Mechanism of nitrogen fixation by nitrogenase: the next stage

Proteomic analysis dissects the impact of nodulation and biological nitrogen fixation on Vicia faba root nodule physiology

Symbiotic nitrogen fixation in root nodules of legumes is a highly important biological process which is only poorly understood. Root nodule metabolism differs from that of roots. Differences in root and nodule metabolism are expressed by altered protein abundances and amenable to quantitative proteome analyses. Differences in the proteomes may either be tissue specific and related to the presence of temporary endosymbionts (the bacteroids) or related to nitrogen fixation activity. An experimental setup including WT bacterial strains and strains not able to conduct symbiotic nitrogen fixation as well as root controls enables identification of tissue and nitrogen fixation specific proteins. Root nodules are specialized plant organs housing and regulating the mutual symbiosis of legumes with nitrogen fixing rhizobia. As such, these organs fulfill unique functions in plant metabolism. Identifying the proteins required for the metabolic reactions of nitrogen fixation and those merely involved in sustaining the rhizobia:plant symbiosis, is a challenging task and requires an experimental setup which allows to differentiate between these two physiological processes. Here, quantitative proteome analyses of nitrogen fixing and non-nitrogen fixing nodules as well as fertilized and non-fertilized roots were performed using Vicia faba and Rhizobium leguminosarum. Pairwise comparisons revealed altered enzyme abundance between active and inactive nodules. Similarly, general differences between nodules and root tissue were observed. Together, these results allow distinguishing the proteins directly involved in nitrogen fixation from those related to nodulation. Further observations relate to the control of nodulation by hormones and provide supportive evidence for the previously reported correlation of nitrogen and sulfur fixation in these plant organs. Additionally, data on altered protein abundance relating to alanine metabolism imply that this amino acid may be exported from the symbiosomes of V. faba root nodules in addition to ammonia. Data are available via ProteomeXchange with identifier PXD008548.

Catalytic Dinitrogen Reduction to Ammonia at a Triamidoamine-Titanium Complex

Catalytic reduction of N2 to NH3 by a Ti complex has been achieved, thus now adding an early d-block metal to the small group of mid- and late-d-block metals (Mo, Fe, Ru, Os, Co) that catalytically produce NH3 by N2 reduction and protonolysis under homogeneous, abiological conditions. Reduction of [TiIV (TrenTMS )X] (X=Cl, 1A; I, 1B; TrenTMS =N(CH2 CH2 NSiMe3 )3 ) with KC8 affords [TiIII (TrenTMS )] (2). Addition of N2 affords [{(TrenTMS )TiIII }2 (μ-η1 :η1 -N2 )] (3); further reduction with KC8 gives [{(TrenTMS )TiIV }2 (μ-η1 :η1 :η2 :η2 -N2 K2 )] (4). Addition of benzo-15-crown-5 ether (B15C5) to 4 affords [{(TrenTMS )TiIV }2 (μ-η1 :η1 -N2 )][K(B15C5)2 ]2 (5). Complexes 3-5 treated under N2 with KC8 and [R3 PH][I], (the weakest H+ source yet used in N2 reduction) produce up to 18 equiv of NH3 with only trace N2 H4 . When only acid is present, N2 H4 is the dominant product, suggesting successive protonation produces [{(TrenTMS )TiIV }2 (μ-η1 :η1 -N2 H4 )][I]2 , and that extruded N2 H4 reacts further with [R3 PH][I]/KC8 to form NH3 .

Carbon Dots Enhance the Nitrogen Fixation Activity of Azotobacter Chroococcum

Biological nitrogen fixation is critical for the nitrogen cycle on the earth. Nitrogen-fixing bacteria, as an environmentally friendly microorganism, convert atmospheric nitrogen to available nitrogen source for plants. In this study, we found that carbon dots (CDs) could significantly enhance the nitrogen-fixing activity of azotobacter chroococcum, in which the activity of azotobacter treated with CDs (4 μg/mL) was increased by 158% compared to that of the control one. A series of experiments suggest that CDs can combine with the nitrogenase, affect the secondary structure of nitrogenase, improve the electron transfer in the biocatalytic process, and finally improve nitrogenase activity for nitrogen fixation. Our findings may offer an economical and environmentally friendly means of improving the biological nitrogen fixation as well as solving the insufficiency of nitrogen fertilizer.

Radical S-Adenosyl-l-Methionine (SAM) Enzyme Involved in the Maturation of the Nitrogenase Cluster

Nitrogenase is the only known enzymatic system that converts atmospheric dinitrogen (N₂) into bioavailable ammonia (NH₃). The active-site cofactor responsible for this reactivity is a [(R-homocitrate)MoFe₇S₉C] cluster that is designated as the M-cluster. This important cofactor is assembled stepwise from a pair of [Fe₄S₄] clusters that become fused into a [Fe₈S₉C] core before additional refinements take place to complete the biosynthesis. NifB, a member of the radical S-adenosyl-l-methionine (SAM) superfamily, facilitates the conversion of the [Fe₄S₄] clusters (called the K-cluster) to the [Fe₈S₉C] core (called the L-cluster). This transformation includes a SAM-dependent carbide insertion with concomitant incorporation of an additional sulfur. While difficulties with the purification of NifB have historically prevented detailed biochemical analyses, we have developed a heterologous expression system in Escherichia coli that yields stable NifB proteins from various N₂-fixing methanogenic organisms that can be used for studies. This chapter details the procedures necessary to prepare an active NifB protein. The methods used for the biochemical characterization of the SAM-dependent carbide insertion reactions are also described.

Efficient Nitrogen Fixation via a Redox-Flexible Single-Iron Site with Reverse-Dative Iron → Boron σ Bonding

Model systems of the FeMo cofactor of nitrogenase have been explored extensively in catalysis to gain insights into their ability for nitrogen fixation that is of vital importance to the human society. Here we investigate the trigonal pyramidal borane-ligand Fe complex by first-principles calculations, and find that the variation of oxidation state of Fe along the reaction path correlates with that of the reverse-dative Fe → B bonding. The redox-flexibility of the reverse-dative Fe → B bonding helps to provide an electron reservoir that buffers and stabilizes the evolution of Fe oxidation state, which is essential for forming the key intermediates of N₂ activation. Our work provides insights for understanding and optimizing homogeneous and surface single-atom catalysts with reverse-dative donating ligands for efficient dinitrogen fixation. The extension of this kind of molecular catalytic active center to heterogeneous catalysts with surface single-clusters is also discussed.

An S = 1/2 Iron Complex Featuring N2, Thiolate, and Hydride Ligands: Reductive Elimination of H2 and Relevant Thermochemical Fe-H Parameters

Believed to accumulate on the Fe sites of the FeMo-cofactor (FeMoco) of MoFe-nitrogenase under turnover, strongly donating hydrides have been proposed to facilitate N₂ binding to Fe and may also participate in the hydrogen evolution process concomitant to nitrogen fixation. Here, we report the synthesis and characterization of a thiolate-coordinated Fe^III(H)(N₂) complex, which releases H₂ upon warming to yield an Fe^II-N₂-Fe^II complex. Bimolecular reductive elimination of H₂ from metal hydrides is pertinent to the hydrogen evolution processes of both enzymes and electrocatalysts, but well-defined examples are uncommon and usually observed from diamagnetic second- and third-row transition metals. Kinetic data obtained on the HER of this ferric hydride species are consistent with a bimolecular reductive elimination pathway, arising from cleavage of the Fe-H bond with a computationally determined BDFE of 55.6 kcal/mol.

Functional expression of an oxygen-labile nitrogenase in an oxygenic photosynthetic organism

Transfer of nitrogen fixation ability to plants, especially crops, is a promising approach to mitigate dependence on chemical nitrogen fertilizer and alleviate environmental pollution caused by nitrogen fertilizer run-off. However, the need to transfer a large number of nitrogen fixation (nif) genes and the extreme vulnerability of nitrogenase to oxygen constitute major obstacles for transfer of nitrogen-fixing ability to plants. Here we demonstrate functional expression of a cyanobacterial nitrogenase in the non-diazotrophic cyanobacterium Synechocystis sp. PCC 6803 (Synechocystis 6803). A 20.8-kb chromosomal fragment containing 25 nif and nif-related genes of the diazotrophic cyanobacterium Leptolyngbya boryana was integrated into a neutral genome site of Synechocystis 6803 by five-step homologous recombination together with the cnfR gene encoding the transcriptional activator of the nif genes to isolate CN1. In addition, two other transformants CN2 and CN3 carrying additional one and four genes, respectively, were isolated from CN1. Low but significant nitrogenase activity was detected in all transformants. This is the first example of nitrogenase activity detected in non-diazotrophic photosynthetic organisms. These strains provide valuable platforms to investigate unknown factors that enable nitrogen-fixing growth of non-diazotrophic photosynthetic organisms, including plants.

A bound reaction intermediate sheds light on the mechanism of nitrogenase

Reduction of N₂ by nitrogenases occurs at an organometallic iron cofactor that commonly also contains either molybdenum or vanadium. The well-characterized resting state of the cofactor does not bind substrate, so its mode of action remains enigmatic. Carbon monoxide was recently found to replace a bridging sulfide, but the mechanistic relevance was unclear. Here we report the structural analysis of vanadium nitrogenase with a bound intermediate, interpreted as a μ²-bridging, protonated nitrogen that implies the site and mode of substrate binding to the cofactor. Binding results in a flip of amino acid glutamine 176, which hydrogen-bonds the ligand and creates a holding position for the displaced sulfide. The intermediate likely represents state E₆ or E₇ of the Thorneley-Lowe model and provides clues to the remainder of the catalytic cycle.

A Thermodynamic Model for Redox-Dependent Binding of Carbon Monoxide at Site-Differentiated, High Spin Iron Clusters

Binding of N2 and CO by the FeMo-cofactor of nitrogenase depends on the redox level of the cluster, but the extent to which pure redox chemistry perturbs the affinity of high spin iron clusters for π-acids is not well understood. Here, we report a series of site-differentiated iron clusters that reversibly bind CO in redox states FeII4 through FeIIFeIII3. One electron redox events result in small changes in the affinity for (at most ∼400-fold) and activation of CO (at most 28 cm-1 for νCO). The small influence of redox chemistry on the affinity of these high spin, valence-localized clusters for CO is in stark contrast to the large enhancements (105-1022 fold) in π-acid affinity reported for monometallic and low spin, bimetallic iron complexes, where redox chemistry occurs exclusively at the ligand binding site. While electron-loading at metal centers remote from the substrate binding site has minimal influence on the CO binding energetics (∼1 kcal·mol-1), it provides a conduit for CO binding at an FeIII center. Indeed, internal electron transfer from these remote sites accommodates binding of CO at an FeIII, with a small energetic penalty arising from redox reorganization (∼2.6 kcal·mol-1). The ease with which these clusters redistribute electrons in response to ligand binding highlights a potential pathway for coordination of N2 and CO by FeMoco, which may occur on an oxidized edge of the cofactor.

Heterogeneous Fe3 single-cluster catalyst for ammonia synthesis via an associative mechanism

The current industrial ammonia synthesis relies on Haber–Bosch process that is initiated by the dissociative mechanism, in which the adsorbed N₂ dissociates directly, and thus is limited by Brønsted–Evans–Polanyi (BEP) relation. Here we propose a new strategy that an anchored Fe₃ cluster on the θ-Al₂O₃(010) surface as a heterogeneous catalyst for ammonia synthesis from first-principles theoretical study and microkinetic analysis. We have studied the whole catalytic mechanism for conversion of N₂ to NH₃ on Fe₃/θ-Al₂O₃(010), and find that an associative mechanism, in which the adsorbed N₂ is first hydrogenated to NNH, dominates over the dissociative mechanism, which we attribute to the large spin polarization, low oxidation state of iron, and multi-step redox capability of Fe₃ cluster. The associative mechanism liberates the turnover frequency (TOF) for ammonia production from the limitation due to the BEP relation, and the calculated TOF on Fe₃/θ-Al₂O₃(010) is comparable to Ru B5 site.

The current industrial ammonia synthesis relies on the Haber-Bosch process that is limited by the Brønsted–Evans–Polanyi relation. Here, the authors propose a new strategy that an anchored Fe₃ on θ-Al₂O₃(010) surface serves as a heterogeneous single cluster catalyst for ammonia synthesis from first-principles calculations and microkinetic analysis.

Functional Single-Cell Approach to Probing Nitrogen-Fixing Bacteria in Soil Communities by Resonance Raman Spectroscopy with 15N2 Labeling

Nitrogen (N) fixation is the conversion of inert nitrogen gas (N₂) to bioavailable N essential for all forms of life. N₂-fixing microorganisms (diazotrophs), which play a key role in global N cycling, remain largely obscure because a large majority are uncultured. Direct probing of active diazotrophs in the environment is still a major challenge. Herein, a novel culture-independent single-cell approach combining resonance Raman (RR) spectroscopy with ¹⁵N₂ stable isotope probing (SIP) was developed to discern N₂-fixing bacteria in a complex soil community. Strong RR signals of cytochrome c (Cyt c, frequently present in diverse N₂-fixing bacteria), along with a marked ¹⁵N₂-induced Cyt c band shift, generated a highly distinguishable biomarker for N₂ fixation. ¹⁵N₂-induced shift was consistent well with ¹⁵N abundance in cell determined by isotope ratio mass spectroscopy. By applying this biomarker and Raman imaging, N₂-fixing bacteria in both artificial and complex soil communities were discerned and imaged at the single-cell level. The linear band shift of Cyt c versus ¹⁵N₂ percentage allowed quantification of N₂ fixation extent of diverse soil bacteria. This single-cell approach will advance the exploration of hitherto uncultured diazotrophs in diverse ecosystems.

Hydride Conformers of the Nitrogenase FeMo-cofactor Two-Electron Reduced State E2(2H), Assigned Using Cryogenic Intra Electron Paramagnetic Resonance Cavity Photolysis

Early studies in which nitrogenase was freeze-trapped during enzymatic turnover revealed the presence of high-spin ( S = ³/₂) electron paramagnetic resonance (EPR) signals from the active-site FeMo-cofactor (FeMo-co) in electron-reduced intermediates of the MoFe protein. Historically denoted as 1b and 1c, each of the signals is describable as a fictitious spin system, S' = ¹/₂, with anisotropic g' tensor, 1b with g' = [4.21, 3.76, ?] and 1c with g' = [4.69, ∼3.20, ?]. A clear discrepancy between the magnetic properties of 1b and 1c and the kinetic analysis of their appearance during pre-steady-state turnover left their identities in doubt, however. We subsequently associated 1b with the state having accumulated 2[e^-/H⁺], denoted as E₂(2H), and suggested that the reducing equivalents are stored on the catalytic FeMo-co cluster as an iron hydride, likely an [Fe-H-Fe] hydride bridge. Intra-EPR cavity photolysis (450 nm; temperature-independent from 4 to 12 K) of the E₂(2H)/1b state now corroborates the identification of this state as storing two reducing equivalents as a hydride. Photolysis converts E₂(2H)/1b to a state with the same EPR spectrum, and thus the same cofactor structure as pre-steady-state turnover 1c, but with a different active-site environment. Upon annealing of the photogenerated state at temperature T = 145 K, it relaxes back to E₂(2H)/1b. This implies that the 1c signal comes from an E₂(2H) hydride isomer of E₂(2H)/1b that stores its two reducing equivalents either as a hydride bridge between a different pair of iron atoms or an Fe-H terminal hydride.

Characterization of an M-Cluster-Substituted Nitrogenase VFe Protein

The Mo- and V-nitrogenases are two homologous members of the nitrogenase family that are distinguished mainly by the presence of different heterometals (Mo or V) at their respective cofactor sites (M- or V-cluster). However, the V-nitrogenase is ~600-fold more active than its Mo counterpart in reducing CO to hydrocarbons at ambient conditions. Here, we expressed an M-cluster-containing, hybrid V-nitrogenase in Azotobacter vinelandii and compared it to its native, V-cluster-containing counterpart in order to assess the impact of protein scaffold and cofactor species on the differential reactivities of Mo- and V-nitrogenases toward CO. Housed in the VFe protein component of V-nitrogenase, the M-cluster displayed electron paramagnetic resonance (EPR) features similar to those of the V-cluster and demonstrated an ~100-fold increase in hydrocarbon formation activity from CO reduction, suggesting a significant impact of protein environment on the overall CO-reducing activity of nitrogenase. On the other hand, the M-cluster was still ~6-fold less active than the V-cluster in the same protein scaffold, and it retained its inability to form detectable amounts of methane from CO reduction, illustrating a fine-tuning effect of the cofactor properties on this nitrogenase-catalyzed reaction. Together, these results provided important insights into the two major determinants for the enzymatic activity of CO reduction while establishing a useful framework for further elucidation of the essential catalytic elements for the CO reactivity of nitrogenase.

This is the first report on the in vivo generation and in vitro characterization of an M-cluster-containing V-nitrogenase hybrid. The “normalization” of the protein scaffold to that of the V-nitrogenase permits a direct comparison between the cofactor species of the Mo- and V-nitrogenases (M- and V-clusters) in CO reduction, whereas the discrepancy between the protein scaffolds of the Mo- and V-nitrogenases (MoFe and VFe proteins) housing the same cofactor (M-cluster) allows for an effective assessment of the impact of the protein environment on the CO reactivity of nitrogenase. The results of this study provide a first look into the “weighted” contributions of protein environment and cofactor properties to the overall activity of CO reduction; more importantly, they establish a useful platform for further investigation of the structural elements attributing to the CO-reducing activity of nitrogenase.

Evaluation of the Catalytic Relevance of the CO-Bound States of V-Nitrogenase

Binding and activation of CO by nitrogenase is a topic of interest because CO is isoelectronic to N₂ , the physiological substrate of this enzyme. The catalytic relevance of one- and multi-CO-bound states (the lo-CO and hi-CO states) of V-nitrogenase to C-C coupling and N₂ reduction was examined. Enzymatic and spectroscopic studies demonstrate that the multiple CO moieties in the hi-CO state cannot be coupled as they are, suggesting that C-C coupling requires further activation and/or reduction of the bound CO entity. Moreover, these studies reveal an interesting correlation between decreased activity of N₂ reduction and increased population of the lo-CO state, pointing to the catalytic relevance of the belt Fe atoms that are bridged by the single CO moiety in the lo-CO state. Together, these results provide a useful framework for gaining insights into the nitrogenase-catalyzed reaction via further exploration of the utility of the lo-CO conformation of V-nitrogenase.

Trace metal metabolism in plants

Many trace metals are essential micronutrients, but also potent toxins. Due to natural and anthropogenic causes, vastly different trace metal concentrations occur in various habitats, ranging from deficient to toxic levels. Therefore, one focus of plant research is on the response to trace metals in terms of uptake, transport, sequestration, speciation, physiological use, deficiency, toxicity, and detoxification. In this review, we cover most of these aspects for the essential micronutrients copper, iron, manganese, molybdenum, nickel, and zinc to provide a broader overview than found in other recent reviews, to cross-link aspects of knowledge in this very active research field that are often seen in a separated way. For example, individual processes of metal usage, deficiency, or toxicity often were not mechanistically interconnected. Therefore, this review also aims to stimulate the communication of researchers following different approaches, such as gene expression analysis, biochemistry, or biophysics of metalloproteins. Furthermore, we highlight recent insights, emphasizing data obtained under physiologically and environmentally relevant conditions.

A Comparative Analysis of the CO-Reducing Activities of MoFe Proteins Containing Mo- and V-Nitrogenase Cofactors

The Mo and V nitrogenases are structurally homologous yet catalytically distinct in their abilities to reduce CO to hydrocarbons. Here we report a comparative analysis of the CO-reducing activities of the Mo- and V-nitrogenase cofactors (i.e., the M and V clusters) upon insertion of the respective cofactor into the same, cofactor-deficient MoFe protein scaffold. Our data reveal a combined contribution from the protein environment and cofactor properties to the reactivity of nitrogenase toward CO, thus laying a foundation for further mechanistic investigation of the enzymatic CO reduction, while suggesting the potential of targeting both the protein scaffold and the cofactor species for nitrogenase-based applications in the future.

Catalytic Silylation of N2 and Synthesis of NH3 and N2H4 by Net Hydrogen Atom Transfer Reactions Using a Chromium P4 Macrocycle

We report the first discrete molecular Cr-based catalysts for the reduction of N₂. This study is focused on the reactivity of the Cr-N₂ complex, trans-[Cr(N₂)₂(P^Ph₄N^Bn₄)] (P₄Cr(N₂)₂), bearing a 16-membered tetraphosphine macrocycle. The architecture of the [16]-P^Ph₄N^Bn₄ ligand is critical to preserve the structural integrity of the catalyst. P₄Cr(N₂)₂ was found to mediate the reduction of N₂ at room temperature and 1 atm pressure by three complementary reaction pathways: (1) Cr-catalyzed reduction of N₂ to N(SiMe₃)₃ by Na and Me₃SiCl, affording up to 34 equiv N(SiMe₃)₃; (2) stoichiometric reduction of N₂ by protons and electrons (for example, the reaction of cobaltocene and collidinium triflate at room temperature afforded 1.9 equiv of NH₃, or at -78 °C afforded a mixture of NH₃ and N₂H₄); and (3) the first example of NH₃ formation from the reaction of a terminally bound N₂ ligand with a traditional H atom source, TEMPOH (2,2,6,6-tetramethylpiperidine-1-ol). We found that trans-[Cr(¹⁵N₂)₂(P^Ph₄N^Bn₄)] reacts with excess TEMPOH to afford 1.4 equiv of ¹⁵NH₃. Isotopic labeling studies using TEMPOD afforded ND₃ as the product of N₂ reduction, confirming that the H atoms are provided by TEMPOH.

Negative cooperativity in the nitrogenase Fe protein electron delivery cycle

Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen (N₂) to two ammonia (NH₃) molecules through the participation of its two protein components, the MoFe and Fe proteins. Electron transfer (ET) from the Fe protein to the catalytic MoFe protein involves a series of synchronized events requiring the transient association of one Fe protein with each αβ half of the α₂β₂ MoFe protein. This process is referred to as the Fe protein cycle and includes binding of two ATP to an Fe protein, association of an Fe protein with the MoFe protein, ET from the Fe protein to the MoFe protein, hydrolysis of the two ATP to two ADP and two P_i for each ET, P_i release, and dissociation of oxidized Fe protein-(ADP)₂ from the MoFe protein. Because the MoFe protein tetramer has two separate αβ active units, it participates in two distinct Fe protein cycles. Quantitative kinetic measurements of ET, ATP hydrolysis, and P_i release during the presteady-state phase of electron delivery demonstrate that the two halves of the ternary complex between the MoFe protein and two reduced Fe protein-(ATP)₂ do not undergo the Fe protein cycle independently. Instead, the data are globally fit with a two-branch negative-cooperativity kinetic model in which ET in one-half of the complex partially suppresses this process in the other. A possible mechanism for communication between the two halves of the nitrogenase complex is suggested by normal-mode calculations showing correlated and anticorrelated motions between the two halves.

Mechanism of N2 Reduction Catalyzed by Fe-Nitrogenase Involves Reductive Elimination of H2

Of the three forms of nitrogenase (Mo-nitrogenase, V-nitrogenase, and Fe-nitrogenase), Fe-nitrogenase has the poorest ratio of N2 reduction relative to H2 evolution. Recent work on the Mo-nitrogenase has revealed that reductive elimination of two bridging Fe-H-Fe hydrides on the active site FeMo-cofactor to yield H2 is a key feature in the N2 reduction mechanism. The N2 reduction mechanism for the Fe-nitrogenase active site FeFe-cofactor was unknown. Here, we have purified both component proteins of the Fe-nitrogenase system, the electron-delivery Fe protein (AnfH) plus the catalytic FeFe protein (AnfDGK), and established its mechanism of N2 reduction. Inductively coupled plasma optical emission spectroscopy and mass spectrometry show that the FeFe protein component does not contain significant amounts of Mo or V, thus ruling out a requirement of these metals for N2 reduction. The fully functioning Fe-nitrogenase system was found to have specific activities for N2 reduction (1 atm) of 181 ± 5 nmol NH3 min-1 mg-1 FeFe protein, for proton reduction (in the absence of N2) of 1085 ± 41 nmol H2 min-1 mg-1 FeFe protein, and for acetylene reduction (0.3 atm) of 306 ± 3 nmol C2H4 min-1 mg-1 FeFe protein. Under turnover conditions, N2 reduction is inhibited by H2 and the enzyme catalyzes the formation of HD when presented with N2 and D2. These observations are explained by the accumulation of four reducing equivalents as two metal-bound hydrides and two protons at the FeFe-cofactor, with activation for N2 reduction occurring by reductive elimination of H2.

Steric and Acidity Control in Hydrogen Bonding and Proton Transfer to trans-W(N2)2(dppe)2

The interaction of trans-W(N₂)₂(dppe)₂ (1; dppe = 1,2-bis(diphenylphosphino)ethane) with relatively weak acids (p-nitrophenol, fluorinated alcohols, CF₃COOH) was studied by means of variable temperature IR and NMR spectroscopy and complemented by DFT/B3PW91-D3 calculations. The results show, for the first time, the formation of a hydrogen bond to the coordinated dinitrogen, W-N≡N···H-O, that is preferred over H-bonding to the metal atom, W···H-O, despite the higher proton affinity of the latter. Protonation of the core metal-the undesirable side step in the conversion of N₂ to NH₃-can be avoided by using weaker and, more importantly, bulkier acids.

Fe-mediated HER vs N2RR: Exploring Factors that Contribute to Selectivity in P3 EFe(N2) (E = B, Si, C) Catalyst Model Systems

Mitigation of the hydrogen evolution reaction (HER) is a key challenge in selective small molecule reduction catalysis. This is especially true of catalytic nitrogen (N₂) and carbon dioxide (CO₂) reduction reactions (N₂RR and CO₂RR, respectively) using H⁺/e^- currency. Here we explore, via DFT calculations, three iron model systems, P₃ ^EFe (E = B, Si, C), known to mediate both N₂RR and HER, but with different selectivity depending on the identity of the auxiliary ligand. It is suggested that the respective efficiencies of these systems for N₂RR trend with the predicted N-H bonds strengths of two putative hydrazido intermediates of the proposed catalytic cycle, P₃ ^EFe(NNH₂)⁺ and P₃ ^EFe(NNH₂). Further, a mechanism is presented for undesired HER consistent with DFT studies, and previously reported experimental data, for these systems; bimolecular proton-coupled-electron-transfer (PCET) from intermediates with weak N-H bonds is posited as an important source of H_2' instead of more traditional scenarios that proceed via metal hydride intermediates and proton transfer/electron transfer (PT/ET) pathways. Wiberg bond indices provide additional insight into key factors related to the degree of stabilization of P₃ ^EFe(NNH₂) species, factors that trend with overall product selectivity.

Cluster-Dependent Charge-Transfer Dynamics in Iron-Sulfur Proteins

Photoinduced charge-transfer dynamics and the influence of cluster size on the dynamics were investigated using five iron-sulfur clusters: the 1Fe-4S cluster in Pyrococcus furiosus rubredoxin, the 2Fe-2S cluster in Pseudomonas putida putidaredoxin, the 4Fe-4S cluster in nitrogenase iron protein, and the 8Fe-7S P-cluster and the 7Fe-9S-1Mo FeMo cofactor in nitrogenase MoFe protein. Laser excitation promotes the iron-sulfur clusters to excited electronic states that relax to lower states. The electronic relaxation lifetimes of the 1Fe-4S, 8Fe-7S, and 7Fe-9S-1Mo clusters are on the picosecond time scale, although the dynamics of the MoFe protein is a mixture of the dynamics of the latter two clusters. The lifetimes of the 2Fe-2S and 4Fe-4S clusters, however, extend to several nanoseconds. A competition between reorganization energies and the density of electronic states (thus electronic coupling between states) mediates the charge-transfer lifetimes, with the 2Fe-2S cluster of Pdx and the 4Fe-4S cluster of Fe protein lying at the optimum leading to them having significantly longer lifetimes. Their long lifetimes make them the optimal candidates for long-range electron transfer and as external photosensitizers for other photoactivated chemical reactions like solar hydrogen production. Potential electron-transfer and hole-transfer pathways that possibly facilitate these charge transfers are proposed.

Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilumT

Leptospirillum ferriphilum plays a major role in acidic, metal-rich environments, where it represents one of the most prevalent iron oxidizers. These milieus include acid rock and mine drainage as well as biomining operations. Despite its perceived importance, no complete genome sequence of the type strain of this model species is available, limiting the possibilities to investigate the strategies and adaptations that Leptospirillum ferriphilum DSM 14647^T (here referred to as Leptospirillum ferriphilum ^T) applies to survive and compete in its niche. This study presents a complete, circular genome of Leptospirillum ferriphilum ^T obtained by PacBio single-molecule real-time (SMRT) long-read sequencing for use as a high-quality reference. Analysis of the functionally annotated genome, mRNA transcripts, and protein concentrations revealed a previously undiscovered nitrogenase cluster for atmospheric nitrogen fixation and elucidated metabolic systems taking part in energy conservation, carbon fixation, pH homeostasis, heavy metal tolerance, the oxidative stress response, chemotaxis and motility, quorum sensing, and biofilm formation. Additionally, mRNA transcript counts and protein concentrations were compared between cells grown in continuous culture using ferrous iron as the substrate and those grown in bioleaching cultures containing chalcopyrite (CuFeS₂). Adaptations of Leptospirillum ferriphilum ^T to growth on chalcopyrite included the possibly enhanced production of reducing power, reduced carbon dioxide fixation, as well as elevated levels of RNA transcripts and proteins involved in heavy metal resistance, with special emphasis on copper efflux systems. Finally, the expression and translation of genes responsible for chemotaxis and motility were enhanced.IMPORTANCE Leptospirillum ferriphilum is one of the most important iron oxidizers in the context of acidic and metal-rich environments during moderately thermophilic biomining. A high-quality circular genome of Leptospirillum ferriphilum ^T coupled with functional omics data provides new insights into its metabolic properties, such as the novel identification of genes for atmospheric nitrogen fixation, and represents an essential step for further accurate proteomic and transcriptomic investigation of this acidophile model species in the future. Additionally, light is shed on adaptation strategies of Leptospirillum ferriphilum ^T for growth on the copper mineral chalcopyrite. These data can be applied to deepen our understanding and optimization of bioleaching and biooxidation, techniques that present sustainable and environmentally friendly alternatives to many traditional methods for metal extraction.

A Major Structural Change of the Homocitrate Ligand of Probable Importance for the Nitrogenase Mechanism

Mo-containing nitrogenase is the main enzyme that is able to take N₂ from the air and form ammonia. The active-site cofactor of the enzyme, termed FeMoco, is unique in nature. It has seven Fe and one Mo atoms connected by S bridges, with a C atom in the center of the cofactor. Another unusual feature is that it has a large homocitrate ligand known to be of importance for catalysis. In the present computational study, the role of the homocitrate ligand is investigated. It is found that a large structural change, which makes Mo^III five-coordinated, is energetically favorable in the more reduced states. This is of probable importance for the nitrogenase mechanism.