Literature DB >> 16723394

Water properties from first principles: simulations by a general-purpose quantum mechanical polarizable force field.

A G Donchev1, N G Galkin, A A Illarionov, O V Khoruzhii, M A Olevanov, V D Ozrin, M V Subbotin, V I Tarasov.   

Abstract

We have recently introduced a quantum mechanical polarizable force field (QMPFF) fitted solely to high-level quantum mechanical data for simulations of biomolecular systems. Here, we present an improved form of the force field, QMPFF2, and apply it to simulations of liquid water. The results of the simulations show excellent agreement with a variety of experimental thermodynamic and structural data, as good or better than that provided by specialized water potentials. In particular, QMPFF2 is the only ab initio force field to accurately reproduce the anomalous temperature dependence of water density to our knowledge. The ability of the same force field to successfully simulate the properties of both organic molecules and water suggests it will be useful for simulations of proteins and protein-ligand interactions in the aqueous environment.

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Year:  2006        PMID: 16723394      PMCID: PMC1466545          DOI: 10.1073/pnas.0602982103

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  9 in total

1.  An ab initio molecular dynamics study of the aqueous liquid-vapor interface.

Authors:  I-Feng W Kuo; Christopher J Mundy
Journal:  Science       Date:  2004-01-30       Impact factor: 47.728

2.  Towards an assessment of the accuracy of density functional theory for first principles simulations of water.

Authors:  Jeffrey C Grossman; Eric Schwegler; Erik W Draeger; François Gygi; Giulia Galli
Journal:  J Chem Phys       Date:  2004-01-01       Impact factor: 3.488

3.  Unified approach for molecular dynamics and density-functional theory.

Authors: 
Journal:  Phys Rev Lett       Date:  1985-11-25       Impact factor: 9.161

4.  Static and dynamic quantum effects in molecular liquids: a linearized path integral description of water.

Authors:  Jens Aage Poulsen; Gunnar Nyman; Peter J Rossky
Journal:  Proc Natl Acad Sci U S A       Date:  2005-04-28       Impact factor: 11.205

5.  A quantum mechanical polarizable force field for biomolecular interactions.

Authors:  A G Donchev; V D Ozrin; M V Subbotin; O V Tarasov; V I Tarasov
Journal:  Proc Natl Acad Sci U S A       Date:  2005-05-23       Impact factor: 11.205

6.  What don't we know?

Authors:  Donald Kennedy; Colin Norman
Journal:  Science       Date:  2005-07-01       Impact factor: 47.728

7.  Refinement of protein conformations using a macromolecular energy minimization procedure.

Authors:  M Levitt; S Lifson
Journal:  J Mol Biol       Date:  1969-12-14       Impact factor: 5.469

8.  Hydrogen bonding in water.

Authors:  Bin Chen; Ivaylo Ivanov; Michael L Klein; Michele Parrinello
Journal:  Phys Rev Lett       Date:  2003-11-20       Impact factor: 9.161

9.  Consistent treatment of inter- and intramolecular polarization in molecular mechanics calculations.

Authors:  Pengyu Ren; Jay W Ponder
Journal:  J Comput Chem       Date:  2002-12       Impact factor: 3.376

  9 in total
  11 in total

1.  Application of a polarizable force field to calculations of relative protein-ligand binding affinities.

Authors:  Oleg Khoruzhii; Alexander G Donchev; Nikolay Galkin; Alexei Illarionov; Mikhail Olevanov; Vladimir Ozrin; Cary Queen; Vladimir Tarasov
Journal:  Proc Natl Acad Sci U S A       Date:  2008-07-24       Impact factor: 11.205

Review 2.  Modeling kinetics of subcellular disposition of chemicals.

Authors:  Stefan Balaz
Journal:  Chem Rev       Date:  2009-05       Impact factor: 60.622

3.  Remarkable patterns of surface water ordering around polarized buckminsterfullerene.

Authors:  Gaurav Chopra; Michael Levitt
Journal:  Proc Natl Acad Sci U S A       Date:  2011-08-15       Impact factor: 11.205

4.  Polarizable molecular interactions in condensed phase and their equivalent nonpolarizable models.

Authors:  Igor V Leontyev; Alexei A Stuchebrukhov
Journal:  J Chem Phys       Date:  2014-07-07       Impact factor: 3.488

5.  Improved parameterization of interatomic potentials for rare gas dimers with density-based energy decomposition analysis.

Authors:  Nengjie Zhou; Zhenyu Lu; Qin Wu; Yingkai Zhang
Journal:  J Chem Phys       Date:  2014-06-07       Impact factor: 3.488

6.  Prediction of cyclohexane-water distribution coefficient for SAMPL5 drug-like compounds with the QMPFF3 and ARROW polarizable force fields.

Authors:  Ganesh Kamath; Igor Kurnikov; Boris Fain; Igor Leontyev; Alexey Illarionov; Oleg Butin; Michael Olevanov; Leonid Pereyaslavets
Journal:  J Comput Aided Mol Des       Date:  2016-09-01       Impact factor: 3.686

7.  A statistical mechanical theory for a two-dimensional model of water.

Authors:  Tomaz Urbic; Ken A Dill
Journal:  J Chem Phys       Date:  2010-06-14       Impact factor: 3.488

8.  Analytical model for three-dimensional Mercedes-Benz water molecules.

Authors:  T Urbic
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2012-06-25

Review 9.  An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications.

Authors:  Justin A Lemkul; Jing Huang; Benoît Roux; Alexander D MacKerell
Journal:  Chem Rev       Date:  2016-01-27       Impact factor: 60.622

10.  Quantum Calculations On Hydrogen Bonds In Certain Water Clusters Show Cooperative Effects.

Authors:  Vasiliy S Znamenskiy; Michael E Green
Journal:  J Chem Theory Comput       Date:  2007-01       Impact factor: 6.006

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