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The chemical reactions occurring at the Fe 7 MoS 9 C(homocitrate) cluster, FeMo-co, the active site of the enzyme nitrogenase (N 2 → NH 3 ), are enigmatic. Experimental information collected over a long period reveals aspects of the roles of N 2 and H 2 , each with more than one type of reactivity. This paper reports investigations of the binding of H 2 and N 2 at intact FeMo-co, using density functional simulations of a large 486 atom relevant portion of the protein, resulting in 27 new structures containing H 2 and/or N 2 bound at the exo and endo coordination sites of the participating Fe atoms, Fe2 and Fe6. Binding energies and transition states for association/dissociation are determined, and trajectories for the approach, binding and separation of H 2 /N 2 are described, including diffusion of these small molecules through proximal protein. Influences of surrounding amino acids are identified. FeMo-co deforms geometrically when binding H 2 or N 2 , and a procedure for calculating the energy cost involved, the adaptation energy, is introduced here. Adaptation energies, which range from 7 to 36 kcal mol -1 for the reported structures, are influenced by the protonation state of the His195 side chain. Seven N 2 structures and three H 2 structures have negative binding free energies, which include the estimated entropy penalties for binding of N 2 , H 2 from proximal protein. These favoured structures have N 2 bound end-on at exo -Fe2, exo -Fe6 and endo -Fe2 positions of FeMo-co, and H 2 bound at the endo -Fe2 position. Various postulated structures with N 2 bridging Fe2 and Fe6 revert to end-on-N 2 at endo positions. The structures are also assessed via the calculated potential energy barriers for association and dissociation. Barriers to the binding of H 2 range from 1 to 20 kcal mol -1 and barriers to dissociation of H 2 range from 3 to 18 kcal mol -1 . Barriers to the binding of N 2 , in either side-on or end-on mode, range from 2 to 18 kcal mol -1 , while dissociation of bound N 2 encounters barriers of 3 to 8 kcal mol -1 for side-on bonding and 7 to 18 kcal mol -1 for end-on bonding. These results allow formulation of mechanisms for the H 2 /N 2 exchange reaction, and three feasible mechanisms for associative exchange and three for dissociative exchange are identified. Consistent electronic structures and potential energy surfaces are maintained throughout. Changes in the spin populations of Fe2 and Fe6 connected with cluster deformation and with metal-ligand bond formation are identified.

The active site of the N2 fixing enzyme nitrogenase is a C-centred Fe7MoS cluster (FeMo-co) containing a trigonal prism of six Fe atoms connected by a central belt of three doubly-bridging S atoms. The trigonal faces of the prism are capped via triply-bridging S atoms to Fe1 at one end and Mo at the other end. One of the central belt atoms, S2B, considered to be important in the chemical mechanism of the enzyme, has been shown by Spatzal, Rees et al. to undergo substitution by CO, and also substitution by Se in the presence of SeCN(-), under turnover conditions. Further, when turning over under C2H2 or N2/CO there is migration of Se to the other two belt bridging positions. These reactions are extraordinary, and unprecedented in metal chalcogenide cluster chemistry. Using density functional simulations, mechanisms for all of these reactions have been developed, involving the small molecules SCO, SeCO, C2H2S, C2H2Se, SeCN(-), SCN(-) functioning as carriers of S and Se atoms. The possibility that the S2B bridge position is vacant is discounted, because the barrier to formation of a bridge-void intermediate with two contiguous three-coordinate Fe atoms is too large. A bridging ligand is retained throughout the proposed mechanisms. Intermediates with Fe-C(O)-S/Se-Fe cycles and with SCO/SeCO C-bound to Fe are predicted. The energetics of the reaction trajectories show them to be feasible and easily reversible, consistent with experiment. Alternative mechanisms involving intramolecular differential rotatory rearrangements of the cluster to scramble the Se bridges are also examined, and shown to be very unlikely. The implications of these new facets of the reactivity of the FeMo-co cluster are discussed: it is considered that they are unlikely to be part of the mechanism of the physiological reactions of nitrogenase.

Density functional calculations reveal that protonation of a μ3-S in [Fe4S4X4](2-) clusters (X = halide, thiolate, phenoxide) results in the breaking of one S-Fe bond (to >3 Å, from 2.3 Å). This creates a doubly-bridging SH ligand (μ3-SH is not stable), and a unique three-coordinated planar Fe atom. The under-coordination of this unique Fe atom is the basis of revised mechanisms for the acid-catalysed ligand substitution reactions in which substitution of X by PhS occurs at the unique Fe site by an indirect pathway involving initial displacement of X by acetonitrile (solvent), followed by displacement of coordinated acetonitrile by PhSH. When X = Cl or Br the rate of attack by PhSH is slower than the dissociation of X(-), and is the rate-determining step; in contrast, when X = SEt, SBu(t) or OPh the rate of dissociation of XH is slower than attack by PhSH and is rate-determining for these clusters. A full and consistent interpretation of all kinetic data is presented including new explanations of many of the kinetic observations on the acid-catalysed substitution reactions of [Fe4S4X4](2-) clusters. The proposed mechanisms are supported by density functional calculations of the structures of intermediates, and simulations of some of the steps. These findings are expected to have widespread ramifications for the reaction chemistry of both natural and synthetic clusters with the {Fe4S4} core.

Density functional calculations show that Fe-S clusters undergo unexpected large structural changes when protonated at S. Protonation of prototypical cubanoid [Fe4S4X4](2-) to [Fe4S3(SH)X4](-) (X = Cl, SR, OR) results in formation of doubly-bridging SH, severance of one Fe-S bond, and creation of a three-coordinate Fe. These findings explain previously enigmatic results concerning the reactivity of these clusters, including the rates of protonation, pKa data, and the kinetics of acid-catalysed ligand substitution.

The iron-molybdenum cofactor (FeMo-co), which is the catalytic center for the enzymatic conversion of N(2) to NH(3), has the composition [NFe(7)MoS(9)(homocitrate)], and, with a cluster of eight transition metal atoms and nine sulfur atoms, has a complex delocalized electronic structure. The electronic dimensions of FeMo-co and of each of its derivatives appear as sets of electronic states lying close in energy. These electronic dimensions naturally partner the geometrical changes and the reactivity patterns during the catalytic cycle, and also connect with spectroscopic investigations of the mechanism. This paper describes straightforward computational procedures for the determination and management of the low-lying electronic states of FeMo-co and of its coordinated intermediates and transition states during density functional simulations of steps in the catalytic mechanism. General principles for the distribution of electron spin density over all atoms are presented, using several proposed intermediates as examples. A tough general irony arises in the distribution of spin density over FeMo-co and its derivatives: the less interesting atoms get the spin, and the most interesting atoms do not.

The preceding paper (Dalton Trans., 2008, DOI: 10.1039/b806100a) describes the logical development of a chemical mechanism for the catalysis of hydrogenation of N(2) to 2NH(3) that occurs at the Fe(7)MoS(9)N(c)(homocitrate) cofactor (FeMo-co) of the enzyme nitrogenase. The mechanism uses a single replenishable path for serial supply of protons which become H atoms on FeMo-co, migrating to become S-H and Fe-H donors to N(2) and to the intermediates that follow. This chemical catalysis at FeMo-co is distinctly intramolecular: transition states and reaction profiles for the preferred 21 step pathway were presented. This paper describes a number of alternative intermediates and pathways that were considered in developing the mechanism. These results reveal further relevant principles of the reactivity of hydrogenated FeMo-co, and the reasons why these pathways are less likely to be part of the mechanism. The intramolecular character of the mechanism, and the relatively small distances over which H atoms transfer, lead to expectations of extensive quantum mechanical hydrogen tunneling as part of the catalytic rate enhancement. This possibility is supported by comparisons of reaction profiles with those for enzyme reactions for which tunneling is established.

Biological nitrogen reduction is catalyzed by a complex two-component metalloenzyme called nitrogenase. For the Mo-dependent enzyme, the site of substrate reduction is provided by a [7Fe-9S-Mo-X-homocitrate] metallocluster, where X is proposed to be an N atom. Recent progress with organometallic model compounds, theoretical calculations, and biochemical, kinetic, and biophysical studies on nitrogenase has led to the formulation of two opposing models of where N(2) or alternative substrates might bind during catalysis. One model involves substrate binding to the Mo atom, whereas the other model involves the participation of one or more Fe atoms located in the central region of the metallocluster. Recently gathered evidence that has provided the basis for both models is summarized, and a perspective on future research in resolving this fundamental mechanistic question is presented.

The active site of the enzyme nitrogenase is the FeMo-cofactor (FeMo-co), a C-centred Fe 7 MoS 9 cluster, connected to the surrounding MoFe protein via ligands Cys 275 and His 442 . Density functional calculations, involving 14 additional surrounding amino acids, focus on His 195 because its mutation causes important reactivity changes, including almost complete loss of ability to reduce N 2 to NH 3 . The Nε side-chain of His 195 is capable of hydrogen bonding to S2B, bridging Fe2 and Fe6 of FeMo-co, believed to be the main reaction domain of nitrogenase. Details are presented for the possible ways in which protonated or deprotonated Nε of His 195 interact with S2B or S2B-H or Fe2 or Fe2-H or Fe-(H 2 ). Movements of the His 195 side-chain allow formation of a significant short dihydrogen bond between Nε of His 195 and H on Fe2: Nε-H••H-Fe2, with H–H = 1.39 Å. It is shown that a 180° rotation of the imidazole ring of His 195 is not able to facilitate transfer of protons from the protein surface to FeMo-co. His 195 is able to move H atoms to and from S2B, and the characteristics of H transfer between S2B and Nε of His 195 are described, together with their dependence on the protonation state of His 195 and the redox state of FeMo-co. The water molecule on the posterior Nδ side of His 195 can mediate proton transfer to and from the side-chain of Tyr 228 . The accumulated results suggest that protonated His 195 could be the agent for the first, most difficult, transfer of H to bound substrate N 2 . [ABSTRACT FROM AUTHOR]

Density functional calculations show that Fe-S clusters undergo unexpected large structural changes when protonated at S. Protonation of prototypical cubanoid [Fe4S4X4]2- to [Fe4S3(SH)X4]- (X = Cl, SR, OR) results in formation of doubly-bridging SH, severance of one Fe-S bond, and creation of a three-coordinate Fe. These findings explain previously enigmatic results concerning the reactivity of these clusters, including the rates of protonation, pKa data, and the kinetics of acid-catalysed ligand substitution. [ABSTRACT FROM AUTHOR]

Abstract: We report density functional theoretical investigations of the experiments described by Pilgrim and Duncan [J.S. Pilgrim, M.A. Duncan, J. Am. Chem. Soc., 115 (1993) 6958] in which [Fe x C y ]+ clusters are generated by laser vapourisation of Fe atoms in a plasma containing acetylene. Many possible structures for the clusters [Fe12C12], [Fe10C12], [Fe8C12], [Fe6C12], [Fe4C12], [Fe3C12] and [Fe2C12] are evaluated, with the following conclusions: [Fe12C12] is a slightly distorted 2×3×4 nanocrystallite fragment of a face-centered cubic FeC lattice; [Fe10C12] is distorted [Fe12C12] depleted by two three-coordinate Fe atoms; [Fe8C12], with the prototypical composition for metallocarbohedrenes, has a C 3v structure containing only C2 groups and with a short axial Fe[Fe6C12] has the [Fe8C12] structure but without the two axial Fe atoms, such that each C2 group has two end-on Fee:glyph name="sbnd" />C2 bonds and one side-on Fee:glyph name="sbnd" />C2 interaction; at [Fe4C12] there are two cumulenic C6 chains separated by four Fe atoms; [Fe3C12] is a monocyclic alternation of cumulenic C4 chains and Fe atoms, while [Fe2C12] is a monocyclic alternation of cumulenic C6 chains and Fe atoms. Mechanisms are proposed for the experiments in which photodissociation of Fe atoms converts [Fe12C12] to [Fe8C12], and in which [Fe8C12] photodissociates to [Fe6C12], [Fe4C12], and [Fe2C12]. The formation of Cnd of C n chains initiated by the withdrawal of Fe atoms in these processes is related to the Fe catalysed formation of carbon nanotubes. [Copyright &y& Elsevier]

The migration of H atoms over S and Fe atoms in the reaction domain of FeMo-co, the active site of nitrogenase, is described and used to explain mechanistic data on the catalyzed reductions of N2 and C2H2. After electron transfer to FeMo-co, H atoms are generated by fast proton supply to S3B (atom labels from structure 1MlN) and migrate vectorially via several pathways from S3B to locations on the FeMo-co face, specifically Fe6, S2B, Fe2, and S2A (calculated reaction profiles are reported). The EnHn reduction levels (n = 1-4) in the Thorneley-Lowe kinetic-mechanistic schemes are each potential sequences of substructures with different distributions of H atoms. The positions of H atoms influence the binding of substrates N2 and C2H2, and the bound substrate subsequently blocks further migration of H atoms past the binding site. This model provides a consistent structural interpretation of (a) the two-site reactivity of C2H2 and the differentiation of the high- and low-affinity sites as due to different preparatory H migration; (b) the differing mutual inhibitions of N2 and C2H2 in wild-type protein; (c) the modified reactivity of the Azotobacter vinelandii α-Gly69Ser mutant with N2 and C2H2 and (d) the basis for the stereoselectivity of hydrogenation of C2D2 and its loss in some mutant proteins. Some structures for initially bound N2 and C2H2, and their hydrogenated intermediates, are presented. The key new concept is that binding sites and binding states for substrates and intermediates are characterized not only by their locations on the FeMo-co face but also by the structural and temporal status of the distribution of H atoms over the FeMo-co reaction domain. [ABSTRACT FROM AUTHOR]