The mechanism for nitrogenase including all steps

The catalytic cofactor of the most common form of nitrogenase contains seven irons and one molybdenum bound together by sulfide bonds. Surprisingly, a central carbide has been demonstrated by experiments. Another noteworthy structural component is a large homocitrate ligand. In recent theoretical studies it has been shown that the central carbide is needed as a place for the incoming protons that are necessary parts of a reduction process. It has also been shown that a role for the homocitrate ligand could be that it may be rotated to release one bond to molybdenum. In the present study, the carbide protonation steps are reinvestigated with similar results to those reported before. The actual activation of N2 in the E4 state is an extremely complicated process. It has been found experimentally that two hydrides should leave as H2, in a reductive elimination process, to allow N2 activation in E4 in an easily reversible step. It is here suggested that after H2 is released, it is necessary for the metal cofactor to get rid of one proton. This is achieved by protonating the homocitrate and then rotating it to release one of the bonds to Mo. After this rotation, N2 can bind. In the E5 step, the homocitrate is rotated back to its original position and remains that way until the end of the catalytic process. The N2 protonation steps are energetically easy. Since a protonated carbide has never been observed experimentally, it is necessary to also have a mechanism for deprotonating the carbon at the end of the catalytic cycles. Such a mechanism is suggested here.