Alexander V. Soudackov

Alexander V. Soudackov
Yale University | YU · Department of Chemistry

Ph.D. in Chemical Physics

About

90
Publications
6,503
Reads
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3,433
Citations
Additional affiliations
June 2018 - present
Yale University
Position
  • Researcher
February 2013 - May 2018
University of Illinois, Urbana-Champaign
Position
  • Professor (Assistant)
August 2002 - January 2013
Pennsylvania State University
Position
  • Research Assistant Professor
Education
August 1986 - May 1992
Karpov Institute of Physical Chemistry
Field of study
  • Chemical Physics
June 1981 - June 1986
Lomonosov Moscow State University
Field of study
  • Chemistry

Publications

Publications (90)
Article
The enzyme ribonucleotide reductase (RNR), which catalyzes the reduction of ribonucleotides to deoxynucleotides, is vital for DNA synthesis, replication, and repair in all living organisms. Its mechanism requires long-range radical translocation over ∼32 Å through two protein subunits and the intervening aqueous interface. Herein, a kinetic model i...
Conference Paper
Full-text available
A new semiempirical effective Hamiltonian method capable of taking into account d-electron correlations, the weak covalency of the metal-ligand bonds, and electronic structure of ligand sphere for transition metal complexes is described. The technique is characterized by the use of variation wave function which differs from Hartree-Fock antisymmetr...
Article
Hydrogen energy-based electrochemical energy conversion technologies offer the promise of enabling a transition of the global energy landscape from fossil fuels to renewable energy. Here, we present a comprehensive review of the fundamentals of electrocatalysis in alkaline media and applications in alkaline-based energy technologies, particularly a...
Article
Full-text available
Artificial neural networks (ANNs) have become important in quantum chemistry. Herein, applications to nuclear quantum effects, such as zero-point energy, vibrationally excited states, and hydrogen tunneling, are explored. ANNs are used to solve the time-independent Schrödinger equation for single- and double-well potentials representing hydrogen-bo...
Article
The cytochrome bc1 complex is a transmembrane enzymatic protein complex that plays a central role in cellular energy production and is present in both photosynthetic and respiratory chain organelles. Its reaction mechanism is initiated by the binding of a quinol molecule to an active site, followed by a series of charge transfer reactions between t...
Article
Long-range electron transfer is coupled to proton transfer in a wide range of chemically and biologically important processes. Recently the proton-coupled electron transfer (PCET) rate constants for a series of biomimetic oligoproline peptides linking Ru(bpy)32+ to tyrosine were shown to exhibit a substantially shallower dependence on the number of...
Article
Proton discharge on metal electrodes, also denoted the Volmer reaction, is a critical step in a wide range of electrochemical processes. This electrochemical proton-coupled electron transfer (PCET) reaction is predominantly electronically adiabatic in aqueous solution and is typically treated as fully adiabatic. Recently, a theoretical model for th...
Article
The first step of the hydrogen evolution reaction, an important reaction for the storage of renewable energy, is the formation of a surface-adsorbed hydrogen atom through proton discharge to the electrode surface, commonly known as the Volmer reaction. Herein a theoretical description of the Volmer reaction is presented. In this formulation, the el...
Article
Photoinduced proton-coupled electron transfer (PCET) plays a key role in a wide range of energy conversion processes, and understanding how to design systems to control the PCET rate constant is a significant challenge. Herein a theoretical formulation of PCET is utilized to identify the conditions under which photoinduced PCET may exhibit inverted...
Article
The discharge of protons on electrode surfaces, known as the Volmer reaction, is a ubiquitous reaction in heterogeneous electrocatalysis and plays an important role in renewable energy technologies. Recent experiments with triethylammonium (TEAH+) donating the proton to a gold electrode in acetonitrile demonstrate significantly different Tafel slop...
Article
Soybean lipoxygenase catalyzes a proton-coupled electron transfer (PCET) reaction and serves as a prototype for hydrogen tunneling in enzymes due to the unusually high kinetic isotope effect and significant modulation of the rate constant and kinetic isotope effect by mutation. Herein these experimental observations are interpreted in the context o...
Article
The proton-coupled electron transfer (PCET) reaction catalyzed by soybean lipoxygenase has served as a prototype for understanding hydrogen tunneling in enzymes. Herein this PCET reaction is studied with mixed quantum mechanical/molecular mechanical (QM/MM) free energy simulations. The free energy surfaces are computed as functions of the proton do...
Article
Full-text available
Experiments have suggested that photoreduced ZnO nanocrystals transfer an electron and a proton to organic radicals through a concerted proton-coupled electron transfer (PCET) mechanism. The kinetics of this process was studied by monitoring the decay of the absorbance that reflects the concentration of electrons in the conduction bands of the nano...
Article
Soybean lipoxygenase (SLO) is a prototype for nonadiabatic hydrogen tunneling reactions and, as such, has served as the subject of numerous theoretical studies. In this work, we report a nearly temperature-independent kinetic isotope effect (KIE) with an average KIE value of 661 ± 27 for a double mutant (DM) of SLO at six temperatures. The data are...
Article
Full-text available
A general theory has been developed for proton-coupled electron transfer (PCET), which is vital to a wide range of chemical and biological processes. This theory describes PCET reactions in terms of nonadiabatic transitions between reactant and product electron-proton vibronic states and includes the effects of thermal fluctuations of the solvent o...
Article
Soybean lipoxygenase (SLO) serves as a prototype for fundamental understanding of hydrogen tunneling in enzymes. Its reactivity depends on the active site structure around a mononuclear, non-heme iron center. The available crystal structures indicate five-coordinate iron, while magnetic circular dichroism experiments suggest significant populations...
Article
Full-text available
Electron transfer and proton coupled electron transfer (PCET) reactions at electrochemical interfaces play an essential role in a broad range of energy conversion processes. The reorganization energy, which is a measure of the free energy change associated with solute and solvent rearrangements, is a key quantity for calculating rate constants for...
Article
Full-text available
We review the basics of the Effective Hamiltonian Crystal Field (EHCF) method originally targeted for calculations of the intra-shell excitations in the d-shells of coordination compounds of the first row transition metal. The formalism employs in the concerted way the McWeeny's group-function approximation and the Lowdin partition technique. It is...
Article
Nonadiabatic dynamics simulations of photoinduced proton-coupled electron transfer (PCET) in a phenol-amine complex in solution were performed. The electronic potential energy surfaces were generated on-the-fly with a hybrid quantum mechanical/molecular mechanical approach that described the solute with a multiconfigurational method in a bath of ex...
Article
Full-text available
Rate constant expressions for vibronically nonadiabatic proton transfer and proton-coupled electron transfer reactions are presented and analyzed. The regimes covered include electronically adiabatic and nonadiabatic reactions, as well as high-frequency and low-frequency proton donor-acceptor vibrational modes. These rate constants differ from prev...
Article
Full-text available
The rate constants for typical concerted proton-coupled electron transfer (PCET) reactions depend on the vibronic coupling between the diabatic reactant and product states. The form of the vibronic coupling is different for electronically adiabatic and nonadiabatic reactions, which are associated with hydrogen atom transfer (HAT) and electron-proto...
Article
Photoinduced concerted electron-proton transfer (EPT), denoted photo-EPT, is important for a wide range of energy conversion processes. Transient absorption and Raman spectroscopy experiments on the hydrogen-bonded p-nitrophenylphenol–t-butylamine complex, solvated in 1,2-dichloroethane, suggested that this complex may undergo photo-EPT. The experi...
Article
Full-text available
The fundamentals of the Effective Hamiltonian Crystal Field (EHCF) method, used originally to calculate intra-shell excitations in the d-shells of coordination compounds of the first row transition metals, are reviewed. The formalism of effective operators is applied to derive an explicit form of the effective operator for a dipole moment in d-shel...
Article
Full-text available
Three-dimensional non-oxidic extended frameworks offer the possibility to design novel materials with unique properties, which can be different from their oxide analogues. Here, we present first experimental results concerning unusual magnetic properties of FeNCN, investigated using Mossbauer spectroscopy and magnetometry between 5 and 380 K. This...
Article
Proton-coupled electron transfer (PCET) plays a vital role in many biological and chemical processes. PCET rate constant expressions are available for various well-defined regimes, and determining which expression is appropriate for a given system is essential for reliable modeling. Quantitative diagnostics have been devised to characterize the vib...
Article
The enzyme soybean lipoxygenase (SLO) has served as a prototype for hydrogen-tunneling reactions, as a result of its unusual kinetic isotope effects (KIEs) and their temperature dependencies. Using a synergy of kinetic, structural, and theoretical studies, we show how the interplay between donor-acceptor distance and active-site flexibility leads t...
Data
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Article
Full-text available
The development of efficient theoretical methods for describing electron transfer (ET) reactions in condensed phases is important for a variety of chemical and biological applications. Previously, dynamical dielectric continuum theory was used to derive Langevin equations for a single collective solvent coordinate describing ET in a polar solvent....
Article
Proton-coupled electron transfer can occur via concerted (EPT) or sequential mechanisms, but this distinction becomes less well-defined for photoinduced reactions. These issues have been examined with transient absorption experiments on a hydrogen-bonded complex comprised of p-nitrophenyl-phenol and t-butylamine. These experiments revealed two spec...
Article
Theoretical approaches for simulating the ultrafast dynamics of photoinduced proton-coupled electron transfer (PCET) reactions in solution are developed and applied to a series of model systems. These processes are simulated by propagating nonadiabatic surface hopping trajectories on electron-proton vibronic surfaces that depend on the solute and s...
Article
Full-text available
The design of molecular electrocatalysts for H(2) oxidation and production is important for the development of alternative renewable energy sources that are abundant, inexpensive, and environmentally benign. Recently, nickel-based molecular electrocatalysts with pendant amines that act as proton relays for the nickel center were shown to effectivel...
Article
Full-text available
A theoretical approach for the multidimensional treatment of photoinduced proton-coupled electron transfer (PCET) processes in solution is presented. This methodology is based on the multistate continuum theory with an arbitrary number of diabatic electronic states representing the relevant charge distributions in a general PCET system. The active...
Article
The hydrogen/deuterium isotope effects on the ultrafast dynamics of photoinduced proton-coupled electron transfer (PCET) are investigated with a recently developed nonadiabatic dynamics approach. An ensemble of surface hopping trajectories is propagated according to a Langevin equation on electron−proton vibronic free energy surfaces that depend on...
Article
A theoretical formulation for modeling photoinduced nonequilibrium proton-coupled electron transfer (PCET) reactions in solution is presented. In this formulation, the PCET system is described by donor and acceptor electron-proton vibronic free energy surfaces that depend on a single collective solvent coordinate. Dielectric continuum theory is use...
Article
The impact of distal mutation on the hydrogen transfer interface properties and on the substrate mobility, conformation, and orientation in soybean lipoxygenase-1 (SLO) is examined. SLO catalyzes a hydrogen abstraction reaction that occurs by a proton-coupled electron transfer mechanism. Mutation of isoleucine 553 to less bulky residues has been fo...
Article
Electrochemical proton-coupled electron transfer of an osmium aquo complex attached to a self-assembled monolayer on a gold electrode is studied with a recently developed theoretical formulation. The calculated hydrogen/deuterium kinetic isotope effect for the standard rate constant, the cathodic transfer coefficient at zero overpotential, and the...
Article
A theoretical model for describing the dynamics of photoinduced proton-coupled electron transfer (PCET) at molecule−semiconductor interfaces is presented. In this model, the electron is photoexcited to a molecular electronic state near the semiconductor surface, and the subsequent electron transfer to the conduction band of the semiconductor is cou...
Article
Full-text available
A model Hamiltonian for photoinduced homogeneous proton-coupled electron transfer reactions is presented, and the equations of motion for the reduced density matrix elements in an electron-proton vibronic basis are derived. This formalism enables a detailed analysis of the proton vibrational dynamics, as well as the dynamics of the electronic state...
Article
The driving force dependence of the rate constants for nonadiabatic electron transfer (ET), proton transfer (PT), and proton-coupled electron transfer (PCET) reactions is examined. Inverted region behavior, where the rate constant decreases as the reaction becomes more exoergic (i.e., as DeltaG(0) becomes more negative), has been observed experimen...
Article
Hybrid quantum/classical molecular dynamics simulations of the two proton transfer reactions catalyzed by ketosteroid isomerase are presented. The potential energy surfaces for the proton transfer reactions are described with the empirical valence bond method. Nuclear quantum effects of the transferring hydrogen increase the rates by a factor of ap...
Article
In this paper we present theoretical calculations on model biomimetic systems for quinol oxidation. In these model systems, an excited-state [Ru(bpy)(2)(pbim)](+) complex (bpy = 2,2'-dipyridyl, pbim = 2-(2-pyridyl)benzimidazolate) oxidizes a ubiquinol or plastoquinol analogue in acetonitrile. The charge transfer reaction occurs via a proton-coupled...
Article
A computationally efficient approach for ranking mutant enzymes according to the catalytic reaction rates is presented. This procedure requires the generation and equilibration of the mutant structures, followed by the calculation of partial free energy curves using an empirical valence bond potential in conjunction with biased molecular dynamics s...
Article
Full-text available
The coupling between proton and electron transfer reactions is vital for a wide range of chemical and biological processes, including photosynthesis,1 - 7 respiration,8,9 and numerous enzyme reactions.10 In this chapter, reactions involving the simultaneous transfer of at least one proton and one electron are denoted proton-coupled electron transfe...
Article
Recent advances in the theoretical treatment of proton-coupled electron transfer (PCET) reactions are reviewed. These reactions play an important role in a wide range of biological processes, as well as in fuel cells, solar cells, chemical sensors, and electrochemical devices. A unified theoretical framework has been developed to describe both sequ...
Article
Expressions are derived for the nonadiabatic transition probabilities, the heterogeneous rate constants, and the current densities of electrochemical proton-coupled electron transfer (PCET) reactions. In these reactions, an electron is transferred between a solute complex and a metal electrode concurrently with proton transfer within the hydrogen-b...
Article
Full-text available
An extension of the Anderson-Newns-Schmickler model for electrochemical proton-coupled electron transfer (PCET) is presented. This model describes reactions in which electron transfer between a solute complex in solution and an electrode is coupled to proton transfer within the solute complex. The model Hamiltonian is derived in a basis of electron...
Article
The umbrella integration method for calculating the potential of mean force (PMF) for a chemical reaction is implemented within the empirical valence bond (EVB) framework. In this implementation, the PMF is generated along the energy gap reaction coordinate, and the biasing potential is the difference between the mapping potential, which is defined...
Article
Theoretical studies of proton-coupled electron transfer (PCET) reactions for model systems provide insight into fundamental concepts relevant to bioenergetics. A dynamical theoretical formulation for vibronically nonadiabatic PCET reactions has been developed. This theory enables the calculation of rates and kinetic isotope effects, as well as the...
Article
The mechanism for tyrosyl radical generation in the [Re(P-Y)(phen)(CO)3]PF6 complex is investigated with a multistate continuum theory for proton-coupled electron transfer (PCET) reactions. Both water and the phosphate buffer are considered as potential proton acceptors. The calculations indicate that the model in which the proton acceptor is the p...
Article
The dynamical behavior and the temperature dependence of the kinetic isotope effects (KIEs) are examined for the proton-coupled electron transfer reaction catalyzed by the enzyme soybean lipoxygenase. The calculations are based on a vibronically nonadiabatic formulation that includes the quantum mechanical effects of the active electrons and the tr...
Article
The vibronic couplings for the phenoxyl/phenol and the benzyl/toluene self-exchange reactions are calculated with a semiclassical approach, in which all electrons and the transferring hydrogen nucleus are treated quantum mechanically. In this formulation, the vibronic coupling is the Hamiltonian matrix element between the reactant and product mixed...
Article
Full-text available
A nonadiabatic rate expression for hydrogen tunneling reactions in the condensed phase is derived for a model system described by a modified spin-boson Hamiltonian with a tunneling matrix element exponentially dependent on the hydrogen donor-acceptor distance. In this model, the two-level system representing the localized hydrogen vibrational state...
Article
Dihydroorotate dehydrogenase (DHOD) catalyzes the only redox reaction in the pathway for pyrimidine biosynthesis. In this reaction, a proton is transferred from a carbon atom of the substrate to a serine residue, and a hydride is transferred from another carbon atom of the substrate to a cofactor. The deprotonation of the substrate is postulated to...
Article
Full-text available
The multistate empirical valence bond (MS-EVB) model, which was developed for molecular dynamics simulations of proton transport in water and biomolecular systems, is extended for the modeling of protonatable amino acid residues in aqueous environments, specifically histidine and glutamic acid. The parameters of the MS-EVB force field are first det...
Article
An expression for the transition state theory rate constant is provided in terms of the potential of mean force for a general reaction coordinate and the mass-weighted gradient of this reaction coordinate. The form of the rate constant enables the straightforward calculation of rates for infrequent events with conventional umbrella sampling and fre...
Article
The dynamical aspects of a model proton-coupled electron transfer (PCET) reaction in solution are analyzed with molecular dynamics simulations. The rate for nonadiabatic PCET is expressed in terms of a time-dependent probability flux correlation function. The impact of the proton donor–acceptor and solvent dynamics on the probability flux is examin...
Article
Fundamental aspects of proton-coupled electron transfer (PCET) reactions in solution are analyzed with molecular dynamics simulations for a series of model systems. The analysis addresses the impact of the solvent reorganization energy, the proton donor-acceptor mode vibrational frequency, and the distance dependence of the nonadiabatic coupling on...
Article
Full-text available
This paper presents a general theoretical formulation for proton-coupled electron transfer (PCET) reactions. The solute is represented by a multistate valence bond model, and the active electrons and transferring proton(s) are treated quantum mechanically. This formulation enables the classical or quantum mechanical treatment of the proton donor-ac...
Article
Full-text available
With use of cumulants of two-electron density matrices semiempirical methods are analyzed from a point of view of their suitability to describe qualitative features of electronic correlation important for calculation of electronic structure of the transition metal complexes (TMC). It is shown that traditional semiempirical methods relying upon the...
Article
The proton-coupled electron transfer reaction catalyzed by soybean lipoxygenase-1 is studied with a multistate continuum theory that represents the transferring hydrogen nucleus as a quantum mechanical wave function. The inner-sphere reorganization energy of the iron cofactor is calculated with density functional theory, and the outer-sphere reorga...