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Field-SEA: A Model for Computing the Solvation Free Energies of Nonpolar, Polar, and Charged Solutes in Water
[Image: see text] Previous work describes a computational solvation model called semi-explicit assembly (SEA). The SEA water model computes the free energies of solvation of nonpolar and polar solutes in water with good efficiency and accuracy. However, SEA gives systematic errors in the solvation f...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Chemical
Society
2013
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4065164/ https://www.ncbi.nlm.nih.gov/pubmed/24299013 http://dx.doi.org/10.1021/jp4115139 |
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author | Li, Libo Fennell, Christopher J. Dill, Ken A. |
author_facet | Li, Libo Fennell, Christopher J. Dill, Ken A. |
author_sort | Li, Libo |
collection | PubMed |
description | [Image: see text] Previous work describes a computational solvation model called semi-explicit assembly (SEA). The SEA water model computes the free energies of solvation of nonpolar and polar solutes in water with good efficiency and accuracy. However, SEA gives systematic errors in the solvation free energies of ions and charged solutes. Here, we describe field-SEA, an improved treatment that gives accurate solvation free energies of charged solutes, including monatomic and polyatomic ions and model dipeptides, as well as nonpolar and polar molecules. Field-SEA is computationally inexpensive for a given solute because explicit-solvent model simulations are relegated to a precomputation step and because it represents solvating waters in terms of a solute’s free-energy field. In essence, field-SEA approximates the physics of explicit-model simulations within a computationally efficient framework. A key finding is that an atom’s solvation shell inherits characteristics of a neighboring atom, especially strongly charged neighbors. Field-SEA may be useful where there is a need for solvation free-energy computations that are faster than explicit-solvent simulations and more accurate than traditional implicit-solvent simulations for a wide range of solutes. |
format | Online Article Text |
id | pubmed-4065164 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | American Chemical
Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-40651642014-06-23 Field-SEA: A Model for Computing the Solvation Free Energies of Nonpolar, Polar, and Charged Solutes in Water Li, Libo Fennell, Christopher J. Dill, Ken A. J Phys Chem B [Image: see text] Previous work describes a computational solvation model called semi-explicit assembly (SEA). The SEA water model computes the free energies of solvation of nonpolar and polar solutes in water with good efficiency and accuracy. However, SEA gives systematic errors in the solvation free energies of ions and charged solutes. Here, we describe field-SEA, an improved treatment that gives accurate solvation free energies of charged solutes, including monatomic and polyatomic ions and model dipeptides, as well as nonpolar and polar molecules. Field-SEA is computationally inexpensive for a given solute because explicit-solvent model simulations are relegated to a precomputation step and because it represents solvating waters in terms of a solute’s free-energy field. In essence, field-SEA approximates the physics of explicit-model simulations within a computationally efficient framework. A key finding is that an atom’s solvation shell inherits characteristics of a neighboring atom, especially strongly charged neighbors. Field-SEA may be useful where there is a need for solvation free-energy computations that are faster than explicit-solvent simulations and more accurate than traditional implicit-solvent simulations for a wide range of solutes. American Chemical Society 2013-12-04 2014-06-19 /pmc/articles/PMC4065164/ /pubmed/24299013 http://dx.doi.org/10.1021/jp4115139 Text en Copyright © 2013 American Chemical Society Terms of Use (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html) |
spellingShingle | Li, Libo Fennell, Christopher J. Dill, Ken A. Field-SEA: A Model for Computing the Solvation Free Energies of Nonpolar, Polar, and Charged Solutes in Water |
title | Field-SEA:
A Model for Computing the Solvation Free Energies of Nonpolar, Polar,
and Charged Solutes in Water |
title_full | Field-SEA:
A Model for Computing the Solvation Free Energies of Nonpolar, Polar,
and Charged Solutes in Water |
title_fullStr | Field-SEA:
A Model for Computing the Solvation Free Energies of Nonpolar, Polar,
and Charged Solutes in Water |
title_full_unstemmed | Field-SEA:
A Model for Computing the Solvation Free Energies of Nonpolar, Polar,
and Charged Solutes in Water |
title_short | Field-SEA:
A Model for Computing the Solvation Free Energies of Nonpolar, Polar,
and Charged Solutes in Water |
title_sort | field-sea:
a model for computing the solvation free energies of nonpolar, polar,
and charged solutes in water |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4065164/ https://www.ncbi.nlm.nih.gov/pubmed/24299013 http://dx.doi.org/10.1021/jp4115139 |
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