Electronic structure, bonding, spectroscopy and energetics of Fe-dependent nitrile hydratase active-site models

Fe-type nitrile hydratase (NHase) is a non-heme Fe(III)-dependent enzyme that catalyzes the hydration of nitriles to the corresponding amides. Despite experimental studies of the enzyme and model Fe(III)-containing complexes, many questions concerning the electronic structure and spectroscopic transitions of the metal center remain unanswered. In addition, the catalytic mechanism of nitrile hydration has not yet been determined. We now report density functional theory (B3LYP/6-31G) calculations on three models of the Fe(III) center in the active site of NHase corresponding to hypothetical intermediates in the enzyme-catalyzed hydration of acetonitrile. Together with natural bond orbital (NBO) analysis of the chemical bonding in these active-site models and INDO/S CIS calculations of their electronic spectra, this theoretical investigation gives new insight into the molecular origin of the unusual low-spin preference and spectroscopic properties of the Fe(III) center. In addition, the low-energy electronic transition observed for the active form of NHase is assigned to a dd transition that is coupled with charge-transfer transitions involving the metal and its sulfur ligands. Calculations of isodesmic ligand-exchange reaction energies provide support for coordination of the Fe(III) center in free NHase by a water molecule rather than a hydroxide ion and suggest that the activation of the nitrile substrate by binding to the metal in the sixth coordination site during catalytic turnover cannot yet be definitively ruled out.