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Implementation and Optimization of the Embedded Cluster Reference Interaction Site Model with Atomic Charges
[Image: see text] In this work, we implemented the embedded cluster reference interaction site model (EC-RISM) originally developed by Kloss, Heil, and Kast (J. Phys. Chem. B2008, 112, 4337–4343). This method combines quantum mechanical calculations with the 3D reference interaction site model (3D-R...
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/PMC9036516/ https://www.ncbi.nlm.nih.gov/pubmed/35394778 http://dx.doi.org/10.1021/acs.jpca.1c07904 |
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author | Ganyecz, Ádám Kállay, Mihály |
author_facet | Ganyecz, Ádám Kállay, Mihály |
author_sort | Ganyecz, Ádám |
collection | PubMed |
description | [Image: see text] In this work, we implemented the embedded cluster reference interaction site model (EC-RISM) originally developed by Kloss, Heil, and Kast (J. Phys. Chem. B2008, 112, 4337–4343). This method combines quantum mechanical calculations with the 3D reference interaction site model (3D-RISM). Numerous options, such as buffer, grid space, basis set, charge model, water model, closure relation, and so forth, were investigated to find the best settings. Additionally, the small point charges, which are derived from the solvent distribution from the 3D-RISM solution to represent the solvent in the QM calculation, were neglected to reduce the overhead without the loss of accuracy. On the MNSOL[a], MNSOL, and FreeSolv databases, our implemented and optimized method provides solvation free energies in water with 5.70, 6.32, and 6.44 kJ/mol root-mean-square deviations, respectively, but with different settings, 5.22, 6.08, and 6.63 kJ/mol can also be achieved. Only solvent models containing fitting parameters, like COSMO-RS and EC-RISM with universal correction and directly used electrostatic potential, perform better than our EC-RISM implementation with atomic charges. |
format | Online Article Text |
id | pubmed-9036516 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | American Chemical Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-90365162022-04-26 Implementation and Optimization of the Embedded Cluster Reference Interaction Site Model with Atomic Charges Ganyecz, Ádám Kállay, Mihály J Phys Chem A [Image: see text] In this work, we implemented the embedded cluster reference interaction site model (EC-RISM) originally developed by Kloss, Heil, and Kast (J. Phys. Chem. B2008, 112, 4337–4343). This method combines quantum mechanical calculations with the 3D reference interaction site model (3D-RISM). Numerous options, such as buffer, grid space, basis set, charge model, water model, closure relation, and so forth, were investigated to find the best settings. Additionally, the small point charges, which are derived from the solvent distribution from the 3D-RISM solution to represent the solvent in the QM calculation, were neglected to reduce the overhead without the loss of accuracy. On the MNSOL[a], MNSOL, and FreeSolv databases, our implemented and optimized method provides solvation free energies in water with 5.70, 6.32, and 6.44 kJ/mol root-mean-square deviations, respectively, but with different settings, 5.22, 6.08, and 6.63 kJ/mol can also be achieved. Only solvent models containing fitting parameters, like COSMO-RS and EC-RISM with universal correction and directly used electrostatic potential, perform better than our EC-RISM implementation with atomic charges. American Chemical Society 2022-04-08 2022-04-21 /pmc/articles/PMC9036516/ /pubmed/35394778 http://dx.doi.org/10.1021/acs.jpca.1c07904 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 | Ganyecz, Ádám Kállay, Mihály Implementation and Optimization of the Embedded Cluster Reference Interaction Site Model with Atomic Charges |
title | Implementation and Optimization of the Embedded Cluster
Reference Interaction Site Model with Atomic Charges |
title_full | Implementation and Optimization of the Embedded Cluster
Reference Interaction Site Model with Atomic Charges |
title_fullStr | Implementation and Optimization of the Embedded Cluster
Reference Interaction Site Model with Atomic Charges |
title_full_unstemmed | Implementation and Optimization of the Embedded Cluster
Reference Interaction Site Model with Atomic Charges |
title_short | Implementation and Optimization of the Embedded Cluster
Reference Interaction Site Model with Atomic Charges |
title_sort | implementation and optimization of the embedded cluster
reference interaction site model with atomic charges |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9036516/ https://www.ncbi.nlm.nih.gov/pubmed/35394778 http://dx.doi.org/10.1021/acs.jpca.1c07904 |
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