Calculation of the free energy of solvation for neutral analogs of amino acid side chains

Villa, A. and Mark, A. E. (2002) Calculation of the free energy of solvation for neutral analogs of amino acid side chains. Journal of Computational Chemistry, 23 5: 548-553. doi:10.1002/jcc.10052


Author Villa, A.
Mark, A. E.
Title Calculation of the free energy of solvation for neutral analogs of amino acid side chains
Journal name Journal of Computational Chemistry   Check publisher's open access policy
ISSN 0192-8651
Publication date 2002-01-01
Sub-type Article (original research)
DOI 10.1002/jcc.10052
Volume 23
Issue 5
Start page 548
End page 553
Total pages 6
Place of publication Hoboken
Publisher John Wiley & Sons Inc
Language eng
Abstract The ability of the GROMOS96 force field to reproduce partition constants between water and two less polar solvents (cyclohexane and chloroform) for analogs of 18 of the 20 naturally occurring amino acids has been investigated. The estimations of the solvation free energies in water, in cyclohexane solution, and chloroform solution are based on thermodynamic integration free energy calculations using molecular dynamics simulations. The calculations show that while the force field reproduces the experimental solvation free energies of nonpolar analogs with reasonable accuracy the solvation free energies of polar analogs in water are systematically overestimated (too positive). The dependence of the calculated free energies on the atomic partial charges was also studied. (C) 2002 Wiley Periodicals, Inc.
Keyword Chemistry, Multidisciplinary
GROMOS96 force field
free energy calculations
partition constants
amino acid analogs
GROMACS
Molecular-dynamics
Aqueous-solution
Organic Solutes
Force-field
Simulations
Coefficients
Proteins
Water
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Unknown

Document type: Journal Article
Sub-type: Article (original research)
Collections: Excellence in Research Australia (ERA) - Collection
School of Chemistry and Molecular Biosciences
 
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Citation counts: TR Web of Science Citation Count  Cited 106 times in Thomson Reuters Web of Science Article | Citations
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Created: Thu, 20 Sep 2007, 01:48:43 EST