Reported here is a comprehensive theoretical investigation of the binding of N(2) to the Fe(7)MoS(9)N(homocitrate)(cysteine)(histidine) active site (FeMo-co) of the enzyme nitrogenase, as a prerequisite to elucidation of the chemical mechanism of the catalyzed reduction to NH(3). The degree and type of hydrogenation of FeMo-co, with H atoms and possibly an H(2) molecule, are key variables, following the Thorneley-Lowe kinetic scheme. Ninety-four local energy minima were located for N(2) coordinated in eta(2) (side) and eta(1) (end) modes at the endo and exo coordination positions of Fe2 and Fe6. The stabilities of 57 representative structures are assessed by calculation of the reaction profiles and activation energies for the association and dissociation of N(2). Barriers to association of N(2) depend mainly on the location of the hydrogenation and the location of N(2) coordination, while dissociation barriers depend primarily on whether N(2) is eta(2)- and eta(1)-coordinated, and secondarily on the location of the hydrogenation. Increased negative charge on FeMo-co increases the barriers, while C in place of N at the center of FeMo-co has little effect. The interactions of the models of ligated FeMo-co with the surrounding protein, including proteins with mutations of key amino acids, are assessed by in silico cofactor transplantations and calculations of protein strain energies. From these results, which identify models involving contacts and interactions with the surrounding residues that have been shown by mutation to affect the N(2) activity of nitrogenase, and from the N(2) coordination profiles, it is concluded that endo-eta(1)-N(2) coordination at Fe6 is most probable. There is strong reason to believe that the mechanism of nitrogenase will involve one or more of the preferred models presented here, and a detailed foundation of structures and principles is now available for postulation and calculation of the profiles of the steps in which H atoms bound to FeMo-co are transferred to bound N(2).