Literature DB >> 26593000

The Solvation Structure of Na(+) and K(+) in Liquid Water Determined from High Level ab Initio Molecular Dynamics Simulations.

Christopher N Rowley1, Benoıt Roux1.   

Abstract

Knowledge of the hydration structure of Na(+) and K(+) in the liquid phase has wide ranging implications in the field of biological chemistry. Despite numerous experimental and computational studies, even basic features such as the coordination number of these alkali ions in liquid water, thought to play a critical role in selectivity, continue to be the subject of intensive debates. Simulations based on accurate potential energy surfaces offer one approach to resolve these issues by providing reliable results on ion hydration. In this article, we report the results from molecular dynamics simulations of Na(+) and K(+) hydration based on a novel and rigorous strategy designed to overcome the challenges of QM/MM simulations of solvent molecules in the liquid phase. In this method, which we call Flexible Inner Region Ensemble Separator (FIRES), the ion and a fixed number of nearest water molecules form a dynamical and flexible inner region that is represented with high level ab initio quantum mechanical (QM) methods, while the water molecules from the surrounding bulk form an outer region that is represented by a polarizable molecular mechanical (MM) force field. Simulations yield rigorously correct thermodynamic averages as long as the solvent molecules in the flexible inner and outer regions are not allowed to exchange. Extensive FIRES simulations were carried out based on a QM/MM model in which the Na(+) or K(+) ion and the 12 nearest water molecules were represented by high level ab initio methods (RI-MP2/def2-TZVP and density functional theory with PBE/def2-TZVP), while the surrounding MM water molecules were represented by the polarizable SWM4-NDP potential. On the basis of these results, the ion coordination numbers are estimated to be within the range of 5.7-5.8 for Na(+) and 6.9-7.0 for K(+).

Entities:  

Year:  2012        PMID: 26593000     DOI: 10.1021/ct300091w

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


  26 in total

1.  Copper Oxidation/Reduction in Water and Protein: Studies with DFTB3/MM and VALBOND Molecular Dynamics Simulations.

Authors:  Haiyun Jin; Puja Goyal; Akshaya Kumar Das; Michael Gaus; Markus Meuwly; Qiang Cui
Journal:  J Phys Chem B       Date:  2015-12-17       Impact factor: 2.991

2.  Pairwise-additive force fields for selected aqueous monovalent ions from adaptive force matching.

Authors:  Jicun Li; Feng Wang
Journal:  J Chem Phys       Date:  2015-11-21       Impact factor: 3.488

3.  Polarizable molecular dynamics simulations of ionic liquids: Influence of temperature control.

Authors:  Esther Heid; Stefan Boresch; Christian Schröder
Journal:  J Chem Phys       Date:  2020-03-07       Impact factor: 3.488

4.  Accelerated Computation of Free Energy Profile at Ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semiempirical Reference Potential. 4. Adaptive QM/MM.

Authors:  Jia-Ning Wang; Wei Liu; Pengfei Li; Yan Mo; Wenxin Hu; Jun Zheng; Xiaoliang Pan; Yihan Shao; Ye Mei
Journal:  J Chem Theory Comput       Date:  2021-02-16       Impact factor: 6.006

5.  A Many-Body, Fully Polarizable Approach to QM/MM Simulations.

Authors:  Eleftherios Lambros; Filippo Lipparini; Gerardo Andrés Cisneros; Francesco Paesani
Journal:  J Chem Theory Comput       Date:  2020-11-19       Impact factor: 6.006

6.  Regulation and Plasticity of Catalysis in Enzymes: Insights from Analysis of Mechanochemical Coupling in Myosin.

Authors:  Xiya Lu; Victor Ovchinnikov; Darren Demapan; Daniel Roston; Qiang Cui
Journal:  Biochemistry       Date:  2017-03-01       Impact factor: 3.162

7.  QM/MM free energy simulations: recent progress and challenges.

Authors:  Xiya Lu; Dong Fang; Shingo Ito; Yuko Okamoto; Victor Ovchinnikov; Qiang Cui
Journal:  Mol Simul       Date:  2016-07-05       Impact factor: 2.178

8.  Leaving Group Ability Observably Affects Transition State Structure in a Single Enzyme Active Site.

Authors:  Daniel Roston; Darren Demapan; Qiang Cui
Journal:  J Am Chem Soc       Date:  2016-06-02       Impact factor: 15.419

9.  Substrate and Transition State Binding in Alkaline Phosphatase Analyzed by Computation of Oxygen Isotope Effects.

Authors:  Daniel Roston; Qiang Cui
Journal:  J Am Chem Soc       Date:  2016-08-31       Impact factor: 15.419

10.  Critical Comparison of the Superoxide Dismutase-like Activity of Carbon Antioxidant Nanozymes by Direct Superoxide Consumption Kinetic Measurements.

Authors:  Gang Wu; Vladimir Berka; Paul J Derry; Kimberly Mendoza; Eugenia Kakadiaris; Trenton Roy; Thomas A Kent; James M Tour; Ah-Lim Tsai
Journal:  ACS Nano       Date:  2019-09-17       Impact factor: 15.881

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.