Mechanism of nitrogen fixation by nitrogenase: the next stage

Multifaceted investigation of metabolites during nitrogen fixation in Medicago via high resolution MALDI-MS imaging and ESI-MS

Legumes have developed the unique ability to establish a symbiotic relationship with soil bacteria known as rhizobia. This interaction results in the formation of root nodules in which rhizobia thrive and reduce atmospheric dinitrogen into plant-usable ammonium through biological nitrogen fixation (BNF). Owing to the availability of genetic information for both of the symbiotic partners, the Medicago truncatula-Sinorhizobium meliloti association is an excellent model for examining the BNF process. Although metabolites are important in this symbiotic association, few studies have investigated the array of metabolites that influence this process. Of these studies, most target only a few specific metabolites, the roles of which are either well known or are part of a well-characterized metabolic pathway. Here, we used a multifaceted mass spectrometric (MS) approach to detect and identify the key metabolites that are present during BNF using the Medicago truncatula-Sinorhizobium meliloti association as the model system. High mass accuracy and high resolution matrix-assisted laser desorption/ionization (MALDI) and electrospray ionization (ESI) Orbitrap instruments were used in this study and provide complementary results for more in-depth characterization of the nitrogen-fixation process. We used well-characterized plant and bacterial mutants to highlight differences between the metabolites that are present in functional versus nonfunctional nodules. Our study highlights the benefits of using a combination of mass spectrometric techniques to detect differences in metabolite composition and the distributions of these metabolites in plant biology.

Cu-mediated nitrogen atom transfer via CN bond cleavage

A nitrogen atom transfer to organic molecules affording aryl nitriles via Cu-mediated C–N triple bond cleavage is firstly developed.

Misconception of reductive elimination of H2, in the context of the mechanism of nitrogenase

Calculated atom partial charges reveal misconceptions of reductive elimination of H₂.

Mechanisms and rates of proton transfer to coordinated carboxydithioates: studies on [Ni(S2CR){PhP(CH2CH2PPh2)2}]+ (R = Me, Et, Bun or Ph)

Kinetics of protonation of [Ni(S₂CR)(PhP{CH₂CH₂PPh₂}₂)]⁺ (R = Me, Et, Buⁿ or Ph) with HCl reveals hydrogen-bonded precursor and subsequent chelate opening.

Structural characterization of α-amino acid complexes of molybdates: a spectroscopic and DFT study

A joint spectroscopic and computational study has allowed us to determine the dinuclear structural core of the products of the reactions between molybdates and α-amino acids in aqueous medium.

Alternative mechanisms for O2release and O–O bond formation in the oxygen evolving complex of photosystem II

A new transition state for O₂release has been found. An alternative, nearly competitive, mechanism for O–O bond formation is described, which is very similar to the one previously suggested.

The discovery of Mo(III) in FeMoco: reuniting enzyme and model chemistry

Biological nitrogen fixation is enabled by molybdenum-dependent nitrogenase enzymes, which effect the reduction of dinitrogen to ammonia using an Fe₇MoS₉C active site, referred to as the iron molybdenum cofactor or FeMoco. In this mini-review, we summarize the current understanding of the molecular and electronic structure of FeMoco. The advances in our understanding of the active site structure are placed in context with the parallel evolution of synthetic model studies. The recent discovery of Mo(III) in the FeMoco active site is highlighted with an emphasis placed on the important role that model studies have played in this finding. In addition, the reactivities of synthetic models are discussed in terms of their relevance to the enzymatic system.

Nitrogenase and homologs

Nitrogenase catalyzes biological nitrogen fixation, a key step in the global nitrogen cycle. Three homologous nitrogenases have been identified to date, along with several structural and/or functional homologs of this enzyme that are involved in nitrogenase assembly, bacteriochlorophyll biosynthesis and methanogenic process, respectively. In this article, we provide an overview of the structures and functions of nitrogenase and its homologs, which highlights the similarity and disparity of this uniquely versatile group of enzymes.

The role of X-ray spectroscopy in understanding the geometric and electronic structure of nitrogenase

X-ray absorption (XAS) and X-ray emission spectroscopy (XES) provide element specific probes of the geometric and electronic structures of metalloprotein active sites. As such, these methods have played an integral role in nitrogenase research beginning with the first EXAFS studies on nitrogenase in the late 1970s. Herein, we briefly explain the information that can be extracted from XAS and XES. We then highlight the recent applications of these methods in nitrogenase research. The influence of X-ray spectroscopy on our current understanding of the atomic structure and electronic structure of iron molybdenum cofactor (FeMoco) is emphasized. Contributions of X-ray spectroscopy to understanding substrate interactions and cluster biosynthesis are also discussed. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.

Alkali metal control over N-N cleavage in iron complexes

Though N2 cleavage on K-promoted Fe surfaces is important in the large-scale Haber-Bosch process, there is still ambiguity about the number of Fe atoms involved during the N-N cleaving step and the interactions responsible for the promoting ability of K. This work explores a molecular Fe system for N2 reduction, particularly focusing on the differences in the results obtained using different alkali metals as reductants (Na, K, Rb, Cs). The products of these reactions feature new types of Fe-N2 and Fe-nitride cores. Surprisingly, adding more equivalents of reductant to the system gives a product in which the N-N bond is not cleaved, indicating that the reducing power is not the most important factor that determines the extent of N2 activation. On the other hand, the results suggest that the size of the alkali metal cation can control the number of Fe atoms that can approach N2, which in turn controls the ability to achieve N2 cleavage. The accumulated results indicate that cleaving the triple N-N bond to nitrides is facilitated by simultaneous approach of least three low-valent Fe atoms to a single molecule of N2.

α-Hydroxy coordination of mononuclear vanadyl citrate, malate and S-citramalate with N-heterocycle ligand, implying a new protonation pathway of iron-vanadium cofactor in nitrogenase

Unlike the most of α-alkoxy coordination in α-hydroxycarboxylates to vanadium, novel α-hydroxy coordination to vanadium(IV) has been observed for a series of chiral and achiral monomeric α-hydroxycarboxylato vanadyl complexes [VO(H2cit)(bpy)]·2H2O (1), [VO(Hmal)(bpy)]·H2O (2), [VO(H2cit)(phen)]·1.5H2O (3), [VO(Hmal)(phen)]·H2O (4), and [(Δ)VO(S-Hcitmal)(bpy)]·2H2O (5), [VO(H2cit)(phen)]2·6.5H2O (6), which were isolated from the reactions of vanadyl sulfate with α-hydroxycarboxylates and N-heterocycle ligands in acidic solution. The complexes feature a tridentate citrate, malate or citramalate that chelates to vanadium atom through their α-hydroxy, α-carboxy and β-carboxy groups; while the other β-carboxylic acidic group of citrate is free to participate strong hydrogen bonds with lattice water molecule. The neutral α-hydroxy group also forms strong intermolecular hydrogen bonds with water molecule and the negatively-charged α-carboxy group in the environment. The inclusion of a hydrogen ion in α-alkoxy group results in the formation of a series of neutral complexes with one less positive charge. There are two different configurations of citrate with respect to the trans-position of axial oxo group, where the complex with trans-hydroxy configuration seems more stable with less hindrance. The average bond distances of V-Ohydroxy and V-Oα-carboxy are 2.196 and 2.003Å respectively, which are comparable to the VO distance (2.15Å) of homocitrate in FeV-cofactor of V-nitrogenase. A new structural model is suggested for R-homocitrato iron vanadium cofactor as VFe7S9C(R-Hhomocit) (H4homocit=homocitric acid) with one more proton in homocitrate ligand.

Molybdenum complexes supported by mixed NHC/phosphine ligands: activation of N2 and reaction with P(OMe)3 to the first meta-phosphite complex

Molybdenum(0) dinitrogen complexes, supported by the mixed NHC/phosphine pincer ligand PCP, exhibit an extreme activation of the N2 ligand due to a very π-electron-rich metal center. The low thermal stability of these compounds can be increased using phosphites instead of phosphines as coligands. Through an amalgam reduction of [MoCl3(PCP)] in the presence of trimethyl phosphite and N2 the highly activated and room-temperature stable dinitrogen complex [Mo(N2)(PCP)(P(OMe)3)2] is obtained. As a second product, the first transition metal complex containing the meta-phosphite ligand P(O)(OMe) originates from this reaction.

Photocrystallographic observation of halide-bridged intermediates in halogen photoeliminations

Polynuclear transition metal complexes, which frequently constitute the active sites of both biological and chemical catalysts, provide access to unique chemical transformations that are derived from metal-metal cooperation. Reductive elimination via ligand-bridged binuclear intermediates from bimetallic cores is one mechanism by which metals may cooperate during catalysis. We have established families of Rh2 complexes that participate in HX-splitting photocatalysis in which metal-metal cooperation is credited with the ability to achieve multielectron photochemical reactions in preference to single-electron transformations. Nanosecond-resolved transient absorption spectroscopy, steady-state photocrystallography, and computational modeling have allowed direct observation and characterization of Cl-bridged intermediates (intramolecular analogues of classical ligand-bridged intermediates in binuclear eliminations) in halogen elimination reactions. On the basis of these observations, a new class of Rh2 complexes, supported by CO ligands, has been prepared, allowing for the isolation and independent characterization of the proposed halide-bridged intermediates. Direct observation of halide-bridged structures establishes binuclear reductive elimination as a viable mechanism for photogenerating energetic bonds.

Differential reduction of CO₂ by molybdenum and vanadium nitrogenases

The molybdenum and vanadium nitrogenases are two homologous enzymes with distinct structural and catalytic features. Previously, it was demonstrated that the V nitrogenase was nearly 700 times more active than its Mo counterpart in reducing CO to hydrocarbons. Herein, a similar discrepancy between the two nitrogenases in the reduction of CO2 is reported, with the V nitrogenase being capable of reducing CO2 to CO, CD4, C2D4, and C2D6, and its Mo counterpart only capable of reducing CO2 to CO. Furthermore, it is shown that the V nitrogenase may direct the formation of CD4 in part via CO2-derived CO, but that it does not catalyze the formation of C2D4 and C2D6 along this route. The exciting observation of a V nitrogenase-catalyzed C-C coupling with CO2 as the origin of the building blocks adds another interesting reaction to the catalytic repertoire of this unique enzyme system. The differential activities of the V and Mo nitrogenases in CO2 reduction provide an important framework for systematic investigations of this reaction in the future.

EPR, ENDOR, and electronic structure studies of the Jahn-Teller distortion in an Fe(V) nitride

The recently synthesized and isolated low-coordinate Fe(V) nitride complex has numerous implications as a model for high-oxidation states in biological and industrial systems. The trigonal [PhB((t)BuIm)3Fe(V)≡N](+) (where (PhB((t)BuIm)3(-) = phenyltris(3-tert-butylimidazol-2-ylidene)), (1) low-spin d(3) (S = 1/2) coordination compound is subject to a Jahn-Teller (JT) distortion of its doubly degenerate (2)E ground state. The electronic structure of this complex is analyzed by a combination of extended versions of the formal two-orbital pseudo Jahn-Teller (PJT) treatment and of quantum chemical computations of the PJT effect. The formal treatment is extended to incorporate mixing of the two e orbital doublets (30%) that results from a lowering of the idealized molecular symmetry from D3h to C3v through strong "doming" of the Fe-C3 core. Correspondingly we introduce novel DFT/CASSCF computational methods in the computation of electronic structure, which reveal a quadratic JT distortion and significant e-e mixing, thus reaching a new level of synergism between computational and formal treatments. Hyperfine and quadrupole tensors are obtained by pulsed 35 GHz ENDOR measurements for the (14/15)N-nitride and the (11)B axial ligands, and spectra are obtained from the imidazole-2-ylidene (13)C atoms that are not bound to Fe. Analysis of the nitride ENDOR tensors surprisingly reveals an essentially spherical nitride trianion bound to Fe, with negative spin density and minimal charge density anisotropy. The four-coordinate (11)B, as expected, exhibits negligible bonding to Fe. A detailed analysis of the frontier orbitals provided by the electronic structure calculations provides insight into the reactivity of 1: JT-induced symmetry lowering provides an orbital selection mechanism for proton or H atom transfer reactivity.

Nitrite and hydroxylamine as nitrogenase substrates: mechanistic implications for the pathway of N₂ reduction

Investigations of reduction of nitrite (NO₂^–) to ammonia (NH₃) by nitrogenase indicate a limiting stoichiometry, NO₂^– + 6e^– + 12ATP + 7H⁺ → NH₃ + 2H₂O + 12ADP + 12P_i. Two intermediates freeze-trapped during NO₂^– turnover by nitrogenase variants and investigated by Q-band ENDOR/ESEEM are identical to states, denoted H and I, formed on the pathway of N₂ reduction. The proposed NO₂^– reduction intermediate hydroxylamine (NH₂OH) is a nitrogenase substrate for which the H and I reduction intermediates also can be trapped. Viewing N₂ and NO₂^– reductions in light of their common reduction intermediates and of NO₂^– reduction by multiheme cytochrome c nitrite reductase (ccNIR) leads us to propose that NO₂^– reduction by nitrogenase begins with the generation of NO₂H bound to a state in which the active-site FeMo-co (M) has accumulated two [e^–/H⁺] (E₂), stored as a (bridging) hydride and proton. Proton transfer to NO₂H and H₂O loss leaves M–[NO⁺]; transfer of the E₂ hydride to the [NO⁺] directly to form HNO bound to FeMo-co is one of two alternative means for avoiding formation of a terminal M–[NO] thermodynamic “sink”. The N₂ and NO₂^– reduction pathways converge upon reduction of NH₂NH₂ and NH₂OH bound states to form state H with [−NH₂] bound to M. Final reduction converts H to I, with NH₃ bound to M. The results presented here, combined with the parallels with ccNIR, support a N₂ fixation mechanism in which liberation of the first NH₃ occurs upon delivery of five [e^–/H⁺] to N₂, but a total of seven [e^–/H⁺] to FeMo-co when obligate H₂ evolution is considered, and not earlier in the reduction process.

A confirmation of the quench-cryoannealing relaxation protocol for identifying reduction states of freeze-trapped nitrogenase intermediates

We have advanced a mechanism for nitrogenase catalysis that rests on the identification of a low-spin EPR signal (S = 1/2) trapped during turnover of a MoFe protein as the E4 state, which has accumulated four reducing equivalents as two [Fe-H-Fe] bridging hydrides. Because electrons are delivered to the MoFe protein one at a time, with the rate-limiting step being the off-rate of oxidized Fe protein, it is difficult to directly control, or know, the degree of reduction, n, of a trapped intermediate, denoted En, n = 1-8. To overcome this previously intractable problem, we introduced a quench-cryoannealing relaxation protocol for determining n of an EPR-active trapped En turnover state. The trapped "hydride" state was allowed to relax to the resting E0 state in frozen medium, which prevents additional accumulation of reducing equivalents; binding of reduced Fe protein and release of oxidized protein from the MoFe protein both are abolished in a frozen solid. Relaxation of En was monitored by periodic EPR analysis at cryogenic temperature. The protocol rests on the hypothesis that an intermediate trapped in the frozen solid can relax toward the resting state only by the release of a stable reduction product from FeMo-co. In turnover under Ar, the only product that can be released is H2, which carries two reducing equivalents. This hypothesis implicitly predicts that states that have accumulated an odd number of electrons/protons (n = 1, 3) during turnover under Ar cannot relax to E0: E3 can relax to E1, but E1 cannot relax to E0 in the frozen state. The present experiments confirm this prediction and, thus, the quench-cryoannealing protocol and our assignment of E4, the foundation of the proposed mechanism for nitrogenase catalysis. This study further gives insights into the identity of the En intermediates with high-spin EPR signals, 1b and 1c, trapped under high electron flux.

Challenges in reduction of dinitrogen by proton and electron transfer

Catalytic reduction of dinitrogen with protons and electrons is a very challenging alternative to the energy expensive Haber–Bosch reaction.