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An Efficient Approach to Large-Scale Ab Initio Conformational Energy Profiles of Small Molecules

Accurate conformational energetics of molecules are of great significance to understand maby chemical properties. They are also fundamental for high-quality parameterization of force fields. Traditionally, accurate conformational profiles are obtained with density functional theory (DFT) methods. Ho...

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Autores principales: Wang, Yanxing, Walker, Brandon Duane, Liu, Chengwen, Ren, Pengyu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9738817/
https://www.ncbi.nlm.nih.gov/pubmed/36500658
http://dx.doi.org/10.3390/molecules27238567
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author Wang, Yanxing
Walker, Brandon Duane
Liu, Chengwen
Ren, Pengyu
author_facet Wang, Yanxing
Walker, Brandon Duane
Liu, Chengwen
Ren, Pengyu
author_sort Wang, Yanxing
collection PubMed
description Accurate conformational energetics of molecules are of great significance to understand maby chemical properties. They are also fundamental for high-quality parameterization of force fields. Traditionally, accurate conformational profiles are obtained with density functional theory (DFT) methods. However, obtaining a reliable energy profile can be time-consuming when the molecular sizes are relatively large or when there are many molecules of interest. Furthermore, incorporation of data-driven deep learning methods into force field development has great requirements for high-quality geometry and energy data. To this end, we compared several possible alternatives to the traditional DFT methods for conformational scans, including the semi-empirical method GFN2-xTB and the neural network potential ANI-2x. It was found that a sequential protocol of geometry optimization with the semi-empirical method and single-point energy calculation with high-level DFT methods can provide satisfactory conformational energy profiles hundreds of times faster in terms of optimization.
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spelling pubmed-97388172022-12-11 An Efficient Approach to Large-Scale Ab Initio Conformational Energy Profiles of Small Molecules Wang, Yanxing Walker, Brandon Duane Liu, Chengwen Ren, Pengyu Molecules Article Accurate conformational energetics of molecules are of great significance to understand maby chemical properties. They are also fundamental for high-quality parameterization of force fields. Traditionally, accurate conformational profiles are obtained with density functional theory (DFT) methods. However, obtaining a reliable energy profile can be time-consuming when the molecular sizes are relatively large or when there are many molecules of interest. Furthermore, incorporation of data-driven deep learning methods into force field development has great requirements for high-quality geometry and energy data. To this end, we compared several possible alternatives to the traditional DFT methods for conformational scans, including the semi-empirical method GFN2-xTB and the neural network potential ANI-2x. It was found that a sequential protocol of geometry optimization with the semi-empirical method and single-point energy calculation with high-level DFT methods can provide satisfactory conformational energy profiles hundreds of times faster in terms of optimization. MDPI 2022-12-05 /pmc/articles/PMC9738817/ /pubmed/36500658 http://dx.doi.org/10.3390/molecules27238567 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Wang, Yanxing
Walker, Brandon Duane
Liu, Chengwen
Ren, Pengyu
An Efficient Approach to Large-Scale Ab Initio Conformational Energy Profiles of Small Molecules
title An Efficient Approach to Large-Scale Ab Initio Conformational Energy Profiles of Small Molecules
title_full An Efficient Approach to Large-Scale Ab Initio Conformational Energy Profiles of Small Molecules
title_fullStr An Efficient Approach to Large-Scale Ab Initio Conformational Energy Profiles of Small Molecules
title_full_unstemmed An Efficient Approach to Large-Scale Ab Initio Conformational Energy Profiles of Small Molecules
title_short An Efficient Approach to Large-Scale Ab Initio Conformational Energy Profiles of Small Molecules
title_sort efficient approach to large-scale ab initio conformational energy profiles of small molecules
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9738817/
https://www.ncbi.nlm.nih.gov/pubmed/36500658
http://dx.doi.org/10.3390/molecules27238567
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