Literature DB >> 21898465

Modeling the interactions between polyoxometalates and their environment.

Blandine Courcot1, Adam J Bridgeman.   

Abstract

To develop a force field suitable both for polyoxometalates (POMs) and organic cations, the Merck molecular force field 94x (MMFF94x) has been selected to describe the counterions used in POMs synthesis and has been combined with our force field optimized for type-II POMs with electrostatic and Van der Waals interactions included in the potential. Nontransferability of force fields is well-known and, to overcome this limitation, a charge-scaling factor (SF) has been introduced and optimized to tune the POMs force field parameters and adapt them to MMFF94x. The mixed MMFF94x/POMFF-II force field has been optimized and tested on different clusters based on hepta-molybdate. To validate our mixed force field comparison of the results obtained after molecular mechanics (MM), geometry optimizations with density-functional (DFT) calculations have been performed on the smallest system of interest. This has enabled a study of the accuracy of different functionals, especially on the description of hydrogen bonding, to be made. Results are promising in terms of structural accuracy. MM geometry optimization can be used on small POM clusters, competing reasonably well with DFT. When quantum approaches increase considerably the computational cost because of the size of the system studied, MM can be used, with the small reservation that even if the charge SF introduced improves the performance of the force field, further optimizations of the nonbonded term and the model used for the atomic charges may be necessary in further studies.
Copyright © 2011 Wiley Periodicals, Inc.

Entities:  

Year:  2011        PMID: 21898465     DOI: 10.1002/jcc.21894

Source DB:  PubMed          Journal:  J Comput Chem        ISSN: 0192-8651            Impact factor:   3.376


  4 in total

1.  In-silico guided discovery of novel CCR9 antagonists.

Authors:  Xin Zhang; Jason B Cross; Jan Romero; Alexander Heifetz; Eric Humphries; Katie Hall; Yuchuan Wu; Sabrina Stucka; Jing Zhang; Haoqun Chandonnet; Blaise Lippa; M Dominic Ryan; J Christian Baber
Journal:  J Comput Aided Mol Des       Date:  2018-03-26       Impact factor: 3.686

2.  DFT study of α-Keggin, lacunary Keggin, and ironII-VI substituted Keggin polyoxometalates: the effect of oxidation state and axial ligand on geometry, electronic structures and oxygen transfer.

Authors:  Soheila Mir; Bahram Yadollahi; Reza Omidyan; Gholamhasan Azimi
Journal:  RSC Adv       Date:  2020-09-11       Impact factor: 4.036

3.  Toward an understanding of agonist binding to human Orexin-1 and Orexin-2 receptors with G-protein-coupled receptor modeling and site-directed mutagenesis.

Authors:  Alexander Heifetz; Oliver Barker; G Benjamin Morris; Richard J Law; Mark Slack; Philip C Biggin
Journal:  Biochemistry       Date:  2013-11-08       Impact factor: 3.162

4.  Identification of Novel Src Inhibitors: Pharmacophore-Based Virtual Screening, Molecular Docking and Molecular Dynamics Simulations.

Authors:  Yi Zhang; Ting-Jian Zhang; Shun Tu; Zhen-Hao Zhang; Fan-Hao Meng
Journal:  Molecules       Date:  2020-09-08       Impact factor: 4.411

  4 in total

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