Literature DB >> 21789033

A Kirkwood-Buff Derived Force Field for Aqueous Alkali Halides.

Moon Bae Gee1, Nicholas R Cox, Yuanfang Jiao, Nikolaos Bentenitis, Samantha Weeerasinghe, Paul E Smith.   

Abstract

A classical nonpolarizable force field is presented for the simulation of aqueous alkali halide solutions (MX), where M = Li(+), Na(+), K(+), Rb(+), Cs(+) and X = F(-), Cl(-), Br(-), I(-), and their interactions with biomolecules. The models are specifically designed to reproduce the experimental Kirkwood-Buff integrals, and thereby the solution salt activities, as a function of salt concentration. Additionally, we demonstrate that these models reasonably reproduce other experimental properties including ion diffusion constants, dielectric decrements, and the excess heats of mixing. The parameters are developed by considering the properties of aqueous NaX and MCl solutions using a previously established model for NaCl. Transferability of the parameters to other salts is then established by the successful simulation of additional aqueous salt solutions, KI and CsBr, not originally included in the parameterization procedure.

Entities:  

Year:  2011        PMID: 21789033      PMCID: PMC3141341          DOI: 10.1021/ct100517z

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


  26 in total

1.  Systematic comparison of force fields for microscopic simulations of NaCl in aqueous solutions: diffusion, free energy of hydration, and structural properties.

Authors:  Michael Patra; Mikko Karttunen
Journal:  J Comput Chem       Date:  2004-04-15       Impact factor: 3.376

2.  Spontaneous Formation of KCl Aggregates in Biomolecular Simulations: A Force Field Issue?

Authors:  Pascal Auffinger; Thomas E Cheatham; Andrea C Vaiana
Journal:  J Chem Theory Comput       Date:  2007-09       Impact factor: 6.006

3.  The Kirkwood-Buff theory and the effect of cosolvents on biochemical reactions.

Authors:  Seishi Shimizu; Chandra L Boon
Journal:  J Chem Phys       Date:  2004-11-08       Impact factor: 3.488

4.  Molecular basis of the apparent near ideality of urea solutions.

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

5.  On the Kirkwood-Buff inversion procedure.

Authors:  Paul E Smith
Journal:  J Chem Phys       Date:  2008-09-28       Impact factor: 3.488

6.  Cation specific binding with protein surface charges.

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.  The effect of urea on the morphology of NaCl crystals: A combined theoretical and simulation study.

Authors:  Paul E Smith
Journal:  Fluid Phase Equilib       Date:  2010-03-25       Impact factor: 2.775

8.  Developing Force Fields from the Microscopic Structure of Solutions.

Authors:  Elizabeth A Ploetz; Nikolaos Bentenitis; Paul E Smith
Journal:  Fluid Phase Equilib       Date:  2010-03-25       Impact factor: 2.775

9.  Kirkwood-Buff derived force field for alkali chlorides in simple point charge water.

Authors:  Benjamin Klasczyk; Volker Knecht
Journal:  J Chem Phys       Date:  2010-01-14       Impact factor: 3.488

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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  12 in total

1.  A Kirkwood-Buff force field for the aromatic amino acids.

Authors:  Elizabeth A Ploetz; Paul E Smith
Journal:  Phys Chem Chem Phys       Date:  2011-09-19       Impact factor: 3.676

2.  Structural and technical details of the Kirkwood-Buff integrals from the optimization of ionic force fields: focus on fluorides.

Authors:  M Fyta
Journal:  Eur Phys J E Soft Matter       Date:  2012-03-22       Impact factor: 1.890

3.  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 4.  Interacting ions in biophysics: real is not ideal.

Authors:  Bob Eisenberg
Journal:  Biophys J       Date:  2013-05-07       Impact factor: 4.033

5.  Kirkwood-Buff integrals for hard-core Yukawa fluids.

Authors:  Han-Fei Chen; Jiang-Tao Li; Fang Gu; Hai-Jun Wang
Journal:  Eur Phys J E Soft Matter       Date:  2017-11-03       Impact factor: 1.890

6.  Mass Action in Ionic Solutions.

Authors:  Bob Eisenberg
Journal:  Chem Phys Lett       Date:  2011-07-26       Impact factor: 2.328

7.  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

Review 8.  Aqueous ionic liquids in comparison with standard co-solutes : Differences and common principles in their interaction with protein and DNA structures.

Authors:  Ewa Anna Oprzeska-Zingrebe; Jens Smiatek
Journal:  Biophys Rev       Date:  2018-04-02

9.  Proteins maintain hydration at high [KCl] concentration regardless of content in acidic amino acids.

Authors:  Hosein Geraili Daronkola; Ana Vila Verde
Journal:  Biophys J       Date:  2021-06-02       Impact factor: 3.699

10.  Salt Bridge in Aqueous Solution: Strong Structural Motifs but Weak Enthalpic Effect.

Authors:  Svetlana Pylaeva; Martin Brehm; Daniel Sebastiani
Journal:  Sci Rep       Date:  2018-09-11       Impact factor: 4.379

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