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 0 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 [(CI)(Fe6FeMoS9)-Fe-II-Mo-III-S-IV(H+)(3)N3-(GI)(Im)](2-), [I-N-3H](2-), and [(CI)(Fe4Fe3MoS9)-Fe-II-Mo-III-S-IV(H+)(3)N3-(GI)(Im)], [I-N-3H](0) (GI = deprotonated glycol; Im = imidazole). These are the triply protonated ENDOR/ESEEM [I-N](5-) and Mossbauer [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 DeltaE's associated with the individual steps of the proposed mechanism are small and either positive or negative. The largest positive DeltaE is +121 kJ/mol. The largest negative DeltaE of -333 kJ/mol is for the FeMoco with a N3- in the center (the isolated form) and an intermediate in the proposed mechanism.