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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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2022
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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. |
format | Online Article Text |
id | pubmed-9738817 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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