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Title: Direct simulation of proton-coupled electron transfer across multiple regimes

Abstract

The coupled transfer of electrons and protons is a central feature of biological and molecular catalysis, yet fundamental aspects of these reactions remain poorly understood. In this study, we extend the ring polymer molecular dynamics (RPMD) method to enable direct simulation of proton-coupled electron transfer (PCET) reactions across a wide range of physically relevant regimes. In a system-bath model for symmetric, co-linear PCET in the condensed phase, RPMD trajectories reveal distinct kinetic pathways associated with sequential and concerted PCET reaction mechanisms, and it is demonstrated that concerted PCET proceeds by a solvent-gating mechanism in which the reorganization energy is mitigated by charge cancellation among the transferring particles. We further employ RPMD to study the kinetics and mechanistic features of concerted PCET reactions across multiple coupling regimes, including the fully non-adiabatic (both electronically and vibrationally non-adiabatic), partially adiabatic (electronically adiabatic, but vibrationally non-adiabatic), and fully adiabatic (both electronically and vibrationally adiabatic) limits. Comparison of RPMD with the results of PCET rate theories demonstrates the applicability of the direct simulation method over a broad range of conditions; it is particularly notable that RPMD accurately predicts the crossover in the thermal reaction rates between different coupling regimes while avoiding a priori assumptions aboutmore » the PCET reaction mechanism. Finally, by utilizing the connections between RPMD rate theory and semiclassical instanton theory, we show that analysis of ring-polymer configurations in the RPMD transition path ensemble enables the a posteriori determination of the coupling regime for the PCET reaction. This analysis reveals an intriguing and distinct “transient-proton-bridge” mechanism for concerted PCET that emerges in the transition between the proton-mediated electron superexchange mechanism for fully non-adiabatic PCET and the hydrogen atom transfer mechanism for partially adiabatic PCET. Taken together, these results provide a unifying picture of the mechanisms and physical driving forces that govern PCET across a wide range of physical regimes, and they raise the possibility for PCET mechanisms that have not been previously reported.« less

Authors:
 [1];  [1]
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  1. California Inst. of Technology (CalTech), Pasadena, CA (United States)
Publication Date:
Research Org.:
California Institute of Technology (CalTech), Pasadena, CA (United States); Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1565003
Grant/Contract Number:  
AC02-05CH11231; AC05-00OR22725; SC0006598
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 138; Journal Issue: 13; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Chemistry; Physics

Citation Formats

Kretchmer, Joshua S., and Miller, Thomas F. Direct simulation of proton-coupled electron transfer across multiple regimes. United States: N. p., 2013. Web. doi:10.1063/1.4797462.
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Kretchmer, Joshua S., & Miller, Thomas F. Direct simulation of proton-coupled electron transfer across multiple regimes. United States. https://doi.org/10.1063/1.4797462
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Kretchmer, Joshua S., and Miller, Thomas F. Tue . "Direct simulation of proton-coupled electron transfer across multiple regimes". United States. https://doi.org/10.1063/1.4797462. https://www.osti.gov/servlets/purl/1565003.
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@article{osti_1565003,
title = {Direct simulation of proton-coupled electron transfer across multiple regimes},
author = {Kretchmer, Joshua S. and Miller, Thomas F.},
abstractNote = {The coupled transfer of electrons and protons is a central feature of biological and molecular catalysis, yet fundamental aspects of these reactions remain poorly understood. In this study, we extend the ring polymer molecular dynamics (RPMD) method to enable direct simulation of proton-coupled electron transfer (PCET) reactions across a wide range of physically relevant regimes. In a system-bath model for symmetric, co-linear PCET in the condensed phase, RPMD trajectories reveal distinct kinetic pathways associated with sequential and concerted PCET reaction mechanisms, and it is demonstrated that concerted PCET proceeds by a solvent-gating mechanism in which the reorganization energy is mitigated by charge cancellation among the transferring particles. We further employ RPMD to study the kinetics and mechanistic features of concerted PCET reactions across multiple coupling regimes, including the fully non-adiabatic (both electronically and vibrationally non-adiabatic), partially adiabatic (electronically adiabatic, but vibrationally non-adiabatic), and fully adiabatic (both electronically and vibrationally adiabatic) limits. Comparison of RPMD with the results of PCET rate theories demonstrates the applicability of the direct simulation method over a broad range of conditions; it is particularly notable that RPMD accurately predicts the crossover in the thermal reaction rates between different coupling regimes while avoiding a priori assumptions about the PCET reaction mechanism. Finally, by utilizing the connections between RPMD rate theory and semiclassical instanton theory, we show that analysis of ring-polymer configurations in the RPMD transition path ensemble enables the a posteriori determination of the coupling regime for the PCET reaction. This analysis reveals an intriguing and distinct “transient-proton-bridge” mechanism for concerted PCET that emerges in the transition between the proton-mediated electron superexchange mechanism for fully non-adiabatic PCET and the hydrogen atom transfer mechanism for partially adiabatic PCET. Taken together, these results provide a unifying picture of the mechanisms and physical driving forces that govern PCET across a wide range of physical regimes, and they raise the possibility for PCET mechanisms that have not been previously reported.},
doi = {10.1063/1.4797462},
journal = {Journal of Chemical Physics},
number = 13,
volume = 138,
place = {United States},
year = {Tue Apr 02 00:00:00 EDT 2013},
month = {Tue Apr 02 00:00:00 EDT 2013}
}
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https://doi.org/10.1063/1.4797462
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Figures / Tables:

FIG. 1 FIG. 1: (a) Schematic illustration of a co-linear PCET reaction, where De/Dp and Ae/Ap are the respective donor and acceptor for the electron/proton. (b) Schematic illustration of sequential and concerted PCET reaction mechanisms, indicating the rate constants for the individual charge transfer processes. The sequential mechanism proceeds along the horizontalmore » and vertical edges of the schematic, whereas the concerted mechanism proceeds along the diagonal.« less
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    • Menzeleev, Artur R.; Bell, Franziska; Miller, Thomas F.
    • The Journal of Chemical Physics, Vol. 140, Issue 6
    • DOI: 10.1063/1.4863919

    A mapping variable ring polymer molecular dynamics study of condensed phase proton-coupled electron transfer.
    text, January 2017

    • Pierre, Sadrach; Duke, Jessica R.; Hele, Tim
    • Apollo - University of Cambridge Repository
    • DOI: 10.17863/cam.18757

    Non-equilibrium dynamics from RPMD and CMD
    text, January 2016

    • Welsch, R.; Song, K.; Shi, Q.
    • Apollo - University of Cambridge Repository
    • DOI: 10.17863/cam.7492

    Coherent state mapping ring polymer molecular dynamics for non-adiabatic quantum propagations
    journal, December 2017

    • Chowdhury, Sutirtha N.; Huo, Pengfei
    • The Journal of Chemical Physics, Vol. 147, Issue 21
    • DOI: 10.1063/1.4995616

    Communication: Full dimensional quantum rate coefficients and kinetic isotope effects from ring polymer molecular dynamics for a seven-atom reaction OH + CH 4 → CH 3 + H 2 O
    journal, June 2013

    • Allen, Joshua W.; Green, William H.; Li, Yongle
    • The Journal of Chemical Physics, Vol. 138, Issue 22
    • DOI: 10.1063/1.4811329

    Quantum theory of multiscale coarse-graining
    journal, March 2018

    • Han, Yining; Jin, Jaehyeok; Wagner, Jacob W.
    • The Journal of Chemical Physics, Vol. 148, Issue 10
    • DOI: 10.1063/1.5010270

    Boltzmann-conserving classical dynamics in quantum time-correlation functions: “Matsubara dynamics”
    journal, April 2015

    • Hele, Timothy J. H.; Willatt, Michael J.; Muolo, Andrea
    • The Journal of Chemical Physics, Vol. 142, Issue 13
    • DOI: 10.1063/1.4916311

    Path-integral dynamics of water using curvilinear centroids
    journal, August 2019

    • Trenins, George; Willatt, Michael J.; Althorpe, Stuart C.
    • The Journal of Chemical Physics, Vol. 151, Issue 5
    • DOI: 10.1063/1.5100587

    Ring-polymer instanton theory of electron transfer in the nonadiabatic limit
    journal, October 2015

    • Richardson, Jeremy O.
    • The Journal of Chemical Physics, Vol. 143, Issue 13
    • DOI: 10.1063/1.4932362

    Biochemistry and Theory of Proton-Coupled Electron Transfer
    journal, January 2014

    • Migliore, Agostino; Polizzi, Nicholas F.; Therien, Michael J.
    • Chemical Reviews, Vol. 114, Issue 7
    • DOI: 10.1021/cr4006654

    On the calculation of quantum mechanical electron transfer rates
    journal, September 2019

    • Lawrence, Joseph E.; Fletcher, Theo; Lindoy, Lachlan P.
    • The Journal of Chemical Physics, Vol. 151, Issue 11
    • DOI: 10.1063/1.5116800

    Path-integral isomorphic Hamiltonian for including nuclear quantum effects in non-adiabatic dynamics
    journal, March 2018

    • Tao, Xuecheng; Shushkov, Philip; Miller, Thomas F.
    • The Journal of Chemical Physics, Vol. 148, Issue 10
    • DOI: 10.1063/1.5005544

    Mapping variable ring polymer molecular dynamics: A path-integral based method for nonadiabatic processes
    journal, September 2013

    • Ananth, Nandini
    • The Journal of Chemical Physics, Vol. 139, Issue 12
    • DOI: 10.1063/1.4821590

    Mean-field Matsubara dynamics: Analysis of path-integral curvature effects in rovibrational spectra
    journal, July 2018

    • Trenins, George; Althorpe, Stuart C.
    • The Journal of Chemical Physics, Vol. 149, Issue 1
    • DOI: 10.1063/1.5038616

    Isotopic Separation of Helium through Nanoporous Graphene Membranes: A Ring Polymer Molecular Dynamics Study
    text, January 2021

    Path-integral dynamics of water using curvilinear centroids
    journalarticle, January 2019

    Kinetically Constrained Ring-Polymer Molecular Dynamics for Non-adiabatic Chemical Reactions
    text, January 2014

    Proton-Coupled Electron Transfer: Moving Together and Charging Forward
    journal, July 2015

    • Hammes-Schiffer, Sharon
    • Journal of the American Chemical Society, Vol. 137, Issue 28
    • DOI: 10.1021/jacs.5b04087

    Nonadiabatic quantum transition-state theory in the golden-rule limit. II. Overcoming the pitfalls of the saddle-point and semiclassical approximations
    journal, December 2019

    • Fang, Wei; Thapa, Manish J.; Richardson, Jeremy O.
    • The Journal of Chemical Physics, Vol. 151, Issue 21
    • DOI: 10.1063/1.5131092

    Coupled-perturbed DFTB-QM/MM metadynamics: Application to proton-coupled electron transfer
    journal, August 2018

    • Gillet, Natacha; Elstner, Marcus; Kubař, Tomáš
    • The Journal of Chemical Physics, Vol. 149, Issue 7
    • DOI: 10.1063/1.5027100

    Mean-field Matsubara dynamics: analysis of path-integral curvature effects in rovibrational spectra
    text, January 2018

    • Althorpe, Stuart; Trenins, Georgijs
    • Apollo - University of Cambridge Repository
    • DOI: 10.17863/cam.30834

    Nonadiabatic quantum transition-state theory in the golden-rule limit. I. Theory and application to model systems
    journal, March 2019

    • Thapa, Manish J.; Fang, Wei; Richardson, Jeremy O.
    • The Journal of Chemical Physics, Vol. 150, Issue 10
    • DOI: 10.1063/1.5081108

    State dependent ring polymer molecular dynamics for investigating excited nonadiabatic dynamics
    journal, June 2019

    • Chowdhury, Sutirtha N.; Huo, Pengfei
    • The Journal of Chemical Physics, Vol. 150, Issue 24
    • DOI: 10.1063/1.5096276
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