Mechanism of nitrogen fixation by nitrogenase: the next stage

Elucidating reaction mechanisms on quantum computers

With rapid recent advances in quantum technology, we are close to the threshold of quantum devices whose computational powers can exceed those of classical supercomputers. Here, we show that a quantum computer can be used to elucidate reaction mechanisms in complex chemical systems, using the open problem of biological nitrogen fixation in nitrogenase as an example. We discuss how quantum computers can augment classical computer simulations used to probe these reaction mechanisms, to significantly increase their accuracy and enable hitherto intractable simulations. Our resource estimates show that, even when taking into account the substantial overhead of quantum error correction, and the need to compile into discrete gate sets, the necessary computations can be performed in reasonable time on small quantum computers. Our results demonstrate that quantum computers will be able to tackle important problems in chemistry without requiring exorbitant resources.

Ambient nitrogen reduction cycle using a hybrid inorganic-biological system

We demonstrate the synthesis of NH3 from N2 and H2O at ambient conditions in a single reactor by coupling hydrogen generation from catalytic water splitting to a H2-oxidizing bacterium Xanthobacter autotrophicus, which performs N2 and CO2 reduction to solid biomass. Living cells of X. autotrophicus may be directly applied as a biofertilizer to improve growth of radishes, a model crop plant, by up to ∼1,440% in terms of storage root mass. The NH3 generated from nitrogenase (N2ase) in X. autotrophicus can be diverted from biomass formation to an extracellular ammonia production with the addition of a glutamate synthetase inhibitor. The N2 reduction reaction proceeds at a low driving force with a turnover number of 9 × 109 cell-1 and turnover frequency of 1.9 × 104 s-1⋅cell-1 without the use of sacrificial chemical reagents or carbon feedstocks other than CO2 This approach can be powered by renewable electricity, enabling the sustainable and selective production of ammonia and biofertilizers in a distributed manner.

Ionic liquid promotes N2 coordination to titanocene(iii) monochloride

Coordination of N₂ to [(Cp₂TiCl)₂] in a non-coordinating ionic liquid, Pyr₄FAP, was studied by UV-vis/NIR and EPR spectroscopies. [(Cp₂TiCl)₂] is in equilibrium between monomeric [Cp₂TiCl] and dimeric species [(Cp₂TiCl)₂]. The frozen solution EPR spectrum revealed the coordination of N₂ to [Cp₂TiCl], suggesting that Pyr₄FAP promotes N₂ coordination to the Ti(iii) center.

Formation of Nitrogenase NifDK Tetramers in the Mitochondria of Saccharomyces cerevisiae

Transferring the prokaryotic enzyme nitrogenase into a eukaryotic host with the final aim of developing N₂ fixing cereal crops would revolutionize agricultural systems worldwide. Targeting it to mitochondria has potential advantages because of the organelle's high O₂ consumption and the presence of bacterial-type iron-sulfur cluster biosynthetic machinery. In this study, we constructed 96 strains of Saccharomyces cerevisiae in which transcriptional units comprising nine Azotobacter vinelandii nif genes (nifHDKUSMBEN) were integrated into the genome. Two combinatorial libraries of nif gene clusters were constructed: a library of mitochondrial leading sequences consisting of 24 clusters within four subsets of nif gene expression strength, and an expression library of 72 clusters with fixed mitochondrial leading sequences and nif expression levels assigned according to factorial design. In total, 29 promoters and 18 terminators were combined to adjust nif gene expression levels. Expression and mitochondrial targeting was confirmed at the protein level as immunoblot analysis showed that Nif proteins could be efficiently accumulated in mitochondria. NifDK tetramer formation, an essential step of nitrogenase assembly, was experimentally proven both in cell-free extracts and in purified NifDK preparations. This work represents a first step toward obtaining functional nitrogenase in the mitochondria of a eukaryotic cell.

Teaching old compounds new tricks: efficient N2 fixation by simple Fe(N2)(diphosphine)2 complexes

The Fe(0) species Fe(N2)(dmpe)2 exists in equilibrium with the previously unreported dimer, [Fe(dmpe2)2(μ-N2)]. For the first time these complexes, alongside Fe(N2)(depe)2, are shown unambiguously to produce N2H4 and/or NH3 upon addition of triflic acid; for Fe(N2)(depe)2 this represents one of the highest electron conversion efficiencies for Fe complexes to date.

N2 -to-NH3 Conversion by a triphos-Iron Catalyst and Enhanced Turnover under Photolysis

Bridging iron hydrides are proposed to form at the active site of MoFe-nitrogenase during catalytic dinitrogen reduction to ammonia and may be key in the binding and activation of N2 via reductive elimination of H2 . This possibility inspires the investigation of well-defined molecular iron hydrides as precursors for catalytic N2 -to-NH3 conversion. Herein, we describe the synthesis and characterization of new P2P'Ph Fe(N2 )(H)x systems that are active for catalytic N2 -to-NH3 conversion. Most interestingly, we show that the yields of ammonia can be significantly increased if the catalysis is performed in the presence of mercury lamp irradiation. Evidence is provided to suggest that photo-elimination of H2 is one means by which the enhanced activity may arise.

Remarkably Stereospecific Utilization of ATP α,β-Halomethylene Analogues by Protein Kinases

ATP analogues containing a CXY group in place of the α,β-bridging oxygen atom are powerful chemical probes for studying ATP-dependent enzymes. A limitation of such probes has been that conventional synthetic methods generate a mixture of diastereomers when the bridging carbon substitution is nonequivalent (X ≠ Y). We report here a novel method based on derivatization of a bisphosphonate precursor with a d-phenylglycine chiral auxiliary that enables preparation of the individual diastereomers of α,β-CHF-ATP and α,β-CHCl-ATP, which differ only in the configuration at the CHX carbon. When tested on a dozen divergent protein kinases, these individual diastereomers exhibit remarkable diastereospecificity (up to over 1000-fold) in utilization by the enzymes. This high selectivity can be exploited in an enzymatic approach to obtain the otherwise inaccessible diastereomers of α,β-CHBr-ATP. The crystal structure of a tyrosine kinase Src bound to α,β-CHX-ADP establishes the absolute configuration of the CHX carbon and helps clarify the origin of the remarkable diastereospecificity observed. We further synthesized the individual diastereomers of α,β-CHF-γ-thiol-ATP and demonstrated their utility in labeling a wide spectrum of kinase substrates. The novel ATP substrate analogues afforded by these two complementary strategies should have broad application in the study of the structure and function of ATP-dependent enzymes.

Coordination chemistry insights into the role of alkali metal promoters in dinitrogen reduction

The Haber-Bosch process is a major contributor to fixed nitrogen that supports the world's nutritional needs and is one of the largest-scale industrial processes known. It has also served as a testing ground for chemists' understanding of surface chemistry. Thus, it is significant that the most thoroughly developed catalysts for N2 reduction use potassium as an electronic promoter. In this review, we discuss the literature on alkali metal cations as promoters for N2 reduction, in the context of the growing knowledge about cooperative interactions between N2, transition metals, and alkali metals in coordination compounds. Because the structures and properties are easier to characterize in these compounds, they give useful information on alkali metal interactions with N2. Here, we review a variety of interactions, with emphasis on recent work on iron complexes by the authors. Finally, we draw conclusions about the nature of these interactions and areas for future research.

Cluster assembly in nitrogenase

The versatile enzyme system nitrogenase accomplishes the challenging reduction of N2and other substrates through the use of two main metalloclusters. For molybdenum nitrogenase, the catalytic component NifDK contains the [Fe8S7]-core P-cluster and a [MoFe7S9C-homocitrate] cofactor called the M-cluster. These chemically unprecedented metalloclusters play a critical role in the reduction of N2, and both originate from [Fe4S4] clusters produced by the actions of NifS and NifU. Maturation of P-cluster begins with a pair of these [Fe4S4] clusters on NifDK called the P*-cluster. An accessory protein NifZ aids in P-cluster fusion, and reductive coupling is facilitated by NifH in a stepwise manner to form P-cluster on each half of NifDK. For M-cluster biosynthesis, two [Fe4S4] clusters on NifB are coupled with a carbon atom in a radical-SAM dependent process, and concomitant addition of a ‘ninth’ sulfur atom generates the [Fe8S9C]-core L-cluster. On the scaffold protein NifEN, L-cluster is matured to M-cluster by the addition of Mo and homocitrate provided by NifH. Finally, matured M-cluster in NifEN is directly transferred to NifDK, where a conformational change locks the cofactor in place. Mechanistic insights into these fascinating biosynthetic processes are detailed in this chapter.

Reactivity of hydride bridges in a high-spin [Fe3(μ-H)3]3+ cluster: reversible H2/CO exchange and Fe-H/B-F bond metathesis

The triiron trihydride complex Fe₃H₃L (1) [where L^3– is a tris(β-diketiminate)cyclophanate] reacts with CO and with BF₃·OEt₂ to afford (Fe^ICO)₂Fe^II(μ₃-H)L (2) and Fe₃F₃L (3), respectively.

The triiron trihydride complex Fe₃H₃L (1) [where L^3– is a tris(β-diketiminate)cyclophanate] reacts with CO and with BF₃·OEt₂ to afford (Fe^ICO)₂Fe^II(μ₃-H)L (2) and Fe₃F₃L (3), respectively. Variable-temperature and applied-field Mössbauer spectroscopy support the assignment of two high-spin (HS) iron(i) centers and one HS iron(ii) ion in 2. Preliminary studies support a CO-induced reductive elimination of H₂ from 1, rather than CO trapping a species from an equilibrium mixture. This complex reacts with H₂ to regenerate 1 under a dihydrogen atmosphere, which represents a rare example of reversible CO/H₂ exchange and the first to occur at high-spin metal centers, as well as the first example of a reversible multielectron redox reaction at a designed high-spin metal cluster. The formation of 3 proceeds through a previously unreported net fluoride-for-hydride substitution, and 3 is surprisingly chemically inert to Si–H bonds and points to an unexpectedly large difference between the Fe–F and Fe–H bonds in this high-spin system.

Testing the Push-Pull Hypothesis: Lewis Acid Augmented N2 Activation at Iron

We present a systematic investigation of the structural and electronic changes that occur in an Fe(0)-N2 unit (Fe(depe)2(N2); depe = 1,2-bis(diethylphosphino)ethane) upon the addition of exogenous Lewis acids. Addition of neutral boranes, alkali metal cations, and an Fe2+ complex increases the N-N bond activation (Δ νNN up to 172 cm-1), decreases the Fe(0)-N2 redox potential, polarizes the N-N bond, and enables -N protonation at uncommonly anodic potentials. These effects were rationalized using combined experimental and theoretical studies.

Ammonia Synthesis from a Pincer Ruthenium Nitride via Metal-Ligand Cooperative Proton-Coupled Electron Transfer

The conversion of metal nitride complexes to ammonia may be essential to dinitrogen fixation. We report a new reduction pathway that utilizes ligating acids and metal-ligand cooperation to effect this conversion without external reductants. Weak acids such as 4-methoxybenzoic acid and 2-pyridone react with nitride complex [(H-PNP)RuN]⁺ (H-PNP = HN(CH₂CH₂P^tBu₂)₂) to generate octahedral ammine complexes that are κ²-chelated by the conjugate base. Experimental and computational mechanistic studies reveal the important role of Lewis basic sites proximal to the acidic proton in facilitating protonation of the nitride. The subsequent reduction to ammonia is enabled by intramolecular 2H⁺/2e^- proton-coupled electron transfer from the saturated pincer ligand backbone.

Remarkable catalytic activity of dinitrogen-bridged dimolybdenum complexes bearing NHC-based PCP-pincer ligands toward nitrogen fixation

Intensive efforts for the transformation of dinitrogen using transition metal-dinitrogen complexes as catalysts under mild reaction conditions have been made. However, limited systems have succeeded in the catalytic formation of ammonia. Here we show that newly designed and prepared dinitrogen-bridged dimolybdenum complexes bearing N-heterocyclic carbene- and phosphine-based PCP-pincer ligands [{Mo(N₂)₂(PCP)}₂(μ-N₂)] (1) work as so far the most effective catalysts towards the formation of ammonia from dinitrogen under ambient reaction conditions, where up to 230 equiv. of ammonia are produced based on the catalyst. DFT calculations on 1 reveal that the PCP-pincer ligand serves as not only a strong σ-donor but also a π-acceptor. These electronic properties are responsible for a solid connection between the molybdenum centre and the pincer ligand, leading to the enhanced catalytic activity for nitrogen fixation.

Catalytic N2-to-NH3 Conversion by Fe at Lower Driving Force: A Proposed Role for Metallocene-Mediated PCET

We have recently reported on several Fe catalysts for N₂-to-NH₃ conversion that operate at low temperature (-78 °C) and atmospheric pressure while relying on a very strong reductant (KC₈) and acid ([H(OEt₂)₂][BAr^F₄]). Here we show that our original catalyst system, P₃^BFe, achieves both significantly improved efficiency for NH₃ formation (up to 72% for e^- delivery) and a comparatively high turnover number for a synthetic molecular Fe catalyst (84 equiv of NH₃ per Fe site), when employing a significantly weaker combination of reductant (Cp*₂Co) and acid ([Ph₂NH₂][OTf] or [PhNH₃][OTf]). Relative to the previously reported catalysis, freeze-quench Mössbauer spectroscopy under turnover conditions suggests a change in the rate of key elementary steps; formation of a previously characterized off-path borohydrido-hydrido resting state is also suppressed. Theoretical and experimental studies are presented that highlight the possibility of protonated metallocenes as discrete PCET reagents under the present (and related) catalytic conditions, offering a plausible rationale for the increased efficiency at reduced driving force of this Fe catalyst system.

Dinitrogen Reduction: Interfacing the Enzyme Nitrogenase with Electrodes

Potential for nitrogenase: Milton, Minteer, and co-workers report the first evidence for the bioelectrochemical reduction of N₂ to ammonia by nitrogenase. This complex enzyme could be wired to an electrode by using the soluble mediator methyl viologen; this very simple approach makes it possible to develop a variety of biotechnological devices.

Photoinduced Reductive Elimination of H2 from the Nitrogenase Dihydride (Janus) State Involves a FeMo-cofactor-H2 Intermediate

N₂ reduction by nitrogenase involves the accumulation of four reducing equivalents at the active site FeMo-cofactor to form a state with two [Fe-H-Fe] bridging hydrides (denoted E₄(4H), the Janus intermediate), and we recently demonstrated that the enzyme is activated to cleave the N≡N triple bond by the reductive elimination (re) of H₂ from this state. We are exploring a photochemical approach to obtaining atomic-level details of the re activation process. We have shown that, when E₄(4H) at cryogenic temperatures is subjected to 450 nm irradiation in an EPR cavity, it cleanly undergoes photoinduced re of H₂ to give a reactive doubly reduced intermediate, denoted E₄(2H)*, which corresponds to the intermediate that would form if thermal dissociative re loss of H₂ preceded N₂ binding. Experiments reported here establish that photoinduced re primarily occurs in two steps. Photolysis of E₄(4H) generates an intermediate state that undergoes subsequent photoinduced conversion to [E₄(2H)* + H₂]. The experiments, supported by DFT calculations, indicate that the trapped intermediate is an H₂ complex on the ground adiabatic potential energy suface that connects E₄(4H) with [E₄(2H)* + H₂]. We suggest that this complex, denoted E₄(H₂; 2H), is a thermally populated intermediate in the catalytically central re of H₂ by E₄(4H) and that N₂ reacts with this complex to complete the activated conversion of [E₄(4H) + N₂] into [E₄(2N2H) + H₂].

Solar Water Splitting and Nitrogen Fixation with Layered Bismuth Oxyhalides

Hydrogen and ammonia are the chemical molecules that are vital to Earth's energy, environmental, and biological processes. Hydrogen with renewable, carbon-free, and high combustion-enthalpy hallmarks lays the foundation of next-generation energy source, while ammonia furnishes the building blocks of fertilizers and proteins to sustain the lives of plants and organisms. Such merits fascinate worldwide scientists in developing viable strategies to produce hydrogen and ammonia. Currently, at the forefronts of hydrogen and ammonia syntheses are solar water splitting and nitrogen fixation, because they go beyond the high temperature and pressure requirements of methane stream reforming and Haber-Bosch reaction, respectively, as the commercialized hydrogen and ammonia production routes, and inherit the natural photosynthesis virtues that are green and sustainable and operate at room temperature and atmospheric pressure. The key to propelling such photochemical reactions lies in searching photocatalysts that enable water splitting into hydrogen and nitrogen fixation to make ammonia efficiently. Although the past 40 years have witnessed significant breakthroughs using the most widely studied TiO₂, SrTiO₃, (Ga_1-xZn_x)(N_1-xO_x), CdS, and g-C₃N₄ for solar chemical synthesis, two crucial yet still unsolved issues challenge their further progress toward robust solar water splitting and nitrogen fixation, including the inefficient steering of electron transportation from the bulk to the surface and the difficulty of activating the N≡N triple bond of N₂. This Account details our endeavors that leverage layered bismuth oxyhalides as photocatalysts for efficient solar water splitting and nitrogen fixation, with a focus on addressing the above two problems. We first demonstrate that the layered structures of bismuth oxyhalides can stimulate an internal electric field (IEF) that is capable of efficiently separating electrons and holes after their formation and of precisely channeling their migration from the bulk to the surface along the different directions, thus enabling more electrons to reach the surface for water splitting and nitrogen fixation. Simultaneously, their oxygen termination feature and the strain differences between interlayers and intralayers render the easy generation of surface oxygen vacancies (OVs) that afford Lewis-base and unsaturated-unsaturated sites for nitrogen activation. With these rationales as the guideline, we can obtain striking visible-light hydrogen- and ammonia-evolving rates without using any noble-metal cocatalysts. Then we show how to utilize IEF and OV based strategies to improve the solar water splitting and nitrogen fixation performances of bismuth oxyhalide photocatalysts. Finally, we highlight the challenges remaining in using bismuth oxyhalides for solar hydrogen and ammonia syntheses, and the prospect of further development of this research field. We believe that our mechanistic insights could serve as a blueprint for the design of more efficient solar water splitting and nitrogen fixation systems, and layered bismuth oxyhalides might open up new photocatalyst paradigm for such two solar chemical syntheses.

Catalytic Amyloid Fibrils That Bind Copper to Activate Oxygen

Amyloid-like fibrils assembled from de novo designed peptides lock ligands in a conformation optimal for metal binding and catalysis in a manner similar to how metalloenzymes provide proper coordination environment through fold. These supramolecular assemblies efficiently catalyze p-nitrophenyl ester hydrolysis in the presence of zinc and phenol oxidation by dioxygen in the presence of copper. The resulting heterogeneous catalysts are inherently switchable, as addition and removal of the metal ions turns the catalytic activity on and off, respectively. The ease of peptide preparation and self-assembly makes amyloid-like fibrils an attractive platform for developing catalysts for a broad range of chemical reactions. Here, we present a detailed protocol for the preparation of copper-containing fibrils and for kinetic characterization of their abilities to oxidize phenols.

Direct Raman Spectroscopic Measurements of Biological Nitrogen Fixation under Natural Conditions: An Analytical Approach for Studying Nitrogenase Activity

Biological N₂ fixation is a major input of bioavailable nitrogen, which represents the most frequent factor limiting the agricultural production throughout the world. Especially, the symbiotic association between legumes and Rhizobium bacteria can provide substantial amounts of nitrogen (N) and reduce the need for industrial fertilizers. Despite its importance in the global N cycle, rates of biological nitrogen fixation have proven difficult to quantify. In this work, we propose and demonstrate a simple analytical approach to measure biological N₂ fixation rates directly without a proxy or isotopic labeling. We determined a mean N₂ fixation rate of 78 ± 5 μmol N₂ (g dry weight nodule)^-1 h^-1 of a Medicago sativa-Rhizobium consortium by continuously analyzing the amount of atmospheric N₂ in static environmental chambers with Raman gas spectroscopy. By simultaneously analyzing the CO₂ uptake and photosynthetic plant activity, we think that a minimum CO₂ mixing ratio might be needed for natural N₂ fixation and only used the time interval above this minimum CO₂ mixing ratio for N₂ fixation rate calculations. The proposed approach relies only on noninvasive measurements of the gas phase and, given its simplicity, indicates the potential to estimate biological nitrogen fixation of legume symbioses not only in laboratory experiments. The same methods can presumably also be used to detect N₂ fluxes by denitrification from ecosystems to the atmosphere.

The in vivo hydrocarbon formation by vanadium nitrogenase follows a secondary metabolic pathway

The vanadium (V)-nitrogenase of Azotobacter vinelandii catalyses the in vitro conversion of carbon monoxide (CO) to hydrocarbons. Here we show that an A. vinelandii strain expressing the V-nitrogenase is capable of in vivo reduction of CO to ethylene (C₂H₄), ethane (C₂H₆) and propane (C₃H₈). Moreover, we demonstrate that CO is not used as a carbon source for cell growth, being instead reduced to hydrocarbons in a secondary metabolic pathway. These findings suggest a possible role of the ancient nitrogenase as an evolutionary link between the carbon and nitrogen cycles on Earth and establish a solid foundation for biotechnological adaptation of a whole-cell approach to recycling carbon wastes into hydrocarbon products. Thus, this study has several repercussions for evolution-, environment- and energy-related areas.

Nitrogenases reduce inorganic nitrogen to organic ammonia in a crucial step of the nitrogen cycle. Here the authors show that the vanadium-nitrogenase of Azotobacter vinelandii can also catalyse the in vivo conversion of carbon monoxide to hydrocarbons in a secondary non-biosynthetic pathway.