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QM/MM Energy Decomposition Using the Interacting Quantum Atoms Approach
[Image: see text] The interacting quantum atoms (IQA) method decomposes the quantum mechanical (QM) energy of a molecular system in terms of one- and two-center (atomic) contributions within the context of the quantum theory of atoms in molecules. Here, we demonstrate that IQA, enhanced with molecul...
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/PMC8965874/ https://www.ncbi.nlm.nih.gov/pubmed/35212531 http://dx.doi.org/10.1021/acs.jcim.1c01372 |
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author | López, Roberto Díaz, Natalia Francisco, Evelio Martín-Pendás, Angel Suárez, Dimas |
author_facet | López, Roberto Díaz, Natalia Francisco, Evelio Martín-Pendás, Angel Suárez, Dimas |
author_sort | López, Roberto |
collection | PubMed |
description | [Image: see text] The interacting quantum atoms (IQA) method decomposes the quantum mechanical (QM) energy of a molecular system in terms of one- and two-center (atomic) contributions within the context of the quantum theory of atoms in molecules. Here, we demonstrate that IQA, enhanced with molecular mechanics (MM) and Poisson–Boltzmann surface-area (PBSA) solvation methods, is naturally extended to the realm of hybrid QM/MM methodologies, yielding intra- and inter-residue energy terms that characterize all kinds of covalent and noncovalent bonding interactions. To test the robustness of this approach, both metal–water interactions and QM/MM boundary artifacts are characterized in terms of the IQA descriptors derived from QM regions of varying size in Zn(II)– and Mg(II)–water clusters. In addition, we analyze a homologous series of inhibitors in complex with a matrix metalloproteinase (MMP-12) by carrying out QM/MM–PBSA calculations on their crystallographic structures followed by IQA energy decomposition. Overall, these applications not only show the advantages of the IQA QM/MM approach but also address some of the challenges lying ahead for expanding the QM/MM methodology. |
format | Online Article Text |
id | pubmed-8965874 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-89658742022-03-30 QM/MM Energy Decomposition Using the Interacting Quantum Atoms Approach López, Roberto Díaz, Natalia Francisco, Evelio Martín-Pendás, Angel Suárez, Dimas J Chem Inf Model [Image: see text] The interacting quantum atoms (IQA) method decomposes the quantum mechanical (QM) energy of a molecular system in terms of one- and two-center (atomic) contributions within the context of the quantum theory of atoms in molecules. Here, we demonstrate that IQA, enhanced with molecular mechanics (MM) and Poisson–Boltzmann surface-area (PBSA) solvation methods, is naturally extended to the realm of hybrid QM/MM methodologies, yielding intra- and inter-residue energy terms that characterize all kinds of covalent and noncovalent bonding interactions. To test the robustness of this approach, both metal–water interactions and QM/MM boundary artifacts are characterized in terms of the IQA descriptors derived from QM regions of varying size in Zn(II)– and Mg(II)–water clusters. In addition, we analyze a homologous series of inhibitors in complex with a matrix metalloproteinase (MMP-12) by carrying out QM/MM–PBSA calculations on their crystallographic structures followed by IQA energy decomposition. Overall, these applications not only show the advantages of the IQA QM/MM approach but also address some of the challenges lying ahead for expanding the QM/MM methodology. American Chemical Society 2022-02-25 2022-03-28 /pmc/articles/PMC8965874/ /pubmed/35212531 http://dx.doi.org/10.1021/acs.jcim.1c01372 Text en © 2022 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 | López, Roberto Díaz, Natalia Francisco, Evelio Martín-Pendás, Angel Suárez, Dimas QM/MM Energy Decomposition Using the Interacting Quantum Atoms Approach |
title | QM/MM Energy Decomposition Using the Interacting Quantum
Atoms Approach |
title_full | QM/MM Energy Decomposition Using the Interacting Quantum
Atoms Approach |
title_fullStr | QM/MM Energy Decomposition Using the Interacting Quantum
Atoms Approach |
title_full_unstemmed | QM/MM Energy Decomposition Using the Interacting Quantum
Atoms Approach |
title_short | QM/MM Energy Decomposition Using the Interacting Quantum
Atoms Approach |
title_sort | qm/mm energy decomposition using the interacting quantum
atoms approach |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8965874/ https://www.ncbi.nlm.nih.gov/pubmed/35212531 http://dx.doi.org/10.1021/acs.jcim.1c01372 |
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