Literature DB >> 22397577

Simple liquid models with corrected dielectric constants.

Christopher J Fennell1, Libo Li, Ken A Dill.   

Abstract

Molecular simulations often use explicit-solvent models. Sometimes explicit-solvent models can give inaccurate values for basic liquid properties, such as the density, heat capacity, and permittivity, as well as inaccurate values for molecular transfer free energies. Such errors have motivated the development of more complex solvents, such as polarizable models. We describe an alternative here. We give new fixed-charge models of solvents for molecular simulations--water, carbon tetrachloride, chloroform, and dichloromethane. Normally, such solvent models are parametrized to agree with experimental values of the neat liquid density and enthalpy of vaporization. Here, in addition to those properties, our parameters are chosen to give the correct dielectric constant. We find that these new parametrizations also happen to give better values for other properties, such as the self-diffusion coefficient. We believe that parametrizing fixed-charge solvent models to fit experimental dielectric constants may provide better and more efficient ways to treat solvents in computer simulations.

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Year:  2012        PMID: 22397577      PMCID: PMC3729351          DOI: 10.1021/jp3002383

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


  9 in total

1.  A novel approach for designing simple point charge models for liquid water with three interaction sites.

Authors:  Alice Glättli; Xavier Daura; Wilfred F Van Gunsteren
Journal:  J Comput Chem       Date:  2003-07-15       Impact factor: 3.376

2.  Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew.

Authors:  Hans W Horn; William C Swope; Jed W Pitera; Jeffry D Madura; Thomas J Dick; Greg L Hura; Teresa Head-Gordon
Journal:  J Chem Phys       Date:  2004-05-22       Impact factor: 3.488

3.  A reoptimization of the five-site water potential (TIP5P) for use with Ewald sums.

Authors:  Steven W Rick
Journal:  J Chem Phys       Date:  2004-04-01       Impact factor: 3.488

4.  GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.

Authors:  Berk Hess; Carsten Kutzner; David van der Spoel; Erik Lindahl
Journal:  J Chem Theory Comput       Date:  2008-03       Impact factor: 6.006

5.  Flexible simple point-charge water model with improved liquid-state properties.

Authors:  Yujie Wu; Harald L Tepper; Gregory A Voth
Journal:  J Chem Phys       Date:  2006-01-14       Impact factor: 3.488

6.  A general purpose model for the condensed phases of water: TIP4P/2005.

Authors:  J L F Abascal; C Vega
Journal:  J Chem Phys       Date:  2005-12-15       Impact factor: 3.488

7.  A computational investigation of thermodynamics, structure, dynamics and solvation behavior in modified water models.

Authors:  Swaroop Chatterjee; Pablo G Debenedetti; Frank H Stillinger; Ruth M Lynden-Bell
Journal:  J Chem Phys       Date:  2008-03-28       Impact factor: 3.488

8.  The spatial structure in liquid water.

Authors:  P G Kusalik; I M Svishchev
Journal:  Science       Date:  1994-08-26       Impact factor: 47.728

9.  The Origin of Layer Structure Artifacts in Simulations of Liquid Water.

Authors:  David van der Spoel; Paul J van Maaren
Journal:  J Chem Theory Comput       Date:  2006-01       Impact factor: 6.006

  9 in total
  15 in total

1.  Adapting the semi-explicit assembly solvation model for estimating water-cyclohexane partitioning with the SAMPL5 molecules.

Authors:  Emiliano Brini; S Shanaka Paranahewage; Christopher J Fennell; Ken A Dill
Journal:  J Comput Aided Mol Des       Date:  2016-09-08       Impact factor: 3.686

2.  Testing the semi-explicit assembly model of aqueous solvation in the SAMPL4 challenge.

Authors:  Libo Li; Ken A Dill; Christopher J Fennell
Journal:  J Comput Aided Mol Des       Date:  2014-01-29       Impact factor: 3.686

3.  Accuracy limit of rigid 3-point water models.

Authors:  Saeed Izadi; Alexey V Onufriev
Journal:  J Chem Phys       Date:  2016-08-21       Impact factor: 3.488

Review 4.  Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems.

Authors:  Fernando Luís Barroso daSilva; Luis Gustavo Dias
Journal:  Biophys Rev       Date:  2017-09-18

5.  Dielectric screening effect of electronic polarization and intramolecular hydrogen bonding.

Authors:  Shen-Shu Sung
Journal:  Protein Sci       Date:  2017-07-28       Impact factor: 6.725

6.  Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation.

Authors:  Saeed Izadi; Boris Aguilar; Alexey V Onufriev
Journal:  J Chem Theory Comput       Date:  2015-08-21       Impact factor: 6.006

7.  Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive.

Authors:  Kyle A Beauchamp; Julie M Behr; Ariën S Rustenburg; Christopher I Bayly; Kenneth Kroenlein; John D Chodera
Journal:  J Phys Chem B       Date:  2015-09-29       Impact factor: 2.991

Review 8.  Water in Nanopores and Biological Channels: A Molecular Simulation Perspective.

Authors:  Charlotte I Lynch; Shanlin Rao; Mark S P Sansom
Journal:  Chem Rev       Date:  2020-08-25       Impact factor: 60.622

9.  Polarizable Water Potential Derived from a Model Electron Density.

Authors:  Joshua A Rackers; Roseane R Silva; Zhi Wang; Jay W Ponder
Journal:  J Chem Theory Comput       Date:  2021-10-26       Impact factor: 6.006

10.  A fixed-charge model for alcohol polarization in the condensed phase, and its role in small molecule hydration.

Authors:  Christopher J Fennell; Karisa L Wymer; David L Mobley
Journal:  J Phys Chem B       Date:  2014-04-17       Impact factor: 2.991

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