show that, given
             recent developments in methods, a general quantum
             mechanical-based treatment can be constructed. We report a
             molecular dynamics simulation of a protein, crambin, in
             solution for 350 ps in which we combine a semiempirical
             quantum-mechanical description of the entire protein with a
             description of the surrounding solvent, and solvent-protein
             interactions based on a molecular mechanics force field.
             Comparison with a recent very high-resolution crystal
             structure of crambin (Jelsch et al., Proc Natl Acad Sci USA
             2000;102:2246-2251) shows that geometrical detail is better
             reproduced in this simulation than when several alternate
             molecular mechanics force fields are used to describe the
             entire system of protein and solvent, even though the
             structure is no less flexible. Individual atomic charges
             deviate in both directions from "canonical" values, and some
             charge transfer is found between the N and C-termini. The
             capability of simulating protein dynamics on and beyond the
             few hundred ps timescale with a demonstrably accurate
             quantum mechanical model will bring new opportunities to
             extend our understanding of a range of basic processes in
             biology such as molecular recognition and enzyme
             catalysis.},
   Key = {fds235086}
}

@article{fds24464,
   Author = {Mu-Hyun Baik and Joel S. Silverman and Patricia A. Ropp and Ivana V.
             Yang and Veronika A. Szalai and Weitao Yang and H. Holden
             Thorp},
   Title = {Using density functional theory to design dna base analogues
             with low oxidation potentials},
   Journal = {J. Phys. Chem. B.},
   Volume = {105},
   Number = {27},
   Pages = {6437-6444},
   Year = {2001},
   Key = {fds24464}
}

@article{fds235160,
   Author = {Baik, M-H and Silverman, JS and Yang, IV and Ropp, PA and Szalai, VA and Yang, W and Thorp, HH},
   Title = {Using density functional theory to design DNA base analogues
             with low oxidation potentials},
   Journal = {Journal of Physical Chemistry B Materials},
   Volume = {105},
   Number = {27},
   Pages = {6437-6444},
   Year = {2001},
   ISSN = {1089-5647},
   url = {http://dx.doi.org/10.1021/jp010643g},
   Abstract = {The oxidizability of substituted nucleobases was evaluated
             through theoretical calculations and the ability of
             individual bases to induce current enhancement in the cyclic
             voltammograms of metal complexes. Formation of the guanine
             derivatives 7-deazaguanine and 8-oxoguanine is known to
             lower the energy for oxidation of guanine. The similar
             derivatives of adenine were examined and gave lower
             predicted redox energies as well as current enhancement with
             Ru(bpy)32+ (7-deazaadenine) and Fe(bpy)32+ (8-oxoadenine).
             Oxidizable, substituted pyrimidines were identified using a
             computational library that gave 5-aminocytosine and
             5-aminouracil as promising electron donors. Again, these
             predictions were verified using catalytic electrochemistry.
             In addition, the computations predicted that 6-aminocytosine
             would be redox-active but not as easily oxidized as
             5-aminocytosine, which was also confirmed experimentally. In
             addition to calculating the relative one-electron redox
             potentials, we used calculations to evaluate the loss of a
             proton that occurs from the initially formed radical cation.
             These calculations gave results consistent with the
             experiments, and in the case of 8-oxoadenine, the relative
             redox reactivity could be predicted only when the proton
             loss step was considered. These substituted bases constitute
             building blocks for highly redox-active nucleic acids, and
             the associated theoretical model provides powerful
             predictability for designing new redox-active
             nucleobases.},
   Doi = {10.1021/jp010643g},
   Key = {fds235160}
}

@article{fds235158,
   Author = {Yang, W and Zhang, Y and Ayers, PW},
   Title = {Degenerate ground states and a fractional number of
             electrons in density and reduced density matrix functional
             theory},
   Journal = {Physical Review Letters},
   Volume = {84},
   Number = {22},
   Pages = {5172-5175},
   Year = {2000},
   Month = {May},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/10990895},
   Abstract = {For a linear combination of electron densities of degenerate
             ground states, it is shown that the value of any energy
             functional is the ground state energy, if the energy
             functional is exact for ground state densities, size
             consistent, and translational invariant. The corresponding
             functional of kinetic and interaction energy is the linear
             combination of the functionals of the degenerate densities.
             Without invoking ensembles, it is shown that the energy
             functional of fractional number electrons is a series of
             straight lines interpolating its values at integers. These
             results underscore the importance of grand canonical
             ensemble formulation in density functional
             theory.},
   Doi = {10.1103/PhysRevLett.84.5172},
   Key = {fds235158}
}

@article{fds24462,
   Author = {Haiyan Liu and Yingkai Zhang and Weitao Yang},
   Title = {How is the active-site of enolase organized to achieve
             overall efficiency in catalyzing a two step
             reaction},
   Journal = {J. Am. Chem. Soc.},
   Volume = {122},
   Pages = {6560-6570},
   Year = {2000},
   Key = {fds24462}
}

@article{fds234896,
   Author = {Liu, H and Zhang, Y and Yang, W},
   Title = {How is the active site of enolase organized to catalyze two
             different reaction steps?},
   Journal = {Journal of the American Chemical Society},
   Volume = {122},
   Number = {28},
   Pages = {6560-6570},
   Year = {2000},
   url = {http://dx.doi.org/10.1021/ja9936619},
   Abstract = {Using a combined ab initio quantum mechanical/molecular
             mechanical approach developed in our laboratory, we obtained
             the reaction paths and free energy barriers for the two
             steps of the reaction catalyzed by enolase. In the first
             step, the α-proton of the substrate, 2-phospho-D-glycerate
             (PGA), is removed by Lys345, resulting in an enolic
             intermediate. In the second step, the β-hydroxyl group
             leaves the enolic intermediate with the assistance of a
             general acid, Glu211. The calculated free energies of
             activation are 13.1 and 9.4 kcal mol -1 for the first and
             the second step, respectively. The barrier heights are
             consistent with the reaction rates measured from
             experiments. The calculations indicate that the
             electrostatic interactions between the substrate and two
             divalent metal cations at the active site strongly favor the
             first step. However, the same metal cations strongly
             disfavor the second step because the change in charge of the
             substrate is of an opposite sign compared with that in the
             first step. We conclude that the enzyme environment
             (excluding Lys345, Glu211, and the metal cations) forms an
             essential part of the reaction mechanism. It counterbalances
             the disfavoring effects of the metal cations in the second
             step without interfering with the first step despite the
             reversed charge changes of the substrate in the two steps.
             This capability of the enzyme originates from the
             three-dimensional organization of polar and charged groups
             in the active site of enolase, as indicated by correlations
             between the three-dimensional structure and energetic
             analyses based on our calculations. To achieve overall
             catalytic efficiency, the structure of the enolase active
             site takes advantage of the fact that the charge
             reorganization procedures accompanying the two reaction
             steps take place in two different directions in
             space.},
   Doi = {10.1021/ja9936619},
   Key = {fds234896}
}

@article{fds234897,
   Author = {Enkvist, C and Zhang, Y and Yang, W},
   Title = {Density functional study of a weakly hydrogen-bonded
             benzene-ammonia complex: The importance of the exchange
             functional},
   Journal = {International Journal of Quantum Chemistry},
   Volume = {79},
   Number = {5},
   Pages = {325-329},
   Year = {2000},
   url = {http://dx.doi.org/10.1002/1097-461X(2000)79:5<325::AID-QUA6>3.0.CO;2-B},
   Abstract = {Density functional theory calculations on the
             benzene-ammonia complex have been performed. The
             benzene-ammonia complex is weakly hydrogen bonded, and
             crucial for obtaining good agreement with experimental
             results is the choice of the exchange functional used, as in
             the case of van der Waals interactions. It is found that the
             behavior of the exchange functional in the region where the
             density is small and the density gradient large plays an
             important role in describing the weak hydrogen-bonding
             interaction. Calculations show that generalized gradient
             approximation functionals, which behave properly in this
             region, have achieved an accuracy similar to the
             second-order Moller-Plesset (MP2) method for the
             benzene-ammonia complex.},
   Doi = {10.1002/1097-461X(2000)79:5<325::AID-QUA6>3.0.CO;2-B},
   Key = {fds234897}
}

@article{fds235154,
   Author = {Zhang, Y and Yang, W},
   Title = {Perspective on "Density-functional theory for fractional
             particle number: Derivative discontinuities of the
             energy"},
   Journal = {Theoretical Chemistry Accounts},
   Volume = {103},
   Number = {3-4},
   Pages = {346-348},
   Year = {2000},
   ISSN = {1432-881X},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000085419900057&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Abstract = {This paper provides an overview of the title paper by
             Perdew, Parr, Levy and Balduz [Phys Rev Lett 49:1691
             (1982)]. The title paper extended density functional theory
             to fractional electron number by an ensemble approach and
             proved that the energy is a series of straight lines
             interpolating its values at integer numbers of electrons. It
             also established that the highest-occupied exact Kohn-Sham
             orbital energy is the negative of the ionization energy, and
             showed that the exchange-correlation potential jumps by a
             constant as the number of electrons increases by an integer.
             These results are fundamental and continue to inspire
             developments in density functional theory.},
   Doi = {10.1007/s002149900021},
   Key = {fds235154}
}

@article{fds235155,
   Author = {Liu, H and Zhang, Y and Yang, W},
   Title = {How is the active-site of enolase organized to achieve
             overall efficiency in catalyzing a two step
             reaction},
   Journal = {J. Am. Chem. Soc.},
   Volume = {122},
   Pages = {6560},
   Year = {2000},
   Key = {fds235155}
}

@article{fds235156,
   Author = {Zhang, Y and Liu, H and Yang, W},
   Title = {Free energy calculation on enzyme reactions with an
             efficient iterative procedure to determine minimum energy
             paths on a combined ab initio QM/MM potential energy
             surface},
   Journal = {Journal of Chemical Physics},
   Volume = {112},
   Number = {8},
   Pages = {3483-3492},
   Year = {2000},
   Abstract = {A new practical approach to studying enzyme reactions by
             combining ab initio QM/MM calculations with free energy
             perturbation is presented. An efficient iterative
             optimization procedure has been developed to determine
             optimized structures and minimum energy paths for a system
             with thousands of atoms on the ab initio QM/MM potential:
             the small QM sub-system is optimized using a quasi-Newton
             minimizer in redundant internal coordinates with ab initio
             QM/MM calculations, while the large MM sub-system is
             minimized by the truncated Newton method in Cartesian
             coordinates with only molecular mechanical calculations. The
             above two optimization procedures are performed iteratively
             until they converge. With the determined minimum energy
             paths, free energy perturbation calculations are carried out
             to determine the change in free energy along the reaction
             coordinate. Critical to the success of the iterative
             optimization procedure and the free energy calculations is
             the smooth connection between the QM and MM regions provided
             by a recently proposed pseudobond QM/MM approach [J. Chem.
             Phys. 110, 46 (1999)], The methods have been demonstrated by
             studying the initial proton transfer step in the reaction
             catalyzed by the enzyme triosephosphate isomerase (TIM). ©
             2000 American Institute of Physics.},
   Key = {fds235156}
}

@article{fds235157,
   Author = {Enkvist, C and Zhang, Y and Yang, W},
   Title = {Density Functional Study of A Weakly Hydrogen Bonded System:
             the Benzene-Ammonia Complex},
   Journal = {The International Journal of Quantum Chemistry},
   Volume = {79},
   Pages = {325-329},
   Year = {2000},
   Key = {fds235157}
}

@article{fds235159,
   Author = {Liu, S and Pérez-Jordâ, JM and Yang, W},
   Title = {Nonorthogonal localized molecular orbitals in electronic
             structure theory},
   Journal = {Journal of Chemical Physics},
   Volume = {112},
   Number = {4},
   Pages = {1634-1644},
   Year = {2000},
   Abstract = {The concept of nonorthogonal localized molecular orbital
             (NOLMO) is investigated in this paper. Given a set of the
             commonly used canonical molecular orbitals, a direct
             minimization algorithm is proposed to obtain both the
             orthogonal localized molecular orbitals (OLMO) and NOLMO by
             using the Boys criterion and conjugate gradient
             minimization. To avoid the multiple-minimum problem, the
             absolute energy minimization principle of Yang is employed
             to obtain initial guesses. Contrary to the early conclusion
             drawn by Lipscomb and co-workers who claimed that OLMOs and
             the corresponding NOLMOs are more or less the same, we found
             that NOLMOs are about 10%-30% more localized than OLMOs.
             More importantly, the so-called "delocalization tail" that
             plagues OLMOs is not present in NOLMOs, showing that NOLMOs
             are more compact and less oscillatory and capable of
             providing greater transferability in describing the
             electronic structure of molecules. We also found that main
             lobes of NOLMOs are slightly larger in size than those of
             OLMOs because of the normalization requirement. These
             features establish NOLMOs to be valuable as building blocks
             in electronic structure theory and for the understanding of
             chemical bonding. They show the promise for the utilization
             of NOLMOs - the most localized possible - in the linear
             scaling approaches of the electronic structure theory for
             molecules and solids. © 2000 American Institute of
             Physics.},
   Key = {fds235159}
}

@article{fds235087,
   Author = {Zhang, Y and Lee, T and Yang, W},
   Title = {A psuedo-bond approach to combining quantum mechanical and
             molecular mechanical methods},
   Journal = {J. Chem. Phys.},
   Volume = {110},
   Number = {1},
   Pages = {46-54},
   Year = {1999},
   url = {http://dx.doi.org/10.1063/1.478083},
   Abstract = {A major challenge for combined quantum mechanical and
             molecular mechanical methods (QM/MM) to study large
             molecules is how to treat the QM/MM boundary that bisects
             some covalent bonds. Here a pseudobond approach has been
             developed to solve this problem for ab initio QM/MM
             calculations: a one-free-valence atom with an effective core
             potential is constructed to replace the boundary atom of the
             environment part and to form a pseudobond with the boundary
             atom of the active part. This pseudobond, which is described
             only by the QM method, is designed to mimic the original
             bond with similar bond length and strength, and similar
             effects on the rest of the active part. With this pseudobond
             approach, some well-known deficiencies of the link atom
             approach have been circumvented and a well-defined potential
             energy surface of the whole QM/MM system has been provided.
             The construction of the effective core potential for the
             pseudobond is independent of the molecular mechanical force
             field and the same effective core potential is applicable to
             both Hartree-Fock and density functional methods. Tests on a
             series of molecules yield very good structural, electronic,
             and energetic results in comparison with the corresponding
             full ab initio quantum mechanical calculations. © 1999
             American Institute of Physics.},
   Doi = {10.1063/1.478083},
   Key = {fds235087}
}

@article{fds235088,
   Author = {Little, SB and Rabinowitz, JR and Wei, P and Yang,
             W},
   Title = {A comparison of calculated and experimental geometries for
             crowded polycyclic aromatic hydrocarbons and their
             metabolites},
   Journal = {Polycyclic Aromatic Compounds},
   Volume = {1999},
   Number = {14-15},
   Pages = {53-61},
   Year = {1999},
   Abstract = {It has become useful to consider the subclass of PAHs with a
             crowded bay region because of similar biological activity
             within the subclass. Crowding in the bay region of a
             polycyclic aromatic hydrocarbon results in a twisted
             molecular geometry. The purpose of this study is to help
             gauge the utility of various computational methods for
             determining the molecular geometry of molecules in this
             subclass and their metabolites. The results from
             semi-empirical methods AMI and PM3, ab initio Hartree-Fock
             methods and density functional methods will be compared to
             experimentally determined geometries for crowded PAHs. It
             will be seen that excellent geometries for all local minimum
             energy structures are obtained from semi-empirical methods.
             More exact and computationally extensive methods yield
             equivalent or somewhat better results only with good basis
             sets. However, methods disagree on the relative energies of
             the isomers of diol-epoxides.},
   Key = {fds235088}
}

@article{fds235089,
   Author = {Lewis, JP and Liu, S and Lee, T-S and Yang, W},
   Title = {A Linear-Scaling Quantum Mechanical Investigation of
             Cytidine Deaminase},
   Journal = {Journal of Computational Physics},
   Volume = {151},
   Number = {1},
   Pages = {242-263},
   Year = {1999},
   url = {http://dx.doi.org/10.1006/jcph.1999.6219},
   Abstract = {We describe the divide-and-conquer technique for
             linear-scaling semiempirical quantum mechanical
             calculations. This method has been successfully applied to
             study cytidine deaminase. Large-scale simulations were
             performed for optimizing geometries surrounding the active
             site of the enzyme and obtaining related energetics. The
             results of the minimizations provide a significant
             complement to experimental efforts and aid in the
             understanding of the enzymatic profile of cytidine
             deaminase. More specifically, we present our predictions
             about the structure of the active species and the structure
             of the active site for low pH. Finally, we present our
             results for the structure of the zinc ion coordination for
             different substrates which represent points along the
             reaction profile. In particular, we find that our results
             for the Zn-Sγ132 and the Zn-Sγ129 bondlengths yield
             similar trends compared to x-ray crystallography data as the
             enzyme structure changes from the ground-state to the
             transition-state analog and from the transition-state analog
             to the product. © 1999 Academic Press.},
   Doi = {10.1006/jcph.1999.6219},
   Key = {fds235089}
}

@article{fds304404,
   Author = {Zhang, Y and Lee, T-S and Yang, W},
   Title = {A pseudobond approach to combining quantum mechanical and
             molecular mechanical methods},
   Journal = {Journal of Chemical Physics},
   Volume = {110},
   Number = {1},
   Pages = {46-54},
   Year = {1999},
   url = {http://dx.doi.org/10.1063/1.478083},
   Abstract = {A major challenge for combined quantum mechanical and
             molecular mechanical methods (QM/MM) to study large
             molecules is how to treat the QM/MM boundary that bisects
             some covalent bonds. Here a pseudobond approach has been
             developed to solve this problem for ab initio QM/MM
             calculations: a one-free-valence atom with an effective core
             potential is constructed to replace the boundary atom of the
             environment part and to form a pseudobond with the boundary
             atom of the active part. This pseudobond, which is described
             only by the QM method, is designed to mimic the original
             bond with similar bond length and strength, and similar
             effects on the rest of the active part. With this pseudobond
             approach, some well-known deficiencies of the link atom
             approach have been circumvented and a well-defined potential
             energy surface of the whole QM/MM system has been provided.
             The construction of the effective core potential for the
             pseudobond is independent of the molecular mechanical force
             field and the same effective core potential is applicable to
             both Hartree-Fock and density functional methods. Tests on a
             series of molecules yield very good structural, electronic,
             and energetic results in comparison with the corresponding
             full ab initio quantum mechanical calculations. © 1999
             American Institute of Physics.},
   Doi = {10.1063/1.478083},
   Key = {fds304404}
}

@article{fds313877,
   Author = {Yang, WT and Levy, M and Trickey, S},
   Title = {Special issue: Symposium on density functional and
             applications (Part I of II) - Introduction},
   Journal = {International Journal of Quantum Chemistry},
   Volume = {69},
   Number = {3},
   Pages = {227-227},
   Year = {1998},
   Month = {August},
   ISSN = {0020-7608},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000075006800001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds313877}
}

@article{fds234985,
   Author = {Acker, JC and Marks, LB and Spencer, DP and Yang, W and Avery, MA and Dodge, RK and Rosner, GL and Dewhirst, MW},
   Title = {Serial in vivo observations of cerebral vasculature after
             treatment with a large single fraction of
             radiation.},
   Journal = {Radiation Research},
   Volume = {149},
   Number = {4},
   Pages = {350-359},
   Year = {1998},
   Month = {April},
   ISSN = {0033-7587},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/9525499},
   Abstract = {To test whether single high doses of radiation, similar to
             those used with radiosurgery, given to normal cerebral
             vasculature can cause changes in leukocyte-vessel wall
             interactions and tissue perfusion, a rat pial window model
             was used to view the cerebral vasculature, facilitating
             repeated in vivo observations of microcirculatory function.
             An attachment for a 4 MV linear accelerator was designed to
             deliver a well-collimated 2.2-mm beam of radiation to a
             selected region of rat brain. Sequential measurements of
             leukocyte-endothelial cell interactions, relative change in
             blood flow with laser Doppler flowmetry and vessel length
             density were performed prior to and at 24 h and 3 weeks
             after treatment with 15, 22.5 or 30 Gy, given in a single
             fraction. Significant increases in leukocyte-endothelial
             cell interactions were seen 24 h and 3 weeks after
             irradiation that were dependent on dose, particularly in
             arteries. Changes were apparent in both arteries and veins
             at 24 h, but by 3 weeks the effects in arteries
             predominated. Decreases in vessel length density and blood
             flow were observed and became greater with time after
             treatment. A variety of morphological changes were observed
             in irradiated arteries, including formation of aneurysmal
             structures, endothelial denudation and thrombus formation.
             These results suggest that: (1) An increase in
             leukocyte-vessel wall interactions occurs after irradiation;
             (2) cerebral arterioles are more sensitive than veins to
             radiation administered in this fashion; and (3) the increase
             in leukocyte-vessel wall interactions likely contributes to
             reduction of or loss of arteriolar flow, with resultant loss
             of flow to dependent microvascular vessels.},
   Key = {fds234985}
}

@article{fds313881,
   Author = {Lewis, JP and Carter, CW and Hermans, J and Pan, W and Lee, TS and Yang,
             WT},
   Title = {Quantum mechanical methods for large biomolecular systems:
             Applications in the study of the cytidine deaminase
             enzyme},
   Journal = {Biophysical Journal},
   Volume = {74},
   Number = {2},
   Pages = {A132-A132},
   Year = {1998},
   Month = {February},
   ISSN = {0006-3495},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000073445400759&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds313881}
}

@article{fds235090,
   Author = {Zhang, YK and Yang, WT},
   Title = {Comment on "Generalized gradient approximation made
             simple"},
   Journal = {Physical Review Letters},
   Volume = {80},
   Number = {4},
   Pages = {890-890},
   Year = {1998},
   Month = {January},
   ISSN = {0031-9007},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000071717100066&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Doi = {10.1103/PhysRevLett.80.890},
   Key = {fds235090}
}

@article{fds235091,
   Author = {Zhang, Y and Yang, W},
   Title = {A challenge for density functionals: Self-interaction error
             increases for systems with a noninteger number of
             electrons},
   Journal = {Journal of Chemical Physics},
   Volume = {109},
   Number = {7},
   Pages = {2604-2608},
   Year = {1998},
   url = {http://dx.doi.org/10.1063/1.476859},
   Abstract = {The difficulty of widely used density functionals in
             describing the dissociation behavior of some homonuclear and
             heteronuclear diatomic radicals is analyzed. It is shown
             that the self-interaction error of these functionals
             accounts for the problem - it is much larger for a system
             with a noninteger number of electrons than a system with an
             integer number of electrons. We find the condition for the
             erroneous dissociation behavior described by approximate
             density functionals: when the ionization energy of one
             dissociation partner differs from the electron affinity of
             the other partner by a small amount, the self-interaction
             error will lead to wrong dissociation limit. Systems with a
             noninteger number of electrons and hence the large amount of
             self-interaction error in approximate density functionals
             arise also in the transition states of some chemical
             reactions and in some charge-transfer complexes. In the
             course of analysis, we derive a scaling relation necessary
             for an exchange-correlation functional to be
             self-interaction free. © 1998 American Institute of
             Physics.},
   Doi = {10.1063/1.476859},
   Key = {fds235091}
}

@article{fds235092,
   Author = {York, DM and Lee, T-S and Yang, W},
   Title = {Quantum mechanical treatment of biological macromolecules in
             solution using linear-scaling electronic structure
             methods},
   Journal = {Physical Review Letters},
   Volume = {80},
   Number = {22},
   Pages = {5011-5014},
   Year = {1998},
   Abstract = {A linear-scaling self-consistent field method for
             calculation of the electronic structure of biological
             macromolecules in solution is presented. The method is
             applied at the semiempirical Hartree-Fock level to the
             determination of heats of formation, solvation free
             energies, and density of electronic states for several
             protein and DNA systems.},
   Key = {fds235092}
}

@article{fds235093,
   Author = {Yang, W and Levy, M and Trickey, S},
   Title = {Symposium on density functional and applications (part 1 of
             ii) - introduction},
   Journal = {Int. J. Quantum Chem.},
   Volume = {69},
   Pages = {227},
   Year = {1998},
   Key = {fds235093}
}

@article{fds235094,
   Author = {Yang, W},
   Title = {Generalized adiabatic connection in density functional
             theory},
   Journal = {Journal of Chemical Physics},
   Volume = {109},
   Number = {23},
   Pages = {10107-10110},
   Year = {1998},
   url = {http://dx.doi.org/10.1063/1.477701},
   Abstract = {A generalized adiabatic connection is developed for density
             functional theory. The method extends the well-known
             adiabatic connection formula and provides a general link
             between the Kohn-Sham and the physical system. When the
             complimentary error function is used as a special case, the
             expression for the exchange-correlation functional does not
             have the 1/r12 Coulomb component. The exact contributions
             from the physical system and the noninteracting system are
             established: The physical system limit has a dominant
             contribution, while the noninteracting system limit has no
             contribution. © 1998 American Institute of
             Physics.},
   Doi = {10.1063/1.477701},
   Key = {fds235094}
}

@article{fds235095,
   Author = {Pérez-Jordá, JM and Yang, W},
   Title = {On the scaling of multipole methods for particle-particle
             interactions},
   Journal = {Chemical Physics Letters},
   Volume = {282},
   Number = {1},
   Pages = {71-78},
   Year = {1998},
   Abstract = {There is some controversy regarding the scaling of the fast
             multipole method (FMM). It has recently been proven by Aluru
             that the FMM is not a linear scaling method, but an O(N log4
             N) method. Aluru's proof cannot be applied to typical
             computational chemistry calculations where the required
             precision is smaller than the machine accuracy. In this
             Letter, we deal with this kind of situation and give a
             rigorous bound to the scaling and a statistical estimate. We
             also perform numerical tests. Our results agree with Aluru's
             proof. The scaling of other methods that use multipoles is
             also discussed.},
   Key = {fds235095}
}

@article{fds235096,
   Author = {Pan, W and Lee, T-S and Yang, W},
   Title = {Parallel implementation of divide-and-conquer semiempirical
             quantum chemistry calculations},
   Journal = {Journal of Computational Chemistry},
   Volume = {19},
   Number = {9},
   Pages = {1101-1109},
   Year = {1998},
   Abstract = {We have implemented a parallel divide-and-conquer method for
             semiempircal quantum mechanical calculations. The standard
             message passing library, the message passing interface
             (MPI), was used. In this parallel version, the memory needed
             to store the Fock and density matrix elements is distributed
             among the processors. This memory distribution solves the
             problem of demanding requirement of memory for very large
             molecules. While the parallel calculation for construction
             of matrix elements is straightforward, the parallel
             calculation of Fock matrix diagonalization is achieved via
             the divide-and-conquer method. Geometry optimization is also
             implemented with parallel gradient calculations. The code
             has been tested on a Cray T3E parallel computer, and
             impressive speedup of calculations has been achieved. Our
             results indicate that the divide-and-conquer method is
             efficient for parallel implementation. © 1998 John Wiley
             &amp; Sons, Inc.},
   Key = {fds235096}
}

@article{fds235097,
   Author = {Lewis, JP and Jr, CWC and Hermans, J and Pan, W and Lee, T-S and Yang,
             W},
   Title = {Active species for the ground-state complex of cytidine
             deaminase: A linear-scaling quantum mechanical
             investigation},
   Journal = {Journal of the American Chemical Society},
   Volume = {120},
   Number = {22},
   Pages = {5407-5410},
   Year = {1998},
   ISSN = {0002-7863},
   url = {http://dx.doi.org/10.1021/ja973522w},
   Abstract = {We present results of large-scale (1330 atoms)
             linear-scaling quantum mechanical semiempirical (PM3)
             simulations done to optimize geometries surrounding the
             active site within the enzyme cytidine deaminase. We make a
             strong prediction about the structure of the active site for
             the active species, based on the energetics of the
             calculated structures and comparisons to X-ray
             crystallographic data. The lowest energy structure indicates
             that Zn-OH- is the active species formed prior to
             nucleophilic attack of the ligand, that the active species
             of Glu-104 is with Oε2 protonated and hydrogen-bonded with
             N3 of the ligand, and that the C4 and OH- atoms are
             significantly closer than is permitted by their van der
             Waals radii. In addition, we predict structures
             corresponding to the low-pH and high-pH states in the active
             site of the enzyme.},
   Doi = {10.1021/ja973522w},
   Key = {fds235097}
}

@article{fds235098,
   Author = {Lee, T-S and Lewis, JP and Yang, W},
   Title = {Linear-scaling quantum mechanical calculations of biological
             molecules: The divide-and-conquer approach},
   Journal = {Computational Materials Science},
   Volume = {12},
   Number = {3},
   Pages = {259-277},
   Year = {1998},
   Abstract = {The divide-and-conquer technique for linear-scaling quantum
             mechanical calculations is reviewed. The method divides a
             large system into many subsystems, determines the density
             matrix of each subsystem separately, and sums the
             corresponding subsystem contributions to obtain the total
             density matrix and the energy of the system. There is a
             uniform chemical potential to allow transfer of electrons
             between subsystems and to insure the normalization of the
             electron density. The implementation of the method for
             semiempirical quantum chemistry Hamiltonians is described.
             The review describes the application to the study of the
             catalytic mechanisms of cytidine deaminase, an enzyme which
             accelerates the rate of hydrolytic deamination of cytidine
             to uridine. The linear-scaling quantum mechanical
             calculations determined the active species of the
             ground-state complex and the structure of the reaction
             transition-state analog complex. © 1998 Elsevier Science
             B.V. All rights reserved.},
   Key = {fds235098}
}

@article{fds235099,
   Author = {Lee, T-S and Yang, W},
   Title = {Frozen density matrix approach for electronic structure
             calculations},
   Journal = {International Journal of Quantum Chemistry},
   Volume = {69},
   Number = {3},
   Pages = {397-404},
   Year = {1998},
   Abstract = {A frozen density matrix approach for determining local
             geometry changes of large molecules is proposed based on the
             density matrix divide-and-conquer method. This approach
             divides a large molecule into a small active part and the
             rest as the frozen part. After a single-point
             self-consistent field (SCF) calculation for the whole
             molecule, only the local molecular orbitals of the active
             part and its neighbor are updated when the geometry of the
             active part changes. The updated density matrix is
             calculated from the new local molecular orbitals of the
             active part and the stored local molecular orbitals of the
             frozen part. The electron transfer between the active and
             the frozen part is allowed via a common and variable
             chemical potential. The preliminary tests using
             semiempirical quantum chemical methods show this approach
             predicts the local geometry change well. The error in
             geometric parameters is less than 0.002 Å and less than
             0.5° for bond length and bond angle, respectively. © 1998
             John Wiley &amp; Sons, Inc.},
   Key = {fds235099}
}

@article{fds235100,
   Author = {Zhu, TH and Pan, W and Yang, WT},
   Title = {Divide-and-conquer calculations for clean surfaces and
             surface adsorption},
   Journal = {Theoretical Chemistry Accounts},
   Volume = {96},
   Number = {1},
   Pages = {2-6},
   Year = {1997},
   Month = {April},
   ISSN = {1432-881X},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1997XF32500001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Doi = {10.1007/s002140050195},
   Key = {fds235100}
}

@article{fds235101,
   Author = {Zhang, Y and Pan, W and Yang, W},
   Title = {Describing van der Waals interaction in diatomic molecules
             with generalized gradient approximations: The role of the
             exchange functional},
   Journal = {Journal of Chemical Physics},
   Volume = {107},
   Number = {19},
   Pages = {7921-7925},
   Year = {1997},
   ISSN = {0021-9606},
   Abstract = {Generalized gradient approximations have been used to
             calculate the potential energy curves for six rare gas
             diatomic molecules. Several generalized gradient
             approximations are found to provide a good description of
             binding in these diatomic molecules and show a significant
             improvement over the local density approximation in the
             prediction of bond lengths and dissociation energies. It is
             shown here that the behavior of an exchange functional in
             the region of small density and large density gradient plays
             a very important role in the ability of the functional to
             describe this type of van der Waals attraction. © 1997
             American Institute of Physics.},
   Key = {fds235101}
}

@article{fds235102,
   Author = {Yang, W},
   Title = {Absolute-energy-minimum principles for linear-scaling
             electronic-structure calculations},
   Journal = {Physical Review B - Condensed Matter and Materials
             Physics},
   Volume = {56},
   Number = {15},
   Pages = {9294-9297},
   Year = {1997},
   Abstract = {Two absolute energy minimum principles are developed for
             first-principle linear-scaling electronic structure
             calculations. One is with a normalization constraint and the
             other without any constraint. The density matrix is
             represented by a set of nonorthogonal localized orbitals and
             an auxiliary matrix which at the minimum becomes a
             generalized inverse of the overlap matrix of the localized
             orbitals. The number of localized orbitals is allowed to
             exceed the number of occupied orbitals. Comparison with
             other variational principles is made and numerical tests
             presented.},
   Key = {fds235102}
}

@article{fds235103,
   Author = {Pérez-Jordá, JM and Yang, W},
   Title = {Fast evaluation of the Coulomb energy for electron
             densities},
   Journal = {Journal of Chemical Physics},
   Volume = {107},
   Number = {4},
   Pages = {1218-1226},
   Year = {1997},
   Abstract = {The evaluation of the Coulomb interaction of the electron
             density with itself dominates the cost of a
             density-functional theory calculation, due to its quadratic
             scaling with the size of the system. A similar problem is
             found in simulations of systems of particles, where the cost
             is dominated by the particle-particle interactions.
             Recently, we have presented a simple method for the
             particle-particle problem [J. M. Pérez-Jordá and W. Yang,
             Chem. Phys. Lett. 247, 484 (1995)]. In this paper, our
             scheme is generalized to densities, in particular for
             calculations with Gaussian basis functions. Near linear
             scaling is observed for molecules with about 400 first-row
             atoms. CPU time savings of up to one order of magnitude are
             observed for these molecules. The method distinguishes
             between localized and diffuse distributions in a much
             simpler way than in other proposed approaches. © 1997
             American Institute of Physics.},
   Key = {fds235103}
}

@article{fds235104,
   Author = {Pan, W and Zhu, T and Yang, W},
   Title = {First-principles study of the structural and electronic
             properties of ethylene adsorption on Si(100)-(2×1)
             surface},
   Journal = {Journal of Chemical Physics},
   Volume = {107},
   Number = {10},
   Pages = {3981-3985},
   Year = {1997},
   ISSN = {0021-9606},
   Abstract = {We present a first-principles density-functional study for
             ethylene adsorption on the Si(100)-(2×1) surface. Ethylene
             is di-σ bonded to the surface Si dimers with the adsorption
             energy of 1.81 eV. The dimer-maintained adsorption structure
             is found to be more stable than the dimer-cleaved one by
             0.91 eV. Our calculations on the post-exposure of the
             ethylene-saturated surface to atomic hydrogen demonstrate
             the formation of Si-H bonds, the cleavage of the Si dimer
             bonds, and the minor changes for the chemisorbed ethylene,
             which is in good agreement with the recent experimental
             observations. © 1997 American Institute of
             Physics.},
   Key = {fds235104}
}

@article{fds235105,
   Author = {Zhu, T and Pan, W and Yang, W},
   Title = {Structure of solid-state systems from embedded-cluster
             calculations: A divide-and-conquer approach},
   Journal = {Physical Review B - Condensed Matter and Materials
             Physics},
   Volume = {53},
   Number = {19},
   Pages = {12713-12724},
   Year = {1996},
   Abstract = {The first-principles divide-and-conquer density-functional
             approach has been extended to solid-state systems. The
             method has the following features. (1) It divides a periodic
             solid-state system into equivalent primitive cells and
             further divides each cell into subsystems. The electron
             density of each subsystem is determined through the local
             representation of the one-electron Hamiltonian and used to
             form the total density per primitive cell. The method
             calculates the electronic structure of solids without
             involving the reciprocal space and its associated band
             structure. (2) It uses numerical atomic orbitals as basis
             functions with great variational flexibility. The
             Hamiltonian and other matrix elements are evaluated by
             numerical integration without any shape approximation to the
             effective one-electron potential. (3) This method, based on
             real space partition, can be applied to extended solid-state
             systems without translational symmetry, such as defects and
             surface chemisorption. As the first step, we have applied
             and tested the method to the electronic structure
             calculations of various crystalline solids: metallic lithium
             and copper, ionic sodium chloride, and covalent diamond and
             silicon. The self-consistently computed cohesive energies,
             structural properties, and density of states are in good
             agreement with those from the local-density approximation
             band-structure calculations and experimental
             results.},
   Key = {fds235105}
}

@article{fds235106,
   Author = {York, DM and Lee, T-S and Yang, W},
   Title = {Parameterization and efficient implementation of a solvent
             model for linear-scaling semiempirical quantum mechanical
             calculations of biological macromolecules},
   Journal = {Chemical Physics Letters},
   Volume = {263},
   Number = {1-2},
   Pages = {297-304},
   Year = {1996},
   Abstract = {A method is developed to include solvation effects in
             linear-scaling semiempirical quantum calculations. Favorable
             scaling of computational effort for large molecules is
             achieved using a preconditioned conjugate gradient technique
             in conjunction with a linear-scaling recursive bisection
             method for evaluation of electrostatic interactions. The
             method requires approximately 30% computational overhead
             relative to gas-phase calculations. Effective atomic radii
             for biological macromolecules are derived from fitting to
             experimental and theoretical solvation energies for small
             molecules homologous to amino-and nucleic acid
             residues.},
   Key = {fds235106}
}

@article{fds235107,
   Author = {York, DM and Yang, W},
   Title = {A chemical potential equalization method for molecular
             simulations},
   Journal = {Journal of Chemical Physics},
   Volume = {104},
   Number = {1},
   Pages = {159-172},
   Year = {1996},
   ISSN = {0021-9606},
   Abstract = {A formulation of the chemical potential (electronegativity)
             equalization principle is presented from the perspective of
             density-functional theory. The resulting equations provide a
             linear-response framework for describing the redistribution
             of electrons upon perturbation by an applied field. The
             method has two main advantages over existing
             electronegativity equalization and charge equilibration
             methods that allow extension to accurate molecular dynamics
             simulations. Firstly, the expansion of the energy is taken
             about the molecular ground state instead of the neutral atom
             ground states; hence, in the absence of an external field,
             the molecular charge distribution can be represented by
             static point charges and dipoles obtained from fitting to
             high-level ab initio calculations without modification.
             Secondly, in the presence of applied fields or interactions
             with other molecules, the density response can be modeled
             accurately using basis functions. Inclusion of basis
             functions with dipolar or higher order multipolar character
             allows molecules or chemical groups to have correct local
             anisotropic polarizabilities. A modified semiempirical form
             of the hardness matrix has been introduced that can be
             evaluated efficiently using Gaussians, and requires only one
             parameter per basis function. Applications at two basis-set
             levels demonstrate the method can accurately reproduce
             induced dipole moments 'and estimated chemical potentials
             obtained from density-functional calculations for a variety
             of molecules. Inclusion of basis functions beyond the
             conventional spherical-atom type is essential in some
             instances. The present formulation provides the foundation
             for a promising semi-empirical model for polarization and
             charge transfer in molecular simulations. © 1996 American
             Institute of Physics.},
   Key = {fds235107}
}

@article{fds235108,
   Author = {York, DM and Lee, T-S and Yang, W},
   Title = {Quantum mechanical study of aqueous polarization effects on
             biological macromolecules},
   Journal = {Journal of the American Chemical Society},
   Volume = {118},
   Number = {44},
   Pages = {10940-10941},
   Year = {1996},
   url = {http://dx.doi.org/10.1021/ja961937w},
   Doi = {10.1021/ja961937w},
   Key = {fds235108}
}

@article{fds235109,
   Author = {Pérez-Jordá, JM and Yang, W},
   Title = {A concise redefinition of the solid spherical harmonics and
             its use in fast multipole methods},
   Journal = {Journal of Chemical Physics},
   Volume = {104},
   Number = {20},
   Pages = {8003-8006},
   Year = {1996},
   Abstract = {Several fast algorithms for the approximation of
             particle-particle interactions by means of multipole
             expansions in spherical harmonics have appeared recently. In
             this letter we present a redefinition of the solid spherical
             harmonics that is real and gives simple expressions for the
             evaluation of the functions and their derivatives.
             Application to the recursive bisection method [J. M.
             Pérez-Jordá and W. Yang, Chem. Phys. Lett. 247, 484
             (1995)] greatly improves its performance. © 1996 American
             Institute of Physics.},
   Key = {fds235109}
}

@article{fds235110,
   Author = {Ni, H and York, DM and Bartolotti, L and Wells, RL and Yang,
             W},
   Title = {Density-functional study of the geometries, stabilities, and
             bond energies of group III-V (13-15) four-membered-ring
             compounds},
   Journal = {Journal of the American Chemical Society},
   Volume = {118},
   Number = {24},
   Pages = {5732-5736},
   Year = {1996},
   url = {http://dx.doi.org/10.1021/ja951706+},
   Abstract = {A theoretical investigation has been carried out on several
             group III-V (13-15) four-membered-ring compounds which, if
             experimentally attainable, are potentially useful as
             precursors to nanocrystalline electronic and semiconductor
             materials. Four-membered-ring compounds considered in this
             study have core structures of the following form: MEME' and
             MEMX (M, M' = In, Ga, Al; E, E' = P, As; X = Cl, Br).
             Equilibrium geometries, binding energies, and bond energies
             were determined based on local density approximation (LDA)
             and gradient-corrected density-functional methods. Optimized
             ring geometries obtained with LDA agree closely with
             single-crystal X-ray crystallographic structures of known
             compounds with the same four-membered-ring cores. The
             following trends in bond energies are observed: M-Cl
             &gt;&gt; M-P &gt; M-As &gt;&gt; M-Br (M = In, Ga, Al), and
             Al-Y &gt; Ga-Y &gt; In-Y (Y = P, As, Cl, Br). Although only
             one M-Br-containing mixed-bridge four-membered-ring compound
             has been reported and no such Al-Cl-containing mixed-bridge
             species have yet been synthesized, our calculations suggest
             that compounds containing these two ring systems are
             stable.},
   Doi = {10.1021/ja951706+},
   Key = {fds235110}
}

@article{fds235111,
   Author = {Lee, T-S and York, DM and Yang, W},
   Title = {Linear-scaling semiempirical quantum calculations for
             macromolecules},
   Journal = {Journal of Chemical Physics},
   Volume = {105},
   Number = {7},
   Pages = {2744-2750},
   Year = {1996},
   Abstract = {A linear-scaling method to carry out semiempirical quantum
             mechanical calculations for large systems has been developed
             based on the density matrix version of the
             divide-and-conquer approach. The method has been tested and
             demonstrated to be accurate and efficient. With this
             implementation, semiempirical quantum mechanical
             calculations are made possible for large molecules over 9000
             atoms on a typical workstation. For biological
             macromolecules, solvent effects are included with a
             dielectric continuum model. © 1996 American Institute of
             Physics.},
   Key = {fds235111}
}

@article{fds235073,
   Author = {Wei, P and Yang, W},
   Title = {Structure and stability of molybdenum carbide clusters
             (MoC4)n (n=1 to 4) and their anions},
   Journal = {Physical Review B - Condensed Matter and Materials
             Physics},
   Volume = {51},
   Number = {11},
   Pages = {7224-7230},
   Year = {1995},
   ISSN = {0163-1829},
   url = {http://dx.doi.org/10.1103/PhysRevB.51.7224},
   Abstract = {We study the structure and stability of recently discovered
             molybdenum carbide clusters (MoC4)n and (MoC4)n- (n=1 to 4)
             using local-density-functional calculations. Our results
             suggest that small clusters are planar and larger ones have
             three-dimensional structures. The carbon atoms in the
             clusters have the tendency to form a chain or ring structure
             similar to that in small all-carbon clusters. The molybdenum
             carbide clusters are stable with binding energies per atom
             comparable to those of the metallo-carbohedrene and
             fullerene clusters. The electron affinities and
             fragmentation pathways of these clusters have also been
             determined and compared with available experimental data. ©
             1995 The American Physical Society.},
   Doi = {10.1103/PhysRevB.51.7224},
   Key = {fds235073}
}

@article{fds235112,
   Author = {Zhao, Q and Yang, W},
   Title = {Analytical energy gradients and geometry optimization in the
             divide-and-conquer method for large molecules},
   Journal = {Journal of Chemical Physics},
   Volume = {102},
   Number = {24},
   Pages = {9598-9603},
   Year = {1995},
   ISSN = {0021-9606},
   Abstract = {Based on the divide-and-conquer method in the
             density-functional theory, an efficient approach is
             developed to compute analytically the energy gradients with
             respect to the nuclear coordinates. Tests performed show
             that both energy gradients and optimized molecular geometry
             converge to the corresponding results of the Kohn-Sham
             method when the nearest neighbor contributions are
             increased. © 1995 American Institute of
             Physics.},
   Key = {fds235112}
}

@article{fds235113,
   Author = {York, DM and Yang, W and Lee, H and Darden, T and Pedersen,
             LG},
   Title = {Toward the accurate modeling of DNA: The importance of
             long-range electrostatics},
   Journal = {Journal of the American Chemical Society},
   Volume = {117},
   Number = {17},
   Pages = {5001-5002},
   Year = {1995},
   Key = {fds235113}
}

@article{fds235114,
   Author = {Yang, W and Lee, T-S},
   Title = {A density-matrix divide-and-conquer approach for electronic
             structure calculations of large molecules},
   Journal = {Journal of Chemical Physics},
   Volume = {103},
   Number = {13},
   Pages = {5674-5678},
   Year = {1995},
   ISSN = {0021-9606},
   Abstract = {A density matrix divide-and-conquer method is proposed for
             electronic structure calculation of large molecules. It is
             based on partition of density matrix and thus applicable to
             both density-functional and Hartree-Fock method. Compared to
             the original formulation with electron density, the present
             method is more efficient and as accurate. © 1995 American
             Institute of Physics.},
   Key = {fds235114}
}

@article{fds235115,
   Author = {Pérez-Jordá, J and Yang, W},
   Title = {A simple O(N log N) algorithm for the rapid evaluation of
             particle-particle interactions},
   Journal = {Chemical Physics Letters},
   Volume = {247},
   Number = {4-6},
   Pages = {484-490},
   Year = {1995},
   ISSN = {0009-2614},
   Abstract = {Exact simulations of huge systems of charged particles are
             impossible in practice, because their cost proportional to
             N2, where N is the number of particles. We present an
             approximate and simple O(N log N) algorithm based upon the
             idea of recursive bisection of the set of particles. A small
             fraction of the particle-particle interactions is evaluated
             exactly by direct summation, while the rest is approximated
             via multipole expansions. Our algorithm is easy to program
             (in particular, in parallel, which is trivial), and it is
             well suited for system with a non-uniform distribution of
             particles. For uniform systems, its accuracy and execution
             time are comparable to other fast methods such as tree codes
             and the fast multipole method. © 1995.},
   Key = {fds235115}
}

@article{fds235116,
   Author = {Pérez-Jorda, J and Yang, W},
   Title = {An algorithm for 3D numerical integration that scales
             linearly with the size of the molecule},
   Journal = {Chemical Physics Letters},
   Volume = {241},
   Number = {4},
   Pages = {469-476},
   Year = {1995},
   ISSN = {0009-2614},
   Abstract = {The cost of numerical integration in density-functional
             theory scales as the cube of the size of the molecule: it is
             proportional to the number of grid points and to the square
             of the number of basis functions. We describe a scheme that
             makes this cost independent of the number of basis
             functions, thus yielding an algorithm that scales linearly
             with the size of the molecule. The error introduced by the
             present scheme can be made as small as desired by lowering a
             threshold T. The method can be applied to any quadrature
             rule and local basis set. © 1995.},
   Key = {fds235116}
}

@article{fds235117,
   Author = {Parr, RG and Yang, W},
   Title = {Density-functional theory of the electronic structure of
             molecules},
   Journal = {Annual Review of Physical Chemistry},
   Volume = {46},
   Number = {1},
   Pages = {701-728},
   Year = {1995},
   Abstract = {Recent fundamental advances in the density-functional theory
             of electronic structure are summarized. Emphasis is given to
             four aspects of the subject: (a) tests of functional, (b)
             new methods for determining accurate exchange-correlation
             functional, (c) linear scaling methods, and (d) developments
             in the description of chemical reactivity.},
   Key = {fds235117}
}

@article{fds235118,
   Author = {Lee, T-S and York, DM and Yang, W},
   Title = {A new definition of atomic charges based on a variational
             principle for the electrostatic potential
             energy},
   Journal = {Journal of Chemical Physics},
   Volume = {102},
   Number = {19},
   Pages = {7549-7556},
   Year = {1995},
   ISSN = {0021-9606},
   Abstract = {A unique definition of atomic charges in molecules is
             presented based on a variational principle involving the
             electrostatic potential energy. The method requires only the
             electron density as input, and does not rely on an arbitrary
             set of fitting points as do conventional electrostatic
             potential fitting procedures. The dipole moments and
             electrostatic potentials calculated from atomic charges
             obtained from this method agree well with those from
             self-consistent-field calculations. The new method also
             provides a spherical-atom potential model that may be useful
             in future generation molecular simulation force fields. ©
             1995 American Institute of Physics.},
   Key = {fds235118}
}

@article{fds235119,
   Author = {ZHU, TH and YANG, WT},
   Title = {STRUCTURE OF THE AMMONIA DIMER STUDIED BY DENSITY-FUNCTIONAL
             THEORY},
   Journal = {International Journal of Quantum Chemistry},
   Volume = {49},
   Number = {5},
   Pages = {613-623},
   Year = {1994},
   Month = {February},
   ISSN = {0020-7608},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1994MU69800006&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Doi = {10.1002/qua.560490507},
   Key = {fds235119}
}

@article{fds235120,
   Author = {York, D and Yang, W},
   Title = {The fast Fourier Poisson method for calculating Ewald
             sums},
   Journal = {Journal of Chemical Physics},
   Volume = {101},
   Number = {4},
   Pages = {3298-3300},
   Year = {1994},
   ISSN = {0021-9606},
   Abstract = {The conventional Ewald expression for the electrostatic
             energy and forces is recast in a form that can be evaluated
             to high accuracy in order N log(N) steps using fast Fourier
             transforms. The fast Fourier Poisson method does not rely on
             interpolation approaches or Taylor/multipole expansions, and
             can be easily integrated with conventional molecular
             dynamics algorithms. © 1994 American Institute of
             Physics.},
   Key = {fds235120}
}

@article{fds235121,
   Author = {Lu, JP and Yang, W},
   Title = {Shape of large single- and multiple-shell
             fullerenes},
   Journal = {Physical Review B - Condensed Matter and Materials
             Physics},
   Volume = {49},
   Number = {16},
   Pages = {11421-11424},
   Year = {1994},
   ISSN = {0163-1829},
   url = {http://dx.doi.org/10.1103/PhysRevB.49.11421},
   Abstract = {The morphology of multiple-shell fullerenes is investigated
             by ab initio calculations using Yang's O(N) method. It is
             found that for large single-shell fullerenes with Ih
             symmetry, the spherical morphology has lower energy than
             that of polyhedrons. The formation energy per atom follows a
             simple scaling law. Including an estimate of intershell van
             de Waals interactions leads to the conclusion that spherical
             multiple-shell fullerenes are likely the most stable
             structure of large carbon clusters. These results are in
             good agreement with recent experiments. © 1994 The American
             Physical Society.},
   Doi = {10.1103/PhysRevB.49.11421},
   Key = {fds235121}
}

@article{fds235123,
   Author = {York, D and Lu, JP and Yang, W},
   Title = {Density-functional calculations of the structure and
             stability of C240},
   Journal = {Physical Review B - Condensed Matter and Materials
             Physics},
   Volume = {49},
   Number = {12},
   Pages = {8526-8528},
   Year = {1994},
   ISSN = {0163-1829},
   url = {http://dx.doi.org/10.1103/PhysRevB.49.8526},
   Abstract = {Density-functional calculations have been performed to
             determine optimized geometries and energies of C240 using
             the divide-and-conquer method. Six initial geometries were
             considered, resulting in convergence to two optimized
             configurations. The formation energies of the optimized
             structures are separated by approximately 0.07 eV/carbon
             atom. The lower-energy structure is highly spherical in
             agreement with preliminary studies and experimental
             observations. The higher-energy structure is polyhedrally
             faceted. The results support the conclusion that the most
             stable form of large carbon clusters is that of dense
             spherical caged structures. © 1994 The American Physical
             Society.},
   Doi = {10.1103/PhysRevB.49.8526},
   Key = {fds235123}
}

@article{fds318107,
   Author = {ZHU, TH and LEE, CT and YANG, WT},
   Title = {EXAMINATION OF SEVERAL EXCHANGE-CORRELATION ENERGY
             FUNCTIONALS BY ACCURATE SELF-CONSISTENT ATOMIC CALCULATIONS
             (VOL 98, PG 4814, 1993)},
   Journal = {Journal of Chemical Physics},
   Volume = {99},
   Number = {5},
   Pages = {4239-4239},
   Year = {1993},
   Month = {September},
   url = {http://dx.doi.org/10.1063/1.466236},
   Doi = {10.1063/1.466236},
   Key = {fds318107}
}

@article{fds234974,
   Author = {Zhu, T and Lee, C and Yang, W},
   Title = {Erratum: Examination of several exchange-correlation energy
             functionals by accurate self-consistent atomic calculations
             (Journal of Chemical Physics (1993) 98 (4814))},
   Journal = {Journal of Chemical Physics},
   Volume = {99},
   Number = {5},
   Pages = {4239-},
   Year = {1993},
   ISSN = {0021-9606},
   Key = {fds234974}
}

@article{fds234975,
   Author = {Bemish, RJ and Block, PA and Pedersen, LG and Weitao, Y and Miller,
             RE},
   Title = {The Ar-C2H2 intermolecular potential
             from high resolution spectroscopy and ab initio theory: A
             case for multicenter interactions},
   Journal = {Journal of Chemical Physics},
   Volume = {99},
   Number = {11},
   Pages = {8585-8598},
   Year = {1993},
   ISSN = {0021-9606},
   Abstract = {Infrared spectra have been obtained for the Ar-C2H2 complex,
             which include a combination band associated with the low
             frequency bending mode. These data are used, together with
             ab initio calculations and the results of previous studies
             of this system, to construct a two-dimensional Hartree-Fock
             plus damped dispersion (HFD) intermolecular potential
             surface corresponding to the C-H stretch excited vibrational
             state. A high quality SCF surface, which includes ghost
             orbital corrections, has been used to fix the repulsive part
             of the potential. The remaining potential parameters were
             initially estimated with the aid of various combining rules
             and the collocation technique was used to solve the bound
             state problem for this potential and to calculate the
             spectrum of the Ar-C2H2 complex. To obtain good agreement
             between the calculated and experimental spectra it was
             necessary to distribute the dispersion interaction over the
             length of the acetylene subunit. The result is a double
             minimum potential upon which the complex executes wide
             amplitude bending motion. &amp;copy; 1993 American Institute
             of Physics.},
   Key = {fds234975}
}

@article{fds235122,
   Author = {Zhu, T and Lee, C and Yang, W},
   Title = {Examination of several exchange-correlation energy
             functionals by accurate self-consistent atomic
             calculations},
   Journal = {Journal of Chemical Physics},
   Volume = {98},
   Number = {6},
   Pages = {4814-4821},
   Year = {1993},
   ISSN = {0021-9606},
   Abstract = {Several local and nonlocal exchange-correlation functionals
             are tested through accurate Kohn-Sham self-consistent
             calculations for six nobel gas atoms and three isoelectronic
             series (with two, four, and ten electrons and atomic numbers
             up to 20). The calculated exchange, correlation, and total
             energies have been compared with those from accurate
             Hartree-Fock calculations and accurate estimates of
             correlation energies available recently. Improvements over
             local-density approximation are found for all the tested
             nonlocal exchange-correlation functionals. In particular,
             nonlocal correlation energy functionals are shown to perform
             significantly better than the local approximations when both
             are used in conjunction with the nonlocal Becke's exchange
             energy functional. However, in most cases, all the
             functionals fail to predict the correct trends of exchange
             and correlation energies as the atomic charge increases. ©
             1993 American Institute of Physics.},
   Key = {fds235122}
}

@article{fds235124,
   Author = {Lee, C and Fitzgerald, G and Yang, W},
   Title = {Nonlocal density functional calculations: Comparison of two
             implementation schemes},
   Journal = {Journal of Chemical Physics},
   Volume = {98},
   Number = {4},
   Pages = {2971-2974},
   Year = {1993},
   ISSN = {0021-9606},
   Abstract = {We have carried out nonlocal density-functional calculations
             of bond dissociation and isomerization energies of several
             polyatomic molecules in two schemes. In the first scheme,
             the nonlocal energy functional is incorporated into the
             optimization of both the electronic and nuclear degrees of
             freedom. In the second scheme, the nonlocal energy
             functional is only included in a non-self-consistent fashion
             in which we just use the molecular geometry and electron
             density determined by the corresponding local density
             calculations. Our study reveals that the differences of the
             energies are very small between these two schemes. © 1993
             American Institute of Physics.},
   Key = {fds235124}
}

@article{fds235125,
   Author = {Bemish, RJ and Block, PA and Pedersen, LG and Yang, W and Miller,
             RE},
   Title = {The ar-c2h2 inter-molecular potential from high resolution
             spectroscopy and ab initio theory: A case for multi-center
             interactions},
   Journal = {J. Chem. Phys.},
   Volume = {99},
   Number = {11},
   Pages = {8593-8598},
   Year = {1993},
   ISSN = {0021-9606},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1993MJ90200025&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Doi = {10.1063/1.465582},
   Key = {fds235125}
}

@article{fds313234,
   Author = {LEE, CT and YANG, WT},
   Title = {THE DIVIDE-AND-CONQUER DENSITY-FUNCTIONAL APPROACH -
             MOLECULAR INTERNAL-ROTATION AND DENSITY OF
             STATES},
   Journal = {Journal of Chemical Physics},
   Volume = {96},
   Number = {3},
   Pages = {2408-2411},
   Year = {1992},
   Month = {February},
   ISSN = {0021-9606},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1992HC61000082&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Doi = {10.1063/1.462039},
   Key = {fds313234}
}

@article{fds24416,
   Author = {Chengteh Lee and Weitao Lee},
   Title = {The divide-functional approach: molecular internal rotation
             and density of states},
   Journal = {J. Chem. Phys.},
   Volume = {96},
   Pages = {2408-2411},
   Year = {1992},
   Key = {fds24416}
}

@article{fds235126,
   Author = {Yang, W},
   Title = {Electron density as the basic variable: a divide-and-conquer
             approach to the ab initio computation of large
             molecules},
   Journal = {Journal of Molecular Structure: THEOCHEM},
   Volume = {255},
   Number = {C},
   Pages = {461-479},
   Year = {1992},
   ISSN = {0166-1280},
   url = {http://dx.doi.org/10.1016/0166-1280(92)85024-F},
   Abstract = {A recently developed approach for calculations of ground
             states of many-electron systems is described. The method is
             based on density-functional theory. It uses the electron
             density as the basic computational variable and does not
             invoke molecular orbitais. A divide-and-conquer strategy is
             employed: a large system is first divided into subsystems in
             the physical space, then the densities of subsystems are
             calculated separately, and finally the total energy and the
             electron density are obtained as the sums of subsystem
             contributions. Various molecular calculations are presented
             to show that the new method is capable of describing
             electronic structure with accuracy comparable to the
             Kohn-Sham orbital approach. The method is expected to enable
             efficient first-principle calculations of large molecules
             beyond the reach of conventional approaches. Analysis is
             presented to address the physics underlying the method, the
             relation of the method to the traditional Thomas-Fermi-type
             theory, the effect of molecular symmetry, the scaling of
             computational effort, and the suitability for parallel
             computation. © 1992.},
   Doi = {10.1016/0166-1280(92)85024-F},
   Key = {fds235126}
}

@article{fds235127,
   Author = {Crawford, TD and Yang, W},
   Title = {The Hartley basis functions and transform: alternatives to
             plane waves and the Fourier transform},
   Journal = {Chemical Physics Letters},
   Volume = {192},
   Number = {1},
   Pages = {45-48},
   Year = {1992},
   ISSN = {0009-2614},
   Abstract = {The Hartley "cas" basis functions are presented as
             alternatives to the well-known plane waves in electronic
             structure and molecular dynamics calculations. The cas
             functions are real, amenable to a fast transform, and thus
             offer the advantage of improved computational efficiency.
             The basis functions are tested in the calculation of the
             energy eigenvalues of a Morse oscillator, and are found to
             give results equal in accuracy to the plane waves. ©
             1992.},
   Key = {fds235127}
}

@article{fds235128,
   Author = {Yang, W},
   Title = {Direct calculation of electron density in density-functional
             theory: Implementation for benzene and a
             tetrapeptide},
   Journal = {Physical Review A - Atomic, Molecular, and Optical
             Physics},
   Volume = {44},
   Number = {11},
   Pages = {7823-7826},
   Year = {1991},
   ISSN = {1050-2947},
   url = {http://dx.doi.org/10.1103/PhysRevA.44.7823},
   Abstract = {A recently developed approach for the direct calculation of
             electron density is implemented for polyatomic molecules:
             benzene and a tetrapeptide with four glycine residues. The
             method uses the density as the basic variable, divides a
             system into subsystems, and determines the density for each
             subsystem. It is found that the method is capable of
             describing the electronic structure with accuracy comparable
             to the Kohn-Sham method. This substantiates the hope for ab
             initio calculations of large systems beyond the reach of
             conventional methods. © 1991 The American Physical
             Society.},
   Doi = {10.1103/PhysRevA.44.7823},
   Key = {fds235128}
}

@article{fds235129,
   Author = {Yang, W},
   Title = {Direct calculation of electron density in density-functional
             theory},
   Journal = {Physical Review Letters},
   Volume = {66},
   Number = {11},
   Pages = {1438-1441},
   Year = {1991},
   ISSN = {0031-9007},
   url = {http://dx.doi.org/10.1103/PhysRevLett.66.1438},
   Abstract = {A new approach for the study of ground states of
             many-electron systems is developed via direct calculation of
             the density in density-functional theory. Not using the
             Kohn-Sham equations, the method divides a system into
             subsystems in physical space and determines the density for
             each subsystem. The method is demonstrated with calculations
             for the nitrogen molecule, which is divided into two atomic
             subsystems. We expect this approach to enable calcultions
             for large molecules beyond the reach of conventional
             methods. © 1991 The American Physical Society.},
   Doi = {10.1103/PhysRevLett.66.1438},
   Key = {fds235129}
}

@article{fds235130,
   Author = {Yang, W},
   Title = {A local projection method for the linear combination of
             atomic orbital implementation of density-functional
             theory},
   Journal = {Journal of Chemical Physics},
   Volume = {94},
   Number = {2},
   Pages = {1208-1214},
   Year = {1991},
   ISSN = {0021-9606},
   Abstract = {A local projection method is proposed for obtaining the
             solution of the Kohn-Sham equation within the
             density-functional theory of molecules. The method uses the
             conventional linear combination of atomic orbitals as the
             approximate orbitals. However, it does not require
             multicenter integration in the construction of algebraic
             eigenvalue equations, and thus significantly reduces the
             corresponding computational effort. The method is tested on
             the self-consistent calculations of nitrogen molecules, N2,
             with basis sets of various accuracies and found to give
             results which are as accurate as the conventional approach.
             It is also shown that the local projection method can be
             applied to the non-self-consistent calculation scheme and
             provides a most efficient method for carrying out this type
             of electronic structure calculations. © 1991 American
             Institute of Physics.},
   Key = {fds235130}
}

@article{fds234973,
   Author = {Yang, W},
   Title = {Integral Formulation of Density-Functional
             Theory},
   Journal = {Advances in Quantum Chemistry},
   Volume = {21},
   Number = {C},
   Pages = {293-302},
   Editor = {Samuel B. Trickey},
   Year = {1990},
   ISSN = {0065-3276},
   url = {http://dx.doi.org/10.1016/S0065-3276(08)60601-2},
   Abstract = {The Hohenberg-Kohn-Sham density-functional theory is
             reformulated in terms of explicit relations between the
             electron density and the effective potential through the use
             of Feynman path integrals. In this formulation electron
             density is the only basic variable as in the Thomas-Fermi
             theory and orbitals are not needed. Possible applications to
             calculations in large molecules and the present limitations
             of the method are discussed. © 1990 Academic Press,
             Inc.},
   Doi = {10.1016/S0065-3276(08)60601-2},
   Key = {fds234973}
}

@article{fds235131,
   Author = {Yang, W and Peet, AC},
   Title = {A method for calculating vibrational bound states: Iterative
             solution of the collocation equations constructed from
             localized basis sets},
   Journal = {Journal of Chemical Physics},
   Volume = {92},
   Number = {1},
   Pages = {522-526},
   Year = {1990},
   ISSN = {0021-9606},
   Abstract = {We propose a simple and efficient method for calculating
             vibrational bound states of molecular systems. The technique
             is based upon iterative solution of the collocation
             equations. A localized basis set is used which is very
             efficient for strongly coupled modes and also leads to a
             diagonally dominant set of collocation equations. The
             iterative scheme developed is based upon Davidson's method
             and takes advantage of this diagonal dominance. The approach
             is capable of exploiting the efficiency with which the
             matrix elements are calculated in the collocation method by
             evaluating the matrix elements as they are required. This
             combination of techniques should allow the method to be used
             for systems which have more degrees of freedom than have
             been treated by conventional methods. © 1990 American
             Institute of Physics.},
   Key = {fds235131}
}

@article{fds235132,
   Author = {Morrison, RC and Yang, W and Parr, RG and Lee, C},
   Title = {Approximate density matrices and wigner distribution
             functions from density, kinetic energy density and
             idempotency constraints},
   Journal = {Int. J. Quantum Chem.},
   Volume = {38},
   Pages = {819},
   Year = {1990},
   Key = {fds235132}
}

@article{fds235133,
   Author = {Yang, W and Peet, AC and Miller, WH},
   Title = {A collocation approach for quantum scattering based on the
             S-matrix version of the Kohn variational
             principle},
   Journal = {Journal of Chemical Physics},
   Volume = {91},
   Number = {12},
   Pages = {7537-7542},
   Year = {1989},
   ISSN = {0021-9606},
   Abstract = {A collocation approach to quantum scattering is presented.
             The method is based on the S-matrix version of the Kohn
             variational principle with a different linear expansion used
             for the two wave functions - one is a linear combination of
             basis functions and the other is a pointwise representation
             with proper asymptotic conditions imposed. The resulting
             equations are similar in structure to the usual version of
             the Kohn variational principle, however, in the present
             approach there are no integrals between the square
             integrable (L2) basis functions. In addition, the method
             does not require the knowledge of quadrature weights
             associated with the collocation points as was the case in a
             previous pointwise method for quantum scattering. This
             property means that the method is readily applicable to
             reactive scattering problems which use different sets of
             coordinates for reactants and products. Appliction to a
             simple inelastic test problem (collinear He-H2 vibrationally
             inelastic scattering) shows the accuracy of the approach to
             be comparable to that of the usual variatinal form of the
             S-matrix Kohn method. © 1989 American Institute of
             Physics.},
   Key = {fds235133}
}

@article{fds235134,
   Author = {Yang, W and Miller, WH},
   Title = {Block Lanczos approach combined with matrix continued
             fraction for the S-matrix Kohn variational principle in
             quantum scattering},
   Journal = {Journal of Chemical Physics},
   Volume = {91},
   Number = {6},
   Pages = {3504-3508},
   Year = {1989},
   ISSN = {0021-9606},
   Abstract = {An iterative method is proposed for calculating the S matrix
             in the Kohn variational approach. Instead of solving the
             system of linear equations directly, the method consists of
             a block Lanczos algorithm extended to complex symmetric
             matrices and a matrix continued fraction procedure.
             Applications to inelastic and reactive scattering
             calculations indicate a reasonable rate of convergence. ©
             1989 American Institute of Physics.},
   Key = {fds235134}
}

@article{fds235135,
   Author = {Peet, AC and Yang, W},
   Title = {An adapted form of the collocation method for calculating
             energy levels of rotating atom-diatom complexes},
   Journal = {Journal of Chemical Physics},
   Volume = {91},
   Number = {11},
   Pages = {6598-6612},
   Year = {1989},
   ISSN = {0021-9606},
   Abstract = {A method is presented for calculating energy levels of
             atom-rigid-diatom systems for various values of the total
             angular momentum (J) of the complex. The technique is based
             upon the collocation method for the vibrational motions of
             the system and the Galerkin approach for the total rotation.
             Unlike the Rayleigh-Ritz variational principle, the method
             does not require the evaluation of integrals over the
             Hamiltonian and so is very simple to implement. An important
             feature of the method is that the wave function is obtained
             in an analytic form and so it is a simple matter to
             calculate many quantities of spectroscopic interest such as
             rotational constants and spectral intensities. It is also
             shown that contracted basis sets can be used in conjunction
             with the collocation method to enhance the efficiency of the
             calculation. The method is demonstrated by calculating
             rovibrational levels of the van der Waals complex ArHCl for
             J up to 10. © 1989 American Institute of
             Physics.},
   Key = {fds235135}
}

@article{fds235136,
   Author = {Peet, AC and Yang, W},
   Title = {The collocation method for calculating vibrational bound
             states of molecular systems - with application to
             Ar-HCl},
   Journal = {Journal of Chemical Physics},
   Volume = {90},
   Number = {3},
   Pages = {1746-1751},
   Year = {1989},
   ISSN = {0021-9606},
   Abstract = {The ability of the collocation method to calculate
             vibrational bound states of molecules is investigated. The
             technique is simpler to implement than conventional
             variational methods; no integration over the basis functions
             is involved. We apply the method to the weakly bound complex
             Ar-HCl, a real multidimensional system of considerable
             physical interest, and find the procedure to be of
             equivalent accuracy to the corresponding variational
             approach at all times. This confirms the conclusions of our
             previous studies on one-dimensional test problems [W. Yang
             and A. C. Peet, Chem. Phys. Lett. 153, 98 (1988) ]. Both low
             lying and highly excited states are examined and the
             conclusions hold even for levels very close to the
             dissociation limit. A test of the wave functions obtained
             also finds these to be of good accuracy and very similar to
             the ones given by the variational procedure. © 1989
             American Institute of Physics.},
   Key = {fds235136}
}

@article{fds24398,
   Author = {Chengteh Lee and Weitao Yang and Robert G.
             Parr},
   Title = {Local softness and chemical reactivity in the molecules co,
             scn, and h co},
   Volume = {163},
   Pages = {305},
   Year = {1988},
   Key = {fds24398}
}

@article{fds234972,
   Author = {Lee, C and Yang, W and Parr, RG},
   Title = {Local softness and chemical reactivity in the molecules CO,
             SCN- and H2CO},
   Journal = {Journal of Molecular Structure: THEOCHEM},
   Volume = {163},
   Number = {C},
   Pages = {305-313},
   Year = {1988},
   ISSN = {0166-1280},
   Abstract = {Fukui functions (softnesses) are calculated for three
             species - formaldehyde, the thiocyanate ion and carbon
             monoxide. The fukui function for a molecule has been defined
             as the derivative of electron density with respect to the
             change of number of electrons, keeping the positions of
             nuclei unchanged; this differentiation is performed by
             finite difference. Local softness and fukui function are
             proportional. The calculated results, expressed in terms of
             contour maps and condensed values of fukui functions,
             substantiate the previous argument that fukui functions
             serve as reactivity indices for chemical reactions.
             Particularly, it is confirmed that: (1) a nucleophilic
             reagent approaches the carbon atom in formaldehyde from the
             direction perpendicular to the molecular plane, while an
             electrophilic reagent approaches the oxygen atom in the
             molecular plane; (2) the sulphur end is softer than the
             nitrogen end in the thiocyanate ion; and (3) carbon monoxide
             behaves like a Lewis acid in bonding with transition metals.
             © 1988.},
   Key = {fds234972}
}

@article{fds235137,
   Author = {Yang, W and Peet, AC},
   Title = {The collocation method for bound solutions of the
             Schrödinger equation},
   Journal = {Chemical Physics Letters},
   Volume = {153},
   Number = {1},
   Pages = {98-104},
   Year = {1988},
   ISSN = {0009-2614},
   url = {http://dx.doi.org/10.1016/0009-2614(88)80139-8},
   Abstract = {The collocation method for obtaining the bound solutions of
             the Schrödinger equation is investigated. The technique
             does not require the evaluation of integrals and is very
             simple to implement. It is closely connected with other
             pointwise representations used recently, but has the
             advantage of requiring less effort to construct the
             algebraic eigenvalue equations. The method is tested on two
             Morse oscillator problems and found to give results which
             are as accurate as the conventional variational approach. In
             conjunction with a distributed Gaussian basis the
             collocation method is shown to be capable of describing
             highly excited states. © 1988.},
   Doi = {10.1016/0009-2614(88)80139-8},
   Key = {fds235137}
}

@article{fds235138,
   Author = {Yang, W},
   Title = {Dynamic linear response of many-electron systems: An
             integral formulation of density-functional
             theory},
   Journal = {Physical Review A - Atomic, Molecular, and Optical
             Physics},
   Volume = {38},
   Number = {11},
   Pages = {5512-5519},
   Year = {1988},
   ISSN = {1050-2947},
   url = {http://dx.doi.org/10.1103/PhysRevA.38.5512},
   Abstract = {A new approach for the calculation of the linear response of
             both the ground and thermal-equilibrium states of
             many-electron systems is proposed via an integral
             formulation of the density-functional theory. Based on the
             path-integral representation of the one-particle Greens
             function, the frequency-dependent linear-response function
             for the Kohn-Sham noninteracting system is expressed as an
             explicit functional of the Kohn-Sham local potential,
             instead of the summation over the single-electron orbitals.
             Thus the dynamic linear density response can be determined
             as the solution of self-consistent equations which only need
             as input the total electron density of the ground or the
             equilibrium state. Exchange and correlation effects are
             incorporated. Because orbitals are not employed, the
             formulation provides the possibility for calculations of
             linear-response properties, such as dynamic polarizability
             and photoabsorption cross sections of systems with very many
             electrons. The present formulation can also be applied to
             general fermions. © 1988 The American Physical
             Society.},
   Doi = {10.1103/PhysRevA.38.5512},
   Key = {fds235138}
}

@article{fds235139,
   Author = {Yang, W},
   Title = {Thermal properties of many-electron systems: An integral
             formulation of density-functional theory},
   Journal = {Physical Review A - Atomic, Molecular, and Optical
             Physics},
   Volume = {38},
   Number = {11},
   Pages = {5504-5511},
   Year = {1988},
   ISSN = {1050-2947},
   url = {http://dx.doi.org/10.1103/PhysRevA.38.5504},
   Abstract = {A new approach for the calculation of thermal properties of
             many-electron systems is proposed via an integral
             formulation of the Mermin-Kohn-Sham finite-temperature
             density-functional theory. The electron density of a
             thermal-equilibrium state can be determined by solving
             self-consistently equations for the electron density without
             using orbitals. Exchange and correlation effects are
             incorporated. In place of the set of the single-electron
             equations, the total electron density is explicitly
             expressed in terms of the Kohn-Sham effective local
             potential through multidimensional integrations. The
             development is based on the first-order density matrix as
             obtained from the one-body Greens function in polygonal and
             Fourier path-integral representations. The formulation can
             also be applied to general fermions. © 1988 The American
             Physical Society.},
   Doi = {10.1103/PhysRevA.38.5504},
   Key = {fds235139}
}

@article{fds235140,
   Author = {Yang, W},
   Title = {Ab initio approach for many-electron systems without
             invoking orbitals: An integral formulation of
             density-functional theory},
   Journal = {Physical Review A - Atomic, Molecular, and Optical
             Physics},
   Volume = {38},
   Number = {11},
   Pages = {5494-5503},
   Year = {1988},
   ISSN = {1050-2947},
   url = {http://dx.doi.org/10.1103/PhysRevA.38.5494},
   Abstract = {A new approach for the calculation of ground states of
             many-electron systems is proposed via an integral
             formulation of the Hohenberg-Kohn-Sham density-functional
             theory. Only equations for the total electron density are
             involved; orbitals are not employed. Exchange and
             correlation effects are incorporated. In place of the set of
             single-electron equations, the total electron density is
             explicitly expressed in terms of the Kohn-Sham effective
             local potential through multidimensional integrations. The
             development is based on the first-order density matrix as
             obtained from the one-body Greens function in polygonal and
             Fourier path-integral representations. This might open up
             the possibility of ab initio calculations for molecules with
             very many electrons. It also provides explicit solutions to
             two long-standing problems: electron kinetic energy and
             momentum density as functionals of the total electron
             density. The formulation can also be used in calculations
             for general fermions. © 1988 The American Physical
             Society.},
   Doi = {10.1103/PhysRevA.38.5494},
   Key = {fds235140}
}

@article{fds235141,
   Author = {Lee, C and Yang, W and Parr, RG},
   Title = {Development of the Colle-Salvetti correlation-energy formula
             into a functional of the electron density},
   Journal = {Physical Review B - Condensed Matter and Materials
             Physics},
   Volume = {37},
   Number = {2},
   Pages = {785-789},
   Year = {1988},
   ISSN = {0163-1829},
   url = {http://dx.doi.org/10.1103/PhysRevB.37.785},
   Abstract = {A correlation-energy formula due to Colle and Salvetti
             [Theor. Chim. Acta 37, 329 (1975)], in which the correlation
             energy density is expressed in terms of the electron density
             and a Laplacian of the second-order Hartree-Fock density
             matrix, is restated as a formula involving the density and
             local kinetic-energy density. On insertion of gradient
             expansions for the local kinetic-energy density,
             density-functional formulas for the correlation energy and
             correlation potential are then obtained. Through numerical
             calculations on a number of atoms, positive ions, and
             molecules, of both open- and closed-shell type, it is
             demonstrated that these formulas, like the original
             Colle-Salvetti formulas, give correlation energies within a
             few percent. © 1988 The American Physical
             Society.},
   Doi = {10.1103/PhysRevB.37.785},
   Key = {fds235141}
}

@article{fds235142,
   Author = {Yang, W and Parr, RG and Uytterhoeven, L},
   Title = {New relation between hardness and compressibility of
             minerals},
   Journal = {Physics and Chemistry of Minerals},
   Volume = {15},
   Number = {2},
   Pages = {191-195},
   Year = {1987},
   ISSN = {0342-1791},
   url = {http://dx.doi.org/10.1007/BF00308783},
   Abstract = {A relation between hardness (H) for minerals and
             compressibility (β) is proposed: {Mathematical expression},
             where M is the molecular weight, ρ the density and q the
             number of atoms in a formula unit. The relation is derived
             from thermodynamics and is based on an analogy between
             mineral hardness and the concept of hardness assumed for the
             classification of reactivity of molecular species. It is
             confirmed with 27 elemental solids and 66 crystalline
             compounds, that this simple relation fairly well describes
             the trend of experimental hardnesses of minerals, and that
             the new relation has advantages over one earlier proposed
             [Plendl et al. (1965)] for connecting hardness to
             compressibility. © 1987 Springer-Verlag.},
   Doi = {10.1007/BF00308783},
   Key = {fds235142}
}

@article{fds235143,
   Author = {Yang, W},
   Title = {Ab initio approach for many-electron systems without
             invoking orbitals: An integral formulation of
             density-functional theory},
   Journal = {Physical Review Letters},
   Volume = {59},
   Number = {14},
   Pages = {1569-1572},
   Year = {1987},
   ISSN = {0031-9007},
   url = {http://dx.doi.org/10.1103/PhysRevLett.59.1569},
   Abstract = {A new approach for the calculation of ground states of
             many-electron systems is developed via an integral
             formulation of the Hohenberg-Kohn-Sham density-functional
             theory. Orbitals are not employed. In place of the set of
             one-electron equations, the total electron density is
             explicitly expressed in terms of the Kohn-Sham local
             potential through a multidimensional integration. This
             offers the possibility of ab initio calculations for
             molecules with very many electrons. The method can also be
             applied to calculate Compton profiles. © 1987 The American
             Physical Society.},
   Doi = {10.1103/PhysRevLett.59.1569},
   Key = {fds235143}
}

@article{fds235144,
   Author = {Xue, W and Yang, W},
   Title = {Application of a scaled particle theory to polar solute
             system and calculation of the salt effect
             constant},
   Journal = {Acta Physica-Chimica Sinica},
   Volume = {3},
   Pages = {258},
   Year = {1987},
   Key = {fds235144}
}

@article{fds235145,
   Author = {Yang, W and Mortier, WJ},
   Title = {The use of global and local molecular parameters for the
             analysis of the gas-phase basicity of amines},
   Journal = {Journal of the American Chemical Society},
   Volume = {108},
   Number = {19},
   Pages = {5708-5711},
   Year = {1986},
   ISSN = {0002-7863},
   Abstract = {It is demonstrated that the variation of the gas-phase
             basicities of amines can be analyzed by using two
             parameters: one global and one local (that is,
             site-dependent). Two global quantities (the average
             "effective" electronegativity and the geometric average of
             the isolated-atom electronegativities) and two local
             quantities (the fukui function and the residual charges) are
             tested. A two-parameter linear model containing one global
             and one local quantity produces satisfactory correlations
             with the experimental gas-phase basicities. It is shown how
             to express the fukui function, which reflects the site
             reactivity in density functional theory (f(r⇒) =
             [∂ρ(r→)/∂N]ν(7), in terms of the variation of the
             Mulliken gross charges (qi) of an atom in a molecule, which
             is accompanied with a change in the total number of
             electrons (N) in this molecule: fi+ = qi(N + 1) - qi(N); fi-
             = qi(N) - qi(N-1) and f1° = 1/2[qi(N + 1) - qi(N - 1)]. ©
             1986 American Chemical Society.},
   Key = {fds235145}
}

@article{fds235146,
   Author = {Yang, W and Parr, RG and Lee, C},
   Title = {Various functionals for the kinetic energy density of an
             atom or molecule},
   Journal = {Physical Review A - Atomic, Molecular, and Optical
             Physics},
   Volume = {34},
   Number = {6},
   Pages = {4586-4590},
   Year = {1986},
   ISSN = {1050-2947},
   url = {http://dx.doi.org/10.1103/PhysRevA.34.4586},
   Abstract = {Various approximate density functionals for the kinetic
             energy density of atoms and molecules are analyzed. These
             include the results of a gradient expansion to first and
             second orders and a form recently derived from a new Greens
             function approximation [W. Yang, preceding paper, Phys. Rev.
             A 34, 4575 (1986)]. All the approximate functionals studied
             diverge to minus infinity at a nucleus, due to the 2 term
             that is in them, while the exact functional is positive and
             finite everywhere. Away from nuclei, however, the
             Hartree-Fock results are well reproduced, including the
             atomic shell structure. New functionals are proposed to
             correct the divergent behavior, and accurate total kinetic
             energy values are obtained from a new formula for kinetic
             energy density tMP(r)=Ck(r)5/3 +(1/72)(r)2/(r)+ (1/12)2(r),
             with a divergence correction. © 1986 The American Physical
             Society.},
   Doi = {10.1103/PhysRevA.34.4586},
   Key = {fds235146}
}

@article{fds235147,
   Author = {Yang, W},
   Title = {Gradient correction in Thomas-Fermi theory},
   Journal = {Physical Review A - Atomic, Molecular, and Optical
             Physics},
   Volume = {34},
   Number = {6},
   Pages = {4575-4585},
   Year = {1986},
   ISSN = {1050-2947},
   url = {http://dx.doi.org/10.1103/PhysRevA.34.4575},
   Abstract = {A new derivation of the Weizsacker-type gradient corrections
             to Thomas-Fermi (TF) kinetic energy functional is presented.
             The development is based on the first-order reduced density
             matrix as obtained from the one-body Greens function in the
             mean-path approximation devised for the purpose, using the
             Feynman path-integral approach; the mean-path approximation
             turns out to be essentially equivalent to the eikonal
             approximation used in quantum collision theory for
             high-energy collisions. This derivation agrees with the
             conventional gradient expansion truncated at second order,
             in that it gives the kinetic energy functional of the
             TF-(1/9)W model, that is, the sum of the original TF kinetic
             energy and (1/9) of the Weizsacker gradient correction.
             However, in the present derivation, TF-(1/9)W results from a
             reduced density matrix of closed form; the original TF local
             relation between particle, density, and one-body potential
             is preserved; and the kinetic energy density contains a
             Laplacian of particle density with a factor half of that
             from the gradient expansion. Most significantly, the
             TF-(1/9)W kinetic energy functional is the consequence of
             representing both the diagonal and off-diagonal elements of
             the density matrix correctly to zero order through the
             mean-path approximation to the one-body Greens function,
             whereas in the conventional TF approximation, the zero order
             of the gradient expansion, off-diagonal elements are not
             correct to the same order. Other results of the present
             approach include a nonlocal exchange energy functional of
             density, a one-body effective potential that contains a
             contribution from the kinetic energy functional derivative,
             and the construction of closed-form density matrices that
             give various kinetic energy functionals of TF-W form
             (justifying various existing empirical values). Also
             presented are the results of numerical calculation for
             rare-gas atoms of TFD-W models (TFD denotes
             Thomas-Fermi-Dirac) with =(1/3), 0.186, (1/6), and (1/9)..
             AE. © 1986 The American Physical Society.},
   Doi = {10.1103/PhysRevA.34.4575},
   Key = {fds235147}
}

@article{fds235148,
   Author = {Yang, W and Harriman, JE},
   Title = {Analysis of the kinetic energy functional in density
             functional theory},
   Journal = {Journal of Chemical Physics},
   Volume = {84},
   Number = {6},
   Pages = {3320-3323},
   Year = {1986},
   ISSN = {0021-9606},
   Abstract = {The density matrix that leads to a minimum kinetic energy
             for a given density is considered as a convex superposition
             of pure states. It is shown that the conditions of
             stationarity of the kinetic energy and collapse to the given
             density require that each of the pure state wave functions
             involved be a single determinant in the same eigenspace of a
             particular, n-electron Hamiltonian and that all of the
             orbitals are eigenfunctions of the same effective
             one-electron Hamiltonian. The potential function arises
             originally as a Lagrange multiplier associated with the
             density constraint. In some cases it can (at least in
             principle) be determined. The role of electron-electron
             interactions and possible treatment of excited states are
             considered. © 1986 American Institute of
             Physics.},
   Key = {fds235148}
}

@article{fds235149,
   Author = {Yang, W and Parr, RG},
   Title = {Hardness, softness, and the fukui function in the electronic
             theory of metals and catalysis.},
   Journal = {Proceedings of the National Academy of Sciences of the
             United States of America},
   Volume = {82},
   Number = {20},
   Pages = {6723-6726},
   Year = {1985},
   Abstract = {The concepts of hardness eta = (2E/N2)nu and fukui function
             f(r) = [rho (r)/N]nu, which have recently been associated
             with the theory of chemical reactivity in molecules, are
             extended to the theory of metals. It is shown that at T = 0,
             1/eta = g(epsilon F) and f(r) = g(epsilon F, r)/g(epsilon
             F), where g(epsilon F), and g(epsilon F, r) are the density
             of states and the local density of states, at the Fermi
             energy epsilon F. Softness S and local softness s(r) are
             defined as 1/eta and Sf(r), respectively, and it is shown
             that (formula; see text) where the averages are over a grand
             canonical ensemble. It is pointed out that the postulate
             that f(r) or g(epsilon F, r) determines site selectivity for
             metals in chemisorption and catalysis is synonymous with the
             recent argument by Falicov and Somorjai [Falicov, L. M.
             &amp; Somorjai, G. A. (1985) Proc. Natl. Acad. Sci. USA 82,
             2207-2211] that such selectivity is determined by low-energy
             density fluctuations.},
   Key = {fds235149}
}

@article{fds235150,
   Author = {Yang, W and Lee, C and Ghosh, SK},
   Title = {Molecular softness as the average of atomic softnesses:
             Companion principle to the geometric mean principle for
             electronegativity equalization},
   Journal = {Journal of Physical Chemistry},
   Volume = {89},
   Number = {25},
   Pages = {5412-5414},
   Year = {1985},
   ISSN = {0022-3654},
   Abstract = {It is demonstrated that, for a molecule consisting of M
             atoms, the relation, 1/(I - A) = (1/M)ΣiM[1/(Ii - Ai)], is
             valid to a reasonable approximation, where I and A are the
             ionization potential and electron affinity of the molecule
             and Ii, Ai denote the same quantities for the ith atom. This
             relation is the arithmetic average principle for molecular
             softness where the softness, S, is defined [W. Yang and R.
             G. Parr, Proc. Natl. Acad. Sci. U.S.A., 82, 6723 (1985)] as
             the inverse of the hardness (η) i.e. S = 1/η = 1/(I - A).
             The calculated values of I - A for 33 molecules show
             agreement with experimental results. The conditions for the
             validity of this principle are shown to be analogous to
             those for the geometric mean principle for electronegativity
             equalization in molecules. © 1985 American Chemical
             Society.},
   Key = {fds235150}
}

@article{fds235151,
   Author = {Levy, M and Yang, W and Parr, RG},
   Title = {A new functional with homogeneous coordinate scaling in
             density functional theory: F[ρ, λ]},
   Journal = {Journal of Chemical Physics},
   Volume = {83},
   Number = {5},
   Pages = {2334-2336},
   Year = {1985},
   ISSN = {0021-9606},
   Abstract = {As previously shown [M. Levy and J. P. Perdew, Phys. Rev. A
             (in press)], the customary Hohenberg-Kohn density
             functional, based on the universal functional F[ρ], does
             not exhibit naively expected scaling properties. Namely, if
             ρλ = λ3ρ(λr) is the scaled density corresponding to
             ρ(r), the expected scaling, not satisfied, is T[ρλ ] =
             λ2T[ρ] and V[ρλ] = λV[ρ], where T and V are the
             kinetic and potential energy components. By defining a new
             functional of ρ and λ, F[ρ, λ], it is now shown how the
             naive scaling can be preserved. The definition isF[ρ(r),λ]
             = 〈λ 3N/2Φρλmin(λr 1⋯λrN)|T̂(r1⋯r N) +
             Vee(r1⋯rN) λ3N/2Φρλmin(λ r1⋯λrN)〉,where λ3N/2
             Ωρλmin(λr 1⋯λrN) is that antisymmetric function Ω
             which yields ρλ(r) = λ3ρ(λr) and simultaneously
             minimizes 〈Ω|T̂(r1⋯r N) + λVee(r1⋯r N)|Ω〉. The
             corresponding variational principle is E G.S.v = Infλ,ρ(r)
             {∫drv(r)ρλ(r) + λ2T[ρ(r)] + λV ee[ρ(r)]}, where
             EG.S.v is the ground-state energy for potential v(r). One is
             thus allowed to lower the energy and satisfy the virial
             theorem by optimum scaling just as if the naive scaling
             relations were correct for F[ρ]. © 1985 American Institute
             of Physics.},
   Key = {fds235151}
}

@article{fds235152,
   Author = {Yang, W and Parr, RG and Pucci, R},
   Title = {Electron density, Kohn-Sham frontier orbitals, and Fukui
             functions},
   Journal = {Journal of Chemical Physics},
   Volume = {81},
   Number = {6},
   Pages = {2862-2863},
   Year = {1984},
   ISSN = {0021-9606},
   Key = {fds235152}
}

@article{fds235153,
   Author = {Parr, RG and Yang, W},
   Title = {Density functional approach to the frontier-electron theory
             of chemical reactivity},
   Journal = {Journal of the American Chemical Society},
   Volume = {106},
   Number = {14},
   Pages = {4049-4050},
   Year = {1984},
   ISSN = {0002-7863},
   Key = {fds235153}
}


%% Chapter in Book   
@misc{fds169962,
   Author = {G. A. CISNEROS and W. T. YANG},
   Title = {Comparison of reaction barriers in energy and free energy
             for enzyme catalysis},
   Pages = {57-78},
   Booktitle = {Multi-scale Quantum Models for Biocatalysis},
   Publisher = {London: Springer-Verlag},
   Editor = {D. York and T.-S. Lee},
   Year = {2009},
   Key = {fds169962}
}

@misc{fds24471,
   Author = {Paul W. Ayers and Weitao Yang},
   Title = {Density-functional theory},
   Booktitle = {Computational Medicinal Chemistry and Drug
             Discovery},
   Editor = {Wilfried Langenaeker},
   Year = {2003},
   Key = {fds24471}
}

@misc{fds24466,
   Author = {Yingkai Zhang and Haiyan Liu and Weitao Yang},
   Title = {Ab initio qm/mm and free energy calculations of enzyme
             reactions},
   Series = {Springer Verlag's Lecture Notes Series in Computational
             Science and Engineering},
   Pages = {332=354},
   Booktitle = {Computational Methods for Macromolecules-Challenges and
             Applications},
   Publisher = {Springer, New York},
   Editor = {T. Schlick and H.H. Gan},
   Year = {2002},
   Key = {fds24466}
}

@misc{fds24468,
   Author = {Zhenyu Lu and Haiyan Liu and Marcus Elstner and Weitao
             Yang},
   Title = {Parameterization of cosmo solvent model for self-consistent
             charge density-functional based tight-binding
             calculations},
   Pages = {1606-1614},
   Booktitle = {Reviews in Modern Quantum Chemistry: A Celebration Of The
             Contributions of R.G. PARR},
   Publisher = {World Scientific, Singapore},
   Editor = {K.D. Sen},
   Year = {2002},
   Key = {fds24468}
}

@misc{fds24453,
   Author = {Weitao Yang and José M. Pérez-Jordá},
   Title = {Linear scaling methods for electronic structure
             calculations},
   Pages = {1496-1513},
   Booktitle = {Encyclopedia of Computational Chemistry},
   Publisher = {John Wiley & Sons},
   Editor = {P.v.R. Schleyer},
   Year = {1998},
   Key = {fds24453}
}

@misc{fds24424,
   Author = {Weitao Yang and Zhongxiang Zhou},
   Title = {Electronic structure of solid-state systems via the
             divide-and-conquer method},
   Pages = {177-188},
   Booktitle = {Electronic Functional Theory of Molecules, Clusters, and
             Solids},
   Publisher = {Kluwer Academic Publishers, Dordrecht},
   Editor = {D.E. Ellis},
   Year = {1994},
   Key = {fds24424}
}

@misc{fds24420,
   Author = {Weitao Yang},
   Title = {Density-functional theory of large systems: a
             divide-and-conquer approach},
   Volume = {8},
   Pages = {367-372},
   Booktitle = {Condensed-Matter Theories},
   Publisher = {Plenum Press, Berlin},
   Editor = {L. Blum and F.B. Malik},
   Year = {1993},
   Key = {fds24420}
}

@misc{fds24397,
   Author = {Weitao Yang},
   Title = {Some remarks on scaling relations in density-functional
             theory},
   Pages = {499-506},
   Booktitle = {Density Matrices and Density-Functionals},
   Publisher = {D. Reidel Publishing Company, Dordrecht,
             Holland},
   Editor = {R. Erdahl and Jr. V. H. Smith},
   Year = {1987},
   Key = {fds24397}
}