Literature DB >> 19203258

Hydration of sodium(I) and potassium(I) revisited: a comparative QM/MM and QMCF MD simulation study of weakly hydrated ions.

S Sikander Azam1, Thomas S Hofer, Bernhard R Randolf, Bernd M Rode.   

Abstract

Quantum mechanical/molecular mechanical (QM/MM) and quantum mechanical charge field (QMCF) molecular (MD) simulations have been performed to describe structural and dynamical properties of Na(I) and K(I) in water and to compare the two approaches. The first and second hydration shells were treated by ab initio quantum mechanics at the restricted Hartree-Fock (RHF) level. The structural data are in good agreement with previously published experimental and theoretical results. A considerable number of water exchange reactions were observed within the first shell during the simulation time of 12 ps. The number of exchange events in both shells is higher in the case of K(I) than Na(I) reflecting the weaker ion-ligand bond strength of K(I). Comparison of the "conventional" QM/MM framework with the QMCF method clearly indicates the latter to be advantageous, as ambiguities arising from the coupling of the subregions occurring in the QM/MM MD simulations did not evolve when the QMCF ansatz was applied.

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Year:  2009        PMID: 19203258     DOI: 10.1021/jp8093462

Source DB:  PubMed          Journal:  J Phys Chem A        ISSN: 1089-5639            Impact factor:   2.781


  8 in total

1.  Coordination numbers of K(+) and Na(+) Ions inside the selectivity filter of the KcsA potassium channel: insights from first principles molecular dynamics.

Authors:  Denis Bucher; Leonardo Guidoni; Paolo Carloni; Ursula Rothlisberger
Journal:  Biophys J       Date:  2010-05-19       Impact factor: 4.033

Review 2.  Biomolecular electrostatics and solvation: a computational perspective.

Authors:  Pengyu Ren; Jaehun Chun; Dennis G Thomas; Michael J Schnieders; Marcelo Marucho; Jiajing Zhang; Nathan A Baker
Journal:  Q Rev Biophys       Date:  2012-11       Impact factor: 5.318

3.  Investigation of rubidium(I) ion solvation in liquid ammonia using QMCF-MD simulation and NBO analysis of first solvation shell structure.

Authors:  Yuniawan Hidayat; Ria Armunanto; Harno Dwi Pranowo
Journal:  J Mol Model       Date:  2018-04-27       Impact factor: 1.810

4.  Docking and molecular dynamics simulation studies on glycation-induced conformational changes of human paraoxonase 1.

Authors:  Ammara Saleem; S Sikander Azam; Shamshad Zarina
Journal:  Eur Biophys J       Date:  2011-12-23       Impact factor: 1.733

5.  Entropy from state probabilities: hydration entropy of cations.

Authors:  Roland G Huber; Julian E Fuchs; Susanne von Grafenstein; Monika Laner; Hannes G Wallnoefer; Nejma Abdelkader; Romano T Kroemer; Klaus R Liedl
Journal:  J Phys Chem B       Date:  2013-05-20       Impact factor: 2.991

6.  A study of the hydration of the alkali metal ions in aqueous solution.

Authors:  Johan Mähler; Ingmar Persson
Journal:  Inorg Chem       Date:  2011-12-14       Impact factor: 5.165

7.  Cation Selectivity in Biological Cation Channels Using Experimental Structural Information and Statistical Mechanical Simulation.

Authors:  Justin John Finnerty; Alexander Peyser; Paolo Carloni
Journal:  PLoS One       Date:  2015-10-13       Impact factor: 3.240

8.  Hydration of trivalent lanthanum revisited - An ab initio QMCF-MD approach.

Authors:  Oliver M D Lutz; Thomas S Hofer; Bernhard R Randolf; Bernd M Rode
Journal:  Chem Phys Lett       Date:  2012-05-21       Impact factor: 2.328

  8 in total

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