Literature DB >> 18570394

Revised charge equilibration potential for liquid alkanes.

Joseph E Davis1, G Lee Warren, Sandeep Patel.   

Abstract

We present a revised liquid alkane force field based on the charge equilibration formalism for incorporating electrostatic nonadditive effects arising from local polarization. The model is a revision of earlier work by Patel and Brooks, specifically addressing deficiencies in the dihedral potential, electrostatic, and Lennard-Jones (van der Waals) parameters of the force field. We discuss refinement of the alkane backbone torsion potential to match high-level ab initio relative conformational energetics for pentane, hexane, and heptane. We further discuss refinement of the electrostatic and Lennard-Jones (van der Waals) parameters to reproduce the experimental polarizability, liquid density, and vaporization enthalpy of hexane. Finally, we calculate bulk liquid properties including densities, vaporization enthalpies, self-diffusion constants, isothermal compressibilities, constant pressure heat capacities, and NMR T 1 relaxation times for a series of linear alkanes ranging from hexane to pentadecane based on the current revised model. We also compute free energies of hydration for pentane, hexane, and heptane. The revised force field offers a significantly improved overall description of these properties relative to the original parametrization. The current alkane force field represents a platform for ongoing development of a CHARMM (Chemistry at Harvard Molecular Mechanics) polarizable force field for lipids and integral membrane proteins.

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Year:  2008        PMID: 18570394     DOI: 10.1021/jp8003129

Source DB:  PubMed          Journal:  J Phys Chem B        ISSN: 1520-5207            Impact factor:   2.991


  16 in total

1.  Incorporation of charge transfer into the explicit polarization fragment method by grand canonical density functional theory.

Authors:  Miho Isegawa; Jiali Gao; Donald G Truhlar
Journal:  J Chem Phys       Date:  2011-08-28       Impact factor: 3.488

2.  Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications.

Authors:  Pedro E M Lopes; Benoit Roux; Alexander D Mackerell
Journal:  Theor Chem Acc       Date:  2009-09       Impact factor: 1.702

3.  Nonadditive empirical force fields for short-chain linear alcohols: methanol to butanol. Hydration free energetics and Kirkwood-Buff analysis using charge equilibration models.

Authors:  Yang Zhong; Sandeep Patel
Journal:  J Phys Chem B       Date:  2010-09-02       Impact factor: 2.991

4.  Polarizable empirical force field for sulfur-containing compounds based on the classical Drude oscillator model.

Authors:  Xiao Zhu; Alexander D MacKerell
Journal:  J Comput Chem       Date:  2010-09       Impact factor: 3.376

5.  Phase-transfer energetics of small-molecule alcohols across the water-hexane interface: molecular dynamics simulations using charge equilibration models.

Authors:  Brad A Bauer; Yang Zhong; David J Meninger; Joseph E Davis; Sandeep Patel
Journal:  J Mol Graph Model       Date:  2010-10-01       Impact factor: 2.518

Review 6.  Charge equilibration force fields for molecular dynamics simulations of lipids, bilayers, and integral membrane protein systems.

Authors:  Timothy R Lucas; Brad A Bauer; Sandeep Patel
Journal:  Biochim Biophys Acta       Date:  2011-09-24

7.  Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field.

Authors:  Christopher M Baker; Pedro E M Lopes; Xiao Zhu; Benoît Roux; Alexander D Mackerell
Journal:  J Chem Theory Comput       Date:  2010-03-01       Impact factor: 6.006

8.  Exploring ion permeation energetics in gramicidin A using polarizable charge equilibration force fields.

Authors:  Sandeep Patel; Joseph E Davis; Brad A Bauer
Journal:  J Am Chem Soc       Date:  2009-10-07       Impact factor: 15.419

9.  Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers.

Authors:  Christopher M Baker; Alexander D Mackerell
Journal:  J Mol Model       Date:  2009-08-25       Impact factor: 1.810

10.  Binding structures of tri-N-acetyl-β-glucosamine in hen egg white lysozyme using molecular dynamics with a polarizable force field.

Authors:  Yang Zhong; Sandeep Patel
Journal:  J Comput Chem       Date:  2012-10-29       Impact factor: 3.376

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