Cargando…

Construction of a Gaussian Process Regression Model of Formamide for Use in Molecular Simulations

[Image: see text] FFLUX, a novel force field based on quantum chemical topology, can perform molecular dynamics simulations with flexible multipole moments that change with geometry. This is enabled by Gaussian process regression machine learning models, which accurately predict atomic energies and...

Descripción completa

Detalles Bibliográficos
Autores principales: Brown, Matthew L., Skelton, Jonathan M., Popelier, Paul L. A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2023
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9969515/
https://www.ncbi.nlm.nih.gov/pubmed/36756842
http://dx.doi.org/10.1021/acs.jpca.2c06566
_version_ 1784897751762337792
author Brown, Matthew L.
Skelton, Jonathan M.
Popelier, Paul L. A.
author_facet Brown, Matthew L.
Skelton, Jonathan M.
Popelier, Paul L. A.
author_sort Brown, Matthew L.
collection PubMed
description [Image: see text] FFLUX, a novel force field based on quantum chemical topology, can perform molecular dynamics simulations with flexible multipole moments that change with geometry. This is enabled by Gaussian process regression machine learning models, which accurately predict atomic energies and multipole moments up to the hexadecapole. We have constructed a model of the formamide monomer at the B3LYP/aug-cc-pVTZ level of theory capable of sub-kJ mol(–1) accuracy, with the maximum prediction error for the molecule being 0.8 kJ mol(–1). This model was used in FFLUX simulations along with Lennard-Jones parameters to successfully optimize the geometry of formamide dimers with errors smaller than 0.1 Å compared to those obtained with D3-corrected B3LYP/aug-cc-pVTZ. Comparisons were also made to a force field constructed with static multipole moments and Lennard-Jones parameters. FFLUX recovers the expected energy ranking of dimers compared to the literature, and changes in C=O and C–N bond lengths associated with hydrogen bonding were found to be consistent with density functional theory.
format Online
Article
Text
id pubmed-9969515
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher American Chemical Society
record_format MEDLINE/PubMed
spelling pubmed-99695152023-02-28 Construction of a Gaussian Process Regression Model of Formamide for Use in Molecular Simulations Brown, Matthew L. Skelton, Jonathan M. Popelier, Paul L. A. J Phys Chem A [Image: see text] FFLUX, a novel force field based on quantum chemical topology, can perform molecular dynamics simulations with flexible multipole moments that change with geometry. This is enabled by Gaussian process regression machine learning models, which accurately predict atomic energies and multipole moments up to the hexadecapole. We have constructed a model of the formamide monomer at the B3LYP/aug-cc-pVTZ level of theory capable of sub-kJ mol(–1) accuracy, with the maximum prediction error for the molecule being 0.8 kJ mol(–1). This model was used in FFLUX simulations along with Lennard-Jones parameters to successfully optimize the geometry of formamide dimers with errors smaller than 0.1 Å compared to those obtained with D3-corrected B3LYP/aug-cc-pVTZ. Comparisons were also made to a force field constructed with static multipole moments and Lennard-Jones parameters. FFLUX recovers the expected energy ranking of dimers compared to the literature, and changes in C=O and C–N bond lengths associated with hydrogen bonding were found to be consistent with density functional theory. American Chemical Society 2023-02-09 /pmc/articles/PMC9969515/ /pubmed/36756842 http://dx.doi.org/10.1021/acs.jpca.2c06566 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 Brown, Matthew L.
Skelton, Jonathan M.
Popelier, Paul L. A.
Construction of a Gaussian Process Regression Model of Formamide for Use in Molecular Simulations
title Construction of a Gaussian Process Regression Model of Formamide for Use in Molecular Simulations
title_full Construction of a Gaussian Process Regression Model of Formamide for Use in Molecular Simulations
title_fullStr Construction of a Gaussian Process Regression Model of Formamide for Use in Molecular Simulations
title_full_unstemmed Construction of a Gaussian Process Regression Model of Formamide for Use in Molecular Simulations
title_short Construction of a Gaussian Process Regression Model of Formamide for Use in Molecular Simulations
title_sort construction of a gaussian process regression model of formamide for use in molecular simulations
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9969515/
https://www.ncbi.nlm.nih.gov/pubmed/36756842
http://dx.doi.org/10.1021/acs.jpca.2c06566
work_keys_str_mv AT brownmatthewl constructionofagaussianprocessregressionmodelofformamideforuseinmolecularsimulations
AT skeltonjonathanm constructionofagaussianprocessregressionmodelofformamideforuseinmolecularsimulations
AT popelierpaulla constructionofagaussianprocessregressionmodelofformamideforuseinmolecularsimulations