Deeth, Robert J.. (2008) General molecular mechanics method for transition metal carboxylates and its application to the multiple coordination modes in mono- and dinuclear Mn(II) complexes. Inorganic Chemistry, Vol.47 (No.15). pp. 6711-6725. ISSN 0020-1669

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Abstract

A general molecular mechanics method is presented for modeling the symmetric bidentate, asymmetric bidentate, and bridging modes of metal-carboxylates with a single parameter set by using a double-minimum M-O-C angle-bending potential. The method is implemented within the Molecular Operating Environment (MOE) with parameters based on the Merck molecular force field although, with suitable modifications, other MM packages and force fields could easily be used. Parameters for high-spin d(5) manganese(II) bound to carboxylate and water plus amine, pyridyl, imidazolyl, and pyrazolyl donors are developed based on 26 mononuclear and 29 dinuclear crystallographically characterized complexes. The average rmsd for Mn-L distances is 0.08 angstrom, which is comparable to the experimental uncertainty required to cover multiple binding modes, and the average rmsd in heavy atom positions is around 0.5 angstrom. In all cases, whatever binding mode is reported is also computed to be a stable local minimum. In addition, the structure-based parametrization implicitly captures the energetics and gives the same relative energies of symmetric and asymmetric coordination modes as density functional theory calculations in model and "real" complexes. Molecular dynamics simulations show that carboxylate rotation is favored over "flipping" while a stochastic search algorithm is described for randomly searching conformational space. The model reproduces Mn-Mn distances in dinuclear systems especially accurately, and this feature is employed to illustrate how MM calculations on models for the dimanganese active site of methionine aminopeptidase can help determine some of the details which may be missing from the experimental structure.

Item Type:	Journal Article
Subjects:	Q Science > QD Chemistry
Divisions:	Faculty of Science > Chemistry
Library of Congress Subject Headings (LCSH):	Molecular structure, Carboxylic acids -- Derivatives, Transition metals, Molecules -- Models, Manganese, Molecular dynamics -- Mathematical models
Journal or Publication Title:	Inorganic Chemistry
Publisher:	American Chemical Society
ISSN:	0020-1669
Date:	4 August 2008
Volume:	Vol.47
Number:	No.15
Number of Pages:	15
Page Range:	pp. 6711-6725
Identification Number:	10.1021/ic800313s
Status:	Peer Reviewed
Publication Status:	Published
Funder:	Chemical Computing Group, GlaxoSmithKline
URI:	http://wrap.warwick.ac.uk/id/eprint/29635

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