Document Detail


Parameterization of a geometric flow implicit solvation model.
MedLine Citation:
PMID:  23212974     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Implicit solvent models are popular for their high computational efficiency and simplicity over explicit solvent models and are extensively used for computing molecular solvation properties. The accuracy of implicit solvent models depends on the geometric description of the solute-solvent interface and the solvent dielectric profile that is defined near the surface of the solute molecule. Typically, it is assumed that the dielectric profile is spatially homogeneous in the bulk solvent medium and varies sharply across the solute-solvent interface. However, the specific form of this profile is often described by ad hoc geometric models rather than physical solute-solvent interactions. Hence, it is of significant interest to improve the accuracy of these implicit solvent models by more realistically defining the solute-solvent boundary within a continuum setting. Recently, a differential geometry-based geometric flow solvation model was developed, in which the polar and nonpolar free energies are coupled through a characteristic function that describes a smooth dielectric interface profile across the solvent-solute boundary in a thermodynamically self-consistent fashion. The main parameters of the model are the solute/solvent dielectric coefficients, solvent pressure on the solute, microscopic surface tension, solvent density, and molecular force-field parameters. In this work, we investigate how changes in the pressure, surface tension, solute dielectric coefficient, and choice of different force-field charge and radii parameters affect the prediction accuracy for hydration free energies of 17 small organic molecules based on the geometric flow solvation model. The results of our study provide insights on the parameterization, accuracy, and predictive power of this new implicit solvent model.
Authors:
Dennis G Thomas; Jaehun Chun; Zhan Chen; Guowei Wei; Nathan A Baker
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Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural     Date:  2012-12-05
Journal Detail:
Title:  Journal of computational chemistry     Volume:  34     ISSN:  1096-987X     ISO Abbreviation:  J Comput Chem     Publication Date:  2013 Mar 
Date Detail:
Created Date:  2013-02-21     Completed Date:  2013-07-30     Revised Date:  2014-04-01    
Medline Journal Info:
Nlm Unique ID:  9878362     Medline TA:  J Comput Chem     Country:  United States    
Other Details:
Languages:  eng     Pagination:  687-95     Citation Subset:  IM    
Copyright Information:
Copyright © 2012 Wiley Periodicals, Inc.
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MeSH Terms
Descriptor/Qualifier:
Models, Chemical*
Molecular Structure
Solvents / chemistry*
Grant Support
ID/Acronym/Agency:
R01 GM069702/GM/NIGMS NIH HHS; R01 GM069702/GM/NIGMS NIH HHS; R01 GM090208/GM/NIGMS NIH HHS; R01 GM090208/GM/NIGMS NIH HHS
Chemical
Reg. No./Substance:
0/Solvents
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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