Literature DB >> 17313226

Free energy of liquid water from a computer simulation via cell theory.

Richard H Henchman1.   

Abstract

A method to calculate the free energy of water from computer simulation is presented. Based on cell theory, it approximates the potential energy surface sampled in the simulation by an anisotropic six-dimensional harmonic potential to model the three hindered translations and three hindered rotations of a single rigid water molecule. The potential is parametrized from the magnitude of the forces and torques measured in the simulation. The entropy of these six harmonic oscillators is calculated and summed with a conformational term to give the total entropy. Combining this with the simulation enthalpy yields the free energy. The six water models examined are TIP3P, SPC, TIP4P, SPC/E, TIP5P, and TIP4P-Ew. The results reproduce experiment well: free energies for all models are within 1.6 kJ mol(-1) and entropies are within 3.6 J K(-1) mol(-1). Approximately two-thirds of the entropy comes from translation, a third from rotation, and 5% from conformation. Vibrational frequencies match those in the experimental infrared spectrum and assist in their assignment. Intermolecular quantum effects are found to be small, with free energies for the classical oscillator lying 0.5-0.7 kJ mol(-1) higher than in the quantum case. Molecular displacements and vibrational and zero point energies are also calculated. Altogether, these results validate the harmonic oscillator as a quantitative model for the liquid state.

Entities:  

Year:  2007        PMID: 17313226     DOI: 10.1063/1.2434964

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  11 in total

1.  Binding Thermodynamics and Kinetics Calculations Using Chemical Host and Guest: A Comprehensive Picture of Molecular Recognition.

Authors:  Zhiye Tang; Chia-En A Chang
Journal:  J Chem Theory Comput       Date:  2017-12-14       Impact factor: 6.006

2.  Comparison of entropic contributions to binding in a "hydrophilic" versus "hydrophobic" ligand-protein interaction.

Authors:  Neil R Syme; Caitriona Dennis; Agnieszka Bronowska; Guido C Paesen; Steve W Homans
Journal:  J Am Chem Soc       Date:  2010-06-30       Impact factor: 15.419

3.  Thermodynamic properties of liquid water: an application of a nonparametric approach to computing the entropy of a neat fluid.

Authors:  Lingle Wang; Robert Abel; Richard A Friesner; B J Berne
Journal:  J Chem Theory Comput       Date:  2009-06-09       Impact factor: 6.006

4.  Entropy from state probabilities: hydration entropy of cations.

Authors:  Roland G Huber; Julian E Fuchs; Susanne von Grafenstein; Monika Laner; Hannes G Wallnoefer; Nejma Abdelkader; Romano T Kroemer; Klaus R Liedl
Journal:  J Phys Chem B       Date:  2013-05-20       Impact factor: 2.991

5.  Entropy of Simulated Liquids Using Multiscale Cell Correlation.

Authors:  Hafiz Saqib Ali; Jonathan Higham; Richard H Henchman
Journal:  Entropy (Basel)       Date:  2019-07-31       Impact factor: 2.524

6.  Correlations in liquid water for the TIP3P-Ewald, TIP4P-2005, TIP5P-Ewald, and SWM4-NDP models.

Authors:  David J Huggins
Journal:  J Chem Phys       Date:  2012-02-14       Impact factor: 3.488

7.  Assessing the accuracy of inhomogeneous fluid solvation theory in predicting hydration free energies of simple solutes.

Authors:  David J Huggins; Mike C Payne
Journal:  J Phys Chem B       Date:  2013-06-26       Impact factor: 2.991

8.  Current and emerging opportunities for molecular simulations in structure-based drug design.

Authors:  Julien Michel
Journal:  Phys Chem Chem Phys       Date:  2014-03-14       Impact factor: 3.676

9.  Energy-entropy prediction of octanol-water logP of SAMPL7 N-acyl sulfonamide bioisosters.

Authors:  Fabio Falcioni; Jas Kalayan; Richard H Henchman
Journal:  J Comput Aided Mol Des       Date:  2021-07-10       Impact factor: 3.686

10.  Energy-entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host-guest challenge.

Authors:  Hafiz Saqib Ali; Arghya Chakravorty; Jas Kalayan; Samuel P de Visser; Richard H Henchman
Journal:  J Comput Aided Mol Des       Date:  2021-07-15       Impact factor: 3.686

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