The chemical mechanism of nitrogenase: calculated details of the intramolecular mechanism for hydrogenation of eta(2)-N(2) on FeMo-co to NH(3).

Using density functional calculations, a complete chemical mechanism has been developed for the reaction N(2) + 6e(-) + 6H(+)--> 2NH(3) catalyzed by the Fe(7)MoS(9)N(c)(homocitrate) cofactor (FeMo-co) of the enzyme nitrogenase. The mechanism is based on previous descriptions of the generation of H atoms on FeMo-co by proton relay through a protein path terminating in water molecule 679, and preserves the model (which explains much biochemical data) for vectorial migration of H atoms to two S atoms and two Fe atoms of FeMo-co. After calculation of the energy profiles for the many possible sequences of steps in which these H atoms are transferred to N(2) and its hydrogenated intermediates, a favourable pathway to 2NH(3) was developed. Transition states and activation potential energies for the 21 step mechanism are presented, together with results for some alternative branches. The mechanism develops logically from the eta(2)-coordination of N(2) at the endo position of one Fe atom of prehydrogenated FeMo-co, consistent with the previous kinetic-mechanistic scheme of Thorneley and Lowe, and passes through bound N(2)H(2) and N(2)H(4) intermediates. This mechanism is different from others in the literature because it uses a single replenishable path for serial supply of protons which become H atoms on FeMo-co, migrating to become S-H and Fe-H donors to N(2) and to the intermediates that follow. The new paradigm for the chemical catalysis is that hydrogenation of N(2) and intermediates is intramolecular and does not involve direct protonation from surrounding residues which appear to be unable to provide a replenishable supply of 6H(+). Many steps in this intramolecular hydrogenation are expected to be enhanced by H tunneling.