David N. Beratan

Journal Article Nature materials · June 2024 Coupling of spin and charge currents to structural chirality in non-magnetic materials, known as chirality-induced spin selectivity, is promising for application in spintronic devices at room temperature. Although the chirality-induced spin selectivity eff ... Full text Cite

Control of Photoinduced Donor-to-Acceptor Transfer Yield with Polarized Light

Journal Article Journal of Physical Chemistry C · May 9, 2024 Molecular species with near-degenerate excited states may be photoexcited into superpositions of these states with specific phase relationships. The subsequent photochemistry can depend on the nature of this superposition if the photochemistry proceeds mor ... Full text Cite

Seeking a quantum advantage with trapped-ion quantum simulations of condensed-phase chemical dynamics.

Journal Article Nature reviews. Chemistry · May 2024 Simulating the quantum dynamics of molecules in the condensed phase represents a longstanding challenge in chemistry. Trapped-ion quantum systems may serve as a platform for the analog-quantum simulation of chemical dynamics that is beyond the reach of cur ... Full text Cite

Electron transfer rate modulation with mid-IR in butadiyne-bridged donor-bridge-acceptor compounds.

Journal Article Physical chemistry chemical physics : PCCP · January 2024 Controlling electron transfer (ET) processes in donor-bridge-acceptor (DBA) compounds by mid-IR excitation can enhance our understanding of the ET dynamics and may find practical applications in molecular sensing and molecular-scale electronics. Alkyne moi ... Full text Cite

Electron-donating functional groups strengthen ligand-induced chiral imprinting on CsPbBr₃ quantum dots.

Journal Article Scientific reports · January 2024 Chiral perovskite nanoparticles and films are promising for integration in emerging spintronic and optoelectronic technologies, yet few design rules exist to guide the development of chiral material properties. The chemical space of potential building bloc ... Full text Cite

Quantum Simulation of Polarized Light-Induced Electron Transfer with a Trapped-Ion Qutrit System.

Journal Article The journal of physical chemistry letters · July 2023 Electron transfer within and between molecules is crucial in chemistry, biochemistry, and energy science. This study describes a quantum simulation method that explores the influence of light polarization on electron transfer between two molecules. By impl ... Full text Cite

Correlated particle transport enables biological free energy transduction.

Journal Article Biophysical journal · May 2023 Studies of biological transport frequently neglect the explicit statistical correlations among particle site occupancies (i.e., they use a mean-field approximation). Neglecting correlations sometimes captures biological function, even for out-of-equilibriu ... Full text Cite

Adenine Fine-Tunes DNA Photolyase's Repair Mechanism.

Journal Article The journal of physical chemistry. B · April 2023 The comparative study of DNA repair by mesophilic and extremophilic photolyases helps us understand the evolution of these enzymes and their role in preserving life on our changing planet. The mechanism of repair of cyclobutane pyrimidine dimer lesions in ... Full text Cite

Electron transfer reactions

Chapter · January 1, 2023 Cite

Interference between Molecular and Photon Field-Mediated Electron Transfer Coupling Pathways in Cavities.

Journal Article The journal of physical chemistry letters · October 2022 Cavity polaritonics creates novel opportunities to direct chemical reactions. Electron transfer (ET) reactions are among the simplest reactions, and they underpin energy conversion. New strategies to manipulate and direct electron flow at the nanoscale are ... Full text Cite

Suppressing the entanglement growth in matrix product state evolution of quantum systems through nonunitary similarity transformations

Journal Article Physical Review B · September 1, 2022 In strong-coupling regimes, quantum dynamical effects can alter conventional physics described by perturbation theories, but the dynamical simulations of these quantum systems using matrix product states - such as multilevel vibronic systems that are relev ... Full text Cite

Mapping Simulated Two-Dimensional Spectra to Molecular Models Using Machine Learning.

Journal Article The journal of physical chemistry letters · August 2022 Two-dimensional (2D) spectroscopy encodes molecular properties and dynamics into expansive spectral data sets. Translating these data into meaningful chemical insights is challenging because of the many ways chemical properties can influence the spectra. T ... Full text Cite

Regulating Singlet-Triplet Energy Gaps through Substituent-Driven Modulation of the Exchange and Coulomb Interactions.

Journal Article Journal of the American Chemical Society · August 2022 Control of the singlet-triplet energy gap (ΔEST) is central to realizing productive energy conversion reactions, photochemical reaction trajectories, and emergent applications that exploit molecular spin physics. Despite this, no systemat ... Full text Cite

Cofactor Dynamics Couples the Protein Surface to the Heme in Cytochrome c, Facilitating Electron Transfer.

Journal Article The journal of physical chemistry. B · May 2022 Electron transport through biomolecules and in biological transport networks is of great importance to bioenergetics and biocatalysis. More generally, it is of crucial importance to understand how the pathways that connect buried metallocofactors to other ... Full text Cite

A Chirality-Based Quantum Leap.

Journal Article ACS nano · April 2022 There is increasing interest in the study of chiral degrees of freedom occurring in matter and in electromagnetic fields. Opportunities in quantum sciences will likely exploit two main areas that are the focus of this Review: (1) recent observations of the ... Full text Cite

Synthetic Control of Exciton Dynamics in Bioinspired Cofacial Porphyrin Dimers.

Journal Article Journal of the American Chemical Society · April 2022 Understanding how the complex interplay among excitonic interactions, vibronic couplings, and reorganization energy determines coherence-enabled transport mechanisms is a grand challenge with both foundational implications and potential payoffs for energy ... Full text Cite

Discovery of the Xenon-Protein Interactome Using Large-Scale Measurements of Protein Folding and Stability.

Journal Article Journal of the American Chemical Society · March 2022 The intermolecular interactions of noble gases in biological systems are associated with numerous biochemical responses, including apoptosis, inflammation, anesthesia, analgesia, and neuroprotection. The molecular modes of action underlying these responses ... Full text Cite

Improving the efficiency of open-quantum-system simulations using matrix product states in the interaction picture

Journal Article Physical Review A · March 1, 2022 Modeling open quantum systems-quantum systems coupled to a bath-is of value in condensed-matter theory, cavity quantum electrodynamics, nanosciences, and biophysics. The real-time simulation of open quantum systems was advanced significantly by the recent ... Full text Cite

Twisted molecular wires polarize spin currents at room temperature.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · February 2022 A critical spintronics challenge is to develop molecular wires that render efficiently spin-polarized currents. Interplanar torsional twisting, driven by chiral binucleating ligands in highly conjugated molecular wires, gives rise to large near-infrared ro ... Full text Cite

Ligand Coverage and Exciton Delocalization Control Chiral Imprinting in Perovskite Nanoplatelets

Journal Article Journal of Physical Chemistry C · January 1, 2022 Chiral perovskites have recently generated significant interest, yet little is known about how their chiro-optical properties arise. In this study, chiral methylammonium lead halide perovskite nanoplatelets (NPLs) with varied halide and ligand compositions ... Full text Cite

Inverse chirality-induced spin selectivity effect in chiral assemblies of π-conjugated polymers.

Control of Photoinduced Donor-to-Acceptor Transfer Yield with Polarized Light

Seeking a quantum advantage with trapped-ion quantum simulations of condensed-phase chemical dynamics.

Electron transfer rate modulation with mid-IR in butadiyne-bridged donor-bridge-acceptor compounds.

Electron-donating functional groups strengthen ligand-induced chiral imprinting on CsPbBr₃ quantum dots.

Quantum Simulation of Polarized Light-Induced Electron Transfer with a Trapped-Ion Qutrit System.

Correlated particle transport enables biological free energy transduction.

Adenine Fine-Tunes DNA Photolyase's Repair Mechanism.

Electron transfer reactions

Chapter · January 1, 2023 Cite

Interference between Molecular and Photon Field-Mediated Electron Transfer Coupling Pathways in Cavities.

Suppressing the entanglement growth in matrix product state evolution of quantum systems through nonunitary similarity transformations

Mapping Simulated Two-Dimensional Spectra to Molecular Models Using Machine Learning.

Regulating Singlet-Triplet Energy Gaps through Substituent-Driven Modulation of the Exchange and Coulomb Interactions.

Cofactor Dynamics Couples the Protein Surface to the Heme in Cytochrome c, Facilitating Electron Transfer.

A Chirality-Based Quantum Leap.

Synthetic Control of Exciton Dynamics in Bioinspired Cofacial Porphyrin Dimers.

Discovery of the Xenon-Protein Interactome Using Large-Scale Measurements of Protein Folding and Stability.

Improving the efficiency of open-quantum-system simulations using matrix product states in the interaction picture

Twisted molecular wires polarize spin currents at room temperature.

Ligand Coverage and Exciton Delocalization Control Chiral Imprinting in Perovskite Nanoplatelets

Interference between Molecular and Photon Field-Mediated Electron Transfer Coupling Pathways in Cavities br

Journal Article JOURNAL OF PHYSICAL CHEMISTRY LETTERS · 2022 Full text Cite

Mechanism of Side Chain-Controlled Proton Conductivity in Bioinspired Peptidic Nanostructures.

Journal Article The journal of physical chemistry. B · November 2021 Bioinspired peptide assemblies are promising candidates for use as proton-conducting materials in electrochemical devices and other advanced technologies. Progress toward applications requires establishing foundational structure-function relationships for ... Full text Cite

Energy transduction by reversible electron bifurcation

Journal Article Current Opinion in Electrochemistry · October 1, 2021 Electron bifurcation is a biological energy conversion process that oxidizes a two-electron donor at medium potential, coupled to the reduction of a high- and a low-potential acceptor species. This process is often fully reversible (can occur close to ΔG≈0 ... Full text Cite

Multiple hops move electrons from bacteria to rocks.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · October 2021 Full text Cite

Excited-State Dynamics and Nonlinear Optical Properties of Hyperpolarizable Chromophores Based on Conjugated Bis(terpyridyl)Ru(II) and Palladium and Platinum Porphyrinic Components: Impact of Heavy Metals upon Supermolecular Electro-Optic Properties.

Journal Article Inorganic chemistry · October 2021 A new series of strongly coupled oscillators based upon (porphinato)Pd, (porphinato)Pt, and bis(terpyridyl)ruthenium(II) building blocks is described. These RuPPd, RuPPt, RuPPdRu, and RuPPtRu chromophores feature bis(terpyridyl) ... Full text Cite

Electron ratcheting in self-assembled soft matter.

Journal Article The Journal of chemical physics · August 2021 Ratcheted multi-step hopping electron transfer systems can plausibly produce directional charge transport over very large distances without requiring a source-drain voltage bias. We examine molecular strategies to realize ratcheted charge transport based o ... Full text Cite

Efficient and reversible electron bifurcation with either normal or inverted potentials at the bifurcating cofactor

Journal Article Chem · July 8, 2021 A longstanding mystery surrounding electron bifurcation is the significance of inverted (or “crossed”) reduction potentials of the two-electron bifurcating cofactor. Using a many-electron open-system kinetic model, we show that reversible and efficient ele ... Full text Cite

Oxalate decarboxylase uses electron hole hopping for catalysis.

Journal Article The Journal of biological chemistry · July 2021 The hexameric low-pH stress response enzyme oxalate decarboxylase catalyzes the decarboxylation of the oxalate mono-anion in the soil bacterium Bacillus subtilis. A single protein subunit contains two Mn-binding cupin domains, and catalysis depends on Mn(I ... Full text Cite

Why Do Most Aromatics Fail to Support Hole Hopping in the Cytochrome c Peroxidase-Cytochrome c Complex?

Journal Article The journal of physical chemistry. B · July 2021 Electron transport through aromatic species (especially tryptophan and tyrosine) plays a central role in water splitting, redox signaling, oxidative damage protection, and bioenergetics. The cytochrome c peroxidase (CcP)-cytochrome c (Cc) com ... Full text Cite

Delocalization-Assisted Transport through Nucleic Acids in Molecular Junctions.

Journal Article Biochemistry · May 2021 The flow of charge through molecules is central to the function of supramolecular machines, and charge transport in nucleic acids is implicated in molecular signaling and DNA repair. We examine the transport of electrons through nucleic acids to understand ... Full text Cite

Temperature Dependence of Charge and Spin Transfer in Azurin.

Journal Article The journal of physical chemistry. C, Nanomaterials and interfaces · May 2021 The steady-state charge and spin transfer yields were measured for three different Ru-modified azurin derivatives in protein films on silver electrodes. While the charge-transfer yields exhibit weak temperature dependences, consistent with operation of a n ... Full text Cite

Correlation between Charge Transport and Base Excision Repair in the MutY-DNA Glycosylase.

Journal Article The journal of physical chemistry. B · January 2021 Experimental evidence suggests that DNA-mediated redox signaling between high-potential [Fe4S4] proteins is relevant to DNA replication and repair processes, and protein-mediated charge transfer (CT) between [Fe4S4 Full text Cite

Charge Transfer and Spin Dynamics in a Zinc Porphyrin Donor Covalently Linked to One or Two Naphthalenediimide Acceptors.

Journal Article The journal of physical chemistry. A · January 2021 Quantum coherence effects on charge transfer and spin dynamics in a system having two degenerate electron acceptors are studied using a zinc 5,10,15-tri(n-pentyl)-20-phenylporphyrin (ZnP) electron donor covalently linked to either one or two naphtha ... Full text Cite

Predicting Dexter Energy Transfer Interactions from Molecular Orbital Overlaps

Journal Article Journal of Physical Chemistry C · September 3, 2020 Featured Publication Dexter energy transfer (DET), also known as spin forbidden energy transfer (e.g., 3D1A → 1D3A), is undergoing a resurgence of interest because of its utility in energy science, photocatalysis, and biomedical imaging. The DET reactions enable exciton fissio ... Full text Cite

Universal free-energy landscape produces efficient and reversible electron bifurcation.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · September 2020 Featured Publication For decades, it was unknown how electron-bifurcating systems in nature prevented energy-wasting short-circuiting reactions that have large driving forces, so synthetic electron-bifurcating molecular machines could not be designed and built. The underpinnin ... Full text Cite

Electrostatic Field-Induced Oscillator Strength Focusing in Molecules.

Journal Article The journal of physical chemistry. B · July 2020 The development of light-harvesting devices based on molecular materials depends critically on the ability to focus the electronic oscillator strength of molecules into the UV-vis spectral window. Typical molecular chromophores have only about 1% of their ... Full text Cite

Conductance and configuration of molecular gold-water-gold junctions under electric fields.

Journal Article Matter · July 2020 Water molecules can mediate charge transfer in biological and chemical reactions by forming electronic coupling pathways. Understanding the mechanism requires a molecular-level electrical characterization of water. Here, we describe the measurement of sing ... Full text Cite

Mutation effects on charge transport through the p58c iron-sulfur protein.

Journal Article Chemical science · July 2020 Featured Publication Growing experimental evidence indicates that iron-sulfur proteins play key roles in DNA repair and replication. In particular, charge transport between [Fe4S4] clusters, mediated by proteins and DNA, may convey signals to coordinate e ... Full text Cite

A Robust Bioderived Wavelength-Specific Photosensor Based on BLUF Proteins.

Journal Article Sensors and actuators. B, Chemical · May 2020 Photosensitive proteins are naturally evolved photosensors that often respond to light signals of specific wavelengths. However, their poor stability under ambient conditions hinders their applications in non-biological settings. In this proof-of-principle ... Full text Cite

Symmetry controlled photo-selection and charge separation in butadiyne-bridged donor-bridge-acceptor compounds.

Journal Article Physical chemistry chemical physics : PCCP · May 2020 Electron transfer (ET) in donor-bridge-acceptor (DBA) compounds depends strongly on the structural and electronic properties of the bridge. Among the bridges that support donor-acceptor conjugation, alkyne bridges have attractive and unique properties: the ... Full text Cite

Revisiting the Hole Size in Double Helical DNA with Localized Orbital Scaling Corrections.

Journal Article The journal of physical chemistry. B · April 2020 The extent of electronic wave function delocalization for the charge carrier (electron or hole) in double helical DNA plays an important role in determining the DNA charge transfer mechanism and kinetics. The size of the charge carrier's wave function delo ... Full text Cite

Autobiography of David N. Beratan.

Journal Article The journal of physical chemistry. B · April 2020 Full text Cite

Unsymmetrical Bis-Alkynyl Complexes Based on Co(III)(cyclam): Synthesis, Ultrafast Charge Separation, and Analysis.

Journal Article Inorganic chemistry · November 2019 Donor-bridge-acceptor (D-B-A) systems with a polarizable bridge can afford rapid photoinduced electron transfer dynamics that may be susceptible to rate modulation by infrared excitation. We describe the synthesis, characterization, and electronic structur ... Full text Cite

Electron bifurcation: progress and grand challenges.

Journal Article Chemical communications (Cambridge, England) · October 2019 Electron bifurcation moves electrons from a two-electron donor to reduce two spatially separated one-electron acceptors. If one of the electrons reduces a high-potential (lower energy) acceptor, then the other electron may proceed "uphill" to reduce a low- ... Full text Cite

Mapping hole hopping escape routes in proteins.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · August 2019 A recently proposed oxidative damage protection mechanism in proteins relies on hole hopping escape routes formed by redox-active amino acids. We present a computational tool to identify the dominant charge hopping pathways through these residues based on ... Full text Cite

Quantum interferences among Dexter energy transfer pathways.

Journal Article Faraday discussions · July 2019 Dexter energy transfer in chemical systems moves an exciton (i.e., an electron-hole pair) from a donor chromophore to an acceptor chromophore through a bridge by a combination of bonded and non-bonded interactions. The transition is enabled by both one-ele ... Full text Cite

Engineering opposite electronic polarization of singlet and triplet states increases the yield of high-energy photoproducts.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · July 2019 Efficient photosynthetic energy conversion requires quantitative, light-driven formation of high-energy, charge-separated states. However, energies of high-lying excited states are rarely extracted, in part because the congested density of states in the ex ... Full text Cite

Photo-induced electron transfer: general discussion.

Journal Article Faraday discussions · July 2019 Full text Cite

Assessing Possible Mechanisms of Micrometer-Scale Electron Transfer in Heme-Free Geobacter sulfurreducens Pili.

Journal Article The journal of physical chemistry. B · June 2019 The electrically conductive pili of Geobacter sulfurreducens are of both fundamental and practical interest. They facilitate extracellular and interspecies electron transfer (ET) and also provide an electrical interface between living and nonliving systems ... Full text Cite

Why Are DNA and Protein Electron Transfer So Different?

Journal Article Annual review of physical chemistry · June 2019 The corpus of electron transfer (ET) theory provides considerable power to describe the kinetics and dynamics of electron flow at the nanoscale. How is it, then, that nucleic acid (NA) ET continues to surprise, while protein-mediated ET is relatively free ... Full text Cite

Correction: Charge Transfer between [4Fe4S] Proteins and DNA Is Unidirectional: Implications for Biomolecular Signaling.

Journal Article Chem · June 2019 [This corrects the article PMC6350243.]. ... Full text Cite

Voltage-induced long-range coherent electron transfer through organic molecules.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · March 2019 Biological structures rely on kinetically tuned charge transfer reactions for energy conversion, biocatalysis, and signaling as well as for oxidative damage repair. Unlike man-made electrical circuitry, which uses metals and semiconductors to direct curren ... Full text Cite

Charge Transfer between [4Fe4S] Proteins and DNA Is Unidirectional: Implications for Biomolecular Signaling.

Journal Article Chem · January 2019 Recent experiments suggest that DNA-mediated charge transport might enable signaling between the [4Fe4S] clusters in the C-terminal domains of human DNA primase and polymerase α, as well as the signaling between other replication and repair high-potential ... Full text Cite

A new era for electron bifurcation.

Journal Article Current opinion in chemical biology · December 2018 Electron bifurcation, or the coupling of exergonic and endergonic oxidation-reduction reactions, was discovered by Peter Mitchell and provides an elegant mechanism to rationalize and understand the logic that underpins the Q cycle of the respiratory chain. ... Full text Cite

Control of electron transfer in nitrogenase.

Journal Article Current opinion in chemical biology · December 2018 The bacterial enzyme nitrogenase achieves the reduction of dinitrogen (N2) to ammonia (NH3) utilizing electrons, protons, and energy from the hydrolysis of ATP. Building on earlier foundational knowledge, recent studies provide molecu ... Full text Cite

Editorial overview: Biological pathways for electrons, protons and photo-excitations.

Journal Article Current opinion in chemical biology · December 2018 Full text Cite

A single AT-GC exchange can modulate charge transfer-induced p53-DNA dissociation.

Journal Article Chemical communications (Cambridge, England) · December 2018 Using molecular dynamics simulations and electronic structure theory, we shed light on the charge dynamics that causes the differential interaction of tumor suppressor protein p53 with the p21 and Gadd45 genes in response to oxidative stress. We show that ... Full text Cite

Electron transfer characteristics of 2'-deoxy-2'-fluoro-arabinonucleic acid, a nucleic acid with enhanced chemical stability.

Journal Article Physical chemistry chemical physics : PCCP · November 2018 The non-biological nucleic acid 2'-deoxy-2'-fluoro-arabinonucleic acid (2'F-ANA) may be of use because of its higher chemical stability than DNA in terms of resistance to hydrolysis and nuclease degradation. In order to investigate the charge transfer char ... Full text Cite

Directing Charge Transfer in Quantum Dot Assemblies.

Journal Article Accounts of chemical research · October 2018 The optical and electronic properties of semiconductor quantum dots (QDs) make them attractive candidates for applications in photovoltaics, spintronics, photocatalysis, and optoelectronics. Understanding how to control the flow of charge in QD assemblies ... Full text Cite

A Nonequilibrium Molecular Dynamics Study of Infrared Perturbed Electron Transfer.

Journal Article Journal of chemical theory and computation · September 2018 Infrared (IR) excitation is known to change electron-transfer kinetics in molecules. We use nonequilibrium molecular dynamics (NEqMD) simulations to explore the molecular underpinnings of how vibrational excitation may influence nonadiabatic electron-trans ... Full text Cite

Energy Transduction in Nitrogenase.

Journal Article Accounts of chemical research · September 2018 Nitrogenase is a complicated two-component enzyme system that uses ATP binding and hydrolysis energy to achieve one of the most difficult chemical reactions in nature, the reduction of N2 to NH3. One component of the Mo-based nitrogen ... Full text Cite

How can infra-red excitation both accelerate and slow charge transfer in the same molecule?

Journal Article Chemical science · August 2018 A UV-IR-Vis 3-pulse study of infra-red induced changes to electron transfer (ET) rates in a donor-bridge-acceptor species finds that charge-separation rates are slowed, while charge-recombination rates are accelerated as a result of IR excitation during th ... Full text Cite

Charge splitters and charge transport junctions based on guanine quadruplexes.

Journal Article Nature nanotechnology · April 2018 Self-assembling circuit elements, such as current splitters or combiners at the molecular scale, require the design of building blocks with three or more terminals. A promising material for such building blocks is DNA, wherein multiple strands can self-ass ... Full text Cite

On the nature of organic and inorganic centers that bifurcate electrons, coupling exergonic and endergonic oxidation-reduction reactions.

Journal Article Chemical communications (Cambridge, England) · April 2018 Bifurcating electrons to couple endergonic and exergonic electron-transfer reactions has been shown to have a key role in energy conserving redox enzymes. Bifurcating enzymes require a redox center that is capable of directing electron transport along two ... Full text Cite

Improving Solar Cell Performance Using Quantum Dot Triad Charge-Separation Engines

Journal Article Journal of Physical Chemistry C · March 22, 2018 We use kinetic modeling to explore the current-voltage, power-voltage, and power conversion efficiency characteristics of quantum dot dyads and triads as possible light absorption and charge separation engines in quantum dot, bulk heterojunction solar cell ... Full text Cite

Determinants of Photolyase's DNA Repair Mechanism in Mesophiles and Extremophiles.

Journal Article Journal of the American Chemical Society · February 2018 Light-driven DNA repair by extremophilic photolyases is of tremendous importance for understanding the early development of life on Earth. The mechanism for flavin adenine dinucleotide repair of DNA lesions is the subject of debate and has been studied mai ... Full text Cite

Where's my oscillator strength?

Conference ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · 2018 Cite

Toward a theory of infra-red perturbed electron transfer reactions

Conference ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · 2018 Cite

De novo design of a hyperstable non-natural protein-ligand complex with sub-Å accuracy.

Journal Article Nature chemistry · December 2017 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 demonstr ... Full text Cite

Electron Bifurcation: Thermodynamics and Kinetics of Two-Electron Brokering in Biological Redox Chemistry.

Journal Article Accounts of chemical research · September 2017 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 app ... Full text Cite

Controlling the excited-state dynamics of low band gap, near-infrared absorbers via proquinoidal unit electronic structural modulation.

Journal Article Chemical science · September 2017 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 s ... Full text Cite

Charge and spin transport through nucleic acids

Journal Article Current Opinion in Electrochemistry · August 1, 2017 Recent developments in our understanding of charge and spin transport through nucleic acid duplexes are discussed. Particular emphasis is placed on recent findings that point to the importance of nucleobase fluctuations, transient but extended length-scale ... Full text Cite

Controlling the Electron-Transfer Kinetics of Quantum-Dot Assemblies

Journal Article Journal of Physical Chemistry C · July 13, 2017 Electron transfer theory is used to explore the size-dependence of electron transfer (ET) between dithiol-bridged quantum dots (QDs) and make predictions that can be tested experimentally. Electronic couplings, electronic densities of states, and reaction- ... Full text Cite

Chirality Control of Electron Transfer in Quantum Dot Assemblies.

Journal Article Journal of the American Chemical Society · July 2017 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 ch ... Full text Cite

Effects of the Backbone and Chemical Linker on the Molecular Conductance of Nucleic Acid Duplexes.

Journal Article Journal of the American Chemical Society · May 2017 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 ho ... Full text Cite

Large Hyperpolarizabilities at Telecommunication-Relevant Wavelengths in Donor-Acceptor-Donor Nonlinear Optical Chromophores.

Journal Article ACS central science · December 2016 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 ... Full text Open Access Cite

Mean First-Passage Times in Biology.

Journal Article Israel journal of chemistry · November 2016 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 phys ... Full text Cite

DNA charge transport: Moving beyond 1D

Journal Article Surface Science · October 1, 2016 Charge transport across novel DNA junctions has been studied for several decades. From early attempts to move charge across DNA double crossover junctions to recent studies on DNA three-way junctions and G4 motifs, it is becoming clear that efficient cross ... Full text Cite

Engineering nanometre-scale coherence in soft matter.

Journal Article Nature chemistry · October 2016 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-mono ... Full text Cite

DNA charge transfer: Hot holes break the speed limit.

Journal Article Nature chemistry · October 2016 Full text Cite

Dexter energy transfer pathways.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · July 2016 Energy transfer with an associated spin change of the donor and acceptor, Dexter energy transfer, is critically important in solar energy harvesting assemblies, damage protection schemes of photobiology, and organometallic opto-electronic materials. Dexter ... Full text Cite

Diverse Optimal Molecular Libraries for Organic Light-Emitting Diodes.

Journal Article Journal of chemical theory and computation · April 2016 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 ... Full text Cite

Coarse-Grained Theory of Biological Charge Transfer with Spatially and Temporally Correlated Noise.

Journal Article The journal of physical chemistry. B · April 2016 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-env ... Full text Cite

Where Is the Electronic Oscillator Strength? Mapping Oscillator Strength across Molecular Absorption Spectra.

Journal Article The journal of physical chemistry. A · March 2016 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 ... Full text Cite

Photoinduced Electron Transfer Elicits a Change in the Static Dielectric Constant of a de Novo Designed Protein.

Journal Article Journal of the American Chemical Society · February 2016 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), ... Full text Cite

Correction: Electron transfer rate modulation in a compact Re(i) donor-acceptor complex.

Journal Article Dalton transactions (Cambridge, England : 2003) · January 2016 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. ... Full text Cite

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 Article The journal of physical chemistry. B · January 2016 Full text Cite

Correction to Full Electron Ligand-to-Ligand Charge Transfer in a Compact Rhenium(I) Complex.

Journal Article The journal of physical chemistry. A · January 2016 Full text Cite

Vibrational control of electron-transfer reactions: a feasibility study for the fast coherent transfer regime.

Journal Article Physical chemistry chemical physics : PCCP · December 2015 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 ... Full text Cite

Open-Access, Interactive Explorations for Teaching and Learning Quantum Dynamics

Journal Article Journal of Chemical Education · November 5, 2015 While the research field of quantum dynamics (QD) benefits from advances in modern computational power, the educational field of QD paradoxically does not. We have developed an open-access, interactive, electronic notebook that leverages a user-friendly in ... Full text Cite

Defusing redox bombs?

Journal Article Proceedings of the National Academy of Sciences of the United States of America · September 2015 Full text Cite

Conformationally Gated Charge Transfer in DNA Three-Way Junctions.

Journal Article The journal of physical chemistry letters · July 2015 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 junct ... Full text Cite

Two-Electron Transfer Pathways.

Journal Article The journal of physical chemistry. B · June 2015 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 probab ... Full text Cite

Correction for Migliore et al., Sensing of molecules using quantum dynamics.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · June 2015 Full text Cite

Electron transfer rate modulation in a compact Re(I) donor-acceptor complex.

Journal Article Dalton transactions (Cambridge, England : 2003) · May 2015 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'-(dic ... Full text Cite

Sensing of molecules using quantum dynamics.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · May 2015 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 phenome ... Full text Cite

Charge Transport across DNA-Based Three-Way Junctions.

Journal Article Journal of the American Chemical Society · April 2015 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 ... Full text Cite

Strategy to discover diverse optimal molecules in the small molecule universe.

Journal Article Journal of chemical information and modeling · March 2015 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 stru ... Full text Cite

Charge transfer in dynamical biosystems, or the treachery of (static) images.

Journal Article Accounts of chemical research · February 2015 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 regardi ... Full text Cite

Full-electron ligand-to-ligand charge transfer in a compact Re(I) complex.

Journal Article The journal of physical chemistry. A · November 2014 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) compl ... Full text Cite

Biological charge transfer via flickering resonance.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · July 2014 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 an ... Full text Cite

Structural and electronic properties of bare and capped Cd 33Se33 and Cd33Te33 quantum dots

Journal Article Journal of Physical Chemistry C · April 3, 2014 We performed comparative DFT (B3LYP/Lanl2dz) studies of the structural and electronic properties of bare and NH3-, SCH3-, and OPH3-capped Cd33Se33 and Cd33Te 33 quantum dots (QDs). The capping groups were chosen as simple models for capping ligands used br ... Full text Cite

Biochemistry and theory of proton-coupled electron transfer.

Journal Article Chemical reviews · April 2014 Full text Cite

Breaking the simple proportionality between molecular conductances and charge transfer rates.

Journal Article Faraday discussions · January 2014 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 u ... Full text Cite

Evaluating the extent of intramolecular charge transfer in the excited states of rhenium(I) donor-acceptor complexes with time-resolved vibrational spectroscopy.

Journal Article The journal of physical chemistry. B · December 2013 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 ... Full text Cite

Correction to "Enthalpic Signature of Methonium Desolvation Revealed in a Synthetic Host-Guest System Based on Cucurbit[7]uril".

Journal Article J Am Chem Soc · November 20, 2013 Full text Link to item Cite

Ligand-induced changes in the characteristic size-dependent electronic energies of CdSe nanocrystals

Journal Article Journal of Physical Chemistry C · October 31, 2013 This work explores the electronic energy of CdSe nanoparticles as a function of nanoparticle (NP) size and capping ligand. Differential pulse voltammetry was used to determine the valence band edge of CdSe NPs that are capped with three different ligands ( ... Full text Cite

Triplet excitation energy dynamics in metal-organic frameworks

Journal Article Journal of Physical Chemistry C · October 31, 2013 Metal-organic frameworks (MOFs) are appealing candidates for use in energy harvesting and concentrating because of their high chromophore density and structural tunability. The ability to engineer electronic excitation energy transport pathways is of parti ... Full text Cite

Distance-independent charge recombination kinetics in cytochrome c-cytochrome c peroxidase complexes: compensating changes in the electronic coupling and reorganization energies.

Journal Article The journal of physical chemistry. B · August 2013 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 ... Full text Cite

The single-molecule conductance and electrochemical electron-transfer rate are related by a power law.

Journal Article ACS nano · June 2013 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 experi ... Full text Cite

Stochastic voyages into uncharted chemical space produce a representative library of all possible drug-like compounds.

Journal Article Journal of the American Chemical Society · May 2013 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 des ... Full text Cite

Enthalpic signature of methonium desolvation revealed in a synthetic host-guest system based on cucurbit[7]uril.

Journal Article Journal of the American Chemical Society · April 2013 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 transmitt ... Full text Cite

Inverse design of molecules with optimal reactivity properties: acidity of 2-naphthol derivatives.

Journal Article Physical chemistry chemical physics : PCCP · December 2012 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 de ... Full text Cite

Effects of S-containing ligands on the structure and electronic properties of CdnSen/CdnTen nanoparticles (n = 3, 4, 6, and 9)

Journal Article Chemical Physics · October 15, 2012 To understand ligand capping effects on the structure and electronic properties of CdnXn (X = Se, Te; n = 3, 4, 6, and 9) species, we performed density functional theory studies of SCH2COOH-, SCH2CH2CO2H-, and SCH2CH 2NH2-capped nanoparticles. CdnXn cappin ... Full text Cite

Redox redux.

Journal Article Physical chemistry chemical physics : PCCP · October 2012 Full text Cite

Interfacial hydration, dynamics and electron transfer: multi-scale ET modeling of the transient [myoglobin, cytochrome b5] complex.

Journal Article Physical chemistry chemical physics : PCCP · October 2012 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 ... Full text Cite

Correction to effect of backbone flexibility on charge transfer rates in Peptide nucleic Acid duplexes.

Journal Article Journal of the American Chemical Society · August 2012 Full text Cite

Effect of backbone flexibility on charge transfer rates in peptide nucleic acid duplexes.

Journal Article Journal of the American Chemical Society · June 2012 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 ... Full text Cite

Design of coupled porphyrin chromophores with unusually large hyperpolarizabilities

Journal Article Journal of Physical Chemistry C · May 3, 2012 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 crit ... Full text Cite

Structural and electronic properties of bare and capped Cd nSen/CdnTen Nanoparticles (n = 6, 9)

Journal Article Journal of Physical Chemistry C · March 29, 2012 Relationships between structures and properties (energy gaps, vertical ionization potentials (IPv), vertical electron affinities (EA v), and ligand binding energies) in small capped CdSe/CdTe nanoparticles (NPs) are poorly understood. We have performed the ... Full text Cite

Exploring biological electron transfer pathway dynamics with the Pathways plugin for VMD.

Journal Article Journal of computational chemistry · March 2012 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 in ... Full text Cite

Physical constraints on charge transport through bacterial nanowires.

Journal Article Faraday discussions · January 2012 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, ... Full text Cite

B-DNA to zip-DNA: simulating a DNA transition to a novel structure with enhanced charge-transport characteristics.

Journal Article The journal of physical chemistry. A · September 2011 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 s ... Full text Cite

Electronic structure of self-assembled peptide nucleic acid thin films

Journal Article Journal of Physical Chemistry C · September 1, 2011 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 photoemiss ... Full text Cite

Two-photon absorption properties of proquinoidal D-A-D and A-D-A quadrupolar chromophores.

Journal Article The journal of physical chemistry. A · June 2011 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-accepto ... Full text Cite

Floquet analysis for vibronically modulated electron tunneling.

Journal Article The journal of physical chemistry. B · May 2011 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 tunn ... Full text Cite

Nucleic Acid Charge Transfer: Black, White and Gray.

Journal Article Coordination chemistry reviews · April 2011 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 tran ... Full text Cite

Topics in Current Chemistry: Preface

Journal Article Topics in Current Chemistry · February 25, 2011 Cite

Evidence for a near-resonant charge transfer mechanism for double-stranded peptide nucleic acid.

Journal Article Journal of the American Chemical Society · January 2011 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 sequenc ... Full text Cite

Chiral control of current transfer in molecules.

Journal Article Topics in current chemistry · January 2011 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 theo ... Full text Cite

Electron transfer in nucleic acids: Black, white, and gray

Journal Article Coord. Chem. Revs. · 2011 Cite

Coherence in electron tunneling pathways

Journal Article Procedia Chemistry · 2011 Cite

NCIPLOT: a program for plotting non-covalent interaction regions

Journal Article J. Chem. Theory Comput. · 2011 Cite

Is MD geometry sampling sufficient for nucleobase electronic structure analysis of et reactions? Comparing classical MD and QM/MM methods

Journal Article Journal of Physical Chemistry C · December 9, 2010 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' th ... Full text Cite

Analysis of the unusual wavelength dependence of the first hyperpolarizability of porphyrin derivatives

Journal Article Proceedings of SPIE - The International Society for Optical Engineering · October 22, 2010 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 absorpt ... Full text Cite

A gradient-directed Monte Carlo approach for protein design.

Journal Article Journal of computational chemistry · August 2010 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 Mon ... Full text Cite

Optimizing single-molecule conductivity of conjugated organic oligomers with carbodithioate linkers.

Journal Article Journal of the American Chemical Society · June 2010 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 ... Full text Open Access Cite

Steady-state theory of current transfer

Journal Article Journal of Physical Chemistry C · May 6, 2010 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 pola ... Full text Open Access Cite

Synthesis and chemical diversity analysis of bicyclo[3.3.1]non-3-en-2-ones

Journal Article Tetrahedron · 2010 Cite

Predicting the Frequency Dispersion of Electronic Hyperpolarizabilities on the Basis of Absorption Data and Thomas-Kuhn Sum Rules

Journal Article J. Phys. Chem. C · 2010 Open Access Cite

Fluctuations in biological and bioinspired electron-transfer reactions.

Journal Article Annual review of physical chemistry · January 2010 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-l ... Full text Cite

Modulating unimolecular charge transfer by exciting bridge vibrations.

Journal Article Journal of the American Chemical Society · December 2009 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). ... Full text Open Access Cite

Steering electrons on moving pathways.

Journal Article Accounts of chemical research · October 2009 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 ... Full text Cite

A gradient-directed Monte Carlo method for global optimization in a discrete space: application to protein sequence design and folding.

Journal Article The Journal of chemical physics · October 2009 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 ... Full text Cite

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 Article Mol Biosyst · September 2009 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. ... Full text Link to item Cite

Coarse-grained modeling of allosteric regulation in protein receptors.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · August 2009 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 ... Full text Cite

Optical signatures of molecular dissymmetry: combining theory with experiments to address stereochemical puzzles.

Journal Article Accounts of chemical research · June 2009 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 spect ... Full text Cite

Turning charge transfer on and off in a molecular interferometer with vibronic pathways.

Journal Article Nano letters · May 2009 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 ... Full text Cite

Role of nucleobase energetics and nucleobase interactions in single-stranded peptide nucleic acid charge transfer.

Journal Article Journal of the American Chemical Society · May 2009 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 ... Full text Cite

Role of Nucleobase Energetics in Single Stranded Peptide Nucleic Acid Charge Transfer

Journal Article J. Am. Chem. Soc · 2009 Cite

Emergent strategies for inverse molecular design

Journal Article Science in China B: Chemistry · 2009 Cite

Discrete optimization of electronic hyperpolarizabilities in a chemical subspace

Journal Article Army Research Laboratory Publication ARL-TR-4833 · 2009 Cite

Photoconductivity and current-voltage characteristics of thin DNA films: Experiments and modeling

Journal Article Proceedings of SPIE - The International Society for Optical Engineering · January 1, 2009 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 ... Full text Cite

Chiral control of electron transmission through molecules.

Journal Article Physical review letters · December 2008 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--a ... Full text Cite

Exploring chemical space with discrete, gradient, and hybrid optimization methods.

Journal Article The Journal of chemical physics · November 2008 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 ... Full text Cite

Molecular design of porphyrin-based nonlinear optical materials.

Journal Article The journal of physical chemistry. A · November 2008 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 ... Full text Cite

Persistence of structure over fluctuations in biological electron-transfer reactions.

Journal Article Physical review letters · October 2008 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 ... Full text Cite

Solution structure of a peptide nucleic acid duplex from NMR data: features and limitations.

Journal Article Journal of the American Chemical Society · October 2008 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 fo ... Full text Cite

PNA versus DNA: effects of structural fluctuations on electronic structure and hole-transport mechanisms.

Journal Article Journal of the American Chemical Society · September 2008 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 ade ... Full text Cite

Computational design, synthesis and biological evaluation of para-quinone-based inhibitors for redox regulation of the dual-specificity phosphatase Cdc25B.

Journal Article Organic & biomolecular chemistry · September 2008 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 model ... Full text Cite

A donor-nanotube paradigm for nonlinear optical materials.

Journal Article Nano letters · September 2008 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 ... Full text Cite

A gradient-directed Monte Carlo approach to molecular design.

Journal Article The Journal of chemical physics · August 2008 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 prop ... Full text Cite

Inverse molecular design in a tight-binding framework.

Journal Article The Journal of chemical physics · July 2008 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 optim ... Full text Cite

Single-and Multi-Electron Transfer Processes

Chapter · April 15, 2008 Full text Cite

Hepatitis C virus NS5B polymerase: QM/MM calculations show the important role of the internal energy in ligand binding.

Journal Article The journal of physical chemistry. B · March 2008 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 ... Full text Cite

Exploring the optical activity tensor by anisotropic Rayleigh optical activity scattering.

Journal Article Chemphyschem : a European journal of chemical physics and physical chemistry · February 2008 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 bac ... Full text Cite

Hepatitis C virus NS5B polymerase: Important roles of the internal energy and van der Waals interactions from QM/MM calculations

Journal Article J.Phys.Chem.B · 2008 Cite

Heme-copper oxidases use tunneling pathways.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · January 2008 Full text Cite

Characterizing aqueous solution conformations of a peptide backbone with theoretical analysis of the Raman optical activity spectra

Journal Article Biophys. J. · 2008 Cite

Orientational Dependence of Cofacial Porphyrin-Quinone Electronic Interactions within the Strong Coupling Regime

Journal Article J. Am. Chem. Soc. · 2008 Cite

A molecular double slit paradigm

Journal Article AIP Conference Proceedings · December 1, 2007 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 pathw ... Full text Cite

Biochemistry. Photosynthesis from the protein's perspective.

Journal Article Science (New York, N.Y.) · May 2007 Full text Cite

Protein phosphorylation and intermolecular electron transfer: a joint experimental and computational study of a hormone biosynthesis pathway.

Journal Article Journal of the American Chemical Society · April 2007 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 ... Full text Cite

Coupling coherence distinguishes structure sensitivity in protein electron transfer.

Journal Article Science (New York, N.Y.) · February 2007 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 ... Full text Cite

Contribution of a solute's chiral solvent imprint to optical rotation.

Journal Article Angewandte Chemie (International ed. in English) · January 2007 Full text Cite

Photoselected electron transfer pathways in DNA photolyase.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · January 2007 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 flav ... Full text Cite

Designing molecules with optimal properties using the linear combination of atomic potentials approach in an AM1 semiempirical framework.

Journal Article The journal of physical chemistry. A · January 2007 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 mo ... Full text Cite

Flavin Charge Transfer Transitions Assist DNA Photolyase Electron Transfer.

Journal Article AIP conference proceedings · January 2007 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 elec ... Full text Cite

Solvent effect on optical rotation: A case study of methyloxirane in water.

Journal Article Chemphyschem : a European journal of chemical physics and physical chemistry · December 2006 Full text Cite

The effects of bridge motion on electron transfer reactions mediated by tunneling

Journal Article · December 1, 2006 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 dyna ... Full text Cite

Binding of warfarin influences the acid-base equilibrium of H242 in sudlow site I of human serum albumin.

Journal Article Photochemistry and photobiology · September 2006 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 ca ... Full text Cite

Guest editorial: Electron transfer

Journal Article Molecular Simulation · August 1, 2006 Full text Cite

Electron transfer between cofactors in protein domains linked by a flexible tether

Journal Article Chemical Physics · July 11, 2006 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 conformation ... Full text Cite

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 Article Mol Endocrinol · June 2006 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 es ... Full text Link to item Cite

Designing molecules by optimizing potentials.

Journal Article Journal of the American Chemical Society · March 2006 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 electro ... Full text Cite

Conformationally averaged score functions for electronic propagation in proteins.

Journal Article The journal of physical chemistry. B · March 2006 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 sco ... Full text Cite

The chiroptical signature of achiral metal clusters induced by dissymmetric adsorbates.

Journal Article Physical chemistry chemical physics : PCCP · January 2006 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, 2630-26 ... Full text Cite

Systematic assignment of the configuration of flexible natural products by spectroscopic and computational methods: the bistramide C analysis.

Journal Article Organic letters · November 2005 [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 stereoiso ... Full text Cite

The nature of aqueous tunneling pathways between electron-transfer proteins.

Journal Article Science (New York, N.Y.) · November 2005 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 coupl ... Full text Cite

Assignment of the absolute configuration of [n]-ladderanes by TD-DFT optical rotation calculations.

Journal Article Chirality · October 2005 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 ... Full text Cite

Charge transfer through chemisorbed organic molecules - Neutralization of ionization processes at local sites in the molecule

Journal Article Chemical Physics Letters · August 25, 2005 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. ... Full text Cite

Generalized Mulliken-Hush analysis of electronic coupling interactions in compressed pi-stacked porphyrin-bridge-quinone systems.

Journal Article Journal of the American Chemical Society · August 2005 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 th ... Full text Cite

Electron Transfer through Proteins

Journal Article · May 23, 2005 Full text Cite

Towards Raman optical activity calculations of large molecules.

Journal Article Chemphyschem : a European journal of chemical physics and physical chemistry · April 2005 Full text Cite

Simulation of electron transfer between cytochrome C2 and the bacterial photosynthetic reaction center: Brownian dynamics analysis of the native proteins and double mutants.

Journal Article The journal of physical chemistry. B · April 2005 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 ... Full text Cite

Electronic conductivity pathways in chemisorbed molecules: Connections to molecular electronic issues.

Conference ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · March 13, 2005 Link to item Cite

Protein dynamics and electron transfer: electronic decoherence and non-Condon effects.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · March 2005 We compute the autocorrelation function of the donor-acceptor tunneling matrix element 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 cowo ... Full text Cite

Ab initio based calculations of electron-transfer rates in metalloproteins.

Journal Article The journal of physical chemistry. B · February 2005 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 th ... Full text Cite

Simulation of scanning tunneling microscope images of 1,3-cyclohexadiene bound to a silicon surface.

Journal Article The journal of physical chemistry. B · February 2005 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 ... Full text Cite

Atomic scale simulations of sulfite oxidase structure and function

Conference BIOPHYSICAL JOURNAL · 2005 Cite

Water -mediated tunneling between proteins

Journal Article Science · 2005 Link to item Cite

Simulation of STM images of 1,4 cyclohexadiene bound to a silicon surface

Journal Article J. Phys. Chem B · 2005 Link to item Cite

Structure of the ochratoxin a binding site within human serum albumin

Journal Article Journal of Physical Chemistry B · October 28, 2004 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 co ... Full text Cite

Inelastic electron tunneling erases coupling-pathway interferences

Journal Article Journal of Physical Chemistry B · October 7, 2004 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 el ... Full text Cite

Erratum: Optical rotation of noncovalent aggregates (Journal of the American Chemical Society (2003) 125 (15696-15697))

Journal Article Journal of the American Chemical Society · August 4, 2004 Full text Cite

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 Article Biophysical journal · August 2004 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 tra ... Full text Cite

Tunneling while pulling: The dependence of tunneling current on end-to-end distance in a flexible molecule

Journal Article Journal of Physical Chemistry A · July 1, 2004 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 curre ... Full text Cite

The degree of charge transfer in ground and charge-separated states revealed by ultrafast visible pump/mid-IR probe spectroscopy.

Journal Article Journal of the American Chemical Society · April 2004 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 ... Full text Cite

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 Article Journal of the American Chemical Society · March 2004 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 ... Full text Cite

Quantitave prediction of electron-transfer rates in metallo-proteins.

Conference ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · 2004 Cite

Conformational control of electron tunneling in sulfite oxidase

Conference BIOPHYSICAL JOURNAL · 2004 Cite

Diffusion controlled intra-molecular electron transfer in protein: A simple model of the sulfite oxidase

Conference BIOPHYSICAL JOURNAL · 2004 Cite

Computer modeling and simulation on ATP-driven large conformational change in proteins

Conference BIOPHYSICAL JOURNAL · 2004 Cite

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 Article J. Am. Chem. Soc. · 2004 Link to item Cite

Loss of Pathway Coherence in Inelastic Bridge-mediated Electron Transfer

Journal Article J. Phys. Chem. B · 2004 Link to item Cite

DNA electron transfer processes: Some theoretical notions

Journal Article Top. Curr. Chem. · 2004 Cite

Optical rotation of noncovalent aggregates.

Journal Article Journal of the American Chemical Society · December 2003 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 f ... Full text Cite

Binding of ochratoxin a to human serum albumin stabilized by a protein-ligand ion pair

Journal Article Journal of Physical Chemistry B · August 7, 2003 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 a ... Full text Cite

Theoretical studies of the effects of phosphorylation on protein electron transfer chains

Conference BIOPHYSICAL JOURNAL · 2003 Cite

A protein-ligand ion pair stabilizes the binding of Ochratoxin A to human serum albumin

Journal Article J. Phys. Chem. B. · 2003 Cite

Molecular control of electron transfer events within and between biomolecules

Conference MOLECULAR ELECTRONICS: BIO-SENSORS AND BIO-COMPUTERS · January 1, 2003 Link to item Cite

Donor-bridge-acceptor energetics determine the distance dependence of electron tunneling in DNA.

Journal Article Proceedings of the National Academy of Sciences of the United States of America · October 2002 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 ... Full text Cite

Dynamic docking and electron transfer between Zn-myoglobin and cytochrome b(5).

Journal Article Journal of the American Chemical Society · June 2002 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 ... Full text Cite

The nature of tunneling pathway and average packing density models for protein-mediated electron transfer

Journal Article Journal of Physical Chemistry A · March 14, 2002 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 ... Full text Cite

Tunneling energy effects on GC oxidation in DNA

Journal Article Journal of Physical Chemistry B · March 7, 2002 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 ... Full text Cite

Hole size and energetics in double helical DNA: Competition between quantum delocalization and solvation localization

Journal Article Journal of Physical Chemistry B · January 10, 2002 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 ... Full text Cite

Electrostatics, electron tunneling, and energy transduction in biomolecules.

Conference ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · 2002 Cite

Tunneling energy controls DNA electron transfer distance dependence

Journal Article Proc. Natl. Acad. Sci. (USA) · 2002 Link to item Cite

Optical activity: From structure - Function to structure prediction

Journal Article ACS Symposium Series · January 1, 2002 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 ap ... Full text Cite

Determining absolute configuration in flexible molecules: a case study.

Journal Article Journal of the American Chemical Society · September 2001 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 molecula ... Full text Cite

From ATP to electron transfer: Electrostatics and free-energy transduction in nitrogenase

Journal Article Journal of Physical Chemistry B · June 14, 2001 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 prote ... Full text Cite

New peroxylactones from the Jamaican sponge Plakinastrella onkodes, with inhibitory activity against the AIDS opportunistic parasitic infection Toxoplasma gondii

Journal Article Tetrahedron · February 18, 2001 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 determ ... Full text Cite

Monte-Carlo simulations of bimolecular electron transfer between myoglobin and cytochrome B5.

Conference ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · 2001 Cite

Energetic analysis of F1 ATP synthase conformations and substrate binding.

Conference BIOPHYSICAL JOURNAL · 2001 Cite

Electrostatic and electron transfer coupling control in the mechanism of energy transduction of nitrogenase.

Conference BIOPHYSICAL JOURNAL · 2001 Cite

The nature of tunnel splitting mediated by stacked aromatics

Journal Article Journal of Physical Chemistry A · August 17, 2000 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; ... Full text Cite

Chiral action at a distance: remote substituent effects on the optical activity of calyculins A and B.

Journal Article Organic letters · June 2000 [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 b ... Full text Cite

Optical rotation computation, total synthesis, and stereochemistry assignment of the marine natural product pitiamide A

Journal Article Journal of the American Chemical Society · May 17, 2000 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 m ... Full text Cite

Bond-mediated electron tunneling in ruthenium-modified high-potential iron-sulfur protein [13]

Journal Article Journal of the American Chemical Society · May 10, 2000 Full text Cite

Electrostatic control of electron transfer between myoglobin and cytochrome b5: Effect of methylating the heme propionates of Zn-myoglobin [16]

Journal Article Journal of the American Chemical Society · April 12, 2000 Full text Cite

Theoretical approaches to biological electron transfer in multi-component systems.

Conference ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · 2000 Cite

Electrostatic control of electron transfer within protein complexes.

Conference ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · 2000 Cite

Electronic propagation in DNA.

Conference ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · 2000 Cite

Optical activity: From structure-function to structure prediction.

Conference ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · 2000 Cite

Theories of structure-function relationships for bridge-mediated electron transfer reactions

Journal Article Advances in Chemical Physics · December 1, 1999 Cite

Determination of the absolute configuration of 1,3,5,7-tetramethyl-1,3- dihydroindol-2-one by optical rotation computation

Journal Article Tetrahedron Asymmetry · October 29, 1999 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 ini ... Full text Cite

Structural and Conformational Dependence of Optical Rotation Angles

Journal Article Journal of Physical Chemistry A · August 19, 1999 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 calcul ... Full text Cite

Electron transfer in three-center chemical systems

Journal Article Journal of Chemical Physics · June 1, 1999 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 s ... Full text Cite

How does nitrogenase work?.

Conference ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · 1999 Cite

Electron transfer in three-state systems

Journal Article J. Chem. Phys. · 1999 Link to item Cite

Atomic contributions to the optical rotation angle as a quantitative probe of molecular chirality.

Journal Article Science (New York, N.Y.) · December 1998 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 th ... Full text Cite

Binding and Electron Transfer between Putidaredoxin and Cytochrome P450cam. Theory and Experiments

Journal Article Journal of the American Chemical Society · September 1, 1998 Full text Cite

Electron transfer in the photosynthetic reaction center: mechanistic implications of mutagenesis studies.

Journal Article Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy · August 1998 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 w ... Full text Cite

Use of modern electron transfer theories to determine electronic coupling matrix elements in intramolecular systems

Journal Article Journal of Physical Chemistry A · July 9, 1998 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 sem ... Full text Cite

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 Article Chemtracts · May 1, 1998 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 whi ... Cite

DNA-mediated electron transfer

Journal Article Journal of Biological Inorganic Chemistry · April 1, 1998 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 ... Full text Cite

Electron transfer mechanisms.

Journal Article Current opinion in chemical biology · April 1998 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 ... Full text Cite

Theory-assisted determination of absolute stereochemistry for complex natural products via computation of molar rotation angles [17]

Journal Article Journal of the American Chemical Society · March 11, 1998 Full text Cite

Divide-and-conquer approach to calculate electronic response properties of macromolecules.

Conference ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · 1998 Cite

A three-state model for two-electron transfer reactions.

Conference ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · 1998 Cite

Electron transfer in the photosynthetic reaction center: Mechanistic implications of mutagenesis studies.

Conference ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY · 1998 Cite

Structure of the electrical double layer in high-temperature superconductors. Origin of the dip in the double-layer capacitance near the superconducting transition

Journal Article Journal of Physical Chemistry B · September 4, 1997 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 ... Full text Cite

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 Article Journal of the American Chemical Society · June 18, 1997 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 couplin ... Full text Cite

Three-state model for two-electron transfer reactions

Journal Article Journal of Physical Chemistry A · May 29, 1997 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 uns ... Full text Cite

Electron transfer contact maps

Journal Article Journal of Physical Chemistry B · February 13, 1997 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 prote ... Full text Cite

High and low resolution theories of protein electron transfer

Journal Article Journal of Biological Inorganic Chemistry · January 1, 1997 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 descri ... Full text Cite

DNA: wire or insulator?

Journal Article Chemistry and Biology · 1997 Link to item Cite

Synthetic and model computational studies of optical angle additivity for interacting chiral centers: A reinvestigation of van't Hoff's principle

Journal Article Chirality · 1997 Link to item Cite

Secondary structure conformations and long range electronic interactions in oligopeptides

Journal Article J. Phys. Chem. B. · 1997 Link to item Cite

Synthetic and model computational studies of molar rotation additivity for interacting chiral centers: a reinvestigation of van't Hoff's principle.

Journal Article Chirality · January 1997 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 ... Full text Cite

Theory and Practice of Electron Transfer within Proteinminus signProtein Complexes: Application to the Multidomain Binding of Cytochrome c by Cytochrome c Peroxidase.

Journal Article Chemical reviews · November 1996 Full text Cite

DNA is not a molecular wire: Protein-like electron-transfer predicted for an extended π-electron system

Journal Article Journal of Physical Chemistry · October 31, 1996 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 un ... Full text Cite

Inverse strategies for molecular design

Journal Article Journal of Physical Chemistry · June 20, 1996 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 pa ... Full text Cite

Bridge-mediated electronic interactions: Differences between Hamiltonian and Green function partitioning in a non-orthogonal basis

Journal Article Journal of Chemical Physics · June 15, 1996 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 sem ... Full text Cite

A method to analyze multi-pathway effects on protein mediated donor-acceptor coupling interactions

Journal Article Inorganica Chimica Acta · February 29, 1996 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 balan ... Full text Cite

Acetylenyl-linked, porphyrin-bridged, donor-acceptor molecules: A theoretical analysis of the molecular first hyperpolarizability in highly conjugated push-pull chromophore structures

Journal Article Journal of the American Chemical Society · February 14, 1996 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 1.0 ... Full text Cite

DNA double helix mediated long range electron transfer

Journal Article Int. J. Quantum Chem. Quantun Biol. Symp. · 1996 Cite

Two-electron transfer reactions in polar solvents

Journal Article Journal of Chemical Physics · January 1, 1996 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 s ... Full text Cite

Ab initio based effective Hamiltonians for long-range electron transfer: Hartree-Fock analysis

Journal Article Journal of Chemical Physics · January 1, 1996 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 calculatio ... Full text Cite

Docking and electron transfer between cytochrome c2 and the photosynthetic reaction center

Journal Article Chemical Physics · August 15, 1995 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 sep ... Full text Cite

Pathways, pathway tubes, pathway docking, and propagators in electron transfer proteins.

Journal Article Journal of bioenergetics and biomembranes · June 1995 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 c ... Full text Cite