Publications of David N. Beratan    :chronological  alphabetical  by type listing:

%%    
@article{fds329887,
   Author = {Polizzi, NF and Wu, Y and Lemmin, T and Maxwell, AM and Zhang, S-Q and Rawson, J and Beratan, DN and Therien, MJ and DeGrado,
             WF},
   Title = {De novo design of a hyperstable non-natural protein-ligand
             complex with sub-Å accuracy.},
   Journal = {Nature Chemistry},
   Volume = {9},
   Number = {12},
   Pages = {1157-1164},
   Year = {2017},
   Month = {December},
   url = {http://dx.doi.org/10.1038/nchem.2846},
   Abstract = {Protein catalysis requires the atomic-level orchestration of
             side chains, substrates and cofactors, and yet the ability
             to design a small-molecule-binding protein entirely from
             first principles with a precisely predetermined structure
             has not been demonstrated. Here we report the design of a
             novel protein, PS1, that binds a highly electron-deficient
             non-natural porphyrin at temperatures up to 100 °C. The
             high-resolution structure of holo-PS1 is in sub-Å agreement
             with the design. The structure of apo-PS1 retains the remote
             core packing of the holoprotein, with a flexible binding
             region that is predisposed to ligand binding with the
             desired geometry. Our results illustrate the unification of
             core packing and binding-site definition as a central
             principle of ligand-binding protein design.},
   Doi = {10.1038/nchem.2846},
   Key = {fds329887}
}

@article{fds328791,
   Author = {Zhang, P and Yuly, JL and Lubner, CE and Mulder, DW and King, PW and Peters, JW and Beratan, DN},
   Title = {Electron Bifurcation: Thermodynamics and Kinetics of
             Two-Electron Brokering in Biological Redox
             Chemistry.},
   Journal = {Accounts of Chemical Research},
   Volume = {50},
   Number = {9},
   Pages = {2410-2417},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.1021/acs.accounts.7b00327},
   Abstract = {How can proteins drive two electrons from a redox active
             donor onto two acceptors at very different potentials and
             distances? And how can this transaction be conducted without
             dissipating very much energy or violating the laws of
             thermodynamics? Nature appears to have addressed these
             challenges by coupling thermodynamically uphill and downhill
             electron transfer reactions, using two-electron donor
             cofactors that have very different potentials for the
             removal of the first and second electron. Although electron
             bifurcation is carried out with near perfection from the
             standpoint of energy conservation and electron delivery
             yields, it is a biological energy transduction paradigm that
             has only come into focus recently. This Account provides an
             exegesis of the biophysical principles that underpin
             electron bifurcation. Remarkably, bifurcating electron
             transfer (ET) proteins typically send one electron uphill
             and one electron downhill by similar energies, such that the
             overall reaction is spontaneous, but not profligate.
             Electron bifurcation in the NADH-dependent reduced
             ferredoxin: NADP+ oxidoreductase I (Nfn) is explored in
             detail here. Recent experimental progress in understanding
             the structure and function of Nfn allows us to dissect its
             workings in the framework of modern ET theory. The first
             electron that leaves the two-electron donor flavin (L-FAD)
             executes a positive free energy "uphill" reaction, and the
             departure of this electron switches on a second
             thermodynamically spontaneous ET reaction from the flavin
             along a second pathway that moves electrons in the opposite
             direction and at a very different potential. The singly
             reduced ET products formed from the bifurcating flavin are
             more than two nanometers distant from each other. In Nfn,
             the second electron to leave the flavin is much more
             reducing than the first: the potentials are said to be
             "crossed." The eventually reduced cofactors, NADH and
             ferredoxin in the case of Nfn, perform crucial downstream
             redox processes of their own. We dissect the thermodynamics
             and kinetics of electron bifurcation in Nfn and find that
             the key features of electron bifurcation are (1) spatially
             separated transfer pathways that diverge from a two-electron
             donor, (2) one thermodynamically uphill and one downhill
             redox pathway, with a large negative shift in the donor's
             reduction potential after departure of the first electron,
             and (3) electron tunneling and activation factors that
             enable bifurcation, producing a 1:1 partitioning of
             electrons onto the two pathways. Electron bifurcation is
             found in the CO2 reducing pathways of methanogenic archaea,
             in the hydrogen pathways of hydrogenases, in the nitrogen
             fixing pathway of Fix, and in the mitochondrial charge
             transfer chain of complex III, cytochrome bc1. While crossed
             potentials may offer the biological advantage of producing
             tightly regulated high energy reactive species, neither
             kinetic nor thermodynamic considerations mandate crossed
             potentials to generate successful electron bifurcation.
             Taken together, the theoretical framework established here,
             focusing on the underpinning electron tunneling barriers and
             activation free energies, explains the logic of electron
             bifurcation that enables energy conversion and conservation
             in Nfn, points toward bioinspired schemes to execute
             multielectron redox chemistry, and establishes a roadmap for
             examining novel electron bifurcation networks in
             nature.},
   Doi = {10.1021/acs.accounts.7b00327},
   Key = {fds328791}
}

@article{fds328571,
   Author = {Bai, Y and Rawson, J and Roget, SA and Olivier, J-H and Lin, J and Zhang,
             P and Beratan, DN and Therien, MJ},
   Title = {Controlling the excited-state dynamics of low band gap,
             near-infrared absorbers via proquinoidal unit electronic
             structural modulation.},
   Journal = {Chemical Science},
   Volume = {8},
   Number = {9},
   Pages = {5889-5901},
   Year = {2017},
   Month = {September},
   url = {http://dx.doi.org/10.1039/c7sc02150j},
   Abstract = {While the influence of proquinoidal character upon the
             linear absorption spectrum of low optical bandgap
             π-conjugated polymers and molecules is well understood, its
             impact upon excited-state relaxation pathways and dynamics
             remains obscure. We report the syntheses, electronic
             structural properties, and excited-state dynamics of a
             series of model highly conjugated near-infrared
             (NIR)-absorbing chromophores based on a (porphinato)metal(ii)-proquinoidal
             spacer-(porphinato)metal(ii) (PM-Sp-PM) structural motif. A
             combination of excited-state dynamical studies and
             time-dependent density functional theory calculations: (i)
             points to the cardinal role that excited-state configuration
             interaction (CI) plays in determining the magnitudes of S1
             → S0 radiative (kr), S1 → T1 intersystem crossing
             (kISC), and S1 → S0 internal conversion (kIC) rate
             constants in these PM-Sp-PM chromophores, and (ii) suggests
             that a primary determinant of CI magnitude derives from the
             energetic alignment of the PM and Sp fragment LUMOs (ΔEL).
             These insights not only enable steering of excited-state
             relaxation dynamics of high oscillator strength NIR
             absorbers to realize either substantial fluorescence or
             long-lived triplets (τT1 > μs) generated at unit quantum
             yield (ΦISC = 100%), but also crafting of those having
             counter-intuitive properties: for example, while
             (porphinato)platinum compounds are well known to generate
             non-emissive triplet states (ΦISC = 100%) upon optical
             excitation at ambient temperature, diminishing the extent of
             excited-state CI in these systems realizes long-wavelength
             absorbing heavy-metal fluorophores. This work highlights
             approaches to: (i) modulate low-lying singlet excited-state
             lifetime over the picosecond-to-nanosecond time domain, (ii)
             achieve NIR fluorescence with quantum yields up to 25%,
             (iii) tune the magnitude of S1-T1 ISC rate constant from 109
             to 1012 s-1 and (iv) realize T1-state lifetimes that range
             from ∼0.1 to several μs, for these model PM-Sp-PM
             chromophores, and renders new insights to evolve bespoke
             photophysical properties for low optical bandgap
             π-conjugated polymers and molecules based on proquinoidal
             conjugation motifs.},
   Doi = {10.1039/c7sc02150j},
   Key = {fds328571}
}

@article{fds327360,
   Author = {Liu, R and Bloom, BP and Waldeck, DH and Zhang, P and Beratan,
             DN},
   Title = {Controlling the Electron-Transfer Kinetics of Quantum-Dot
             Assemblies},
   Journal = {The Journal of Physical Chemistry C},
   Volume = {121},
   Number = {27},
   Pages = {14401-14412},
   Year = {2017},
   Month = {July},
   url = {http://dx.doi.org/10.1021/acs.jpcc.7b02261},
   Doi = {10.1021/acs.jpcc.7b02261},
   Key = {fds327360}
}

@article{fds327163,
   Author = {Bloom, BP and Graff, BM and Ghosh, S and Beratan, DN and Waldeck,
             DH},
   Title = {Chirality Control of Electron Transfer in Quantum Dot
             Assemblies.},
   Journal = {Journal of the American Chemical Society},
   Volume = {139},
   Number = {26},
   Pages = {9038-9043},
   Year = {2017},
   Month = {July},
   url = {http://dx.doi.org/10.1021/jacs.7b04639},
   Abstract = {Electron spin and molecular chirality are emerging as
             factors that can be used effectively to direct charge flow
             at the molecular scale. We report order of magnitude effects
             of molecular chirality on electron-transfer rates between
             quantum dots (QDs) in chiral QD assemblies. Indeed, both the
             circular polarization of the light that excites the electron
             donor and the imprinted chirality of the acceptor QDs affect
             the dot-to-dot electron-transfer kinetics. We define a
             polarization for the electron-transfer rate constant and
             show that it correlates with the strength of the acceptor QD
             circular dichroism (CD) spectrum. These findings imply that
             the CD strength of the QD exciton transition(s) may be used
             as a predictor for the spin-dependent electron transfer,
             indicating that chiral imprinting of the dots may lie at the
             origin of this phenomenon.},
   Doi = {10.1021/jacs.7b04639},
   Key = {fds327163}
}

@article{fds326592,
   Author = {Beall, E and Ulku, S and Liu, C and Wierzbinski, E and Zhang, Y and Bae, Y and Zhang, P and Achim, C and Beratan, DN and Waldeck,
             DH},
   Title = {Effects of the Backbone and Chemical Linker on the Molecular
             Conductance of Nucleic Acid Duplexes.},
   Journal = {Journal of the American Chemical Society},
   Volume = {139},
   Number = {19},
   Pages = {6726-6735},
   Year = {2017},
   Month = {May},
   url = {http://dx.doi.org/10.1021/jacs.7b02260},
   Abstract = {Scanning tunneling microscope break junction measurements
             are used to examine how the molecular conductance of nucleic
             acids depends on the composition of their backbone and the
             linker group to the electrodes. Molecular conductances of 10
             base pair long homoduplexes of DNA, aeg-PNA, γ-PNA, and a
             heteroduplex of DNA/aeg-PNA with identical nucleobase
             sequence were measured. The molecular conductance was found
             to vary by 12 to 13 times with the change in backbone.
             Computational studies show that the molecular conductance
             differences between nucleic acids of different backbones
             correlate with differences in backbone structural
             flexibility. The molecular conductance was also measured for
             duplexes connected to the electrode through two different
             linkers, one directly to the backbone and one directly to
             the nucleobase stack. While the linker causes an
             order-of-magnitude increase in the overall conductance for a
             particular duplex, the differences in the electrical
             conductance with backbone composition are preserved. The
             highest molecular conductance value, 0.06G0, was measured
             for aeg-PNA duplexes with a base stack linker. These
             findings reveal an important new strategy for creating
             longer and more complex electroactive, nucleic acid
             assemblies.},
   Doi = {10.1021/jacs.7b02260},
   Key = {fds326592}
}

@article{fds326931,
   Author = {Nayak, A and Park, J and De Mey and K and Hu, X and Duncan, TV and Beratan,
             DN and Clays, K and Therien, MJ},
   Title = {Large Hyperpolarizabilities at Telecommunication-Relevant
             Wavelengths in Donor-Acceptor-Donor Nonlinear Optical
             Chromophores.},
   Journal = {ACS Central Science},
   Volume = {2},
   Number = {12},
   Pages = {954-966},
   Year = {2016},
   Month = {December},
   url = {http://dx.doi.org/10.1021/acscentsci.6b00291},
   Abstract = {Octopolar D2-symmetric chromophores, based on the MPZnM
             supermolecular motif in which (porphinato)zinc(II) (PZn) and
             ruthenium(II) polypyridyl (M) structural units are connected
             via ethyne linkages, were synthesized. These structures take
             advantage of electron-rich meso-arylporphyrin or
             electron-poor meso-(perfluoroalkyl)porphyrin macrocycles,
             unsubstituted terpyridyl and 4'-pyrrolidinyl-2,2';6',2″-terpyridyl
             ligands, and modulation of metal(II) polypyridyl-to-(porphinato)zinc
             connectivity, to probe how electronic and geometric factors
             impact the measured hyperpolarizability. Transient
             absorption spectra obtained at early time delays (tdelay <
             400 fs) demonstrate fast excited-state relaxation, and
             formation of a highly polarized T1 excited state; the T1
             states of these chromophores display expansive, intense T1
             → T n absorption manifolds that dominate the 800-1200 nm
             region of the NIR, long (μs) triplet-state lifetimes, and
             unusually large NIR excited absorptive extinction
             coefficients [ε(T1 → T n ) ∼ 105 M-1 cm-1]. Dynamic
             hyperpolarizability (βλ) values were determined from
             hyper-Rayleigh light scattering (HRS) measurements, carried
             out at multiple incident irradiation wavelengths spanning
             the 800-1500 nm spectral domain. The measured βHRS value
             (4600 ± 1200 × 10-30 esu) for one of these complexes,
             RuPZnRu, is the largest yet reported for any chromophore at
             a 1500 nm irradiation wavelength, highlighting that
             appropriate engineering of strong electronic coupling
             between multiple charge-transfer oscillators provides a
             critical design strategy to realize octopolar NLO
             chromophores exhibiting large βHRS values at
             telecom-relevant wavelengths. Generalized Thomas-Kuhn sum
             (TKS) rules were utilized to compute the effective
             excited-state-to-excited-state transition dipole moments
             from experimental linear-absorption spectra; these data were
             then utilized to compute hyperpolarizabilities as a function
             of frequency, that include two- and three-state
             contributions for both β zzz and β xzx tensor components
             to the RuPZnRu hyperpolarizability spectrum. This analysis
             predicts that the β zzz and β xzx tensor contributions to
             the RuPZnRu hyperpolarizability spectrum maximize near 1550
             nm, in agreement with experimental data. The TKS analysis
             suggests that relative to analogous dipolar chromophores,
             octopolar supermolecules will be likely characterized by
             more intricate dependences of the measured
             hyperpolarizability upon irradiation wavelength due to the
             interactions among multiple different β tensor
             components.},
   Doi = {10.1021/acscentsci.6b00291},
   Key = {fds326931}
}

@article{fds318053,
   Author = {Polizzi, NF and Therien, MJ and Beratan, DN},
   Title = {Mean First-Passage Times in Biology.},
   Journal = {Israel Journal of Chemistry},
   Volume = {56},
   Number = {9-10},
   Pages = {816-824},
   Year = {2016},
   Month = {November},
   url = {http://dx.doi.org/10.1002/ijch.201600040},
   Abstract = {Many biochemical processes, such as charge hopping or
             protein folding, can be described by an average timescale to
             reach a final state, starting from an initial state. Here,
             we provide a pedagogical treatment of the mean first-passage
             time (MFPT) of a physical process, which depends on the
             number of intervening states between the initial state and
             the target state. Our aim in this tutorial review is to
             provide a clear development of the mean first-passage time
             formalism and to show some of its practical utility. The
             MFPT treatment can provide a useful link between microscopic
             rates and the average timescales often probed by
             experiment.},
   Doi = {10.1002/ijch.201600040},
   Key = {fds318053}
}

@article{fds318052,
   Author = {Beratan, DN and Waldeck, DH},
   Title = {DNA charge transfer: Hot holes break the speed
             limit.},
   Journal = {Nature Chemistry},
   Volume = {8},
   Number = {11},
   Pages = {992-993},
   Year = {2016},
   Month = {October},
   url = {http://dx.doi.org/10.1038/nchem.2655},
   Doi = {10.1038/nchem.2655},
   Key = {fds318052}
}

@article{fds318054,
   Author = {Liu, C and Xiang, L and Zhang, Y and Zhang, P and Beratan, DN and Li, Y and Tao, N},
   Title = {Engineering nanometre-scale coherence in soft
             matter.},
   Journal = {Nature Chemistry},
   Volume = {8},
   Number = {10},
   Pages = {941-945},
   Year = {2016},
   Month = {October},
   url = {http://dx.doi.org/10.1038/nchem.2545},
   Abstract = {Electronic delocalization in redox-active polymers may be
             disrupted by the heterogeneity of the environment that
             surrounds each monomer. When the differences in monomer
             redox-potential induced by the environment are small (as
             compared with the monomer-monomer electronic interactions),
             delocalization persists. Here we show that guanine (G) runs
             in double-stranded DNA support delocalization over 4-5
             guanine bases. The weak interaction between delocalized G
             blocks on opposite DNA strands is known to support partially
             coherent long-range charge transport. The
             molecular-resolution model developed here finds that the
             coherence among these G blocks follows an even-odd
             orbital-symmetry rule and predicts that weakening the
             interaction between G blocks exaggerates the resistance
             oscillations. These findings indicate how sequence can be
             exploited to change the balance between coherent and
             incoherent transport. The predictions are tested and
             confirmed using break-junction experiments. Thus, tailored
             orbital symmetry and structural fluctuations may be used to
             produce coherent transport with a length scale of multiple
             nanometres in soft-matter assemblies, a length scale
             comparable to that of small proteins.},
   Doi = {10.1038/nchem.2545},
   Key = {fds318054}
}

@article{fds314839,
   Author = {Zhang, Y and Zhang, WB and Liu, C and Zhang, P and Balaeff, A and Beratan,
             DN},
   Title = {DNA charge transport: Moving beyond 1D},
   Journal = {Surface Science},
   Volume = {652},
   Pages = {33-38},
   Year = {2016},
   Month = {October},
   ISSN = {0039-6028},
   url = {http://dx.doi.org/10.1016/j.susc.2016.03.011},
   Doi = {10.1016/j.susc.2016.03.011},
   Key = {fds314839}
}

@article{fds315336,
   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 = {fds315336}
}

@article{fds315911,
   Author = {Liu, C and Beratan, DN and Zhang, P},
   Title = {Coarse-Grained Theory of Biological Charge Transfer with
             Spatially and Temporally Correlated Noise.},
   Journal = {The Journal of Physical Chemistry Part B: Condensed Matter,
             Materials, Surfaces, Interfaces and Biophysical},
   Volume = {120},
   Number = {15},
   Pages = {3624-3633},
   Year = {2016},
   Month = {April},
   ISSN = {1520-6106},
   url = {http://dx.doi.org/10.1021/acs.jpcb.6b01018},
   Abstract = {System-environment interactions are essential in determining
             charge-transfer (CT) rates and mechanisms. We developed a
             computationally accessible method, suitable to simulate CT
             in flexible molecules (i.e., DNA) with hundreds of sites,
             where the system-environment interactions are explicitly
             treated with numerical noise modeling of time-dependent site
             energies and couplings. The properties of the noise are
             tunable, providing us a flexible tool to investigate the
             detailed effects of correlated thermal fluctuations on CT
             mechanisms. The noise is parametrizable by molecular
             simulation and quantum calculation results of specific
             molecular systems, giving us better molecular resolution in
             simulating the system-environment interactions than sampling
             fluctuations from generic spectral density functions. The
             spatially correlated thermal fluctuations among different
             sites are naturally built-in in our method but are not
             readily incorporated using approximate spectral densities.
             Our method has quantitative accuracy in systems with small
             redox potential differences (<kbT) and provides qualitative
             insights into systems with wide redox potential differences
             (≫kbT). Specifically, we find that the temporal
             correlations of site energies are critical in determining
             the coherent-incoherent transition, while the role of
             spatial correlations depends on the nature of the systems.
             In a system with repeated bridge units of the same
             chemistry, spatially correlated fluctuations enhance the
             charge delocalization and charge-transfer rates; however, in
             a system of units with different site energies, spatial
             correlations slow the fluctuations to bring units into
             degeneracy, in turn, slowing the charge-transfer rates. The
             spatial and temporal correlations of condensed phase medium
             fluctuations provide another source to control and tune the
             kinetics and dynamics of charge-transfer
             systems.},
   Doi = {10.1021/acs.jpcb.6b01018},
   Key = {fds315911}
}

@article{fds314840,
   Author = {Zheng, L and Polizzi, NF and Dave, AR and Migliore, A and Beratan,
             DN},
   Title = {Where Is the Electronic Oscillator Strength? Mapping
             Oscillator Strength across Molecular Absorption
             Spectra.},
   Journal = {The Journal of Physical Chemistry Part A: Molecules,
             Spectroscopy, Kinetics, Environment and General
             Theory},
   Volume = {120},
   Number = {11},
   Pages = {1933-1943},
   Year = {2016},
   Month = {March},
   ISSN = {1089-5639},
   url = {http://dx.doi.org/10.1021/acs.jpca.6b00692},
   Abstract = {The effectiveness of solar energy capture and conversion
             materials derives from their ability to absorb light and to
             transform the excitation energy into energy stored in free
             carriers or chemical bonds. The Thomas-Reiche-Kuhn (TRK) sum
             rule mandates that the integrated (electronic) oscillator
             strength of an absorber equals the total number of electrons
             in the structure. Typical molecular chromophores place only
             about 1% of their oscillator strength in the UV-vis window,
             so individual chromophores operate at about 1% of their
             theoretical limit. We explore the distribution of oscillator
             strength as a function of excitation energy to understand
             this circumstance. To this aim, we use familiar
             independent-electron model Hamiltonians as well as
             first-principles electronic structure methods. While model
             Hamiltonians capture the qualitative electronic spectra
             associated with π electron chromophores, these Hamiltonians
             mistakenly focus the oscillator strength in the fewest
             low-energy transitions. Advanced electronic structure
             methods, in contrast, spread the oscillator strength over a
             very wide excitation energy range, including transitions to
             Rydberg and continuum states, consistent with experiment.
             Our analysis rationalizes the low oscillator strength in the
             UV-vis spectral region in molecules, a step toward the goal
             of oscillator strength manipulation and focusing.},
   Doi = {10.1021/acs.jpca.6b00692},
   Key = {fds314840}
}

@article{fds313542,
   Author = {Polizzi, NF and Eibling, MJ and Perez-Aguilar, JM and Rawson, J and Lanci, CJ and Fry, HC and Beratan, DN and Saven, JG and Therien,
             MJ},
   Title = {Photoinduced Electron Transfer Elicits a Change in the
             Static Dielectric Constant of a de Novo Designed
             Protein.},
   Journal = {Journal of the American Chemical Society},
   Volume = {138},
   Number = {7},
   Pages = {2130-2133},
   Year = {2016},
   Month = {February},
   ISSN = {0002-7863},
   url = {http://dx.doi.org/10.1021/jacs.5b13180},
   Abstract = {We provide a direct measure of the change in effective
             dielectric constant (ε(S)) within a protein matrix after a
             photoinduced electron transfer (ET) reaction. A linked
             donor-bridge-acceptor molecule, PZn-Ph-NDI, consisting of a
             (porphinato)Zn donor (PZn), a phenyl bridge (Ph), and a
             naphthalene diimide acceptor (NDI), is shown to be a "meter"
             to indicate protein dielectric environment. We calibrated
             PZn-Ph-NDI ET dynamics as a function of solvent dielectric,
             and computationally de novo designed a protein SCPZnI3 to
             bind PZn-Ph-NDI in its interior. Mapping the protein ET
             dynamics onto the calibrated ET catalogue shows that SCPZnI3
             undergoes a switch in the effective dielectric constant
             following photoinduced ET, from ε(S) ≈ 8 to ε(S) ≈
             3.},
   Doi = {10.1021/jacs.5b13180},
   Key = {fds313542}
}

@article{fds316543,
   Author = {Yue, Y and Grusenmeyer, T and Ma, Z and Zhang, P and Schmehl, RH and Beratan, DN and Rubtsov, IV},
   Title = {Correction to Full Electron Ligand-to-Ligand Charge Transfer
             in a Compact Rhenium(I) Complex.},
   Journal = {The Journal of Physical Chemistry Part A: Molecules,
             Spectroscopy, Kinetics, Environment and General
             Theory},
   Volume = {120},
   Number = {3},
   Pages = {473},
   Year = {2016},
   Month = {January},
   ISSN = {1089-5639},
   url = {http://dx.doi.org/10.1021/acs.jpca.6b00093},
   Doi = {10.1021/acs.jpca.6b00093},
   Key = {fds316543}
}

@article{fds316544,
   Author = {Yue, Y and Grusenmeyer, T and Ma, Z and Zhang, P and Pham, TT and Mague,
             JT and Donahue, JP and Schmehl, RH and Beratan, DN and Rubtsov,
             IV},
   Title = {Correction to "Evaluating the Extent of Intramolecular
             Charge Transfer in the Excited States of Rhenium(I)
             Donor-Acceptor Complexes with Time-Resolved Vibrational
             Spectroscopy".},
   Journal = {The Journal of Physical Chemistry Part B: Condensed Matter,
             Materials, Surfaces, Interfaces and Biophysical},
   Volume = {120},
   Number = {3},
   Pages = {596},
   Year = {2016},
   Month = {January},
   ISSN = {1520-6106},
   url = {http://dx.doi.org/10.1021/acs.jpcb.5b12238},
   Doi = {10.1021/acs.jpcb.5b12238},
   Key = {fds316544}
}

@article{fds313541,
   Author = {Yue, Y and Grusenmeyer, T and Ma, Z and Zhang, P and Schmehl, RH and Beratan, DN and Rubtsov, IV},
   Title = {Correction: Electron transfer rate modulation in a compact
             Re(i) donor-acceptor complex.},
   Journal = {Dalton Transactions},
   Volume = {45},
   Number = {2},
   Pages = {842},
   Year = {2016},
   Month = {January},
   ISSN = {1477-9226},
   url = {http://dx.doi.org/10.1039/c5dt90221e},
   Abstract = {Correction for 'Electron transfer rate modulation in a
             compact Re(i) donor-acceptor complex' by Yuankai Yue et al.,
             Dalton Trans., 2015, 44, 8609-8616.},
   Doi = {10.1039/c5dt90221e},
   Key = {fds313541}
}

@article{fds323625,
   Author = {Polizzi, NF and Beratan, DN},
   Title = {Open-Access, Interactive Explorations for Teaching and
             Learning Quantum Dynamics},
   Journal = {Journal of Chemical Education},
   Volume = {92},
   Number = {12},
   Pages = {2161-2164},
   Year = {2015},
   Month = {December},
   url = {http://dx.doi.org/10.1021/acs.jchemed.5b00662},
   Doi = {10.1021/acs.jchemed.5b00662},
   Key = {fds323625}
}

@article{fds231847,
   Author = {Antoniou, P and Ma, Z and Zhang, P and Beratan, DN and Skourtis,
             SS},
   Title = {Vibrational control of electron-transfer reactions: a
             feasibility study for the fast coherent transfer
             regime.},
   Journal = {Physical Chemistry Chemical Physics},
   Volume = {17},
   Number = {46},
   Pages = {30854-30866},
   Year = {2015},
   Month = {December},
   ISSN = {1463-9076},
   url = {http://dx.doi.org/10.1039/c5cp00610d},
   Abstract = {Molecular vibrations and electron-vibrational interactions
             are central to the control of biomolecular electron and
             energy-transfer rates. The vibrational control of molecular
             electron-transfer reactions by infrared pulses may enable
             the precise probing of electronic-vibrational interactions
             and of their roles in determining electron-transfer
             mechanisms. This type of electron-transfer rate control is
             advantageous because it does not alter the electronic state
             of the molecular electron-transfer system or irreversibly
             change its molecular structure. For bridge-mediated
             electron-transfer reactions, infrared (vibrational)
             excitation of the bridge linking the electron donor to the
             electron acceptor was suggested as being capable of
             influencing the electron-transfer rate by modulating the
             bridge-mediated donor-to-acceptor electronic coupling. This
             kind of electron-transfer experiment has been realized,
             demonstrating that bridge-mediated electron-transfer rates
             can be changed by exciting vibrational modes of the bridge.
             Here, we use simple models and ab initio computations to
             explore the physical constraints on one's ability to
             vibrationally perturb electron-transfer rates using infrared
             excitation. These constraints stem from the nature of
             molecular vibrational spectra, the strengths of the
             electron-vibrational coupling, and the interaction between
             molecular vibrations and infrared radiation. With these
             constraints in mind, we suggest parameter regimes and
             molecular architectures that may enhance the vibrational
             control of electron transfer for fast coherent
             electron-transfer reactions.},
   Doi = {10.1039/c5cp00610d},
   Key = {fds231847}
}

@article{fds231843,
   Author = {Polizzi, NF and Migliore, A and Therien, MJ and Beratan,
             DN},
   Title = {Defusing redox bombs?},
   Journal = {Proceedings of the National Academy of Sciences of
             USA},
   Volume = {112},
   Number = {35},
   Pages = {10821-10822},
   Year = {2015},
   Month = {September},
   ISSN = {0027-8424},
   url = {http://dx.doi.org/10.1073/pnas.1513520112},
   Doi = {10.1073/pnas.1513520112},
   Key = {fds231843}
}

@article{fds231844,
   Author = {Zhang, Y and Young, RM and Thazhathveetil, AK and Singh, APN and Liu, C and Berlin, YA and Grozema, FC and Lewis, FD and Ratner, MA and Renaud, N and Siriwong, K and Voityuk, AA and Wasielewski, MR and Beratan,
             DN},
   Title = {Conformationally Gated Charge Transfer in DNA Three-Way
             Junctions.},
   Journal = {Journal of Physical Chemistry Letters},
   Volume = {6},
   Number = {13},
   Pages = {2434-2438},
   Year = {2015},
   Month = {July},
   url = {http://dx.doi.org/10.1021/acs.jpclett.5b00863},
   Abstract = {Molecular structures that direct charge transport in two or
             three dimensions possess some of the essential functionality
             of electrical switches and gates. We use theory, modeling,
             and simulation to explore the conformational dynamics of DNA
             three-way junctions (TWJs) that may control the flow of
             charge through these structures. Molecular dynamics
             simulations and quantum calculations indicate that DNA TWJs
             undergo dynamic interconversion among "well stacked"
             conformations on the time scale of nanoseconds, a feature
             that makes the junctions very different from linear DNA
             duplexes. The studies further indicate that this
             conformational gating would control charge flow through
             these TWJs, distinguishing them from conventional (larger
             size scale) gated devices. Simulations also find that
             structures with polyethylene glycol linking groups
             ("extenders") lock conformations that favor CT for 25 ns or
             more. The simulations explain the kinetics observed
             experimentally in TWJs and rationalize their transport
             properties compared with double-stranded
             DNA.},
   Doi = {10.1021/acs.jpclett.5b00863},
   Key = {fds231844}
}

@article{fds231845,
   Author = {D.N. Beratan},
   Title = {Correction for Migliore et al., Sensing of molecules using
             quantum dynamics.},
   Journal = {Proceedings of the National Academy of Sciences of
             USA},
   Volume = {112},
   Number = {25},
   Pages = {E3310},
   Year = {2015},
   Month = {June},
   ISSN = {0027-8424},
   url = {http://dx.doi.org/10.1073/pnas.1509993112},
   Doi = {10.1073/pnas.1509993112},
   Key = {fds231845}
}

@article{fds231851,
   Author = {Lin, J and Balamurugan, D and Zhang, P and Skourtis, SS and Beratan,
             DN},
   Title = {Two-Electron Transfer Pathways.},
   Journal = {The Journal of Physical Chemistry Part B: Condensed Matter,
             Materials, Surfaces, Interfaces and Biophysical},
   Volume = {119},
   Number = {24},
   Pages = {7589-7597},
   Year = {2015},
   Month = {June},
   ISSN = {1520-6106},
   url = {http://dx.doi.org/10.1021/jp511429z},
   Abstract = {The frontiers of electron-transfer chemistry demand that we
             develop theoretical frameworks to describe the delivery of
             multiple electrons, atoms, and ions in molecular systems.
             When electrons move over long distances through high
             barriers, where the probability for thermal population of
             oxidized or reduced bridge-localized states is very small,
             the electrons will tunnel from the donor (D) to acceptor
             (A), facilitated by bridge-mediated superexchange
             interactions. If the stable donor and acceptor redox states
             on D and A differ by two electrons, it is possible that the
             electrons will propagate coherently from D to A. While
             structure-function relations for single-electron
             superexchange in molecules are well established, strategies
             to manipulate the coherent flow of multiple electrons are
             largely unknown. In contrast to one-electron superexchange,
             two-electron superexchange involves both one- and
             two-electron virtual intermediate states, the number of
             virtual intermediates increases very rapidly with system
             size, and multiple classes of pathways interfere with one
             another. In the study described here, we developed simple
             superexchange models for two-electron transfer. We explored
             how the bridge structure and energetics influence
             multielectron superexchange, and we compared two-electron
             superexchange interactions to single-electron superexchange.
             Multielectron superexchange introduces interference between
             singly and doubly oxidized (or reduced) bridge virtual
             states, so that even simple linear donor-bridge-acceptor
             systems have pathway topologies that resemble those seen for
             one-electron superexchange through bridges with multiple
             parallel pathways. The simple model systems studied here
             exhibit a richness that is amenable to experimental
             exploration by manipulating the multiple pathways, pathway
             crosstalk, and changes in the number of donor and acceptor
             species. The features that emerge from these studies may
             assist in developing new strategies to deliver multiple
             electrons in condensed-phase redox systems, including
             multiple-electron redox species, multimetallic/multielectron
             redox catalysts, and multiexciton excited
             states.},
   Doi = {10.1021/jp511429z},
   Key = {fds231851}
}

@article{fds231848,
   Author = {Migliore, A and Naaman, R and Beratan, DN},
   Title = {Sensing of molecules using quantum dynamics.},
   Journal = {Proceedings of the National Academy of Sciences of
             USA},
   Volume = {112},
   Number = {19},
   Pages = {E2419-E2428},
   Year = {2015},
   Month = {May},
   ISSN = {0027-8424},
   url = {http://dx.doi.org/10.1073/pnas.1502000112},
   Abstract = {We design sensors where information is transferred between
             the sensing event and the actuator via quantum relaxation
             processes, through distances of a few nanometers. We thus
             explore the possibility of sensing using intrinsically
             quantum mechanical phenomena that are also at play in
             photobiology, bioenergetics, and information processing.
             Specifically, we analyze schemes for sensing based on charge
             transfer and polarization (electronic relaxation) processes.
             These devices can have surprising properties. Their
             sensitivity can increase with increasing separation between
             the sites of sensing (the receptor) and the actuator (often
             a solid-state substrate). This counterintuitive response and
             other quantum features give these devices favorable
             characteristics, such as enhanced sensitivity and
             selectivity. Using coherent phenomena at the core of
             molecular sensing presents technical challenges but also
             suggests appealing schemes for molecular sensing and
             information transfer in supramolecular structures.},
   Doi = {10.1073/pnas.1502000112},
   Key = {fds231848}
}

@article{fds231852,
   Author = {Yue, Y and Grusenmeyer, T and Ma, Z and Zhang, P and Schmehl, RH and Beratan, DN and Rubtsov, IV},
   Title = {Electron transfer rate modulation in a compact Re(I)
             donor-acceptor complex.},
   Journal = {Dalton Transactions},
   Volume = {44},
   Number = {18},
   Pages = {8609-8616},
   Year = {2015},
   Month = {May},
   ISSN = {1477-9226},
   url = {http://dx.doi.org/10.1039/c4dt02145b},
   Abstract = {Formation of the charge transfer state with the rate
             constant of (10 ps)(-1) has recently been reported for the
             complex fac-[Re(I)(CO)3(DCEB)(3DMABN)] (ReEBA); where 3DMABN
             is 3-dimethylaminobenzonitrile, serving as an electron
             donor, and DCEB is 4,4'-(dicarboxyethyl)-2,2-bipyridine,
             serving as an electron acceptor (Y. Yue et al., J. Phys.
             Chem. A, 118, 10407). 3-Pulse UV-pump - IR-pump - IR-probe
             spectroscopy is used in this work to study how the charge
             separation reaction in ReEBA to form a ligand to ligand
             charge transfer state (LLCT) can be modulated by vibrational
             excitation of various modes of the complex. While no
             significant rate modulation was found when the cyano group
             stretching mode of the 3DMABN donor was excited, a sizable
             effect was found when the ring stretching mode of the DCEB
             acceptor was excited. The accumulation of the charge
             separated state (LLCT state) in the 3-pulse experiment was
             observed as a sharp excited-state vibrational peak of the
             symmetric stretch of the three facial carbonyl groups,
             νSS(CO). Modeling indicates that the rate of charge
             separation is increased by ca. 28% when vibrational
             excitation is present. The vibronic coupling signal of the
             bpy ring mode and νSS(CO) as well as the energy transport
             dynamics from bpy to carbonyl contributed to the 3-pulse
             signal and was studied as well using the 3-pulse method.
             Energy transport between the same modes in the ground
             electronic state was measured by relaxation-assisted
             two-dimensional infrared (RA 2DIR) spectroscopy. The energy
             transport times of 4 ± 0.7 and 5 ± 1.5 ps were found for
             the ground and excited electronic states.},
   Doi = {10.1039/c4dt02145b},
   Key = {fds231852}
}

@article{fds231846,
   Author = {Young, RM and Singh, APN and Thazhathveetil, AK and Cho, VY and Zhang,
             Y and Renaud, N and Grozema, FC and Beratan, DN and Ratner, MA and Schatz,
             GC and Berlin, YA and Lewis, FD and Wasielewski, MR},
   Title = {Charge Transport across DNA-Based Three-Way
             Junctions},
   Journal = {Journal of the American Chemical Society},
   Volume = {137},
   Number = {15},
   Pages = {5113-5122},
   Year = {2015},
   Month = {April},
   ISSN = {0002-7863},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000353606700043&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Doi = {10.1021/jacs.5b00931},
   Key = {fds231846}
}

@article{fds231849,
   Author = {Young, RM and Singh, APN and Thazhathveetil, AK and Cho, VY and Zhang,
             Y and Renaud, N and Grozema, FC and Beratan, DN and Ratner, MA and Schatz,
             GC and Berlin, YA and Lewis, FD and Wasielewski, MR},
   Title = {Charge Transport across DNA-Based Three-Way
             Junctions.},
   Journal = {Journal of the American Chemical Society},
   Volume = {137},
   Number = {15},
   Pages = {5113-5122},
   Year = {2015},
   Month = {April},
   ISSN = {0002-7863},
   url = {http://dx.doi.org/10.1021/jacs.5b00931},
   Abstract = {DNA-based molecular electronics will require charges to be
             transported from one site within a 2D or 3D architecture to
             another. While this has been shown previously in linear,
             π-stacked DNA sequences, the dynamics and efficiency of
             charge transport across DNA three-way junction (3WJ) have
             yet to be determined. Here, we present an investigation of
             hole transport and trapping across a DNA-based three-way
             junction systems by a combination of femtosecond transient
             absorption spectroscopy and molecular dynamics simulations.
             Hole transport across the junction is proposed to be gated
             by conformational fluctuations in the ground state which
             bring the transiently populated hole carrier nucleobases
             into better aligned geometries on the nanosecond time scale,
             thus modulating the π-π electronic coupling along the base
             pair sequence.},
   Doi = {10.1021/jacs.5b00931},
   Key = {fds231849}
}

@article{fds231850,
   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 = {fds231850}
}

@article{fds231853,
   Author = {Beratan, DN and Liu, C and Migliore, A and Polizzi, NF and Skourtis, SS and Zhang, P and Zhang, Y},
   Title = {Charge transfer in dynamical biosystems, or the treachery of
             (static) images.},
   Journal = {Accounts of Chemical Research},
   Volume = {48},
   Number = {2},
   Pages = {474-481},
   Year = {2015},
   Month = {February},
   ISSN = {0001-4842},
   url = {http://dx.doi.org/10.1021/ar500271d},
   Abstract = {CONSPECTUS: The image is not the thing. Just as a pipe
             rendered in an oil painting cannot be smoked, quantum
             mechanical coupling pathways rendered on LCDs do not convey
             electrons. The aim of this Account is to examine some of our
             recent discoveries regarding biological electron transfer
             (ET) and transport mechanisms that emerge when one moves
             beyond treacherous static views to dynamical frameworks.
             Studies over the last two decades introduced both atomistic
             detail and macromolecule dynamics to the description of
             biological ET. The first model to move beyond the
             structureless square-barrier tunneling description is the
             Pathway model, which predicts how protein secondary motifs
             and folding-induced through-bond and through-space tunneling
             gaps influence kinetics. Explicit electronic structure
             theory is applied routinely now to elucidate ET mechanisms,
             to capture pathway interferences, and to treat redox
             cofactor electronic structure effects. Importantly,
             structural sampling of proteins provides an understanding of
             how dynamics may change the mechanisms of biological ET, as
             ET rates are exponentially sensitive to structure. Does
             protein motion average out tunneling pathways? Do
             conformational fluctuations gate biological ET? Are
             transient multistate resonances produced by energy gap
             fluctuations? These questions are becoming accessible as the
             static view of biological ET recedes and dynamical
             viewpoints take center stage. This Account introduces ET
             reactions at the core of bioenergetics, summarizes our
             team's progress toward arriving at an atomistic-level
             description, examines how thermal fluctuations influence ET,
             presents metrics that characterize dynamical effects on ET,
             and discusses applications in very long (micrometer scale)
             bacterial nanowires. The persistence of structural effects
             on the ET rates in the face of thermal fluctuations is
             considered. Finally, the flickering resonance (FR) view of
             charge transfer is presented to examine how fluctuations
             control low-barrier transport among multiple groups in van
             der Waals contact. FR produces exponential distance
             dependence in the absence of tunneling; the exponential
             character emerges from the probability of matching multiple
             vibronically broadened electronic energies within a
             tolerance defined by the rms coupling among interacting
             groups. FR thus produces band like coherent transport on the
             nanometer length scale, enabled by conformational
             fluctuations. Taken as a whole, the emerging context for ET
             in dynamical biomolecules provides a robust framework to
             design and interpret the inner workings of bioenergetics
             from the molecular to the cellular scale and beyond, with
             applications in biomedicine, biocatalysis, and energy
             science.},
   Doi = {10.1021/ar500271d},
   Key = {fds231853}
}

@article{fds231855,
   Author = {Yue, Y and Grusenmeyer, T and Ma, Z and Zhang, P and Schmehl, RH and Beratan, DN and Rubtsov, IV},
   Title = {Full-electron ligand-to-ligand charge transfer in a compact
             Re(I) complex.},
   Journal = {The Journal of Physical Chemistry Part A: Molecules,
             Spectroscopy, Kinetics, Environment and General
             Theory},
   Volume = {118},
   Number = {45},
   Pages = {10407-10415},
   Year = {2014},
   Month = {November},
   ISSN = {1089-5639},
   url = {http://dx.doi.org/10.1021/jp5039877},
   Abstract = {Ligand-to-ligand charge transfer (LLCT) states in transition
             metal complexes are often characterized by fractional
             electron transfer due to coupling of the LLCT state with
             many other states via the metal. We designed and
             characterized a compact Re(I) complex that displays
             essentially full-electron charge transfer in the LLCT
             excited state. The complex, [Re(DCEB)(CO)3(L)](+) (DCEB =
             4,4'-dicarboxyethyl-2,2'-bipyridine), referred to as ReEBA,
             features two redox active ligands with strong electron
             accepting (DCEB) and electron donating (L is
             3-dimethylaminobenzonitrile (3DMABN)) properties. The lowest
             energy excited state formed with a ca. 10 ps time constant
             and was characterized as the full-electron 3DMABN → DCEB
             LLCT state using time-resolved infrared spectroscopy (TRIR),
             transient absorption spectroscopy, and DFT computations.
             Analysis of a range of vibrational modes helped to assign
             the charge transfer characteristics of the complex. The LLCT
             state lifetime in ReEBA shows a strong dependence on the
             solvent polarity and features solvent dependent frequency
             shifts for several vibrational reporters. The formation of a
             full-electron LLCT state (∼92%) was enabled by tuning the
             redox properties of the electron accepting ligand (DCEB) and
             simultaneously decoupling the redox active group of the
             electron donating ligand (3DMABN) from the metal center.
             This strategy is generally applicable for designing compact
             transition metal complexes that have full-electron LLCT
             states.},
   Doi = {10.1021/jp5039877},
   Key = {fds231855}
}

@article{fds231856,
   Author = {Zhang, Y and Liu, C and Balaeff, A and Skourtis, SS and Beratan,
             DN},
   Title = {Biological charge transfer via flickering
             resonance.},
   Journal = {Proceedings of the National Academy of Sciences of
             USA},
   Volume = {111},
   Number = {28},
   Pages = {10049-10054},
   Year = {2014},
   Month = {July},
   ISSN = {0027-8424},
   url = {http://dx.doi.org/10.1073/pnas.1316519111},
   Abstract = {Biological electron-transfer (ET) reactions are typically
             described in the framework of coherent two-state electron
             tunneling or multistep hopping. However, these ET reactions
             may involve multiple redox cofactors in van der Waals
             contact with each other and with vibronic broadenings on the
             same scale as the energy gaps among the species. In this
             regime, fluctuations of the molecular structures and of the
             medium can produce transient energy level matching among
             multiple electronic states. This transient degeneracy, or
             flickering electronic resonance among states, is found to
             support coherent (ballistic) charge transfer. Importantly,
             ET rates arising from a flickering resonance (FR) mechanism
             will decay exponentially with distance because the
             probability of energy matching multiple states is
             multiplicative. The distance dependence of FR transport thus
             mimics the exponential decay that is usually associated with
             electron tunneling, although FR transport involves real
             carrier population on the bridge and is not a tunneling
             phenomenon. Likely candidates for FR transport are
             macromolecules with ET groups in van der Waals contact: DNA,
             bacterial nanowires, multiheme proteins, strongly coupled
             porphyrin arrays, and proteins with closely packed
             redox-active residues. The theory developed here is used to
             analyze DNA charge-transfer kinetics, and we find that
             charge-transfer distances up to three to four bases may be
             accounted for with this mechanism. Thus, the observed rapid
             (exponential) distance dependence of DNA ET rates over
             distances of ≲ 15 Å does not necessarily prove a
             tunneling mechanism.},
   Doi = {10.1073/pnas.1316519111},
   Key = {fds231856}
}

@article{fds231857,
   Author = {Kuznetsov, AE and Beratan, DN},
   Title = {Structural and Electronic Properties of Bare and Capped Cd
             33 Se 33 and Cd 33 Te 33 Quantum Dots},
   Journal = {The Journal of Physical Chemistry C},
   Volume = {118},
   Number = {13},
   Pages = {7094-7109},
   Year = {2014},
   Month = {April},
   ISSN = {1932-7447},
   url = {http://dx.doi.org/10.1021/jp4007747},
   Doi = {10.1021/jp4007747},
   Key = {fds231857}
}

@article{fds231858,
   Author = {Migliore, A and Polizzi, NF and Therien, MJ and Beratan,
             DN},
   Title = {Biochemistry and theory of proton-coupled electron
             transfer.},
   Journal = {Chemical Reviews},
   Volume = {114},
   Number = {7},
   Pages = {3381-3465},
   Year = {2014},
   Month = {April},
   ISSN = {0009-2665},
   url = {http://dx.doi.org/10.1021/cr4006654},
   Doi = {10.1021/cr4006654},
   Key = {fds231858}
}

@article{fds231854,
   Author = {Venkatramani, R and Wierzbinski, E and Waldeck, DH and Beratan,
             DN},
   Title = {Breaking the simple proportionality between molecular
             conductances and charge transfer rates.},
   Journal = {Faraday Discussions},
   Volume = {174},
   Pages = {57-78},
   Year = {2014},
   Month = {January},
   ISSN = {1359-6640},
   url = {http://dx.doi.org/10.1039/c4fd00106k},
   Abstract = {A theoretical framework is presented to describe and to
             understand the observed relationship between molecular
             conductances and charge transfer rates across molecular
             bridges as a function of length, structure, and charge
             transfer mechanism. The approach uses a reduced density
             matrix formulation with a phenomenological treatment of
             system-bath couplings to describe charge transfer kinetics
             and a Green's function based Landauer-Buttiker method to
             describe steady-state currents. Application of the framework
             is independent of the transport regime and includes
             bath-induced decoherence effects. This model shows that the
             relationship between molecular conductances and charge
             transfer rates follows a power-law. The nonlinear
             rate-conductance relationship is shown to arise from
             differences in the charge transport barrier heights and from
             differences in environmental decoherence rates for the two
             experiments. This model explains otherwise puzzling
             correlations between molecular conductances and
             electrochemical kinetics.},
   Doi = {10.1039/c4fd00106k},
   Key = {fds231854}
}

@article{fds231864,
   Author = {Yue, Y and Grusenmeyer, T and Ma, Z and Zhang, P and Pham, TT and Mague,
             JT and Donahue, JP and Schmehl, RH and Beratan, DN and Rubtsov,
             IV},
   Title = {Evaluating the extent of intramolecular charge transfer in
             the excited states of rhenium(I) donor-acceptor complexes
             with time-resolved vibrational spectroscopy.},
   Journal = {The Journal of Physical Chemistry Part B: Condensed Matter,
             Materials, Surfaces, Interfaces and Biophysical},
   Volume = {117},
   Number = {49},
   Pages = {15903-15916},
   Year = {2013},
   Month = {December},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/24117405},
   Abstract = {Excited states in transition-metal complexes, even in those
             featuring ligands with strong electron donating and
             accepting properties, often involve only partial charge
             transfer between the donor and acceptor ligands. The
             excited-state properties of [Re(bpy)(CO)3L](+) compounds
             were studied, where L is 4-dimethylaminobenzonitrile
             (Re4DMABN), 3-dimethylaminobenzonitrile (Re3DMABN), and
             benzonitrile (ReBN) using time-resolved infrared (TRIR) and
             electronic spectroscopy methods as well as electronic
             structure computations. The DMABN complexes exhibit strongly
             solvent-dependent luminescence; the excited state lifetime
             decreases from microseconds in dichloromethane to several
             nanoseconds in mixed MeOH:DCM (1:1) solvent. Despite the
             similarities in the solvent dependence of the excited state
             dynamics and redox properties for Re3DMABN and Re4DMABN, the
             nature of the lowest energy excited states formed in these
             two compounds is drastically different. For example, the
             lowest energy excited state for Re4DMABN in the mixed
             solvent is assigned to the (4DMABN → bpy) ligand-to-ligand
             charge transfer (LLCT) state featuring partial charge
             transfer character. An equilibrium between a 3DMABN
             intraligand triplet ((3)IL) and a metal-ligand-to-ligand
             charge transfer (MLLCT) state is found for Re3DMABN in the
             mixed solvent with the latter at ca. 400 cm(-1) lower
             energy. The origin of such a drastic difference between the
             states involved in Re4DMABN and Re3DMABN is attributed to a
             difference in the energies of polarized quinoidal resonance
             structures in 4DMABN and 3DMABN ligands.},
   Doi = {10.1021/jp409628e},
   Key = {fds231864}
}

@article{fds231860,
   Author = {Wang, Y and King, JR and Wu, P and Pelzman, DL and Beratan, DN and Toone,
             EJ},
   Title = {Erratum: Eenthalpic signature of methonium desolvation
             revealed in a synthetic host-guest system based on
             cucurbit[7]uril (Journal of the American Chemical Society
             (2013) 135 (6084-6091) DOI: 10.1021/ja311327v)},
   Journal = {Journal of the American Chemical Society},
   Volume = {135},
   Number = {46},
   Pages = {17650},
   Year = {2013},
   Month = {November},
   ISSN = {0002-7863},
   url = {http://dx.doi.org/10.1021/ja408346j},
   Doi = {10.1021/ja408346j},
   Key = {fds231860}
}

@article{fds231863,
   Author = {Wang, Y and King, JR and Wu, P and Pelzman, DL and Beratan, DN and Toone,
             EJ},
   Title = {Correction to "Enthalpic Signature of Methonium Desolvation
             Revealed in a Synthetic Host-Guest System Based on
             Cucurbit[7]uril".},
   Journal = {Journal of the American Chemical Society},
   Volume = {135},
   Number = {46},
   Pages = {17650},
   Year = {2013},
   Month = {November},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/24215303},
   Doi = {10.1021/ja408346j},
   Key = {fds231863}
}

@article{fds231861,
   Author = {Lin, J and Hu, X and Zhang, P and Van Rynbach and A and Beratan, DN and Kent,
             CA and Mehl, BP and Papanikolas, JM and Meyer, TJ and Lin, W and Skourtis,
             SS and Constantinou, M},
   Title = {Triplet Excitation Energy Dynamics in Metal-Organic
             Frameworks},
   Journal = {The Journal of Physical Chemistry C},
   Volume = {117},
   Number = {43},
   Pages = {22250-22259},
   Year = {2013},
   Month = {October},
   ISSN = {1932-7447},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000326608200013&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Doi = {10.1021/jp401515r},
   Key = {fds231861}
}

@article{fds285284,
   Author = {Bloom, BP and Zhao, L-B and Wang, Y and Waldeck, DH and Liu, R and Zhang,
             P and Beratan, DN},
   Title = {Ligand-Induced Changes in the Characteristic Size-Dependent
             Electronic Energies of CdSe Nanocrystals},
   Journal = {The Journal of Physical Chemistry C},
   Volume = {117},
   Number = {43},
   Pages = {22401-22411},
   Year = {2013},
   Month = {October},
   ISSN = {1932-7447},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000326608200031&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Doi = {10.1021/jp403164w},
   Key = {fds285284}
}

@article{fds231866,
   Author = {Jiang, N and Kuznetsov, A and Nocek, JM and Hoffman, BM and Crane, BR and Hu, X and Beratan, DN},
   Title = {Distance-independent charge recombination kinetics in
             cytochrome c-cytochrome c peroxidase complexes: compensating
             changes in the electronic coupling and reorganization
             energies.},
   Journal = {The Journal of Physical Chemistry Part B: Condensed Matter,
             Materials, Surfaces, Interfaces and Biophysical},
   Volume = {117},
   Number = {31},
   Pages = {9129-9141},
   Year = {2013},
   Month = {August},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23895339},
   Abstract = {Charge recombination rate constants vary no more than 3-fold
             for interprotein ET in the Zn-substituted wild type (WT)
             cytochrome c peroxidase (CcP):cytochrome c (Cc) complex and
             in complexes with four mutants of the Cc protein (i.e.,
             F82S, F82W, F82Y, and F82I), despite large differences in
             the ET distance. Theoretical analysis indicates that charge
             recombination for all complexes involves a combination of
             tunneling and hopping via Trp191. For three of the five
             structures (WT and F82S(W)), the protein favors hopping more
             than that in the other two structures that have longer heme
             → ZnP distances (F82Y(I)). Experimentally observed
             biexponential ET kinetics is explained by the complex
             locking in alternative coupling pathways, where the acceptor
             hole state is either primarily localized on ZnP (slow phase)
             or on Trp191 (fast phase). The large conformational
             differences between the CcP:Cc interface for the F82Y(I)
             mutants compared to that the WT and F82S(W) complexes are
             predicted to change the reorganization energies for the
             CcP:Cc ET reactions because of changes in solvent exposure
             and interprotein ET distances. Since the recombination
             reaction is likely to occur in the inverted Marcus regime,
             an increased reorganization energy compensates the decreased
             role for hopping recombination (and the longer transfer
             distance) in the F82Y(I) mutants. Taken together, coupling
             pathway and reorganization energy effects for the five
             protein complexes explain the observed insensitivity of
             recombination kinetics to donor-acceptor distance and
             docking pose and also reveals how hopping through aromatic
             residues can accelerate long-range ET.},
   Doi = {10.1021/jp401551t},
   Key = {fds231866}
}

@article{fds231867,
   Author = {Wierzbinski, E and Venkatramani, R and Davis, KL and Bezer, S and Kong,
             J and Xing, Y and Borguet, E and Achim, C and Beratan, DN and Waldeck,
             DH},
   Title = {The single-molecule conductance and electrochemical
             electron-transfer rate are related by a power
             law.},
   Journal = {ACS Nano},
   Volume = {7},
   Number = {6},
   Pages = {5391-5401},
   Year = {2013},
   Month = {June},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23692478},
   Abstract = {This study examines quantitative correlations between
             molecular conductances and standard electrochemical rate
             constants for alkanes and peptide nucleic acid (PNA)
             oligomers as a function of the length, structure, and charge
             transport mechanism. The experimental data show a power-law
             relationship between conductances and charge transfer rates
             within a given class of molecules with the same bridge
             chemistry, and a lack of correlation when a more diverse
             group of molecules is compared, in contrast with some
             theoretical predictions. Surprisingly, the PNA duplexes
             exhibit the lowest charge-transfer rates and the highest
             molecular conductances. The nonlinear rate-conductance
             relationships for structures with the same bridging
             chemistries are attributed to differences in the
             charge-mediation characteristics of the molecular bridge,
             energy barrier shifts and electronic dephasing, in the two
             different experimental settings.},
   Doi = {10.1021/nn401321k},
   Key = {fds231867}
}

@article{fds231869,
   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 = {fds231869}
}

@article{fds231868,
   Author = {Wang, Y and King, JR and Wu, P and Pelzman, DL and Beratan, DN and Toone,
             EJ},
   Title = {Enthalpic signature of methonium desolvation revealed in a
             synthetic host-guest system based on cucurbit[7]uril.},
   Journal = {Journal of the American Chemical Society},
   Volume = {135},
   Number = {16},
   Pages = {6084-6091},
   Year = {2013},
   Month = {April},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23510488},
   Abstract = {Methonium (N(+)Me3) is an organic cation widely distributed
             in biological systems. As an organic cation, the binding of
             methonium to protein receptors requires the removal of a
             positive charge from water. The appearance of methonium in
             biological transmitters and receptors seems at odds with the
             large unfavorable desolvation free energy reported for
             tetramethylammonium (TMA(+)), a frequently utilized
             surrogate of methonium. Here, we report an experimental
             system that facilitates incremental internalization of
             methonium within the molecular cavity of cucurbit[7]uril
             (CB[7]). Using a combination of experimental and
             computational studies, we show that the transfer of
             methonium from bulk water (partially solvated methonium
             state) to the CB[7] cavity (mostly desolvated methonium
             state) is accompanied by a remarkably small desolvation
             enthalpy of just 0.5 ± 0.3 kcal·mol(-1), a value
             significantly less endothermic than those values suggested
             from gas-phase model studies. Our results are in accord with
             neutron scattering measurements that suggest methonium
             produces only a minimal perturbation in the bulk water
             structure, which highlights the limitations of gas-phase
             models. More surprisingly, the incremental withdrawal of the
             methonium surface from water produces a nonmonotonic
             response in desolvation enthalpy. A partially desolvated
             state exists, in which a portion of the methonium group
             remains exposed to solvent. This structure incurs an
             increased enthalpic penalty of ~3 kcal·mol(-1) compared to
             other solvation states. We attribute this observation to the
             pre-encapsulation dewetting of the methonium surface.
             Together, our results offer a rationale for the wide
             distribution of methonium in a biological context and
             suggest limitations to computational estimates of binding
             affinities based on simple parametrization of
             solvent-accessible surface area.},
   Doi = {10.1021/ja311327v},
   Key = {fds231868}
}

@article{fds222349,
   Author = {B.P. Bloom and J-B. Zhao and Y. Wang and D.H. Waldeck and R. Liu and P.
             Zhang and D.N. Beratan},
   Title = {Ligand-induced changes in the characteristic size-dependent
             electronic energies of CdSe nanocrystals},
   Journal = {J. Phys Chem. C},
   Year = {2013},
   url = {http://dx.doi.org/10.1021/jp403164w},
   Doi = {10.1021/jp403164w},
   Key = {fds222349}
}

@article{fds222350,
   Author = {J. Lin and X. Hu and P. Zhang and A. Van Rynbach and D.N. Beratan and C.
             Kent, B. Mehl and J. Papanikolas and T.J. Meyer and Thomas and W. Lin and S.S. Skourtis and M. Constantinou},
   Title = {Ligand-induced changes in the characteristic size-dependent
             electronic energies of CdSe nanocrystals},
   Journal = {J. Phys Chem. C},
   Year = {2013},
   url = {http://dx.doi.org/10.1021/jp401515r},
   Doi = {10.1021/jp401515r},
   Key = {fds222350}
}

@article{fds222353,
   Author = {Y. Wang and J.R. King and P. Wu and D.L. Pelzman and D.N. Beratan and E.J. Toone},
   Title = {Enthalpic signature of methonium desolvation revealed in a
             synthetic host-guest system based on curcurbit[7]uril},
   Journal = {J. Am. Chem. Soc.},
   Number = {135},
   Pages = {6084-6091},
   Year = {2013},
   Key = {fds222353}
}

@misc{fds222354,
   Author = {D.N. Beratan and S.S. Skourtis},
   Title = {Electron transfer through proteins},
   Pages = {625-630},
   Booktitle = {Encyclopedia of Biophysics},
   Publisher = {Springer Verlag},
   Editor = {G. Roberts and ed},
   Year = {2013},
   Key = {fds222354}
}

@article{fds222356,
   Author = {Y. Zhang and C. Liu and A. Balaeff and S. S. Skourtis and D.N.
             Beratan},
   Title = {A flickering resonance mechanism for biological charge
             transfer},
   Journal = {PNAS},
   Year = {2013},
   Key = {fds222356}
}

@article{fds222357,
   Author = {A. Kuznetsov and D.N. Beratan},
   Title = {Structural and Electronic Properties of Bare and Capped
             Cd33Se33/Cd33Te33 Nanoparticles},
   Journal = {J. Phys. Chem. C},
   Year = {2013},
   Key = {fds222357}
}

@article{fds231900,
   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 = {fds231900}
}

@article{fds231910,
   Author = {Keinan, S and Nocek, JM and Hoffman, BM and Beratan,
             DN},
   Title = {Interfacial hydration, dynamics and electron transfer:
             multi-scale ET modeling of the transient [myoglobin,
             cytochrome b5] complex.},
   Journal = {Physical Chemistry Chemical Physics},
   Volume = {14},
   Number = {40},
   Pages = {13881-13889},
   Year = {2012},
   Month = {October},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22955681},
   Abstract = {Formation of a transient [myoglobin (Mb), cytochrome b(5)
             (cyt b(5))] complex is required for the reductive repair of
             inactive ferri-Mb to its functional ferro-Mb state. The [Mb,
             cyt b(5)] complex exhibits dynamic docking (DD), with its
             cyt b(5) partner in rapid exchange at multiple sites on the
             Mb surface. A triple mutant (Mb(3M)) was designed as part of
             efforts to shift the electron-transfer process to the simple
             docking (SD) regime, in which reactive binding occurs at a
             restricted, reactive region on the Mb surface that dominates
             the docked ensemble. An electrostatically-guided brownian
             dynamics (BD) docking protocol was used to generate an
             initial ensemble of reactive configurations of the complex
             between unrelaxed partners. This ensemble samples a broad
             and diverse array of heme-heme distances and orientations.
             These configurations seeded all-atom constrained molecular
             dynamics simulations (MD) to generate relaxed complexes for
             the calculation of electron tunneling matrix elements
             (T(DA)) through tunneling-pathway analysis. This procedure
             for generating an ensemble of relaxed complexes combines the
             ability of BD calculations to sample the large variety of
             available conformations and interprotein distances, with the
             ability of MD to generate the atomic level information,
             especially regarding the structure of water molecules at the
             protein-protein interface, that defines electron-tunneling
             pathways. We used the calculated T(DA) values to compute ET
             rates for the [Mb(wt), cyt b(5)] complex and for the complex
             with a mutant that has a binding free energy strengthened by
             three D/E → K charge-reversal mutations, [Mb(3M), cyt
             b(5)]. The calculated rate constants are in agreement with
             the measured values, and the mutant complex ensemble has
             many more geometries with higher T(DA) values than does the
             wild-type Mb complex. Interestingly, water plays a double
             role in this electron-transfer system, lowering the
             tunneling barrier as well as inducing protein interface
             remodeling that screens the repulsion between the
             negatively-charged propionates of the two
             hemes.},
   Doi = {10.1039/c2cp41949a},
   Key = {fds231910}
}

@article{fds231911,
   Author = {Beratan, DN and Onuchic, JN},
   Title = {Redox redux.},
   Journal = {Physical Chemistry Chemical Physics},
   Volume = {14},
   Number = {40},
   Pages = {13728},
   Year = {2012},
   Month = {October},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22960628},
   Doi = {10.1039/c2cp90148j},
   Key = {fds231911}
}

@article{fds231897,
   Author = {Wierzbinski, E and de Leon, A and Yin, X and Balaeff, A and Davis, KL and Rapireddy, S and Venkatramani, R and Keinan, S and Ly, DH and Madrid, M and Beratan, DN and Achim, C and Waldeck, DH},
   Title = {Correction to effect of backbone flexibility on charge
             transfer rates in Peptide nucleic Acid duplexes.},
   Journal = {Journal of the American Chemical Society},
   Volume = {134},
   Number = {31},
   Pages = {13141},
   Year = {2012},
   Month = {August},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22834983},
   Doi = {10.1021/ja306598z},
   Key = {fds231897}
}

@article{fds231899,
   Author = {Wierzbinski, E and de Leon, A and Yin, X and Balaeff, A and Davis, KL and Rapireddy, S and Venkatramani, R and Keinan, S and Ly, DH and Madrid, M and Beratan, DN and Achim, C and Waldeck, DH},
   Title = {Effect of backbone flexibility on charge transfer rates in
             peptide nucleic acid duplexes.},
   Journal = {Journal of the American Chemical Society},
   Volume = {134},
   Number = {22},
   Pages = {9335-9342},
   Year = {2012},
   Month = {June},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22548314},
   Abstract = {Charge transfer (CT) properties are compared between peptide
             nucleic acid structures with an aminoethylglycine backbone
             (aeg-PNA) and those with a γ-methylated backbone (γ-PNA).
             The common aeg-PNA is an achiral molecule with a flexible
             structure, whereas γ-PNA is a chiral molecule with a
             significantly more rigid structure than aeg-PNA.
             Electrochemical measurements show that the CT rate constant
             through an aeg-PNA bridging unit is twice the CT rate
             constant through a γ-PNA bridging unit. Theoretical
             calculations of PNA electronic properties, which are based
             on a molecular dynamics structural ensemble, reveal that the
             difference in the CT rate constant results from the
             difference in the extent of backbone fluctuations of aeg-
             and γ-PNA. In particular, fluctuations of the backbone
             affect the local electric field that broadens the energy
             levels of the PNA nucleobases. The greater flexibility of
             the aeg-PNA gives rise to more broadening, and a more
             frequent appearance of high-CT rate conformations than in
             γ-PNA.},
   Doi = {10.1021/ja301677z},
   Key = {fds231899}
}

@article{fds231912,
   Author = {Balabin, IA and Hu, X and Beratan, DN},
   Title = {Exploring biological electron transfer pathway dynamics with
             the Pathways plugin for VMD.},
   Journal = {Journal of Computational Chemistry},
   Volume = {33},
   Number = {8},
   Pages = {906-910},
   Year = {2012},
   Month = {March},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22298319},
   Abstract = {We describe the new Pathways plugin for the molecular
             visualization program visual molecular dynamics. The plugin
             identifies and visualizes tunneling pathways and pathway
             families in biomolecules, and calculates relative electronic
             couplings. The plugin includes unique features to estimate
             the importance of individual atoms for mediating the
             coupling, to analyze the coupling sensitivity to thermal
             motion, and to visualize pathway fluctuations. The Pathways
             plugin is open source software distributed under the terms
             of the GNU's Not Unix (GNU) public license.},
   Doi = {10.1002/jcc.22927},
   Key = {fds231912}
}

@article{fds231895,
   Author = {Kuznetsov, AE and Balamurugan, D and Skourtis, SS and Beratan,
             DN},
   Title = {Structural and electronic properties of bare and capped Cd
             nSe n/Cd nTe n
             Nanoparticles (n = 6, 9)},
   Journal = {The Journal of Physical Chemistry C},
   Volume = {116},
   Number = {12},
   Pages = {6817-6830},
   Year = {2012},
   ISSN = {1932-7447},
   url = {http://dx.doi.org/10.1021/jp2109187},
   Abstract = {Relationships between structures and properties (energy
             gaps, vertical ionization potentials (IP v), vertical
             electron affinities (EA v), and ligand binding energies) in
             small capped CdSe/CdTe nanoparticles (NPs) are poorly
             understood. We have performed the first systematic density
             functional theory (DFT) (B3LYP/Lanl2dz) study of the
             structural (geometries and ligand binding energies) and
             electronic (HOMO/LUMO energy gaps, IPs v, and EAs v)
             properties of Cd nSe n/Cd nTe n NPs (n = 6, 9), both bare
             and capped with NH 3, SCH 3, and OPH 3 ligands. NH 3 and OPH
             3 ligands cause HOMO/LUMO energy destabilization in capped
             NPs, more pronounced for the LUMOs than for the HOMOs.
             Orbital destabilization drastically reduces both the IP v
             and EA v of the NPs compared with the bare species. For SCH
             3-capped Cd 6X 6 NPs, formation of expanded structures was
             found to be preferable to crystal-like structures. SCH 3
             groups cause destabilization of the HOMOs of the capped NPs
             and stabilization of their LUMOs, which indicates a
             reduction of the IP v of the capped NPs compared with the
             bare species. For the Cd 9X 9 NPs, similar trends in
             stabilization/destabilization of frontier orbitals were
             observed in comparison with the capped Cd 6X 6 species.
             Also, pinning of the HOMO energies was observed for the NH
             3- and SCH 3-capped NPs as a function of a NP size. © 2012
             American Chemical Society.},
   Doi = {10.1021/jp2109187},
   Key = {fds231895}
}

@article{fds231896,
   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 = {fds231896}
}

@article{fds231898,
   Author = {Lim, E and Kuznetsov, AE and Beratan, DN},
   Title = {Effects of S-containing ligands on the structure and
             electronic properties of Cd nSe n/Cd
             nTe n nanoparticles (n = 3, 4, 6, and
             9)},
   Journal = {Chemical Physics},
   Volume = {407},
   Pages = {97-109},
   Year = {2012},
   ISSN = {0301-0104},
   url = {http://dx.doi.org/10.1016/j.chemphys.2012.09.005},
   Abstract = {To understand ligand capping effects on the structure and
             electronic properties of Cd nX n (X = Se, Te; n = 3, 4, 6,
             and 9) species, we performed density functional theory
             studies of SCH 2COOH-, SCH 2CH 2CO 2H-, and SCH 2CH 2NH
             2-capped nanoparticles. Cd nX n capping with all three
             capping groups was found to produce significant NP
             distortions. All three ligands destabilize the NP HOMOs and
             either stabilize or destabilize their LUMOs, leading to
             closure of the HOMO/LUMO gaps for all of the capped species,
             because the HOMO destabilization effect is generally large
             than the LUMO destabilization effect. The calculated
             absorption spectra of bare and capped NPs, exemplified by Cd
             nX n with n = 4 and 6, show that all capping groups cause
             noticeable red shifts for n = 4 and mostly blue shifts for n
             = 6. © 2012 Elsevier B.V. All rights reserved.},
   Doi = {10.1016/j.chemphys.2012.09.005},
   Key = {fds231898}
}

@article{fds231913,
   Author = {Polizzi, NF and Skourtis, SS and Beratan, DN},
   Title = {Physical constraints on charge transport through bacterial
             nanowires.},
   Journal = {Faraday Discussions},
   Volume = {155},
   Pages = {43-62},
   Year = {2012},
   ISSN = {1359-6640},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/22470966},
   Abstract = {Extracellular appendages of the dissimilatory metal-reducing
             bacterium Shewanella oneidensis MR-1 were recently shown to
             sustain currents of 10(10) electrons per second over
             distances of 0.5 microns [El-Naggar et al., Proc. Natl.
             Acad. Sci. U. S. A., 2010, 107, 18127]. However, the
             identity of the charge localizing sites and their
             organization along the "nanowire" remain unknown. We use
             theory to predict redox cofactor separation distances that
             would permit charge flow at rates of 10(10) electrons per
             second over 0.5 microns for voltage biases of < or = IV,
             using a steady-state analysis governed by a non-adiabatic
             electron transport mechanism. We find the observed currents
             necessitate a multi-step hopping transport mechanism, with
             charge localizing sites separated by less than 1 nm and
             reorganization energies that rival the lowest known in
             biology.},
   Key = {fds231913}
}

@article{fds231919,
   Author = {Balaeff, A and Craig, SL and Beratan, DN},
   Title = {B-DNA to zip-DNA: simulating a DNA transition to a novel
             structure with enhanced charge-transport
             characteristics.},
   Journal = {The Journal of Physical Chemistry Part A: Molecules,
             Spectroscopy, Kinetics, Environment and General
             Theory},
   Volume = {115},
   Number = {34},
   Pages = {9377-9391},
   Year = {2011},
   Month = {September},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21598926},
   Abstract = {The forced extension of a DNA segment is studied in a series
             of steered molecular dynamics simulations, employing a broad
             range of pulling forces. Throughout the entire force range,
             the formation of a zipper-like (zip-) DNA structure is
             observed. In that structure, first predicted by Lohikoski et
             al., the bases of the DNA strands interdigitate with each
             other and form a single-base aromatic stack. Similar motifs,
             albeit only a few base pairs in extent, have been observed
             in experimental crystal structures. Analysis of the dynamics
             of structural changes in pulled DNA shows that S-form DNA,
             thought to be adopted by DNA under applied force, serves as
             an intermediate between B-DNA and zip-DNA. Therefore, the
             phase transition plateau observed in force-extension curves
             of DNA is suggested to reflect the B-DNA to zip-DNA
             structural transition. Electronic structure analysis of
             purine bases in zip-DNA indicates a several-fold to order of
             magnitude increase in the π-π electronic coupling among
             nearest-neighbor nucleobases, compared to B-DNA. We further
             observe that zip-DNA does not require base pair
             complementarity between DNA strands, and we predict that the
             increased electronic coupling in zip-DNA will result in a
             much higher rate of charge transfer through an all-purine
             zip-DNA compared to B-DNA of equal length.},
   Doi = {10.1021/jp110871g},
   Key = {fds231919}
}

@article{fds231918,
   Author = {Susumu, K and Fisher, JAN and Zheng, J and Beratan, DN and Yodh, AG and Therien, MJ},
   Title = {Two-photon absorption properties of proquinoidal D-A-D and
             A-D-A quadrupolar chromophores.},
   Journal = {The Journal of Physical Chemistry Part A: Molecules,
             Spectroscopy, Kinetics, Environment and General
             Theory},
   Volume = {115},
   Number = {22},
   Pages = {5525-5539},
   Year = {2011},
   Month = {June},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21568299},
   Abstract = {We report the synthesis, one- and two-photon absorption
             spectroscopy, fluorescence, and electrochemical properties
             of a series of quadrupolar molecules that feature
             proquinoidal π-aromatic acceptors. These quadrupolar
             molecules possess either donor-acceptor-donor (D-A-D) or
             acceptor-donor-acceptor (A-D-A) electronic motifs, and
             feature 4-N,N-dihexylaminophenyl, 4-dodecyloxyphenyl,
             4-(N,N-dihexylamino)benzo[c][1,2,5]thiadiazolyl or
             2,5-dioctyloxyphenyl electron donor moieties and
             benzo[c][1,2,5]thiadiazole (BTD) or 6,7-bis(3',7'-dimethyloctyl)[1,2,5]thiadiazolo[3,4-g]quinoxaline
             (TDQ) electron acceptor units. These conjugated structures
             are highly emissive in nonpolar solvents and exhibit large
             spectral red-shifts of their respective lowest energy
             absorption bands relative to analogous reference compounds
             that incorporate phenylene components in place of BTD and
             TDQ moieties. BTD-based D-A-D and A-D-A chromophores exhibit
             increasing fluorescence emission red-shifts, and a
             concomitant decrease of the fluorescence quantum yield
             (Φ(f)) with increasing solvent polarity; these data
             indicate that electronic excitation augments
             benzothiadiazole electron density via an internal charge
             transfer mechanism. The BTD- and TDQ-containing structures
             exhibit blue-shifted two-photon absorption (TPA) spectra
             relative to their corresponding one-photon absorption (OPA)
             spectra, and display high TPA cross sections (>100 GM)
             within these spectral windows. D-A-D and A-D-A structures
             that feature more extensive conjugation within this series
             of compounds exhibit larger TPA cross sections consistent
             with computational simulation. Factors governing TPA
             properties of these quadrupolar chromophores are discussed
             within the context of a three-state model.},
   Doi = {10.1021/jp2000738},
   Key = {fds231918}
}

@article{fds231917,
   Author = {Carias, H and Beratan, DN and Skourtis, SS},
   Title = {Floquet analysis for vibronically modulated electron
             tunneling.},
   Journal = {The Journal of Physical Chemistry Part B: Condensed Matter,
             Materials, Surfaces, Interfaces and Biophysical},
   Volume = {115},
   Number = {18},
   Pages = {5510-5518},
   Year = {2011},
   Month = {May},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21476504},
   Abstract = {Electron tunneling provides the primary reaction channel for
             electron transfer (ET) in many molecular systems. The
             analysis of such systems therefore requires the
             consideration of electronic coherence and interference
             effects. A model system for which tunneling may be either
             symmetry forbidden or allowed is considered here in the
             presence of a driving infrared (IR) field. It was previously
             shown that inelastic tunneling allows ET in the symmetry
             forbidden system via vibronic interactions. We show here
             that explicit considerations of IR interactions with these
             systems further changes the ET kinetics. Analysis in the
             framework of Floquet theory reveals that interaction with an
             IR field may increase the probability of inelastic tunneling
             and thus enhance the ET rate for a system in which elastic
             ET is forbidden. It is shown that IR driving of a nuclear
             oscillator promotes the oscillator into excited states that
             couple more strongly to the tunneling electron. Furthermore,
             it is shown that IR driving may suppress the ET rate in this
             same system, depending on system energetics. In a model
             where elastic tunneling is symmetry allowed, we examine
             vibronic modulation of ET in the Floquet framework. ET rates
             are computed for symmetry allowed and forbidden model
             systems, and vibronic interactions are found to suppress or
             enhance ET in both systems. The inelastic ET rate may be
             enhanced over 4 orders of magnitude in the symmetry
             disfavored case or suppressed by 15% in the same system.
             Effects of IR on ET rates in the symmetry-allowed system are
             weaker with enhancements up to 34% over the undriven rate
             and suppression of about 3% with IR driving present. This
             study is the first theoretical and computational exploration
             of ET rate control by IR irradiation of the
             bridge.},
   Doi = {10.1021/jp111097a},
   Key = {fds231917}
}

@article{fds231894,
   Author = {Venkatramani, R and Keinan, S and Balaeff, A and Beratan,
             DN},
   Title = {Nucleic Acid Charge Transfer: Black, White and
             Gray.},
   Journal = {Coordination Chemistry Reviews},
   Volume = {255},
   Number = {7-8},
   Pages = {635-648},
   Year = {2011},
   Month = {April},
   ISSN = {0010-8545},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21528017},
   Abstract = {Theoretical studies of charge transport in deoxyribonucleic
             acid (DNA) and peptide nucleic acid (PNA) indicate that
             structure and dynamics modulate the charge transfer rates,
             and that different members of a structural ensemble support
             different charge transport mechanisms. Here, we review the
             influences of nucleobase geometry, electronic structure,
             solvent environment, and thermal conformational fluctuations
             on the charge transfer mechanism. We describe an emerging
             framework for understanding the diversity of charge
             transport mechanisms seen in nucleic acids.},
   Doi = {10.1016/j.ccr.2010.12.010},
   Key = {fds231894}
}

@article{fds231916,
   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 = {fds231916}
}

@article{fds231921,
   Author = {Venkatramani, R and Davis, KL and Wierzbinski, E and Bezer, S and Balaeff, A and Keinan, S and Paul, A and Kocsis, L and Beratan, DN and Achim, C and Waldeck, DH},
   Title = {Evidence for a near-resonant charge transfer mechanism for
             double-stranded peptide nucleic acid.},
   Journal = {Journal of the American Chemical Society},
   Volume = {133},
   Number = {1},
   Pages = {62-72},
   Year = {2011},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21141966},
   Abstract = {We present evidence for a near-resonant mechanism of charge
             transfer in short peptide nucleic acid (PNA) duplexes
             obtained through electrochemical, STM break junction
             (STM-BJ), and computational studies. A seven base pair
             (7-bp) PNA duplex with the sequence (TA)(3)-(XY)-(TA)(3) was
             studied, in which XY is a complementary nucleobase pair. The
             experiments showed that the heterogeneous charge transfer
             rate constant (k(0)) and the single-molecule conductance
             (σ) correlate with the oxidation potential of the purine
             base in the XY base pair. The electrochemical measurements
             showed that the enhancement of k(0) is independent, within
             experimental error, of which of the two PNA strands contains
             the purine base of the XY base pair. 7-bp PNA duplexes with
             one or two GC base pairs had similar measured k(0) and
             conductance values. While a simple superexchange model,
             previously used to rationalize charge transfer in single
             stranded PNA (Paul et al. J. Am. Chem. Soc. 2009, 131,
             6498-6507), describes some of the experimental observations,
             the model does not explain the absence of an enhancement in
             the experimental k(0) and σ upon increasing the G content
             in the duplexes from one to two. Moreover, the superexchange
             model is not consistent with other studies (Paul et al. J.
             Phys. Chem. B 2010, 114, 14140), that showed a hopping
             charge transport mechanism is likely important for PNA
             duplexes longer than seven base pairs. A quantitative
             computational analysis shows that a near-resonant charge
             transfer regime, wherein a mix of superexchange and hopping
             mechanisms are expected to coexist, can rationalize all of
             the experimental results.},
   Doi = {10.1021/ja107622m},
   Key = {fds231921}
}

@misc{fds197284,
   Author = {D.N. Beratan and S.S. Skourtis},
   Title = {Electron transfer through proteins},
   Booktitle = {Encyclopedia of Biophysics},
   Publisher = {Springer Verlag},
   Year = {2011},
   Key = {fds197284}
}

@book{fds197288,
   Title = {Electronic and magnetic properties of chiral molecules and
             supramolecular architectures},
   Volume = {298},
   Publisher = {Springer},
   Editor = {D.N. Beratan},
   Year = {2011},
   Key = {fds197288}
}

@article{fds231892,
   Author = {Beratan, DN and Naaman, R and Waldeck, DH},
   Title = {Topics in Current Chemistry: Preface},
   Journal = {Topics in current chemistry},
   Volume = {298},
   Pages = {ix-x},
   Year = {2011},
   ISSN = {0340-1022},
   Key = {fds231892}
}

@article{fds231893,
   Author = {Skourtis, S and Beratan, DN and Waldeck, DH},
   Title = {Coherence in electron tunneling pathways},
   Journal = {Procedia Chemistry},
   Number = {3},
   Pages = {99-104},
   Year = {2011},
   Key = {fds231893}
}

@article{fds231914,
   Author = {Wolak, MA and Balaeff, A and Gutmann, S and Helmrich, HJ and Vosloo, R and Beerbom, MM and Wierzbinski, E and Waldeck, DH and Bezer, S and Achim,
             C and Beratan, DN and Schlaf, R},
   Title = {Electronic structure of self-assembled peptide nucleic acid
             thin films},
   Journal = {The Journal of Physical Chemistry C},
   Volume = {115},
   Number = {34},
   Pages = {17123-17135},
   Year = {2011},
   ISSN = {1932-7447},
   url = {http://dx.doi.org/10.1021/jp201602j},
   Abstract = {The electronic structure of self-assembled monolayers (SAMs)
             of peptide nucleic acid (PNA) formed on Au substrates was
             investigated. Cys-appended PNA 7-mers of thymine (Cys-T7)
             were incubated on Au substrates in a nitrogen glovebox
             attached to a photoemission spectrometer. Ultraviolet and
             X-ray photoemission spectroscopy (UPS and XPS) measurements
             on the resulting SAMs revealed the hole injection barrier at
             the interface and the interface dipole. Electronic structure
             calculations based on molecular dynamics sampling of the PNA
             structure yielded the HOMO-LUMO gap and the electronic
             density of states for PNA. Combined with the UPS data, the
             theoretical calculation enabled estimation of the charge
             injection barriers at the interface, as well as the
             assignment of individual UP spectral features to specific
             molecular orbitals. Interestingly, the dipole moment of the
             PNA backbone is predicted to polarize PNA MOs, shifting the
             preferred HOMO localization toward the C-terminus of PNA.
             Control measurements on Cys-appended, abasic PNA backbone
             7-mers (Cys-Bckb7) allowed the identification of the
             emissions related to the PNA backbone in the UP spectra. The
             orbital line-up at the interface between the Au substrate
             and the Cys-PNA indicates a significant interface dipole
             resulting in the alignment of the Au Fermi level near the
             center of the PNA HOMO-LUMO gap. This alignment causes large
             charge injection barriers for both holes and electrons, and
             thus impedes charge transfer from Au into the Cys-PNA SAM.
             © 2011 American Chemical Society.},
   Doi = {10.1021/jp201602j},
   Key = {fds231914}
}

@article{fds231915,
   Author = {Venkatramani, R and Keinan, S and Balaeff, A and Beratan,
             DN},
   Title = {Electron transfer in nucleic acids: Black, white, and
             gray},
   Journal = {Coord. Chem. Revs.},
   Number = {255},
   Pages = {635-648},
   Year = {2011},
   Key = {fds231915}
}

@article{fds231920,
   Author = {Ben-Moshe, V and Beratan, DN and Nitzan, A and Skourtis,
             SS},
   Title = {Chiral control of current transfer in molecules.},
   Journal = {Topics in current chemistry},
   Volume = {298},
   Number = {298},
   Pages = {259-278},
   Year = {2011},
   ISSN = {0340-1022},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/21321805},
   Abstract = {Electron transmission through chiral molecules induced by
             circularly polarized light can be very different for mirror
             image structures. This behavior is described in terms of
             current transfer: the transfer of both charge and momentum.
             We review recent theoretical developments on the theory of
             current transfer and discuss related experimental studies of
             electron transmission through chiral molecular structures
             adsorbed on surfaces.},
   Doi = {10.1007/128_2010_101},
   Key = {fds231920}
}

@article{fds231926,
   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 = {fds231926}
}

@article{fds231924,
   Author = {Xing, Y and Park, T-H and Venkatramani, R and Keinan, S and Beratan, DN and Therien, MJ and Borguet, E},
   Title = {Optimizing single-molecule conductivity of conjugated
             organic oligomers with carbodithioate linkers.},
   Journal = {Journal of the American Chemical Society},
   Volume = {132},
   Number = {23},
   Pages = {7946-7956},
   Year = {2010},
   Month = {June},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20433175},
   Abstract = {In molecular electronics, the linker group, which attaches
             the functional molecular core to the electrode, plays a
             crucial role in determining the overall conductivity of the
             molecular junction. While much focus has been placed on
             optimizing molecular core conductivity, there have been
             relatively few attempts at designing optimal linker groups
             to metallic or semiconducting electrodes. The vast majority
             of molecular electronic studies use thiol linker groups;
             work probing alternative amine linker systems has only
             recently been explored. Here, we probe single-molecule
             conductances in phenylene-ethynylene molecules terminated
             with thiol and carbodithioate linkers, experimentally using
             STM break-junction methods and theoretically using a
             nonequilibrium Green's function approach. Experimental
             studies demonstrate that the carbodithioate linker augments
             electronic coupling to the metal electrode and lowers the
             effective barrier for charge transport relative to the
             conventional thiol linker, thus enhancing the conductance of
             the linker-phenylene-ethynylene-linker unit; these data
             underscore that phenylene-ethynylene-based structures are
             more highly conductive than originally appreciated in
             molecular electronics applications. The theoretical analysis
             shows that the nature of sulfur hybridization in these
             species is responsible for the order-of-magnitude increased
             conductance in carbodithioate-terminated systems relative to
             identical conjugated structures that feature classic thiol
             linkers, independent of the mechanism of charge transport.
             Interestingly, in these systems, the tunneling current is
             not dominated by the frontier molecular orbitals. While
             barriers <k(B)T are expected to produce low beta values, we
             show that the competition between tunneling and resonant
             transport processes allows barriers >k(B)T to produce the
             low beta values seen in our experiments. Taken together,
             these experimental and theoretical studies indicate a
             promising role for carbodithioate-based connectivity in
             molecular-scale electronics applications involving metallic
             and semiconducting electrodes.},
   Doi = {10.1021/ja909559m},
   Key = {fds231924}
}

@misc{fds184126,
   Author = {D.N. Beratan and S.S. Skourtis},
   Title = {Electron tunneling through proteins},
   Booktitle = {Encyclopedia of Biophysics (In Press)},
   Publisher = {Springer Press},
   Year = {2010},
   Key = {fds184126}
}

@article{fds184132,
   Author = {Y. Xing and T-H. Park and R. Venkatramani and S. Keinan and D.N.
             Beratan, M.J. Therien and E. Borguet},
   Title = {Optimizing single molecule conductivity of conjugated
             organic oligomers with conjugated carbodithioate
             linkers},
   Journal = {J. Am. Chem. Soc.},
   Number = {132},
   Pages = {7946-7956},
   Year = {2010},
   Key = {fds184132}
}

@article{fds231891,
   Author = {Mey, KD and Clays, K and Therien, MJ and Beratan, DN and Asselberghs,
             I},
   Title = {Analysis of the unusual wavelength dependence of the first
             hyperpolarizability of porphyrin derivatives},
   Journal = {Proceedings of SPIE - The International Society for Optical
             Engineering},
   Volume = {7774},
   Year = {2010},
   ISSN = {0277-786X},
   url = {http://dx.doi.org/10.1117/12.859819},
   Abstract = {Successfully predicting the frequency dispersion of
             electronic hyperpolarizabilities is an unresolved challenge
             in materials science and electronic structure theory. It has
             been shown1 that the generalized Thomas-Kuhn sum rules
             combined with linear absorption data and measured
             hyperpolarizabilities 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 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.
             Importantly, this approach provides a quantitative scheme to
             use linear optical absorption spectra and very few
             individual hyperpolarizability values to predict the entire
             frequency-dependent nonlinear optical response. In addition
             we provide here experimental dynamic hyperpolarizability
             values determined by hyper-Rayleigh scattering that
             underscore the validity of our approach. © 2010
             SPIE.},
   Doi = {10.1117/12.859819},
   Key = {fds231891}
}

@article{fds231922,
   Author = {Skourtis, SS and Waldeck, DH and Beratan, DN},
   Title = {Fluctuations in biological and bioinspired electron-transfer
             reactions.},
   Journal = {Annual Review of Physical Chemistry},
   Volume = {61},
   Number = {61},
   Pages = {461-485},
   Year = {2010},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/20192814},
   Abstract = {Central to theories of electron transfer (ET) is the idea
             that nuclear motion generates a transition state that
             enables electron flow to proceed, but nuclear motion also
             induces fluctuations in the donor-acceptor (DA) electronic
             coupling that is the rate-limiting parameter for
             nonadiabatic ET. The interplay between the DA energy gap and
             DA coupling fluctuations is particularly noteworthy in
             biological ET, where flexible protein and mobile water
             bridges take center stage. Here, we discuss the critical
             timescales at play for ET reactions in fluctuating media,
             highlighting issues of the Condon approximation, average
             medium versus fluctuation-controlled electron tunneling,
             gated and solvent relaxation controlled electron transfer,
             and the influence of inelastic tunneling on electronic
             coupling pathway interferences. Taken together, one may use
             this framework to establish principles to describe how
             macromolecular structure and structural fluctuations
             influence ET reactions. This framework deepens our
             understanding of ET chemistry in fluctuating media.
             Moreover, it provides a unifying perspective for biophysical
             charge-transfer processes and helps to frame new questions
             associated with energy harvesting and transduction in
             fluctuating media.},
   Doi = {10.1146/annurev.physchem.012809.103436},
   Key = {fds231922}
}

@article{fds231923,
   Author = {Ben-Moshe, V and Nitzan, A and Skourtis, SS and Beratan,
             DN},
   Title = {Steady-state theory of current transfer},
   Journal = {The Journal of Physical Chemistry C},
   Volume = {114},
   Number = {17},
   Pages = {8005-8013},
   Year = {2010},
   ISSN = {1932-7447},
   url = {http://hdl.handle.net/10161/4066 Duke open
             access},
   Abstract = {Current transfer is defined as a charge-transfer process
             where the transferred charge carries information about its
             original motion. We have recently suggested that such
             transfer causes the asymmetry observed in electron transfer
             induced by circularly polarized light through helical wires.
             This paper presents the steady-state theory of current
             transfer within a tight binding model of coupled wires
             systems. The asymmetry in the system response to a steady
             current imposed in a particular direction on one of the
             wires is used to define the efficiency of current transfer.
             © 2010 American Chemical Society.},
   Doi = {10.1021/jp100661f},
   Key = {fds231923}
}

@article{fds231925,
   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 = {fds231925}
}

@article{fds231927,
   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 = {fds231927}
}

@article{fds231928,
   Author = {Keinan, S and Venkatramani, R and Balaeff, A and Beratan,
             DN},
   Title = {Is MD geometry sampling sufficient for nucleobase electronic
             structure analysis of et reactions? Comparing classical MD
             and QM/MM methods},
   Journal = {The Journal of Physical Chemistry C},
   Volume = {114},
   Number = {48},
   Pages = {20496-20502},
   Year = {2010},
   ISSN = {1932-7447},
   url = {http://dx.doi.org/10.1021/jp104919g},
   Abstract = {It has been shown in many experimental studies that one of
             the major charge-transfer mechanisms in nucleic acids is
             that by positive charge carriers (holes), residing
             predominantly on G bases. Theoretical charge-transfer
             calculations often use Koopmans' theorem to approximate the
             relaxed doublet cation hole energies from simulations of the
             neutral ground state (GS). An assumption in these
             calculations is that the geometry and interactions of the
             doublet cation (DC) hole with the solvent is the same as
             that for the neutral GS. Here, we simulate the DC hole on
             solvated G and A nucleobases using combined quantum
             mechanics/molecular mechanics (QM/MM) methods and compare
             the geometries and electronic structure of the charged bases
             to those of the neutral bases. We also study the effects of
             the solvent environment on the nucleobase electronic
             structure and estimate the size of the smallest solvent
             shell that needs to be included in order to achieve
             convergence of the nucleobase energy levels. We find that
             Koopmans' theorem based methods provide a satisfactory
             description of the nucleobase energy levels, with the
             largest deviation (̃0.1eV) for charged bases in explicit
             water. We also find that the size of the solvent shell is
             crucial for describing the nucleobase electronic structure.
             When the solvent is properly accounted for, we find that the
             average energy separation between the hole energy levels on
             isolated G and A is ̃0.2 eV, and the hole energy levels
             fluctuate by ̃0.3 eV. These findings suggest important
             corrections to earlier theoretical studies that
             overestimated the hole energy separation among nucleobases
             and underestimated or neglected the base energy distribution
             due to thermal fluctuations of the nucleobases and their
             environment. Our results further suggest that hopping charge
             transport plays an important role even at short distances.
             © 2010 American Chemical Society.},
   Doi = {10.1021/jp104919g},
   Key = {fds231928}
}

@article{fds231933,
   Author = {Lin, Z and Lawrence, CM and Xiao, D and Kireev, VV and Skourtis, SS and Sessler, JL and Beratan, DN and Rubtsov, IV},
   Title = {Modulating unimolecular charge transfer by exciting bridge
             vibrations.},
   Journal = {Journal of the American Chemical Society},
   Volume = {131},
   Number = {50},
   Pages = {18060-18062},
   Year = {2009},
   Month = {December},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19928957},
   Abstract = {Ultrafast UV-vibrational spectroscopy was used to
             investigate how vibrational excitation of the bridge changes
             photoinduced electron transfer between donor
             (dimethylaniline) and acceptor (anthracene) moieties bridged
             by a guanosine-cytidine base pair (GC). The charge-separated
             (CS) state yield is found to be lowered by high-frequency
             bridge mode excitation. The effect is linked to a dynamic
             modulation of the donor-acceptor coupling interaction by
             weakening of H-bonding and/or by disruption of the bridging
             base-pair planarity.},
   Doi = {10.1021/ja907041t},
   Key = {fds231933}
}

@article{fds231931,
   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 = {fds231931}
}

@article{fds231935,
   Author = {Beratan, DN and Skourtis, SS and Balabin, IA and Balaeff, A and Keinan,
             S and Venkatramani, R and Xiao, D},
   Title = {Steering electrons on moving pathways.},
   Journal = {Accounts of Chemical Research},
   Volume = {42},
   Number = {10},
   Pages = {1669-1678},
   Year = {2009},
   Month = {October},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19645446},
   Abstract = {Electron transfer (ET) reactions provide a nexus among
             chemistry, biochemistry, and physics. These reactions
             underpin the "power plants" and "power grids" of
             bioenergetics, and they challenge us to understand how
             evolution manipulates structure to control ET kinetics.
             Ball-and-stick models for the machinery of electron
             transfer, however, fail to capture the rich electronic and
             nuclear dynamics of ET molecules: these static
             representations disguise, for example, the range of
             thermally accessible molecular conformations. The influence
             of structural fluctuations on electron-transfer kinetics is
             amplified by the exponential decay of electron tunneling
             probabilities with distance, as well as the delicate
             interference among coupling pathways. Fluctuations in the
             surrounding medium can also switch transport between
             coherent and incoherent ET mechanisms--and may gate ET so
             that its kinetics is limited by conformational
             interconversion times, rather than by the intrinsic ET time
             scale. Moreover, preparation of a charge-polarized donor
             state or of a donor state with linear or angular momentum
             can have profound dynamical and kinetic consequences. In
             this Account, we establish a vocabulary to describe how the
             conformational ensemble and the prepared donor state
             influence ET kinetics in macromolecules. This framework is
             helping to unravel the richness of functional biological ET
             pathways, which have evolved within fluctuating
             macromolecular structures. The conceptual framework for
             describing nonadiabatic ET seems disarmingly simple: compute
             the ensemble-averaged (mean-squared) donor-acceptor (DA)
             tunneling interaction, <H(DA)(2)>, and the Franck-Condon
             weighted density of states, rho(FC), to describe the rate,
             (2pi/variant Planck's over 2pi)<H(DA)(2)>rho(FC). Modern
             descriptions of the thermally averaged electronic coupling
             and of the Franck-Condon factor establish a useful
             predictive framework in biology, chemistry, and nanoscience.
             Describing the influence of geometric and energetic
             fluctuations on ET allows us to address a rich array of
             mechanistic and kinetic puzzles. How strongly is a protein's
             fold imprinted on the ET kinetics, and might thermal
             fluctuations "wash out" signatures of structure? What is the
             influence of thermal fluctuations on ET kinetics beyond
             averaging of the tunneling barrier structure? Do electronic
             coupling mechanisms change as donor and acceptor reposition
             in a protein, and what are the consequences for the ET
             kinetics? Do fluctuations access minority species that
             dominate tunneling? Can energy exchanges between the
             electron and bridge vibrations generate vibronic signatures
             that label some of the D-to-A pathways traversed by the
             electron, thus eliminating unmarked pathways that would
             otherwise contribute to the DA coupling (as in other "which
             way" or double-slit experiments)? Might medium fluctuations
             drive tunneling-hopping mechanistic transitions? How does
             the donor-state preparation, in particular, its polarization
             toward the acceptor and its momentum characteristics (which
             may introduce complex rather than pure real relationships
             among donor orbital amplitudes), influence the electronic
             dynamics? In this Account, we describe our recent studies
             that address puzzling questions of how conformational
             distributions, excited-state polarization, and electronic
             and nuclear dynamical effects influence ET in
             macromolecules. Indeed, conformational and dynamical effects
             arise in all transport regimes, including the tunneling,
             resonant transport, and hopping regimes. Importantly, these
             effects can induce switching among ET mechanisms.},
   Doi = {10.1021/ar900123t},
   Key = {fds231935}
}

@article{fds231929,
   Author = {Yuan, L and Seo, J-S and Kang, NS and Keinan, S and Steele, SE and Michelotti, GA and Wetsel, WC and Beratan, DN and Gong, Y-D and Lee, TH and Hong, J},
   Title = {Identification of 3-hydroxy-2-(3-hydroxyphenyl)-4H-1-benzopyran-4-ones
             as isoform-selective PKC-zeta inhibitors and potential
             therapeutics for psychostimulant abuse.},
   Journal = {Molecular BioSystems},
   Volume = {5},
   Number = {9},
   Pages = {927-930},
   Year = {2009},
   Month = {September},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19668856},
   Abstract = {From a screen of small molecule libraries to identify
             potential therapeutics for psychostimulant abuse,
             3-hydroxy-2-(3-hydroxyphenyl)-4H-1-benzopyran-4-ones were
             shown to be isoform-selective PKC-zeta inhibitors.},
   Doi = {10.1039/b903036k},
   Key = {fds231929}
}

@article{fds231936,
   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 = {fds231936}
}

@article{fds231932,
   Author = {Mukhopadhyay, P and Wipf, P and Beratan, DN},
   Title = {Optical signatures of molecular dissymmetry: combining
             theory with experiments to address stereochemical
             puzzles.},
   Journal = {Accounts of Chemical Research},
   Volume = {42},
   Number = {6},
   Pages = {809-819},
   Year = {2009},
   Month = {June},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19378940},
   Abstract = {Modern chemistry emerged from the quest to describe the
             three-dimensional structure of molecules: van't Hoff's
             tetravalent carbon placed symmetry and dissymmetry at the
             heart of chemistry. In this Account, we explore how modern
             theory, synthesis, and spectroscopy can be used in concert
             to elucidate the symmetry and dissymmetry of molecules and
             their assemblies. Chiroptical spectroscopy, including
             optical rotatory dispersion (ORD), electronic circular
             dichroism (ECD), vibrational circular dichroism (VCD), and
             Raman optical activity (ROA), measures the response of
             dissymmetric structures to electromagnetic radiation. This
             response can in turn reveal the arrangement of atoms in
             space, but deciphering the molecular information encoded in
             chiroptical spectra requires an effective theoretical
             approach. Although important correlations between ECD and
             molecular stereochemistry have existed for some time, a
             battery of accurate new theoretical methods that link a much
             wider range of chiroptical spectroscopies to structure have
             emerged over the past decade. The promise of this field is
             considerable: theory and spectroscopy can assist in
             assigning the relative and absolute configurations of
             complex products, revealing the structure of noncovalent
             aggregates, defining metrics for molecular diversity based
             on polarization response, and designing chirally imprinted
             nanomaterials. The physical organic chemistry of chirality
             is fascinating in its own right: defining atomic and group
             contributions to optical rotation (OR) is now possible.
             Although the common expectation is that chiroptical response
             is determined solely by a chiral solute's electronic
             structure in a given environment, chiral imprinting effects
             on the surrounding medium and molecular assembly can, in
             fact, dominate the chiroptical signatures. The theoretical
             interpretation of chiroptical markers is challenging because
             the optical properties are subtle, resulting from the strong
             electric dipole and the weaker electric quadrupole and
             magnetic dipole perturbations by the electromagnetic field.
             Moreover, OR arises from a combination of nearly canceling
             contributions to the electronic response. Indeed, the
             challenge posed by the chiroptical properties delayed the
             advent of even qualitatively accurate descriptions for some
             chiroptical signatures until the past decade when, for
             example, prediction of the observed sign of experimental OR
             became accessible to theory. The computation of chiroptical
             signatures, in close coordination with synthesis and
             spectroscopy, provides a powerful framework to diagnose and
             interpret the dissymmetry of chemical structures and
             molecular assemblies. Chiroptical theory now produces new
             schemes to elucidate structure, to describe the specific
             molecular sources of chiroptical signatures, and to assist
             in our understanding of how dissymmetry is templated and
             propagated in the condensed phase.},
   Doi = {10.1021/ar8002859},
   Key = {fds231932}
}

@article{fds231890,
   Author = {Paul, A and Bezer, S and Venkatramani, R and Kocsis, L and Wierzbinski,
             E and Balaeff, A and Keinan, S and Beratan, DN and Achim, C and Waldeck,
             DH},
   Title = {Role of nucleobase energetics and nucleobase interactions in
             single-stranded peptide nucleic acid charge
             transfer.},
   Journal = {Journal of the American Chemical Society},
   Volume = {131},
   Number = {18},
   Pages = {6498-6507},
   Year = {2009},
   Month = {May},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19382798},
   Abstract = {Self-assembled monolayers of single-stranded (ss) peptide
             nucleic acids (PNAs) containing seven nucleotides (TTTXTTT),
             a C-terminus cysteine, and an N-terminus ferrocene redox
             group were formed on gold electrodes. The PNA monomer group
             (X) was selected to be either cytosine (C), thymine (T),
             adenine (A), guanine (G), or a methyl group (Bk). The charge
             transfer rate through the oligonucleotides was found to
             correlate with the oxidation potential of X. Kinetic
             measurements and computational studies of the ss-PNA
             fragments show that a nucleobase mediated charge transport
             mechanism in the deep tunneling superexchange regime can
             explain the observed dependence of the kinetics of charge
             transfer on the PNA sequence. Theoretical analysis suggests
             that the charge transport is dominantly hole-mediated and
             takes place through the filled bridge orbitals. The
             strongest contribution to conductance comes from the highest
             filled orbitals (HOMO, HOMO-1, and HOMO-2) of individual
             bases, with a rapid drop off in contributions from lower
             lying filled orbitals. Our studies further suggest that the
             linear correlation observed between the experimental charge
             transfer rates and the oxidation potential of base X arises
             from weak average interbase couplings and similar stacking
             geometries for the four TTTXTTT systems.},
   Doi = {10.1021/ja9000163},
   Key = {fds231890}
}

@article{fds231937,
   Author = {Xiao, D and Skourtis, SS and Rubtsov, IV and Beratan,
             DN},
   Title = {Turning charge transfer on and off in a molecular
             interferometer with vibronic pathways.},
   Journal = {Nano Letters},
   Volume = {9},
   Number = {5},
   Pages = {1818-1823},
   Year = {2009},
   Month = {May},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19435376},
   Abstract = {Inelastic electron-transfer kinetics in molecules with
             electron donor and acceptor units connected by a bridge is
             expected to be sensitive to bridge-localized vibronic
             interactions. Here, we show how inelastic electron transfer
             may be turned on and off in a double-slit style experiment
             that uses the molecule as an interferometer. We describe
             donor-acceptor interactions in terms of interfering vibronic
             coupling pathways that can be actively selected ("labeled")
             when pathway-specific vibrations are excited by infrared
             radiation. Thus, inelastic tunneling may be actively
             controlled, and we suggest strategies for building molecular
             scale quantum interferometers and switches based on this
             phenomenon.},
   Doi = {10.1021/nl8037695},
   Key = {fds231937}
}

@article{fds167417,
   Author = {R. Venkatramani and D.Y. Zang and C. Oh and J. Grote and D.
             Beratan},
   Title = {Photoconductivity and current-voltage characteristics in
             thin DNA},
   Journal = {Proceedings of SPIE-The Society of Photo-Optical
             Instrumentation Engineers, 7403, 74030B-1 to
             74030B-12},
   Year = {2009},
   Key = {fds167417}
}

@article{fds167393,
   Author = {X. Hu and D.N. Beratan and W. Yang},
   Title = {A gradient-directed Monte Caro method for global
             optimization in discrete space: Application to protein
             sequence design and folding},
   Journal = {J. Chem. Phys},
   Number = {131},
   Pages = {154117},
   Year = {2009},
   Key = {fds167393}
}

@article{fds167395,
   Author = {B.C. Rinderspacher and J. Andzelm and A. Rawlett and J. Dougherty and D.N. Beratan and W. Yang},
   Title = {Discrete optimization of electronic hyperpolarizabilities in
             a chemical subspace},
   Journal = {J. Chem. Theory Comput},
   Number = {5},
   Pages = {3321-3329},
   Year = {2009},
   Key = {fds167395}
}

@article{fds167397,
   Author = {L. Yuan and J. Seo and N.S. Kang and S. Keinan and S.E. Steele and G.A.
             Michelotti, W.C. Wetsel and D.N. Beratan and Y-D. Gong and T.H. Lee and J. Hong},
   Title = {Identification of 3-Hydroxy-2-(3-Hydroxyphenyl)-4H-1-Benzopyran-4-Ones
             as Isoform-Selective PKC-ζ Inhibitors and Potential
             Therapeutics for Psychostimulant Abuse},
   Journal = {Mol. BioSyst},
   Number = {5},
   Pages = {927-930},
   Year = {2009},
   Key = {fds167397}
}

@article{fds231889,
   Author = {Venkatramani, R and Zang, DY and Oh, C and Grote, J and Beratan,
             D},
   Title = {Photoconductivity and current-voltage characteristics of
             thin DNA films: Experiments and modeling},
   Journal = {Proceedings of SPIE - The International Society for Optical
             Engineering},
   Volume = {7403},
   Year = {2009},
   ISSN = {0277-786X},
   url = {http://dx.doi.org/10.1117/12.831024},
   Abstract = {We report experimental observations and theoretical modeling
             of an unusual photoelectric effect in deoxyribonucleic acid
             (DNA) thin-film devices, under visible and near-infrared
             illumination. The devices also show diode-type rectifying
             current-voltage (I-V) characteristics. An equivalent circuit
             model was constructed that fits the experimental data, and
             physical processes likely to arise in the devices are
             discussed. We envisage the formation of a Schottky barrier
             at the DNA film-metal interface and infer that the
             photoresponse arises from photoinjection of electrons from
             the metal into the DNA film. © 2009 SPIE.},
   Doi = {10.1117/12.831024},
   Key = {fds231889}
}

@article{fds231930,
   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 = {fds231930}
}

@article{fds231934,
   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 = {fds231934}
}

@article{fds231938,
   Author = {Paul, and Bezer, S and Venkatramani, R and Kocsis, L and Wierzbinski,
             E and Balaeff, A and Keinan, S and Beratan, DN and Achim, C and Waldeck,
             DH},
   Title = {Role of Nucleobase Energetics in Single Stranded Peptide
             Nucleic Acid Charge Transfer},
   Journal = {J. Am. Chem. Soc},
   Number = {131},
   Pages = {6498-6507},
   Year = {2009},
   Key = {fds231938}
}

@article{fds231946,
   Author = {Skourtis, SS and Beratan, DN and Naaman, R and Nitzan, A and Waldeck,
             DH},
   Title = {Chiral control of electron transmission through
             molecules.},
   Journal = {Physical Review Letters},
   Volume = {101},
   Number = {23},
   Pages = {238103},
   Year = {2008},
   Month = {December},
   ISSN = {0031-9007},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/19113598},
   Abstract = {Electron transmission through chiral molecules induced by
             circularly polarized light can be very different for
             mirror-image structures, a peculiar fact given that the
             electronic energy spectra of the systems are identical. We
             propose that this asymmetry--as large as 10% for resonant
             transport--arises from different dynamical responses of the
             mirrored structures to coherent excitation. This behavior is
             described in the context of a general novel phenomenon of
             current transfer (transfer of charge with its momentum
             information) and accounts for the observed asymmetry and its
             dependence on structure.},
   Doi = {10.1103/PhysRevLett.101.238103},
   Key = {fds231946}
}

@article{fds231947,
   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 = {fds231947}
}

@article{fds231943,
   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 = {fds231943}
}

@article{fds231948,
   Author = {Balabin, IA and Beratan, DN and Skourtis, SS},
   Title = {Persistence of structure over fluctuations in biological
             electron-transfer reactions.},
   Journal = {Physical Review Letters},
   Volume = {101},
   Number = {15},
   Pages = {158102},
   Year = {2008},
   Month = {October},
   ISSN = {0031-9007},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18999647},
   Abstract = {In the soft-wet environment of biomolecular electron
             transfer, it is possible that structural fluctuations could
             wash out medium-specific electronic effects on electron
             tunneling rates. We show that beyond a transition distance
             (2-3 A in water and 6-7 A in proteins), fluctuation
             contributions to the mean-squared donor-to-acceptor
             tunneling matrix element are likely to dominate over the
             average matrix element. Even though fluctuations dominate
             the tunneling mechanism at larger distances, we find that
             the protein fold is "remembered" by the electronic coupling,
             and structure remains a key determinant of electron transfer
             kinetics.},
   Doi = {10.1103/PhysRevLett.101.158102},
   Key = {fds231948}
}

@article{fds231941,
   Author = {He, W and Hatcher, E and Balaeff, A and Beratan, DN and Gil, RR and Madrid,
             M and Achim, C},
   Title = {Solution structure of a peptide nucleic acid duplex from NMR
             data: features and limitations.},
   Journal = {Journal of the American Chemical Society},
   Volume = {130},
   Number = {40},
   Pages = {13264-13273},
   Year = {2008},
   Month = {October},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18781753},
   Abstract = {This paper describes the results of a 1D and 2D NMR
             spectroscopy study of a palindromic 8-base pair PNA duplex
             GGCATGCC in H2O and H2O-D2O solutions. The (1)H NMR peaks
             have been assigned for most of the protons of the six
             central base pairs, as well as for several amide protons of
             the backbone. The resulting 36 interbase and base-backbone
             distance restraints were used together with Watson-Crick
             restraints to generate the PNA duplex structure in the
             course of 10 independent simulated annealing runs followed
             by restrained molecular dynamics (MD) simulations in
             explicit water. The resulting PNA structures correspond to a
             P-type helix with helical parameters close to those observed
             in the crystal structures of PNA. Based on the current
             limited number of restraints obtained from NMR spectra,
             alternative structures obtained by MD from starting PNA
             models based on DNA cannot be ruled out and are also
             discussed.},
   Doi = {10.1021/ja800652h},
   Key = {fds231941}
}

@article{fds231940,
   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 = {fds231940}
}

@article{fds231944,
   Author = {Hatcher, E and Balaeff, A and Keinan, S and Venkatramani, R and Beratan,
             DN},
   Title = {PNA versus DNA: effects of structural fluctuations on
             electronic structure and hole-transport mechanisms.},
   Journal = {Journal of the American Chemical Society},
   Volume = {130},
   Number = {35},
   Pages = {11752-11761},
   Year = {2008},
   Month = {September},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18693722},
   Abstract = {The effects of structural fluctuations on charge transfer in
             double-stranded DNA and peptide nucleic acid (PNA) are
             investigated. A palindromic sequence with two guanine bases
             that play the roles of hole donor and acceptor, separated by
             a bridge of two adenine bases, was analyzed using combined
             molecular dynamics (MD) and quantum-chemical methods.
             Surprisingly, electronic structure calculations on
             individual MD snapshots show significant frontier orbital
             electronic population on the bridge in approximately 10% of
             the structures. Electron-density delocalization to the
             bridge is found to be gated by fluctuations of the covalent
             conjugated bond structure of the aromatic rings of the
             nucleic bases. It is concluded, therefore, that both thermal
             hopping and superexchange should contribute significantly to
             charge transfer even in short DNA/PNA fragments. PNA is
             found to be more flexible than DNA, and this flexibility is
             predicted to produce larger rates of charge
             transfer.},
   Doi = {10.1021/ja802541e},
   Key = {fds231944}
}

@article{fds231939,
   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 = {fds231939}
}

@article{fds231942,
   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},
   ISSN = {0021-9606},
   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 = {fds231942}
}

@article{fds231949,
   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 = {fds231949}
}

@article{fds231887,
   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 = {fds231887}
}

@article{fds231951,
   Author = {Zuber, G and Wipf, P and Beratan, DN},
   Title = {Exploring the optical activity tensor by anisotropic
             Rayleigh optical activity scattering},
   Journal = {Chemphyschem},
   Volume = {9},
   Number = {2},
   Pages = {265-271},
   Year = {2008},
   Month = {February},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18219646},
   Abstract = {Rayleigh optical activity (RayOA) spectroscopy promises to
             provide an elegant and robust analytical method to probe
             molecular stereochemistry. A careful selection of RayOA
             variants such as right-angle depolarized ICP (incident
             circular polarization) or backscattering DCP(I) (in-phase
             dual circular polarization) allows analysis of the
             anisotropic component of the scattered light. In this study,
             we show that calculated anisotropic Rayleigh optical
             activity quantities provide key advantages over isotropic
             chiroptical quantities (such as optical rotation and RayOA
             variants dominated by isotropic invariants): 1) higher
             sensitivity for probing the chiroptical tensor G', 2)
             reduced dependence on small geometry changes, and 3) much
             less stringent computational demand for predicting an
             accurate sign than for optical rotation. Moreover, the
             stereochemical information provided by anisotropic RayOA and
             its invariants can be used to develop chirality descriptors
             because of the apparent correlation between
             structure/stereochemistry and the sign and magnitude of the
             anisotropic Rayleigh optical activity quantities.},
   Doi = {10.1002/cphc.200700660},
   Key = {fds231951}
}

@article{fds231945,
   Author = {Beratan, DN and Balabin, IA},
   Title = {Heme-copper oxidases use tunneling pathways.},
   Journal = {Proceedings of the National Academy of Sciences of
             USA},
   Volume = {105},
   Number = {2},
   Pages = {403-404},
   Year = {2008},
   Month = {January},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/18180451},
   Doi = {10.1073/pnas.0711343105},
   Key = {fds231945}
}

@misc{fds154732,
   Author = {I.A. Balabin and D.N. Beratan and S.S. Skourtis},
   Title = {The chemical roles of water in biological electron
             transfer},
   Booktitle = {Wiley Encyclopedia of Chemical Biology, Vol.
             1},
   Editor = {T.P. Begley},
   Year = {2008},
   url = {http://mrw.interscience.wiley.com/emrw/9780470048672/home/},
   Key = {fds154732}
}

@misc{fds154734,
   Author = {D.N. Beratan},
   Title = {Methods and systems for selecting molecular structures,”
             provisional patent application, submitted 2/16/07; patent
             filed 6/12/08},
   Year = {2008},
   Key = {fds154734}
}

@article{fds231888,
   Author = {Mukhopadhyay, P and Zuber, G and Beratan, DN},
   Title = {Characterizing aqueous solution conformations of a peptide
             backbone with theoretical analysis of the Raman optical
             activity spectra},
   Journal = {Biophys. J.},
   Number = {95},
   Pages = {5574-5586},
   Year = {2008},
   Key = {fds231888}
}

@article{fds231950,
   Author = {Parks, JM and Kondru, RK and Hua, H and Beratan, DN and Yang,
             W},
   Title = {Hepatitis C virus NS5B polymerase: Important roles of the
             internal energy and van der Waals interactions from QM/MM
             calculations},
   Journal = {J.Phys.Chem.B},
   Number = {112},
   Pages = {3168-3176},
   Year = {2008},
   Key = {fds231950}
}

@article{fds231955,
   Author = {Skourtis, SS and Beratan, DN},
   Title = {Biochemistry. Photosynthesis from the protein's
             perspective.},
   Journal = {Science},
   Volume = {316},
   Number = {5825},
   Pages = {703-704},
   Year = {2007},
   Month = {May},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17478711},
   Doi = {10.1126/science.1142330},
   Key = {fds231955}
}

@article{fds231952,
   Author = {Zöllner, A and Pasquinelli, MA and Bernhardt, R and Beratan,
             DN},
   Title = {Protein phosphorylation and intermolecular electron
             transfer: a joint experimental and computational study of a
             hormone biosynthesis pathway.},
   Journal = {Journal of the American Chemical Society},
   Volume = {129},
   Number = {14},
   Pages = {4206-4216},
   Year = {2007},
   Month = {April},
   ISSN = {0002-7863},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17358057},
   Abstract = {Protein phosphorylation is a common regulator of enzyme
             activity. Chemical modification of a protein surface,
             including phosphorylation, could alter the function of
             biological electron-transfer reactions. However, the
             sensitivity of intermolecular electron-transfer kinetics to
             post-translational protein modifications has not been widely
             investigated. We have therefore combined experimental and
             computational studies to assess the potential role of
             phosphorylation in electron-transfer reactions. We
             investigated the steroid hydroxylating system from bovine
             adrenal glands, which consists of adrenodoxin (Adx),
             adrenodoxin reductase (AdR), and a cytochrome P450, CYP11A1.
             We focused on the phosphorylation of Adx at Thr-71, since
             this residue is located in the acidic interaction domain of
             Adx, and a recent study has demonstrated that this residue
             is phosphorylated by casein kinase 2 (CK2) in vitro.1
             Optical biosensor experiments indicate that the presence of
             this phosphorylation slightly increases the binding affinity
             of oxidized Adx with CYP11A1ox but not AdRox. This tendency
             was confirmed by KA values extracted from Adx
             concentration-dependent stopped-flow experiments that
             characterize the interaction between AdRred and Adxox or
             between Adxred and CYP11A1ox. In addition, acceleration of
             the electron-transfer kinetics measured with stopped-flow is
             seen only for the phosphorylated Adx-CYP11A1 reaction.
             Biphasic reaction kinetics are observed only when Adx is
             phosphorylated at Thr-71, and the Brownian dynamics (BD)
             simulations suggest that this phosphorylation may enhance
             the formation of a secondary Adx-CYP11A1 binding complex
             that provides an additional electron-transfer pathway with
             enhanced coupling.},
   Doi = {10.1021/ja064803j},
   Key = {fds231952}
}

@article{fds231956,
   Author = {Prytkova, TR and Kurnikov, IV and Beratan, DN},
   Title = {Coupling coherence distinguishes structure sensitivity in
             protein electron transfer.},
   Journal = {Science},
   Volume = {315},
   Number = {5812},
   Pages = {622-625},
   Year = {2007},
   Month = {February},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17272715},
   Abstract = {Quantum mechanical analysis of electron tunneling in nine
             thermally fluctuating cytochrome b562 derivatives reveals
             two distinct protein-mediated coupling limits. A
             structure-insensitive regime arises for redox partners
             coupled through dynamically averaged multiple-coupling
             pathways (in seven of the nine derivatives) where heme-edge
             coupling leads to the multiple-pathway regime. A
             structure-dependent limit governs redox partners coupled
             through a dominant pathway (in two of the nine derivatives)
             where axial-ligand coupling generates the single-pathway
             limit and slower rates. This two-regime paradigm provides a
             unified description of electron transfer rates in 26
             ruthenium-modified heme and blue-copper proteins, as well as
             in numerous photosynthetic proteins.},
   Doi = {10.1126/science.1134862},
   Key = {fds231956}
}

@article{fds231954,
   Author = {Prytkova, TR and Beratan, DN and Skourtis, SS},
   Title = {Photoselected electron transfer pathways in DNA
             photolyase.},
   Journal = {Proceedings of the National Academy of Sciences of
             USA},
   Volume = {104},
   Number = {3},
   Pages = {802-807},
   Year = {2007},
   Month = {January},
   ISSN = {0027-8424},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17209014},
   Abstract = {Cyclobutane dimer photolyases are proteins that bind to
             UV-damaged DNA containing cyclobutane pyrimidine dimer
             lesions. They repair these lesions by photo-induced electron
             transfer. The electron donor cofactor of a photolyase is a
             two-electron-reduced flavin adenine dinucleotide (FADH(-)).
             When FADH(-) is photo-excited, it transfers an electron from
             an excited pi --> pi* singlet state to the pyrimidine dimer
             lesion of DNA. We compute the lowest excited singlet states
             of FADH(-) using ab initio (time-dependent density
             functional theory and time-dependent Hartree-Fock), and
             semiempirical (INDO/S configuration interaction) methods.
             The calculations show that the two lowest pi --> pi* singlet
             states of FADH(-) are localized on the side of the flavin
             ring that is proximal to the dimer lesion of DNA. For the
             lowest-energy donor excited state of FADH(-), we compute the
             conformationally averaged electronic coupling to acceptor
             states of the thymine dimer. The coupling calculations are
             performed at the INDO/S level, on donor-acceptor cofactor
             conformations obtained from molecular dynamics simulations
             of the solvated protein with a thymine dimer docked in its
             active site. These calculations demonstrate that the
             localization of the (1)FADH(-)* donor state on the flavin
             ring enhances the electronic coupling between the flavin and
             the dimer by permitting shorter electron-transfer pathways
             to the dimer that have single through-space jumps.
             Therefore, in photolyase, the photo-excitation itself
             enhances the electron transfer rate by moving the electron
             towards the dimer.},
   Doi = {10.1073/pnas.0605319104},
   Key = {fds231954}
}

@article{fds231953,
   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 = {fds231953}
}

@article{fds231885,
   Author = {Skourtis, SS and Beratan, DN},
   Title = {A molecular double slit paradigm},
   Journal = {AIP Conference Proceedings},
   Volume = {963},
   Number = {2},
   Pages = {809-812},
   Year = {2007},
   ISSN = {0094-243X},
   url = {http://dx.doi.org/10.1063/1.2836214},
   Abstract = {This contribution describes a simple model of a molecular
             interferometer. We consider an electron transfer molecule
             consisting of electron-donating and electron-acceptor parts
             that are connected by a bridge. The bridge provides two
             parallel tunneling pathways for electron transfer from donor
             to acceptor. In each pathway the electron can interact with
             a pathway-specific bridge vibration. We study electron
             transfer from donor to acceptor mediated by inelastic
             tunneling, where the tunneling electron exchanges energy
             with the local bridge vibrations. When the tunneling
             electron excites or is excited by a bridge vibration
             specific to one of the tunneling pathways, the tunneling
             pathway is "labeled" and the interference between tunneling
             pathways is lost. We discuss types of molecules and
             optical-spectroscopy experiments which could allow the
             observation of this effect. © 2007 American Institute of
             Physics.},
   Doi = {10.1063/1.2836214},
   Key = {fds231885}
}

@article{fds231886,
   Author = {Skourtis, SS and Prytkova, T and Beratan, DN},
   Title = {Flavin Charge Transfer Transitions Assist DNA Photolyase
             Electron Transfer.},
   Journal = {AIP Conference Proceedings},
   Volume = {963},
   Pages = {674-677},
   Year = {2007},
   ISSN = {0094-243X},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/23226907},
   Abstract = {This contribution describes molecular dynamics,
             semi-empirical and ab-initio studies of the primary
             photo-induced electron transfer reaction in DNA photolyase.
             DNA photolyases are FADH(-)-containing proteins that repair
             UV-damaged DNA by photo-induced electron transfer. A DNA
             photolyase recognizes and binds to cyclobutatne pyrimidine
             dimer lesions of DNA. The protein repairs a bound lesion by
             transferring an electron to the lesion from FADH(-), upon
             photo-excitation of FADH(-) with 350-450 nm light. We
             compute the lowest singlet excited states of FADH(-) in DNA
             photolyase using INDO/S configuration interaction,
             time-dependent density-functional, and time-dependent
             Hartree-Fock methods. The calculations identify the lowest
             singlet excited state of FADH(-) that is populated after
             photo-excitation and that acts as the electron donor. For
             this donor state we compute conformationally-averaged
             tunneling matrix elements to empty electron- acceptor states
             of a thymine dimer bound to photolyase. The conformational
             averaging involves different FADH(-) - thymine dimer
             confromations obtained from molecular dynamics simulations
             of the solvated protein with a thymine dimer docked in its
             active site. The tunneling matrix element computations use
             INDO/S-level Green's function, energy splitting, and
             Generalized Mulliken-Hush methods. These calculations
             indicate that photo-excitation of FADH(-) causes a π →
             π(*) charge-transfer transition that shifts electron
             density to the side of the flavin isoalloxazine ring that is
             adjacent to the docked thymine dimer. This shift in electron
             density enhances the FADH(-) - to - dimer electronic
             coupling, thus inducing rapid electron transfer.},
   Doi = {10.1063/1.2836174},
   Key = {fds231886}
}

@article{fds231957,
   Author = {Mukhopadhyay, P and Zuber, G and Wipf, P and Beratan,
             DN},
   Title = {Contribution of a solute's chiral solvent imprint to optical
             rotation.},
   Journal = {Angewandte Chemie International Edition},
   Volume = {46},
   Number = {34},
   Pages = {6450-6452},
   Year = {2007},
   ISSN = {1433-7851},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17645276},
   Doi = {10.1002/anie.200702273},
   Key = {fds231957}
}

@article{fds231884,
   Author = {Mukhopadhyay, P and Zuber, G and Goldsmith, M-R and Wipf, P and Beratan,
             DN},
   Title = {Solvent effect on optical rotation: A case study of
             methyloxirane in water.},
   Journal = {Chemphyschem},
   Volume = {7},
   Number = {12},
   Pages = {2483-2486},
   Year = {2006},
   Month = {December},
   ISSN = {1439-4235},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17072929},
   Doi = {10.1002/cphc.200600477},
   Key = {fds231884}
}

@article{fds231883,
   Author = {Perry, JL and Goldsmith, MR and Williams, TR and Radack, KP and Christensen, T and Gorham, J and Pasquinelli, MA and Toone, EJ and Beratan, DN and Simon, JD},
   Title = {Binding of warfarin influences the acid-base equilibrium of
             H242 in sudlow site I of human serum albumin.},
   Journal = {Photochemistry & Photobiology},
   Volume = {82},
   Number = {5},
   Pages = {1365-1369},
   Year = {2006},
   Month = {September},
   ISSN = {0031-8655},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16563025},
   Abstract = {Sudlow Site I of human serum albumin (HSA) is located in
             subdomain IIA of the protein and serves as a binding cavity
             for a variety of ligands. In this study, the binding of
             warfarin (W) is examined using computational techniques and
             isothermal titration calorimetry (ITC). The structure of the
             docked warfarin anion (W-) to Site I is similar to that
             revealed by X-ray crystallography, with a calculated binding
             constant of 5.8 x 10(5) M(-1). ITC experiments (pH 7.13 and
             I = 0.1) carried out in three different buffers (MOPs,
             phosphate and Tris) reveal binding of W- is accompanied by
             uptake of 0.30+/-0.02 protons from the solvent. This
             measurement suggests that the binding of W- is stabilized by
             an ion-pair interaction between protonated H242 and the
             phenoxide group of W-.},
   Doi = {10.1562/2006-02-23-RA-811},
   Key = {fds231883}
}

@article{fds231958,
   Author = {Kazmin, D and Prytkova, T and Cook, CE and Wolfinger, R and Chu, T-M and Beratan, D and Norris, JD and Chang, C-Y and McDonnell,
             DP},
   Title = {Linking ligand-induced alterations in androgen receptor
             structure to differential gene expression: a first step in
             the rational design of selective androgen receptor
             modulators.},
   Journal = {Molecular endocrinology (Baltimore, Md.)},
   Volume = {20},
   Number = {6},
   Pages = {1201-1217},
   Year = {2006},
   Month = {June},
   ISSN = {0888-8809},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16574741},
   Abstract = {We have previously identified a family of novel androgen
             receptor (AR) ligands that, upon binding, enable AR to adopt
             structures distinct from that observed in the presence of
             canonical agonists. In this report, we describe the use of
             these compounds to establish a relationship between AR
             structure and biological activity with a view to defining a
             rational approach with which to identify useful selective AR
             modulators. To this end, we used combinatorial peptide phage
             display coupled with molecular dynamic structure analysis to
             identify the surfaces on AR that are exposed specifically in
             the presence of selected AR ligands. Subsequently, we used a
             DNA microarray analysis to demonstrate that differently
             conformed receptors facilitate distinct patterns of gene
             expression in LNCaP cells. Interestingly, we observed a
             complete overlap in the identity of genes expressed after
             treatment with mechanistically distinct AR ligands. However,
             it was differences in the kinetics of gene regulation that
             distinguished these compounds. Follow-up studies, in
             cell-based assays of AR action, confirmed the importance of
             these alterations in gene expression. Together, these
             studies demonstrate an important link between AR structure,
             gene expression, and biological outcome. This relationship
             provides a firm underpinning for mechanism-based screens
             aimed at identifying SARMs with useful clinical
             profiles.},
   Doi = {10.1210/me.2005-0309},
   Key = {fds231958}
}

@article{fds231960,
   Author = {Kawatsu, T and Beratan, DN and Kakitani, T},
   Title = {Conformationally averaged score functions for electronic
             propagation in proteins.},
   Journal = {The Journal of Physical Chemistry Part B: Condensed Matter,
             Materials, Surfaces, Interfaces and Biophysical},
   Volume = {110},
   Number = {11},
   Pages = {5747-5757},
   Year = {2006},
   Month = {March},
   ISSN = {1520-6106},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16539520},
   Abstract = {We explore the influence of conformational dynamics on
             protein-mediated electron donor-acceptor interactions. We
             introduce a thermally averaged score function to
             characterize electronic propagation from redox cofactors
             into the protein and solvent. The score function is explored
             for myoglobin at the extended-Hückel level, and the results
             are compared with those of simpler models. The
             conformationally averaged quantum results are consistent
             with the empirical analysis of the Pathways model. Notably,
             subtle effects of quantum interference among multiple
             coupling pathways that arise in static structures are
             largely averaged out when protein thermal motion is
             included. Propagation through bulk water near the
             single-protein interface decays rapidly with
             distance.},
   Doi = {10.1021/jp052194g},
   Key = {fds231960}
}

@article{fds231961,
   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 = {fds231961}
}

@article{fds231962,
   Author = {Goldsmith, M-R and George, CB and Zuber, G and Naaman, R and Waldeck,
             DH and Wipf, P and Beratan, DN},
   Title = {The chiroptical signature of achiral metal clusters induced
             by dissymmetric adsorbates.},
   Journal = {Physical Chemistry Chemical Physics},
   Volume = {8},
   Number = {1},
   Pages = {63-67},
   Year = {2006},
   Month = {January},
   ISSN = {1463-9076},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16482245},
   Abstract = {Using a dissymmetrically-perturbed particle-in-a-box model,
             we demonstrate that the induced optical activity of chiral
             monolayer protected clusters, such as Whetten's Au28(SG)16
             glutathione-passivated gold nanoclusters (J. Phys. Chem. B,
             2000, 104, 2630-2641), could arise from symmetric metal
             cores perturbed by a dissymmetric or chiral field
             originating from the adsorbates. This finding implies that
             the electronic states of the nanocluster core are chiral,
             yet the lattice geometries of these cores need not be
             geometrically distorted by the chiral adsorbates. Based on
             simple chiral monolayer protected cluster models, we
             rationalize how the adsorption pattern of the tethering
             sulfur atoms has a substantial effect on the induced CD in
             the NIR spectral region, and we show how the chiral image
             charge produced in the core provides a convenient means of
             visualizing dissymmetric perturbations to the achiral gold
             nanocluster core.},
   Doi = {10.1039/b511563a},
   Key = {fds231962}
}

@misc{fds231865,
   Author = {Skourtis, SS and Lin, J and Beratan, DN},
   Title = {The effects of bridge motion on electron transfer reactions
             mediated by tunneling},
   Journal = {Modern Methods for Theoretical Physical Chemistry of
             Biopolymers},
   Pages = {357-382},
   Booktitle = {Modern Methods for Theoretical Physical Chemistry of
             Biopolymers},
   Publisher = {Elsevier},
   Editor = {E.B. Starikov and J.P. Lewis and S. Tanaka},
   Year = {2006},
   url = {http://dx.doi.org/10.1016/B978-044452220-7/50082-4},
   Abstract = {This chapter provides an in-depth review of recent
             developments associated with dynamical effects on electron
             transfer (ET) processes. It discusses the regimens of
             validity for standard rate formulations and presents in
             detail the explicit examples of dynamically coupled electron
             transfer reactions. It also discusses methods for the
             computation of tunneling matrix elements, bridge mediated
             electron transfer rates for fluctuating bridges, the
             influence of tunneling matrix element fluctuations on the ET
             rate, the qualitative picture of tunneling matrix element
             fluctuation effects on the ET rate, quantum nuclear motion
             and inelastic tunneling, tunneling through a bridge with
             large conformational freedom, and bimolecular ET kinetics:
             exploring numerous protein-protein conformations and aqueous
             coupling pathways between proteins. In conclusion, the
             theoretical framework and specific applications outlined
             show a richness that emerges as bridge dynamical effects are
             added explicitly to the considerations of electron transfer
             kinetics. Quantum interferences can be manipulated by
             inelastic tunneling effects; reaction mechanisms can be
             switched, and bridge-mediated tunneling can be dominated by
             minority population species. © 2006 Elsevier B.V. All
             rights reserved.},
   Doi = {10.1016/B978-044452220-7/50082-4},
   Key = {fds231865}
}

@article{fds231882,
   Author = {Skourtis, SS and Beratan, DN},
   Title = {Guest editorial: Electron transfer},
   Journal = {Molecular Simulation},
   Volume = {32},
   Number = {9},
   Pages = {675-676},
   Year = {2006},
   ISSN = {0892-7022},
   url = {http://dx.doi.org/10.1080/08927020600991120},
   Doi = {10.1080/08927020600991120},
   Key = {fds231882}
}

@article{fds231959,
   Author = {Kawatsu, T and Beratan, DN},
   Title = {Electron transfer between cofactors in protein domains
             linked by a flexible tether},
   Journal = {Chemical Physics},
   Volume = {326},
   Number = {1},
   Pages = {259-269},
   Year = {2006},
   ISSN = {0301-0104},
   url = {http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6TFM-4JBGJBR-2-4B&_cdi=5230&_user=38557&_orig=browse&_coverDate=07%2F11%2F2006&_sk=996739998&view=c&wchp=dGLbVzb-zSkWz&md5=4d2f73f773a8820794bf297c7a6a0854&ie=/sdarticle.pdf},
   Abstract = {Some key electron-transfer (ET) proteins have domains
             containing redox cofactors connected by a flexible tether.
             The relative motion of the domains is essential for reaction
             because of the strong ET rate dependence on distance. The
             constrained conformational flexibility produces a kinetic
             regime intermediate between "unimolecular" and
             "bimolecular". We used a simple model for ET coupled to
             conformational diffusion to explore the structure dependence
             of the ET kinetics. The model describes the evolution of an
             initially prepared reduced donor state, and recovers the
             diffusion and electron tunneling-limited regimes. The
             restriction of the conformational space imposed by the
             tether introduces an entropic component to the effective
             donor-acceptor interaction potential. As such, the tether
             length may control the transition between the electron
             tunneling and diffusion-limited regimes. © 2006 Elsevier
             B.V. All rights reserved.},
   Doi = {10.1016/j.chemphys.2006.01.020},
   Key = {fds231959}
}

@article{fds304362,
   Author = {Lin, J and Balabin, IA and Beratan, DN},
   Title = {The nature of aqueous tunneling pathways between
             electron-transfer proteins.},
   Journal = {Science},
   Volume = {310},
   Number = {5752},
   Pages = {1311-1313},
   Year = {2005},
   Month = {November},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16311331},
   Abstract = {Structured water molecules near redox cofactors were found
             recently to accelerate electron-transfer (ET) kinetics in
             several systems. Theoretical study of interprotein electron
             transfer across an aqueous interface reveals three
             distinctive electronic coupling mechanisms that we describe
             here: (i) a protein-mediated regime when the two proteins
             are in van der Waals contact; (ii) a structured
             water-mediated regime featuring anomalously weak distance
             decay at relatively close protein-protein contact distances;
             and (iii) a bulk water-mediated regime at large distances.
             Our analysis explains a range of otherwise puzzling
             biological ET kinetic data and provides a framework for
             including explicit water-mediated tunneling effects on ET
             kinetics.},
   Doi = {10.1126/science.1118316},
   Key = {fds304362}
}

@article{fds232021,
   Author = {Zuber, G and Goldsmith, M-R and Hopkins, TD and Beratan, DN and Wipf,
             P},
   Title = {Systematic assignment of the configuration of flexible
             natural products by spectroscopic and computational methods:
             the bistramide C analysis.},
   Journal = {Organic Letters},
   Volume = {7},
   Number = {23},
   Pages = {5269-5272},
   Year = {2005},
   Month = {November},
   ISSN = {1523-7060},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16268555},
   Abstract = {[reaction: see text] The combination of NMR NOE, chemical
             shift, and J-coupling measurements with molar rotation and
             circular dichroism (CD) determinations, including RI-DFT
             BP86/aug-cc-pVDZ calculations, reduced a candidate pool of
             1024 possible stereoisomers of (+)-bistramide C to a single
             absolute configuration assignment for the 10 stereogenic
             carbons of the marine natural product.},
   Doi = {10.1021/ol052154v},
   Key = {fds232021}
}

@article{fds232013,
   Author = {Zuber, G and Goldsmith, M-R and Beratan, DN and Wipf,
             P},
   Title = {Assignment of the absolute configuration of [n]-ladderanes
             by TD-DFT optical rotation calculations.},
   Journal = {Chirality},
   Volume = {17},
   Number = {8},
   Pages = {507-510},
   Year = {2005},
   Month = {October},
   ISSN = {0899-0042},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16121333},
   Abstract = {In this study, we report theoretical specific rotation
             values for a series of cis-/trans-alkylated-[5]-ladderanes
             and cis-/trans-methylated-[n]-ladderanes. Using
             time-dependent density functional response theory optical
             rotation calculations, we can assign (+) and (-) optical
             rotation signs to trans-(S)-alkyl-[5]-ladderane and
             trans-(R)-alkyl-[5]-ladderane configurations, respectively.
             In order to qualitatively validate our absolute
             configuration predictions, we computed optical rotation
             values at three different levels of theory--B3LYP, RI-BP86,
             and Hartree-Fock--using the aug-cc-pVDZ basis set. We
             observe a novel rung-parity-controlled oscillatory optical
             rotatory phenomenon in our computations, which, to the best
             of our knowledge, has never been reported or observed
             before. Furthermore, this preliminary analysis of optical
             rotation properties in this class of compounds should
             facilitate the correct absolute stereochemical assignment of
             natural and synthetic ladderanes, such as the trans-isomer
             of pentacyclic C(20)-fatty acid methyl ester
             (pentacycloanammoxic methyl ester), without the need for
             derivatization, in particular for cases where NMR or X-ray
             crystal structures are not readily available.},
   Doi = {10.1002/chir.20190},
   Key = {fds232013}
}

@article{fds232014,
   Author = {Zheng, J and Kang, YK and Therien, MJ and Beratan,
             DN},
   Title = {Generalized Mulliken-Hush analysis of electronic coupling
             interactions in compressed pi-stacked porphyrin-bridge-quinone
             systems.},
   Journal = {Journal of the American Chemical Society},
   Volume = {127},
   Number = {32},
   Pages = {11303-11310},
   Year = {2005},
   Month = {August},
   ISSN = {0002-7863},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16089459},
   Abstract = {Donor-acceptor interactions were investigated in a series of
             unusually rigid, cofacially compressed pi-stacked
             porphyrin-bridge-quinone systems. The two-state generalized
             Mulliken-Hush (GMH) approach was used to compute the
             coupling matrix elements. The theoretical coupling values
             evaluated with the GMH method were obtained from
             configuration interaction calculations using the INDO/S
             method. The results of this analysis are consistent with the
             comparatively soft distance dependences observed for both
             the charge separation and charge recombination reactions.
             Theoretical studies of model structures indicate that the
             phenyl units dominate the mediation of the donor-acceptor
             coupling and that the relatively weak exponential decay of
             rate with distance arises from the compression of this
             pi-electron stack.},
   Doi = {10.1021/ja050984y},
   Key = {fds232014}
}

@misc{fds231859,
   Author = {Winkler, JR and Gray, HB and Prytkova, TR and Kurnikov, IV and Beratan,
             DN},
   Title = {Electron Transfer through Proteins},
   Pages = {15-33},
   Booktitle = {Bioelectronics},
   Publisher = {Wiley-VCH},
   Editor = {I. Willner and E. Katz},
   Year = {2005},
   Month = {May},
   url = {http://dx.doi.org/10.1002/352760376X.ch2},
   Doi = {10.1002/352760376X.ch2},
   Key = {fds231859}
}

@article{fds232016,
   Author = {Lin, J and Beratan, DN},
   Title = {Simulation of electron transfer between cytochrome C2 and
             the bacterial photosynthetic reaction center: Brownian
             dynamics analysis of the native proteins and double
             mutants.},
   Journal = {The Journal of Physical Chemistry Part B: Condensed Matter,
             Materials, Surfaces, Interfaces and Biophysical},
   Volume = {109},
   Number = {15},
   Pages = {7529-7534},
   Year = {2005},
   Month = {April},
   ISSN = {1520-6106},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16851864},
   Abstract = {Electron transfer is essential for bacterial photosynthesis
             which converts light energy into chemical energy. This paper
             theoretically studies the interprotein electron transfer
             from cytochrome c(2) of Rhodobacter capsulatus to the
             photosynthetic reaction center of Rhodobacter sphaeroides in
             native and mutated systems. Brownian dynamics is used with
             an exponential distance-dependent electron-transfer rate
             model to compute bimolecular rate constants, which are
             consistent with experimental data when reasonable prefactors
             and decay constants are used. Interestingly, switching of
             the reaction mechanism from the diffusion-controlled limit
             in the native proteins to the activation-controlled limit in
             one of the mutants (DK(L261)/KE(C99)) was found. We also
             predict that the second-order rate for the native reaction
             center/cytochrome c(2) system will decrease with increasing
             ionic strength, a characteristic of electrostatically
             controlled docking.},
   Doi = {10.1021/jp045417w},
   Key = {fds232016}
}

@article{fds232020,
   Author = {Zuber, G and Goldsmith, M-R and Beratan, DN and Wipf,
             P},
   Title = {Towards Raman optical activity calculations of large
             molecules.},
   Journal = {Chemphyschem},
   Volume = {6},
   Number = {4},
   Pages = {595-597},
   Year = {2005},
   Month = {April},
   ISSN = {1439-4235},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15881572},
   Doi = {10.1002/cphc.200400544},
   Key = {fds232020}
}

@article{fds232017,
   Author = {Skourtis, SS and Balabin, IA and Kawatsu, T and Beratan,
             DN},
   Title = {Protein dynamics and electron transfer: electronic
             decoherence and non-Condon effects.},
   Journal = {Proceedings of the National Academy of Sciences of
             USA},
   Volume = {102},
   Number = {10},
   Pages = {3552-3557},
   Year = {2005},
   Month = {March},
   ISSN = {0027-8424},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15738409},
   Abstract = {We compute the autocorrelation function of the
             donor-acceptor tunneling matrix element <T(DA)(t)T(DA)(0)>
             for six Ru-azurin derivatives. Comparison of this decay time
             to the decay time of the time-dependent Franck-Condon factor
             {computed by Rossky and coworkers [Lockwood, D. M., Cheng,
             Y.-K. & Rossky, P. J. (2001) Chem. Phys. Lett. 345,
             159-165]} reveals the extent to which non-Condon effects
             influence the electron-transfer rate. <T(DA)(t)T(DA)(0)> is
             studied as a function of donor-acceptor distance, tunneling
             pathway structure, tunneling energy, and temperature to
             explore the structural and dynamical origins of non-Condon
             effects. For azurin, the correlation function is remarkably
             insensitive to tunneling pathway structure. The decay time
             is only slightly shorter than it is for solvent-mediated
             electron transfer in small organic molecules and originates,
             largely, from fluctuations of valence angles rather than
             bond lengths.},
   Doi = {10.1073/pnas.0409047102},
   Key = {fds232017}
}

@article{fds232018,
   Author = {Prytkova, TR and Kurnikov, IV and Beratan, DN},
   Title = {Ab initio based calculations of electron-transfer rates in
             metalloproteins.},
   Journal = {The Journal of Physical Chemistry Part B: Condensed Matter,
             Materials, Surfaces, Interfaces and Biophysical},
   Volume = {109},
   Number = {4},
   Pages = {1618-1625},
   Year = {2005},
   Month = {February},
   ISSN = {1520-6106},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16851133},
   Abstract = {A long-standing challenge in electron-transfer theory is to
             compute accurate rates of long-distance reactions in
             proteins. We describe an ab initio Hartree-Fock approach to
             compute electronic-coupling interactions and
             electron-transfer rates in proteins that allows the
             favorable comparison with experiment. The method includes
             the following key features; each is essential for reliable
             rate computations: (1) summing contributions over multiple
             tunneling pathways, (2) averaging couplings over thermally
             accessible protein conformations, (3) describing donor and
             acceptor electronic structure explicitly, including
             solvation effects, and averaging coupling over multiple
             energy-level crossings of the nearly degenerate
             donor-acceptor ligand-field states, and (4) eliminating
             basis set artifacts associated with diffuse basis functions.
             The strong dependence of coupling on donor-acceptor distance
             and on pathway interferences causes large variations of the
             computed electron-coupling values with protein geometry, and
             the strongest coupled conformers dominate the
             electron-transfer rate. As such, averaging over thermally
             accessible conformers of the protein and of the redox
             cofactors is essential. This approach was tested on six
             ruthenium-modified azurin derivatives using the high
             temperature nonadiabatic rate expression and compared with
             simpler pathways, average barrier, and semiempirical INDO
             models. Results of ab initio Hartree-Fock calculations with
             a split-valence basis set are in good agreement with the
             experimental rates. Predicted rates in the longer-distance
             derivatives are underestimated by 3-8-fold. This analysis
             indicates that the key ingredients needed for quantitatively
             reliable protein electron-transfer rate calculations are
             accessible.},
   Doi = {10.1021/jp0457491},
   Key = {fds232018}
}

@article{fds303173,
   Author = {Galperin, M and Beratan, DN},
   Title = {Simulation of scanning tunneling microscope images of
             1,3-cyclohexadiene bound to a silicon surface.},
   Journal = {The Journal of Physical Chemistry Part B: Condensed Matter,
             Materials, Surfaces, Interfaces and Biophysical},
   Volume = {109},
   Number = {4},
   Pages = {1473-1480},
   Year = {2005},
   Month = {February},
   ISSN = {1520-6106},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/16851118},
   Abstract = {Scanning tunneling microscope (STM) images of
             1,3-cyclohexadiene bound to silicon are interpreted using a
             nonequilibrium Green's function method. The resolution of
             the carbon-carbon double bond for positive bias voltages but
             not for negative bias voltages is explained using a
             quasiprobability density analysis. The asymmetry in the
             images arises from the system's voltage dependent electronic
             structure. A pi* orbital is found to be responsible for the
             empty state STM images of the carbon-carbon double bond,
             which is observed experimentally. The pi orbital relevant
             for the opposite bias does not produce an STM image sharply
             localized in the bond region because the molecule induces a
             Si-surface dipole dependent on the bias. The dipole voltage
             dependence arises from molecular charging. This result
             emphasizes the importance of simulating the molecule as an
             element in an open quantum system.},
   Doi = {10.1021/jp045783f},
   Key = {fds303173}
}

@misc{fds43098,
   Author = {S.S. Skourtis and J. Lin and D.N. Beratan},
   Title = {The effects of bridge motion on electron transfer reactions
             mediated by tunneling},
   Booktitle = {Modern Methods for Theoretical Physical Chemistry of
             Biopolymers},
   Editor = {E.B. Starikov and S. Tanaka and J.P. Lewis},
   Year = {2005},
   Key = {fds43098}
}

@article{fds232015,
   Author = {Lee, J and Balabin, IA and Beratan, DN and Lee, J-G and Jr,
             JTY},
   Title = {Charge transfer through chemisorbed organic molecules -
             Neutralization of ionization processes at local sites in the
             molecule},
   Journal = {Chemical Physics Letters},
   Volume = {412},
   Number = {1-3},
   Pages = {171-175},
   Year = {2005},
   url = {http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6TFN-4GNKRVG-1-N&_cdi=5231&_user=38557&_orig=browse&_coverDate=08%2F25%2F2005&_sk=995879998&view=c&wchp=dGLzVlz-zSkzk&md5=7ddc456a040d0561556a211cb6c30a39&ie=/sdarticle.pdf},
   Abstract = {The charge transfer through chemisorbed molecules has been
             studied by using normally oriented pyridine and benzoate
             molecules, chemisorbed on the Cu(1 1 0) surface. They yield
             H+ ions from the outer three C-H bond locations when ionized
             by electron impact. The local yield of these H+ ions allows
             the determination of the rate of electron transport through
             the molecule from the molecular contact point to the
             ionization position, causing ion neutralization. A
             superexchange (molecule-assisted tunneling) electron
             transfer process is found to control the electron-transfer
             event. © 2005 Elsevier B.V. All rights reserved.},
   Doi = {10.1016/j.cplett.2005.05.101},
   Key = {fds232015}
}

@article{fds232019,
   Author = {Galperin, M and Beratan, DN},
   Title = {Simulation of STM images of 1,4 cyclohexadiene bound to a
             silicon surface},
   Journal = {J. Phys. Chem B},
   Volume = {109},
   Number = {4},
   Pages = {1473-1480},
   Year = {2005},
   ISSN = {1520-6106},
   url = {http://pubs.acs.org/cgi-bin/article.cgi/jpcbfk/2005/109/i04/pdf/jp045783f.pdf},
   Abstract = {Scanning tunneling microscope (STM) images of
             1,3-cyclohexadiene bound to silicon are interpreted using a
             nonequilibrium Green's function method. The resolution of
             the carbon-carbon double bond for positive bias voltages but
             not for negative bias voltages is explained using a
             quasiprobability density analysis. The asymmetry in the
             images arises from the system's voltage dependent electronic
             structure. A pi* orbital is found to be responsible for the
             empty state STM images of the carbon-carbon double bond,
             which is observed experimentally. The pi orbital relevant
             for the opposite bias does not produce an STM image sharply
             localized in the bond region because the molecule induces a
             Si-surface dipole dependent on the bias. The dipole voltage
             dependence arises from molecular charging. This result
             emphasizes the importance of simulating the molecule as an
             element in an open quantum system.},
   Doi = {10.1021/jp045783f},
   Key = {fds232019}
}

@article{fds232022,
   Author = {Lin, J and Balabin, IA and Beratan, DN},
   Title = {Water -mediated tunneling between proteins},
   Journal = {Science},
   Volume = {310},
   Number = {5752},
   Pages = {1311-1313},
   Year = {2005},
   url = {http://www.sciencemag.org/cgi/reprint/310/5752/1311.pdf},
   Abstract = {Structured water molecules near redox cofactors were found
             recently to accelerate electron-transfer (ET) kinetics in
             several systems. Theoretical study of interprotein electron
             transfer across an aqueous interface reveals three
             distinctive electronic coupling mechanisms that we describe
             here: (i) a protein-mediated regime when the two proteins
             are in van der Waals contact; (ii) a structured
             water-mediated regime featuring anomalously weak distance
             decay at relatively close protein-protein contact distances;
             and (iii) a bulk water-mediated regime at large distances.
             Our analysis explains a range of otherwise puzzling
             biological ET kinetic data and provides a framework for
             including explicit water-mediated tunneling effects on ET
             kinetics.},
   Doi = {10.1126/science.1118316},
   Key = {fds232022}
}

@article{fds231968,
   Author = {Liao, J-L and Beratan, DN},
   Title = {How does protein architecture facilitate the transduction of
             ATP chemical-bond energy into mechanical work? The cases of
             nitrogenase and ATP binding-cassette proteins.},
   Journal = {Biophysical Journal},
   Volume = {87},
   Number = {2},
   Pages = {1369-1377},
   Year = {2004},
   Month = {August},
   ISSN = {0006-3495},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15298939},
   Abstract = {Transduction of adenosine triphosphate (ATP) chemical-bond
             energy into work to drive large-scale conformational changes
             is common in proteins. Two specific examples of
             ATP-utilizing proteins are the nitrogenase iron protein and
             the ATP binding-cassette transporter protein, BtuCD.
             Nitrogenase catalyzes biological nitrogen fixation whereas
             BtuCD transports vitamin B(12) across membranes. Both
             proteins drive their reactions with ATP. To interpret how
             the mechanical force generated by ATP binding and hydrolysis
             is propagated in these proteins, a coarse-grained elastic
             network model is employed. The analysis shows that subunits
             of the proteins move against each other in a concerted
             manner. The lowest-frequency modes of the nitrogenase iron
             protein and of the ATP binding-cassette transporter BtuCD
             protein are found to link the functionally critical domains,
             and these modes are suggested to be responsible for (at
             least the initial stages) large-scale ATP-coupled
             conformational changes.},
   Doi = {10.1529/biophysj.103.038653},
   Key = {fds231968}
}

@article{fds231965,
   Author = {Rubtsov, IV and Kang, YK and Redmore, NP and Allen, RM and Zheng, J and Beratan, DN and Therien, MJ},
   Title = {The degree of charge transfer in ground and charge-separated
             states revealed by ultrafast visible pump/mid-IR probe
             spectroscopy.},
   Journal = {Journal of the American Chemical Society},
   Volume = {126},
   Number = {16},
   Pages = {5022-5023},
   Year = {2004},
   Month = {April},
   ISSN = {0002-7863},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/15099057},
   Abstract = {We demonstrate a new femtosecond visible pump/mid-IR probe
             spectroscopic approach to assess directly the ground- and
             excited-state degrees of charge transfer (CT) in
             donor-spacer-acceptor (D-Sp-A) structures. Two classes of
             (porphinato)zinc(II) (PZn)-based D-Sp-A compounds with
             either quinonyl (Q) or N-(N'-octyl)pyromellitic diimide (PI)
             electron acceptors were interrogated. Carbonyl antisymmetric
             stretching mode frequency domain transient-IR spectra of
             these species were recorded and analyzed for the Q/PI
             moieties. These data show that the acceptor mode frequency
             shift, DeltanuA, determined by this method provides a more
             accurate measure of the degree of CT in ground and
             charge-separated states relative to other techniques which
             rely on the ground-state frequency shift alone. This
             approach enables determination of new experimental
             benchmarks to test the power of complimentary computational
             methods and provides a means to probe the degree of CT in
             transitions that either overlap strongly with other bands or
             possess low oscillator strength.},
   Doi = {10.1021/ja030674k},
   Key = {fds231965}
}

@article{fds304360,
   Author = {Liang, Z-X and Kurnikov, IV and Nocek, JM and Mauk, AG and Beratan, DN and Hoffman, BM},
   Title = {Dynamic docking and electron-transfer between cytochrome b5
             and a suite of myoglobin surface-charge mutants.
             Introduction of a functional-docking algorithm for
             protein-protein complexes.},
   Journal = {Journal of the American Chemical Society},
   Volume = {126},
   Number = {9},
   Pages = {2785-2798},
   Year = {2004},
   Month = {March},
   ISSN = {0002-7863},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/14995196},
   Abstract = {Horse myoglobin (Mb) provides a convenient "workbench" for
             probing the effects of electrostatics on binding and
             reactivity in the dynamic [Mb, cytochrome b(5)]
             electron-transfer (ET) complex. We have combined mutagenesis
             and heme neutralization to prepare a suite of six Mb
             surface-charge variants: the [S92D]Mb and [V67R]Mb mutants
             introduce additional charges on the "front" face, and
             incorporation of the heme di-ester into each of these
             neutralizes the charge on the heme propionates which further
             increases the positive charge on the "front" face. For this
             set of mutants, the nominal charge of Mb changes by -1 to +3
             units relative to that for native Mb. For each member of
             this set, we have measured the bimolecular quenching rate
             constant (k(2)) for the photoinitiated (3)ZnDMb -->
             Fe(3+)b(5) ET reaction as a function of ionic strength. We
             find: (i) a dramatic decoupling of binding and reactivity,
             in which k(2) varies approximately 10(3)-fold within the
             suite of Mbs without a significant change in binding
             affinity; (ii) the ET reaction occurs within the
             "thermodynamic" or "rapid exchange" limit of the "Dynamic
             Docking" model, in which a large ensemble of weakly bound
             protein-protein configurations contribute to binding, but
             only a few are reactive, as shown by the fact that the
             zero-ionic-strength bimolecular rate constant varies
             exponentially with the net charge on Mb; (iii) Brownian
             dynamic docking profiles allow us to visualize the
             microscopic basis of dynamic docking. To describe these
             results we present a new theoretical approach which
             mathematically combines PATHWAY donor/acceptor coupling
             calculations with Poisson-Boltzmann-based electrostatics
             estimates of the docking energetics in a Monte Carlo (MC)
             sampling framework that is thus specially tailored to the
             intermolecular ET problem. This procedure is extremely
             efficient because it targets only the functionally active
             complex geometries by introducing a "reactivity filter" into
             the computations themselves, rather than as a subsequent
             step. This efficiency allows us to employ more
             computationally expensive and accurate methods to describe
             the relevant intermolecular interaction energies and the
             protein-mediated donor/acceptor coupling interactions. It is
             employed here to compute the changes in the bimolecular rate
             constant for ET between Mb and cyt b(5) upon variations in
             the myoglobin surface charge, pH, and ionic
             strength.},
   Doi = {10.1021/ja038163l},
   Key = {fds304360}
}

@article{fds231879,
   Author = {Goldsmith, M-R and Jayasuriya, N and Beratan, DN and Wipf,
             P},
   Title = {Erratum: Optical rotation of noncovalent aggregates (Journal
             of the American Chemical Society (2003) 125
             (15696-15697))},
   Journal = {Journal of the American Chemical Society},
   Volume = {126},
   Number = {30},
   Pages = {9464-},
   Year = {2004},
   url = {http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ja047614e},
   Doi = {10.1021/ja047614e},
   Key = {fds231879}
}

@article{fds231963,
   Author = {Jianping, L and Beratan, DN},
   Title = {Tunneling while pulling: The dependence of tunneling current
             on end-to-end distance in a flexible molecule},
   Journal = {The Journal of Physical Chemistry Part A: Molecules,
             Spectroscopy, Kinetics, Environment and General
             Theory},
   Volume = {108},
   Number = {26},
   Pages = {5655-5661},
   Year = {2004},
   ISSN = {1089-5639},
   url = {http://dx.doi.org/10.1021/jp0379502},
   Abstract = {Most molecules access a broad range of conformations at room
             temperature. Since electron-tunneling interactions are
             exponentially sensitive to geometry changes, thermal
             fluctuations are expected to have a large influence on
             room-temperature tunneling currents and scanning tunneling
             microscope images. We explore the influence of
             conformational freedom on tunneling currents in a simple
             model for tunneling mediated by a single small molecule that
             bridges between a model tip and substrate. The tip and
             substrate are described as semi-infinite structures. The
             bridging molecule and the metals are all described with
             tight-binding Hamiltonians. The conformationally averaged
             tunneling matrix element, proportional to the tunneling
             currents, is computed from thermally accessible molecular
             conformations. We vary the sulfur-to-sulfur separation
             distance in -S-(CH 2) 8-S- (n-octanedithiol) and, at each of
             these separations, compute the family of thermally
             accessible conformers. The two sulfur atoms are constrained
             to positions along a line perpendicular to the substrate
             surface. The conformationally averaged tunneling current
             computed for each fixed sulfur-to-sulfur distance is
             predicted to display an average distance dependence that is
             strikingly similar to the decay found in experiments
             performed on families of extended ("all trans") n-alkanes.
             That is, the tunneling current is predicted to decay
             exponentially with a decay parameter of ∼1.0 Å -1 based
             on the tip to substrate distance. This observation supports
             the notion that the most strongly coupled conformers in the
             ensemble dominate the STM tunneling current. This conclusion
             is also consistent with the analysis of protein
             electron-transfer systems, where thermal fluctuations are
             predicted to shorten coupling pathways and to minimize the
             influence on the rate of destructive interferences among
             multiple coupling pathways.},
   Doi = {10.1021/jp0379502},
   Key = {fds231963}
}

@article{fds231964,
   Author = {Berlin, YA and Kurnikov, IV and Ratner, MA and Burin, AL and Beratan,
             DN},
   Title = {DNA electron transfer processes: Some theoretical
             notions},
   Journal = {Top. Curr. Chem.},
   Volume = {237},
   Pages = {1-36},
   Year = {2004},
   Key = {fds231964}
}

@article{fds231966,
   Author = {Skourtis, SS and Waldeck, DH and Beratan, DN},
   Title = {Loss of Pathway Coherence in Inelastic Bridge-mediated
             Electron Transfer},
   Journal = {J. Phys. Chem. B},
   Volume = {108},
   Number = {40},
   Pages = {15511-15518},
   Year = {2004},
   ISSN = {1520-6106},
   url = {http://pubs.acs.org/cgi-bin/article.cgi/jpcbfk/2004/108/i40/pdf/jp0485340.pdf},
   Abstract = {Theoretical analysis of nonadiabatic electron-transfer
             reactions in molecules usually assumes that electron
             amplitude propagates coherently from the reductant to the
             oxidant via covalent and noncovalent coupling pathways. We
             show that when the tunneling electron excites local bridge
             vibrations (inelastic tunneling), the excitation "labels"
             the physical pathway traversed. As such, the coherence among
             the bridge-mediated tunneling pathways is destroyed. We
             illustrate this effect using a simple model Hamiltonian and
             show how the donor-acceptor interaction, and thus the
             electron-transfer rate, is modified by inelastic effects.
             Pathway coherence loss provides a mechanism to relax
             orbital-symmetry constraints on electron-transfer reactions.
             This effect may be of particular significance in
             macromolecules with destructively interfering pathways or
             low tunneling barriers. Pathway decoherence that arises from
             inelastic effects in molecules is analogous to coherence
             loss in mesoscopic "which way" interferometers and might
             provide an approach to gate electron flow in molecular-scale
             devices.},
   Doi = {10.1021/jp0485340},
   Key = {fds231966}
}

@article{fds231967,
   Author = {Perry, JL and Goldsmith, MR and Peterson, MA and Beratan, DN and Wozniak, G and Rüker, F and Simon, JD},
   Title = {Structure of the ochratoxin a binding site within human
             serum albumin},
   Journal = {The Journal of Physical Chemistry Part B: Condensed Matter,
             Materials, Surfaces, Interfaces and Biophysical},
   Volume = {108},
   Number = {43},
   Pages = {16960-16964},
   Year = {2004},
   ISSN = {1520-6106},
   url = {http://pubs.acs.org/cgi-bin/article.cgi/jpcbfk/2004/108/i43/pdf/jp0480652.pdf},
   Abstract = {The binding site of ochratoxin A (OTA) within domain 2A of
             human serum albumin (HSA) is examined by theoretical
             simulations and site-directed mutagenesis experiments. The
             calculated binding constant, based on docking experiments
             and theoretical affinity constants derived from the
             empirical free energy of binding as implemented in AutoDock
             3.0, for the OTA dianion (3.7 × 10 6 M -1) is in good
             agreement with experimental value of 5.2 × 10 6 M -1. The
             carboxy terminus of OTA associates with R218 and R222 of the
             protein. Binding is reduced by over an order of magnitude
             for the mutant R218A in both experiments and theoretical
             simulations. The carbonyl of the lactone and the phenolic
             group of OTA are in close proximity to R257. The
             experimental binding constant of OTA to the R257A mutant is
             1.6 × 10 5 M -1, over an order of magnitude smaller than
             for the wild-type protein. The predicted binding constant
             based on a comparison of the lowest-energy conformer from
             docking studies performed in AutoDock 3.0 of OTA to the
             R257A mutant (8.3 × 10 4 M -1) is also in good agreement
             with the experimental result. R257 clearly plays an
             important role in the binding of the isocoumarin ring of OTA
             by serving as a proton acceptor and stabilizing the binding
             through the creation of an ion pair with the phenoxide group
             on OTA.},
   Doi = {10.1021/jp0480652},
   Key = {fds231967}
}

@article{fds232023,
   Author = {Liang, Z-X and Kurnikov, IV and Nocek, JM and Mauk, AG and Beratan, DN and Hoffman, BM},
   Title = {Electron transfer between cytochrome b5 and a suite of
             myoglobin surface-charge mutants; Introduction of a
             funtional-docking algorithm for dynamically-docked
             protein-protein complexes},
   Journal = {J. Am. Chem. Soc.},
   Volume = {126},
   Number = {9},
   Pages = {2785-2798},
   Year = {2004},
   ISSN = {0002-7863},
   url = {http://pubs.acs.org/cgi-bin/article.cgi/jacsat/2004/126/i09/pdf/ja038163l.pdf},
   Abstract = {Horse myoglobin (Mb) provides a convenient "workbench" for
             probing the effects of electrostatics on binding and
             reactivity in the dynamic [Mb, cytochrome b(5)]
             electron-transfer (ET) complex. We have combined mutagenesis
             and heme neutralization to prepare a suite of six Mb
             surface-charge variants: the [S92D]Mb and [V67R]Mb mutants
             introduce additional charges on the "front" face, and
             incorporation of the heme di-ester into each of these
             neutralizes the charge on the heme propionates which further
             increases the positive charge on the "front" face. For this
             set of mutants, the nominal charge of Mb changes by -1 to +3
             units relative to that for native Mb. For each member of
             this set, we have measured the bimolecular quenching rate
             constant (k(2)) for the photoinitiated (3)ZnDMb -->
             Fe(3+)b(5) ET reaction as a function of ionic strength. We
             find: (i) a dramatic decoupling of binding and reactivity,
             in which k(2) varies approximately 10(3)-fold within the
             suite of Mbs without a significant change in binding
             affinity; (ii) the ET reaction occurs within the
             "thermodynamic" or "rapid exchange" limit of the "Dynamic
             Docking" model, in which a large ensemble of weakly bound
             protein-protein configurations contribute to binding, but
             only a few are reactive, as shown by the fact that the
             zero-ionic-strength bimolecular rate constant varies
             exponentially with the net charge on Mb; (iii) Brownian
             dynamic docking profiles allow us to visualize the
             microscopic basis of dynamic docking. To describe these
             results we present a new theoretical approach which
             mathematically combines PATHWAY donor/acceptor coupling
             calculations with Poisson-Boltzmann-based electrostatics
             estimates of the docking energetics in a Monte Carlo (MC)
             sampling framework that is thus specially tailored to the
             intermolecular ET problem. This procedure is extremely
             efficient because it targets only the functionally active
             complex geometries by introducing a "reactivity filter" into
             the computations themselves, rather than as a subsequent
             step. This efficiency allows us to employ more
             computationally expensive and accurate methods to describe
             the relevant intermolecular interaction energies and the
             protein-mediated donor/acceptor coupling interactions. It is
             employed here to compute the changes in the bimolecular rate
             constant for ET between Mb and cyt b(5) upon variations in
             the myoglobin surface charge, pH, and ionic
             strength.},
   Doi = {10.1021/ja038163l},
   Key = {fds232023}
}

@article{fds304361,
   Author = {Skourtis, SS and Waldeck, DH and Beratan, DN},
   Title = {Inelastic electron tunneling erases coupling-pathway
             interferences},
   Journal = {The Journal of Physical Chemistry Part B: Condensed Matter,
             Materials, Surfaces, Interfaces and Biophysical},
   Volume = {108},
   Number = {40},
   Pages = {15511-15518},
   Year = {2004},
   ISSN = {1520-6106},
   url = {http://dx.doi.org/10.1021/jp0485340},
   Abstract = {Theoretical analysis of nonadiabatic electron-transfer
             reactions in molecules usually assumes that electron
             amplitude propagates coherently from the reductant to the
             oxidant via covalent and noncovalent coupling pathways. We
             show that when the tunneling electron excites local bridge
             vibrations (inelastic tunneling), the excitation "labels"
             the physical pathway traversed. As such, the coherence among
             the bridge-mediated tunneling pathways is destroyed. We
             illustrate this effect using a simple model Hamiltonian and
             show how the donor-acceptor interaction, and thus the
             electron-transfer rate, is modified by inelastic effects.
             Pathway coherence loss provides a mechanism to relax
             orbital-symmetry constraints on electron-transfer reactions.
             This effect may be of particular significance in
             macromolecules with destructively interfering pathways or
             low tunneling barriers. Pathway decoherence that arises from
             inelastic effects in molecules is analogous to coherence
             loss in mesoscopic "which way" interferometers and might
             provide an approach to gate electron flow in molecular-scale
             devices.},
   Doi = {10.1021/jp0485340},
   Key = {fds304361}
}

@article{fds232024,
   Author = {Goldsmith, M-R and Jayasuriya, N and Beratan, DN and Wipf,
             P},
   Title = {Optical rotation of noncovalent aggregates.},
   Journal = {Journal of the American Chemical Society},
   Volume = {125},
   Number = {51},
   Pages = {15696-15697},
   Year = {2003},
   Month = {December},
   ISSN = {0002-7863},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/14677931},
   Abstract = {Dilute solutions of (R)-(-)-pantolactone in CCl4 were
             studied by polarimetry in conjunction with theoretical
             calculations of [alpha]D. Our data demonstrate that the
             self-association of a chiral solute results in a change in
             [alpha]D that can be accounted for by the presence of
             hydrogen-bonded dimeric species. The theoretical analysis
             predicts a concentration-dependent specific rotation in good
             agreement with experiment. Further exploration of monomer
             and dimer [alpha]D differences, through atomic map analysis,
             reveals large contributions to [alpha]D from the
             hydrogen-bonded hydroxyl groups in the tightly-coupled
             dimer. This study extends the computation of chiroptical
             properties to the accurate concentration-dependent
             prediction of [alpha]D for noncovalently interacting
             self-associating species.},
   Doi = {10.1021/ja0376893},
   Key = {fds232024}
}

@article{fds232056,
   Author = {Perry, JL and Christensen, T and Goldsmith, MR and Toone, EJ and Beratan, DN and Simon, JD},
   Title = {A protein-ligand ion pair stabilizes the binding of
             Ochratoxin A to human serum albumin},
   Journal = {J. Phys. Chem. B.},
   Volume = {107},
   Number = {31},
   Pages = {7884-7888},
   Year = {2003},
   Abstract = {Ochratoxin A (OTA), a fungal metabolite of strains of
             Penicillium and Aspergillus, binds in its dianion form to
             Sudlow site I of human serum albumin (HSA) with high
             affinity. In this study, isothermal calorimetry (ITC) is
             used to study the binding of OTA and its O-methyl derivative
             (MOA). Calculations of the equilibrium geometry of the
             monoanion and dianion of OTA reveal only small structural
             changes among the lowest energy conformers. The ITC data
             show the binding of MOA, which lacks the phenolic proton of
             OTA, is accompanied by the uptake of a proton from the
             surrounding solvent. At pH 7.13, the binding of OTA is
             accompanied by uptake of 0.43 ± 0.15 protons from the
             solvent. At this pH, the monoanion (0.54) and dianion (0.46)
             forms of OTA are both present in solution. However, the pKa
             of the phenolic group of OTA decreases by more than three
             units upon protein binding, and so all available OTA is
             bound to the protein as the dianion. To account for the ITC
             data, a model is proposed in which the proton is provided by
             the phenolic moiety of OTA in the case of initial binding of
             the monoanion, and a proton is taken up from the surrounding
             solvent for initial binding of the dianion. The binding
             constant of MOA is 2 orders of magnitude smaller than that
             of OTA, indicating the ion pair between the phenoxide group
             of OTA and the protonated amino acid is a major contributor
             to the high binding affinity of OTA to HSA. To identify the
             specific amino acid involved, the binding of OTA to bovine,
             rat, and porcine serum albumins was examined. Deprotonation
             of the monoanion of OTA occurred upon binding to all
             species. Assuming the amino acid is conserved between
             species and taking into account crystal structures of
             ligands bound to site I of HSA and their ability to displace
             OTA from HSA, either R218 or R257 is involved in the ion
             pairing with OTA. These two amino acids sit across the
             binding cavity from one other in site I.},
   Key = {fds232056}
}

@article{fds304358,
   Author = {Perry, JL and Christensen, T and Goldsmith, MR and Toone, EJ and Beratan, DN and Simon, JD},
   Title = {Binding of ochratoxin a to human serum albumin stabilized by
             a protein-ligand ion pair},
   Journal = {Journal of Physical Chemistry B},
   Volume = {107},
   Number = {31},
   Pages = {7884-7888},
   Year = {2003},
   Abstract = {Ochratoxin A (OTA), a fungal metabolite of strains of
             Penicillium and Aspergillus, binds in its dianion form to
             Sudlow site I of human serum albumin (HSA) with high
             affinity. In this study, isothermal calorimetry (ITC) is
             used to study the binding of OTA and its O-methyl derivative
             (MOA). Calculations of the equilibrium geometry of the
             monoanion and dianion of OTA reveal only small structural
             changes among the lowest energy conformers. The ITC data
             show the binding of MOA, which lacks the phenolic proton of
             OTA, is accompanied by the uptake of a proton from the
             surrounding solvent. At pH 7.13, the binding of OTA is
             accompanied by uptake of 0.43 ± 0.15 protons from the
             solvent. At this pH, the monoanion (0.54) and dianion (0.46)
             forms of OTA are both present in solution. However, the pKa
             of the phenolic group of OTA decreases by more than three
             units upon protein binding, and so all available OTA is
             bound to the protein as the dianion. To account for the ITC
             data, a model is proposed in which the proton is provided by
             the phenolic moiety of OTA in the case of initial binding of
             the monoanion, and a proton is taken up from the surrounding
             solvent for initial binding of the dianion. The binding
             constant of MOA is 2 orders of magnitude smaller than that
             of OTA, indicating the ion pair between the phenoxide group
             of OTA and the protonated amino acid is a major contributor
             to the high binding affinity of OTA to HSA. To identify the
             specific amino acid involved, the binding of OTA to bovine,
             rat, and porcine serum albumins was examined. Deprotonation
             of the monoanion of OTA occurred upon binding to all
             species. Assuming the amino acid is conserved between
             species and taking into account crystal structures of
             ligands bound to site I of HSA and their ability to displace
             OTA from HSA, either R218 or R257 is involved in the ion
             pairing with OTA. These two amino acids sit across the
             binding cavity from one other in site I.},
   Key = {fds304358}
}

@article{fds304359,
   Author = {Lewis, FD and Liu, J and Weigel, W and Rettig, W and Kurnikov, IV and Beratan, DN},
   Title = {Donor-bridge-acceptor energetics determine the distance
             dependence of electron tunneling in DNA.},
   Journal = {Proceedings of the National Academy of Sciences of
             USA},
   Volume = {99},
   Number = {20},
   Pages = {12536-12541},
   Year = {2002},
   Month = {October},
   ISSN = {0027-8424},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12228728},
   Abstract = {Electron transfer (ET) processes in DNA are of current
             interest because of their involvement in oxidative strand
             cleavage reactions and their relevance to the development of
             molecular electronics. Two mechanisms have been identified
             for ET in DNA, a single-step tunneling process and a
             multistep charge-hopping process. The dynamics of tunneling
             reactions depend on both the distance between the electron
             donor and acceptor and the nature of the molecular bridge
             separating the donor and acceptor. In the case of protein
             and alkane bridges, the distance dependence is not strongly
             dependent on the properties of the donor and acceptor. In
             contrast, we show here that the distance decay of DNA ET
             rates varies markedly with the energetics of the donor and
             acceptor relative to the bridge. Specifically, we find that
             an increase in the energy of the bridge states by 0.25 eV (1
             eV = 1.602 x 10(-19) J) relative to the donor and acceptor
             energies for photochemical oxidation of nucleotides, without
             changing the reaction free energy, results in an increase in
             the characteristic exponential distance decay constant for
             the ET rates from 0.71 to 1.1 A(-1). These results show
             that, in the small tunneling energy gap regime of DNA ET,
             the distance dependence is not universal; it varies strongly
             with the tunneling energy gap. These DNA ET reactions fill a
             "missing link" or transition regime between the large
             barrier (rapidly decaying) tunneling regime and the (slowly
             decaying) hopping regime in the general theory of
             bridge-mediated ET processes.},
   Doi = {10.1073/pnas.192432899},
   Key = {fds304359}
}

@article{fds232035,
   Author = {Liang, Z-X and Nocek, JM and Huang, K and Hayes, RT and Kurnikov, IV and Beratan, DN and Hoffman, BM},
   Title = {Dynamic docking and electron transfer between Zn-myoglobin
             and cytochrome b(5).},
   Journal = {Journal of the American Chemical Society},
   Volume = {124},
   Number = {24},
   Pages = {6849-6859},
   Year = {2002},
   Month = {June},
   ISSN = {0002-7863},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/12059205},
   Abstract = {We present a broad study of the effect of neutralizing the
             two negative charges of the Mb propionates on the
             interaction and electron transfer (ET) between horse Mb and
             bovine cyt b(5), through use of Zn-substituted Mb (ZnMb, 1)
             to study the photoinitiated reaction, ((3)ZnP)Mb + Fe(3+)cyt
             b(5) --> (ZnP)(+)Mb + Fe(2+)cyt b(5). The charge
             neutralization has been carried out both by replacing the Mb
             heme with zinc-deuteroporphyrin dimethylester (ZnMb(dme),
             2), which replaces the charges by small neutral hydrophobic
             patches, and also by replacement with the newly prepared
             zinc-deuteroporphyrin diamide (ZnMb(diamide), 3), which
             converts the charged groups to neutral, hydrophilic ones.
             The effect of propionate neutralization on the conformation
             of the zinc-porphyrin in the Mb heme pocket has been studied
             by multinuclear NMR with an (15)N labeled zinc porphyrin
             derivative (ZnMb((15)N-diamide), 4). The rates of
             photoinitiated ET between the Mb's (1-3) and cyt b(5) have
             been measured over a range of pH values and ionic strengths.
             Isothermal titration calorimetry (ITC) and NMR methods have
             been used to independently investigate the effect of charge
             neutralization on Mb/b(5) binding. The neutralization of the
             two heme propionates of ZnMb by formation of the heme
             diester or, for the first time, the diamide increases the
             second-order rate constant of the ET reaction between ZnMb
             and cyt b(5) by as much as several 100-fold, depending on pH
             and ionic strength, while causing negligible changes in
             binding affinity. Brownian dynamic (BD) simulations and ET
             pathway calculations provide insight into the protein
             docking and ET process. The results support a new "dynamic
             docking" paradigm for protein-protein reactions in which
             numerous weakly bound conformations of the docked complex
             contribute to the binding of cyt b(5) to Mb and Hb, but only
             a very small subset of these are ET active, and this subset
             does not include the conformations most favorable for
             binding; the Mb surface is a large "target" with a small
             "bullseye" for the cyt b(5) "arrow". This paradigm differs
             sharply from the more familiar, "simple" docking within a
             single, or narrow range of conformations, where binding
             strength and ET reactivity increase in parallel. Likewise,
             it is distinct from, although complementary to, the
             well-known picture of conformational control of ET through
             "gating", or a related picture of "conformational coupling".
             The new model describes situations in which tight binding
             does not correlate with efficient ET reactivity, and
             explains how it is possible to modulate reactivity without
             changing affinity. Such "decoupling" of reactivity from
             binding clearly is of physiological relevance for the
             reduction of met-Mb in muscle and of met-Hb in a red cell,
             where tight binding of cyt b(5) to the high concentration of
             ferrous-Mb/Hb would prevent the cytochrome from finding and
             reducing the oxidized proteins; it likely is of
             physiological relevance in other situations, as
             well.},
   Key = {fds232035}
}

@misc{fds231874,
   Author = {Beratan, DN and Kondru, RK and Wipf, P},
   Title = {Optical activity: From structure - Function to structure
             prediction},
   Journal = {ACS Symposium Series},
   Volume = {810},
   Pages = {104-118},
   Year = {2002},
   ISSN = {0097-6156},
   Abstract = {Optical rotation is easily measured and provides a
             comprehensive probe of molecular dissymmetry. Reliable
             calculations of optical rotation angles are now accessible
             for organic molecules. These calculations have allowed us to
             establish new computational approaches to assign the
             absolute stereochemistry of complex natural products. These
             methods also allow us to pinpoint chemical group
             contributions to optical rotation, resulting in assignment
             of how particular dissymmetric structural elements influence
             the sign and the magnitude of optical rotations. This
             chapter reviews our recent developments in computing optical
             rotation angles for natural products, in using this data to
             assign absolute stereochemistry, and in establishing
             structure-property relations for rotation
             angles.},
   Key = {fds231874}
}

@article{fds232005,
   Author = {Lewis, FD and Liu, J and Weigel, W and Retting, W and Kurnikov, IV and Beratan, DN},
   Title = {Tunneling energy controls DNA electron transfer distance
             dependence},
   Journal = {Proc. Natl. Acad. Sci. (USA)},
   Volume = {99},
   Number = {20},
   Pages = {12536-12541},
   Year = {2002},
   ISSN = {0027-8424},
   url = {http://www.pnas.org/cgi/content/full/99/20/12536},
   Abstract = {Electron transfer (ET) processes in DNA are of current
             interest because of their involvement in oxidative strand
             cleavage reactions and their relevance to the development of
             molecular electronics. Two mechanisms have been identified
             for ET in DNA, a single-step tunneling process and a
             multistep charge-hopping process. The dynamics of tunneling
             reactions depend on both the distance between the electron
             donor and acceptor and the nature of the molecular bridge
             separating the donor and acceptor. In the case of protein
             and alkane bridges, the distance dependence is not strongly
             dependent on the properties of the donor and acceptor. In
             contrast, we show here that the distance decay of DNA ET
             rates varies markedly with the energetics of the donor and
             acceptor relative to the bridge. Specifically, we find that
             an increase in the energy of the bridge states by 0.25 eV (1
             eV = 1.602 x 10(-19) J) relative to the donor and acceptor
             energies for photochemical oxidation of nucleotides, without
             changing the reaction free energy, results in an increase in
             the characteristic exponential distance decay constant for
             the ET rates from 0.71 to 1.1 A(-1). These results show
             that, in the small tunneling energy gap regime of DNA ET,
             the distance dependence is not universal; it varies strongly
             with the tunneling energy gap. These DNA ET reactions fill a
             "missing link" or transition regime between the large
             barrier (rapidly decaying) tunneling regime and the (slowly
             decaying) hopping regime in the general theory of
             bridge-mediated ET processes.},
   Doi = {10.1073/pnas.192432899},
   Key = {fds232005}
}

@article{fds232006,
   Author = {Jones, ML and Kurnikov, IV and Beratan, DN},
   Title = {The nature of tunneling pathway and average packing density
             models for protein-mediated electron transfer},
   Journal = {The Journal of Physical Chemistry Part A: Molecules,
             Spectroscopy, Kinetics, Environment and General
             Theory},
   Volume = {106},
   Number = {10},
   Pages = {2002-2006},
   Year = {2002},
   ISSN = {1089-5639},
   url = {http://pubs.acs.org/cgi-bin/article.cgi/jpcafh/2002/106/i10/pdf/jp0133743.pdf},
   Abstract = {The last 30 years have witnessed the development of
             increasingly successful theoretical approaches to predicting
             how a protein's chemical composition and three-dimensional
             structure influence its propensity to mediate
             electron-transfer reactions. Analysis has progressed from
             uniform-barrier models that neglect atomic detail, to
             pathway models that incorporate the specific nature of the
             bonding and the protein fold, to multipathway models that
             add coherently the contributions of pathways, to methods
             that average over accessible geometries. Large-scale
             electronic structure methods remain of somewhat limited use
             because: the demands of geometry sampling and electronic
             structure calculation are considerable, especially for
             slower ET events; qualitative new insights arising from the
             more intensive analysis have been moderate; and
             structure-function relations become increasingly difficult
             to derive from more complex models. For these reasons,
             simple models remain both useful and popular. The simplest
             structured-protein models employ tunneling pathway and
             average packing density analysis. These methods are derived
             from the same protein physics: electronic interactions decay
             much more rapidly through-space than through-bond. We show
             that for the majority of 38 donor-acceptor pairs in 28
             proteins with determined X-ray structures, the two models
             are in qualitative agreement. However, for five of these
             donor-acceptor pairs, the pathway and the average packing
             density predictions are qualitatively different. The
             structural reasons for these differences are clear: (1)
             strong coupling pathways may exist in regions of
             unremarkable packing density, (2) explicit water molecules
             added to the X-ray structures can eliminate otherwise costly
             through-space jumps, (3) strong pathways situated beyond the
             zone sampled in average packing density analysis can
             dominate. We suggest that the instances of substantial
             differences between the two models can be used to probe ET
             tunneling mechanism. Differences, where they exist, point to
             specific t structural motifs where pathway effects
             associated with a protein s three-dimensional structure
             might play a central role in ET kinetics.},
   Doi = {10.1021/jp0133743},
   Key = {fds232006}
}

@article{fds232007,
   Author = {Tong, GSM and Kurnikov, IV and Beratan, DN},
   Title = {Tunneling energy effects on GC oxidation in
             DNA},
   Journal = {Journal of Physical Chemistry B Materials},
   Volume = {106},
   Number = {9},
   Pages = {2381-2392},
   Year = {2002},
   ISSN = {1089-5647},
   url = {http://pubs.acs.org/cgi-bin/article.cgi/jpcbfk/2002/106/i09/pdf/jp013387g.pdf},
   Abstract = {Hole-mediated electronic couplings, reorganization energies,
             and electron transfer (ET) rates are examined theoretically
             for hole-transfer reactions in DNA. Electron transfer rates
             are found to depend critically on the energy gap between the
             donor/acceptor states and the intervening bases-the
             tunneling energy gap. The calculated distance decay exponent
             for the square of the electronic coupling, β, for hole
             transfer between GC base pairs (and pi-electron D/A pairs)
             ranges from 0.95 to 1.5 Å-1 in the model structures as the
             tunneling energy gap varies from 0.3 to 0.8 eV (which we
             argue is the range of energy gaps for GC oxidation probed in
             recent experiments). We show that the tunneling energy gap
             depends on the ET reorganization energy, which itself grows
             rapidly with distance for ET over 1-5 base pairs. Inclusion
             of the distance dependence of reorganization energies for
             these hole transfer reactions gives the tunneling rates an
             apparent decay exponent of ∼1.5-2.5 Å-1. We show that ET
             rates observed in DNA across one and two base pairs are
             reasonably well described with single-step ET theories,
             using our calculated couplings and reorganization energies.
             However, the computed single-step tunneling (superexchange)
             ET rates for donor and acceptor species separated by three
             or more base pairs are much smaller than observed. We
             conclude that longer-distance ET probably proceeds through
             thermal population of intermediate hole states of the
             bridging bases. Switching between mechanisms as distance
             grows beyond a few base pairs is likely to be a general
             characteristic of ET in small tunneling energy gap
             systems.},
   Doi = {10.1021/jp013387g},
   Key = {fds232007}
}

@article{fds232012,
   Author = {Kurnikov, IV and Tong, GSM and Madrid, M and Beratan,
             DN},
   Title = {Hole size and energetics in double helical DNA: Competition
             between quantum delocalization and solvation
             localization},
   Journal = {Journal of Physical Chemistry B Materials},
   Volume = {106},
   Number = {1},
   Pages = {7-10},
   Year = {2002},
   ISSN = {1089-5647},
   url = {http://pubs.acs.org/cgi-bin/article.cgi/jpcbfk/2002/106/i01/pdf/jp0132329.pdf},
   Abstract = {The transition between single step long-range tunneling and
             multistep hopping transport in DNA electron transfer depends
             on a myriad of factors including sequence, distance,
             conformation, solvation and, consequently, hole state
             energetics. We show that the solvation energetics of hole
             (radical cation) states in DNA is comparable to the quantum
             delocalization energetics of the hole. That is, the
             solvation forces that tend to localize the hole compete with
             the quantum effects that give rise to hole delocalization.
             The net result is that the hole states are predicted to be
             relatively compact (one to three base pairs in length) and
             that the "trap depth" of these holes is expected to be much
             shallower than anticipated by gas-phase quantum chemical
             analysis of base stacks. This analysis predicts guanine
             oxidation potential dependence on the length of GC runs to
             be modest (differences &lt;0.1 V for holes from one to three
             base pairs). The lowering of the trapped hole binding energy
             has significant implications for the structure and mobility
             of hole states in DNA.},
   Doi = {10.1021/jp0132329},
   Key = {fds232012}
}

@article{fds232039,
   Author = {Specht, KM and Nam, J and Ho, DM and Berova, N and Kondru, RK and Beratan,
             DN and Wipf, P and Pascal, RA and Kahne, D},
   Title = {Determining absolute configuration in flexible molecules: a
             case study.},
   Journal = {Journal of the American Chemical Society},
   Volume = {123},
   Number = {37},
   Pages = {8961-8966},
   Year = {2001},
   Month = {September},
   ISSN = {0002-7863},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11552802},
   Abstract = {Assigning absolute configuration of molecules continues to
             be a major problem. Determining absolute configuration in
             conformationally flexible systems is challenging, even for
             experts. Here, we present a case study in which we use a
             combination of molecular modeling, solution NMR, and X-ray
             crystallography to illustrate why it is difficult to use
             solution methods alone for configuration assignment. For the
             case examined, a comparison of calculated and experimental
             optical rotatory dispersion (ORD) data provides the most
             straightforward way to assign the absolute
             configuration.},
   Key = {fds232039}
}

@misc{fds22196,
   Author = {G.C. Walker and D.N. Beratan},
   Title = {Electron Transfer Reactions},
   Booktitle = {"Electron Transfer Reactions"},
   Publisher = {Institute of Physics Press},
   Editor = {J. Moore and N. Spencer},
   Year = {2001},
   Key = {fds22196}
}

@misc{fds22198,
   Author = {S.S. Skourtis and D.N. Beratan},
   Title = {Multi-center and multi-electron transfer in
             biology},
   Journal = {Electron Transfer Reaction},
   Volume = {1},
   Series = {Electron Transfer Reaction},
   Pages = {109-125},
   Booktitle = {Theory & Principles},
   Editor = {Wiley-VCH (Weinheim), V. Balzani},
   Year = {2001},
   Key = {fds22198}
}

@article{fds232010,
   Author = {Perry, TL and Dickerson, A and Khan, AA and Kondru, RK and Beratan, DN and Wipf, P and Kelly, M and Hamann, MT},
   Title = {New peroxylactones from the Jamaican sponge Plakinastrella
             onkodes, with inhibitory activity against the AIDS
             opportunistic parasitic infection Toxoplasma
             gondii},
   Journal = {Tetrahedron},
   Volume = {57},
   Number = {8},
   Pages = {1483-1487},
   Year = {2001},
   ISSN = {0040-4020},
   url = {http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6THR-42G08W1-5-C&_cdi=5289&_user=38557&_orig=browse&_coverDate=02%2F18%2F2001&_sk=999429991&view=c&wchp=dGLbVtz-zSkzS&md5=9131454337d1599a42c0349a9dc1187a&ie=/sdarticle.pdf},
   Abstract = {An analysis of the chemical constituents of Plakinastrella
             onkodes collected in Jamaica yielded three cyclic peroxides,
             including the known plakortolide (1) and two new analogs of
             1. The absolute configuration of plakortolide G
             ((3R,4R,6R,8S)-3) was determined by ab initio optical
             rotation computations using a coupled Hartree-Fock (CHF)
             method implemented in CADPAC. Plakortolide (1) (J. Org.
             Chem. 1980, 45, 3396) and plakortolide G (3) exhibited
             potent inhibitory activity against the protozoan Toxoplasma
             gondii in HFF cells and represent the first marine natural
             products reported with T. gondii inhibitory activity. ©
             2001 Elsevier Science Ltd.},
   Doi = {10.1016/S0040-4020(00)01134-0},
   Key = {fds232010}
}

@article{fds232011,
   Author = {Kurnikov, IV and Charnley, AK and Beratan, DN},
   Title = {From ATP to electron transfer: Electrostatics and
             free-energy transduction in nitrogenase},
   Journal = {Journal of Physical Chemistry B Materials},
   Volume = {105},
   Number = {23},
   Pages = {5359-5367},
   Year = {2001},
   ISSN = {1089-5647},
   url = {http://pubs.acs.org/cgi-bin/article.cgi/jpcbfk/2001/105/i23/pdf/jp002540o.pdf},
   Abstract = {Nitrogenase consists of two proteins that work in concert to
             reduce atmospheric dinitrogen to a biologically useful form,
             ammonia (Curr. Opin. Chem. Bio. 2000, 4, 559-566; Chem. Rev.
             1996, 96, 2965-2982). The smaller of the proteins (the
             so-called Fe protein) shuttles high-energy electrons to the
             larger subunit (the so-called MoFe protein) where the
             reduction of dinitrogen molecules takes place. The Fe
             protein catalyzes the hydrolysis of two MgATP molecules per
             electron transferred to the MoFe protein. The physical
             mechanism that couples the ATP hydrolysis and
             electron-transfer reactions in nitrogenase is one of the
             "great mysteries" of nitrogen fixation. Our goal is to
             describe the free-energy transformations that occur in
             nitrogenase based upon theoretical analysis of structural
             and electrochemical data. The electrostatic and
             thermodynamic analysis described here, made possible by
             recent X-ray structural data (and motivated by closely
             related electrochemical studies: Biochemistry 1997, 36,
             12976-12983; FEBS Lett. 1998, 432, 55-58), shows that the
             ATP hydrolysis energy in nitrogenase serves the purpose of
             increasing the driving force of the electron-transfer
             reaction in and protein-protein complex. MgATP binding
             induces conformational changes and protein-protein
             association. The protein-protein docking excludes water from
             the negatively charged [Fe4S4]S4cys redox cofactor that lies
             near the Fe-protein surface, boosting its energy through
             diminished solvation. We estimated the induced
             redox-potential change to be equal to or larger than
             one-third of an electronvolt, which is roughly the energy
             associated with the hydrolysis of one MgATP molecule.
             Nitrogenase appears, therefore, to employ a relatively
             simple ATP hydrolysis coupled redox cofactor desolvation
             mechanism to energize, and thus to accelerate, interprotein
             electron transfer. Our analysis also indicates that
             electrostatic interactions play an important role in the
             substitution of MgADP by MgATP upon reduction of the
             [Fe4S4]S4cys cluster in the Fe protein. The nitrogenase
             scheme of energy conversion may suggest alternative
             strategies for the design of new molecular
             devices.},
   Doi = {10.1021/jp002540o},
   Key = {fds232011}
}

@article{fds232009,
   Author = {Kondru, RK and Beratan, DN and Friestad, GK and Smith, AB and Wipf,
             P},
   Title = {Chiral action at a distance: remote substituent effects on
             the optical activity of calyculins A and
             B.},
   Journal = {Organic Letters},
   Volume = {2},
   Number = {11},
   Pages = {1509-1512},
   Year = {2000},
   Month = {June},
   ISSN = {1523-7060},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/10841466},
   Abstract = {[structure--see text] Calyculins A and B differ only by the
             (E)- vs (Z)-configuration at C(2). Yet, they show a large
             difference in optical rotations. We demonstrate a new
             strategy that provides a physical analysis of this
             long-range chiro-optical effect by Boltzmann-averaged atomic
             contribution mapping. The polarizability characteristics of
             the CN substituent rather than the perturbation of the
             stereogenic centers or the introduction of asymmetry into
             the polyene chain give rise to the remarkable difference in
             rotation angles.},
   Key = {fds232009}
}

@article{fds232008,
   Author = {Lee, M and Shephard, MJ and Risser, SM and Priyadarshy, S and Paddon-Row, MN and Beratan, DN},
   Title = {The nature of tunnel splitting mediated by stacked
             aromatics},
   Journal = {The Journal of Physical Chemistry Part A: Molecules,
             Spectroscopy, Kinetics, Environment and General
             Theory},
   Volume = {104},
   Number = {32},
   Pages = {7593-7599},
   Year = {2000},
   ISSN = {1089-5639},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpcafh/2000/104/i32/pdf/jp994372+.pdf},
   Abstract = {We have examined the distance and orientation dependence of
             the energy splitting, ΔE(π*), between the two lowest-lying
             unoccupied molecular orbitals of a pair of
             tetracyanoethylene (TCNE) molecules bridged by a stack of
             noncovalently bonded benzene rings; the stack length ranged
             from one to. six benzene molecules. The distance between
             ring planes was fixed at 3.4 Å, while the orientation of
             the rings and of the TCNE molecules was varied. The
             magnitude of the splitting energy was found to decay
             exponentially with increasing stack length, r; ΔE(π*) = A
             exp(-0.5βer), with the damping factor, βe, ranging in
             value from 1.1 to 1.6 Å-1, as might be anticipated for
             instances where the "tunneling energy" lies several electron
             volts away from the frontier orbitals of the π-electron
             stack. Both ab initio and semiempirical computations predict
             a weak dependence of the coupling upon the orientation of
             the rings. The ab initio HF/3-21G calculations give βe
             values approximately 20% smaller than those values found in
             semiempirical computations using π-stacks in which the
             separation between adjacent benzene molecules (3.4 Å) is
             typical of stacked aromatic systems. This is due to the
             improved capability of the 3-21G basis set to treat the
             nearest-neighbor inter-ring orbital interactions, compared
             to the more contracted complete neglect of differential
             overlap (CNDO) basis set. Comparison to calculations with a
             more extended basis shows the 3-21G basis is accurate for
             rings separated by up to 4.0 Å, but for larger separations,
             ab initio calculations require the use of diffuse functions
             to properly describe the exponential decay of the
             interaction. © 2000 American Chemical Society.},
   Key = {fds232008}
}

@article{fds232036,
   Author = {Ribe, S and Kondru, RK and Beratan, DN and Wipf, P},
   Title = {Optical rotation computation, total synthesis, and
             stereochemistry assignment of the marine natural product
             pitiamide A},
   Journal = {Journal of the American Chemical Society},
   Volume = {122},
   Number = {19},
   Pages = {4608-4617},
   Year = {2000},
   ISSN = {0002-7863},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/2000/122/i19/pdf/ja9945313.pdf},
   Abstract = {We report the joint application of ab initio computations
             and total synthesis to assign the absolute configuration of
             a new natural product. The expected specific rotations of
             the (7S,10R)- and (7R,10R)-isomers of pitiamide A in a CHCl3
             solvent continuum model were determined as +8 and - 39,
             respectively, by CADPAC calculations of the
             electric-dipole-magnetic- dipole polarizability tensor.
             Total syntheses of these two stereoisomers of the marine
             metabolite were achieved by a convergent strategy that
             utilized Evans' oxazolidinone alkylation, a novel
             water-accelerated modification of Negishi's
             zirconocene-catalyzed asymmetric carbometalation as well as
             an unusual segment condensation via Mitsunobu alkylation of
             a nosyl-activated amide. The experimental optical rotation
             measurements confirmed the results of the computational
             optical rotation predictions. On the basis of NMR
             comparisons, the configuration of pitiamide A was assigned
             as (7R,10R). These studies highlight the considerable
             structural significance of [α](D) data, but, because the
             optical rotation of the natural product was different from
             either synthetic diastereomer, our work serves also as an
             illustration of potential problems with obtaining accurate
             experimental [α](D) data for natural samples.},
   Doi = {10.1021/ja9945313},
   Key = {fds232036}
}

@article{fds232037,
   Author = {Liang, Z-X and Nocek, JM and Kurnikov, IV and Beratan, DN and Hoffman,
             BM},
   Title = {Electrostatic control of electron transfer between myoglobin
             and cytochrome b5: Effect of methylating the heme
             propionates of Zn-myoglobin [16]},
   Journal = {Journal of the American Chemical Society},
   Volume = {122},
   Number = {14},
   Pages = {3552-3553},
   Year = {2000},
   ISSN = {0002-7863},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/2000/122/i14/pdf/ja993951p.pdf},
   Doi = {10.1021/ja993951p},
   Key = {fds232037}
}

@article{fds232038,
   Author = {Babini, E and Bertini, I and Borsari, M and Capozzi, F and Luchinat, C and Zhang, X and Moura, GLC and Kurnikov, IV and Beratan, DN and Ponce, A and Bilio, AJD and Winkler, JR and Gray, HB},
   Title = {Bond-mediated electron tunneling in ruthenium-modified
             high-potential iron-sulfur protein [13]},
   Journal = {Journal of the American Chemical Society},
   Volume = {122},
   Number = {18},
   Pages = {4532-4533},
   Year = {2000},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/2000/122/i18/pdf/ja994472t.pdf},
   Doi = {10.1021/ja994472t},
   Key = {fds232038}
}

@article{fds32269,
   Author = {S.S. Skourtis and D.N. Beratan},
   Title = {Theories of structure-function relationships for
             bridge-mediated electron transfer},
   Volume = {106},
   Pages = {377-452},
   Booktitle = {Adv. Chem. Phys.},
   Year = {1999},
   Key = {fds32269}
}

@article{fds231908,
   Author = {Skourtis, SS and Beratan, DN},
   Title = {Theories of structure-function relationships for
             bridge-mediated electron transfer reactions},
   Journal = {Advances in Chemical Physics},
   Volume = {106},
   Pages = {377-452},
   Year = {1999},
   ISSN = {0065-2385},
   Key = {fds231908}
}

@article{fds232002,
   Author = {Zusman, LD and Beratan, DN},
   Title = {Electron transfer in three-state systems},
   Journal = {J. Chem. Phys.},
   Volume = {110},
   Number = {21},
   Pages = {10468-10481},
   Year = {1999},
   url = {http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JCPSA6000110000021010468000001&idtype=cvips},
   Abstract = {Electron transfer is examined in three redox center
             (donor-bridge-acceptor) systems. Here, electron transfer
             cannot be described as arising from one-dimensional
             diffusional motion along the reaction coordinate. Instead,
             two-dimensional diffusion over two statistically independent
             reaction coordinates emerges. We show that electron transfer
             in three-center systems can be reduced to electron transfer
             between the pairs of adjacent centers. The interplay between
             sequential and superexchange mechanisms is examined. New
             expressions for the electron transfer rate, including
             effects of the two-dimensional reaction coordinate and of
             solvent dynamics, are derived. Using this analysis, new
             driving force effects are predicted, and rich behavior is
             revealed. © 1999 American Institute of Physics.},
   Key = {fds232002}
}

@article{fds232003,
   Author = {Kondru, RK and Wipf, P and Beratan, DN},
   Title = {Structural and Conformational Dependence of Optical Rotation
             Angles},
   Journal = {Journal of Physical Chemistry A},
   Volume = {103},
   Number = {33},
   Pages = {6603-6611},
   Year = {1999},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpcafh/1999/103/i33/pdf/jp990697e.pdf},
   Abstract = {The ability to compute and to interpret optical rotation
             angles of chiral molecules is of great value in assigning
             relative and absolute stereochemistry. The molar rotations
             for an indoline and an azetidine, as well as for menthol and
             menthone, were calculated using ab inito methods and
             compared to the experimental values. In one case the
             calculated rotation angle allowed the assignment of the
             absolute configuration of a heterocycle of unknown
             stereochemistry. The critical importance of Boltzmann
             averaging of conformers for reliable prediction of the
             optical rotation angle was established. Comparisons between
             static-field and time-dependent methods were made pointing
             to the limits and validity of the methods as electronic
             resonance is approached. A protocol analogous to population
             analysis was used to analyze atomic contributions to the
             rotation angle in specific conformers. The combination of
             atomic contribution maps and conformational analysis may
             provide an indirect tool to assist in three-dimensional
             structure determination.},
   Key = {fds232003}
}

@article{fds232004,
   Author = {Kondru, RK and Chen, CH-T and Curran, DP and Beratan, DN and Wipf,
             P},
   Title = {Determination of the absolute configuration of
             1,3,5,7-tetramethyl-1,3- dihydroindol-2-one by optical
             rotation computation},
   Journal = {Tetrahedron Asymmetry},
   Volume = {10},
   Number = {21},
   Pages = {4143-4150},
   Year = {1999},
   url = {http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6THT-3Y6HDKJ-G-Y&_cdi=5291&_user=38557&_orig=browse&_coverDate=10%2F29%2F1999&_sk=999899978&view=c&wchp=dGLbVlb-zSkWb&md5=6bd074b42cd870365d7f2e80a7606ca0&ie=/sdarticle.pdf},
   Abstract = {The absolute configuration of 1,3,5,7-tetramethyl-1,3-dihydroindol-2-one
             was determined by quantum chemical calculations of specific
             rotation angles with coupled-perturbed Hartree-Fock methods.
             The computation used molecular geometries obtained from ab
             initio calculations as well as from molecular mechanics and
             semi-empirical optimization. In addition to the dependence
             on geometry optimization strategies, the basis set
             dependence of the computed rotation angle was
             examined.},
   Key = {fds232004}
}

@article{fds304365,
   Author = {Zusman, LD and Beratan, DN},
   Title = {Electron transfer in three-center chemical
             systems},
   Journal = {Journal of Chemical Physics},
   Volume = {110},
   Number = {21},
   Pages = {10468-10481},
   Year = {1999},
   Abstract = {Electron transfer is examined in three redox center
             (donor-bridge-acceptor) systems. Here, electron transfer
             cannot be described as arising from one-dimensional
             diffusional motion along the reaction coordinate. Instead,
             two-dimensional diffusion over two statistically independent
             reaction coordinates emerges. We show that electron transfer
             in three-center systems can be reduced to electron transfer
             between the pairs of adjacent centers. The interplay between
             sequential and superexchange mechanisms is examined. New
             expressions for the electron transfer rate, including
             effects of the two-dimensional reaction coordinate and of
             solvent dynamics, are derived. Using this analysis, new
             driving force effects are predicted, and rich behavior is
             revealed. © 1999 American Institute of Physics.},
   Key = {fds304365}
}

@article{fds232001,
   Author = {Kondru, RK and Wipf, P and Beratan, DN},
   Title = {Atomic contributions to the optical rotation angle as a
             quantitative probe of molecular chirality.},
   Journal = {Science},
   Volume = {282},
   Number = {5397},
   Pages = {2247-2250},
   Year = {1998},
   Month = {December},
   ISSN = {0036-8075},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/9856945},
   Abstract = {Chiral molecules are characterized by a specific rotation
             angle, the angle through which plane-polarized light is
             rotated on passing through an enantiomerically enriched
             solution. Recent developments in methodology allow
             computation of both the sign and the magnitude of these
             rotation angles. However, a general strategy for assigning
             the individual contributions that atoms and functional
             groups make to the optical rotation angle and, more
             generally, to the molecular chirality has remained elusive.
             Here, a method to determine the atomic contributions to the
             optical rotation angle is reported. This approach links
             chemical structure with optical rotation angle and provides
             a quantitative measure of molecular asymmetry propagation
             from a center, axis, or plane of chirality.},
   Key = {fds232001}
}

@article{fds232033,
   Author = {Roitberg, AE and Holden, MJ and Mayhew, MP and Kurnikov, IV and Beratan,
             DN and Vilker, VL},
   Title = {Binding and electron transfer between putidaredoxin and
             cytochrome P450cam. Theory and experiments},
   Journal = {Journal of the American Chemical Society},
   Volume = {120},
   Number = {35},
   Pages = {8927-8932},
   Year = {1998},
   Month = {September},
   ISSN = {0002-7863},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000075860100005&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Doi = {10.1021/ja9739906},
   Key = {fds232033}
}

@article{fds231997,
   Author = {Zusman, LD and Beratan, DN},
   Title = {Electron transfer in the photosynthetic reaction center:
             mechanistic implications of mutagenesis studies.},
   Journal = {Spectrochimica Acta Part A: Molecular and Biomolecular
             Spectroscopy},
   Volume = {54A},
   Number = {9},
   Pages = {1211-1218},
   Year = {1998},
   Month = {August},
   ISSN = {1386-1425},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/9734088},
   Abstract = {A phenomenological analysis of the driving force effects in
             photosynthetic reaction centers modified by mutagenesis and
             also by chemical means is presented. Different parameter
             sets associated with different mechanisms of electron
             transfer are consistent with the mutagenesis experiments.
             However, only one parameter set--connected with a sequential
             mechanism of electron transfer--is consistent with all known
             experimental data. Arguments explaining why the sequential
             mechanism of electron transfer is selected by nature in the
             wild type reaction center are provided. Why the driving
             force of the wild type reaction center is about 0.25 eV is
             explained and new driving force effects are
             predicted.},
   Key = {fds231997}
}

@misc{fds22225,
   Author = {D.N. Beratanand S.S. Skourtis},
   Title = {Protein-mediated electron transfer: pathways, orbital
             interactions and contact maps},
   Pages = {9-27},
   Booktitle = {Biological electron-transfer chains: genetics, composition
             and mode of operation},
   Publisher = {Kluwer Academic Publishers, Dordrecht, The
             Netherlands},
   Editor = {G.W. Canters and E. Vigenboom},
   Year = {1998},
   Key = {fds22225}
}

@article{fds231907,
   Author = {Kurnikov, IV and Zusman, LD and Kurnikova, MG and Farid, RS and Beratan,
             DN},
   Title = {Structural fluctuations, spin, reorganization energy, and
             tunneling energy control of intramolecular electron
             transfer: The surprising case of electron transfer in a
             d8-d8 bimetallic system},
   Journal = {Chemtracts},
   Volume = {11},
   Number = {5},
   Pages = {359-365},
   Year = {1998},
   Abstract = {Theoretical analysis of the ET rates in di-iridium complexes
             with covalently linked pyridinium acceptors has shown the
             crucial role of the conformational dynamics. ET is fast
             enough to occur in the extended conformations of molecules
             with short spacers while it is gated by the conformational
             changes in species with longer, more flexible, spacers.
             Reorganization energies and electronic coupling were
             calculated to be larger then expected from the analysis of
             the singlet ET rate dependence on the reaction driving force
             indicating that all the ET reactions studied occur in the
             normal Marcus region. Electronic coupling is almost the same
             for the reaction from the spin-singlet and -triplet excited
             states of the Ir2 unit. A dip on the dependence of the
             electroniccoupling term on the tunneling energy was
             predicted.},
   Key = {fds231907}
}

@article{fds231998,
   Author = {Kumar, K and Kurnikov, IV and Beratan, DN and Waldeck, DH and Zimmt,
             MB},
   Title = {Use of modern electron transfer theories to determine
             electronic coupling matrix elements in intramolecular
             systems},
   Journal = {Journal of Physical Chemistry A},
   Volume = {102},
   Number = {28},
   Pages = {5529-5541},
   Year = {1998},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpcafh/1998/102/i28/pdf/jp980113t.pdf},
   Abstract = {The dependence of the donor/acceptor electronic coupling on
             the topology of donor-bridge-acceptor (DBA) molecules is
             probed experimentally and theoretically. The temperature
             dependence of photoinduced electron-transfer rate constants
             is analyzed with a semiclassical electron-transfer model to
             extract the donor/acceptor electronic coupling matrix
             elements |V| and the low-frequency reorganization energy at
             295 K, λ0(295 K), for four rigid DBA molecules. The
             sensitivity of the electronic coupling |V| to the models and
             parameters used to fit the data are extensively
             investigated. The treatment of the low-frequency
             reorganization energy's temperature dependence has a
             significant impact on the analysis. The identity of the
             principal coupling pathways is determined for molecular
             linkages that propagate symmetry allowed donor/acceptor
             interactions and molecular linkages that propagate symmetry
             forbidden donor/acceptor interactions. For the symmetry
             forbidden case, these analyses demonstrate that solvent
             molecules provide the dominant coupling pathway in the
             nine-bond bridge, C-shaped molecule 2 but do not
             significantly influence |V| across the seven-bond, linear
             bridge in 1.},
   Key = {fds231998}
}

@article{fds231999,
   Author = {Beratan, DN and Skourtis, SS},
   Title = {Electron transfer mechanisms},
   Journal = {Current Opinion in Chemical Biology},
   Volume = {2},
   Number = {2},
   Pages = {235-243},
   Year = {1998},
   url = {http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6VRX-457KS2R-4K-1&_cdi=6246&_user=38557&_orig=browse&_coverDate=04%2F30%2F1998&_sk=999979997&view=c&wchp=dGLbVzz-zSkWz&md5=18303de1120376b338b92b2c589c551d&ie=/sdarticle.pdf},
   Abstract = {The tunneling pathway framework description of protein
             electron transfer reactions has prompted a lively discussion
             of how structure and evolution influence electron transfer
             rates. Recent protein and model system experiments,
             performed in solution and in organized media, are providing
             answers. The molecular mechanisms of DNA electron transfer
             reactions are being probed as well with new theoretical and
             experimental strategies.},
   Key = {fds231999}
}

@article{fds232000,
   Author = {Priyadarshy, S and Risser, SM and Beratan, DN},
   Title = {DNA-mediated electron transfer},
   Journal = {Journal of Biological Inorganic Chemistry},
   Volume = {3},
   Number = {2},
   Pages = {196-200},
   Year = {1998},
   url = {http://www.springerlink.com/media/2724vnyuxk1kbtm3ng86/contributions/l/w/r/6/lwr6ca0pguppb87d.pdf},
   Abstract = {Electron transfer in DNA has been investigated for decades,
             but recent experiments highlight our limited fundamental
             understanding of these processes. Modern electron transfer
             theory may help to address some of the open mechanistic
             issues. We summarize and analyze the results of recent
             experiments from a theoretical perspective. Future research
             directions are suggested that might help to establish the
             molecular mechanism(s) for long- range DNA electron
             transfer.},
   Doi = {10.1007/s007750050221},
   Key = {fds232000}
}

@article{fds232034,
   Author = {Kondru, RK and Wipf, P and Beratan, DN},
   Title = {Theory-assisted determination of absolute stereochemistry
             for complex natural products via computation of molar
             rotation angles [17]},
   Journal = {Journal of the American Chemical Society},
   Volume = {120},
   Number = {9},
   Pages = {2204-2205},
   Year = {1998},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1998/120/i09/pdf/ja973690o.pdf},
   Doi = {10.1021/ja973690o},
   Key = {fds232034}
}

@misc{fds22240,
   Author = {J. N. Onuchic and S.M. Risser and S.S. Skourtis and D.N.
             Beratan},
   Title = {The design of starburst dendrimer electron transfer
             systems},
   Pages = {369-379},
   Booktitle = {Molecular Electronics},
   Publisher = {Chemistry for the 21st Century Series, Blackwell Science,
             Oxford, Chapter 12},
   Editor = {M. Ratner and J. Jortner},
   Year = {1997},
   Key = {fds22240}
}

@misc{fds26206,
   Author = {D.N. Beratan},
   Title = {Molecular control of electron tunneling processes},
   Publisher = {Chapter 3.2 in IBC Molecular Nanotechology Conference
             Proceedings, IBC Press},
   Year = {1997},
   Key = {fds26206}
}

@article{fds231873,
   Author = {Beratan, DN and Priyadarshy, S and Risser, SM},
   Title = {DNA: wire or insulator?},
   Journal = {Chemistry and Biology},
   Volume = {4},
   Pages = {3-8},
   Year = {1997},
   url = {http://www.sciencedirect.com/science?_ob=MImg&_imagekey=B6VRP-4B616KK-BG-2&_cdi=6240&_user=38557&_coverDate=01%2F31%2F1997&_sk=%23TOC%236240%231997%23999959998%23473703%23FLP%23display%23Volume_4,_Issue_1,_Pages_1-85_(January_1997)%23tagged%23Volume%23first%3D4%23Issue%23first%3D1%23Pages%23first%3D1%23last%3D85%23date%23(January_1997)%23&view=c&_gw=y&wchp=dGLbVtb-zSkWW&md5=82145db032421c4f467734eb72ece26b&ie=/sdarticle.pdf},
   Key = {fds231873}
}

@article{fds231906,
   Author = {Wolfgang, J and Risser, SM and Priyadarshy, S and Beratan,
             DN},
   Title = {Secondary structure conformations and long range electronic
             interactions in oligopeptides},
   Journal = {J. Phys. Chem. B.},
   Volume = {101},
   Pages = {2987-2991},
   Year = {1997},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpcbfk/1997/101/i15/pdf/jp963771r.pdf},
   Key = {fds231906}
}

@article{fds231992,
   Author = {Skourtis, SS and Beratan, DN},
   Title = {Electron transfer contact maps},
   Journal = {Journal of Physical Chemistry B},
   Volume = {101},
   Number = {7},
   Pages = {1215-1234},
   Year = {1997},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpcbfk/1997/101/i07/pdf/jp9619245.pdf},
   Abstract = {An exact approach is introduced to establish and compare
             quantitative structure-function relationships in electron
             transfer proteins. The strategy is based on the idea of an
             electron transfer contact map and is motivated by reduced
             descriptions of 3D protein structure that emphasize the
             folded conformation (ribbon drawings, distance contact maps,
             and Ramachandran plots). Electron transfer contact maps
             render the protein-mediated electronic coupling information
             in a compact and transferable form. The method includes all
             contributions of multiple interfering tunneling pathways to
             the tunneling propagation and can be implemented at many
             levels of electronic structure theory. Contact maps are used
             to interpret the influence of mutations on electronic
             propagation in model peptides.},
   Key = {fds231992}
}

@article{fds231993,
   Author = {Kondru, RK and Lim, S and Wipf, P and Beratan, DN},
   Title = {Synthetic and model computational studies of optical angle
             additivity for interacting chiral centers: A reinvestigation
             of van't Hoff's principle},
   Journal = {Chirality},
   Volume = {9},
   Number = {5-6},
   Pages = {468-477},
   Year = {1997},
   ISSN = {0899-0042},
   url = {http://www3.interscience.wiley.com/cgi-bin/fulltext/54386/PDFSTART},
   Abstract = {When plane-polarized light impinges on a solution of
             optically active molecules, the polarization of the light
             that emerges is rotated. This simple phenomenon arises from
             the interaction of light with matter and is well understood,
             in principle, van't Hoff's rule of optical superposition
             correlates the molar rotation with the individual
             contributions to optical activity of isolated centers of
             asymmetry. This straightforward empirical additivity rule is
             rarely used for structure elucidation nowadays because of
             its limitations in the assessment of conformationally
             restricted or interacting chiral centers. However,
             additivity can be used successfully to assign the
             configuration of complex natural products such as
             hennoxazole A if appropriate synthetic partial structures
             are available. Therefore, van't Hoff's principle is a
             powerful stereochemical complement to natural products'
             total synthesis. The quest for reliable quantitative methods
             to calculate the angle of rotation a priori has been
             underway for a long time. Both classical and quantum methods
             for calculating molar rotation have been developed. Of
             particular practical importance for determining the absolute
             structure of molecules by calculation is the manner in which
             interactions between multiple chiral centers in a single
             molecule are included, leading to additive or non-additive
             optical rotation angles. This problem is addressed here
             using semi-empirical electronic structure models and the
             Rosenfeld equation.},
   Doi = {10.1002/(SICI)1520-636X(1997)9:5/6<469::AID-CHIR13>3.0.CO;2-},
   Key = {fds231993}
}

@article{fds231994,
   Author = {Skourtis, SS and Beratan, DN},
   Title = {High and low resolution theories of protein electron
             transfer},
   Journal = {Journal of Biological Inorganic Chemistry},
   Volume = {2},
   Number = {3},
   Pages = {378-386},
   Year = {1997},
   url = {http://www.springerlink.com/media/e3d054fexk6qwlcbrqau/contributions/g/l/8/9/gl89l5vjc3awtg6f.pdf},
   Abstract = {Protein-mediated electronic interactions facilitate
             biological electron transfer (ET) reactions. Theory and
             experiment are being used extensively to establish
             atomic-scale descriptions of these reactions. The last 20
             years have seen a progression of descriptions ranging from
             square barrier protein approximations to tunneling Pathway
             models, and recently to valence orbital Hamiltonian methods.
             Pathway connectivity, reflecting a protein's secondary and
             tertiary motif, is predicted (and was recently confirmed) to
             determine the ET rate. A critical challenge now is to
             extract from more detailed orbital descriptions, with
             millions of interaction elements between orbitals,
             predictions of how primary sequence and folding-induced
             contacts influence electron transfer rates. Electron
             transfer contact maps reduce the orbital interaction
             information in a manner that allows ready interpretation in
             the context of protein motifs and mutations. We discuss
             these modern models for protein ET and the reduced views
             that are being derived from them.},
   Doi = {10.1007/s007750050147},
   Key = {fds231994}
}

@article{fds231995,
   Author = {Zusman, LD and Beratan, DN},
   Title = {Three-state model for two-electron transfer
             reactions},
   Journal = {Journal of Physical Chemistry A},
   Volume = {101},
   Number = {22},
   Pages = {4136-4141},
   Year = {1997},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpcafh/1997/101/i22/pdf/jp970123e.pdf},
   Abstract = {Much of electron transfer based catalysis relies upon
             multielectron rather than single-electron transfer
             processes. If the multielectron events proceed through
             stable one-electron intermediates, conventional theory
             describes the events However, when an unstable one-electron
             intermediate plays a role, when a stable intermediate lives
             for a brief period of time, or when concerted multielectron
             events occur, the electronic coupling and free energy
             dependence of the rate is distinct from that arising in
             one-electron theories. We describe several new features that
             can arise in multielectron processes, predict their
             experimental signature, and show how these ideas can be
             applied to specific experimental systems.},
   Key = {fds231995}
}

@article{fds231996,
   Author = {Zusman, LD and Beratan, DN},
   Title = {Structure of the electrical double layer in high-temperature
             superconductors. Origin of the dip in the double-layer
             capacitance near the superconducting transition},
   Journal = {Journal of Physical Chemistry B},
   Volume = {101},
   Number = {36},
   Pages = {7095-7099},
   Year = {1997},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpcbfk/1997/101/i36/pdf/jp971026o.pdf},
   Abstract = {A theory of the electrical double layer in high-temperature
             superconductors is developed in the context of a modified
             Ginzburg-Landau equation. Potential and excess charge
             distributions inside the electrode are computed. These
             distributions are shown to be characterized by a new
             fundamental length parameter. This length diverges when the
             electrode temperature approaches the superconducting
             critical temperature. The capacitance of the electrical
             double layer is found to be inversely proportional to this
             length. On the basis of this analysis, the origin of an
             experimentally observed dip in the double-layer capacitance
             is explained. The dependence of this capacitance dip on the
             external field is predicted.},
   Key = {fds231996}
}

@article{fds232032,
   Author = {Kurnikov, IV and Zusman, LD and Kurnikova, MG and Farid, RS and Beratan,
             DN},
   Title = {Structural fluctuations, spin, reorganization energy, and
             tunneling energy control of intramolecular electron
             transfer: The surprising case of electron transfer in a
             d8-d8 bimetallic system},
   Journal = {Journal of the American Chemical Society},
   Volume = {119},
   Number = {24},
   Pages = {5690-5700},
   Year = {1997},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1997/119/i24/pdf/ja970309r.pdf},
   Abstract = {A considerable body of unimolecular electron-transfer rate
             data has been reported recently for Ir2 excited-state donors
             linked to substituted pyridinium acceptors. These data pose
             a substantial paradox. Simple analysis suggested that
             donor-acceptor coupling matrix elements differ by 1 order of
             magnitude for the excited triplet and singlet states. Yet,
             there is no fundamental reason to expect this large
             electronic coupling dependence on spin state. We offer an
             alternative self-consistent interpretation based on a hybrid
             theoretical analysis that includes ab initio quantum
             calculations of electronic couplings, molecular dynamics
             simulations of molecular geometries, and Poisson-Boltzmann
             computations of reorganization energies. Taken together the
             analysis provides a detailed comprehensive interpretation of
             these reactions. In our analysis, we reach the conclusions:
             (1) that reorganization energies in these systems (~1.3-1.7
             eV) are larger than expected from simple analysis of
             experiments, (2) that electronic couplings (~0.005-0.02 eV)
             are also larger than previously believed and differ only by
             a factor of 2 for singlet and triplet states, (3) that the
             molecules have access to multiple conformations differing
             both in reorganization energy and electronic coupling, and
             explicit treatment of this flexibility is crucial to
             interpret the rate data, and (4) that a considerable dip is
             expected in the donor- acceptor coupling dependence on
             tunneling energy, associated with destructively interfering
             electron and hole-mediated coupling pathways, which probably
             leads to a small observed ET rate in one of the compounds.
             Taken together, this analysis explains most of the
             experimental data. Fundamental arguments and detailed
             computations show that the influence of donor spin state on
             long-range electronic interactions is relatively weak. Many
             of the molecular aspects that establish the ET
             characteristics of these molecules exist in other semirigid
             model compounds, making this hybrid theoretical strategy of
             general interest.},
   Doi = {10.1021/ja970309r},
   Key = {fds232032}
}

@article{fds304357,
   Author = {Kondru, RK and Lim, S and Wipf, P and Beratan, DN},
   Title = {Synthetic and model computational studies of molar rotation
             additivity for interacting chiral centers: a reinvestigation
             of van't Hoff's principle.},
   Journal = {Chirality},
   Volume = {9},
   Number = {5-6},
   Pages = {469-477},
   Year = {1997},
   ISSN = {0899-0042},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/9329177},
   Abstract = {When plane-polarized light impinges on a solution of
             optically active molecules, the polarization of the light
             that emerges is rotated. This simple phenomenon arises from
             the interaction of light with matter and is well understood,
             in principle, van't Hoff's rule of optical superposition
             correlates the molar rotation with the individual
             contributions to optical activity of isolated centers of
             asymmetry. This straightforward empirical additivity rule is
             rarely used for structure elucidation nowadays because of
             its limitations in the assessment of conformationally
             restricted or interacting chiral centers. However,
             additivity can be used successfully to assign the
             configuration of complex natural products such as
             hennoxazole A if appropriate synthetic partial structures
             are available. Therefore, van't Hoff's principle is a
             powerful stereochemical complement to natural products'
             total synthesis. The quest for reliable quantitative methods
             to calculate the angle of rotation a priori has been
             underway for a long time. Both classical and quantum methods
             for calculating molar rotation have been developed. Of
             particular practical importance for determining the absolute
             structure of molecules by calculation is the manner in which
             interactions between multiple chiral centers in a single
             molecule are included, leading to additive or non-additive
             optical rotation angles. This problem is addressed here
             using semi-empirical electronic structure models and the
             Rosenfeld equation.},
   Doi = {10.1002/(SICI)1520-636X(1997)9:5/6<469::AID-CHIR13>3.0.CO;2-},
   Key = {fds304357}
}

@article{fds231991,
   Author = {Nocek, JM and Zhou, JS and De Forest and S and Priyadarshy, S and Beratan,
             DN and Onuchic, JN and Hoffman, BM},
   Title = {Theory and Practice of Electron Transfer within Proteinminus
             signProtein Complexes: Application to the Multidomain
             Binding of Cytochrome c by Cytochrome c Peroxidase.},
   Journal = {Chemical Reviews},
   Volume = {96},
   Number = {7},
   Pages = {2459-2490},
   Year = {1996},
   Month = {November},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/11848833},
   Key = {fds231991}
}

@misc{fds22250,
   Author = {D.N. Beratan and J.N. Onuchic},
   Title = {Chapter 2: The protein bridge between redox
             centers},
   Pages = {23-42},
   Booktitle = {Protein Electron Transfer},
   Publisher = {BIOS Scientific Publishers, Oxford},
   Editor = {D.S. Bendall},
   Year = {1996},
   Key = {fds22250}
}

@misc{fds22251,
   Author = {J.N. Onuchic and D.N. Beratan},
   Title = {Appendix A: Electron transfer rate calculations},
   Pages = {273-283},
   Booktitle = {Protein Electron Transfer},
   Publisher = {bios Scientific Publishers, Oxford},
   Editor = {D.S. Bendall},
   Year = {1996},
   Key = {fds22251}
}

@article{fds231870,
   Author = {Kurnikov, IV and Beratan, DN},
   Title = {Ab initio based effective Hamiltonians for long-range
             electron transfer: Hartree-Fock analysis},
   Journal = {Journal of Chemical Physics},
   Volume = {105},
   Number = {21},
   Pages = {9561-9573},
   Year = {1996},
   ISSN = {0021-9606},
   url = {http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JCPSA6000105000021009561000001&idtype=cvips},
   Abstract = {An ab initio electronic structure method is developed to
             describe electron transfer in large systems. The method is
             based on a molecular fragment effective Hamiltonian
             approach. The strategy pieces together results of ab initio
             quantum chemistry calculations on overlapping molecular
             segments in order to build an effective Hamiltonian that
             describes the long-range electronic interactions. This is
             accomplished by constructing fragment effective Hamiltonians
             that properly describe the electronic propagation
             characteristics of each fragment (computed at the ab initio
             Hartree-Fock level in an appropriate basis set). The
             fragment effective Hamiltonian is projected onto the valence
             orbital space of each fragment, and a relatively
             well-localized set of effective interactions is obtained.
             Combining these projected fragment Hamiltonians allows the
             construction of a valence effective Hamiltonian for the
             entire system. We find that the fragment Hamiltonian
             matrices constructed in this way are transferable between
             donor-acceptor systems with homologous electron-transfer
             bridges. The overall strategy of fragmentation and
             construction of valence effective Hamiltonians could enable
             ab initio quality computations of long-range tunneling
             interactions in macromolecules. We demonstrate the use of
             the method in a series of electron-transfer model systems of
             modest size. © 1996 American Institute of
             Physics.},
   Key = {fds231870}
}

@article{fds231871,
   Author = {Priyadarshy, S and Risser, SM and Beratan, DN},
   Title = {DNA double helix mediated long range electron
             transfer},
   Journal = {Int. J. Quantum Chem. Quantun Biol. Symp.},
   Volume = {60},
   Pages = {65-71},
   Year = {1996},
   Key = {fds231871}
}

@article{fds231987,
   Author = {Zusman, LD and Beratan, DN},
   Title = {Two-electron transfer reactions in polar
             solvents},
   Journal = {Journal of Chemical Physics},
   Volume = {105},
   Number = {1},
   Pages = {165-176},
   Year = {1996},
   url = {http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JCPSA6000105000001000165000001&idtype=cvips},
   Abstract = {Chemical, biological, and electrode based electron transfer
             (ET) processes involve multielectron events. However, an
             adequate framework in which to describe these complex
             reactions does not yet exist. A theory for two-electron
             transfer reactions in Debye solvents is developed. The
             theory is formulated by generalizing Zusman's model of ET
             reactions [L. D. Zusman, Chem. Phys. 49, 295 (1980)] to
             those involving three parabolic wells: One for the doubly
             reduced donor, one for the singly reduced donor/singly
             reduced acceptor, and one for the doubly reduced acceptor.
             The ET processes are described in terms of diffusional
             motion along a one-dimensional reaction coordinate with
             tunneling transitions at the intersection points of the
             parabolas. Two competing mechanisms of two-electron transfer
             arise. One is a process with two sequential single electron
             steps D=A→D-A-→DA=. The other involves ET in one
             concerted two-electron step (D=A→DA=). The general rate
             expressions for two-electron transfer are obtained. When the
             stepwise mechanism dominates, the free energy of activation
             is predicted to depend upon the driving forces of the two
             sequential steps but is independent of the overall driving
             force of the reaction. When concerted two-electron transfer
             dominates, the Marcus relation is obtained with a
             reorganization energy associated with the shift of two
             electrons. The dynamical solvent effect in two-electron ET
             processes is predicted to be unusual. Two distinct regimes
             exist, each with essentially linear 1/γL dependence (with
             γL the solvent longitudinal relaxation time): one for slow
             solvents and one for fast solvents. A combination of solvent
             and free energy studies could be used to elucidate the
             mechanism of multielectron processes in chemical and
             biological systems. © 1996 American Institute of
             Physics.},
   Key = {fds231987}
}

@article{fds231988,
   Author = {Kuhn, C and Beratan, DN},
   Title = {Inverse strategies for molecular design},
   Journal = {Journal of Physical Chemistry},
   Volume = {100},
   Number = {25},
   Pages = {10595-10599},
   Year = {1996},
   ISSN = {0022-3654},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1996/100/i25/pdf/jp960518i.pdf},
   Abstract = {An "inverse" molecular design strategy is described to
             assist in the development of new molecules with optimized
             properties. This approach is based on a molecular orbital
             view and can be used to tailor ground state or excited state
             properties subject to particular constraints. In this
             scheme, wave functions are sought that optimize a chemical
             or electronic property, and then a Hamiltonian is
             constructed that generates these optimized wave functions.
             Analysis of the chemical properties in the optimized systems
             may suggest new synthetic targets. Examples are presented
             that optimize the transition dipole moment in some simple
             structures. © 1996 American Chemical Society.},
   Key = {fds231988}
}

@article{fds231989,
   Author = {Priyadarshy, S and Skourtis, SS and Risser, SM and Beratan,
             DN},
   Title = {Bridge-mediated electronic interactions: Differences between
             Hamiltonian and Green function partitioning in a
             non-orthogonal basis},
   Journal = {Journal of Chemical Physics},
   Volume = {104},
   Number = {23},
   Pages = {9473-9481},
   Year = {1996},
   url = {http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JCPSA6000104000023009473000001&idtype=cvips},
   Abstract = {An analysis of the partitioning (projection) technique is
             given with emphasis on non-orthogonal basis sets. The
             general expression for the effective Hamiltonian obtained
             via Löwdin partitioning of the Schrödinger equation is
             discussed in the context of semi-empirical theories and
             electron transfer matrix elements. Numerous pitfalls in
             calculations of matrix elements are pointed out. More
             importantly, it is shown that contrary to the case of an
             orthogonal basis, for a non-orthogonal basis Löwdin
             partitioning of the Schrödinger equation and partitioning
             of the Green function equation are not equivalent. The
             latter method provides a more general prescription for
             deriving effective Hamiltonians. Such Hamiltonians reproduce
             the full propagation in the partitioned subspace. © 1996
             American Institute of Physics.},
   Key = {fds231989}
}

@article{fds231990,
   Author = {Priyadarshy, S and Risser, SM and Beratan, DN},
   Title = {DNA is not a molecular wire: Protein-like electron-transfer
             predicted for an extended π-electron system},
   Journal = {Journal of Physical Chemistry},
   Volume = {100},
   Number = {44},
   Pages = {17678-17682},
   Year = {1996},
   ISSN = {0022-3654},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1996/100/i44/pdf/jp961731h.pdf},
   Abstract = {The earliest studies of electron-transfer proteins1 raised
             the question of whether or not π-electron residues might
             facilitate electron transport.2 Three recent long-range
             electron-transfer experiments utilizing DNA bridges revisit
             this provocative, yet unresolved, question.3,4,5 The
             distance dependence of electron transfer in DNA is not a
             matter of purely academic concern; it controls the mechanism
             of DNA damage and repair in cells and is being exploited in
             new molecular probes of DNA sequence. We present a
             theoretical analysis based upon very large scale
             self-consistent-field quantum calculation of all valence
             electrons (as many as ∼3300) in these three systems This
             computation is the first performed on such large
             macromolecules and also the first to extract long-range
             electronic interactions at this level of theory. DNA
             electron transfer is found to be mediated by through-space
             interactions between the π-electron-containing base pairs,
             but the magnitude of the coupling facilitated by this
             channel drops rapidly with distance, as a consequence of the
             ∼3.4 Å noncovalent gap between base pairs. These,
             predictions are in agreement with most of the experimental
             data. The rapid decay of electron-transfer rates with
             distance computed here suggests that biologically controlled
             DNA electron-transfer events, of importance in DNA repair,6
             must function over relatively short range. Moreover, the
             predicted distance dependence of electron transfer in DNA is
             strikingly close to that found in proteins. © 1996 American
             Chemical Society.},
   Key = {fds231990}
}

@article{fds232031,
   Author = {Priyadarshy, S and Therien, MJ and Beratan, DN},
   Title = {Acetylenyl-linked, porphyrin-bridged, donor-acceptor
             molecules: A theoretical analysis of the molecular first
             hyperpolarizability in highly conjugated push-pull
             chromophore structures},
   Journal = {Journal of the American Chemical Society},
   Volume = {118},
   Number = {6},
   Pages = {1504-1510},
   Year = {1996},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1996/118/i06/pdf/ja952690q.pdf},
   Abstract = {We described the theoretical basis for the exceptionally
             large molecular first hyperpolarizabilities inherent to
             (5,15-diethynyl)porphinato)metal-bridged donor-acceptor
             (D-A) molecules. β values relevant for hyper-Rayleigh
             experiments are calculated at 1.064 and 0.830 μm for a
             complex with such a structure, [5-((4'-dimethylamino)phenyl)ethynyl)-15-((4''-nitrophenyl)ethynyl)-10
             ,20-diphenylporphinato]zinc(II), and are 472 x 10-30 and
             8152 x 10-30 cm5/esu, respectively. The values are 1 order
             of magnitude larger than that calculated for any other
             porphyrin bridged donor-acceptor chromophore studied to
             date. The considerably enhanced hyperpolarizability arises
             from the significant excited-state electronic asymmetry
             manifest in such structures (derived from the strong
             bridge-mediated D-A coupling enabled by the largely
             porphyrin-based excited state) and the large bridge-centered
             oscillator strength in this new class of D-bridge-A
             molecules. Our analysis of NLO properties (based upon
             INDO/SCI calculations within the sum over states formalism)
             shows a sensitivity to the degree of cumulenic character in
             the ground state. Calculations on structurally related
             multiporphyrin systems suggest candidate chromophores with
             further enhanced optical nonlinearities.},
   Doi = {10.1021/ja952690q},
   Key = {fds232031}
}

@article{fds232055,
   Author = {Skourtis, SS and Onuchic, JN and Beratan, DN},
   Title = {A method to analyze multi-pathway effects on protein
             mediated donor-acceptor coupling interactions},
   Journal = {Inorganica Chimica Acta},
   Volume = {243},
   Number = {1-2},
   Pages = {167-175},
   Year = {1996},
   Abstract = {Current strategies for analyzing donor-acceptor interactions
             involve mapping the dominant coupling pathways or families
             of pathways, followed by a numerical estimate of the
             interaction mediated by the paths. This strategy succeeds
             because it properly balances the through-bond versus
             through-space aspects of the protein electron transfer
             problem. Yet, existing analytical tools do not provide
             general predictions of how specific protein motifs might
             favor or disfavor electron transfer. This issue is best
             addressed with methods that incorporate multiple interfering
             pathways and that allow the coupling to be dissected
             systematically into contributing factors. We present such a
             method that probes collective effects arising from secondary
             and tertiary motifs. This analysis indicates when (and why)
             single pathway strategies succeed or fail. Applications of
             this new method to model secondary structures are
             described.},
   Key = {fds232055}
}

@article{fds232054,
   Author = {Curry, WB and Grabe, MD and Kurnikov, IV and Skourtis, SS and Beratan,
             DN and Regan, JJ and Aquino, AJ and Beroza, P and Onuchic,
             JN},
   Title = {Pathways, pathway tubes, pathway docking, and propagators in
             electron transfer proteins.},
   Journal = {Journal of Bioenergetics and Biomembranes},
   Volume = {27},
   Number = {3},
   Pages = {285-293},
   Year = {1995},
   Month = {June},
   ISSN = {0145-479X},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/8847342},
   Abstract = {The simplest views of long-range electron transfer utilize
             flat one-dimensional barrier tunneling models, neglecting
             structural details of the protein medium. The pathway model
             of protein electron transfer reintroduces structure by
             distinguishing between covalent bonds, hydrogen bonds, and
             van der Waals contacts. These three kinds of interactions in
             a tunneling pathway each have distinctive decay factors
             associated with them. The distribution and arrangement of
             these bonded and nonbonded contacts in a folded protein
             varies tremendously between structures, adding a richness to
             the tunneling problem that is absent in simpler views. We
             review the pathway model and the predictions that it makes
             for protein electron transfer rates in small proteins,
             docked proteins, and the photosynthetic reactions center. We
             also review the formulation of the protein electron transfer
             problem as an effective two-level system. New multi-pathway
             approaches and improved electronic Hamiltonians are
             described briefly as well.},
   Key = {fds232054}
}

@article{fds231986,
   Author = {Risser, SM and Beratan, DN},
   Title = {What is the anharmonicity of a molecule's electronic wave
             function?},
   Journal = {Journal of Physical Chemistry},
   Volume = {99},
   Number = {7},
   Pages = {1935-1942},
   Year = {1995},
   ISSN = {0022-3654},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1995/99/i07/pdf/j100007a024.pdf},
   Abstract = {The dependence of a classical spring's hyperpolarizabilities
             on its anharmonicity constants is known, defining a simple
             structure-property relationship. Corresponding
             structure-property relationships for the electronic
             hyperpolarizabilities of quantum many-particle systems,
             molecules, remain elusive. The quasi-harmonic behavior of
             molecular electronic polarization is disguised by the
             Coulombic nature of the interaction potential. Yet, to the
             extent that a perturbation theory description of electronic
             hyperpolarizability is appropriate, the quantum electronic
             hyperpolarizability problem maps onto a single-particle
             effective anharmonic oscillator hamiltonian. Here, we derive
             this relationship, which provides a means of establishing
             the effective anharmonic oscillator constants for a
             molecule. We calculate these electronic anharmonicities
             analytically and show results for some simple hamiltonians.
             One barrier to the design of chemical chromophores with
             tailored nonlinear optical coefficients is an understanding
             of how molecular structure influences hyperpolarizability.
             Restating the problem in terms of anharmonicities
             demystifies the source and magnitude of the electronic
             hyperpolarizabilities. © 1995 American Chemical
             Society.},
   Key = {fds231986}
}

@article{fds232041,
   Author = {Aquino, AJA and Beroza, P and Beratan, DN and Onuchic,
             JN},
   Title = {Docking and electron transfer between cytochrome
             c2 and the photosynthetic reaction
             center},
   Journal = {Chemical Physics},
   Volume = {197},
   Number = {3},
   Pages = {277-288},
   Year = {1995},
   ISSN = {0301-0104},
   Abstract = {Electron transfer between the proteins cytochrome c2 (cytc2)
             and the photosynthetic reaction center (RC) was studied
             using the pathways model of Beratan and Onuchic. To
             investigate the protein structure dependence of this
             electron transfer reaction, we separated the electronic
             coupling decay between electron donor and acceptor into
             three parts: (i) the coupling from the cytochrome heme to
             the surface of the cytochrome, (ii) the coupling from the RC
             surface to the bacteriochlorophyll dimer, and (iii) the
             coupling from the surface of the cytochrome to the surface
             of the reaction center. Calculating the coupling between the
             surface amino acids and the redox center allows the simple
             estimate of inter-protein electronic coupling, and, for a
             given docked structure, provides a functional criterion for
             evaluating that structure. The strongest heme to special
             pair electron transfer pathway in Rps. viridis (an RC with
             fixed heme-special pair structure) included surface residues
             on the cytochrome and RC (when each was treated as a
             separate protein), although it did not involve the most
             strongly coupled surface atoms of the RC. To examine the
             effect of docking orientation on electron transfer in Rb.
             sphaeroides, in which the cytochrome is not bound to the RC,
             we generated surface coupling maps of the electronic
             coupling between the redox sites and solvent exposed atoms
             in each protein. These maps were compared to individual
             pathways calculated for two docked cytc2/RC structures, one
             based on electrostatic complementarity, the other based on
             maximizing electronic coupling. The electronic coupling
             between donor and acceptor for these two docked structures
             was remarkably similar, suggesting that efficient electron
             transfer can be obtained from very different docked
             orientations of the cytochrome. Other factors influencing
             intermolecular electron transfer are discussed. ©
             1995.},
   Key = {fds232041}
}

@article{fds232053,
   Author = {Waldeck, DH and Beratan, DN},
   Title = {Molecular electronics: observation of molecular
             rectification.},
   Journal = {Science},
   Volume = {261},
   Number = {5121},
   Pages = {576-577},
   Year = {1993},
   Month = {July},
   ISSN = {0036-8075},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17758166},
   Doi = {10.1126/science.261.5121.576},
   Key = {fds232053}
}

@article{fds232030,
   Author = {RISSER, SM and BERATAN, DN and MEADE, TJ},
   Title = {ELECTRON-TRANSFER IN DNA - PREDICTIONS OF EXPONENTIAL-GROWTH
             AND DECAY OF COUPLING WITH DONOR-ACCEPTOR
             DISTANCE},
   Journal = {Journal of the American Chemical Society},
   Volume = {115},
   Number = {6},
   Pages = {2508-2510},
   Year = {1993},
   Month = {March},
   ISSN = {0002-7863},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1993KU90200057&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Doi = {10.1021/ja00059a057},
   Key = {fds232030}
}

@article{fds231984,
   Author = {Regan, JJ and Risser, SM and Beratan, DN and Onuchic,
             JN},
   Title = {Protein electron transport: Single versus multiple
             pathways},
   Journal = {Journal of Physical Chemistry},
   Volume = {97},
   Number = {50},
   Pages = {13083-13088},
   Year = {1993},
   ISSN = {0022-3654},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1993/97/i50/pdf/j100152a009.pdf},
   Abstract = {Pathway analysis provides a tool for the design of tailored
             electron-transfer proteins and is a useful starting point
             from which to build up multipathway views of electron
             mediation that include the influence of interference and all
             of the chemical tunability that is accessible. We present a
             new theoretical strategy to determine when a single-pathway
             picture is sufficient or when one must consider multiple
             paths. A definition of a single pathway in the context of a
             Green's function formalism is presented. To illustrate these
             effects, examples are given for cytochrome c. We also show
             that full protein Green's function calculations can be
             carried out at the tight-binding (extended-Hückel) level on
             cytochrome c including all valence orbitals of the protein.
             Although many questions remain about appropriate
             parameterization, the simple Pathway prediction that
             proteins are not structureless isotropic electron-transfer
             barriers holds as multiple pathways are included in the
             calculations and backscattering of electron amplitude within
             and between pathways is added. © 1993 American Chemical
             Society.},
   Key = {fds231984}
}

@article{fds231985,
   Author = {Risser, SM and Beratan, DN and Onuchic, JN},
   Title = {Electronic coupling in starburst dendrimers},
   Journal = {J. Phys. Chem.},
   Volume = {97},
   Number = {17},
   Pages = {4523-4527},
   Year = {1993},
   ISSN = {0022-3654},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1993/97/i17/pdf/j100119a045.pdf},
   Abstract = {We describe the mechanism of electronic coupling in
             starburst dendrimers, where each repeating unit is linked to
             three or more nearest neighbors. The connectivity in these
             molecules, which is that of a Bethe lattice or Cayley tree,
             leads to localization of the electronic states even within
             the "bands" of the material. This localization gives rise to
             electronic coupling properties that are distinct from those
             of the corresponding linear polymers. These differences are
             evident in the predicted electron-transport properties of
             the materials. When disorder is introduced to the structure,
             however, the branched connectivity of the dendrimer can
             enhance the probability of finding some strongly coupled
             pathways between the core and surface sites of the
             dendrimer. The unusual electron mediation properties of
             these molecules make them particularly intriguing frameworks
             for investigating the molecular control of electron
             transport and, especially, the role that disorder can play
             in establishing pathways for electronic communication in
             macromolecules. © 1993 American Chemical
             Society.},
   Key = {fds231985}
}

@article{fds232029,
   Author = {Risser, SM and Beratan, DN and Marder, SR},
   Title = {Structure-function relationships for β, the first molecular
             hyperpolarizability},
   Journal = {Journal of the American Chemical Society},
   Volume = {115},
   Number = {17},
   Pages = {7719-7728},
   Year = {1993},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1993/115/i17/pdf/ja00070a016.pdf},
   Abstract = {A four-orbital model is used to map the overall dependence
             of β, the first electronic hyperpolarizability, on chemical
             parameters such as donor/acceptor strength and coupling
             between bridge and donor/acceptor orbitals. These
             calculations are used to develop general structure-property
             relationships for β and to demonstrate the physical origin
             of maxima, minima, and zeros in β. Comparison with
             multiorbital calculations on specific molecules show that
             the general relationships apply to more complex structures
             as well. A number of strategies for manipulating β by
             varying molecular structure emerge from the analysis. We
             show that the absolute maxima in the β surfaces fall
             outside of the range that has been probed using conventional
             organic donors and acceptors.},
   Key = {fds232029}
}

@article{fds232052,
   Author = {Skourtis, SS and Beratan, DN and Onuchic, JN},
   Title = {The two-state reduction for electron and hole transfer in
             bridge-mediated electron-transfer reactions},
   Journal = {Chemical Physics},
   Volume = {176},
   Number = {2-3},
   Pages = {501-520},
   Year = {1993},
   ISSN = {0301-0104},
   url = {http://dx.doi.org/10.1016/0301-0104(93)80258-B},
   Abstract = {We present a unified analysis of the two-state reduction in
             bridge-mediated electron transfer for both electron and hole
             transfer. The parameter that characterizes the leading error
             associated with a two-state reduction is derived in the
             energy and time domains. A precise definition of the
             tunnelling energy is given. We also derive analytically the
             regimes of validity of the two-state reduction and we
             interpret it in terms of the time evolution of the purely
             electronic part of the electron-transfer probability. ©
             1993.},
   Doi = {10.1016/0301-0104(93)80258-B},
   Key = {fds232052}
}

@article{fds304364,
   Author = {Risser, SM and Beratan, DN and Onuchic, JN},
   Title = {Electronic coupling in starburst dendrimers: Connectivity,
             disorder, and finite size effects in macromolecular Bethe
             lattices},
   Journal = {Journal of Physical Chemistry},
   Volume = {97},
   Number = {17},
   Pages = {4523-4527},
   Year = {1993},
   ISSN = {0022-3654},
   Abstract = {We describe the mechanism of electronic coupling in
             starburst dendrimers, where each repeating unit is linked to
             three or more nearest neighbors. The connectivity in these
             molecules, which is that of a Bethe lattice or Cayley tree,
             leads to localization of the electronic states even within
             the "bands" of the material. This localization gives rise to
             electronic coupling properties that are distinct from those
             of the corresponding linear polymers. These differences are
             evident in the predicted electron-transport properties of
             the materials. When disorder is introduced to the structure,
             however, the branched connectivity of the dendrimer can
             enhance the probability of finding some strongly coupled
             pathways between the core and surface sites of the
             dendrimer. The unusual electron mediation properties of
             these molecules make them particularly intriguing frameworks
             for investigating the molecular control of electron
             transport and, especially, the role that disorder can play
             in establishing pathways for electronic communication in
             macromolecules. © 1993 American Chemical
             Society.},
   Key = {fds304364}
}

@article{fds232040,
   Author = {Beratan, DN and Onuchic, JN and Winkler, JR and Gray,
             HB},
   Title = {Electron-tunneling pathways in proteins.},
   Journal = {Science},
   Volume = {258},
   Number = {5089},
   Pages = {1740-1741},
   Year = {1992},
   Month = {December},
   ISSN = {0036-8075},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/1334572},
   Key = {fds232040}
}

@misc{fds22271,
   Author = {D.N. Beratan},
   Title = {Molecular electronic device concepts},
   Volume = {10},
   Pages = {411-417},
   Booktitle = {1992 Encyclopedia of Physical Science and
             Technology},
   Publisher = {Academic Press},
   Year = {1992},
   Key = {fds22271}
}

@article{fds231982,
   Author = {Onuchic, JN and Beratan, DN and Winkler, JR and Gray,
             HB},
   Title = {Pathway analysis of protein electron-transfer
             reactions.},
   Journal = {Annual Review of Biophysics and Biomolecular
             Structure},
   Volume = {21},
   Pages = {349-377},
   Year = {1992},
   ISSN = {1056-8700},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/1326356},
   Doi = {10.1146/annurev.bb.21.060192.002025},
   Key = {fds231982}
}

@article{fds231983,
   Author = {Beratan, DN and Betts, JN and Onuchic, JN},
   Title = {Tunneling pathway and redox-state-dependent electronic
             couplings at nearly fixed distance in electron-transfer
             proteins},
   Journal = {Journal of Physical Chemistry},
   Volume = {96},
   Number = {7},
   Pages = {2852-2855},
   Year = {1992},
   ISSN = {0022-3654},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1992/96/i07/pdf/j100186a014.pdf},
   Abstract = {The tunneling pathway model for electron transfer, which
             accounts for the unique covalent, hydrogen-bonded, and van
             der Waals contacts linking donor and acceptor in a protein,
             gives a consistent description of electron-transfer rates in
             ruthenated proteins (cytochrome c, myoglobin, and cytochrome
             b5), while simpler exponential decay models are not fully
             adequate. We report several new testable predictions of the
             pathway model relating electron-transfer rates to protein
             structure. The analysis predicts qualitative differences in
             the distance dependence of protein electron transfer at
             short (&lt;5 Å) vs long distance, differences in the nature
             of the coupling through α-helix vs β-sheet, and the
             possibility of switching electronic coupling upon
             oxidation/reduction or ligation/deligation in
             metalloproteins. © 1992 American Chemical
             Society.},
   Key = {fds231983}
}

@article{fds232028,
   Author = {Betts, JN and Beratan, DN and Onuchic, JN},
   Title = {Mapping electron tunneling pathways: An algorithm that finds
             the "minimum lengths"/maximum coupling pathway between
             electron donors and acceptors in proteins},
   Journal = {Journal of the American Chemical Society},
   Volume = {114},
   Number = {11},
   Pages = {4043-4046},
   Year = {1992},
   ISSN = {0002-7863},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1992/114/i11/pdf/ja00037a004.pdf},
   Abstract = {The covalent, hydrogen bonded, and van der Waals
             connectivity of proteins can be represented with geometrical
             objects called graphs. In these graphs, vertices represent
             bonds and the connections between them, edges, represent
             bond-bond interactions. We describe a model in which edge
             lengths are associated with the wave function decay between
             interacting pairs of bonds, and a minimum distance
             graph-search algorithm is used to find the pathways that
             dominate electron donor-acceptor interactions in these
             molecules. Predictions of relative electron transfer rates
             can be made from these pathway lengths. The results are
             consistent with many experimentally measured
             electron-transfer rates, although some anomalies exist.
             Presentation of the pathway coupling between the donor (or
             acceptor) and every other atom in a given protein as a
             color-coded map provides a design tool for tailored
             electron-transfer proteins.},
   Key = {fds232028}
}

@article{fds232051,
   Author = {Beratan, DN and Betts, JN and Onuchic, JN},
   Title = {Protein electron transfer rates set by the bridging
             secondary and tertiary structure.},
   Journal = {Science},
   Volume = {252},
   Number = {5010},
   Pages = {1285-1288},
   Year = {1991},
   Month = {May},
   ISSN = {0036-8075},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/1656523},
   Abstract = {The rate of long-distance electron transfer in proteins
             rapidly decreases with distance, which is indicative of an
             electron tunneling process. Calculations predict that the
             distance dependence of electron transfer in native proteins
             is controlled by the protein's structural motif. The helix
             and sheet content of a protein and the tertiary arrangement
             of these secondary structural units define the distance
             dependence of electronic coupling in that protein. The
             calculations use a tunneling pathway model applied
             previously with success to ruthenated proteins. The analysis
             ranks the average distance decay constant for electronic
             coupling in electron transfer proteins and identifies the
             amino acids that are coupled to the charge localization site
             more strongly or weakly than average for their
             distance.},
   Key = {fds232051}
}

@article{fds232050,
   Author = {Marder, SR and Beratan, DN and Cheng, LT},
   Title = {Approaches for optimizing the first electronic
             hyperpolarizability of conjugated organic
             molecules.},
   Journal = {Science},
   Volume = {252},
   Number = {5002},
   Pages = {103-106},
   Year = {1991},
   Month = {April},
   ISSN = {0036-8075},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17739081},
   Abstract = {A two-state, four-orbital, independent electron analysis of
             the first optical molecular hyperpolarizability, beta, leads
             to the prediction that |beta| maximizes at a combination of
             donor and acceptor strengths for a given conjugated bridge.
             Molecular design strategies that focus on the energetic
             manipulations of the bridge states are proposed for the
             optimization of beta. The limitations of molecular classes
             based on common bridge structures are highlighted and more
             promising candidates are described. Experimental results
             supporting the validity of this approach are
             presented.},
   Doi = {10.1126/science.252.5002.103},
   Key = {fds232050}
}

@misc{fds22276,
   Author = {S.R. Marder and B.G. Tiemann and D.N. Beratan and L-T. Cheng and W.
             Tam},
   Title = {Structure property relationships for organic and
             oranometallic materials with second-order
             nonlinearities},
   Pages = {165-175},
   Booktitle = {Organic Materials for Nonlinear Optics, II},
   Publisher = {Royal Society of Chemistry, Cambridge},
   Editor = {R.A. hann and D. Bloor},
   Year = {1991},
   Key = {fds22276}
}

@misc{fds22277,
   Author = {D.N. Beratan},
   Title = {Electronic hyperpolizability and chemical structure: a
             tutorial},
   Volume = {455},
   Series = {ACS Symposium Series},
   Pages = {89-102},
   Booktitle = {New Materials for Nonlinear Optics},
   Editor = {S.R. Marder and J.E. Sohn and G.D. Stucky},
   Year = {1991},
   Key = {fds22277}
}

@misc{fds22278,
   Author = {D.N. Beratan and J.N. Onuchic and H.B. Gray},
   Title = {Electron tunneling pathways in proteins},
   Volume = {27},
   Pages = {97-127},
   Booktitle = {Metal Ions in Biological Systems},
   Publisher = {Marcel Dekker Press, New York},
   Editor = {H. Sigel and A. Sigel},
   Year = {1991},
   Key = {fds22278}
}

@misc{fds22279,
   Author = {D.N. Beratan and J.N. Onuchic},
   Title = {Electron tunneling pathways: from model compounds to
             proteins},
   Pages = {71-90},
   Booktitle = {ACS Advance in Chemistry Series volume 228, Electron
             transfer in organic, and biological systems},
   Editor = {J.R. Bolton and N. Mataga and G. McLendon},
   Year = {1991},
   Key = {fds22279}
}

@misc{fds22280,
   Author = {D.N. Beratan},
   Title = {Molecular electronic device concepts},
   Pages = {359-364},
   Booktitle = {1991 Encyclopedia of Physical Science and Technology
             Yearbook},
   Publisher = {Academic Press},
   Year = {1991},
   Key = {fds22280}
}

@article{fds231969,
   Author = {Marder, SR and Cheng, L-TA and Tiemann, BG and Beratan,
             DN},
   Title = {Structure/property relationships for molecular second-order
             nonlinear optics (Invited Paper)},
   Journal = {Proceedings of SPIE - The International Society for Optical
             Engineering},
   Volume = {1560},
   Pages = {86-97},
   Year = {1991},
   url = {http://spiedl.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=PSISDG001560000001000086000001&idtype=cvips&prog=normal},
   Abstract = {Using a two-state model, it was recently shown that there is
             an optimal combination of donor and acceptor strengths for a
             given bridge that will maximize the first molecular
             electronic hyperpolarizability (β). To date, molecules with
             sufficiently strong donors and acceptors have not been
             synthesized to reach this ideal point. Here we outline
             synthetic strategies that lead to molecules where β is
             optimized by tuning the degree of bond alternation in the
             π-electron system between the donor and acceptor.
             Implementation of this strategy relies on the realization
             that molecules with strongly aromatic end groups will not
             have the correct balance of two limiting charge transfer
             resonance forms in the ground state to achieve the degree of
             bond alternation required to optimize the molecular
             hyperpolarizability. Electric field induced second harmonic
             generation studies on organic molecules with various bridge
             structures support our hypothesis.},
   Key = {fds231969}
}

@article{fds231981,
   Author = {Onuchic, JN and Andrade, PCPD and Beratan, DN},
   Title = {Electron tunneling pathways in proteins: A method to compute
             tunneling matrix elements in very large systems},
   Journal = {Journal of Chemical Physics},
   Volume = {95},
   Number = {2},
   Pages = {1131-1138},
   Year = {1991},
   ISSN = {0021-9606},
   url = {http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JCPSA6000095000002001131000001&idtype=cvips},
   Abstract = {A tight-binding Hamiltonian and Dyson's equation method are
             described that allow the computation of the tunneling matrix
             elements between electron donor and acceptor sites in a
             protein. The method is exact and computationally tractable.
             The Green's function matrix elements of the bridge are
             computed using a strategy that builds up the bridge one
             orbital at a time, allowing inclusion of all orbitals on
             proposed tunneling pathways and elsewhere. The tunneling
             matrix element is determined directly from the bridge
             Green's function. A simple representation of a helical
             protein segment is used to illustrate the method and its
             ability to include contributions from high-order
             backscattering and multiple pathway interference in the
             donor-acceptor coupling. © 1991 American Institute of
             Physics.},
   Key = {fds231981}
}

@article{fds313865,
   Author = {BERATAN, DN and ONUCHIC, JN},
   Title = {ELECTRON-TRANSFER - FROM MODEL COMPOUNDS TO
             PROTEINS},
   Journal = {Advances in Chemistry Series},
   Number = {228},
   Pages = {71-90},
   Year = {1991},
   ISSN = {0065-2393},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1991GD62900006&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds313865}
}

@article{fds318059,
   Author = {BERATAN, DN},
   Title = {ELECTRONIC HYPERPOLARIZABILITY AND CHEMICAL-STRUCTURE},
   Journal = {ACS Symposium Series},
   Volume = {455},
   Pages = {89-102},
   Year = {1991},
   Key = {fds318059}
}

@misc{fds22275,
   Author = {D.N. Beratan and J.N. Onuchic and J.J. Hopefield},
   Title = {Design of a molecular memory device: the electron transfer
             shift register memory},
   Pages = {107-118},
   Booktitle = {Towards the Biochip},
   Publisher = {World Publishing Company, New Jersey},
   Editor = {C. Nicolini},
   Year = {1990},
   Key = {fds22275}
}

@article{fds231902,
   Author = {Beratan, DN},
   Title = {Strategies for the 'molecular engineering' of chemical,
             electronic, and optical devices},
   Journal = {Proceedings of the Intersociety Energy Conversion
             Engineering Conference},
   Volume = {3},
   Pages = {519-520},
   Year = {1990},
   Abstract = {Theoretical chemistry is assisting in the design of new
             materials for biocatalysis, ultrasmall-scale electronic
             devices, and nonlinear optics. The author discusses of the
             kinds of molecular design and property prediction problems
             which have recently been attacked using these techniques.
             The role of theoretical chemistry for developing the
             structure-property relationships in families of small
             molecules with novel optical properties is
             discussed.},
   Key = {fds231902}
}

@article{fds231904,
   Author = {Onuchic, J and Beratan, D},
   Title = {Tunneling pathways in proteins: From biology to molecular
             electronics},
   Journal = {Proceedings of the Annual Conference on Engineering in
             Medicine and Biology},
   Number = {pt 4},
   Pages = {1764-1765},
   Year = {1990},
   Abstract = {A method is presented for the calculation of tunneling
             matrix elements for electron transfer in proteins. The
             concept of a tunneling pathway is introduced and its
             importance in mediating this coupling is described. Comments
             are presented on how, using the knowledge about electron
             transfer reactions, a molecular shift register memory has
             been designed. Similar to photosynthetic structures, these
             shift register memories have to separate charge (fast
             forward electron transfer) much faster than the charge
             separated states are able to recombine (slow reverse
             electron transfer). This device demonstrates the importance
             of understanding how controlled electron transfer reactions
             work for developing new kinds of technology.},
   Key = {fds231904}
}

@article{fds231979,
   Author = {Beratan, DN and Onuchic, JN and Betts, JN and Bowler, B and Gray,
             HG},
   Title = {Electron mediation pathways in ruthenated
             proteins},
   Journal = {J. Am. Chem. Soc.},
   Volume = {112},
   Number = {22},
   Pages = {7915-7921},
   Year = {1990},
   ISSN = {0002-7863},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1990/112/i22/pdf/ja00178a011.pdf},
   Abstract = {We implement a numerical algorithm to survey proteins for
             electron-tunneling pathways. Insight is gained into the
             nature of the mediation process in long-distance
             electron-transfer reactions. The dominance of covalent and
             hydrogen bond pathways is shown. The method predicts the
             relative electronic couplings in ruthenated myoglobin and
             cytochrome c consistent with measured electron-transfer
             rates. It also allows the design of long-range
             electron-transfer systems. Qualitative differences between
             pathways arise from the protein secondary structure. Effects
             of this sort are not predicted from simpler models that
             neglect various details of the protein electronic
             structure.},
   Key = {fds231979}
}

@article{fds231980,
   Author = {Onuchic, JN and Beratan, DN},
   Title = {A predictive theoretical model for electron tunneling
             pathways in proteins},
   Journal = {Journal of Chemical Physics},
   Volume = {92},
   Number = {1},
   Pages = {722-733},
   Year = {1990},
   ISSN = {0021-9606},
   url = {http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JCPSA6000092000001000722000001&idtype=cvips},
   Abstract = {A practical method is presented for calculating the
             dependence of electron transfer rates on details of the
             protein medium intervening between donor and acceptor. The
             method takes proper account of the relative energetics and
             mutual interactions of the donor, acceptor, and peptide
             groups. It also provides a quantitative search scheme for
             determining the important tunneling pathway(s) [specific
             sequence (s) of localized bonding and antibonding orbitals
             of the protein which dominate the donor-acceptor electronic
             coupling] in native and tailored proteins, provides a tool
             for designing new proteins with prescribed electron transfer
             rates, and provides a consistent description of observed
             electron transfer rates in existing redox labeled
             metalloproteins and small molecule model compounds. © 1990
             American Institute of Physics.},
   Key = {fds231980}
}

@article{fds232049,
   Author = {BERATAN, DN},
   Title = {CONTROLLED ELECTRON-TRANSFER FOR MOLECULAR
             ELECTRONICS},
   Volume = {190},
   Pages = {85-94},
   Year = {1990},
   ISSN = {0140-6566},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1990EF05400010&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Doi = {10.1080/00268949008047835},
   Key = {fds232049}
}

@article{fds304363,
   Author = {Beratan, DN and Onuchic, JN and Betts, JN and Bowler, BE and Gray,
             HB},
   Title = {Electron-tunneling pathways in ruthenated
             proteins},
   Journal = {Journal of the American Chemical Society},
   Volume = {112},
   Number = {22},
   Pages = {7915-7921},
   Year = {1990},
   ISSN = {0002-7863},
   Abstract = {We implement a numerical algorithm to survey proteins for
             electron-tunneling pathways. Insight is gained into the
             nature of the mediation process in long-distance
             electron-transfer reactions. The dominance of covalent and
             hydrogen bond pathways is shown. The method predicts the
             relative electronic couplings in ruthenated myoglobin and
             cytochrome c consistent with measured electron-transfer
             rates. It also allows the design of long-range
             electron-transfer systems. Qualitative differences between
             pathways arise from the protein secondary structure. Effects
             of this sort are not predicted from simpler models that
             neglect various details of the protein electronic
             structure.},
   Key = {fds304363}
}

@misc{fds22289,
   Author = {D.N. Beratan and J.N Onuchic and J.J. Hopfield},
   Title = {Design of a true molecular electronic device:the electron
             transfer shift register memory},
   Pages = {353-360},
   Booktitle = {Molecular Electronics - Biosensors and Diocomputers},
   Publisher = {Plenum Press},
   Editor = {F.T. Hong},
   Year = {1989},
   Key = {fds22289}
}

@misc{fds22290,
   Author = {D.N. Beratan and J.N. Onuchic and J.J. Hopfield},
   Title = {Design of a molecular memory device based on electron
             transfer reactions},
   Pages = {331-357},
   Booktitle = {Molecular Electronics: Science and Technology},
   Publisher = {Engineering Foundation, New York},
   Year = {1989},
   Key = {fds22290}
}

@article{fds231901,
   Author = {Beratan, DN and Hopfield, JJ and Onuchic, J},
   Title = {Ultrasmall memories based on electron transfer
             reactions},
   Journal = {Annual International Conference of the IEEE Engineering in
             Medicine and Biology - Proceedings},
   Volume = {11 pt 4},
   Pages = {1322-},
   Year = {1989},
   Abstract = {Summary form only given. An electronic shift register memory
             at the molecular level is described. The memory elements are
             based on a chain of electron transfer molecules, and the
             information is shifted by photoinduced electron transfer
             reactions. This device integrates designed electronic
             molecules onto a very-large-scale integrated (silicon
             microelectronic) substrate, providing an example of a
             molecular electronic device.},
   Key = {fds231901}
}

@article{fds231977,
   Author = {Hopfield, JJ and Onuchic, JN and Beratan, DN},
   Title = {Electronic shift register memory based on molecular
             electron-transfer reactions},
   Journal = {Journal of Physical Chemistry},
   Volume = {93},
   Number = {17},
   Pages = {6350-6357},
   Year = {1989},
   ISSN = {0022-3654},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1989/93/i17/pdf/j100354a017.pdf},
   Abstract = {The design of a shift register memory at the molecular level
             is described in detail. The memory elements are based on a
             chain of electron-transfer molecules incorporated on a very
             large scale integrated (VLSI) substrate, and the information
             is shifted by photoinduced electron-transfer reactions. The
             design requirements for such a system are discussed, and
             several realistic strategies for synthesizing these systems
             are presented. The immediate advantage of such a hybrid
             molecular/VLSI device would arise from the possible
             information storage density. The prospect of considerable
             savings of energy per bit processed also exists. This
             molecular shift register memory element design solves the
             conceptual problems associated with integrating molecular
             size components with larger (micron) size features on a
             chip. © 1989 American Chemical Society.},
   Key = {fds231977}
}

@article{fds231978,
   Author = {Beratan, DN},
   Title = {Influence of gap states on the nonresonant second
             hyperpolarizabilities of conjugated organic
             polymers},
   Journal = {Journal of physical chemistry},
   Volume = {93},
   Number = {10},
   Pages = {3915-3920},
   Year = {1989},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1989/93/i10/pdf/j100347a012.pdf},
   Abstract = {The presence of conjugation and substitution defects
             introduces 'gap states' in finite polyenes that are shown to
             influence the size and sign of the second molecular
             hyperpolarizability, γxxxx. Using a one-electron
             tight-binding model, we calculate the dependence of γxxxx
             on the defect-state occupancy and energy in finite polyenes.
             Defects can cause a significant decrease or enhancement of
             γxxxx by impeding charge delocalization or by creating
             partly filled bands (mimicking the one-band limit),
             respectively. Concomitant sign changes in γxxxx are
             predicted. Calculations of these effects are made for
             molecules in which a central atom's identity and electron
             occupancy are varied. The results suggest strategies for
             designing molecules that can be either photochemically or
             electrochemically switched between states with considerably
             different second hyperpolarizabilities.},
   Key = {fds231978}
}

@article{fds232046,
   Author = {BERATAN, DN and LEE, MA and ALLENDER, DW and RISSER,
             S},
   Title = {STRUCTURAL DEPENDENCE OF THE PI-ELECTRON CONTRIBUTIONS TO
             THE OPTICAL 2ND HYPERPOLARIZABILITY OF LINEAR CONJUGATED
             ORGANIC-MOLECULES},
   Journal = {LIQUID CRYSTAL CHEMISTRY, PHYSICS, AND APPLICATIONS},
   Volume = {1080},
   Pages = {101-107},
   Year = {1989},
   url = {http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:A1989BP78U00013&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=47d3190e77e5a3a53558812f597b0b92},
   Key = {fds232046}
}

@article{fds232047,
   Author = {Beratan, DN and Onuchic, JN and Hopfield, JJ},
   Title = {Information storage at the molecular level: the design of a
             molecular shift register memory},
   Journal = {Journal of the British Interplanetary Society},
   Volume = {42},
   Pages = {468-473},
   Year = {1989},
   Key = {fds232047}
}

@article{fds232048,
   Author = {Beratan, DN and Onuchic, JN},
   Title = {Electron tunneling pathways in proteins: influences on the
             transfer rate},
   Journal = {Photosynthesis Research},
   Volume = {22},
   Number = {3},
   Pages = {173-186},
   Year = {1989},
   ISSN = {0166-8595},
   url = {http://dx.doi.org/10.1007/BF00048296},
   Abstract = {A strategy for calculating the tunneling matrix element
             dependence on the medium intervening between donor and
             acceptor in specific proteins is described. The scheme is
             based on prior studies of small molecules and is general
             enough to allow inclusion of through bond and through space
             contributions to the electronic tunneling interaction. This
             strategy should allow the prediction of relative electron
             transfer rates in a number of proteins. It will therefore
             serve as a design tool and will be explicitly testable, in
             contrast with calculations on single molecules. As an
             example, the method is applied to ruthenated myoglobin and
             the tunneling matrix elements are estimated. Quantitative
             improvements of the model are described and effects due to
             motion of the bridging protein are discussed. The method
             should be of use for designing target proteins having
             tailored electron transfer rates for production with site
             directed mutagenesis. The relevance of the technique to
             understanding certain photosynthetic reaction center
             electron transfer rates is discussed. © 1989 Kluwer
             Academic Publishers.},
   Doi = {10.1007/BF00048296},
   Key = {fds232048}
}

@article{fds232044,
   Author = {Hopfield, JJ and Onuchic, JN and Beratan, DN},
   Title = {A molecular shift register based on electron
             transfer.},
   Journal = {Science},
   Volume = {241},
   Number = {4867},
   Pages = {817-820},
   Year = {1988},
   Month = {August},
   ISSN = {0036-8075},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/17829175},
   Abstract = {An electronic shift-register memory at the molecular level
             is described. The memory elements are based on a chain of
             electron-transfer molecules and the information is shifted
             by photoinduced electron-transfer reactions. This device
             integrates designed electronic molecules onto a very large
             scale integrated (silicon microelectronic) substrate,
             providing an example of a "molecular electronic device" that
             could actually be made. The design requirements for such a
             device and possible synthetic strategies are discussed.
             Devices along these lines should have lower energy usage and
             enhanced storage density.},
   Doi = {10.1126/science.241.4867.817},
   Key = {fds232044}
}

@article{fds231975,
   Author = {Onuchic, JN and Beratan, DN},
   Title = {Adiabaticity criteria for outer-sphere bimolecular
             electron-transfer reactions},
   Journal = {Journal of Physical Chemistry},
   Volume = {92},
   Number = {17},
   Pages = {4817-4820},
   Year = {1988},
   ISSN = {0022-3654},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1988/92/i17/pdf/j100328a001.pdf},
   Abstract = {A model is presented for outer-sphere bimolecular
             electron-transfer reactions which is correct in the
             adiabatic, nonadiabatic, and intermediate dynamical regimes
             for an overdamped solvent coordinate. From this model we
             deduce the conditions for the transfer to be "adiabatic" or
             "nonadiabatic". Evidence for the two regimes exists in the
             experimental literature, so this work will provide guidance
             for mapping out the transition between these regimes. The
             time-scale separations needed to adequately describe the
             process as an average over (distant dependent) unimolecular
             rates are described. © 1988 American Chemical
             Society.},
   Key = {fds231975}
}

@article{fds231976,
   Author = {Beratan, DN and Onuchic, JN},
   Title = {Adiabaticlty and nonadiabaticity in bimolecular outer-sphere
             charge transfer reactions},
   Journal = {Journal of Chemical Physics},
   Volume = {89},
   Number = {10},
   Pages = {6195-6203},
   Year = {1988},
   ISSN = {0021-9606},
   url = {http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JCPSA6000089000010006195000001&idtype=cvips},
   Abstract = {A model for outer-sphere bimolecular electron transfer
             reactions is presented which is based on a rate expression
             correct in the adiabatic, nonadiabatic, and intermediate
             dynamical regimes for an overdamped solvent coordinate. A
             complete discussion of the time-scale separations needed to
             define a bimolecular rate for these electron transfer
             reactions is given. Bimolecular reaction rates are predicted
             to display distinct solvent and electronic coupling
             dependencies, defined by a few experimentally variable
             parameters, which we now identify. Also, a significant
             intermediate dynamical regime is predicted to exist in which
             the rate is sensitive to both electronic coupling and
             nuclear relaxation. Evidence that both extreme dynamical
             regimes have been accessed experimentally is recalled, and
             strategies are presented for fully mapping out the
             dependence of rate on the electronic coupling and relaxation
             times. © 1988 American Institute of Physics.},
   Key = {fds231976}
}

@article{fds232043,
   Author = {Perry, JW and Stiegman, AE and Marder, SR and Coulter, DR and Beratan,
             DN and Brinza, DE and Klavetter, FL and Grubbs, RH},
   Title = {Second and third order nonlinear optical properties of
             conjugated molecules and polymers},
   Journal = {Proceedings of SPIE-The Society of Photo-Optical
             Instrumentation Engineers},
   Volume = {971},
   Pages = {17-24},
   Year = {1988},
   Key = {fds232043}
}

@article{fds232045,
   Author = {Cowan, JA and Upmacis, RK and Beratan, DN and Onuchic, JN and Gray,
             HB},
   Title = {Long-range electron transfer in myoglobin.},
   Journal = {Annals of the New York Academy of Sciences},
   Volume = {550},
   Pages = {68-84},
   Year = {1988},
   ISSN = {0077-8923},
   url = {http://www.ncbi.nlm.nih.gov/pubmed/3245652},
   Abstract = {The distance and driving-force dependences of electron
             transfer (ET) in a set of four surface-ruthenated
             myoglobins, in which the heme prosthetic group has been
             systematically replaced by a series of metalloporphyrins of
             differing excited-state redox potentials, have provided
             information on the magnitude [Hab(12.7 A) approximately 6.3
             x 10(-3) cm-1] and decay [beta approximately 0.8 A-1, where
             kET alpha exp [-beta(d - do)]] of protein-mediated
             donor-acceptor electronic coupling. A reorganization energy
             lambda approximately 1.3 eV, due to coordination and
             solvation changes both at and between the ET sites, has been
             estimated using a rate expression that allows
             electron-vibration coupling to classical and quantum
             mechanical modes. The contribution to lambda from the
             porphyrin and peptide matrix is approximately 0.7 eV.
             Specific electron-tunneling pathways in the protein have
             been evaluated.},
   Doi = {10.1111/j.1749-6632.1988.tb35324.x},
   Key = {fds232045}
}

@misc{fds22297,
   Author = {D.N. Beratan and J.N. Onuchic and J.J. Hopfield},
   Title = {Through bond and through space limits of the long distance
             electron transfer problem},
   Pages = {488},
   Booktitle = {Protein Structure, Molecular and Electronic
             Reactivity},
   Editor = {R. Austin and et al.},
   Year = {1987},
   Key = {fds22297}
}

@article{fds231973,
   Author = {Beratan, DN and Onuchic, JN and Hopfield, JJ},
   Title = {Electron tunneling through covalent and noncovalent pathways
             in proteins},
   Journal = {Journal of Chemical Physics},
   Volume = {86},
   Number = {8},
   Pages = {4488-4498},
   Year = {1987},
   ISSN = {0021-9606},
   url = {http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JCPSA6000086000008004488000001&idtype=cvips},
   Abstract = {A model is presented for electron tunneling in proteins
             which allows the donor-acceptor interaction to be mediated
             by the covalent bonds between amino acids and noncovalent
             contacts between amino acid chains. The important tunneling
             pathways are predicted to include mostly bonded groups with
             less favorable nonbonded interactions being important when
             the through bond pathway is prohibitively long. In some
             cases, vibrational motion of nonbonded groups along the
             tunneling pathway strongly inluences the temperature
             dependence of the rate. Quantitative estimates for the sizes
             of these noncovalent interactions are made and their role in
             protein mediated electron transport is discussed. © 1987
             American Institute of Physics.},
   Key = {fds231973}
}

@article{fds231974,
   Author = {Beratan, DN and Onuchic, JN and Perry, JW},
   Title = {Nonlinear susceptibilities of finite conjugated organic
             polymers},
   Journal = {Journal of Physical Chemistry},
   Volume = {91},
   Number = {11},
   Pages = {2696-2698},
   Year = {1987},
   ISSN = {0022-3654},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1987/91/i11/pdf/j100295a009.pdf},
   Abstract = {Tight-binding calculations of the length dependence of the
             third-order molecular hyperpolarizability for polyenes and
             polyynes are reported. The π-electron wave functions were
             determined by exploiting the limited translational symmetry
             of the molecules. Perturbation theory was used to calculate
             the longitudinal component of the electronic nonresonant
             hyperpolarizability. To our knowledge, this is the first
             two-"band" calculation of third-order hyperpolarizabilities
             on finite π-electron systems of varying length. In contrast
             to the results of the one-"band" models, the
             hyperpolarizability densities increase rapidly and then,
             after about 10-15 repeating units, approach an asymptotic
             value. © 1987 American Chemical Society.},
   Key = {fds231974}
}

@article{fds232027,
   Author = {Onuchic, JN and Beratan, DN},
   Title = {Molecular bridge effects on distant charge
             tunneling},
   Journal = {Journal of the American Chemical Society},
   Volume = {109},
   Number = {22},
   Pages = {6771-6778},
   Year = {1987},
   ISSN = {0002-7863},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1987/109/i22/pdf/ja00256a035.pdf},
   Abstract = {The question arises as to whether different hydrocarbon
             bridges should give different electron-transfer rates. We
             answer this question on the basis of energetic and
             topological (interference) effects that can be gleaned from
             one-electron models. A discussion of model compound
             electron-transfer rates based on this interpretation is
             given. The approximations implicit in the periodic models
             used here (and in previous work) are carefully justified. ©
             1987 American Chemical Society.},
   Key = {fds232027}
}

@article{fds231972,
   Author = {Onuchic, JN and Beratan, DN and Hopfield, JJ},
   Title = {Some aspects of electron-transfer reaction
             dynamics},
   Journal = {Journal of Physical Chemistry},
   Volume = {90},
   Number = {16},
   Pages = {3707-3721},
   Year = {1986},
   ISSN = {0022-3654},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jpchax/1986/90/i16/pdf/j100407a045.pdf},
   Abstract = {We prissent a simple, but complete, quantum mechanical model
             for electron transfer. It contains the elements necessary to
             calculate a rate: electron, reaction coordinate(s), and
             bath. The completeness of the model allows analysis of the
             dynamical aspects of the transfer (validity of the
             nonadiabatic, Born-Oppenheimer, and Condon approximations,
             for example). Interaction between the reaction coordinate(s)
             and the bath is discussed for "weak" and "strong" coupling,
             and the rate expression is derived in these limits. A model
             for donor and acceptor vibronic wave functions is solved
             exactly by using a molecular orbital approach. The rates are
             calculated from these states and a comparison with the
             standard Born-Oppenheimer/Condon result is made. The nature
             of the "inverted" effect is found to depend on transfer
             distance and details of the vibronic coupling. © 1986
             American Chemical Society.},
   Key = {fds231972}
}

@article{fds232026,
   Author = {Beratan, DN},
   Title = {Electron tunneling through rigid molecular bridges:
             Bicyclo[2.2.2]octane},
   Journal = {Journal of the American Chemical Society},
   Volume = {108},
   Number = {15},
   Pages = {4321-4326},
   Year = {1986},
   ISSN = {0002-7863},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1986/108/i15/pdf/ja00275a014.pdf},
   Abstract = {Electron tunneling through polymers of bicyclo[2.2.2]octane
             is studied. The repeating nature of the linker allows
             prediction of the dependence of the tunneling matrix element
             on distance and electronic energy by a semiempirical method
             exploiting the translational symmetry of the linker.
             Specific predictions for the dependence of rate on distance
             are made for recently synthesized photosynthetic model
             compounds containing porphyrins and quinones linked by this
             bridge. A large difference between the decay of rate with
             distance is predicted for the forward electron transfer in
             these model compounds compared with the reverse electron
             transfer. The effects of linker topology on the
             donor-acceptor interaction in several linkers are compared,
             and a heuristic rule is quantitated. The ability of the
             [2.2.2] linker to mediate the donor-acceptor interaction is
             shown to have an energy dependence determined by the
             symmetry of the donor and acceptor orbitals relative to the
             linker orbitals. © 1986 American Chemical
             Society.},
   Key = {fds232026}
}

@article{fds231971,
   Author = {Beratan, DN and Onuchic, JN and Hopfield, JJ},
   Title = {Limiting forms of the tunneling matrix element in the long
             distance bridge mediated electron transfer
             problem},
   Journal = {Journal of Chemical Physics},
   Volume = {83},
   Number = {10},
   Pages = {5325-5329},
   Year = {1985},
   ISSN = {0021-9606},
   url = {http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JCPSA6000083000010005325000001&idtype=cvips},
   Abstract = {A simple model is presented for long distance electron
             transfer through a bridging medium. Assumptions about the
             bridge mediated interaction, inherent in many other models,
             are shown to be limits of the more general problem. The
             relative importance of through bond and through space
             coupling is discussed. © 1985 American Institute of
             Physics.},
   Key = {fds231971}
}

@article{fds231970,
   Author = {Beratan, DN and Hopfield, JJ},
   Title = {Failure of the Born-Oppenheimer and Franck-Condon
             approximations for long distance electron transfer rate
             calculations},
   Journal = {Journal of Chemical Physics},
   Volume = {81},
   Number = {12},
   Pages = {5753-5759},
   Year = {1984},
   ISSN = {0021-9606},
   url = {http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JCPSA6000081000012005753000001&idtype=cvips},
   Abstract = {Quantum mechanical and semiclassical formulations of
             nonadiabatic electron transfer theory are usually
             implemented within a Born-Oppenheimer regime. Calculations
             on real weakly interacting systems are so difficult that
             this approximation is rarely questioned. The
             Born-Oppenheimer approximation becomes qualitatively wrong
             for electron transfers at very large distances. A model
             vibronic problem is exactly solved and compared with the
             Born-Oppenheimer result. Rate expressions are derived from
             the wave functions using the "golden rule" approximation.
             Electron propagation is intimately correlated with nuclear
             motion so that the vibrational energy left on the donor
             critically affects the electronic decay length. Several
             deviations from the usual predictions appear for transfers
             over very large distances. © 1984 American Institute of
             Physics.},
   Key = {fds231970}
}

@article{fds232025,
   Author = {Beratan, DN and Hopfield, JJ},
   Title = {CALCULATION OF ELECTRON TUNNELING MATRIX ELEMENTS IN RIGID
             SYSTEMS: MIXED-VALENCE DITHIASPIROCYCLOBUTANE
             MOLECULES.},
   Journal = {Journal of the American Chemical Society},
   Volume = {106},
   Number = {6},
   Pages = {1584-1594},
   Year = {1984},
   url = {http://pubs.acs.org/cgi-bin/archive.cgi/jacsat/1984/106/i06/pdf/ja00318a008.pdf},
   Abstract = {A semiempirical model is presented which predicts
             photoassisted electron-transfer rate dependence on distance
             for redox groups connected by rigid polymeric linkers. The
             model approximately reproduces the observed decay of the
             optical tunneling matrix element with distance found for the
             rigid ruthenium dithiaspiro mixed-valence complexes of C. A.
             Stein, N. A. Lewis, G. J. Seitz, and H. Taube. The method
             calculates the through-bond propagation of the wave function
             tail, by a method which emphasizes obtaining the correct
             distance dependence of the tunneling matrix element for
             these weakly interacting donor-acceptor complexes. The
             method also allows prediction of the magnitude of the matrix
             element, the importance of hole or electron tunneling in the
             transport process, the effect of donor and acceptor redox
             potential on the matrix element, and the thermal tunneling
             matrix element for these and other compounds.},
   Key = {fds232025}
}

@article{fds232042,
   Author = {Luken, WL and Beratan, DN},
   Title = {Localized orbitals and the Fermi hole},
   Journal = {Theoretica Chimica Acta},
   Volume = {61},
   Number = {3},
   Pages = {265-281},
   Year = {1982},
   ISSN = {0040-5744},
   url = {http://dx.doi.org/10.1007/BF00550971},
   Abstract = {The relationship between localized orbitals and the Fermi
             hole is demonstrated with contour maps of the Fermi hole in
             the water molecule. These contour maps indicate the presence
             of regions in which the Fermi hole is relatively stable,
             regions in which the shape of the Fermi hole changes
             rapidly, and regions in which the Fermi hole follows the
             probe electron smoothly. If a single orbital dominates any
             region of space, the Fermi hole resembles that orbital for
             any position of the probe electron in the dominated region.
             © 1982 Springer-Verlag.},
   Doi = {10.1007/BF00550971},
   Key = {fds232042}
}

@misc{fds22308,
   Author = {D.N. Beratan and W.L. Luken},
   Title = {Electron Correlation and the Chemical Bond},
   Publisher = {Freewater Film Productions, Durham, NC},
   Year = {1980},
   Key = {fds22308}
}