An atomic-level mechanism for molybdenum nitrogenase. Part 1. Reduction of dinitrogen

The properties of the Fe and Mo sites of the iron-molybdenum cofactor of nitrogenase with respect to binding and activation of N-2 have been studied by molecular mechanics calculations on the local protein environment and by density functional theory (DFT) calculations on subsections of the cofactor. The DFT calculations indicate that the homocitrate ligand of the cofactor can become monodentate on reduction, allowing N-2 to bind at Mo. In addition, the neighboring Fe atom plays a crucial role in N-2 reduction by stabilizing the initial reduced N-2 species and by facilitating cleavage of the N-N bond. The various possible isomers for partially reduced N-2 intermediates have been compared by DFT, and a detailed model for the reduction of N-2 is developed based on these results, together with chemical precedents and the available biochemical data for nitrogenase.