Ivan Rostov - Academia.edu (original) (raw)

Papers by Ivan Rostov

Research paper thumbnail of Continuum level treatment of electronic polarization in the framework of molecular simulations of solvation effects

The Journal of Chemical Physics, 2003

The hybrid molecular-continuum model for polar solvation considered in this paper combines the di... more The hybrid molecular-continuum model for polar solvation considered in this paper combines the dielectric continuum approximation for treating fast electronic (inertialess) polarization effects and a molecular dynamics (MD) simulation for the slow (inertial) polarization component, including orientational and translational solvent modes. The inertial polarization is generated by average charge distributions of solvent particles, composed of permanent and induced (electronic) components.

Research paper thumbnail of Molecular simulations of outersphere reorganization energies for intramolecular electron and hole transfer in polar solvents

Chemical Physics, 2005

Outersphere reorganization energies (λ) for intramolecular electron transfer (ET) and hole transf... more Outersphere reorganization energies (λ) for intramolecular electron transfer (ET) and hole transfer are studied in anion- and cation-radical forms of complex organic substrates (biphenylyl-spacer-naphtyl) in polar solvents simulated by means of the nonpolarizable models of water and 1,2-dichloroethane. The earlier elaborated molecular/continuum approach (the MD/FRCM, J. Chem. Phys., 119 (2003) 8024) is used; this method provides a physically relevant background

Research paper thumbnail of The Mechanism of Catalytic Action of Water in Liquid-Phase Chlorination of Olefins

Russian Journal of Physical Chemistry

Research paper thumbnail of Transition States in Chlorination of Olefins in the Gas and Luquid States

Russian Journal of Physical Chemistry

Research paper thumbnail of Simulations of Enzyme Reaction Mechanisms in Active Sites: Accounting for an Environment Which Is Much More Than a Solvent Perturbation

The goal of this chapter is to outline the special challenges faced in using computational method... more The goal of this chapter is to outline the special challenges faced in using computational methods to define the reaction mechanisms of enzymes. Our approach is to set the problem in the context of the special chemical and structural features which differentiate enzymes from other types of catalysts, and the limitations of experiment in probing these features and defining their contributions to the reaction facilitation. We then briefly discuss the types of computational methods available and how they can be applied to an enzyme problem. Two major features – the roles of active-site protons and water molecules, and enzyme conformational flexibility – are illustrated by results from our simulation work on dihydrofolate reductase. After briefly reviewing published work, we focus on two novel simulation protocols and methods we have recently developed, combining the use of ONIOM ab initio QM/MM calculations and MD simulations with semiempirical QM/MM potentials, to address issues of tr...

Research paper thumbnail of Quantum-chemical evaluation of energy quantities governing electron transfer kinetics: applications to intramolecular processes

Journal of Molecular Structure: THEOCHEM, 1996

Important energy quantities governing electron transfer (ET) kinetics in polar solutions (reorgan... more Important energy quantities governing electron transfer (ET) kinetics in polar solutions (reorganization energy, E,, and net free energy change, AU) are evaluated on the basis of quantum-chemical self-consistent reaction-field (SCRF) models. Either self-consistent field (SCF) or configuration interaction (CI) wavefunctions are used for the solute, which occupies a molecular cavity of realistic shape in a dielectric continuum. A classical SCRF model together with unrestricted Hartree-Fock SCF wavefunctions based on the semiempirical PM3 Hamiltonian is applied to the calculation of the solvent portion of E, (denoted E,) for two different series of radical ion ET systems: radical cations and anions of biphenylyl/naphthyl donor/acceptor (D/A) pairs linked by cyclohexane-based spacer groups and trans-staggered radical anions of the type (CH,),, m = 2-5. Results for E, based on two-configurational CI wavefunctions and an alternative reaction field (the so-called Born-Oppenheimer model, which recognizes the fast timescales of solvent electrons relative to those involved in ET) are also noted. Results for innersphere (i.e. intra-solute) reorganization, Ei, and for AU are also reported. The semiempirical E, results are quite similar to corresponding ab initio results and display the form of the two-sphere Marcus model for E, as a function of D/A separation. Nevertheless, in the one case where direct comparison is possible, the calculated E, result is more than twice the magnitude of the estimate based on experimental ET kinetic data. To reconcile this situation, a generalized SCRF model is proposed, which assigns different effective solute cavity sizes to the optical and inertial components of the solvent response, using ideas based on non-local solvation models.

Research paper thumbnail of Advanced dielectric continuum models of solvation, their connection to microscopic solvent models, and application to electron transfer reactions

Some recent advances in dielectric continuum models for static and dynamic aspects of molecular s... more Some recent advances in dielectric continuum models for static and dynamic aspects of molecular solvation are discussed, and connections with molecular-level solvent models are noted. The traditional Born-Onsager-Kirkwood (BKO) model is compared to a more flexible model (the so-called frequency-resolved cavity model (FRCM)) which assigns distinct inner and outer solute cavities in accommodating, respectively, the inertialess (optical) and inertial solvent response. Sample calculations of solvent reorganization energy (lambdas) are presented for various thermal and optical electron transfer (ET) processes, based on self-consistent reaction field models using molecular orbital (MO) or configuration interaction (CI) solvent wave functions.

Research paper thumbnail of A Theoretical Investigation of Charge Transfer in Several Substituted Acridinium Ions †

The Journal of Physical Chemistry B, 2005

Research paper thumbnail of A two-dimensional Born–Oppenheimer treatment of intramolecular electron transfer reactions

Journal of Electroanalytical Chemistry, 1998

The Born-Oppenheimer (BO) formulation of polar solvation is developed and implemented at the semi... more The Born-Oppenheimer (BO) formulation of polar solvation is developed and implemented at the semiemperical (PM3) configuration interaction (CI) level, yielding estimates of electron transfer (ET) coupling elements (V 0) for intramolecular ET in several families of radical ion systems. In contrast to the traditional treatment based on a single solvent coordinate and a fixed gas-phase coupling element, the present treatment yields a self-consistent characterization of kinetic parameters in a 2-dimensional solvent framework which includes an exchange coordinate. The dependence of V 0 on inertial solvent contributions and on donor/acceptor separation (r DA) is discussed.

Research paper thumbnail of Erratum to “A two-dimensional Born–Oppenheimer treatment of intramolecular electron transfer reactions”

Journal of Electroanalytical Chemistry, 1999

Research paper thumbnail of Calculation of a Complete Enzymic Reaction Surface:  Reaction and Activation Free Energies for Hydride-Ion Transfer in Dihydrofolate Reductase

Journal of Chemical Theory and Computation, 2007

We present a two-dimensional grid method for the calculation of complete free-energy surfaces for... more We present a two-dimensional grid method for the calculation of complete free-energy surfaces for enzyme reactions using a hybrid quantum mechanical/molecular mechanical (QM/MM) potential within the semiempirical (PM3) QM approximation. This implementation is novel in that parallel processing with multiple trajectories (replica-exchange molecular dynamics simulations) is used to sample configuration space. The free energies at each grid point are computed using the thermodynamic integration formalism. From the free-energy surface, the minimum free-energy pathway for the reaction can be defined, and the computed activation and reaction energies can be compared with experimental values. We illustrate its use in a study of the hydride-transfer step in the reduction of dihydrofolate to tetrahydrofolate catalyzed by Escherichia coli dihydrofolate reductase with bound nicotinamide adenine dinucleotide phosphate cofactor. We investigated the effects of changing the QM region, ionization state of the conserved active-site Asp27 residue, and polarization contributions to the activation and reaction free energy. The results clearly show the necessity for including the complete substrate and cofactor molecules in the QM region, and the importance of the overall protein (MM) electrostatic environment in determining the free energy of the transition state (TS) and products relative to reactants. For the model with ionized Asp27, its inclusion in the QM region is essential. We found that the reported [Garcia-Viloca, M.; Truhlar, D. G.; Gao, J. J. Mol. Biol. 2003, 327, 549] stabilization of the TS due to polarization is an artifact that can be attributed to truncation of the electrostatic interactions between the QM and MM atoms. For neutral (protonated) Asp27, our calculated reaction free energy of -4 ± 2 kcal/mol agrees well with the experimental value of -4.4 kcal/mol, although the corresponding activation free-energy estimate is still high at 21 ± 2 kcal/mol compared with the experimental value of 13.4 kcal/mol. The results are less supportive of the ionized Asp27 model, which gives rise to a much higher activation barrier and favors the reverse reaction.

Research paper thumbnail of Theoretical formulation for electron transfer coupled to multiple protons: Application to amidinium–carboxylate interfaces

The Journal of Chemical Physics, 2001

This paper presents a theoretical formulation for electron transfer coupled to the motion of mult... more This paper presents a theoretical formulation for electron transfer coupled to the motion of multiple protons. This theory is applied to proton-coupled electron transfer ͑PCET͒ through amidiniumcarboxylate salt bridges, where the electron transfer reaction is coupled to the motion of two protons at the proton transfer interface. The rate for the donor-͑amidinium-carboxylate͒-acceptor system is found to be substantially slower than the rate for the switched interface donor-͑carboxylate-amidinium͒-acceptor system. This trend is consistent with experimental data for photoinduced PCET in analogous systems. The calculations indicate that this difference in rates is due mainly to the opposite dipole moments at the proton transfer interfaces for the two systems, leading to an endothermic reaction for the donor-͑amidinium-carboxylate͒-acceptor system and an exothermic reaction for the donor-͑carboxylate-amidinium͒-acceptor system. The deuterium kinetic isotope effects are found to be moderate ͑i.e., k H /k D Ͻ3) for both types of systems. These moderate kinetic isotope effects are due to the dominance of vibrationally excited product states, leading to significant overlap between the reactant and product proton vibrational wave functions.

Research paper thumbnail of Semiempirical modeling free energy surfaces for proton transfer in polar aprotic solvents

Chemical Physics, 2000

A method of calculation of a free-energy surface (FES) of the proton transfer (PT) reaction in a ... more A method of calculation of a free-energy surface (FES) of the proton transfer (PT) reaction in a polar aprotic solvent is developed. This is based on the two-state (valence bond) VB description of the solute combined with recent continuum medium models. Its essential new feature is an explicit quantum-chemical treatment of VB wave functions, including internal electronic structure of a

Research paper thumbnail of Studies of the Ground and Excited-State Surfaces of the Retinal Chromophore using CAM-B3LYP

The Journal of Physical Chemistry B, 2010

The isomerization of the 11-cis isomer (PSB11) of the retinal chromophore to its all-trans isomer... more The isomerization of the 11-cis isomer (PSB11) of the retinal chromophore to its all-trans isomer (PSBT) is examined. Optimized structures on both the ground state and the excited state are calculated, and the dependence on torsional angles in the carbon chain is investigated. Time-dependent density functional theory is used to produce excitation energies and the excited-state surface. To avoid problems with the description of excited states that can arise with standard DFT methods, the CAM-B3LYP functional was used. Comparing CAM-B3LYP with B3LYP results indicates that the former is significantly more accurate, as a consequence of which detailed cross sections of the retinal excited-state surface are obtained.

Research paper thumbnail of A correlated ab initio quantum chemical study of the interaction of the Na+, Mg2+, Ca2+ and Zn2+ ions with the tautomers of cytosine in the presence of polar solvent

Physical Chemistry Chemical Physics, 2013

The interactions of the metal ions Na(+), Mg(2+), Ca(2+) and Zn(2+) with cytosine have been inves... more The interactions of the metal ions Na(+), Mg(2+), Ca(2+) and Zn(2+) with cytosine have been investigated with inclusion of solvent effects. Computations have been performed at the density functional and Møller-Plesset levels of theory within the IEFPCM solvent model. It has been found that the inclusion of the solvent environment is essential for giving more biologically realistic results. Earlier gas-phase findings of the stabilisation of rare tautomeric forms by the metal ions have been reproduced, with the presence of the solvent further affecting the relative stabilities.

Research paper thumbnail of Comparing long-range corrected functionals in the cis–trans isomerisation of the retinal chromophore

Research paper thumbnail of A frequency-resolved cavity model (FRCM) for treating equilibrium and non-equilibrium solvation energies

Chemical Physics, 1998

A refined continuum medium model, denoted as the `frequency-resolved cavity model' (FRCM)... more A refined continuum medium model, denoted as the `frequency-resolved cavity model' (FRCM), for describing solvation effects of electrically charged solutes in polar solvents is considered. The principal distinction between the commonly accepted Born–Kirkwood–Onsager model and the FRCM treatment is that in the latter case the medium polarization field induced by the solute charge distribution is subdivided into inertial and inertialess

Research paper thumbnail of Semiempirical modeling free energy surfaces for proton transfer in polar aprotic solvents

Chemical Physics, 2000

A method of calculation of a free-energy surface (FES) of the proton transfer (PT) reaction in a ... more A method of calculation of a free-energy surface (FES) of the proton transfer (PT) reaction in a polar aprotic solvent is developed. This is based on the two-state (valence bond) VB description of the solute combined with recent continuum medium models. Its essential new feature is an explicit quantum-chemical treatment of VB wave functions, including internal electronic structure of a chemical subsystem. The FES includes a pair of intrasolute coordinates, R, the distance between hydrogen-bonded atoms and s, the proton coordinate, together with the collective medium polarization mode. Two hydrogen-bonded systems immersed in a polar solvent (Freon) were considered. The ®rst one is the H 5 O 2 ion, a model system which was used as a benchmark testifying the validity of our semiempirical calculations. The second system is the neutral (CN)(CH 3 )N±HÁ Á ÁN(CH 3 ) 3 complex in Freon. PT for this system has been studied experimentally. The dependencies of basic parameters controlling FES properties (the overlap integral, the coupling matrix element and the reorganization energy E r ) on intrasolute coordinates R and s are evaluated and discussed. In particular, for the neutral complex, E r depends on s linearly, and its dependence on R is weak. The FES, for the neutral system, has two potential wells separated by the energy barrier of $7 kcal/mol. Quantum-mechanical averaging over the proton coordinate, s, reduces the barrier from 7.0 to 1.2 kcal/mol. The value of the nonadiabatic parameter on the averaged FES is equal to 0.13. This implies that the PT in the second system corresponds to an intermediate dynamic regime and that proton tunneling eects are hardly signi®cant for this reaction. Ó

Research paper thumbnail of Molecular simulations of outersphere reorganization energies for intramolecular electron and hole transfer in polar solvents

Chemical Physics, 2005

Outersphere reorganization energies (k) for intramolecular electron transfer (ET) and hole transf... more Outersphere reorganization energies (k) for intramolecular electron transfer (ET) and hole transfer are studied in anion-and cation-radical forms of complex organic substrates (biphenylyl-spacer-naphtyl) in polar solvents simulated by means of the nonpolarizable models of water and 1,2-dichloroethane. The earlier elaborated molecular/continuum approach (the MD/FRCM, J. Chem. Phys., 119 (2003) 8024) is used; this method provides a physically relevant background for separating inertial and inertialess polarization responses within a nonpolarizable MD simulation (the SPC water model). Quantum-chemical calculations of solute charge distributions were performed with semiempirical (AM1) and second ab initio (HF/6-31G(d,p)) approximations. Ab initio charges give lower k-values and are preferable, probably, because of including the effect of the SCRF polarization of the diabatic ET states. Standard Lennard-Jones and charge parameters implemented in MD runs were not specially fitted for reproducing ET effects. The difference in values for a cation and an anion originating from the same parent structure was specially investigated. As shown earlier, this effect, nonlinear in its nature, proved to be extremely large when a model dipolar two-site system was studied. For the present ET structures representing real chemical substrates it has reduced to a plausible value of 6-8 kcal/mol. The study of the temperature dependence of k comprises a first MD simulation of this problem and its slope was found to be in accord with an experimental observation for an anionic species. Calculations of absolute k-values for the hole transfer in 1,2-dichloroethane are the first MD simulations of reorganization energies in experimentally studied reactions. Computed values of k-s are higher than the experimental data. The effect of this magnitude could be eliminated by proper tuning the solvent parameters.

Research paper thumbnail of Continuum level treatment of electronic polarization in the framework of molecular simulations of solvation effects

The Journal of Chemical Physics, 2003

The hybrid molecular-continuum model for polar solvation considered in this paper combines the di... more The hybrid molecular-continuum model for polar solvation considered in this paper combines the dielectric continuum approximation for treating fast electronic ͑inertialess͒ polarization effects and a molecular dynamics ͑MD͒ simulation for the slow ͑inertial͒ polarization component, including orientational and translational solvent modes. The inertial polarization is generated by average charge distributions of solvent particles, composed of permanent and induced ͑electronic͒ components. MD simulations are performed in a manner consistent with the choice of solvent and solute charges such that all electrostatic interactions are scaled by the factor 1/ ϱ , where ϱ is the optical dielectric permittivity. This approach yields an ensemble of equilibrium solvent configurations adjusted to the electric field created by a charged or strongly polar solute. The electrostatic solvent response field is found as the solution of the Poisson equation including both solute and explicit solvent charges, with accurate account of electrostatic boundary conditions at the surfaces separating spatial regions with different dielectric permittivities. Both equilibrium and nonequilibrium solvation effects can be studied by means of this model, and their inertial and inertialess contributions are naturally separated. The methodology for computation of charge transfer reorganization energies is developed and applied to a model two-site dipolar system in the SPC water solvent. Three types of charge transfer reactions are considered. The standard linear-response approach yields high accuracy for each particular reaction, but proves to be significantly in error when reorganization energies of different reactions were compared. This result has a purely molecular origin and is absent within a conventional continuum solvent model.

Research paper thumbnail of Continuum level treatment of electronic polarization in the framework of molecular simulations of solvation effects

The Journal of Chemical Physics, 2003

The hybrid molecular-continuum model for polar solvation considered in this paper combines the di... more The hybrid molecular-continuum model for polar solvation considered in this paper combines the dielectric continuum approximation for treating fast electronic (inertialess) polarization effects and a molecular dynamics (MD) simulation for the slow (inertial) polarization component, including orientational and translational solvent modes. The inertial polarization is generated by average charge distributions of solvent particles, composed of permanent and induced (electronic) components.

Research paper thumbnail of Molecular simulations of outersphere reorganization energies for intramolecular electron and hole transfer in polar solvents

Chemical Physics, 2005

Outersphere reorganization energies (λ) for intramolecular electron transfer (ET) and hole transf... more Outersphere reorganization energies (λ) for intramolecular electron transfer (ET) and hole transfer are studied in anion- and cation-radical forms of complex organic substrates (biphenylyl-spacer-naphtyl) in polar solvents simulated by means of the nonpolarizable models of water and 1,2-dichloroethane. The earlier elaborated molecular/continuum approach (the MD/FRCM, J. Chem. Phys., 119 (2003) 8024) is used; this method provides a physically relevant background

Research paper thumbnail of The Mechanism of Catalytic Action of Water in Liquid-Phase Chlorination of Olefins

Russian Journal of Physical Chemistry

Research paper thumbnail of Transition States in Chlorination of Olefins in the Gas and Luquid States

Russian Journal of Physical Chemistry

Research paper thumbnail of Simulations of Enzyme Reaction Mechanisms in Active Sites: Accounting for an Environment Which Is Much More Than a Solvent Perturbation

The goal of this chapter is to outline the special challenges faced in using computational method... more The goal of this chapter is to outline the special challenges faced in using computational methods to define the reaction mechanisms of enzymes. Our approach is to set the problem in the context of the special chemical and structural features which differentiate enzymes from other types of catalysts, and the limitations of experiment in probing these features and defining their contributions to the reaction facilitation. We then briefly discuss the types of computational methods available and how they can be applied to an enzyme problem. Two major features – the roles of active-site protons and water molecules, and enzyme conformational flexibility – are illustrated by results from our simulation work on dihydrofolate reductase. After briefly reviewing published work, we focus on two novel simulation protocols and methods we have recently developed, combining the use of ONIOM ab initio QM/MM calculations and MD simulations with semiempirical QM/MM potentials, to address issues of tr...

Research paper thumbnail of Quantum-chemical evaluation of energy quantities governing electron transfer kinetics: applications to intramolecular processes

Journal of Molecular Structure: THEOCHEM, 1996

Important energy quantities governing electron transfer (ET) kinetics in polar solutions (reorgan... more Important energy quantities governing electron transfer (ET) kinetics in polar solutions (reorganization energy, E,, and net free energy change, AU) are evaluated on the basis of quantum-chemical self-consistent reaction-field (SCRF) models. Either self-consistent field (SCF) or configuration interaction (CI) wavefunctions are used for the solute, which occupies a molecular cavity of realistic shape in a dielectric continuum. A classical SCRF model together with unrestricted Hartree-Fock SCF wavefunctions based on the semiempirical PM3 Hamiltonian is applied to the calculation of the solvent portion of E, (denoted E,) for two different series of radical ion ET systems: radical cations and anions of biphenylyl/naphthyl donor/acceptor (D/A) pairs linked by cyclohexane-based spacer groups and trans-staggered radical anions of the type (CH,),, m = 2-5. Results for E, based on two-configurational CI wavefunctions and an alternative reaction field (the so-called Born-Oppenheimer model, which recognizes the fast timescales of solvent electrons relative to those involved in ET) are also noted. Results for innersphere (i.e. intra-solute) reorganization, Ei, and for AU are also reported. The semiempirical E, results are quite similar to corresponding ab initio results and display the form of the two-sphere Marcus model for E, as a function of D/A separation. Nevertheless, in the one case where direct comparison is possible, the calculated E, result is more than twice the magnitude of the estimate based on experimental ET kinetic data. To reconcile this situation, a generalized SCRF model is proposed, which assigns different effective solute cavity sizes to the optical and inertial components of the solvent response, using ideas based on non-local solvation models.

Research paper thumbnail of Advanced dielectric continuum models of solvation, their connection to microscopic solvent models, and application to electron transfer reactions

Some recent advances in dielectric continuum models for static and dynamic aspects of molecular s... more Some recent advances in dielectric continuum models for static and dynamic aspects of molecular solvation are discussed, and connections with molecular-level solvent models are noted. The traditional Born-Onsager-Kirkwood (BKO) model is compared to a more flexible model (the so-called frequency-resolved cavity model (FRCM)) which assigns distinct inner and outer solute cavities in accommodating, respectively, the inertialess (optical) and inertial solvent response. Sample calculations of solvent reorganization energy (lambdas) are presented for various thermal and optical electron transfer (ET) processes, based on self-consistent reaction field models using molecular orbital (MO) or configuration interaction (CI) solvent wave functions.

Research paper thumbnail of A Theoretical Investigation of Charge Transfer in Several Substituted Acridinium Ions †

The Journal of Physical Chemistry B, 2005

Research paper thumbnail of A two-dimensional Born–Oppenheimer treatment of intramolecular electron transfer reactions

Journal of Electroanalytical Chemistry, 1998

The Born-Oppenheimer (BO) formulation of polar solvation is developed and implemented at the semi... more The Born-Oppenheimer (BO) formulation of polar solvation is developed and implemented at the semiemperical (PM3) configuration interaction (CI) level, yielding estimates of electron transfer (ET) coupling elements (V 0) for intramolecular ET in several families of radical ion systems. In contrast to the traditional treatment based on a single solvent coordinate and a fixed gas-phase coupling element, the present treatment yields a self-consistent characterization of kinetic parameters in a 2-dimensional solvent framework which includes an exchange coordinate. The dependence of V 0 on inertial solvent contributions and on donor/acceptor separation (r DA) is discussed.

Research paper thumbnail of Erratum to “A two-dimensional Born–Oppenheimer treatment of intramolecular electron transfer reactions”

Journal of Electroanalytical Chemistry, 1999

Research paper thumbnail of Calculation of a Complete Enzymic Reaction Surface:  Reaction and Activation Free Energies for Hydride-Ion Transfer in Dihydrofolate Reductase

Journal of Chemical Theory and Computation, 2007

We present a two-dimensional grid method for the calculation of complete free-energy surfaces for... more We present a two-dimensional grid method for the calculation of complete free-energy surfaces for enzyme reactions using a hybrid quantum mechanical/molecular mechanical (QM/MM) potential within the semiempirical (PM3) QM approximation. This implementation is novel in that parallel processing with multiple trajectories (replica-exchange molecular dynamics simulations) is used to sample configuration space. The free energies at each grid point are computed using the thermodynamic integration formalism. From the free-energy surface, the minimum free-energy pathway for the reaction can be defined, and the computed activation and reaction energies can be compared with experimental values. We illustrate its use in a study of the hydride-transfer step in the reduction of dihydrofolate to tetrahydrofolate catalyzed by Escherichia coli dihydrofolate reductase with bound nicotinamide adenine dinucleotide phosphate cofactor. We investigated the effects of changing the QM region, ionization state of the conserved active-site Asp27 residue, and polarization contributions to the activation and reaction free energy. The results clearly show the necessity for including the complete substrate and cofactor molecules in the QM region, and the importance of the overall protein (MM) electrostatic environment in determining the free energy of the transition state (TS) and products relative to reactants. For the model with ionized Asp27, its inclusion in the QM region is essential. We found that the reported [Garcia-Viloca, M.; Truhlar, D. G.; Gao, J. J. Mol. Biol. 2003, 327, 549] stabilization of the TS due to polarization is an artifact that can be attributed to truncation of the electrostatic interactions between the QM and MM atoms. For neutral (protonated) Asp27, our calculated reaction free energy of -4 ± 2 kcal/mol agrees well with the experimental value of -4.4 kcal/mol, although the corresponding activation free-energy estimate is still high at 21 ± 2 kcal/mol compared with the experimental value of 13.4 kcal/mol. The results are less supportive of the ionized Asp27 model, which gives rise to a much higher activation barrier and favors the reverse reaction.

Research paper thumbnail of Theoretical formulation for electron transfer coupled to multiple protons: Application to amidinium–carboxylate interfaces

The Journal of Chemical Physics, 2001

This paper presents a theoretical formulation for electron transfer coupled to the motion of mult... more This paper presents a theoretical formulation for electron transfer coupled to the motion of multiple protons. This theory is applied to proton-coupled electron transfer ͑PCET͒ through amidiniumcarboxylate salt bridges, where the electron transfer reaction is coupled to the motion of two protons at the proton transfer interface. The rate for the donor-͑amidinium-carboxylate͒-acceptor system is found to be substantially slower than the rate for the switched interface donor-͑carboxylate-amidinium͒-acceptor system. This trend is consistent with experimental data for photoinduced PCET in analogous systems. The calculations indicate that this difference in rates is due mainly to the opposite dipole moments at the proton transfer interfaces for the two systems, leading to an endothermic reaction for the donor-͑amidinium-carboxylate͒-acceptor system and an exothermic reaction for the donor-͑carboxylate-amidinium͒-acceptor system. The deuterium kinetic isotope effects are found to be moderate ͑i.e., k H /k D Ͻ3) for both types of systems. These moderate kinetic isotope effects are due to the dominance of vibrationally excited product states, leading to significant overlap between the reactant and product proton vibrational wave functions.

Research paper thumbnail of Semiempirical modeling free energy surfaces for proton transfer in polar aprotic solvents

Chemical Physics, 2000

A method of calculation of a free-energy surface (FES) of the proton transfer (PT) reaction in a ... more A method of calculation of a free-energy surface (FES) of the proton transfer (PT) reaction in a polar aprotic solvent is developed. This is based on the two-state (valence bond) VB description of the solute combined with recent continuum medium models. Its essential new feature is an explicit quantum-chemical treatment of VB wave functions, including internal electronic structure of a

Research paper thumbnail of Studies of the Ground and Excited-State Surfaces of the Retinal Chromophore using CAM-B3LYP

The Journal of Physical Chemistry B, 2010

The isomerization of the 11-cis isomer (PSB11) of the retinal chromophore to its all-trans isomer... more The isomerization of the 11-cis isomer (PSB11) of the retinal chromophore to its all-trans isomer (PSBT) is examined. Optimized structures on both the ground state and the excited state are calculated, and the dependence on torsional angles in the carbon chain is investigated. Time-dependent density functional theory is used to produce excitation energies and the excited-state surface. To avoid problems with the description of excited states that can arise with standard DFT methods, the CAM-B3LYP functional was used. Comparing CAM-B3LYP with B3LYP results indicates that the former is significantly more accurate, as a consequence of which detailed cross sections of the retinal excited-state surface are obtained.

Research paper thumbnail of A correlated ab initio quantum chemical study of the interaction of the Na+, Mg2+, Ca2+ and Zn2+ ions with the tautomers of cytosine in the presence of polar solvent

Physical Chemistry Chemical Physics, 2013

The interactions of the metal ions Na(+), Mg(2+), Ca(2+) and Zn(2+) with cytosine have been inves... more The interactions of the metal ions Na(+), Mg(2+), Ca(2+) and Zn(2+) with cytosine have been investigated with inclusion of solvent effects. Computations have been performed at the density functional and Møller-Plesset levels of theory within the IEFPCM solvent model. It has been found that the inclusion of the solvent environment is essential for giving more biologically realistic results. Earlier gas-phase findings of the stabilisation of rare tautomeric forms by the metal ions have been reproduced, with the presence of the solvent further affecting the relative stabilities.

Research paper thumbnail of Comparing long-range corrected functionals in the cis–trans isomerisation of the retinal chromophore

Research paper thumbnail of A frequency-resolved cavity model (FRCM) for treating equilibrium and non-equilibrium solvation energies

Chemical Physics, 1998

A refined continuum medium model, denoted as the `frequency-resolved cavity model' (FRCM)... more A refined continuum medium model, denoted as the `frequency-resolved cavity model' (FRCM), for describing solvation effects of electrically charged solutes in polar solvents is considered. The principal distinction between the commonly accepted Born–Kirkwood–Onsager model and the FRCM treatment is that in the latter case the medium polarization field induced by the solute charge distribution is subdivided into inertial and inertialess

Research paper thumbnail of Semiempirical modeling free energy surfaces for proton transfer in polar aprotic solvents

Chemical Physics, 2000

A method of calculation of a free-energy surface (FES) of the proton transfer (PT) reaction in a ... more A method of calculation of a free-energy surface (FES) of the proton transfer (PT) reaction in a polar aprotic solvent is developed. This is based on the two-state (valence bond) VB description of the solute combined with recent continuum medium models. Its essential new feature is an explicit quantum-chemical treatment of VB wave functions, including internal electronic structure of a chemical subsystem. The FES includes a pair of intrasolute coordinates, R, the distance between hydrogen-bonded atoms and s, the proton coordinate, together with the collective medium polarization mode. Two hydrogen-bonded systems immersed in a polar solvent (Freon) were considered. The ®rst one is the H 5 O 2 ion, a model system which was used as a benchmark testifying the validity of our semiempirical calculations. The second system is the neutral (CN)(CH 3 )N±HÁ Á ÁN(CH 3 ) 3 complex in Freon. PT for this system has been studied experimentally. The dependencies of basic parameters controlling FES properties (the overlap integral, the coupling matrix element and the reorganization energy E r ) on intrasolute coordinates R and s are evaluated and discussed. In particular, for the neutral complex, E r depends on s linearly, and its dependence on R is weak. The FES, for the neutral system, has two potential wells separated by the energy barrier of $7 kcal/mol. Quantum-mechanical averaging over the proton coordinate, s, reduces the barrier from 7.0 to 1.2 kcal/mol. The value of the nonadiabatic parameter on the averaged FES is equal to 0.13. This implies that the PT in the second system corresponds to an intermediate dynamic regime and that proton tunneling eects are hardly signi®cant for this reaction. Ó

Research paper thumbnail of Molecular simulations of outersphere reorganization energies for intramolecular electron and hole transfer in polar solvents

Chemical Physics, 2005

Outersphere reorganization energies (k) for intramolecular electron transfer (ET) and hole transf... more Outersphere reorganization energies (k) for intramolecular electron transfer (ET) and hole transfer are studied in anion-and cation-radical forms of complex organic substrates (biphenylyl-spacer-naphtyl) in polar solvents simulated by means of the nonpolarizable models of water and 1,2-dichloroethane. The earlier elaborated molecular/continuum approach (the MD/FRCM, J. Chem. Phys., 119 (2003) 8024) is used; this method provides a physically relevant background for separating inertial and inertialess polarization responses within a nonpolarizable MD simulation (the SPC water model). Quantum-chemical calculations of solute charge distributions were performed with semiempirical (AM1) and second ab initio (HF/6-31G(d,p)) approximations. Ab initio charges give lower k-values and are preferable, probably, because of including the effect of the SCRF polarization of the diabatic ET states. Standard Lennard-Jones and charge parameters implemented in MD runs were not specially fitted for reproducing ET effects. The difference in values for a cation and an anion originating from the same parent structure was specially investigated. As shown earlier, this effect, nonlinear in its nature, proved to be extremely large when a model dipolar two-site system was studied. For the present ET structures representing real chemical substrates it has reduced to a plausible value of 6-8 kcal/mol. The study of the temperature dependence of k comprises a first MD simulation of this problem and its slope was found to be in accord with an experimental observation for an anionic species. Calculations of absolute k-values for the hole transfer in 1,2-dichloroethane are the first MD simulations of reorganization energies in experimentally studied reactions. Computed values of k-s are higher than the experimental data. The effect of this magnitude could be eliminated by proper tuning the solvent parameters.

Research paper thumbnail of Continuum level treatment of electronic polarization in the framework of molecular simulations of solvation effects

The Journal of Chemical Physics, 2003

The hybrid molecular-continuum model for polar solvation considered in this paper combines the di... more The hybrid molecular-continuum model for polar solvation considered in this paper combines the dielectric continuum approximation for treating fast electronic ͑inertialess͒ polarization effects and a molecular dynamics ͑MD͒ simulation for the slow ͑inertial͒ polarization component, including orientational and translational solvent modes. The inertial polarization is generated by average charge distributions of solvent particles, composed of permanent and induced ͑electronic͒ components. MD simulations are performed in a manner consistent with the choice of solvent and solute charges such that all electrostatic interactions are scaled by the factor 1/ ϱ , where ϱ is the optical dielectric permittivity. This approach yields an ensemble of equilibrium solvent configurations adjusted to the electric field created by a charged or strongly polar solute. The electrostatic solvent response field is found as the solution of the Poisson equation including both solute and explicit solvent charges, with accurate account of electrostatic boundary conditions at the surfaces separating spatial regions with different dielectric permittivities. Both equilibrium and nonequilibrium solvation effects can be studied by means of this model, and their inertial and inertialess contributions are naturally separated. The methodology for computation of charge transfer reorganization energies is developed and applied to a model two-site dipolar system in the SPC water solvent. Three types of charge transfer reactions are considered. The standard linear-response approach yields high accuracy for each particular reaction, but proves to be significantly in error when reorganization energies of different reactions were compared. This result has a purely molecular origin and is absent within a conventional continuum solvent model.