Modeling a central ligand in the nitrogenase FeMo cofactor

In very recent work by Einsle et al. (Science 2002, 297, 1696), a new X-ray crystallographic structure of the FeMo cofactor of nitrogenase with a central ligand was presented. The central ligand is a light atom (N, O, or C), and Einsle et al. suggest that it is nitrogen. We present density functional calculations on the FeMo cofactor, and we investigate N, O, and C as central ligands. We show that both N and O lead to energetically stable FeMo cofactor structures, whereas C is energetically unfavorable. By comparison of bond geometries with the crystallographically determined values, we show that the central ligand is most likely nitrogen.     

Ammonia production at the FeMo cofactor of nitrogenase: results from density functional theory

Biological nitrogen fixation has been investigated beginning with the monoprotonated dinitrogen bound to the FeMo cofactor of nitrogenase up to the formation of the two ammonia molecules. The energy differences of the relevant intermediates, the reaction barriers, and potentially relevant side branches are presented. During the catalytic conversion, nitrogen bridges two Fe atoms of the central cage, replacing a sulfur bridge present before dinitrogen binds to the cofactor. A transformation from cis- to trans-diazene has been found. The strongly exothermic cleavage of the dinitrogen bond takes place, while the Fe atoms are bridged by a single nitrogen atom. The dissociation of the second ammonia from the cofactor is facilitated by the closing of the sulfur bridge following an intramolecular proton transfer. This closes the catalytic cycle.     

The consequences of an interstitial N atom in the FeMo cofactor of nitrogenase

The atom-centred FeMo cofactor of nitrogenase most likely contains N, resting at the [NMoFe7]18+ redox level, inserted from N2, and subsequently restricting the modes of binding of substrate to the NFe6 core.     

Chemical activity of the nitrogenase FeMo cofactor with a central nitrogen ligand: density functional study

We investigate the chemical consequences of a central ligand in the nitrogenase FeMo cofactor using density functional calculations. Several studies have shown that the central ligand most probably is a nitrogen atom, but the consequences for the chemical reactivity of the cofactor are unknown. We investigate several possible routes for insertion of the central nitrogen ligand and conclude that all routes involve barriers and intermediate states, which are inaccessible at ambient conditions. On this basis we suggest that the central nitrogen ligand is present at all times during the reaction. Furthermore, we investigate how the FeMoco with the central ligand can interact with N(2) and reduce it.     

Exploring the interstitial atom in the FeMo cofactor of nitrogenase: insights from QM and QM/MM calculations

Density functional theory and combined quantum mechanics and molecular mechanics (QM/MM) calculations have been used to explore structural features of the FeMo cofactor with an interstitial atom X (X = N, C, or O) and its interactions with CO and N 2. Predicted frequencies of the metal-bound CO, QM/MM-optimized geometries, and calculated redox potentials of the FeMo cofactor with different central ligands show that the oxygen atom is the candidate for the interstitial atom. Calculations on the interactions of the FeMo cofactor with CO and N 2 reveal that there is a remarkable dependence of the binding energy on the binding site and the interstitial atom. Generally, the Fe2 site of the FeMo cofactor has stronger interactions with CO and N 2 than Fe6, and both the Fe2 and Fe6 sites in the N-centered and O-centered clusters of the FeMo cofactor can effectively bind N 2 while the coordination of N 2 to the Fe6 site of the C-centered active cluster is unfavorable energetically. Present results indicate that the protein environment is important for computational characterization of the structure of the FeMo cofactor and properties of the metal-bound CO and N 2 are sensitive to the interstitial atom.     

Activation of dinitrogen at binuclear sites

TMC Literature Highlights-22,Transition Met. Chem.,15, 251 (1990).     

Catalytic reduction of acetylene and dinitrogen with the participation of the iron-molybdenum cofactor of nitrogenase and synthetic polynuclear molybdenum(iii) complexes

Catalytic reduction of acetylene and dinitrogen was carried out by sodium, zinc, and europium amalgams in the presence of polymolybdenum clusters and the iron-molybdenum cofactor of nitrogenase isolated from the enzyme. The activity of both catalysts toward acetylene changes in the sequence Zn(Hg)<Eu(Hg)<Na(Hg), increasing as the redox potential of the reducing agent is shifted to the negative region. The catalytic reduction of N₂ occurs only by the action of sodium and europium amalgams and only in the presence of synthetic polymolybdenum complexes; in the case of Na(Hg), the main product is hydrazine; in the case of Eu(Hg), it is ammonia. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 890–896, May, 1998.     

The mechanistically significant coordination chemistry of dinitrogen at FeMo-co, the catalytic site of nitrogenase

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).     

A quantum-chemical study of dinitrogen reduction at mononuclear iron-sulfur complexes with hints to the mechanism of nitrogenase

The mechanism of biological dinitrogen reduction is still unsolved, and the structure of the biological reaction center, the FeMo cofactor with its seven iron atoms bridged by sulfur atoms, is too complicated for direct attack by current sophisticated quantum chemical methods. Therefore, iron-sulfur complexes with biologically compatible ligands are utilized as models for studying particular features of the reduction process: coordination energetics, thermodynamic stability of intermediates, relative stability of isomers of N2H2, end-on versus side-on binding of N2, and the role of states of different multiplicity at a single iron center. From the thermodynamical point of view, the crucial steps are dinitrogen binding and reduction to diazene, while especially the reduction of hydrazine to ammonia is not affected by the transition metal complex, because the complex-free reduction reaction is equally favored. Moreover, the abstraction of coordinated ammonia can be easily achieved and the complex is recovered for the next reduction cycle. Our results are discussed in the light of studies on various model systems in order to identify common features and to arrive at conclusions which are of importance for the biological mechanism.     

FeMo cofactor of nitrogenase: a density functional study of states M(N), M(OX), M(R), and M(I).

The M(N) S = (3)/(2) resting state of the FeMo cofactor of nitrogenase has been proposed to have metal-ion valencies of either Mo(4+)6Fe(2+)Fe(3+) (derived from metal hyperfine interactions) or Mo(4+)4Fe(2+)3Fe(3+) (from M?ssbauer isomer shifts). Spin-polarized broken-symmetry (BS) density functional theory (DFT) calculations have been undertaken to determine which oxidation level best represents the M(N) state and to provide a framework for understanding its energetics and spectroscopy. For the Mo(4+)6Fe(2+)Fe(3+) oxidation state, the spin coupling pattern for several spin state alignments compatible with S = (3)/(2) were generated and assessed by energy and geometric criteria. The most likely BS spin state is composed of a Mo3Fe cluster with spin S(a) = 2 antiferromagnetically coupled to a 4Fe' cluster with spin S(b) = (7)/(2). This state has a low DFT energy for the isolated FeMoco cluster and the lowest energy when the interaction with the protein and solvent environment is included. This spin state also displays calculated metal hyperfine and M?ssbauer isomer shifts compatible with experiment, and optimized geometries that are in excellent agreement with the protein X-ray data. Our best model for the actual spin-coupled state within FeMoco alters this BS state by a slight canting of spins and is analogous in several respects to that found in the 8Fe P-cluster in the same protein. The spin-up and spin-down components of the LUMO contain atomic contributions from Mo(4+) and the homocitrate and from the central prismane Fe sites and muS(2) atoms, respectively. This qualitative picture of the accepting orbitals for M(N) is consistent with observations from M?ssbauer spectra of the one-electron reduced states. Similar calculations for the Mo(4+)4Fe(2+)3Fe(3+) oxidation state yield results that are in poorer agreement with experiment. Using the Mo(4+)6Fe(2+)Fe(3+) oxidation level as the most plausible resting state, the geometric, electronic and energetic properties of the one-electron redox transition to the oxidized state, M(OX), catalytically observed M(R) and radiolytically reduced M(I) states have also been explored.     

Density functional calculations on the binding of dinitrogen to the FeFe cofactor in Fe-only nitrogenase: FeFeco(mu 6-N2) as intermediate in nitrogen fixation

The geometries and stabilities of the FeFe cofactor at different oxidation states and its complexes with N(2) have been determined by density functional calculations. These calculations support an EPR-inactive resting state of the FeFe cofactor with four Fe(2+) and four Fe(3+) sites (4Fe(2+)4Fe(3+)). FeFeco(mu(6)-N(2)) with a central dinitrogen ligand is predicted to be the most stable complex of the FeFe cofactor with N(2). It is easily formed by penetration of N(2) into the trigonal Fe(6) prism of the FeFe cofactor with an approximate barrier of 4 kcal mol(-1). The present DFT results suggest that an FeFeco(mu(6)-N(2)) entity is a plausible intermediate in dinitrogen fixation by nitrogenase. CO is calculated to bind even more strongly than N(2) to the FeFe cofactor so that CO may inhibit the reduction of nitrogen by Fe-only nitrogenase.     

On the reduced and oxidized forms of the FeMo- cofactor of Azotobacter vinelandii nitrogenase

Reduced and oxidized forms of the FeMo- cofactor of Azotobacter vinelandii nitrogenase are examined theoretically within the intermediate neglect of differential overlap model. The results obtained favor one of the experimentally suggested modes of contraction of the metal system which results in an expansion of the central cavity of the cofactor. The bond index analysis indicates marked changes in the Mo coordination upon electron addition which may contribute to an opening of the Mo atom as a possible binding site at the advanced stages of the reduction process. In this work we also compare the 39- and 41-electron [MoFe₇] core as possible native resting states, both compatible with known spin and M?ssbauer spectroscopies. Received: 19 March 1997 / Accepted: 8 May 1997     

Car-Parrinello molecular dynamics study of the initial dinitrogen reduction step in Sellmann-type nitrogenase model complexes

We have studied reduction reactions for nitrogen fixation at Sellmann-type model complexes with Car-Parrinello simulation techniques. These dinuclear complexes are especially designed to emulate the so-called open-side FeMoco model. The main result of this work shows that in order to obtain the reduced species several side reactions have to be suppressed. These involve partial dissociation of the chelate ligands and hydrogen atom transfer to the metal center. Working at low temperature turns out to be one necessary pre-requisite in carrying out successful events. The successful events cannot be described by simple reaction coordinates. Complicated processes are involved during the initiation of the reaction. Our theoretical study emphasizes two experimental strategies which are likely to inhibit the side reactions. Clamping of the two metal fragments by a chelating phosphane ligand should prevent dissociation of the complex. Furthermore, introduction of tert-butyl substituents could improve the solubility and should thus allow usage of a wider range of (mild) acids, reductants, and reaction conditions.     

Selective syntheses of iron-imide-sulfide cubanes, including a partial representation of the Fe-S-X environment in the FeMo cofactor

The dinuclear precursors Fe(2)(N(t)Bu)(2)Cl(2)(NH(2)(t)Bu)(2), [Fe(2)(N(t)Bu)(S)Cl(4)](2-), and Fe(2)(NH(t)Bu)(2)(S)(N{SiMe(3)}(2))(2) allowed the selective syntheses of the cubane clusters [Fe(4)(N(t)Bu)(n)(S)(4-n)Cl(4)](z) with [n, z] = [3, 1-], [2, 2-], [1, 2-]. Weak-field iron-sulfur clusters with heteroleptic, nitrogen-containing cores are of interest with respect to observed or conjectured environments in the iron-molybdenum cofactor of nitrogenase. In this context, the present iron-imide-sulfide clusters constitute a new class of compounds for study, with the Fe(4)NS(3) core of the [1, 2-] cluster affording the first synthetic representation of the corresponding heteroligated Fe(4)S(3)X subunit in the cofactor.     

Theoretical, spectroscopic, and mechanistic studies on transition-metal dinitrogen complexes: implications to reactivity and relevance to the nitrogenase problem

Dinitrogen complexes of transition metals exhibit different binding geometries of N2 (end-on terminal, end-on bridging, side-on bridging, side-on end-on bridging), which are investigated by spectroscopy and DFT calculations, analyzing their electronic structure and reactivity. For comparison, a bis(mu-nitrido) complex, where the N--N bond has been split, has been studied as well. Most of these systems are highly covalent, and have strong metal-nitrogen bonds. In the present review, particular emphasis is put on a consideration of the activation of the coordinated dinitrogen ligand, making it susceptible to protonation, reactions with electrophiles or cleavage. In this context, theoretical, structural, and spectroscopic data giving informations on the amount of charge on the N2 unit are presented. The orbital interactions leading to a charge transfer from the metals to the dinitrogen ligand and the charge distribution within the coordinated N2 group are analyzed. Correlations between the binding mode and the observed reactivity of N2 are discussed.     

Activation of dinitrogen molecule on the surface of iron (or ruthenium) based catalysts

Supported iron (or ruthenium) catalysts prepared by different methods were tested in the ammonia synthesis reaction. A promoter effect of potassium was observed in these catalysts. By means of infrared spectroscopy, the activation of dinitrogen species was observed on the surface of a highly dispersed 3.2 wt. % Ru-alumina non-promoted catalyst.

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Unique peculiarities of the structure of the Fe-Mo cofactor of nitrogenase favorable for multicenter coordination of a nitrogen molecule

The probable coordination mode of a nitrogen molecule on the Fe-Mo cofactor of nitrogenase has been theoretically considered, taking into account both the well-known data on the structure of the Fe-Mo cofactor and the substrate selectivity of nitrogenase and the results of semiempirical calculations of the electronic structures of the cofactor and its complexes with molecular nitrogen. The distances between the Fe atoms in the cofactor are favorable for different multicenter coordination modes of a nitrogen molecule: above the Fe₄ face along its diagonal, through this face, and inside the Fe₆ prism perpendicularly to its axes. It is important that the nitrogen atoms are open for protonation in all coordination modes. The first mode is disadvantageous due to steric hindrances. Of the other variants, the latter is the most favorable both energetically and from the viewpoint of weakening of the N-N bond.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1928–1933, August, 1996.     

An organometallic approach to the synthesis of high nuclearity Mo-Fe-S clusters as potential models for the iron-molybdenum cofactor of nitrogenase

Reaction of the [Fe₂S₂(CO)₆]^2– dianion with molybdenum reagents produces a number of high-nuclearity Mo-Fe-S carbonyl clusters with Fe/Mo ratios 5, as well as a variety of new Fe-S carbonyl clusters. The former are particularly relevant as models or precursors to models for the iron-molybdenum cofactor [FeMo-cofactor] of nitrogenase. General strategies for the synthesis of FeMo-cofactor models are briefly reviewed, and the structures of clusters produced in the [Fe₂S₂(CO)₆]^2–/Mo systems examined to date are described.     

Quantitative geometric descriptions of the belt iron atoms of the iron-molybdenum cofactor of nitrogenase and synthetic iron(II) model complexes

Six of the seven iron atoms in the iron-molybdenum cofactor of nitrogenase display an unusual geometry, which is distorted from the tetrahedral geometry that is most common in iron-sulfur clusters. This distortion pulls the iron along one C3 axis of the tetrahedron toward a trigonal pyramid. The trigonal pyramidal coordination geometry is rare in four-coordinate transition metal complexes. In order to document this geometry in a systematic fashion in iron(II) chemistry, we have synthesized a range of four-coordinate iron(II) complexes that vary from tetrahedral to trigonal pyramidal. Continuous shape measures are used for a quantitative comparison of the stereochemistry of the Fe atoms in the iron-molybdenum cofactor with those of the presently and previously reported model complexes, as well as with those in polynuclear iron-sulfur compounds. This understanding of the iron coordination geometry is expected to assist in the design of synthetic analogues for intermediates in the nitrogenase catalytic cycle.