Calculating the chemical mechanism of nitrogenase: new working hypotheses.

The enzyme nitrogenase converts N to NH with stoichiometry N + 8H + 8e → 2NH + H. The mechanism is chemically complex with multiple steps that must be consistent with much accumulated experimental information, including exchange of H and N and the N-dependent hydrogenation of D to HD. Previous investigations have developed a collection of working hypotheses that guide ongoing density functional investigations of mechanistic steps and sequences. These include (i) hypotheses about the serial provision of protons and their conversion to H atoms bonded to and Fe atoms of the FeMo-co catalytic site, (ii) the migration of H atoms over the surface of FeMo-co, (iii) the roles of His195, (iv) identification of three protein channels, one for the ingress of N, a separate pathway for the passage of exogenous H (D) and product H (HD), and a hydrophilic pathway for egress of product NH. Two additional working hypotheses are described in this paper. N passing along the N channel approaches and binds end-on to the coordination position of Fe2, with favourable energetics when FeMo-co is pre-hydrogenated. This -Fe2-N is apparently not reduced but has a promotional role by expanding the reaction zone. A second N can enter the N ingress channel and bind at the -Fe6 position, where it is surrounded by H atom donors suitable for the N → NH conversion. It is proposed that this -Fe6 position is also the binding site for H (generated or exogenous), accounting for the competitive inhibition of N reduction by H. The HD reaction occurs at the -Fe6 site, promoted by N at the -Fe2 site. The second hypothesis concerns the most stable electronic states of FeMo-co with ligands bound at Fe2 and Fe6, and provides a protocol for management of electronic states in mechanism calculations.