Representation of Zn(II) complexes in polarizable molecular mechanics. Further refinements of the electrostatic and short‐range contributions. Comparisons with parallel ab initio computations

• Published in: Journal of computational chemistry 2005-08, Vol.26 (11), p.1113-1130
• Main Authors: Gresh, Nohad, Piquemal, Jean‐Philip, Krauss, Morris
• Format: Article
• Language: English
• Subjects: ab initio computations; beta-Lactamases - chemistry; Chemical compounds; Chemical Sciences; Comparative analysis; Computer based modeling; energy decomposition; intermolecular interactions; Mathematical Computing; metalloprotein binding sites; Metalloproteins - chemistry; Models, Molecular; Molecular Conformation; Molecular structure; or physical chemistry; Organometallic Compounds - chemistry; polarizable molecular mechanics; Theoretical and; Thermodynamics; Zinc - chemistry; Zn(II) cation
• ISSN: 0192-8651; 1096-987X
• DOI: 10.1002/jcc.20244

We present refinements of the SIBFA molecular mechanics procedure to represent the intermolecular interaction energies of Zn(II). The two first‐order contributions, electrostatic (EMTP), and short‐range repulsion (Erep), are refined following the recent developments due to Piquemal et al. (Piquemal et al. J Phys Chem A 2003, 107, 9800; and Piquemal et al., submitted). Thus, EMTP is augmented with a penetration component, Epen, which accounts for the effects of reduction in electronic density of a given molecular fragment sensed by another interacting fragment upon mutual overlap. Epen is fit in a limited number of selected Zn(II)–mono‐ligated complexes so that the sum of EMTP and Epen reproduces the Coulomb contribution Ec from an ab initio Hartree–Fock energy decomposition procedure. Denoting by S, the overlap matrix between localized orbitals on the interacting monomers, and by R, the distance between their centroids, Erep is expressed by a S2/R term now augmented with an S2/R2 one. It is calibrated in selected monoligated Zn(II) complexes to fit the corresponding exchange repulsion Eexch from ab initio energy decomposition, and no longer as previously the difference between (Ec + Eexch) and EMTP. Along with the reformulation of the first‐order contributions, a limited recalibration of the second‐order contributions was carried out. As in our original formulation (Gresh, J Comput Chem 1995, 16, 856), the Zn(II) parameters for each energy contribution were calibrated to reproduce the radial behavior of its ab initio HF counterpart in monoligated complexes with N, O, and S ligands. The SIBFA procedure was subsequently validated by comparisons with parallel ab initio computations on several Zn(II) polyligated complexes, including binuclear Zn(II) complexes as in models for the Gal4 and β‐lactamase metalloproteins. The largest relative error with respect to the RVS computations is 3%, and the ordering in relative energies of competing structures reproduced even though the absolute numerical values of the ab initio interaction energies can be as large as 1220 kcal/mol. A term‐to‐term identification of the SIBFA contributions to their ab initio counterparts remained possible even for the largest sized complexes. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1113–1130, 2005