Modeling the nitrogenase FeMo cofactor with high‐spin Fe₈S₉X⁺ (XN, C) clusters. Is the first step for N₂ reduction to NH₃ a concerted dihydrogen transfer?

Abstract

A high-spin Fe(8)S(9)X(+) (X=N, C) cluster is used to model the reduction of molecular nitrogen to ammonia by the nitrogenase FeMo cofactor at the B3LYP/6-311G(d,p)/ECP(Fe,SDD) level of theory. A total of seventy-three structures were optimized (including three transition state optimizations) to explore the structure and energetic of N(2), C(2)H(2), and CO coordination to the Fe(8)S(9)X(+) cluster. After three protonation-reduction (PR) steps (modeled by addition of hydrogen atoms), N(2), C(2)H(2), and CO are predicted to bind to a Fe atom in the exo (cage does not open) position with binding energies of 7.6, 14.7, and 11.7 kcal/mol. With additional PR steps the coordination number of the core nitrogen atom is reduced from six to five and the bridging thiol group becomes a terminal SH(2) group. The fifth and sixth PR steps occur on the core nitrogen and the open Fe site. Coordination of N(2) is enhanced after six PR steps to give an intermediate ideally suited for a concerted dihydrogen transfer from the Fe and core nitrogen atoms to the coordinated N(2). The identity of the central atom (nitrogen or carbon) has only a minor effect on the reaction steps.

Photolysis of Hi‐CO Nitrogenase – Observation of a Plethora of Distinct CO Species Using Infrared Spectroscopy

“…Plane‐wave DFT calculations also failed to find a stable bridging CO structure for a variety of models 11. Using an 8‐Fe model for the FeMo cofactor, the most stable CO structure was found to involve terminal CO in an “ exo ” geometry (Scheme , a) at the 3‐electron, 3‐proton reduction level 12. The alternative of terminal CO binding at Mo has also been proposed to explain some of the spectroelectrochemical FT‐IR results from studies of isolated FeMo‐co 9…”

Density Functional Theory Study of NHx (x = 0−3) and N2 Adsorption on IrO2(110) Surfaces

“…In recent years, many computational and experimental studies have been performed to develop low-molecular-weight transition metal complexes that mimic the structural or functional role of nitrogenase. 26,[33][34][35][36][37][38][39] The first step in all N 2 fixation reactions is activation of bonded N 2 ; because N 2 is very inert, the search for a catalyst that could activate it remains a considerable challenge.…”

The chemical mechanism of nitrogenase: calculated details of the intramolecular mechanism for hydrogenation of η2-N2 on FeMo-co to NH3

“…The light atom of unproven elemental identity at the center of FeMo-co is presumed to be nitrogen, N c , on the basis of various theoretical investigations. 10-14 Theory also indicates that the possible alternative elemental identity of the central atom, carbon, has minor influence on the reactivity of FeMo-co. 15, 16 The consequences of site directed mutations suggest very strongly that the reaction domain of FeMo-co is the Fe2,Fe3,Fe6,Fe7 face, [17][18][19] rather than the Mo atom, [20][21][22] and implicate Fe2 and Fe6 as the sites of binding of substrates and intermediates. 9 While most attempts to elucidate the mechanism by direct observation of intermediates have been frustrated by EPR silence during turnover, recent investigations of MoFe proteins modified at residues a-70 and a-195 (labeling for Azotobacter vinelandii, Protein Database (PDB) 1M1N) have detected and partially characterized intermediates believed to involve H, 23,24 N 2 , 25,26 HNNMe 25- 27 and N 2 H 4 , 25,26, 28 as well as alkenes from alternative alkyne substrates.…”

“…Theoretical investigations of model systems related to FeMo-co have also been reported. 16,21,[42][43][44][45][46][47][48] The reduction of N 2 requires six electrons and six protons. The electrons are transferred serially to FeMo-co from the P-cluster.…”