Literature DB >> 23795497

Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field.

Yun Luo1, Wei Jiang, Haibo Yu, Alexander D MacKerell, Benoit Roux.   

Abstract

The accuracy of empirical force fields is critical for meaningful molecular dynamics simulations of concentrated ionic solutions. Current models are typically developed on the basis of single ion properties such as the monohydrate energy in the gas phase, or the absolute hydration free energy at infinite dilution. However, the failure of these models to represent accurately the properties of concentrated solutions cannot be excluded. Here, these issues are illustrated for a polarizable potential based on classical Drude oscillators. To model accurately concentrated ionic solutions, the parameters of the potential functions are optimized to reproduce osmotic pressure data. The sodium-chloride potential of mean force in solution calculated from the empirically-adjusted model is consistent with the results from that calculated from ab initio CPMD simulations.

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Year:  2013        PMID: 23795497      PMCID: PMC3695446          DOI: 10.1039/c2fd20068f

Source DB:  PubMed          Journal:  Faraday Discuss        ISSN: 1359-6640            Impact factor:   4.008


  23 in total

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Authors:  Jia-Wei Shen; Chunli Li; Nico F A van der Vegt; Christine Peter
Journal:  J Chem Theory Comput       Date:  2011-05-05       Impact factor: 6.006

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Authors:  Jörg Rösgen; Bernard Montgomery Pettitt; David Wayne Bolen
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Journal:  Nature       Date:  1995-11-23       Impact factor: 49.962

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Authors:  Hironori Kokubo; Jörg Rösgen; D Wayne Bolen; B Montgomery Pettitt
Journal:  Biophys J       Date:  2007-08-10       Impact factor: 4.033

Review 5.  CHARMM: the biomolecular simulation program.

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Journal:  J Comput Chem       Date:  2009-07-30       Impact factor: 3.376

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Authors:  Berk Hess; Nico F A van der Vegt
Journal:  Proc Natl Acad Sci U S A       Date:  2009-07-28       Impact factor: 11.205

7.  Canonical dynamics: Equilibrium phase-space distributions.

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Journal:  Phys Rev A Gen Phys       Date:  1985-03

8.  High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD.

Authors:  Wei Jiang; David J Hardy; James C Phillips; Alexander D Mackerell; Klaus Schulten; Benoît Roux
Journal:  J Phys Chem Lett       Date:  2011       Impact factor: 6.475

9.  Ion pairing in aqueous electrolyte solutions with biologically relevant anions.

Authors:  Pritam Ganguly; Pim Schravendijk; Berk Hess; Nico F A van der Vegt
Journal:  J Phys Chem B       Date:  2011-03-16       Impact factor: 2.991

10.  Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations.

Authors:  In Suk Joung; Thomas E Cheatham
Journal:  J Phys Chem B       Date:  2008-07-02       Impact factor: 2.991

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  26 in total

1.  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 2.  Metal Ion Modeling Using Classical Mechanics.

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

3.  Polarizable molecular dynamics in a polarizable continuum solvent.

Authors:  Filippo Lipparini; Louis Lagardère; Christophe Raynaud; Benjamin Stamm; Eric Cancès; Benedetta Mennucci; Michael Schnieders; Pengyu Ren; Yvon Maday; Jean-Philip Piquemal
Journal:  J Chem Theory Comput       Date:  2015-02-10       Impact factor: 6.006

4.  Scalable Evaluation of Polarization Energy and Associated Forces in Polarizable Molecular Dynamics: II.Towards Massively Parallel Computations using Smooth Particle Mesh Ewald.

Authors:  Louis Lagardère; Filippo Lipparini; Étienne Polack; Benjamin Stamm; Éric Cancès; Michael Schnieders; Pengyu Ren; Yvon Maday; Jean-Philip Piquemal
Journal:  J Chem Theory Comput       Date:  2014-02-28       Impact factor: 6.006

5.  Force Field for Peptides and Proteins based on the Classical Drude Oscillator.

Authors:  Pedro E M Lopes; Jing Huang; Jihyun Shim; Yun Luo; Hui Li; Benoît Roux; Alexander D Mackerell
Journal:  J Chem Theory Comput       Date:  2013-12-10       Impact factor: 6.006

6.  All-atom polarizable force field for DNA based on the classical Drude oscillator model.

Authors:  Alexey Savelyev; Alexander D MacKerell
Journal:  J Comput Chem       Date:  2014-04-18       Impact factor: 3.376

7.  Competition among Li(+), Na(+), K(+), and Rb(+) monovalent ions for DNA in molecular dynamics simulations using the additive CHARMM36 and Drude polarizable force fields.

Authors:  Alexey Savelyev; Alexander D MacKerell
Journal:  J Phys Chem B       Date:  2015-03-18       Impact factor: 2.991

8.  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

9.  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

10.  Differential Deformability of the DNA Minor Groove and Altered BI/BII Backbone Conformational Equilibrium by the Monovalent Ions Li(+), Na(+), K(+), and Rb(+) via Water-Mediated Hydrogen Bonding.

Authors:  Alexey Savelyev; Alexander D MacKerell
Journal:  J Chem Theory Comput       Date:  2015-08-26       Impact factor: 6.006

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