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Fragmentation Method for Computing Quantum Mechanics and Molecular Mechanics Gradients for Force Matching: Validation with Hydration Free Energy Predictions Using Adaptive Force Matching
[Image: see text] A fragmentation approach referred to as a simple overlapping region method for force matching (SORForM) is presented. SORForM is designed to enable efficient computation of quantum mechanical (QM) forces for large molecules and is validated in the framework of adaptive force matchi...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical Society
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9059759/ https://www.ncbi.nlm.nih.gov/pubmed/35420821 http://dx.doi.org/10.1021/acs.jpca.2c01615 |
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author | Zheng, Dong Yuan, Ying Wang, Feng |
author_facet | Zheng, Dong Yuan, Ying Wang, Feng |
author_sort | Zheng, Dong |
collection | PubMed |
description | [Image: see text] A fragmentation approach referred to as a simple overlapping region method for force matching (SORForM) is presented. SORForM is designed to enable efficient computation of quantum mechanical (QM) forces for large molecules and is validated in the framework of adaptive force matching (AFM) to develop solute models in water. The SORForM method divides a molecule into overlapping QM regions with each region containing a gradient zone and a buffer zone. The buffer zone ensures that the atoms in the gradient zone have their surroundings unchanged with fragmentation. The performance of the method is validated with mefenamic acid and linalyl acetate by comparing the hydration free energies of AFM models developed with and without SORForM. The AFM hydration free energies are also compared with that of the experiments. The models developed with B3LYP-D3(BJ) and def2-TZVP are in excellent agreement with experiments. Our work shows that PBE-D3(BJ) provides less satisfactory results when compared to B3LYP-D3(BJ). The def2-TZVP basis set is found to greatly improve the agreement with experiments when compared to a double-zeta quality basis set. |
format | Online Article Text |
id | pubmed-9059759 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-90597592023-04-14 Fragmentation Method for Computing Quantum Mechanics and Molecular Mechanics Gradients for Force Matching: Validation with Hydration Free Energy Predictions Using Adaptive Force Matching Zheng, Dong Yuan, Ying Wang, Feng J Phys Chem A [Image: see text] A fragmentation approach referred to as a simple overlapping region method for force matching (SORForM) is presented. SORForM is designed to enable efficient computation of quantum mechanical (QM) forces for large molecules and is validated in the framework of adaptive force matching (AFM) to develop solute models in water. The SORForM method divides a molecule into overlapping QM regions with each region containing a gradient zone and a buffer zone. The buffer zone ensures that the atoms in the gradient zone have their surroundings unchanged with fragmentation. The performance of the method is validated with mefenamic acid and linalyl acetate by comparing the hydration free energies of AFM models developed with and without SORForM. The AFM hydration free energies are also compared with that of the experiments. The models developed with B3LYP-D3(BJ) and def2-TZVP are in excellent agreement with experiments. Our work shows that PBE-D3(BJ) provides less satisfactory results when compared to B3LYP-D3(BJ). The def2-TZVP basis set is found to greatly improve the agreement with experiments when compared to a double-zeta quality basis set. American Chemical Society 2022-04-14 2022-04-28 /pmc/articles/PMC9059759/ /pubmed/35420821 http://dx.doi.org/10.1021/acs.jpca.2c01615 Text en © 2022 The Authors. Published by American Chemical Society https://creativecommons.org/licenses/by-nc-nd/4.0/Permits non-commercial access and re-use, provided that author attribution and integrity are maintained; but does not permit creation of adaptations or other derivative works (https://creativecommons.org/licenses/by-nc-nd/4.0/). |
spellingShingle | Zheng, Dong Yuan, Ying Wang, Feng Fragmentation Method for Computing Quantum Mechanics and Molecular Mechanics Gradients for Force Matching: Validation with Hydration Free Energy Predictions Using Adaptive Force Matching |
title | Fragmentation Method for Computing Quantum Mechanics
and Molecular Mechanics Gradients for Force Matching: Validation with
Hydration Free Energy Predictions Using Adaptive Force Matching |
title_full | Fragmentation Method for Computing Quantum Mechanics
and Molecular Mechanics Gradients for Force Matching: Validation with
Hydration Free Energy Predictions Using Adaptive Force Matching |
title_fullStr | Fragmentation Method for Computing Quantum Mechanics
and Molecular Mechanics Gradients for Force Matching: Validation with
Hydration Free Energy Predictions Using Adaptive Force Matching |
title_full_unstemmed | Fragmentation Method for Computing Quantum Mechanics
and Molecular Mechanics Gradients for Force Matching: Validation with
Hydration Free Energy Predictions Using Adaptive Force Matching |
title_short | Fragmentation Method for Computing Quantum Mechanics
and Molecular Mechanics Gradients for Force Matching: Validation with
Hydration Free Energy Predictions Using Adaptive Force Matching |
title_sort | fragmentation method for computing quantum mechanics
and molecular mechanics gradients for force matching: validation with
hydration free energy predictions using adaptive force matching |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9059759/ https://www.ncbi.nlm.nih.gov/pubmed/35420821 http://dx.doi.org/10.1021/acs.jpca.2c01615 |
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