We have used combined quantum mechanical and molecular mechanical (QM/MM) calculations to study the reaction mechanism of nitrogenase, assuming that none of the sulfide ligands dissociates. To avoid the problem that there is no consensus regarding the structure and protonation of the E4 state, we start from a state where N2 is bound to the cluster and is protonated to N2H2, after dissociation of H2. We show that the reaction follows an alternating mechanism with HNNH (possibly protonated to HNNH2) and H2NNH2 as intermediates and the two NH3 products dissociate at the E7 and E8 levels. For all intermediates, coordination to Fe6 is preferred, but for the E4 and E8 intermediates, binding to Fe2 is competitive. For the E4, E5 and E7 intermediates we find that the substrate may abstract a proton from the hydroxy group of the homocitrate ligand of the FeMo cluster, thereby forming HNNH2, H2NNH2 and NH3 intermediates. This may explain why homocitrate is a mandatory component of nitrogenase. All steps in the suggested reaction mechanism are thermodynamically favourable compared to protonation of the nearby His-195 group and in all cases, protonation of the NE2 atom of the latter group is preferred.
- Teoretisk kemi