Literature DB >> 20300554

Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field.

Haibo Yu1, Troy W Whitfield, Edward Harder, Guillaume Lamoureux, Igor Vorobyov, Victor M Anisimov, Alexander D Mackerell, Benoît Roux.   

Abstract

An accurate representation of ion solvation in aqueous solution is critical for meaningful computer simulations of a broad range of physical and biological processes. Polarizable models based on classical Drude oscillators are introduced and parametrized for a large set of monoatomic ions including cations of the alkali metals (Li(+), Na(+), K(+), Rb(+) and Cs(+)) and alkaline earth elements (Mg(2+), Ca(2+), Sr(2+) and Ba(2+)) along with Zn(2+) and halide anions (F(-), Cl(-), Br(-) and I(-)). The models are parameterized, in conjunction with the polarizable SWM4-NDP water model [Lamoureux et al., Chem. Phys. Lett. 418, 245 (2006)], to be consistent with a wide assortment of experimentally measured aqueous bulk thermodynamic properties and the energetics of small ion-water clusters. Structural and dynamic properties of the resulting ion models in aqueous solutions at infinite dilution are presented.

Entities:  

Year:  2010        PMID: 20300554      PMCID: PMC2838399          DOI: 10.1021/ct900576a

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


  40 in total

1.  Structure of the gating domain of a Ca2+-activated K+ channel complexed with Ca2+/calmodulin.

Authors:  M A Schumacher; A F Rivard; H P Bächinger; J P Adelman
Journal:  Nature       Date:  2001-04-26       Impact factor: 49.962

2.  Ion solvation thermodynamics from simulation with a polarizable force field.

Authors:  Alan Grossfield; Pengyu Ren; Jay W Ponder
Journal:  J Am Chem Soc       Date:  2003-12-17       Impact factor: 15.419

Review 3.  Principles governing Mg, Ca, and Zn binding and selectivity in proteins.

Authors:  Todor Dudev; Carmay Lim
Journal:  Chem Rev       Date:  2003-03       Impact factor: 60.622

Review 4.  Ions and RNA folding.

Authors:  David E Draper; Dan Grilley; Ana Maria Soto
Journal:  Annu Rev Biophys Biomol Struct       Date:  2005

5.  Ion permeation through a narrow channel: using gramicidin to ascertain all-atom molecular dynamics potential of mean force methodology and biomolecular force fields.

Authors:  Toby W Allen; Olaf S Andersen; Benoit Roux
Journal:  Biophys J       Date:  2006-02-24       Impact factor: 4.033

6.  Computation of methodology-independent ionic solvation free energies from molecular simulations. I. The electrostatic potential in molecular liquids.

Authors:  M A Kastenholz; Philippe H Hünenberger
Journal:  J Chem Phys       Date:  2006-03-28       Impact factor: 3.488

Review 7.  Metal ions and RNA folding: a highly charged topic with a dynamic future.

Authors:  Sarah A Woodson
Journal:  Curr Opin Chem Biol       Date:  2005-04       Impact factor: 8.822

8.  Zn protein simulations including charge transfer and local polarization effects.

Authors:  Dmitri V Sakharov; Carmay Lim
Journal:  J Am Chem Soc       Date:  2005-04-06       Impact factor: 15.419

9.  Mg2+-dependent folding of a large ribozyme without kinetic traps.

Authors:  X W Fang; T Pan; T R Sosnick
Journal:  Nat Struct Biol       Date:  1999-12

10.  Absolute hydration free energy scale for alkali and halide ions established from simulations with a polarizable force field.

Authors:  Guillaume Lamoureux; Benoît Roux
Journal:  J Phys Chem B       Date:  2006-02-23       Impact factor: 2.991

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  101 in total

1.  Polarizable force field for RNA based on the classical drude oscillator.

Authors:  Justin A Lemkul; Alexander D MacKerell
Journal:  J Comput Chem       Date:  2018-12-15       Impact factor: 3.376

2.  Activation of the edema factor of Bacillus anthracis by calmodulin: evidence of an interplay between the EF-calmodulin interaction and calcium binding.

Authors:  Elodie Laine; Leandro Martínez; Arnaud Blondel; Thérèse E Malliavin
Journal:  Biophys J       Date:  2010-10-06       Impact factor: 4.033

3.  Role of electrostatics in modulating hydrophobic interactions and barriers to hydrophobic assembly.

Authors:  Brad A Bauer; Sandeep Patel
Journal:  J Phys Chem B       Date:  2010-06-24       Impact factor: 2.991

4.  Matching of additive and polarizable force fields for multiscale condensed phase simulations.

Authors:  Christopher M Baker; Robert B Best
Journal:  J Chem Theory Comput       Date:  2013-06-11       Impact factor: 6.006

5.  Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields.

Authors:  Bin Lin; Pedro E M Lopes; Benoît Roux; Alexander D MacKerell
Journal:  J Chem Phys       Date:  2013-08-28       Impact factor: 3.488

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

7.  Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field.

Authors:  Fang-Yu Lin; Jing Huang; Poonam Pandey; Chetan Rupakheti; Jing Li; Benoı T Roux; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2020-04-27       Impact factor: 6.006

8.  Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks.

Authors:  Jing Huang; Justin A Lemkul; Peter K Eastman; Alexander D MacKerell
Journal:  J Comput Chem       Date:  2018-05-04       Impact factor: 3.376

9.  Balancing the Interactions of Mg2+ in Aqueous Solution and with Nucleic Acid Moieties For a Polarizable Force Field Based on the Classical Drude Oscillator Model.

Authors:  Justin A Lemkul; Alexander D MacKerell
Journal:  J Phys Chem B       Date:  2016-10-27       Impact factor: 2.991

10.  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

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