Cargando…
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...
Autores principales: | , , |
---|---|
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 |
_version_ | 1785146850422030336 |
---|---|
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. |
format | Online Article Text |
id | pubmed-10641885 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT koczorbendazsuzsanna directcalculationofelectrontransferrateswiththebinlessdynamichistogramanalysismethod AT mateevateodora directcalculationofelectrontransferrateswiththebinlessdynamichistogramanalysismethod AT rostaedina directcalculationofelectrontransferrateswiththebinlessdynamichistogramanalysismethod |