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J Phys Chem B. 2008 Jan 24;112(3):938-46. doi: 10.1021/jp0764384. Epub 2008 Jan 3.

Treating entropy and conformational changes in implicit solvent simulations of small molecules.

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1
Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA. dmobley@gmail.com

Abstract

Implicit solvent models are increasingly popular for estimating aqueous solvation (hydration) free energies in molecular simulations and other applications. In many cases, parameters for these models are derived to reproduce experimental values for small molecule hydration free energies. Often, these hydration free energies are computed for a single solute conformation, neglecting solute conformational changes upon solvation. Here, we incorporate these effects using alchemical free energy methods. We find significant errors when hydration free energies are estimated using only a single solute conformation, even for relatively small, simple, rigid solutes. For example, we find conformational entropy (TDeltaS) changes of up to 2.3 kcal/mol upon hydration. Interestingly, these changes in conformational entropy correlate poorly (R2 = 0.03) with the number of rotatable bonds. The present study illustrates that implicit solvent modeling can be improved by eliminating the approximation that solutes are rigid.

PMID:
18171044
PMCID:
PMC2745223
DOI:
10.1021/jp0764384
[Indexed for MEDLINE]
Free PMC Article
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