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Predicting water-to-cyclohexane partitioning of the SAMPL5 molecules using dielectric balancing of force fields
Alchemical transformation of solutes using classical fixed-charge force fields is a popular strategy for assessing the free energy of transfer in different environments. Accurate estimations of transfer between phases with significantly different polarities can be difficult because of the static nat...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer International Publishing
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5206264/ https://www.ncbi.nlm.nih.gov/pubmed/27573982 http://dx.doi.org/10.1007/s10822-016-9950-z |
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author | Paranahewage, S. Shanaka Gierhart, Cassidy S. Fennell, Christopher J. |
author_facet | Paranahewage, S. Shanaka Gierhart, Cassidy S. Fennell, Christopher J. |
author_sort | Paranahewage, S. Shanaka |
collection | PubMed |
description | Alchemical transformation of solutes using classical fixed-charge force fields is a popular strategy for assessing the free energy of transfer in different environments. Accurate estimations of transfer between phases with significantly different polarities can be difficult because of the static nature of the force fields. Here, we report on an application of such calculations in the SAMPL5 experiment that also involves an effort in balancing solute and solvent interactions via their expected static dielectric constants. This strategy performs well with respect to predictive accuracy and correlation with unknown experimental values. We follow this by performing a series of retrospective investigations which highlight the potential importance of proper balancing in these systems, and we use a null hypothesis analysis to explore potential biases in the comparisons with experiment. The collective findings indicate that considerations of force field compatibility through dielectric behavior is a potential strategy for future improvements in transfer processes between disparate environments. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s10822-016-9950-z) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5206264 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Springer International Publishing |
record_format | MEDLINE/PubMed |
spelling | pubmed-52062642017-01-18 Predicting water-to-cyclohexane partitioning of the SAMPL5 molecules using dielectric balancing of force fields Paranahewage, S. Shanaka Gierhart, Cassidy S. Fennell, Christopher J. J Comput Aided Mol Des Article Alchemical transformation of solutes using classical fixed-charge force fields is a popular strategy for assessing the free energy of transfer in different environments. Accurate estimations of transfer between phases with significantly different polarities can be difficult because of the static nature of the force fields. Here, we report on an application of such calculations in the SAMPL5 experiment that also involves an effort in balancing solute and solvent interactions via their expected static dielectric constants. This strategy performs well with respect to predictive accuracy and correlation with unknown experimental values. We follow this by performing a series of retrospective investigations which highlight the potential importance of proper balancing in these systems, and we use a null hypothesis analysis to explore potential biases in the comparisons with experiment. The collective findings indicate that considerations of force field compatibility through dielectric behavior is a potential strategy for future improvements in transfer processes between disparate environments. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s10822-016-9950-z) contains supplementary material, which is available to authorized users. Springer International Publishing 2016-08-29 2016 /pmc/articles/PMC5206264/ /pubmed/27573982 http://dx.doi.org/10.1007/s10822-016-9950-z Text en © The Author(s) 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided 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. |
spellingShingle | Article Paranahewage, S. Shanaka Gierhart, Cassidy S. Fennell, Christopher J. Predicting water-to-cyclohexane partitioning of the SAMPL5 molecules using dielectric balancing of force fields |
title | Predicting water-to-cyclohexane partitioning of the SAMPL5 molecules using dielectric balancing of force fields |
title_full | Predicting water-to-cyclohexane partitioning of the SAMPL5 molecules using dielectric balancing of force fields |
title_fullStr | Predicting water-to-cyclohexane partitioning of the SAMPL5 molecules using dielectric balancing of force fields |
title_full_unstemmed | Predicting water-to-cyclohexane partitioning of the SAMPL5 molecules using dielectric balancing of force fields |
title_short | Predicting water-to-cyclohexane partitioning of the SAMPL5 molecules using dielectric balancing of force fields |
title_sort | predicting water-to-cyclohexane partitioning of the sampl5 molecules using dielectric balancing of force fields |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5206264/ https://www.ncbi.nlm.nih.gov/pubmed/27573982 http://dx.doi.org/10.1007/s10822-016-9950-z |
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