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Density functional theory (DFT) calculations have been performed on the nitrogenase cofactor, FeMoco. Issues that have been addressed concern the nature of M-M interactions and the identity and origin of the central light atom, revealed in a recent crystallographic study of the FeMo protein of nitrogenase (Einsle, O.; et al. Science 2002, 297, 871). Introduction of Se in place of the S atoms in the cofactor and energy minimization results in an optimized structure very similar to that in the native enzyme. The nearly identical, short, lengths of the Fe-Fe distances in the Se and S analogues are interpreted in terms of M-M weak bonding interactions. DFT calculations with O or N as the central atoms in the FeMoco marginally support the assignment of the central atom as N rather than O. The assumption was made that the central atom is the N atom, and steps of a catalytic cycle were calculated starting with either of two possible states for the cofactor and maintaining the same charge throughout (by addition of equal numbers of H(+) and e(-)) between steps. The states were [(Cl)Fe(II)(6)Fe(III)Mo(IV)S(9)(H(+))(3)N(3-)(Gl)(Im)](2-), [I-N-3H](2-), and [(Cl)Fe(II)(4)Fe(III)(3)Mo(IV)S(9)(H(+))(3)N(3-)(Gl)(Im)], [I-N-3H](0) (Gl = deprotonated glycol; Im = imidazole). These are the triply protonated ENDOR/ESEEM [I-N](5-) and Mössbauer [I-N](3-) models, respectively. The proposed mechanism explores the possibilities that (a) redox-induced distortions facilitate insertion of N(2) and derivative substrates into the Fe(6) central unit of the cofactor, (b) the central atom in the cofactor is an exchangeable nitrogen, and (c) the individual steps are related by H(+)/e(-) additions (and reduction of substrate) or aquation/dehydration (and distortion of the Fe(6) center). The Delta E's associated with the individual steps of the proposed mechanism are small and either positive or negative. The largest positive Delta E is +121 kJ/mol. The largest negative Delta E of -333 kJ/mol is for the FeMoco with a N(3-) in the center (the isolated form) and an intermediate in the proposed mechanism.

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