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Sharon Hammes-Schiffer

Publications and source records attributed to Sharon Hammes-Schiffer.

At least 19 recordsLinked to original sources
PubMed2007

Proton-coupled electron transfer in soybean lipoxygenase: dynamical behavior and temperature dependence of kinetic isotope effects.

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 transferring proton, as well as the motions of all atoms in the complete solvated enzyme system. The rate constant is represented by the time integral of a probability flux correlation function that depends on the vibronic coupling and on time correlation functions of the energy gap and the proton donor-acceptor mode, which can be calculated from classical molecular dynamics simulations of the entire system. The dynamical behavior of the probability flux correlation function is dominated by the equilibrium protein and solvent motions and is not significantly influenced by the proton donor-acceptor motion. The magnitude of the overall rate is strongly influenced by the proton donor-acceptor frequency, the vibronic coupling, and the protein/solvent reorganization energy. The calculations reproduce the experimentally observed magnitude and temperature dependence of the KIE for the soybean lipoxygenase reaction without fitting any parameters directly to the experimental kinetic data. The temperature dependence of the KIE is determined predominantly by the proton donor-acceptor frequency and the distance dependence of the vibronic couplings for hydrogen and deuterium. The ratio of the overlaps of the hydrogen and deuterium vibrational wavefunctions strongly impacts the magnitude of the KIE but does not significantly influence its temperature dependence. For this enzyme reaction, the large magnitude of the KIE arises mainly from the dominance of tunneling between the ground vibronic states and the relatively large ratio of the overlaps between the corresponding hydrogen and deuterium vibrational wavefunctions. The weak temperature dependence of the KIE is due in part to the dominance of the local component of the proton donor-acceptor motion.

Electron Transport↗
PubMed2006

Calculation of vibronic couplings for phenoxyl/phenol and benzyl/toluene self-exchange reactions: implications for proton-coupled electron transfer mechanisms.

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 electronic-proton vibrational wavefunctions. The magnitude of the vibronic coupling and its dependence on the proton donor-acceptor distance can significantly impact the rates and kinetic isotope effects, as well as the temperature dependences, of proton-coupled electron transfer reactions. Both of these self-exchange reactions are vibronically nonadiabatic with respect to a solvent environment at room temperature, but the proton tunneling is electronically nonadiabatic for the phenoxyl/phenol reaction and electronically adiabatic for the benzyl/toluene reaction. For the phenoxyl/phenol system, the electrons are unable to rearrange fast enough to follow the proton motion on the electronically adiabatic ground state, and the excited electronic state is involved in the reaction. For the benzyl/toluene system, the electrons can respond virtually instantaneously to the proton motion, and the proton moves on the electronically adiabatic ground state. For both systems, the vibronic coupling decreases exponentially with the proton donor-acceptor distance for the range of distances studied. When the transferring hydrogen is replaced with deuterium, the magnitude of the vibronic coupling decreases and the exponential decay with distance becomes faster. Previous studies designated the phenoxyl/phenol reaction as proton-coupled electron transfer and the benzyl/toluene reaction as hydrogen atom transfer. In addition to providing insights into the fundamental physical differences between these two types of reactions, the present analysis provides a new diagnostic for differentiating between the conventionally defined hydrogen atom transfer and proton-coupled electron transfer reactions.

Electrons↗
PubMed2006

Hybrid quantum/classical path integral approach for simulation of hydrogen transfer reactions in enzymes.

A hybrid quantum/classical path integral Monte Carlo (QC-PIMC) method for calculating the quantum free energy barrier for hydrogen transfer reactions in condensed phases is presented. In this approach, the classical potential of mean force along a collective reaction coordinate is calculated using umbrella sampling techniques in conjunction with molecular dynamics trajectories propagated according to a mapping potential. The quantum contribution is determined for each configuration along the classical trajectory with path integral Monte Carlo calculations in which the beads move according to an effective mapping potential. This type of path integral calculation does not utilize the centroid constraint and can lead to more efficient sampling of the relevant region of conformational space than free-particle path integral sampling. The QC-PIMC method is computationally practical for large systems because the path integral sampling for the quantum nuclei is performed separately from the classical molecular dynamics sampling of the entire system. The utility of the QC-PIMC method is illustrated by an application to hydride transfer in the enzyme dihydrofolate reductase. A comparison of this method to the quantized classical path and grid-based methods for this system is presented.

Computer Simulation↗
PubMed2006

Extended spin-boson model for nonadiabatic hydrogen tunneling in the condensed phase.

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 states is linearly coupled to the donor-acceptor vibrational mode and the harmonic bath. The Hamiltonian also includes bilinear coupling between the donor-acceptor mode and the bath oscillators. This coupling provides a mechanism for energy exchange between the two-level system and the bath through the donor-acceptor mode, thereby facilitating convergence of the time integral of the probability flux correlation function for the case of weak coupling between the two-level system and the bath. The dependence of the rate constant on the model parameters and the temperature is analyzed in various regimes. Anomalous behavior of the rate constant is observed in the weak solvation regime for model systems that lack an effective mechanism for energy exchange between the two-level system and the bath. This theoretical formulation is applicable to a wide range of chemical and biological processes, including neutral hydrogen transfer reactions with small solvent reorganization energies.

Electron Transport↗
PubMed2006

Hydrogen bonding pathways in human dihydroorotate dehydrogenase.

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 involve a proton relay mechanism along a hydrogen bonding pathway in the active site. In this paper, molecular dynamics simulations are used to identify and characterize potential hydrogen bonding pathways that could facilitate the redox reaction catalyzed by human DHOD. The observed pathways involve hydrogen bonding of the active base serine to a water molecule, which is hydrogen bonded to the substrate carboxylate group or a threonine residue. The threonine residue is positioned to enable proton transfer to another water molecule leading to the bulk solvent. The impact of mutating the active base serine to cysteine is also investigated. This mutation is found to increase the average donor-acceptor distances for proton and hydride transfer and to disrupt the hydrogen bonding pathways observed for the wild-type enzyme. These effects could lead to a significant decrease in enzyme activity, as observed experimentally for the analogous mutant in Escherichia coli DHOD.

Carbon↗
PubMed2006

Hydride transfer catalysed by Escherichia coli and Bacillus subtilis dihydrofolate reductase: coupled motions and distal mutations.

This paper reviews the results from hybrid quantum/classical molecular dynamics simulations of the hydride transfer reaction catalysed by wild-type (WT) and mutant Escherichia coli and WT Bacillus subtilis dihydrofolate reductase (DHFR). Nuclear quantum effects such as zero point energy and hydrogen tunnelling are significant in these reactions and substantially decrease the free energy barrier. The donor-acceptor distance decreases to ca 2.7 A at transition-state configurations to enable the hydride transfer. A network of coupled motions representing conformational changes along the collective reaction coordinate facilitates the hydride transfer reaction by decreasing the donor-acceptor distance and providing a favourable geometric and electrostatic environment. Recent single-molecule experiments confirm that at least some of these thermally averaged equilibrium conformational changes occur on the millisecond time-scale of the hydride transfer. Distal mutations can lead to non-local structural changes and significantly impact the probability of sampling configurations conducive to the hydride transfer, thereby altering the free-energy barrier and the rate of hydride transfer. E. coli and B. subtilis DHFR enzymes, which have similar tertiary structures and hydride transfer rates with 44% sequence identity, exhibit both similarities and differences in the equilibrium motions and conformational changes correlated to hydride transfer, suggesting a balance of conservation and flexibility across species.

Bacillus subtilis↗
PubMed2006

Explicit dynamical electron-proton correlation in the nuclear-electronic orbital framework.

A method that includes explicit electron-proton correlation directly into the nuclear-electronic orbital self-consistent-field framework is presented. This nuclear-electronic orbital explicitly correlated Hartree-Fock (NEO-XCHF) scheme is formulated using Gaussian basis functions for the electrons and the quantum nuclei in conjunction with Gaussian-type geminal functions. The NEO approach is designed for the quantum treatment of a relatively small number of nuclei, such as the hydrogen nuclei involved in key hydrogen bonding interactions or hydrogen transfer reactions. The conventional nuclear-electronic-orbital-based methods produce nuclear wave functions that are too localized, leading to severe overestimations of hydrogen vibrational frequencies, as well as inaccuracies in geometries, isotope effects, couplings, and tunneling splittings. The application of the NEO-XCHF approach to a model system illustrates that the description of the nuclear wave function is significantly improved by the inclusion of explicit electron-proton correlation. In contrast to the NEO-HF method, the NEO-XCHF method leads to hydrogen vibrational stretch frequencies that are in excellent agreement with those calculated from grid-based methods. This approach is computationally practical for many-electron systems because only a relatively small number of nuclei are treated quantum mechanically and only electron-proton correlation is treated explicitly. Electron-electron dynamical correlation can be included with density functional theory or perturbation theory methods.

Letter↗
PubMed2006

Hybrid quantum/classical molecular dynamics for a proton transfer reaction coupled to a dissipative bath.

A hybrid quantum/classical molecular dynamics approach is applied to a proton transfer reaction represented by a symmetric double well system coupled to a dissipative bath. In this approach, the proton is treated quantum mechanically and all bath modes are treated classically. The transition state theory rate constant is obtained from the potential of mean force, which is generated along a collective reaction coordinate with umbrella sampling techniques. The transmission coefficient, which accounts for dynamical recrossings of the dividing surface, is calculated with a reactive flux approach combined with the molecular dynamics with quantum transitions surface hopping method. The hybrid quantum/classical results agree well with numerically exact results in the spatial-diffusion-controlled regime, which is most relevant for proton transfer in proteins. This hybrid quantum/classical approach has already been shown to be computationally practical for studying proton transfer in large biological systems. These results have important implications for future applications to hydrogen transfer reactions in solution and proteins.

Biophysics↗
PubMed2006

Comparison of coupled motions in Escherichia coli and Bacillus subtilis dihydrofolate reductase.

Hybrid quantum/classical molecular dynamics simulations are used to compare the role of protein motion in the hydride transfer reaction catalyzed by Escherichia coli and Bacillus subtilis dihydrofolate reductase (DHFR). These two enzymes have 44% sequence identity, and the experimentally determined structures and hydride transfer rates are similar. The simulations indicate that the tertiary structures of both enzymes evolve in a similar manner during the hydride transfer reaction. In both enzymes, the donor-acceptor distance decreases to approximately 2.7 Angstroms at the transition state configurations to enable hydride transfer. Zero point energy and hydrogen tunneling effects are found to be significant for both enzymes. Covariance and rank correlation analyses of motions throughout the protein and ligands illustrate that E. coli and B. subtilis DHFR exhibit both similarities and differences in the equilibrium fluctuations and the conformational changes along the collective reaction coordinate for hydride transfer. A common set of residues that play a significant role in the network of coupled motions leading to configurations conducive to hydride transfer for both E. coli and B. subtilis DHFR was identified. These results suggest a balance between conservation and flexibility in the thermal motions and conformational changes during hydride transfer. Homologous protein structures, in conjunction with conformational sampling, enable enzymes with different sequences to catalyze the same hydride transfer reaction with similar efficiency.

Bacillus subtilis↗
PubMed2006

Freezing a single distal motion in dihydrofolate reductase.

Constraining a single motion between distal residues separated by approximately 28 A in hybrid quantum/classical molecular dynamics simulations is found to increase the free energy barrier for hydride transfer in dihydrofolate reductase by approximately 3 kcal/mol. Our analysis indicates that a single distal constraint alters equilibrium motions throughout the enzyme on a wide range of time scales. This alteration of the conformational sampling of the entire system is sufficient to significantly increase the free energy barrier and decrease the rate of hydride transfer. Despite the changes in conformational sampling introduced by the constraint, the system assumes a similar transition state conformation with a donor-acceptor distance of approximately 2.72 A to enable the hydride transfer reaction. The modified thermal sampling leads to a substantial increase in the average donor-acceptor distance for the reactant state, however, thereby decreasing the probability of sampling the transition state conformations with the shorter distances required for hydride transfer. These simulations indicate that fast thermal fluctuations of the enzyme, substrate, and cofactor lead to conformational sampling of configurations that facilitate hydride transfer. The fast thermal motions are in equilibrium as the reaction progresses along the collective reaction coordinate, and the overall average equilibrium conformational changes occur on the slower time scale measured experimentally. Recent single molecule experiments suggest that at least some of these thermally averaged equilibrium conformational changes occur on the millisecond time scale of the hydride transfer reaction. Thus, introducing a constraint that modifies the conformational sampling of an enzyme could significantly impact its catalytic activity.

Biological Transport↗
PubMed2006

Hydrogen tunneling and protein motion in enzyme reactions.

Theoretical perspectives on hydrogen transfer reactions in enzymes are presented. The proton-coupled electron transfer reaction catalyzed by soybean lipoxygenase and the hydride transfer reaction catalyzed by dihydrofolate reductase are discussed. The first reaction is nonadiabatic and involves two distinct electronic states, while the second reaction is predominantly adiabatic and occurs on the electronic ground state. Theoretical studies indicate that hydrogen tunneling and protein motion play significant roles in both reactions. In both cases, the proton donor-acceptor distance decreases relative to its equilibrium value to enable efficient hydrogen tunneling. Equilibrium thermal motions of the protein lead to conformational changes that facilitate hydrogen transfer, but the nonequilibrium dynamical aspects of these motions have negligible impact.

Deuterium↗
PubMed2006

Relating protein motion to catalysis.

This review examines the linkage between protein conformational motions and enzyme catalysis. The fundamental issues related to this linkage are probed in the context of two enzymes that catalyze hydride transfer, namely dihydrofolate reductase and liver alcohol dehydrogenase. The extensive experimental and theoretical studies addressing the role of protein conformational changes in these enzyme reactions are summarized. Evidence is presented for a network of coupled motions throughout the protein fold that facilitate the chemical reaction. This network is comprised of fast thermal motions that are in equilibrium as the reaction progresses along the reaction coordinate and that lead to slower equilibrium conformational changes conducive to the chemical reaction.

Alcohol Dehydrogenase↗
PubMed2005

Impact of nuclear quantum effects on the molecular structure of bihalides and the hydrogen fluoride dimer.

The structural impact of nuclear quantum effects is investigated for a set of bihalides, [XHX](-), X = F, Cl, and Br, and the hydrogen fluoride dimer. Structures are calculated with the vibrational self-consistent-field (VSCF) method, the second-order vibrational perturbation theory method (VPT2), and the nuclear-electronic orbital (NEO) approach. In the VSCF and VPT2 methods, the vibrationally averaged geometries are calculated for the Born-Oppenheimer electronic potential energy surface. In the NEO approach, the hydrogen nuclei are treated quantum mechanically on the same level as the electrons, and mixed nuclear-electronic wave functions are calculated variationally with molecular orbital methods. Electron-electron and electron-proton dynamical correlation effects are included in the NEO approach using second-order perturbation theory (NEO-MP2). The nuclear quantum effects are found to alter the distances between the heavy atoms by 0.02-0.05 A for the systems studied. These effects are of similar magnitude as the electron correlation effects. For the bihalides, inclusion of the nuclear quantum effects with the NEO-MP2 or the VSCF method increases the X-X distance. The bihalide X-X distances are similar for both methods and are consistent with two-dimensional grid calculations and experimental values, thereby validating the use of the computationally efficient NEO-MP2 method for these types of systems. For the hydrogen fluoride dimer, inclusion of nuclear quantum effects decreases the F-F distance with the NEO-MP2 method and increases the F-F distance with the VSCF and VPT2 methods. The VPT2 F-F distances for the hydrogen fluoride dimer and the deuterated form are consistent with the experimentally determined values. The NEO-MP2 F-F distance is in excellent agreement with the distance obtained experimentally for a model that removes the large amplitude bending motions. The analysis of these calculations provides insight into the significance of electron-electron and electron-proton correlation, anharmonicity of the vibrational modes, and nonadiabatic effects for hydrogen-bonded systems.

Dimerization↗
PubMed2005

Nonadiabatic proton-coupled electron transfer reactions: impact of donor-acceptor vibrations, reorganization energies, and couplings on dynamics and rates.

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 the dynamics of the reaction and the magnitude of the rate. The rate for nonadiabatic PCET is expressed in terms of a time-dependent probability flux correlation function. The time dependence of the probability flux correlation function is determined mainly by the solvent reorganization energy and is not significantly influenced by the proton donor-acceptor frequency or the distance dependence of the nonadiabatic coupling. The magnitude of the PCET rate becomes greater as the solvent reorganization energy decreases, the proton donor-acceptor frequency decreases, and the distance dependence of the nonadiabatic coupling increases. The approximations underlying a previously derived analytical PCET rate expression are also investigated. The short-time approximation for the solvent is valid for these types of systems. In addition, solvent damping effects on the proton donor-acceptor motion are not significant on the time scale of the probability flux. The rates calculated from the molecular dynamics simulations agree well with those calculated from the analytical rate expression.

Models, Theoretical↗
PubMed2005

Nuclear-electronic orbital nonorthogonal configuration interaction approach.

The nuclear-electronic orbital nonorthogonal configuration interaction (NEO-NOCI) approach is presented. In this framework, the hydrogen nuclei are treated quantum mechanically on the same level as the electrons, and a mixed nuclear-electronic time-independent Schrodinger equation is solved with molecular orbital techniques. For hydrogen transfer systems, the transferring hydrogen is represented by two basis function centers to allow delocalization of the nuclear wave function. In the two-state NEO-NOCI approach, the ground and excited state delocalized nuclear-electronic wave functions are expressed as linear combinations of two nonorthogonal localized nuclear-electronic wave functions obtained at the NEO-Hartree-Fock level. The advantages of the NEO-NOCI approach are the removal of the adiabatic separation between the electrons and the quantum nuclei, the computational efficiency, the potential for systematic improvement by enhancing the basis sets and number of configurations, and the applicability to a broad range of chemical systems. The tunneling splitting is determined by the energy difference between the two delocalized vibronic states. The hydrogen tunneling splittings calculated with the NEO-NOCI approach for the [He-H-He]+ model system with a range of fixed He-He distances are in excellent agreement with NEO-full CI and Fourier grid calculations. These benchmarking calculations indicate that NEO-NOCI is a promising approach for the calculation of delocalized, bilobal hydrogen wave functions and the corresponding hydrogen tunneling splittings.

Chemical Phenomena↗
PubMed2005

Investigation of isotope effects with the nuclear-electronic orbital approach.

This paper addresses fundamental issues that arise in the application of the nuclear-electronic orbital (NEO) approach to systems with equivalent quantum nuclei. Our analysis illustrates that Hartree-Fock nuclear wave functions do not provide physically reasonable descriptions of systems comprised of equivalent low-spin fermions or equivalent bosons. The physical basis for this breakdown is that the ionic terms dominate due to the localized nature of the nuclear orbitals. Multi-configurational wave functions that include only covalent terms provide physically reasonable descriptions of these types of systems. The application of the NEO approach to a variety of chemical systems is presented to elucidate the isotope effects on the geometries and electronic wave functions. Deuteration of hydrogen halides, water, ammonia, and hydronium ion decreases the bond length and the magnitude of negative partial atomic charge on the heavy atom. These results are consistent with experimental spectroscopic data. Deuteration at the beta position for formate anion and a series of amines increases the magnitude of negative partial atomic charge on the protonation site for the unprotonated species. This observation is consistent with the experimentally observed increase in basicity upon deuteration at the beta position for carboxylic acids and amines.

Amines↗
PubMed2005

Analysis of the nuclear-electronic orbital method for model hydrogen transfer systems.

Fundamental issues associated with the application of the nuclear-electronic orbital (NEO) approach to hydrogen transfer systems are addressed. In the NEO approach, specified nuclei are treated quantum mechanically on the same level as the electrons, and mixed nuclear-electronic wavefunctions are calculated with molecular orbital methods. The positions of the nuclear basis function centers are optimized variationally. In the application of the NEO approach to hydrogen transfer systems, the hydrogen nuclei and all electrons are treated quantum mechanically. Within the NEO framework, the transferring hydrogen atom can be represented by two basis function centers to allow delocalization of the proton vibrational wavefunction. In this paper, the NEO approach is applied to the [He-H-He]+ and [He-H-He]++ model systems. Analyses of technical issues pertaining to flexibility of the basis set to describe both single and double well proton potential energy surfaces, linear dependency of the hydrogen basis functions, multiple minima in the basis function center optimization, convergence of the number of hydrogen basis function centers, and basis set superposition error are presented. The accuracy of the NEO approach is tested by comparison to grid calculations for these model systems.

Chemistry, Physical↗