Literature DB >> 25589343

Determination of partial molar volumes from free energy perturbation theory.

Jonah Z Vilseck1, Julian Tirado-Rives, William L Jorgensen.   

Abstract

Partial molar volume is an important thermodynamic property that gives insights into molecular size and intermolecular interactions in solution. Theoretical frameworks for determining the partial molar volume (V°) of a solvated molecule generally apply Scaled Particle Theory or Kirkwood-Buff theory. With the current abilities to perform long molecular dynamics and Monte Carlo simulations, more direct methods are gaining popularity, such as computing V° directly as the difference in computed volume from two simulations, one with a solute present and another without. Thermodynamically, V° can also be determined as the pressure derivative of the free energy of solvation in the limit of infinite dilution. Both approaches are considered herein with the use of free energy perturbation (FEP) calculations to compute the necessary free energies of solvation at elevated pressures. Absolute and relative partial molar volumes are computed for benzene and benzene derivatives using the OPLS-AA force field. The mean unsigned error for all molecules is 2.8 cm(3) mol(-1). The present methodology should find use in many contexts such as the development and testing of force fields for use in computer simulations of organic and biomolecular systems, as a complement to related experimental studies, and to develop a deeper understanding of solute-solvent interactions.

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Year:  2015        PMID: 25589343      PMCID: PMC4872387          DOI: 10.1039/c4cp05304d

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  34 in total

1.  Development and testing of a general amber force field.

Authors:  Junmei Wang; Romain M Wolf; James W Caldwell; Peter A Kollman; David A Case
Journal:  J Comput Chem       Date:  2004-07-15       Impact factor: 3.376

2.  Molecular dynamics calculation of molecular volumes and volumes of activation.

Authors:  J Spooner; H Wiebe; N Boon; E Deglint; E Edwards; B Yanciw; B Patton; L Thiele; P Dance; N Weinberg
Journal:  Phys Chem Chem Phys       Date:  2012-01-12       Impact factor: 3.676

3.  Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model.

Authors:  Devleena Shivakumar; Yuqing Deng; Benoît Roux
Journal:  J Chem Theory Comput       Date:  2009-03-24       Impact factor: 6.006

4.  Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field.

Authors:  Devleena Shivakumar; Joshua Williams; Yujie Wu; Wolfgang Damm; John Shelley; Woody Sherman
Journal:  J Chem Theory Comput       Date:  2010-04-14       Impact factor: 6.006

Review 5.  Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.

Authors:  William L Jorgensen; Julian Tirado-Rives
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

6.  The application of the thermodynamic perturbation theory to study the hydrophobic hydration.

Authors:  Tomaz Mohoric; Tomaz Urbic; Barbara Hribar-Lee
Journal:  J Chem Phys       Date:  2013-07-14       Impact factor: 3.488

7.  Pressure reentrant assembly: direct simulation of volumes of micellization.

Authors:  Bin Meng; Henry S Ashbaugh
Journal:  Langmuir       Date:  2013-08-13       Impact factor: 3.882

8.  Studying pressure denaturation of a protein by molecular dynamics simulations.

Authors:  Sapna Sarupria; Tuhin Ghosh; Angel E García; Shekhar Garde
Journal:  Proteins       Date:  2010-05-15

9.  Predictions of hydration free energies from all-atom molecular dynamics simulations.

Authors:  David L Mobley; Christopher I Bayly; Matthew D Cooper; Ken A Dill
Journal:  J Phys Chem B       Date:  2009-04-09       Impact factor: 2.991

10.  CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.

Authors:  K Vanommeslaeghe; E Hatcher; C Acharya; S Kundu; S Zhong; J Shim; E Darian; O Guvench; P Lopes; I Vorobyov; A D Mackerell
Journal:  J Comput Chem       Date:  2010-03       Impact factor: 3.376

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  3 in total

1.  Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions.

Authors:  Jonah Z Vilseck; Jakub Kostal; Julian Tirado-Rives; William L Jorgensen
Journal:  J Comput Chem       Date:  2015-08-27       Impact factor: 3.376

2.  1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase Simulations.

Authors:  Leela S Dodda; Jonah Z Vilseck; Julian Tirado-Rives; William L Jorgensen
Journal:  J Phys Chem B       Date:  2017-03-02       Impact factor: 2.991

3.  Evaluation of CM5 Charges for Nonaqueous Condensed-Phase Modeling.

Authors:  Leela S Dodda; Jonah Z Vilseck; Kara J Cutrona; William L Jorgensen
Journal:  J Chem Theory Comput       Date:  2015-08-27       Impact factor: 6.006

  3 in total

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