Extended Zinc AMBER Force Field (EZAFF).

Abstract

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.