Protonation and Reduction of the FeMo Cluster in Nitrogenase Studied by Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations

We have performed a systematic computational study of the relative energies of possible protonation states of the FeMo cluster in nitrogenase in the E₀–E₄ states, i.e., the resting state and states with 1–4 electrons and protons added but before N₂ binds. We use the combined quantum mechanics and molecular mechanics (QM/MM) approach, including the complete solvated heterotetrameric enzyme in the calculations. The QM system consisted of 112 atoms, i.e., the full FeMo cluster, as well all groups forming hydrogen bonds to it within 3.5 Å. It was treated with either the TPSS-D3 or B3LYP-D3 methods with the def2-SV­(P) or def2-TZVPD basis sets. For each redox state, we calculated relative energies of at least 50 different possible positions for the proton, added to the most stable protonation state of the level with one electron less. We show quite conclusively that the resting E₀ state is not protonated using quantum refinement and by comparing geometries to the crystal structure. The E₁ state is protonated on S2B, in agreement with most previous computational studies. However, for the E₂–E₄ states, the two QM methods give diverging results, with relative energies that differ by over 300 kJ/mol for the most stable E₄ states. TPSS favors hydride ions binding to the Fe ions. The first bridges Fe2 and Fe6, whereas the next two bind terminally to either Fe4, Fe5, or Fe6 with nearly equal energies. On the other hand, B3LYP disfavors hydride ions and instead suggests that 1–3 protons bind to the central carbide ion.