PNNL

Abstract

Recent spectroscopic, kinetic, photophysical and thermodynamic measurements have shown that activation of the enzyme nitrogenase for reduction of N2 to two NH3 involves the reductive elimination (re) of H2 from two [Fe-H-Fe] bridging hydrides bound to the catalytic [7Fe-9S-Mo-C-homocitrate] FeMo-cofactor (FeMo-co), thereby rationalizing the Lowe-Thorneley kinetic scheme’s proposal of the mechanistically obligatory formation of one H2 for each N2 reduced. To computationally analyze this process, (i) we critically assessed the density functional and structural model required to obtain accurate structures and energies of nitrogenase intermediates. (ii) We also examined models for the FeMo-co protein environment that are based on molecular dynamics calculations, and exhibit increasing levels of complexity. We show that a reliable analysis of the FeMo-co electron and proton accumulation patterns requires an extended model that includes all the protein residues and water molecules interacting directly with FeMo-co, both via specific H-bonds and non-specific electrostatic interactions. DFT computations thus performed illuminate and provide strong theoretical and computational support for nitrogenase activation by re. of H2. They show that re of H2 is coupled to N2 binding/reduction in a nearly thermoneutral equilibrium, and that obligatory H2 re indeed represents the thermodynamic driving force for N2 reduction to a diazene-like intermediate. Mechanistically, the computations support the experimental conclusion that hydride re involves formation of an H2 complex, and they suggest that N2 displaces H2, forming an end-on N2 complex. They further indicate that sulfide hemilability plays an important role.