Na(+), K (+) and Tl(+) hydration from QM/MM computations and MD simulations with a polarizable force field

Interdisciplinary Sciences, Computational Life Sciences
Bogdan LevSergei Yu Noskov

Abstract

The hydration of three different monovalent cations was studied with a number of theoretical approaches ranging from classical MD simulations to MD simulations with a polarizable force field and finally to QM/MM MD. A particular emphasis was put on the development of a novel polarizable potential function for studies of Tl(+) hydration enabling the ability to reproduce key features observed in QM/MM simulations. We extended the CHARMM-deMon interface developed previously to studies of ion hydration with QM/MM simulations. All simulations reproduce experimental data on the Radial Distribution Function (RDF) accurately. However, notable differences start to emerge in the description of probabilities for coordination states of an ion if explicit account of polarization is included.

References

Jan 30, 1976·Archives of Toxicology·W Lameijer, P A van Zwieten
Nov 4, 1998·Toxicology Letters·S Galván-Arzate, A Santamaría
Sep 15, 1988·Physical Review A: General Physics·A D Becke
Mar 27, 2002·Journal of Computational Chemistry·Martin J Field
Dec 11, 2003·Journal of the American Chemical Society·Alan GrossfieldJay W Ponder
Dec 20, 2003·Physical Review Letters·Bin ChenMichele Parrinello
Mar 24, 2005·Journal of the American Chemical Society·Johannes C HermannHans-Dieter Höltje
Aug 30, 2005·Inorganic Chemistry·Anja-Verena Mudring, Franziska Rieger
Oct 8, 2005·Journal of Computational Chemistry·Markus ChristenWilfred F van Gunsteren
Dec 3, 2005·Science·Eric Gouaux, Roderick Mackinnon
Dec 6, 2005·Inorganic Chemistry·Franziska Rieger, Anja-V Mudring
Feb 24, 2006·The Journal of Physical Chemistry. B·Guillaume Lamoureux, Benoît Roux
May 11, 2006·Chemical Reviews·Stewart A Adcock, J Andrew McCammon
May 16, 2006·Biophysical Chemistry·Alan K Soper, Kristian Weckström
Jun 30, 2006·The Journal of Physical Chemistry. B·Lijiang YangRay Luo
Feb 3, 2007·Journal of Computational Chemistry·Viwat VchirawongkwinBernd M Rode
Mar 6, 2007·Journal of Computational Chemistry·H Lee WoodcockBernard R Brooks
Jul 31, 2007·Journal of the American Chemical Society·D AsthagiriL R Pratt
Oct 16, 2007·The Journal of Chemical Physics·J K ShahM E Paulaitis
Mar 1, 2007·Journal of Chemical Theory and Computation·Hao HuWeitao Yang
Jan 29, 2009·Angewandte Chemie·Hans Martin Senn, Walter Thiel
May 16, 2009·Journal of Computational Chemistry·B R BrooksM Karplus
May 22, 2009·Nature·Harini KrishnamurthyEric Gouaux
Dec 23, 2009·Journal of Computational Chemistry·Bogdan LevSergei Yu Noskov
Jun 26, 2010·Theoretical Chemistry Accounts·Pedro E M LopesAlexander D Mackerell
Jan 1, 2007·Journal of Chemical Theory and Computation·Troy W WhitfieldBenoît Roux
Mar 1, 2008·Journal of Chemical Theory and Computation·Berk HessErik Lindahl
Jul 1, 2005·Journal of Chemical Theory and Computation·Jon R MapleRichard A Friesner

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Citations

Jul 19, 2019·Journal of Biomolecular Structure & Dynamics·Tian-Tian LiuJiang-Xing Zhuang
Jun 28, 2019·Chemical Reviews·Emelie FloodToby W Allen

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