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Direct Calculation of Electron Transfer Rates with the Binless Dynamic Histogram Analysis Method

[Image: see text] Umbrella sampling molecular dynamics simulations are widely used to enhance sampling along the reaction coordinates of chemical reactions. The effect of the artificial bias can be removed using methods such as the dynamic weighted histogram analysis method (DHAM), which in addition...

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Autores principales: Koczor-Benda, Zsuzsanna, Mateeva, Teodora, Rosta, Edina
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2023
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10641885/
https://www.ncbi.nlm.nih.gov/pubmed/37903301
http://dx.doi.org/10.1021/acs.jpclett.3c02624
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author Koczor-Benda, Zsuzsanna
Mateeva, Teodora
Rosta, Edina
author_facet Koczor-Benda, Zsuzsanna
Mateeva, Teodora
Rosta, Edina
author_sort Koczor-Benda, Zsuzsanna
collection PubMed
description [Image: see text] Umbrella sampling molecular dynamics simulations are widely used to enhance sampling along the reaction coordinates of chemical reactions. The effect of the artificial bias can be removed using methods such as the dynamic weighted histogram analysis method (DHAM), which in addition to the global free energy profile also provides kinetic information about barrier-crossing rates directly from the Markov matrix. Here we present a binless formulation of DHAM that extends DHAM to high-dimensional and Hamiltonian-based biasing to allow the study of electron transfer (ET) processes, for which enhanced sampling is usually not possible based on simple geometric grounds. We show the capabilities of binless DHAM on examples such as aqueous ferrous-ferric ET and intramolecular ET in the radical anion of benzoquinone–tetrathiafulvalene–benzoquinone (Q-TTF-Q)(−). From classical Hamiltonian-based umbrella sampling simulations and electronic coupling values from quantum chemistry calculations, binless DHAM provides ET rates for adiabatic and nonadiabatic ET reactions alike in excellent agreement with experimental results.
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spelling pubmed-106418852023-11-15 Direct Calculation of Electron Transfer Rates with the Binless Dynamic Histogram Analysis Method Koczor-Benda, Zsuzsanna Mateeva, Teodora Rosta, Edina J Phys Chem Lett [Image: see text] Umbrella sampling molecular dynamics simulations are widely used to enhance sampling along the reaction coordinates of chemical reactions. The effect of the artificial bias can be removed using methods such as the dynamic weighted histogram analysis method (DHAM), which in addition to the global free energy profile also provides kinetic information about barrier-crossing rates directly from the Markov matrix. Here we present a binless formulation of DHAM that extends DHAM to high-dimensional and Hamiltonian-based biasing to allow the study of electron transfer (ET) processes, for which enhanced sampling is usually not possible based on simple geometric grounds. We show the capabilities of binless DHAM on examples such as aqueous ferrous-ferric ET and intramolecular ET in the radical anion of benzoquinone–tetrathiafulvalene–benzoquinone (Q-TTF-Q)(−). From classical Hamiltonian-based umbrella sampling simulations and electronic coupling values from quantum chemistry calculations, binless DHAM provides ET rates for adiabatic and nonadiabatic ET reactions alike in excellent agreement with experimental results. American Chemical Society 2023-10-30 /pmc/articles/PMC10641885/ /pubmed/37903301 http://dx.doi.org/10.1021/acs.jpclett.3c02624 Text en © 2023 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by/4.0/Permits the broadest form of re-use including for commercial purposes, provided that author attribution and integrity are maintained (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Koczor-Benda, Zsuzsanna
Mateeva, Teodora
Rosta, Edina
Direct Calculation of Electron Transfer Rates with the Binless Dynamic Histogram Analysis Method
title Direct Calculation of Electron Transfer Rates with the Binless Dynamic Histogram Analysis Method
title_full Direct Calculation of Electron Transfer Rates with the Binless Dynamic Histogram Analysis Method
title_fullStr Direct Calculation of Electron Transfer Rates with the Binless Dynamic Histogram Analysis Method
title_full_unstemmed Direct Calculation of Electron Transfer Rates with the Binless Dynamic Histogram Analysis Method
title_short Direct Calculation of Electron Transfer Rates with the Binless Dynamic Histogram Analysis Method
title_sort direct calculation of electron transfer rates with the binless dynamic histogram analysis method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10641885/
https://www.ncbi.nlm.nih.gov/pubmed/37903301
http://dx.doi.org/10.1021/acs.jpclett.3c02624
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