On the accuracy of one- and two-particle solvation entropies

The Journal of Chemical Physics
Benedict W J Irwin, David J Huggins

Abstract

Evaluating solvation entropies directly and combining with direct energy calculations is one way of calculating free energies of solvation and is used by Inhomogeneous Fluid Solvation Theory (IFST). The configurational entropy of a fluid is a function of the interatomic correlations and can thus be expressed in terms of correlation functions. The entropies in this work are directly calculated from a truncated series of integrals over these correlation functions. Many studies truncate all terms higher than the solvent-solute correlations. This study includes an additional solvent-solvent correlation term and assesses the associated free energy when IFST is applied to a fixed Lennard-Jones particle solvated in neon. The strength of the central potential is varied to imitate larger solutes. Average free energy estimates with both levels of IFST are able to reproduce the estimate made using the Free energy Perturbation (FEP) to within 0.16 kcal/mol. We find that the signal from the solvent-solvent correlations is very weak. Our conclusion is that for monatomic fluids simulated by pairwise classical potentials the correction term is relatively small in magnitude. This study shows it is possible to reproduce the free energy from a pa...Continue Reading

References

Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Jul 1, 1988·Physical Review A: General Physics·D C Wallace
May 1, 1989·Physical Review A: General Physics·D C Wallace
Oct 1, 1989·Physical Review A: General Physics·A Baranyai, D J Evans
Sep 24, 2005·The Journal of Chemical Physics·Jan Zielkiewicz
Oct 14, 2005·Journal of Computational Chemistry·James C PhillipsKlaus Schulten
Dec 30, 2006·Journal of Computational Chemistry·Vladimir HnizdoHarshinder Singh
Jan 5, 2007·Annual Review of Biophysics and Biomolecular Structure·Michael K Gilson, Huan-Xiang Zhou
Jan 11, 2007·The Journal of Chemical Physics·Friedemann Reinhard, Helmut Grubmüller
Aug 8, 2009·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Ulf HensenOliver F Lange
Nov 10, 2009·The Journal of Chemical Physics·Alauddin Ahmed, Richard J Sadus
Aug 13, 2010·The Journal of Physical Chemistry. B·Andrew PohorilleChristophe Chipot
Jul 24, 2012·The Journal of Physical Chemistry. B·Bradley M DicksonCarol Beth Post
Mar 8, 2013·The Journal of Chemical Physics·Gabriel J RocklinKen A Dill
Jun 15, 2013·The Journal of Physical Chemistry. B·David J Huggins, Mike C Payne
Jul 16, 2014·Journal of Chemical Theory and Computation·Crystal N NguyenTom Kurtzman
Nov 18, 2015·Journal of Chemical Theory and Computation·Camilo Velez-VegaJosé S Duca
Sep 9, 2014·Journal of Chemical Theory and Computation·David J Huggins
Aug 14, 2012·Journal of Chemical Theory and Computation·Peng LiuChristophe Chipot
Dec 5, 2015·Journal of Chemical Theory and Computation·Crystal N NguyenMichael K Gilson

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Citations

Apr 27, 2019·The Journal of Physical Chemistry. B·Benedict W J IrwinDavid J Huggins
May 2, 2018·Journal of Chemical Theory and Computation·Benedict W J Irwin, David J Huggins

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Software Mentioned

ParseFEP Plugin for Visual Molecular Dynamics ( VMD )
Grid Inhomogeneous Solvation Theory ( GIST
NAMD
NpT
FEP
IFST
gnuplot
GIST
CHARMM27

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