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Systematic optimization of a fragment-based force field against experimental pure-liquid properties considering large compound families: application to oxygen and nitrogen compounds
The CombiFF approach is a workflow for the automated refinement of force-field parameters against experimental condensed-phase data, considering entire classes of organic molecules constructed using a fragment library via combinatorial isomer enumeration. One peculiarity of this approach is that it...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The Royal Society of Chemistry
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8386690/ https://www.ncbi.nlm.nih.gov/pubmed/34350931 http://dx.doi.org/10.1039/d1cp02001c |
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author | P. Oliveira, Marina Hünenberger, Philippe H. |
author_facet | P. Oliveira, Marina Hünenberger, Philippe H. |
author_sort | P. Oliveira, Marina |
collection | PubMed |
description | The CombiFF approach is a workflow for the automated refinement of force-field parameters against experimental condensed-phase data, considering entire classes of organic molecules constructed using a fragment library via combinatorial isomer enumeration. One peculiarity of this approach is that it relies on an electronegativity-equalization scheme to account for induction effects within molecules, with values of the atomic hardness and electronegativity as electrostatic parameters, rather than the partial charges themselves. In a previous article [M. P. Oliveira, M. Andrey, S. R. Rieder, L. Kern, D. F. Hahn, S. Riniker, B. A. C. Horta and P. H. Hünenberger, J. Chem. Theory. Comput. 2020, 16, 7525], CombiFF was introduced and applied to calibrate a GROMOS-compatible united-atom force field for the saturated acyclic (halo-)alkane family. Here, this scheme is employed for the construction of a corresponding force field for saturated acyclic compounds encompassing eight common chemical functional groups involving oxygen and/or nitrogen atoms, namely: ether, aldehyde, ketone, ester, alcohol, carboxylic acid, amine, and amide. Monofunctional as well as homo-polyfunctional compounds are considered. A total of 1712 experimental liquid densities ρ(liq) and vaporization enthalpies ΔH(vap) concerning 1175 molecules are used for the calibration (339 molecules) and validation (836 molecules) of the 102 non-bonded interaction parameters of the force field. Using initial parameter values based on the GROMOS 2016H66 parameter set, convergence is reached after five iterations. Given access to one processor per simulated system, this operation only requires a few days of wall-clock computing time. After optimization, the root-mean-square deviations from experiment are 29.9 (22.4) kg m(−3) for ρ(liq) and 4.1 (5.5) kJ mol(−1) for ΔH(vap) for the calibration (validation) set. Thus, a very good level of agreement with experiment is achieved in terms of these two properties, although the errors are inhomogeneously distributed across the different chemical functional groups. |
format | Online Article Text |
id | pubmed-8386690 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | The Royal Society of Chemistry |
record_format | MEDLINE/PubMed |
spelling | pubmed-83866902021-09-13 Systematic optimization of a fragment-based force field against experimental pure-liquid properties considering large compound families: application to oxygen and nitrogen compounds P. Oliveira, Marina Hünenberger, Philippe H. Phys Chem Chem Phys Chemistry The CombiFF approach is a workflow for the automated refinement of force-field parameters against experimental condensed-phase data, considering entire classes of organic molecules constructed using a fragment library via combinatorial isomer enumeration. One peculiarity of this approach is that it relies on an electronegativity-equalization scheme to account for induction effects within molecules, with values of the atomic hardness and electronegativity as electrostatic parameters, rather than the partial charges themselves. In a previous article [M. P. Oliveira, M. Andrey, S. R. Rieder, L. Kern, D. F. Hahn, S. Riniker, B. A. C. Horta and P. H. Hünenberger, J. Chem. Theory. Comput. 2020, 16, 7525], CombiFF was introduced and applied to calibrate a GROMOS-compatible united-atom force field for the saturated acyclic (halo-)alkane family. Here, this scheme is employed for the construction of a corresponding force field for saturated acyclic compounds encompassing eight common chemical functional groups involving oxygen and/or nitrogen atoms, namely: ether, aldehyde, ketone, ester, alcohol, carboxylic acid, amine, and amide. Monofunctional as well as homo-polyfunctional compounds are considered. A total of 1712 experimental liquid densities ρ(liq) and vaporization enthalpies ΔH(vap) concerning 1175 molecules are used for the calibration (339 molecules) and validation (836 molecules) of the 102 non-bonded interaction parameters of the force field. Using initial parameter values based on the GROMOS 2016H66 parameter set, convergence is reached after five iterations. Given access to one processor per simulated system, this operation only requires a few days of wall-clock computing time. After optimization, the root-mean-square deviations from experiment are 29.9 (22.4) kg m(−3) for ρ(liq) and 4.1 (5.5) kJ mol(−1) for ΔH(vap) for the calibration (validation) set. Thus, a very good level of agreement with experiment is achieved in terms of these two properties, although the errors are inhomogeneously distributed across the different chemical functional groups. The Royal Society of Chemistry 2021-07-19 /pmc/articles/PMC8386690/ /pubmed/34350931 http://dx.doi.org/10.1039/d1cp02001c Text en This journal is © the Owner Societies https://creativecommons.org/licenses/by-nc/3.0/ |
spellingShingle | Chemistry P. Oliveira, Marina Hünenberger, Philippe H. Systematic optimization of a fragment-based force field against experimental pure-liquid properties considering large compound families: application to oxygen and nitrogen compounds |
title | Systematic optimization of a fragment-based force field against experimental pure-liquid properties considering large compound families: application to oxygen and nitrogen compounds |
title_full | Systematic optimization of a fragment-based force field against experimental pure-liquid properties considering large compound families: application to oxygen and nitrogen compounds |
title_fullStr | Systematic optimization of a fragment-based force field against experimental pure-liquid properties considering large compound families: application to oxygen and nitrogen compounds |
title_full_unstemmed | Systematic optimization of a fragment-based force field against experimental pure-liquid properties considering large compound families: application to oxygen and nitrogen compounds |
title_short | Systematic optimization of a fragment-based force field against experimental pure-liquid properties considering large compound families: application to oxygen and nitrogen compounds |
title_sort | systematic optimization of a fragment-based force field against experimental pure-liquid properties considering large compound families: application to oxygen and nitrogen compounds |
topic | Chemistry |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8386690/ https://www.ncbi.nlm.nih.gov/pubmed/34350931 http://dx.doi.org/10.1039/d1cp02001c |
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