Literature DB >> 26636199

Polarizable Force Fields:  History, Test Cases, and Prospects.

Arieh Warshel1, Mitsunori Kato1, Andrei V Pisliakov1.   

Abstract

A consistent treatment of electrostatic energies is arguably the most important requirement for the realistic modeling of biological systems. An important part of electrostatic modeling is the ability to account for the polarizability of the simulated system. This can be done both macroscopically and microscopically, but the use of macroscopic models may lead to conceptual traps, which do not exist in the microscopic treatments. The present work describes the development of microscopic polarizable force fields starting with the introduction of these powerful tools and following some of the subsequent developments in the field. Special effort has been made to review a wide range of applications and emphasize cases when the use of polarizable force fields is important. Finally, a brief perspective is given on the future of this rapidly growing field.

Year:  2007        PMID: 26636199     DOI: 10.1021/ct700127w

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  59 in total

1.  Three applications of path integrals: equilibrium and kinetic isotope effects, and the temperature dependence of the rate constant of the [1,5] sigmatropic hydrogen shift in (Z)-1,3-pentadiene.

Authors:  Tomáš Zimmermann; Jiří Vaníček
Journal:  J Mol Model       Date:  2010-04-30       Impact factor: 1.810

2.  Tautomers and reference 3D-structures: the orphans of in silico drug design.

Authors:  Timothy Clark
Journal:  J Comput Aided Mol Des       Date:  2010-03-27       Impact factor: 3.686

3.  Multibody effects in ion binding and selectivity.

Authors:  Sameer Varma; Susan B Rempe
Journal:  Biophys J       Date:  2010-11-17       Impact factor: 4.033

Review 4.  Biomolecular simulation and modelling: status, progress and prospects.

Authors:  Marc W van der Kamp; Katherine E Shaw; Christopher J Woods; Adrian J Mulholland
Journal:  J R Soc Interface       Date:  2008-12-06       Impact factor: 4.118

Review 5.  Modeling kinetics of subcellular disposition of chemicals.

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

Review 6.  Classical electrostatics for biomolecular simulations.

Authors:  G Andrés Cisneros; Mikko Karttunen; Pengyu Ren; Celeste Sagui
Journal:  Chem Rev       Date:  2013-08-27       Impact factor: 60.622

Review 7.  Metal Ion Modeling Using Classical Mechanics.

Authors:  Pengfei Li; Kenneth M Merz
Journal:  Chem Rev       Date:  2017-01-03       Impact factor: 60.622

8.  Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator.

Authors:  Fang-Yu Lin; Pedro E M Lopes; Edward Harder; Benoît Roux; Alexander D MacKerell
Journal:  J Chem Inf Model       Date:  2018-04-17       Impact factor: 4.956

9.  Charge density distributions derived from smoothed electrostatic potential functions: design of protein reduced point charge models.

Authors:  Laurence Leherte; Daniel P Vercauteren
Journal:  J Comput Aided Mol Des       Date:  2011-09-14       Impact factor: 3.686

10.  Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in.

Authors:  Mark A Ditzler; Michal Otyepka; Jirì Sponer; Nils G Walter
Journal:  Acc Chem Res       Date:  2010-01-19       Impact factor: 22.384

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