Literature DB >> 26929375

Long-ranged contributions to solvation free energies from theory and short-ranged models.

Richard C Remsing1, Shule Liu2, John D Weeks3.   

Abstract

Long-standing problems associated with long-ranged electrostatic interactions have plagued theory and simulation alike. Traditional lattice sum (Ewald-like) treatments of Coulomb interactions add significant overhead to computer simulations and can produce artifacts from spurious interactions between simulation cell images. These subtle issues become particularly apparent when estimating thermodynamic quantities, such as free energies of solvation in charged and polar systems, to which long-ranged Coulomb interactions typically make a large contribution. In this paper, we develop a framework for determining very accurate solvation free energies of systems with long-ranged interactions from models that interact with purely short-ranged potentials. Our approach is generally applicable and can be combined with existing computational and theoretical techniques for estimating solvation thermodynamics. We demonstrate the utility of our approach by examining the hydration thermodynamics of hydrophobic and ionic solutes and the solvation of a large, highly charged colloid that exhibits overcharging, a complex nonlinear electrostatic phenomenon whereby counterions from the solvent effectively overscreen and locally invert the integrated charge of the solvated object.

Keywords:  density functional theory; free energy calculations; hydrophobicity; mean field theory; solvation

Year:  2016        PMID: 26929375      PMCID: PMC4801310          DOI: 10.1073/pnas.1521570113

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


  19 in total

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Authors:  John D Weeks
Journal:  Annu Rev Phys Chem       Date:  2001-10-04       Impact factor: 12.703

2.  Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study.

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Journal:  Biophys Chem       Date:  1999-04-05       Impact factor: 2.352

3.  Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer.

Authors:  Roland Schulz; Benjamin Lindner; Loukas Petridis; Jeremy C Smith
Journal:  J Chem Theory Comput       Date:  2009-10-13       Impact factor: 6.006

4.  Interplay of local hydrogen-bonding and long-ranged dipolar forces in simulations of confined water.

Authors:  Jocelyn M Rodgers; John D Weeks
Journal:  Proc Natl Acad Sci U S A       Date:  2008-12-08       Impact factor: 11.205

5.  Dissecting hydrophobic hydration and association.

Authors:  Richard C Remsing; John D Weeks
Journal:  J Phys Chem B       Date:  2013-08-28       Impact factor: 2.991

6.  Accurate thermodynamics for short-ranged truncations of Coulomb interactions in site-site molecular models.

Authors:  Jocelyn M Rodgers; John D Weeks
Journal:  J Chem Phys       Date:  2009-12-28       Impact factor: 3.488

7.  A new approach for efficient simulation of Coulomb interactions in ionic fluids.

Authors:  Natalia A Denesyuk; John D Weeks
Journal:  J Chem Phys       Date:  2008-03-28       Impact factor: 3.488

8.  Efficient solutions of self-consistent mean field equations for dewetting and electrostatics in nonuniform liquids.

Authors:  Zhonghan Hu; John D Weeks
Journal:  Phys Rev Lett       Date:  2010-09-28       Impact factor: 9.161

9.  Water-mediated ion-ion interactions are enhanced at the water vapor-liquid interface.

Authors:  Vasudevan Venkateshwaran; Srivathsan Vembanur; Shekhar Garde
Journal:  Proc Natl Acad Sci U S A       Date:  2014-06-02       Impact factor: 11.205

10.  Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born.

Authors:  Andreas W Götz; Mark J Williamson; Dong Xu; Duncan Poole; Scott Le Grand; Ross C Walker
Journal:  J Chem Theory Comput       Date:  2012-03-26       Impact factor: 6.006

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  11 in total

1.  The hydrophobic effect, and fluctuations: The long and the short of it.

Authors:  Erte Xi; Amish J Patel
Journal:  Proc Natl Acad Sci U S A       Date:  2016-04-14       Impact factor: 11.205

2.  On the role of water density fluctuations in the inhibition of a proton channel.

Authors:  Eleonora Gianti; Lucie Delemotte; Michael L Klein; Vincenzo Carnevale
Journal:  Proc Natl Acad Sci U S A       Date:  2016-12-12       Impact factor: 11.205

3.  Dielectric response with short-ranged electrostatics.

Authors:  Stephen J Cox
Journal:  Proc Natl Acad Sci U S A       Date:  2020-08-03       Impact factor: 11.205

4.  Short solvent model for ion correlations and hydrophobic association.

Authors:  Ang Gao; Richard C Remsing; John D Weeks
Journal:  Proc Natl Acad Sci U S A       Date:  2020-01-07       Impact factor: 11.205

5.  Theory and simulations for RNA folding in mixtures of monovalent and divalent cations.

Authors:  Hung T Nguyen; Naoto Hori; D Thirumalai
Journal:  Proc Natl Acad Sci U S A       Date:  2019-09-30       Impact factor: 11.205

6.  Playing the long game wins the cohesion-adhesion rivalry.

Authors:  Richard C Remsing
Journal:  Proc Natl Acad Sci U S A       Date:  2019-10-28       Impact factor: 11.205

7.  Solvation Thermodynamics from the Perspective of Endpoints DFT.

Authors:  Ronald M Levy; Nobuyuki Matubayasi; Bin W Zhang
Journal:  J Phys Chem B       Date:  2020-12-11       Impact factor: 2.991

8.  Spatially-Decomposed Free Energy of Solvation Based on the Endpoint Density-Functional Method.

Authors:  Yoshiki Ishii; Naoki Yamamoto; Nobuyuki Matubayasi; Bin W Zhang; Di Cui; Ronald M Levy
Journal:  J Chem Theory Comput       Date:  2019-04-16       Impact factor: 6.006

9.  Ion-dependent protein-surface interactions from intrinsic solvent response.

Authors:  Jesse L Prelesnik; Robert G Alberstein; Shuai Zhang; Harley Pyles; David Baker; Jim Pfaendtner; James J De Yoreo; F Akif Tezcan; Richard C Remsing; Christopher J Mundy
Journal:  Proc Natl Acad Sci U S A       Date:  2021-06-29       Impact factor: 11.205

10.  A molecular twist on hydrophobicity.

Authors:  Sara Gómez; Natalia Rojas-Valencia; Santiago A Gómez; Chiara Cappelli; Gabriel Merino; Albeiro Restrepo
Journal:  Chem Sci       Date:  2021-06-15       Impact factor: 9.825

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