Literature DB >> 35420428

Systematic Evaluation of Ion Diffusion and Water Exchange.

Zhen Li1, Kenneth M Merz1,2.   

Abstract

As a fundamental property of all fluids, diffusion plays myriad roles in both science and our daily lives. Diffusive properties of many liquids including water have been extensively studied both experimentally and theoretically, while for transition metal ions, there exist significant experimental data that have not been extensively studied theoretically. Hence, high-confidence predictions for challenging systems like radioactive ions that are biohazardous cannot be reliably generated. In this work, a workflow named ISAIAH (Ion Simulation using AMBER for dIffusion Action when Hydrated) was designed to accurately simulate the diffusion coefficients of 15 monoatomic ions with charges varying from -1 to +3 in four water models. As the results indicate, good agreement with experimental values was achieved, leading us to select 239Pu4+ (for which no experimental data are available) as a candidate ion to make a theoretical prediction of its diffusion coefficient in water. Among all the force field parameter sets, the ones parametrized using an augmented 12-6-4 Lennard-Jones (LJ) potential showed lower average unsigned errors (AUE) for ions of various radii and electron configurations relative to some 12-6 LJ parameters. This observation agrees well with the fact that diffusion is affected by both the hydration free energy (HFE) and the ion-oxygen distance (IOD) between solute and solvent molecules, both of which are handled well by the 12-6-4 model.

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Year:  2022        PMID: 35420428      PMCID: PMC9124439          DOI: 10.1021/acs.jctc.1c01189

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.578


  38 in total

1.  Ionic self-diffusion in concentrated aqueous electrolyte solutions.

Authors:  J-F Dufrêche; O Bernard; P Turq; A Mukherjee; B Bagchi
Journal:  Phys Rev Lett       Date:  2002-02-19       Impact factor: 9.161

2.  Building Force Fields: An Automatic, Systematic, and Reproducible Approach.

Authors:  Lee-Ping Wang; Todd J Martinez; Vijay S Pande
Journal:  J Phys Chem Lett       Date:  2014-05-16       Impact factor: 6.475

3.  Polarizable Mean-Field Model of Water for Biological Simulations with Amber and Charmm force fields.

Authors:  Igor V Leontyev; Alexei A Stuchebrukhov
Journal:  J Chem Theory Comput       Date:  2012-09-11       Impact factor: 6.006

4.  Accuracy limit of rigid 3-point water models.

Authors:  Saeed Izadi; Alexey V Onufriev
Journal:  J Chem Phys       Date:  2016-08-21       Impact factor: 3.488

5.  Water in Hydration Shell of an Iodide Ion: Structure and Dynamics of Solute-Water Hydrogen Bonds and Vibrational Spectral Diffusion from First-Principles Simulations.

Authors:  Anwesa Karmakar; Amalendu Chandra
Journal:  J Phys Chem B       Date:  2015-06-30       Impact factor: 2.991

6.  Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg(2+) ion models commonly used in biomolecular simulations.

Authors:  Maria T Panteva; George M Giambaşu; Darrin M York
Journal:  J Comput Chem       Date:  2015-03-04       Impact factor: 3.376

7.  Proton transfer and the mobilities of the H+ and OH- ions from studies of a dissociating model for water.

Authors:  Song Hi Lee; Jayendran C Rasaiah
Journal:  J Chem Phys       Date:  2011-09-28       Impact factor: 3.488

8.  Parametrization of Trivalent and Tetravalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models.

Authors:  Zhen Li; Lin Frank Song; Pengfei Li; Kenneth M Merz
Journal:  J Chem Theory Comput       Date:  2021-04-01       Impact factor: 6.006

9.  Kinetic pathways of water exchange in the first hydration shell of magnesium.

Authors:  Nadine Schwierz
Journal:  J Chem Phys       Date:  2020-06-14       Impact factor: 3.488

10.  Combining the Fluctuating Charge Method, Non-Periodic Boundary Conditions and Meta-Dynamics: Aqua Ions as case studies.

Authors:  Giordano Mancini; Giuseppe Brancato; Vincenzo Barone
Journal:  J Chem Theory Comput       Date:  2014-03-11       Impact factor: 6.006

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