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Gregory A. Voth - One of the best experts on this subject based on the ideXlab platform.

  • Efficient Multistate Reactive Molecular Dynamics Approach Based on Short-Range Effective Potentials.
    Journal of Chemical Theory and Computation, 2010
    Co-Authors: Hanning Chen, Pu Liu, Gregory A. Voth
    Abstract:

    NonBonded interactions between molecules usually include the van der Waals force and computationally expensive long-range electrostatic interactions. This article develops a more efficient approach: the effective-interaction multistate Empirical-Valence-Bond (EI-MS-EVB) model. The EI-MS-EVB method relies on a mapping of all interactions onto a short-range and thus, computationally efficient effective potential. The effective potential is tabulated by matching its force to known trajectories obtained from the full-potential Empirical multistate Empirical-Valence-Bond (MS-EVB) model. The effective pairwise interaction depends on and is uniquely determined by the atomic configuration of the system, varying only with respect to the hydrogen-Bonding topology. By comparing the EI-MS-EVB and full MS-EVB calculations of several equilibrium and dynamic properties important to hydrated excess proton solvation and transport, we show that the EI-MS-EVB model produces very accurate results for the specific system in which the tabulated potentials were generated. The EI-MS-EVB potential also transfers reasonably well to similar systems with different temperatures and box sizes. The EI-MS-EVB method also reduces the computational cost of the nonBonded interactions by about 1 order of magnitude in comparison with the full algorithm.

  • Mechanism of fast proton transport along one-dimensional water chains confined in carbon nanotubes.
    Journal of the American Chemical Society, 2010
    Co-Authors: Zhen Cao, Tianying Yan, Yuxing Peng, Gregory A. Voth
    Abstract:

    A reactive molecular dynamics simulation employing the multistate Empirical Valence Bond (MS-EVB) methodology is reported for the hydration structure of an excess proton in a (6,6) carbon nanotube as well as for the mechanism of proton transport (PT) within the nanoconfined environment. The proton is found to be hydrated in a distorted Zundel cation (H5O2+) form within the one-dimensional, confined water chain. Proton transfer events occur via a “Zundel−Zundel” mechanism through a transient H7O3+ intermediate that differs significantly from the “Eigen−Zundel−Eigen” mechanism found in bulk water.

  • Distributed Gaussian Valence Bond Surface Derived from Ab Initio Calculations
    Journal of Chemical Theory and Computation, 2009
    Co-Authors: Jason L. Sonnenberg, Gregory A. Voth, Kim F. Wong, H. Bernhard Schlegel
    Abstract:

    The experimental and computational results for the tautomerization reaction of 2-pyridone are reviewed. G3, G4, CBS-APNO, and W1 model chemistries are used to generate state-of-the-art reaction energetics for the tautomerization reaction with and without catalytic water molecules in both the gas and aqueous phases. Reactive, electronic potential energy surface surfaces for use in molecular dynamics simulations were generated for these reactions following a recently improved Empirical Valence Bond formulation. The form of molecular mechanics potentials needed for a satisfactory fit is also discussed.

  • An Improved Multistate Empirical Valence Bond Model for Aqueous Proton Solvation and Transport
    The Journal of Physical Chemistry B, 2008
    Co-Authors: Hanning Chen, Feng Wang, Francesco Paesani, Gregory A. Voth
    Abstract:

    A new multistate Empirical Valence Bond model (MS-EVB3) is developed for proton solvation and transport in aqueous solutions. The new model and its quantum version (qMS-EVB3) are based on the MS-EVB2 model [Day et al., J. Chem. Phys. 2002, 117, 5839] and recently developed flexible water models-the SPC/Fw model [Wu et al. J. Chem. Phys. 2006, 124, 24503] and the qSPC/Fw model [Paesani et al. J. Chem. Phys. 2006, 125, 184507]-for classical and quantum simulations, respectively. Using ab initio data as benchmarks, the binding energies and optimized geometries calculated with the new model for protonated water clusters, as well as the potential energy surface for proton shuttling between water molecules in a cluster environment, are improved in comparison to the MS-EVB2 model. For aqueous solutions, classical and quantum molecular dynamics simulations with the MS-EVB3 model yield a more accurate description of the solvation structure and diffusive dynamics of the excess proton. New insight is also provided into the proton solvation and hopping dynamics in water, as well as the "amphiphilic" nature of the hydrated proton that has been predicted to give rise to its enhanced concentration at aqueous interfaces and an effectively lower pH of the air-water interface [Petersen et al. J. Phys. Chem. B 2004, 108, 14804].

  • Effect of membrane environment on proton permeation through gramicidin A channels.
    The Journal of Physical Chemistry B, 2007
    Co-Authors: Zhen Qin, Harald L. Tepper, Gregory A. Voth
    Abstract:

    Multistate Empirical Valence Bond simulations were employed to study proton transport through gramicidin A channels embedded in two different lipid bilayers, glycerol 1-monooleate (GMO) and diphytanolphosphatidylcholine (DiPhPC). Free energy barriers to proton permeation were derived using a new internal reaction coordinate describing the proton permeation process. The large quantitative and qualitative differences between the two systems are discussed in terms of local bilayer structures, ordering of interfacial water, and channel flexibility in the two environments.

Eckhard Spohr - One of the best experts on this subject based on the ideXlab platform.

  • Merging Empirical Valence Bond Theory with Quantum Chemistry to Model Proton Transfer Processes in Water
    Electrocatalysis, 2017
    Co-Authors: Sebastian Dohm, Eckhard Spohr, Martin Korth
    Abstract:

    Proton transfer processes in water are of fundamental importance for, among others, electrochemical proton discharge. Empirical Valence Bond (EVB) approaches were shown in the past to be a versatile tool for modeling complex phenomena such as proton discharge at metal electrodes. By replacing Empirical fitting procedures with on-the-fly quantum chemistry (QC) calculations, we arrive at a transferable and systematically tunable description of proton transfer in water with EVB. Graphical Abstract ᅟ

  • Water Structure and Mechanisms of Proton Discharge on Platinum Electrodes: Empirical Valence Bond Molecular Dynamics Trajectory Studies
    Electrocatalysis, 2017
    Co-Authors: Johannes Wiebe, Eckhard Spohr
    Abstract:

    We present a comparative analysis of molecular dynamics trajectory studies of the influence of surface charge, ion strength, and ion adsorption on the interfacial water structure and the possible pathways of proton transport and discharge on negatively charged platinum(111) electrodes. The model used is a reactive force field based on a nine-state Empirical Valence Bond model. It incorporates both proton transfer between water molecules and simultaneous electron and proton transfer to the metal (discharge). The interfacial water polarization is the result of the competition between the electrical field influence of the smooth surface charge and the point-like local charges of adsorbed positive or negative ions, which leads to variations of the prevalent proton discharge pathways depending on system composition. Graphical Abstract In trajectory calculations of proton adsorption and discharge from aqueous solutions onto charged platinum electrodes, the presence of electrolytes in the adsorbate layer influences proton discharge mechanisms via changes in water orientation and via exclusion of discharge sites through repulsive cation-proton interactions.

  • Water Structure and Mechanisms of Proton Discharge on Platinum Electrodes: Empirical Valence Bond Molecular Dynamics Trajectory Studies
    Electrocatalysis, 2017
    Co-Authors: Johannes Wiebe, Eckhard Spohr
    Abstract:

    We present a comparative analysis of molecular dynamics trajectory studies of the influence of surface charge, ion strength, and ion adsorption on the interfacial water structure and the possible pathways of proton transport and discharge on negatively charged platinum(111) electrodes. The model used is a reactive force field based on a nine-state Empirical Valence Bond model. It incorporates both proton transfer between water molecules and simultaneous electron and proton transfer to the metal (discharge). The interfacial water polarization is the result of the competition between the electrical field influence of the smooth surface charge and the point-like local charges of adsorbed positive or negative ions, which leads to variations of the prevalent proton discharge pathways depending on system composition.

  • transport in proton conductors for fuel cell applications simulations elementary reactions and phenomenology
    Chemical Reviews, 2004
    Co-Authors: K D Kreuer, Eckhard Spohr, Stephen J Paddison, Michael Schuster
    Abstract:

    1. Introduction 46372. Theoretical Methodologies and Simulation Tools 46402.1. Ab Initio Quantum Chemistry 46412.2. Molecular Dynamics 46422.2.1. Classical Molecular Dynamics and MonteCarlo Simulations46432.2.2. Empirical Valence Bond Models 46442.2.3. Ab Initio Molecular Dynamics (AIMD) 46452.3. Poisson−Boltzmann Theory 46452.4. Nonequilibrium Statistical Mechanical IonTransport Modeling46462.5. Dielectric Saturation 46473. Transport Mechanisms 46483.1. Proton Conduction Mechanisms 46483.1.1. Homogeneous Media 46483.1.2. Heterogeneous Systems (ConfinementEffects)46553.2. Mechanisms of Parasitic Transport 46613.2.1. Solvated Acidic Polymers 46613.2.2. Oxides 46654. Phenomenology of Transport inProton-Conducting Materials for Fuel-CellApplications46664.1. Hydrated Acidic Polymers 46664.2. PBI−H

Collin D Wick - One of the best experts on this subject based on the ideXlab platform.

  • Comparing hydroxide and hydronium at the instantaneous air-water interface using polarizable multi-state Empirical Valence Bond models
    Computational and Theoretical Chemistry, 2017
    Co-Authors: Collin D Wick
    Abstract:

    Abstract A new molecular model for the hydroxide anion was developed and its propensity for the air-water interface was compared with that of the hydronium ion. The multi-state Empirical Valence Bond approach with polarizable potentials was used for both of these, allowing them to share their charge with adjacent water molecules. The hydroxide anion appeared to have a lower propensity for the air-water interface than that of hydronium when comparing its potential of mean force with respect to the Gibbs dividing surface. However, upon further inspection it was found that the hydroxide and hydronium ions had similar free energies at the instantaneous air-water interface. The reason for this discrepancy is that the hydroxide anion has a greater free energy when it was partially solvated. Or in other words, when the hydroxide anion is one molecular layer from the instantaneous air-water interface, but potentially still near the Gibbs dividing surface, it is less stable than the hydronium in a similar configuration. This shows that using the instantaneous interface can provide additional important insights.

  • hydronium behavior at the air water interface with a polarizable multistate Empirical Valence Bond model
    Journal of Physical Chemistry C, 2012
    Co-Authors: Collin D Wick
    Abstract:

    Molecular dynamics simulations were carried out to understand the propensity of the hydronium ion for the air–water interface with a polarizable multistate Empirical Valence Bond (MS-EVB) model. Reasonable agreement with experiment for radial distribution functions and very good agreement for hydronium diffusion were found for the model. The polarizable MS-EVB model had no free energy minimum at the air–water interface. However, when polarizability on the hydronium ion alone was removed, a free energy of around −1.5 kcal/mol was calculated at the air–water interface. This discrepancy was found to be due to the behavior of water molecules in the first solvation shell of a hydronium ion. These water molecules contained a moderate amount of hydronium character, resulting in the delocalization of the hydronium ion. For the system with polarizable hydronium ions, this delocalization was the same at the interface as in the bulk, but for the system without polarizable hydronium ions, the delocalization increased...

  • Hydronium Behavior at the Air–Water Interface with a Polarizable Multistate Empirical Valence Bond Model
    Journal of Physical Chemistry C, 2012
    Co-Authors: Collin D Wick
    Abstract:

    Molecular dynamics simulations were carried out to understand the propensity of the hydronium ion for the air–water interface with a polarizable multistate Empirical Valence Bond (MS-EVB) model. Reasonable agreement with experiment for radial distribution functions and very good agreement for hydronium diffusion were found for the model. The polarizable MS-EVB model had no free energy minimum at the air–water interface. However, when polarizability on the hydronium ion alone was removed, a free energy of around −1.5 kcal/mol was calculated at the air–water interface. This discrepancy was found to be due to the behavior of water molecules in the first solvation shell of a hydronium ion. These water molecules contained a moderate amount of hydronium character, resulting in the delocalization of the hydronium ion. For the system with polarizable hydronium ions, this delocalization was the same at the interface as in the bulk, but for the system without polarizable hydronium ions, the delocalization increased...

  • Investigating hydroxide anion interfacial activity by classical and multistate Empirical Valence Bond molecular dynamics simulations.
    The Journal of Physical Chemistry A, 2009
    Co-Authors: Collin D Wick, Liem X. Dang
    Abstract:

    Molecular dynamics simulations were carried out to understand the propensity of the hydroxide anion for the air−water interface. Two classes of molecular models were used, a classical polarizable model and a polarizable multistate Empirical Valence Bond (MS-EVB) potential. The latter model was parametrized to reproduce the structures of small hydroxide−water clusters based on proton reaction coordinates. Furthermore, nuclear quantum effects were introduced into the MS-EVB model implicitly by refitting its potential energy function to account for them. The final MS-EVB model showed reasonable agreement with experiment and ab initio molecular dynamics simulations for dynamical and structural properties. The free-energy profiles for both the classical and MS-EVB models were mapped out across the air−water interface, and the classical model gave a higher free energy at the interface with respect to bulk. However, the MS-EVB model gave little free-energy difference between when the hydroxide anion was in the b...

Ilan Benjamin - One of the best experts on this subject based on the ideXlab platform.

  • a molecular dynamics Empirical Valence Bond study of an sn2 reaction at the water chloroform interface
    Journal of Physical Chemistry C, 2010
    Co-Authors: Katherine V. Nelson, Ilan Benjamin
    Abstract:

    Using a recently developed Empirical Valence Bond (EVB) model for the nucleophilic substitution reaction (SN2) in solution, we study the benchmark Cl− + CH3Cl reaction at the water/chloroform liquid/liquid interface. The reaction free energy profile is determined as a function of the reagents’ location relative to the interface. We find that the activation free energy is very sensitive to the reagents’ location and to the orientation of the nucleophilic attack. The barrier height at the interface is equal or slightly larger than the barrier in bulk water and approaches the value in bulk chloroform only when the solute is a few nanometers deep into the organic phase. We show that this is due to the ability of the nucleophile to keep part of its hydration shell. This suggests that for the catalytic effect of the nonpolar solvent to be appreciable, the nucleophile must be transferred away from the interface. The dynamical correction to the rate, the variation in the system’s electronic structure and other sy...

  • A Molecular Dynamics−Empirical Valence Bond Study of an SN2 Reaction at the Water/Chloroform Interface
    The Journal of Physical Chemistry C, 2009
    Co-Authors: Katherine V. Nelson, Ilan Benjamin
    Abstract:

    Using a recently developed Empirical Valence Bond (EVB) model for the nucleophilic substitution reaction (SN2) in solution, we study the benchmark Cl− + CH3Cl reaction at the water/chloroform liquid/liquid interface. The reaction free energy profile is determined as a function of the reagents’ location relative to the interface. We find that the activation free energy is very sensitive to the reagents’ location and to the orientation of the nucleophilic attack. The barrier height at the interface is equal or slightly larger than the barrier in bulk water and approaches the value in bulk chloroform only when the solute is a few nanometers deep into the organic phase. We show that this is due to the ability of the nucleophile to keep part of its hydration shell. This suggests that for the catalytic effect of the nonpolar solvent to be appreciable, the nucleophile must be transferred away from the interface. The dynamical correction to the rate, the variation in the system’s electronic structure and other sy...

  • Empirical Valence Bond model of an SN2 reaction in polar and nonpolar solvents
    The Journal of Chemical Physics, 2008
    Co-Authors: Ilan Benjamin
    Abstract:

    A new model for the substitution nucleophilic reaction (SN2) in solution is described using the Empirical Valence Bond (EVB) method. The model includes a generalization to three dimensions of a collinear gas phase EVB model developed by Mathis et al. [J. Mol. Liq. 61, 81 (1994)] and a parametrization of solute-solvent interactions of four different solvents (water, ethanol, chloroform, and carbon tetrachloride). The model is used to compute (in these four solvents) reaction free energy profiles, reaction and solvent dynamics, a two-dimensional reaction/solvent free energy map, as well as a number of other properties that in the past have mostly been estimated.

Shina Caroline Lynn Kamerlin - One of the best experts on this subject based on the ideXlab platform.

  • Computational physical organic chemistry using the Empirical Valence Bond approach
    Advances in Physical Organic Chemistry, 2019
    Co-Authors: Yashraj Kulkarni, Shina Caroline Lynn Kamerlin
    Abstract:

    Abstract There has been growing interest in applying the Empirical Valence Bond approach to a range of (bio)chemical problems, primarily to study enzymatic and non-enzymatic catalysis, but also to studying other processes such as excited state chemistry and reaction dynamics. Despite its apparent theoretical simplicity, this approach is a powerful computational tool that can be used to reproduce and rationalize a wide range of experimental observables, such as linear free energy relationships, kinetic isotope effects, and temperature effects on reaction rates. We provide here both a theoretical background for this approach, as well as highlighting several of its broad applications in computational physical organic chemistry.

  • Empirical Valence Bond Simulations Suggest a Direct Hydride Transfer Mechanism for Human Diamine Oxidase
    ACS Omega, 2018
    Co-Authors: Aleksandra Maršavelski, Paul Bauer, Dušan Petrović, Robert Vianello, Shina Caroline Lynn Kamerlin
    Abstract:

    Diamine oxidase (DAO) is an enzyme involved in the regulation of cell proliferation and the immune response. This enzyme performs oxidative deamination in the catabolism of biogenic amines, including, among others, histamine, putrescine, spermidine, and spermine. The mechanistic details underlying the reductive half-reaction of the DAO-catalyzed oxidative deamination which leads to the reduced enzyme cofactor and the aldehyde product are, however, still under debate. The catalytic mechanism was proposed to involve a prototropic shift from the substrate–Schiff base to the product–Schiff base, which includes the rate-limiting cleavage of the Cα–H Bond by the conserved catalytic aspartate. Our detailed mechanistic study, performed using a combined quantum chemical cluster approach with Empirical Valence Bond simulations, suggests that the rate-limiting cleavage of the Cα–H Bond involves direct hydride transfer to the topaquinone cofactor—a mechanism that does not involve the formation of a Schiff base. Addit...

  • Q6 : A comprehensive toolkit for Empirical Valence Bond and related free energy calculations
    SoftwareX, 2018
    Co-Authors: Paul Bauer, Alexandre Barrozo, Miha Purg, Beat Anton Amrein, Mauricio Esguerra, Philippe B. Wilson, Dan Thomas Major, Johan Åqvist, Shina Caroline Lynn Kamerlin
    Abstract:

    Q Version 6, a comprehensive toolkit for Empirical Valence Bond and related free energy calculations.

  • Empirical Valence Bond Simulations of Organophosphate Hydrolysis: Theory and Practice.
    Methods in Enzymology, 2018
    Co-Authors: Miha Purg, Shina Caroline Lynn Kamerlin
    Abstract:

    Recent years have seen an explosion of interest in understanding the mechanisms of phosphate ester hydrolysis in biological systems, using a range of computational approaches, each with different advantages and limitations. In this contribution, we present the Empirical Valence Bond (EVB) approach as a powerful tool for modeling biochemical reactivity, using the example of organophosphate hydrolysis by diisopropyl fluorophosphatase as our model reaction. We walk the reader through the protocol for setting up and performing EVB simulations, as well as key technical considerations that need to be taken into account. Finally, we provide examples of the applications of the EVB approach to understanding different experimental observables.

  • Empirical Valence Bond Simulations Suggest a Direct Hydride Transfer Mechanism for Human Diamine Oxidase
    2018
    Co-Authors: Aleksandra Maršavelski, Paul Bauer, Robert Vianello, Dušan Petrović, Shina Caroline Lynn Kamerlin
    Abstract:

    Diamine oxidase (DAO) is an enzyme involved in the regulation of cell proliferation and the immune response. This enzyme performs oxidative deamination in the catabolism of biogenic amines, including, among others, histamine, putrescine, spermidine, and spermine. The mechanistic details underlying the reductive half-reaction of the DAO-catalyzed oxidative deamination which leads to the reduced enzyme cofactor and the aldehyde product are, however, still under debate. The catalytic mechanism was proposed to involve a prototropic shift from the substrate–Schiff base to the product–Schiff base, which includes the rate-limiting cleavage of the Cα–H Bond by the conserved catalytic aspartate. Our detailed mechanistic study, performed using a combined quantum chemical cluster approach with Empirical Valence Bond simulations, suggests that the rate-limiting cleavage of the Cα–H Bond involves direct hydride transfer to the topaquinone cofactora mechanism that does not involve the formation of a Schiff base. Additional investigation of the D373E and D373N variants supported the hypothesis that the conserved catalytic aspartate is indeed essential for the reaction; however, it does not appear to serve as the catalytic base, as previously suggested. Rather, the electrostatic contributions of the most significant residues (including D373), together with the proximity of the Cu2+ cation to the reaction site, lower the activation barrier to drive the chemical reaction