Structures and reaction dynamics of N and H binding at FeMo-co, the active site of nitrogenase.

The chemical reactions occurring at the FeMoSC(homocitrate) cluster, FeMo-co, the active site of the enzyme nitrogenase (N → NH), are enigmatic. Experimental information collected over a long period reveals aspects of the roles of N and H, each with more than one type of reactivity. This paper reports investigations of the binding of H and N at intact FeMo-co, using density functional simulations of a large 486 atom relevant portion of the protein, resulting in 27 new structures containing H and/or N bound at the and coordination sites of the participating Fe atoms, Fe2 and Fe6. Binding energies and transition states for association/dissociation are determined, and trajectories for the approach, binding and separation of H/N are described, including diffusion of these small molecules through proximal protein. Influences of surrounding amino acids are identified. FeMo-co deforms geometrically when binding H or N, and a procedure for calculating the energy cost involved, the adaptation energy, is introduced here. Adaptation energies, which range from 7 to 36 kcal mol for the reported structures, are influenced by the protonation state of the His195 side chain. Seven N structures and three H structures have negative binding free energies, which include the estimated entropy penalties for binding of N, H from proximal protein. These favoured structures have N bound end-on at -Fe2, -Fe6 and -Fe2 positions of FeMo-co, and H bound at the -Fe2 position. Various postulated structures with N bridging Fe2 and Fe6 revert to end-on-N at positions. The structures are also assessed the calculated potential energy barriers for association and dissociation. Barriers to the binding of H range from 1 to 20 kcal mol and barriers to dissociation of H range from 3 to 18 kcal mol. Barriers to the binding of N, in either side-on or end-on mode, range from 2 to 18 kcal mol, while dissociation of bound N encounters barriers of 3 to 8 kcal mol for side-on bonding and 7 to 18 kcal mol for end-on bonding. These results allow formulation of mechanisms for the H/N exchange reaction, and three feasible mechanisms for associative exchange and three for dissociative exchange are identified. Consistent electronic structures and potential energy surfaces are maintained throughout. Changes in the spin populations of Fe2 and Fe6 connected with cluster deformation and with metal-ligand bond formation are identified.