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Abstract
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.