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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...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
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.
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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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