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Accurate determination of solvation free energies of neutral organic compounds from first principles
The main goal of molecular simulation is to accurately predict experimental observables of molecular systems. Another long-standing goal is to devise models for arbitrary neutral organic molecules with little or no reliance on experimental data. While separately these goals have been met to various...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Nature Publishing Group UK
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8776904/ https://www.ncbi.nlm.nih.gov/pubmed/35058472 http://dx.doi.org/10.1038/s41467-022-28041-0 |
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author | Pereyaslavets, Leonid Kamath, Ganesh Butin, Oleg Illarionov, Alexey Olevanov, Michael Kurnikov, Igor Sakipov, Serzhan Leontyev, Igor Voronina, Ekaterina Gannon, Tyler Nawrocki, Grzegorz Darkhovskiy, Mikhail Ivahnenko, Ilya Kostikov, Alexander Scaranto, Jessica Kurnikova, Maria G. Banik, Suvo Chan, Henry Sternberg, Michael G. Sankaranarayanan, Subramanian K. R. S. Crawford, Brad Potoff, Jeffrey Levitt, Michael Kornberg, Roger D. Fain, Boris |
author_facet | Pereyaslavets, Leonid Kamath, Ganesh Butin, Oleg Illarionov, Alexey Olevanov, Michael Kurnikov, Igor Sakipov, Serzhan Leontyev, Igor Voronina, Ekaterina Gannon, Tyler Nawrocki, Grzegorz Darkhovskiy, Mikhail Ivahnenko, Ilya Kostikov, Alexander Scaranto, Jessica Kurnikova, Maria G. Banik, Suvo Chan, Henry Sternberg, Michael G. Sankaranarayanan, Subramanian K. R. S. Crawford, Brad Potoff, Jeffrey Levitt, Michael Kornberg, Roger D. Fain, Boris |
author_sort | Pereyaslavets, Leonid |
collection | PubMed |
description | The main goal of molecular simulation is to accurately predict experimental observables of molecular systems. Another long-standing goal is to devise models for arbitrary neutral organic molecules with little or no reliance on experimental data. While separately these goals have been met to various degrees, for an arbitrary system of molecules they have not been achieved simultaneously. For biophysical ensembles that exist at room temperature and pressure, and where the entropic contributions are on par with interaction strengths, it is the free energies that are both most important and most difficult to predict. We compute the free energies of solvation for a diverse set of neutral organic compounds using a polarizable force field fitted entirely to ab initio calculations. The mean absolute errors (MAE) of hydration, cyclohexane solvation, and corresponding partition coefficients are 0.2 kcal/mol, 0.3 kcal/mol and 0.22 log units, i.e. within chemical accuracy. The model (ARROW FF) is multipolar, polarizable, and its accompanying simulation stack includes nuclear quantum effects (NQE). The simulation tools’ computational efficiency is on a par with current state-of-the-art packages. The construction of a wide-coverage molecular modelling toolset from first principles, together with its excellent predictive ability in the liquid phase is a major advance in biomolecular simulation. |
format | Online Article Text |
id | pubmed-8776904 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-87769042022-02-04 Accurate determination of solvation free energies of neutral organic compounds from first principles Pereyaslavets, Leonid Kamath, Ganesh Butin, Oleg Illarionov, Alexey Olevanov, Michael Kurnikov, Igor Sakipov, Serzhan Leontyev, Igor Voronina, Ekaterina Gannon, Tyler Nawrocki, Grzegorz Darkhovskiy, Mikhail Ivahnenko, Ilya Kostikov, Alexander Scaranto, Jessica Kurnikova, Maria G. Banik, Suvo Chan, Henry Sternberg, Michael G. Sankaranarayanan, Subramanian K. R. S. Crawford, Brad Potoff, Jeffrey Levitt, Michael Kornberg, Roger D. Fain, Boris Nat Commun Article The main goal of molecular simulation is to accurately predict experimental observables of molecular systems. Another long-standing goal is to devise models for arbitrary neutral organic molecules with little or no reliance on experimental data. While separately these goals have been met to various degrees, for an arbitrary system of molecules they have not been achieved simultaneously. For biophysical ensembles that exist at room temperature and pressure, and where the entropic contributions are on par with interaction strengths, it is the free energies that are both most important and most difficult to predict. We compute the free energies of solvation for a diverse set of neutral organic compounds using a polarizable force field fitted entirely to ab initio calculations. The mean absolute errors (MAE) of hydration, cyclohexane solvation, and corresponding partition coefficients are 0.2 kcal/mol, 0.3 kcal/mol and 0.22 log units, i.e. within chemical accuracy. The model (ARROW FF) is multipolar, polarizable, and its accompanying simulation stack includes nuclear quantum effects (NQE). The simulation tools’ computational efficiency is on a par with current state-of-the-art packages. The construction of a wide-coverage molecular modelling toolset from first principles, together with its excellent predictive ability in the liquid phase is a major advance in biomolecular simulation. Nature Publishing Group UK 2022-01-20 /pmc/articles/PMC8776904/ /pubmed/35058472 http://dx.doi.org/10.1038/s41467-022-28041-0 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Article Pereyaslavets, Leonid Kamath, Ganesh Butin, Oleg Illarionov, Alexey Olevanov, Michael Kurnikov, Igor Sakipov, Serzhan Leontyev, Igor Voronina, Ekaterina Gannon, Tyler Nawrocki, Grzegorz Darkhovskiy, Mikhail Ivahnenko, Ilya Kostikov, Alexander Scaranto, Jessica Kurnikova, Maria G. Banik, Suvo Chan, Henry Sternberg, Michael G. Sankaranarayanan, Subramanian K. R. S. Crawford, Brad Potoff, Jeffrey Levitt, Michael Kornberg, Roger D. Fain, Boris Accurate determination of solvation free energies of neutral organic compounds from first principles |
title | Accurate determination of solvation free energies of neutral organic compounds from first principles |
title_full | Accurate determination of solvation free energies of neutral organic compounds from first principles |
title_fullStr | Accurate determination of solvation free energies of neutral organic compounds from first principles |
title_full_unstemmed | Accurate determination of solvation free energies of neutral organic compounds from first principles |
title_short | Accurate determination of solvation free energies of neutral organic compounds from first principles |
title_sort | accurate determination of solvation free energies of neutral organic compounds from first principles |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8776904/ https://www.ncbi.nlm.nih.gov/pubmed/35058472 http://dx.doi.org/10.1038/s41467-022-28041-0 |
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