Can the semiempirical PM3 scheme describe iron‐containing bioinorganic molecules?

Abstract

A set of iron parameters for use in the semiempirical PM3 method have been developed to allow the structure and redox properties of the active sites of iron‐containing proteins to be accurately modeled, focussing on iron–sulfur, iron–heme, and iron‐only hydrogenases. Data computed at the B3LYP/6‐31G* level for a training set of 60 representative complexes have been employed. A gradient‐based optimization algorithm has been used, and important modifications of the core repulsion function have been highlighted. The derived parameters lead in general to good predictions of the structure and energetics of molecules both within and outside the training set, and overcome the extensive deficiencies of a B3LYP/STO‐3G model. Particularly encouraging is the success of the parameters in describing [4Fe‐4S] cubanes. The derived parameter set provides a starting point should greater accuracy for a more restricted range of compounds be required. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 1307–1323, 2006