%% 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 Ru^{2+}-Ru^{3+}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 & 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 & 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 & 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 > MQ > 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 & 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 & 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 >> M-P > M-As >> M-Br (M = In, Ga, Al), and Al-Y > Ga-Y > 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-C_{2}H_{2}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. &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 H_{2}CO}, 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. & 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} }