Literature DB >> 20572683

Assessing the accuracy of approximate treatments of ion hydration based on primitive quasichemical theory.

Benoît Roux1, Haibo Yu.   

Abstract

Quasichemical theory (QCT) provides a framework that can be used to partition the influence of the solvent surrounding an ion into near and distant contributions. Within QCT, the solvation properties of the ion are expressed as a sum of configurational integrals comprising only the ion and a small number of solvent molecules. QCT adopts a particularly simple form if it is assumed that the clusters undergo only small thermal fluctuations around a well-defined energy minimum and are affected exclusively in a mean-field sense by the surrounding bulk solvent. The fluctuations can then be integrated out via a simple vibrational analysis, leading to a closed-form expression for the solvation free energy of the ion. This constitutes the primitive form of quasichemical theory (pQCT), which is an approximate mathematical formulation aimed at reproducing the results from the full many-body configurational averages of statistical mechanics. While the results from pQCT from previous applications are reasonable, the accuracy of the approach has not been fully characterized and its range of validity remains unclear. Here, a direct test of pQCT for a set of ion models is carried out by comparing with the results of free energy simulations with explicit solvent. The influence of the distant surrounding bulk on the cluster comprising the ion and the nearest solvent molecule is treated both with a continuum dielectric approximation and with free energy perturbation molecular dynamics simulations with explicit solvent. The analysis shows that pQCT can provide an accurate framework in the case of a small cation such as Li(+). However, the approximation encounters increasing difficulties when applied to larger cations such as Na(+), and particularly for K(+). This suggests that results from pQCT should be interpreted with caution when comparing ions of different sizes.

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Year:  2010        PMID: 20572683      PMCID: PMC2903185          DOI: 10.1063/1.3436632

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


  17 in total

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Journal:  J Chem Phys       Date:  2004-10-01       Impact factor: 3.488

Review 2.  Ion selectivity in potassium channels.

Authors:  Sergei Yu Noskov; Benoît Roux
Journal:  Biophys Chem       Date:  2006-06-18       Impact factor: 2.352

3.  Role of fluctuations in a snug-fit mechanism of KcsA channel selectivity.

Authors:  D Asthagiri; Lawrence R Pratt; Michael E Paulaitis
Journal:  J Chem Phys       Date:  2006-07-14       Impact factor: 3.488

Review 4.  Importance of hydration and dynamics on the selectivity of the KcsA and NaK channels.

Authors:  Sergei Yu Noskov; Benoît Roux
Journal:  J Gen Physiol       Date:  2007-01-16       Impact factor: 4.086

Review 5.  CHARMM: the biomolecular simulation program.

Authors:  B R Brooks; C L Brooks; A D Mackerell; L Nilsson; R J Petrella; B Roux; Y Won; G Archontis; C Bartels; S Boresch; A Caflisch; L Caves; Q Cui; A R Dinner; M Feig; S Fischer; J Gao; M Hodoscek; W Im; K Kuczera; T Lazaridis; J Ma; V Ovchinnikov; E Paci; R W Pastor; C B Post; J Z Pu; M Schaefer; B Tidor; R M Venable; H L Woodcock; X Wu; W Yang; D M York; M Karplus
Journal:  J Comput Chem       Date:  2009-07-30       Impact factor: 3.376

6.  On the origin of the electrostatic potential difference at a liquid-vacuum interface.

Authors:  Edward Harder; Benoît Roux
Journal:  J Chem Phys       Date:  2008-12-21       Impact factor: 3.488

7.  Modeling molecular and ionic absolute solvation free energies with quasichemical theory bounds.

Authors:  David M Rogers; Thomas L Beck
Journal:  J Chem Phys       Date:  2008-10-07       Impact factor: 3.488

8.  Hydration number, topological control, and ion selectivity.

Authors:  Haibo Yu; Sergei Yu Noskov; Benoît Roux
Journal:  J Phys Chem B       Date:  2009-06-25       Impact factor: 2.991

9.  Ion selectivity from local configurations of ligands in solutions and ion channels.

Authors:  D Asthagiri; P D Dixit; S Merchant; M E Paulaitis; L R Pratt; S B Rempe; S Varma
Journal:  Chem Phys Lett       Date:  2010-01-18       Impact factor: 2.328

10.  Thermodynamically dominant hydration structures of aqueous ions.

Authors:  Safir Merchant; D Asthagiri
Journal:  J Chem Phys       Date:  2009-05-21       Impact factor: 3.488

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  6 in total

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Journal:  J Am Soc Mass Spectrom       Date:  2015-04-09       Impact factor: 3.109

2.  Probing the thermodynamics of competitive ion binding using minimum energy structures.

Authors:  David M Rogers; Susan B Rempe
Journal:  J Phys Chem B       Date:  2011-07-01       Impact factor: 2.991

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

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

4.  Multiple Scales in the Simulation of Ion Channels and Proteins.

Authors:  Bob Eisenberg
Journal:  J Phys Chem C Nanomater Interfaces       Date:  2010-10-21       Impact factor: 4.126

5.  Ion binding sites and their representations by reduced models.

Authors:  Benoît Roux
Journal:  J Phys Chem B       Date:  2012-04-30       Impact factor: 2.991

Review 6.  Ion selectivity in channels and transporters.

Authors:  Benoît Roux; Simon Bernèche; Bernhard Egwolf; Bogdan Lev; Sergei Y Noskov; Christopher N Rowley; Haibo Yu
Journal:  J Gen Physiol       Date:  2011-05       Impact factor: 4.086

  6 in total

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