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Extended Zinc AMBER Force Field (EZAFF)

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Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
Cite this: J. Chem. Theory Comput. 2018, 14, 1, 242–254
Publication Date (Web):November 17, 2017
Copyright © 2017 American Chemical Society

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    An empirical approach based on the previously developed zinc AMBER force field (ZAFF) is proposed for the determination of the parameters for bonds and angles involving zinc. We call it the extended ZAFF (EZAFF) model because the original ZAFF model was only formulated for four-coordinated systems, while EZAFF additionally can tackle five- and six-coordinated systems. Tests were carried out for six metalloproteins and six organometallic compounds with different coordination spheres. Results validated the reliability of the current model to handle a variety of zinc containing complexes. Meanwhile, benchmark calculations were performed to assess the performance of three bonded molecular mechanics models (EZAFF, Seminario, and Z-matrix models), four nonbonded parameter sets (the HFE, IOD, CM, and 12-6-4 models), and four semiempirical quantum mechanical methods (AM1, PM3, PM6, and SCC-DFTB methods) for simulating zinc containing systems. The obtained results indicate that, even with their increased computational cost, the semiempirical quantum methods only offered slightly better accuracy for the computation of relative energies and only afforded similar molecular geometries, when compared to the investigated molecular mechanics models.

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    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jctc.7b00773.

    • Table S1 showing mean errors of relative energies for 12 zinc complexes investigated; Table S2 showing RMSDs of the optimized structure by various methods toward the DFT optimized geometry; Table S3 showing RMSDs of the optimized structure by various methods toward the crystal structure. (PDF)

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