Literature DB >> 19624181

Coarse-grained ions without charges: reproducing the solvation structure of NaCl in water using short-ranged potentials.

Robert C DeMille1, Valeria Molinero.   

Abstract

A coarse-grained model of NaCl in water is presented where the ions are modeled without charge to avoid computationally challenging electrostatics. A monatomic model of water [V. Molinero and E. B. Moore, J. Phys. Chem. B 113, 4008 (2009)] is used as the basis for this coarse-grain approach. The ability of Na(+) to disrupt the native tetrahedral arrangement of water molecules, and of Cl(-) to integrate within this organization, is preserved in this mW-ion model through parametrization focused on water's solvation of these ions. This model successfully reproduces the structural effect of ions on water, referenced to observations from experiments and atomistic molecular dynamics simulations, while using extremely short-ranged potentials. Without Coulomb interactions the model replicates details of the ion-water structure such as distinguishing contact and solvent-separated ion pairs and the free energy barriers between them. The approach of mimicking ionic effects with short-ranged interactions results in performance gains of two orders of magnitude compared to Ewald methods. Explored over a broad range of salt concentration, the model reproduces the solvation structure and trends of diffusion relative to atomistic simulations and experimental results. The functional form of the mW-ion model can be parametrized to represent other electrolytes. With increased computational efficiency and reliable structural fidelity, this model promises to be an asset for accessing significantly longer simulation time scales with an explicit solvent in a coarse-grained system involving, for example, polyelectrolytes such as proteins, nucleic acids, and fuel-cell membranes.

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Year:  2009        PMID: 19624181     DOI: 10.1063/1.3170982

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


  4 in total

1.  A coarse-grain three-site-per-nucleotide model for DNA with explicit ions.

Authors:  Gordon S Freeman; Daniel M Hinckley; Juan J de Pablo
Journal:  J Chem Phys       Date:  2011-10-28       Impact factor: 3.488

2.  Solvation structure of the halides from x-ray absorption spectroscopy.

Authors:  Matthew Antalek; Elisabetta Pace; Britt Hedman; Keith O Hodgson; Giovanni Chillemi; Maurizio Benfatto; Ritimukta Sarangi; Patrick Frank
Journal:  J Chem Phys       Date:  2016-07-28       Impact factor: 3.488

3.  A coarse-grained model of DNA with explicit solvation by water and ions.

Authors:  Robert C DeMille; Thomas E Cheatham; Valeria Molinero
Journal:  J Phys Chem B       Date:  2010-12-14       Impact factor: 2.991

4.  The power of coarse graining in biomolecular simulations.

Authors:  Helgi I Ingólfsson; Cesar A Lopez; Jaakko J Uusitalo; Djurre H de Jong; Srinivasa M Gopal; Xavier Periole; Siewert J Marrink
Journal:  Wiley Interdiscip Rev Comput Mol Sci       Date:  2014-05
  4 in total

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