Literature DB >> 33793233

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

Zhen Li1, Lin Frank Song1, Pengfei Li2,3, Kenneth M Merz1,4.   

Abstract

Commonly seen in rare-earth chemistry and materials science, highly charged metal ions play key roles in many chemical processes. Computer simulations have become an important tool for scientific research nowadays. Meaningful simulations require reliable parameters. In the present work, we parametrized 18 M(III) and 6 M(IV) metal ions for four new water models (OPC3, OPC, TIP3P-FB, TIP4P-FB) in conjunction with each of the 12-6 and 12-6-4 nonbonded models. Similar to what was observed previously, issues with the 12-6 model can be fixed by using the 12-6-4 model. Moreover, the four new water models showed comparable performance or considerable improvement over the previous water models (TIP3P, SPC/E, and TIP4PEW) in the same category (3-point or 4-point water models, respectively). Finally, we reported a study of a metalloprotein system demonstrating the capability of the 12-6-4 model to model metalloproteins. The reported parameters will facilitate accurate simulations of highly charged metal ions in aqueous solution.

Entities:  

Year:  2021        PMID: 33793233      PMCID: PMC8173366          DOI: 10.1021/acs.jctc.0c01320

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


  52 in total

Review 1.  Principles governing Mg, Ca, and Zn binding and selectivity in proteins.

Authors:  Todor Dudev; Carmay Lim
Journal:  Chem Rev       Date:  2003-03       Impact factor: 60.622

2.  Development of an improved four-site water model for biomolecular simulations: TIP4P-Ew.

Authors:  Hans W Horn; William C Swope; Jed W Pitera; Jeffry D Madura; Thomas J Dick; Greg L Hura; Teresa Head-Gordon
Journal:  J Chem Phys       Date:  2004-05-22       Impact factor: 3.488

3.  A scaled-ionic-charge simulation model that reproduces enhanced and suppressed water diffusion in aqueous salt solutions.

Authors:  Z R Kann; J L Skinner
Journal:  J Chem Phys       Date:  2014-09-14       Impact factor: 3.488

4.  MCPB.py: A Python Based Metal Center Parameter Builder.

Authors:  Pengfei Li; Kenneth M Merz
Journal:  J Chem Inf Model       Date:  2016-03-23       Impact factor: 4.956

Review 5.  A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization.

Authors:  E Duboué-Dijon; M Javanainen; P Delcroix; P Jungwirth; H Martinez-Seara
Journal:  J Chem Phys       Date:  2020-08-07       Impact factor: 3.488

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.  Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential.

Authors:  Jiajing Zhang; Wei Yang; Jean-Philip Piquemal; Pengyu Ren
Journal:  J Chem Theory Comput       Date:  2012-01-02       Impact factor: 6.006

8.  Wide-open flaps are key to urease activity.

Authors:  Benjamin P Roberts; Bill R Miller; Adrian E Roitberg; Kenneth M Merz
Journal:  J Am Chem Soc       Date:  2012-06-11       Impact factor: 15.419

9.  Force field independent metal parameters using a nonbonded dummy model.

Authors:  Fernanda Duarte; Paul Bauer; Alexandre Barrozo; Beat Anton Amrein; Miha Purg; Johan Aqvist; Shina Caroline Lynn Kamerlin
Journal:  J Phys Chem B       Date:  2014-04-15       Impact factor: 2.991

10.  Parameterization of highly charged metal ions using the 12-6-4 LJ-type nonbonded model in explicit water.

Authors:  Pengfei Li; Lin Frank Song; Kenneth M Merz
Journal:  J Phys Chem B       Date:  2014-09-12       Impact factor: 2.991

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  2 in total

1.  Systematic Evaluation of Ion Diffusion and Water Exchange.

Authors:  Zhen Li; Kenneth M Merz
Journal:  J Chem Theory Comput       Date:  2022-04-14       Impact factor: 6.578

2.  Advanced Electrostatic Model for Monovalent Ions Based on Ab Initio Energy Decomposition.

Authors:  Zhifeng Jing; Chengwen Liu; Pengyu Ren
Journal:  J Chem Inf Model       Date:  2021-06-07       Impact factor: 6.162

  2 in total

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