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Influence of Ethanol Parametrization on Diffusion Coefficients Using OPLS-AA Force Field
Molecular dynamics simulations employing the all-atom optimized potential for liquid simulations (OPLS-AA) force field were performed for determining self-diffusion coefficients ([Formula: see text]) of ethanol and tracer diffusion coefficients ([Formula: see text]) of solutes in ethanol at several...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10138630/ https://www.ncbi.nlm.nih.gov/pubmed/37108479 http://dx.doi.org/10.3390/ijms24087316 |
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author | Zêzere, Bruno Fonseca, Tiago V. B. Portugal, Inês Simões, Mário M. Q. Silva, Carlos M. Gomes, José R. B. |
author_facet | Zêzere, Bruno Fonseca, Tiago V. B. Portugal, Inês Simões, Mário M. Q. Silva, Carlos M. Gomes, José R. B. |
author_sort | Zêzere, Bruno |
collection | PubMed |
description | Molecular dynamics simulations employing the all-atom optimized potential for liquid simulations (OPLS-AA) force field were performed for determining self-diffusion coefficients ([Formula: see text]) of ethanol and tracer diffusion coefficients ([Formula: see text]) of solutes in ethanol at several temperature and pressure conditions. For simulations employing the original OPLS-AA diameter of ethanol’s oxygen atom ([Formula: see text]), calculated and experimental diffusivities of protic solutes differed by more than 25%. To correct this behavior, the [Formula: see text] was reoptimized using the experimental [Formula: see text] of quercetin and of gallic acid in liquid ethanol as benchmarks. A substantial improvement of the calculated diffusivities was found by changing [Formula: see text] from its original value (0.312 nm) to 0.306 nm, with average absolute relative deviations (AARD) of 3.71% and 4.59% for quercetin and gallic acid, respectively. The new [Formula: see text] value was further tested by computing [Formula: see text] of ibuprofen and butan-1-ol in liquid ethanol with AARDs of 1.55% and 4.81%, respectively. A significant improvement was also obtained for the [Formula: see text] of ethanol with AARD = 3.51%. It was also demonstrated that in the case of diffusion coefficients of non-polar solutes in ethanol, the original [Formula: see text] nm should be used for better agreement with experiment. If equilibrium properties such as enthalpy of vaporization and density are estimated, the original diameter should be once again adopted. |
format | Online Article Text |
id | pubmed-10138630 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-101386302023-04-28 Influence of Ethanol Parametrization on Diffusion Coefficients Using OPLS-AA Force Field Zêzere, Bruno Fonseca, Tiago V. B. Portugal, Inês Simões, Mário M. Q. Silva, Carlos M. Gomes, José R. B. Int J Mol Sci Article Molecular dynamics simulations employing the all-atom optimized potential for liquid simulations (OPLS-AA) force field were performed for determining self-diffusion coefficients ([Formula: see text]) of ethanol and tracer diffusion coefficients ([Formula: see text]) of solutes in ethanol at several temperature and pressure conditions. For simulations employing the original OPLS-AA diameter of ethanol’s oxygen atom ([Formula: see text]), calculated and experimental diffusivities of protic solutes differed by more than 25%. To correct this behavior, the [Formula: see text] was reoptimized using the experimental [Formula: see text] of quercetin and of gallic acid in liquid ethanol as benchmarks. A substantial improvement of the calculated diffusivities was found by changing [Formula: see text] from its original value (0.312 nm) to 0.306 nm, with average absolute relative deviations (AARD) of 3.71% and 4.59% for quercetin and gallic acid, respectively. The new [Formula: see text] value was further tested by computing [Formula: see text] of ibuprofen and butan-1-ol in liquid ethanol with AARDs of 1.55% and 4.81%, respectively. A significant improvement was also obtained for the [Formula: see text] of ethanol with AARD = 3.51%. It was also demonstrated that in the case of diffusion coefficients of non-polar solutes in ethanol, the original [Formula: see text] nm should be used for better agreement with experiment. If equilibrium properties such as enthalpy of vaporization and density are estimated, the original diameter should be once again adopted. MDPI 2023-04-15 /pmc/articles/PMC10138630/ /pubmed/37108479 http://dx.doi.org/10.3390/ijms24087316 Text en © 2023 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 Zêzere, Bruno Fonseca, Tiago V. B. Portugal, Inês Simões, Mário M. Q. Silva, Carlos M. Gomes, José R. B. Influence of Ethanol Parametrization on Diffusion Coefficients Using OPLS-AA Force Field |
title | Influence of Ethanol Parametrization on Diffusion Coefficients Using OPLS-AA Force Field |
title_full | Influence of Ethanol Parametrization on Diffusion Coefficients Using OPLS-AA Force Field |
title_fullStr | Influence of Ethanol Parametrization on Diffusion Coefficients Using OPLS-AA Force Field |
title_full_unstemmed | Influence of Ethanol Parametrization on Diffusion Coefficients Using OPLS-AA Force Field |
title_short | Influence of Ethanol Parametrization on Diffusion Coefficients Using OPLS-AA Force Field |
title_sort | influence of ethanol parametrization on diffusion coefficients using opls-aa force field |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10138630/ https://www.ncbi.nlm.nih.gov/pubmed/37108479 http://dx.doi.org/10.3390/ijms24087316 |
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