Literature DB >> 25005273

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

Igor V Leontyev1, Alexei A Stuchebrukhov1.   

Abstract

Earlier, using phenomenological approach, we showed that in some cases polarizable models of condensed phase systems can be reduced to nonpolarizable equivalent models with scaled charges. Examples of such systems include ionic liquids, TIPnP-type models of water, protein force fields, and others, where interactions and dynamics of inherently polarizable species can be accurately described by nonpolarizable models. To describe electrostatic interactions, the effective charges of simple ionic liquids are obtained by scaling the actual charges of ions by a factor of 1/√(ε(el)), which is due to electronic polarization screening effect; the scaling factor of neutral species is more complicated. Here, using several theoretical models, we examine how exactly the scaling factors appear in theory, and how, and under what conditions, polarizable Hamiltonians are reduced to nonpolarizable ones. These models allow one to trace the origin of the scaling factors, determine their values, and obtain important insights on the nature of polarizable interactions in condensed matter systems.

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Year:  2014        PMID: 25005273      PMCID: PMC4106032          DOI: 10.1063/1.4884276

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


  41 in total

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Review 2.  Molecular dynamics simulations of biomolecules.

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Journal:  Nat Struct Biol       Date:  2002-09

Review 3.  Force fields for protein simulations.

Authors:  Jay W Ponder; David A Case
Journal:  Adv Protein Chem       Date:  2003

4.  Elucidating the mechanism of selective ion adsorption to the liquid water surface.

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Journal:  Proc Natl Acad Sci U S A       Date:  2012-01-10       Impact factor: 11.205

5.  Influence of polarization on structural, thermodynamic, and dynamic properties of ionic liquids obtained from molecular dynamics simulations.

Authors:  Dmitry Bedrov; Oleg Borodin; Zhe Li; Grant D Smith
Journal:  J Phys Chem B       Date:  2010-04-22       Impact factor: 2.991

Review 6.  Accounting for electronic polarization in non-polarizable force fields.

Authors:  Igor Leontyev; Alexei Stuchebrukhov
Journal:  Phys Chem Chem Phys       Date:  2011-01-07       Impact factor: 3.676

7.  Electronic continuum model for molecular dynamics simulations.

Authors:  I V Leontyev; A A Stuchebrukhov
Journal:  J Chem Phys       Date:  2009-02-28       Impact factor: 3.488

8.  Screening of pairs of ions dissolved in ionic liquids.

Authors:  R M Lynden-Bell
Journal:  Phys Chem Chem Phys       Date:  2009-11-12       Impact factor: 3.676

9.  Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers.

Authors:  Igor Vorobyov; Victor M Anisimov; Shannon Greene; Richard M Venable; Adam Moser; Richard W Pastor; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2007-05       Impact factor: 6.006

10.  The Polarizable Atomic Multipole-based AMOEBA Force Field for Proteins.

Authors:  Yue Shi; Zhen Xia; Jiajing Zhang; Robert Best; Chuanjie Wu; Jay W Ponder; Pengyu Ren
Journal:  J Chem Theory Comput       Date:  2013       Impact factor: 6.006

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  10 in total

Review 1.  Metal Ion Modeling Using Classical Mechanics.

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Journal:  Chem Rev       Date:  2017-01-03       Impact factor: 60.622

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3.  Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions.

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4.  Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg(2+) ion models commonly used in biomolecular simulations.

Authors:  Maria T Panteva; George M Giambaşu; Darrin M York
Journal:  J Comput Chem       Date:  2015-03-04       Impact factor: 3.376

5.  A Kirkwood-Buff derived force field for alkaline earth halide salts.

Authors:  Nawavi Naleem; Nikolaos Bentenitis; Paul E Smith
Journal:  J Chem Phys       Date:  2018-06-14       Impact factor: 3.488

6.  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

7.  Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel.

Authors:  Van Ngo; Hui Li; Alexander D MacKerell; Toby W Allen; Benoît Roux; Sergei Noskov
Journal:  J Chem Theory Comput       Date:  2021-02-04       Impact factor: 6.006

8.  Evaluating Force Field Performance in Thermodynamic Calculations of Cyclodextrin Host-Guest Binding: Water Models, Partial Charges, and Host Force Field Parameters.

Authors:  Niel M Henriksen; Michael K Gilson
Journal:  J Chem Theory Comput       Date:  2017-08-04       Impact factor: 6.006

9.  Computational and structural evidence for neurotransmitter-mediated modulation of the oligomeric states of human insulin in storage granules.

Authors:  Vladimír Palivec; Cristina M Viola; Mateusz Kozak; Timothy R Ganderton; Květoslava Křížková; Johan P Turkenburg; Petra Haluŝková; Lenka Žáková; Jiří Jiráĉek; Pavel Jungwirth; Andrzej M Brzozowski
Journal:  J Biol Chem       Date:  2017-03-27       Impact factor: 5.157

10.  On the importance of accounting for nuclear quantum effects in ab initio calibrated force fields in biological simulations.

Authors:  Leonid Pereyaslavets; Igor Kurnikov; Ganesh Kamath; Oleg Butin; Alexey Illarionov; Igor Leontyev; Michael Olevanov; Michael Levitt; Roger D Kornberg; Boris Fain
Journal:  Proc Natl Acad Sci U S A       Date:  2018-08-20       Impact factor: 11.205

  10 in total

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