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The Impact of Electron Correlation on Describing QM/MM Interactions in the Attendant Molecular Dynamics Simulations of CO in Myoglobin
The impact of the dispersion and electron correlation effects on describing quantum mechanics/molecular mechanics (QM/MM) interactions in QM/MM molecular dynamics (MD) simulations was explored by performing a series of up to 2 ns QM/MM MD simulations on the B states of the myoglobin–carbon monoxide...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7244521/ https://www.ncbi.nlm.nih.gov/pubmed/32444817 http://dx.doi.org/10.1038/s41598-020-65475-2 |
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author | Wang, Xianwei Lu, Chenhui Yang, Maoyou |
author_facet | Wang, Xianwei Lu, Chenhui Yang, Maoyou |
author_sort | Wang, Xianwei |
collection | PubMed |
description | The impact of the dispersion and electron correlation effects on describing quantum mechanics/molecular mechanics (QM/MM) interactions in QM/MM molecular dynamics (MD) simulations was explored by performing a series of up to 2 ns QM/MM MD simulations on the B states of the myoglobin–carbon monoxide (MbCO) system. The results indicate that both dispersion and electron correlations play significant roles in the simulation of the ratios of two B states (B(1)/B(2)), which suggests that the inclusion of the electron correlation effects is essential for accurately modeling the interactions between QM and MM subsystems. We found that the QM/MM interaction energies between the CO and the surroundings statistically present a linear correlation with the electric fields along the CO bond. This indicates that QM/MM interactions can be described by a simple physical model of a dipole with constant moment under the action of the electric fields. The treatment provides us with an accurate and effective approach to account for the electron correlation effects in QM/MM MD simulations. |
format | Online Article Text |
id | pubmed-7244521 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-72445212020-05-30 The Impact of Electron Correlation on Describing QM/MM Interactions in the Attendant Molecular Dynamics Simulations of CO in Myoglobin Wang, Xianwei Lu, Chenhui Yang, Maoyou Sci Rep Article The impact of the dispersion and electron correlation effects on describing quantum mechanics/molecular mechanics (QM/MM) interactions in QM/MM molecular dynamics (MD) simulations was explored by performing a series of up to 2 ns QM/MM MD simulations on the B states of the myoglobin–carbon monoxide (MbCO) system. The results indicate that both dispersion and electron correlations play significant roles in the simulation of the ratios of two B states (B(1)/B(2)), which suggests that the inclusion of the electron correlation effects is essential for accurately modeling the interactions between QM and MM subsystems. We found that the QM/MM interaction energies between the CO and the surroundings statistically present a linear correlation with the electric fields along the CO bond. This indicates that QM/MM interactions can be described by a simple physical model of a dipole with constant moment under the action of the electric fields. The treatment provides us with an accurate and effective approach to account for the electron correlation effects in QM/MM MD simulations. Nature Publishing Group UK 2020-05-22 /pmc/articles/PMC7244521/ /pubmed/32444817 http://dx.doi.org/10.1038/s41598-020-65475-2 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Wang, Xianwei Lu, Chenhui Yang, Maoyou The Impact of Electron Correlation on Describing QM/MM Interactions in the Attendant Molecular Dynamics Simulations of CO in Myoglobin |
title | The Impact of Electron Correlation on Describing QM/MM Interactions in the Attendant Molecular Dynamics Simulations of CO in Myoglobin |
title_full | The Impact of Electron Correlation on Describing QM/MM Interactions in the Attendant Molecular Dynamics Simulations of CO in Myoglobin |
title_fullStr | The Impact of Electron Correlation on Describing QM/MM Interactions in the Attendant Molecular Dynamics Simulations of CO in Myoglobin |
title_full_unstemmed | The Impact of Electron Correlation on Describing QM/MM Interactions in the Attendant Molecular Dynamics Simulations of CO in Myoglobin |
title_short | The Impact of Electron Correlation on Describing QM/MM Interactions in the Attendant Molecular Dynamics Simulations of CO in Myoglobin |
title_sort | impact of electron correlation on describing qm/mm interactions in the attendant molecular dynamics simulations of co in myoglobin |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7244521/ https://www.ncbi.nlm.nih.gov/pubmed/32444817 http://dx.doi.org/10.1038/s41598-020-65475-2 |
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