Density Functional Calculations on the Binding of Dinitrogen to the FeFe Cofactor in Fe-Only Nitrogenase: FeFeco(μ6-N2) as Intermediate in Nitrogen Fixation

Evolution of Ferromagnetic and Antiferromagnetic States in Iron Nitride Clusters FenN and FenN2 (n = 1-10)

First-principles density functional theory calculations on neutral and singly negatively and positively charged iron clusters Fe_n and iron nitride clusters Fe_nN and Fe_nN₂ (n = 1-10) in the range of 1 ≤ n ≤ 10 revealed that there is a strong competition between ferromagnetic and antiferromagnetic states especially in the Fe_nN₂^0,±1 cluster series. This phenomenon was related to superexchange via a bridging N atom between two iron atoms in the Fe_nN₂^0,±1 cluster series and to a double superexchange effect via a Fe atom shared by two N atoms in the Fe_nN₂^0,±1 series. A thorough examination of the structure-energy-spin state relationships in these clusters is conducted, leading to new insights and confirmation of available experimental results on structural parameters and dissociation energetics. The bond energies of both nitrogen atoms in the Fe_nN₂ series are approximately the same. They weakly depend on the charge of the host cluster and fluctuate around 5.5 eV when moving along the series. The energy of N₂ desorption is relatively small; it varies by about 1.0 eV and depends on the charge of the cluster. The experimental finding that N₂ dissociates on the Fe_n⁺ clusters beginning with n = 4 was supported by the results of our computations. Our computed values of the Fe_n⁺-N bonding energies agree with the experimental data within the experimental uncertainty bars. It was found that the attachment of one or two N atoms does not seriously affect the polarizability, electron affinity, or ionization energy of the host iron clusters independent of the charge.

Theoretically exploring the key role of the Lys412 residue in the conversion of N2O to N2by nitrous oxide reductase from Achromobacter cycloclastes

The active Cu_Zcluster of NOR provides strong back-donation to coordinated N₂O and activates the O atom of the N₂O group facilitating H-bonding and protonationviathe Lys412 residue.

Catalytic reduction of dinitrogen to ammonia by molybdenum: theory versus experiment

Molybdenum complexes that contain the triamidoamine ligand [(RNCH(2)CH(2))(3)N](3-) (R = 3,5-(2,4,6-iPr(3)C(6)H(2))(2)C(6)H(3)) catalyze the reduction of dinitrogen to ammonia at 22 degrees C and 1 atm with protons from 2,6-dimethylpyridinium and electrons from decamethylchromocene. Several theoretical studies have been published that bear on the proposed intermediates in the catalytic dinitrogen reduction reaction and their reaction characteristics, including DFT calculations on [(HIPTNCH(2)CH(2))(3)N]Mo species (HIPT =hexaisopropylterphenyl = 3,5-(2,4,6-iPr(3)C(6)H(2))(2)C(6)H(3)), which contain the actual triamidoamine ligand that is present in catalytic intermediates. Recent theoretical findings are compared with experimental findings for each proposed step in the catalytic reaction.

Modeling hydrogen evolution from the Fe4S4and Fe8S9X (X = N, C) clusters. Can a FeS high-spin cluster serve as a surrogate for the FeMo cofactor?

A high-spin model of nitrogenase with a Fe(8)S(9)X(+) cluster (X = nitrogen or carbon) is used to test a mechanism for molecular hydrogen production, which is known to accompany ammonia production. The reaction proceeds with a series of protonation-reduction (PR) steps which are considered to be spontaneous if the calculated hydrogen-cluster bond energy exceeds 35-40 kcal/mol. The novel features of this mechanism include the opening of the cluster when one of the bridging sulfides undergoes two PR steps and the direct participation of the central atom when it undergoes a PR step. After the sixth PR step, a cluster is formed which has a low barrier for loss of molecular hydrogen in an exothermic reaction step. The central atom (nitrogen or carbon) has only a minor effect on the reaction steps.

Modeling the nitrogenase FeMo cofactor with high-spin Fe8 S9 X+ (XN, C) clusters. Is the first step for N2 reduction to NH3 a concerted dihydrogen transfer?

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.

Exploring new frontiers of nitrogenase structure and mechanism

The mechanism of the complex enzyme nitrogenase has long been one of the most challenging problems in bioinorganic chemistry. The complexity of the metal centers of nitrogenase has stretched the boundaries of biochemical, physical and computational tools for providing insights into its structure and chemical function. Recently, there have been several key advances in crystallography and spectroscopy that have impacted the way the nitrogenase mechanism is approached. These advances have opened new frontiers in nitrogenase research, which has started to reveal novel details about the molecular structure, substrate binding and reduction. Here, we discuss these recent advances and their implications on the future of nitrogenase research.

Structural insights into a protein-bound iron-molybdenum cofactor precursor

The iron-molybdenum cofactor (FeMoco) of the nitrogenase MoFe protein is a highly complex metallocluster that provides the catalytically essential site for biological nitrogen fixation. FeMoco is assembled outside the MoFe protein in a stepwise process requiring several components, including NifB-co, an iron- and sulfur-containing FeMoco precursor, and NifEN, an intermediary assembly protein on which NifB-co is presumably converted to FeMoco. Through the comparison of Azotobacter vinelandii strains expressing the NifEN protein in the presence or absence of the nifB gene, the structure of a NifEN-bound FeMoco precursor has been analyzed by x-ray absorption spectroscopy. The results provide physical evidence to support a mechanism for FeMoco biosynthesis. The NifEN-bound precursor is found to be a molybdenum-free analog of FeMoco and not one of the more commonly suggested cluster types based on a standard [4Fe-4S] architecture. A facile scheme by which FeMoco and alternative, non-molybdenum-containing nitrogenase cofactors are constructed from this common precursor is presented that has important implications for the biosynthesis and biomimetic chemical synthesis of FeMoco.

Syntheses, crystal structures and biological relevance of glycolato and S-lactato molybdates

Glycolato and S-lactato complexes containing the dioxomolybdenum(VI) moiety have been synthesized for studies on the role of the alpha-hydroxycarboxylato anion in the iron molybdenum cofactor of nitrogenase. The ligands in these complexes, vis K2[MoO2(glyc)2].H2O (H2glyc=glycolic acid, C2H4O3) (1) and (Na2[MoO2(S-lact)2])3.13H2O (H2lact=lactic acid, C3H6O3) (2) chelate through their alpha-alkoxyl and alpha-carboxyl oxygen atoms. In contrast, octanuclear K6[(MoO2)8(glyc)6(Hglyc)2].10H2O (3) formed by the reduction of the glycolato complex (1), features three different ligand binding modes: (i) non-bridging and bridging bidentate coordination of alpha-alkoxyl and alpha-carboxyl groups, and (ii) bidentate bridging using alpha-carboxyl group, leaving the alpha-alkoxyl group free. The octanuclear skeleton shows strong metal-metal interactions. The coordination modes in (1) and (2) mimic that of homocitrate to the iron molybdenum cofactor (FeMo-co) of nitrogenase. The bidentate coordination of alpha-alkoxyl and alpha-carboxyl groups shows that bond of alpha-carboxyl group to Mo is less susceptible to the oxidation state of molybdenum compared with the Mo-alpha-alkoxyl bond. This is supported by the dinuclear coordination of alpha-carboxyl group with free alpha-alkoxyl group in glycolato molybdate(V) (3).

Ground-State Singlet L3Fe-(μ-N)-FeL3 and L3Fe(NR) Complexes Featuring Pseudotetrahedral Fe(II) Centers

Pseudotetrahedral iron(II) coordination complexes that contain bridged nitride and terminal imide linkages, and exhibit singlet ground-state electronic configurations, are described. Sodium amalgam reduction of the ferromagnetically coupled dimer, {[PhBP(3)]Fe(mu-1,3-N(3))}(2) (2) ([PhBP(3)] = [PhB(CH(2)PPh(2))(3)](-)), yields the diamagnetic bridging nitride species [{[PhBP(3)]Fe}(2)(mu-N)][Na(THF)(5)] (3). The Fe-N-Fe linkage featured in the anion of 3 exhibits an unusually bent angle of approximately 135 degrees , and the short Fe-N bond distances (Fe-N(av) approximately equal to 1.70 A) suggest substantial Fe-N multiple bond character. The diamagnetic imide complex {[PhBP(3)]Fe(II)(triple bond)N(1-Ad)}{(n)()Bu(4)N} (4) has been prepared by sodium amalgam reduction of its low-spin iron(III) precursor, [PhBP(3)]Fe(III)(triple bond)N(1-Ad) (5). Complexes 4 and 5 have been structurally characterized, and their respective electronic structures are discussed in the context of a supporting DFT calculation. Diamagnetic 4 provides a bona fide example of a pseudotetrahedral iron(II) center in a low-spin ground-state configuration. Comparative optical data strongly suggest that dinuclear 3 is best described as containing two high-spin iron(II) centers that are strongly antiferromagnetically coupled to give rise to a singlet ground-state at room temperature.