Recent spectroscopic, kinetic, photophysical, and thermodynamic measurements show activation of nitrogenase for N 2 → 2NH 3 reduction involves the reductive elimination (re) of H 2 from two [Fe-H-Fe] bridging hydrides bound to the catalytic [7Fe-9S-Mo-Chomocitrate] FeMo-cofactor (FeMo-co). These studies rationalize the Lowe-Thorneley kinetic scheme's proposal of mechanistically obligatory formation of one H 2 for each N 2 reduced. They also provide an overall framework for understanding the mechanism of nitrogen fixation by nitrogenase. However, they directly pose fundamental questions addressed computationally here. We here report an extensive computational investigation of the structure and energetics of possible nitrogenase intermediates using structural models for the active site with a broad range in complexity, while evaluating a diverse set of density functional theory flavors. (i) This shows that to prevent spurious disruption of FeMo-co having accumulated 4[e − /H + ] it is necessary to include: all residues (and water molecules) interacting directly with FeMo-co via specific H-bond interactions; nonspecific local electrostatic interactions; and steric confinement. (ii) These calculations indicate an important role of sulfide hemilability in the overall conversion of E 0 to a diazene-level intermediate. (iii ) Perhaps most importantly, they explain (iiia) how the enzyme mechanistically couples exothermic H 2 formation to endothermic cleavage of the N≡N triple bond in a nearly thermoneutral re/oxidativeaddition equilibrium, (iiib) while preventing the "futile" generation of two H 2 without N 2 reduction: hydride re generates an H 2 complex, but H 2 is only lost when displaced by N 2 , to form an end-on N 2 complex that proceeds to a diazene-level intermediate.iological nitrogen fixation is one of the most challenging chemical transformations in biology, the conversion of N 2 to ammonia. The catalyst for biological N 2 fixation, the metalloenzyme nitrogenase, is known in three different forms (1) with the most abundant being the Mo-dependent enzyme, which is composed of the electron-donating Fe protein and the catalytic MoFe protein. The Fe protein, a homodimer, delivers one electron at a time during transient association with the MoFe protein heterotetramer with dissociation of the two proteins driven by the hydrolysis of two ATP to two ADP/P i per electron transfer (ET) event (2). The reduction of N 2 takes place on the [7Fe-9S-Mo-C-homocitrate] FeMo-cofactor (FeMo-co) in the active site of the MoFe protein (Fig. 1), with the [8Fe-7S] Pcluster in the MoFe protein acting as an ET intermediary.Lowe and Thorneley put forward a kinetic model for catalysis by the MoFe protein, including rate constants for formation of each intermediate state, designated as E n , where n indicates the number of electrons and protons accumulated. This scheme incorporates a controversial limiting stoichiometry:with an obligatory formation of 1 mol of H 2 per mole of N 2 reduced, and a corresponding requirement of 8[e − /H + ], ...