Photolysis of Hi-CO Nitrogenase - Observation of a Plethora of Distinct CO Species using Infrared Spectroscopy

Partial Deoxygenative CO Homocoupling by a Diiron Complex

One route to address climate change is converting carbon dioxide to synthetic carbon-neutral fuels. Whereas carbon dioxide to CO conversion has precedent in homo- and heterogeneous catalysis, deoxygenative coupling of CO to products with C-C bonds-as in liquid fuels-remains challenging. Here, we report coupling of two CO molecules by a diiron complex. Reduction of Fe2 (CO)2 L (2), where L2- is a bis(β-diketiminate) cyclophane, gives [K(THF)5 ][Fe2 (CO)2 L] (3), which undergoes silylation to Fe2 (CO)(COSiMe3 )L (4). Subsequent C-OSiMe3 bond cleavage and C=C bond formation occurs upon reduction of 4, yielding Fe2 (μ-CCO)L. CO derived ligands in this series mediate weak exchange interactions with the ketenylidene affording the smallest J value, with changes to local metal ion spin states and coupling schemes (ferro- vs. antiferromagnetism) based on DFT calculations, Mössbauer and EPR spectroscopy. Finally, reaction of 5 with KEt3 BH or methanol releases the C2 O2- ligand with retention of the diiron core.

Enzymatic Fischer-Tropsch-Type Reactions

The Fischer-Tropsch (FT) process converts a mixture of CO and H2 into liquid hydrocarbons as a major component of the gas-to-liquid technology for the production of synthetic fuels. Contrary to the energy-demanding chemical FT process, the enzymatic FT-type reactions catalyzed by nitrogenase enzymes, their metalloclusters, and synthetic mimics utilize H+ and e- as the reducing equivalents to reduce CO, CO2, and CN- into hydrocarbons under ambient conditions. The C1 chemistry exemplified by these FT-type reactions is underscored by the structural and electronic properties of the nitrogenase-associated metallocenters, and recent studies have pointed to the potential relevance of this reactivity to nitrogenase mechanism, prebiotic chemistry, and biotechnological applications. This review will provide an overview of the features of nitrogenase enzymes and associated metalloclusters, followed by a detailed discussion of the activities of various nitrogenase-derived FT systems and plausible mechanisms of the enzymatic FT reactions, highlighting the versatility of this unique reactivity while providing perspectives onto its mechanistic, evolutionary, and biotechnological implications.

The HD Reaction of Nitrogenase: a Detailed Mechanism

Nitrogenase is the enzyme that converts N₂ to NH₃ under ambient conditions. The chemical mechanism of this catalysis at the active site FeMo-co [Fe₇ S₉ CMo(homocitrate)] is unknown. An obligatory co-product is H₂ , while exogenous H₂ is a competitive inhibitor. Isotopic substitution using exogenous D₂ revealed the N₂ -dependent reaction D₂ +2H⁺ +2e^- →2HD (the 'HD reaction'), together with a collection of additional experimental characteristics and requirements. This paper describes a detailed mechanism for the HD reaction, developed and elaborated using density functional simulations with a 486-atom model of the active site and surrounding protein. First D₂ binds at one Fe atom (endo-Fe6 coordination position), where it is flanked by H-Fe6 (exo position) and H-Fe2 (endo position). Then there is synchronous transfer of these two H atoms to bound D₂ , forming one HD bound to Fe2 and a second HD bound to Fe6. These two HD dissociate sequentially. The final phase is recovery of the two flanking H atoms. These H atoms are generated, sequentially, by translocation of a proton from the protein surface to S3B of FeMo-co and combination with introduced electrons. The first H atom migrates from S3B to exo-Fe6 and the second from S3B to endo-Fe2. Reaction energies and kinetic barriers are reported for all steps. This mechanism accounts for the experimental data: (a) stoichiometry; (b) the N₂ -dependence results from promotional N₂ bound at exo-Fe2; (c) different N₂ binding K_m for the HD reaction and the NH₃ formation reaction results from involvement of two different sites; (d) inhibition by CO; (e) the non-occurrence of 2HD→H₂ +D₂ results from the synchronicity of the two transfers of H to D₂ ; (f) inhibition of HD production at high pN₂ is by competitive binding of N₂ at endo-Fe6; (g) the non-leakage of D to solvent follows from the hydrophobic environment and irreversibility of proton introduction.

Biological nitrogen fixation in theory, practice, and reality: a perspective on the molybdenum nitrogenase system

Nitrogenase is the sole enzyme responsible for the ATP-dependent conversion of atmospheric dinitrogen into the bioavailable form of ammonia (NH₃ ), making this protein essential for the maintenance of the nitrogen cycle and thus life itself. Despite the widespread use of the Haber-Bosch process to industrially produce NH₃ , biological nitrogen fixation still accounts for half of the bioavailable nitrogen on Earth. An important feature of nitrogenase is that it operates under physiological conditions, where the equilibrium strongly favours ammonia production. This biological, multielectron reduction is a complex catalytic reaction that has perplexed scientists for decades. In this review, we explore the current understanding of the molybdenum nitrogenase system based on experimental and computational research, as well as the limitations of the crystallographic, spectroscopic, and computational techniques employed. Finally, essential outstanding questions regarding the nitrogenase system will be highlighted alongside suggestions for future experimental and computational work to elucidate this essential yet elusive process.

Nitrogenase Chemistry at 10 Kelvin─Phototautomerization and Recombination of CO-Inhibited α-H195Q Enzyme

CO-bound forms of nitrogenase are N₂-reduction inhibited and likely intermediates in Fischer-Tropsch chemistry. Visible-light photolysis at 7 K was used to interrogate all three known CO-related EPR-active forms as exhibited by the α-H195Q variant of Azotobacter vinelandii nitrogenase MoFe protein. The hi(5)-CO EPR signal converted to the hi-CO EPR signal, which reverted at 10 K. FT-IR monitoring revealed an exquisitely light-sensitive "Hi-2" species with bands at 1932 and 1866 cm^-1 that yielded "Hi-1" with bands at 1969 and 1692 cm^-1, which reverted to "Hi-2". The similarities of photochemical behavior and recombination kinetics showed, for the first time, that hi-CO EPR and "Hi-1" IR signals arise from one chemical species. hi(5)-CO EPR and "Hi-2" IR signals are from a second species, and lo-CO EPR and "Lo-2" IR signals, formed after prolonged illumination, are from a third species. Comparing FT-IR data with CO-inhibited MoFe-protein crystal structures allowed assignment of CO-bonding geometries in these species.

Second and Outer Coordination Sphere Effects in Nitrogenase, Hydrogenase, Formate Dehydrogenase, and CO Dehydrogenase

Gases like H₂, N₂, CO₂, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N₂, CO₂, and CO and the production of H₂ require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N₂ fixation by nitrogenase and H₂ production by hydrogenase as well as CO₂ and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.

Carbon Monoxide Binding to the Iron-Molybdenum Cofactor of Nitrogenase: a Detailed Quantum Mechanics/Molecular Mechanics Investigation

Carbon monoxide (CO) is a well-known inhibitor of nitrogenase activity. Under turnover conditions, CO binds to FeMoco, the active site of Mo nitrogenase. Time-resolved IR measurements suggest an initial terminal CO at 1904 cm^-1 that converts to a bridging CO at 1715 cm^-1, and an X-ray structure shows that CO can displace one of the bridging belt sulfides of FeMoco. However, the CO-binding redox state(s) of FeMoco (E_n) and the role of the protein environment in stabilizing specific CO-bound intermediates remain elusive. In this work, we carry out an in-depth analysis of the CO-FeMoco interaction based on quantum chemical calculations addressing different aspects of the electronic structure. (1) The local electronic structure of the Fe-CO bond is studied through diamagnetically substituted FeMoco. (2) A cluster model of FeMoco within a polarizable continuum illustrates how CO binding may affect the spin-coupling between the metal centers. (3) A QM/MM model incorporates the explicit influence of the amino acid residues surrounding FeMoco in the MoFe protein. The QM/MM model predicts both a terminal and a bridging CO in the E₁ redox state. The scaled calculated CO frequencies (1922 and 1716 cm^-1, respectively) are in good agreement with the experimentally observed IR bands supporting CO binding to the E₁ state. Alternatively, an E₂ state QM/MM model, which has the same atomic structure as the CO-bound X-ray structure, features a semi-bridging CO with a scaled calculated frequency (1718 cm^-1) similar to the bridging CO in the E₁ model.

The Conversion of Carbon Monoxide and Carbon Dioxide by Nitrogenases

Nitrogenases are the only known family of enzymes that catalyze the reduction of molecular nitrogen (N₂) to ammonia (NH₃). The N₂ reduction drives biological nitrogen fixation and the global nitrogen cycle. Besides the conversion of N₂, nitrogenases catalyze a whole range of other reductions, including the reduction of the small gaseous substrates carbon monoxide (CO) and carbon dioxide (CO₂) to hydrocarbons. However, it remains an open question whether these ‘side reactivities’ play a role under environmental conditions. Nonetheless, these reactivities and particularly the formation of hydrocarbons have spurred the interest in nitrogenases for biotechnological applications. There are three different isozymes of nitrogenase: the molybdenum and the alternative vanadium and iron‐only nitrogenase. The isozymes differ in their metal content, structure, and substrate‐dependent activity, despite their homology. This minireview focuses on the conversion of CO and CO₂ to methane and higher hydrocarbons and aims to specify the differences in activity between the three nitrogenase isozymes.

Two ligand-binding sites in CO-reducing V nitrogenase reveal a general mechanistic principle

Besides its role in biological nitrogen fixation, vanadium-containing nitrogenase also reduces carbon monoxide (CO) to hydrocarbons, in analogy to the industrial Fischer-Tropsch process. The protein yields 93% of ethylene (C₂H₄), implying a C-C coupling step that mandates the simultaneous binding of two CO at the active site FeV cofactor. Spectroscopic data indicated multiple CO binding events, but structural analyses of Mo and V nitrogenase only confirmed a single site. Here, we report the structure of a two CO-bound state of V nitrogenase at 1.05 Å resolution, with one μ-bridging and one terminal CO molecule. This additional, specific ligand binding site suggests a mechanistic route for CO reduction and hydrocarbon formation, as well as a second access pathway for protons required during the reaction. Moreover, carbonyls are strong-field ligands that are chemically similar to mechanistically relevant hydrides that may be formed and used in a fully analogous fashion.

Structural Characterization of Two CO Molecules Bound to the Nitrogenase Active Site

As an approach towards unraveling the nitrogenase mechanism, we have studied the binding of CO to the active-site FeMo-cofactor. CO is not only an inhibitor of nitrogenase, but it is also a substrate, undergoing reduction to hydrocarbons (Fischer-Tropsch-type chemistry). The C-C bond forming capabilities of nitrogenase suggest that multiple CO or CO-derived ligands bind to the active site. Herein, we report a crystal structure with two CO ligands coordinated to the FeMo-cofactor of the molybdenum nitrogenase at 1.33 Å resolution. In addition to the previously observed bridging CO ligand between Fe2 and Fe6 of the FeMo-cofactor, a new ligand binding mode is revealed through a second CO ligand coordinated terminally to Fe6. While the relevance of this state to nitrogenase-catalyzed reactions remains to be established, it highlights the privileged roles for Fe2 and Fe6 in ligand binding, with multiple coordination modes available depending on the ligand and reaction conditions.

CowN sustains nitrogenase turnover in the presence of the inhibitor carbon monoxide

Nitrogenase is the only enzyme capable of catalyzing nitrogen fixation, the reduction of dinitrogen gas (N₂) to ammonia (NH₃). Nitrogenase is tightly inhibited by the environmental gas carbon monoxide (CO). Nitrogen-fixing bacteria rely on the protein CowN to grow in the presence of CO. However, the mechanism by which CowN operates is unknown. Here, we present the biochemical characterization of CowN and examine how CowN protects nitrogenase from CO. We determine that CowN interacts directly with nitrogenase and that CowN protection observes hyperbolic kinetics with respect to CowN concentration. At a CO concentration of 0.001 atm, CowN restores nearly full nitrogenase activity. Our results further indicate that CowN's protection mechanism involves decreasing the binding affinity of CO to nitrogenase's active site approximately tenfold without interrupting substrate turnover. Taken together, our work suggests CowN is an important auxiliary protein in nitrogen fixation that engenders CO tolerance to nitrogenase.

The Spectroscopy of Nitrogenases

Nitrogenases are responsible for biological nitrogen fixation, a crucial step in the biogeochemical nitrogen cycle. These enzymes utilize a two-component protein system and a series of iron-sulfur clusters to perform this reaction, culminating at the FeMco active site (M = Mo, V, Fe), which is capable of binding and reducing N2 to 2NH3. In this review, we summarize how different spectroscopic approaches have shed light on various aspects of these enzymes, including their structure, mechanism, alternative reactivity, and maturation. Synthetic model chemistry and theory have also played significant roles in developing our present understanding of these systems and are discussed in the context of their contributions to interpreting the nature of nitrogenases. Despite years of significant progress, there is still much to be learned from these enzymes through spectroscopic means, and we highlight where further spectroscopic investigations are needed.

Reduction of Substrates by Nitrogenases

Nitrogenase is the enzyme that catalyzes biological N₂ reduction to NH₃. This enzyme achieves an impressive rate enhancement over the uncatalyzed reaction. Given the high demand for N₂ fixation to support food and chemical production and the heavy reliance of the industrial Haber-Bosch nitrogen fixation reaction on fossil fuels, there is a strong need to elucidate how nitrogenase achieves this difficult reaction under benign conditions as a means of informing the design of next generation synthetic catalysts. This Review summarizes recent progress in addressing how nitrogenase catalyzes the reduction of an array of substrates. New insights into the mechanism of N₂ and proton reduction are first considered. This is followed by a summary of recent gains in understanding the reduction of a number of other nitrogenous compounds not considered to be physiological substrates. Progress in understanding the reduction of a wide range of C-based substrates, including CO and CO₂, is also discussed, and remaining challenges in understanding nitrogenase substrate reduction are considered.

Reactivity, Mechanism, and Assembly of the Alternative Nitrogenases

Biological nitrogen fixation is catalyzed by the enzyme nitrogenase, which facilitates the cleavage of the relatively inert triple bond of N₂. Nitrogenase is most commonly associated with the molybdenum-iron cofactor called FeMoco or the M-cluster, and it has been the subject of extensive structural and spectroscopic characterization over the past 60 years. In the late 1980s and early 1990s, two "alternative nitrogenase" systems were discovered, isolated, and found to incorporate V or Fe in place of Mo. These systems are regulated by separate gene clusters; however, there is a high degree of structural and functional similarity between each nitrogenase. Limited studies with the V- and Fe-nitrogenases initially demonstrated that these enzymes were analogously active as the Mo-nitrogenase, but more recent investigations have found capabilities that are unique to the alternative systems. In this review, we will discuss the reactivity, biosynthetic, and mechanistic proposals for the alternative nitrogenases as well as their electronic and structural properties in comparison to the well-characterized Mo-dependent system. Studies over the past 10 years have been particularly fruitful, though key aspects about V- and Fe-nitrogenases remain unexplored.

Rethinking the Nitrogenase Mechanism: Activating the Active Site

Metalloenzymes called nitrogenases (N₂ases) harness the reactivity of transition metals to reduce N₂ to NH₃. Specifically, N₂ases feature a multimetallic active site, called a cofactor, which binds and reduces N₂. The seven Fe centers and one additional metal center (Mo, V, or Fe) that make up the cofactor are all potential substrate binding sites. Unraveling the mechanism by which the cofactor binds N₂ and reduces N₂ to NH₃ represents a multifaceted challenge because cofactor activation is required for N₂ binding and functionalization to NH₃. Despite decades of fascinating contributions, the nature of N₂ binding to the active site and the structure of the activated cofactor remain unknown. Herein, we discuss the challenges associated with N₂ reduction and how transition metal complexes facilitate N₂ functionalization by coordinating N₂. We also review the activation and/or reaction mechanisms reported for small molecule catalysts and the Haber-Bosch catalyst and discuss their potential relevance to biological N₂ fixation. Finally, we survey what is known about the mechanism of N₂ase and highlight recent X-ray crystallographic studies supporting Fe-S bond cleavage at the active site to generate reactive Fe centers as a potential, underexplored route for cofactor activation. We propose that structural rearrangements, beyond electron and proton transfers, are key in generating the catalytically active state(s) of the cofactor. Understanding the mechanism of activation will be key to understanding N₂ binding and reduction.

Localized Electronic Structure of Nitrogenase FeMoco Revealed by Selenium K-Edge High Resolution X-ray Absorption Spectroscopy

The size and complexity of Mo-dependent nitrogenase, a multicomponent enzyme capable of reducing dinitrogen to ammonia, have made a detailed understanding of the FeMo cofactor (FeMoco) active site electronic structure an ongoing challenge. Selective substitution of sulfur by selenium in FeMoco affords a unique probe wherein local Fe-Se interactions can be directly interrogated via high-energy resolution fluorescence detected X-ray absorption spectroscopic (HERFD XAS) and extended X-ray absorption fine structure (EXAFS) studies. These studies reveal a significant asymmetry in the electronic distribution of the FeMoco, suggesting a more localized electronic structure picture than is typically assumed for iron-sulfur clusters. Supported by experimental small molecule model data in combination with time dependent density functional theory (TDDFT) calculations, the HERFD XAS data is consistent with an assignment of Fe2/Fe6 as an antiferromagnetically coupled diferric pair. HERFD XAS and EXAFS have also been applied to Se-substituted CO-inhibited MoFe protein, demonstrating the ability of these methods to reveal electronic and structural changes that occur upon substrate binding. These results emphasize the utility of Se HERFD XAS and EXAFS for selectively probing the local electronic and geometric structure of FeMoco.

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.

Serendipitous discoveries of new coordination modes of the 1,5-regioisomer of 1,2,3-triazoles enroute to the attempted synthesis of a carbon-anchored tri-mesoionic carbene

Di-, tri-, and tetra-nuclear Ag(i) complexes, a protonated ligand and a hydroxyl–alkyl-substituted triazolium salt with the 1,5-substituted-1,2,3-triazole ligand are presented.

Infrared spectroscopy of the nitrogenase MoFe protein under electrochemical control: potential-triggered CO binding

We demonstrate electrochemical control of the nitrogenase MoFe protein, in the absence of Fe protein or ATP, using europium(iii/ii) polyaminocarboxylate complexes as electron transfer mediators. This allows the potential dependence of proton reduction and inhibitor (CO) binding to the active site FeMo-cofactor to be established. Reduction of protons to H2 is catalyzed by the wild type MoFe protein and β-98Tyr→His and β-99Phe→His variants of the MoFe protein at potentials more negative than -800 mV (vs. SHE), with greater electrocatalytic proton reduction rates observed for the variants compared to the wild type protein. Electrocatalytic proton reduction is strongly attenuated by carbon monoxide (CO), and the potential-dependence of CO binding to the FeMo-cofactor is determined by in situ infrared (IR) spectroelectrochemistry. The vibrational wavenumbers for CO coordinated to the FeMo-cofactor are consistent with earlier IR studies on the MoFe protein with Fe protein/ATP as reductant showing that electrochemically generated states of the protein are closely related to states generated with the native Fe protein as electron donor.

Mechanism of Molybdenum-Mediated Carbon Monoxide Deoxygenation and Coupling: Mono- and Dicarbyne Complexes Precede C-O Bond Cleavage and C-C Bond Formation

Deoxygenative coupling of CO to value-added C_≥2 products is challenging and mechanistically poorly understood. Herein, we report a mechanistic investigation into the reductive coupling of CO, which provides new fundamental insights into a multielectron bond-breaking and bond-making transformation. In our studies, the formation of a bis(siloxycarbyne) complex precedes C-O bond cleavage. At -78 °C, over days, C-C coupling occurs without C-O cleavage. However, upon warming to 0 °C, C-O cleavage is observed from this bis(siloxycarbyne) complex. A siloxycarbyne/CO species undergoes C-O bond cleavage at lower temperatures, indicating that monosilylation, and a more electron-rich Mo center, favors deoxygenative pathways. From the bis(siloxycarbyne), isotopic labeling experiments and kinetics are consistent with a mechanism involving unimolecular silyl loss or C-O cleavage as rate-determining steps toward carbide formation. Reduction of Mo(IV) CO adducts of carbide and silylcarbyne species allowed for the spectroscopic detection of reduced silylcarbyne/CO and mixed silylcarbyne/siloxycarbyne complexes, respectively. Upon warming, both of these silylcarbynes undergo C-C bond formation, releasing silylated C₂O₁ fragments and demonstrating that the multiple bonded terminal Mo≡C moiety is an intermediate on the path to deoxygenated, C-C coupled products. The electronic structures of Mo carbide and carbyne species were investigated quantum mechanically. Overall, the present studies establish the elementary reactions steps by which CO is cleaved and coupled at a single metal site.

Is Trehalose an Effective Quenching Agent of Azotobacter vinelandii Mo-Nitrogenase Turnover?

H₂-evolution assays, plus EPR and FTIR spectroscopies, using CO-inhibited Azotobacter vinelandii Mo-nitrogenase have shown that the disaccharide trehalose is an effective quenching agent of enzymatic turnover and also stabilizes the reaction intermediates formed. Complete inhibition of H₂-evolution activity was achieved at 1.5 M trehalose, which compares favorably to the requirement for 10 M ethylene glycol to achieve similar inhibition. Reaction-intermediate stabilization was demonstrated by monitoring the EPR spectrum of the 'hi-CO' form of CO-inhibited N₂ase, which did not change during 1 hr after trehalose quenching. Similarly, in situ photolysis with FTIR monitoring of 'hi-CO' resulted in the same 1973 and 1681 cm^-1 signals as observed previously in ethylene glycol-quenched systems. [a] These results clearly show that 1.5 M trehalose is an effective quench and stabilization agent for Mo-N₂ase studies. Possible applications are discussed.

Low frequency dynamics of the nitrogenase MoFe protein via femtosecond pump probe spectroscopy - Observation of a candidate promoting vibration

We have used femtosecond pump-probe spectroscopy (FPPS) to study the FeMo-cofactor within the nitrogenase (N2ase) MoFe protein from Azotobacter vinelandii. A sub-20-fs visible laser pulse was used to pump the sample to an excited electronic state, and a second sub-10-fs pulse was used to probe changes in transmission as a function of probe wavelength and delay time. The excited protein relaxes to the ground state with a ~1.2ps time constant. With the short laser pulse we coherently excited the vibrational modes associated with the FeMo-cofactor active site, which are then observed in the time domain. Superimposed on the relaxation dynamics, we distinguished a variety of oscillation frequencies with the strongest band peaks at ~84, 116, 189, and 226cm(-1). Comparison with data from nuclear resonance vibrational spectroscopy (NRVS) shows that the latter pair of signals comes predominantly from the FeMo-cofactor. The frequencies obtained from the FPPS experiment were interpreted with normal mode calculations using both an empirical force field (EFF) and density functional theory (DFT). The FPPS data were also compared with the first reported resonance Raman (RR) spectrum of the N2ase MoFe protein. This approach allows us to outline and assign vibrational modes having relevance to the catalytic activity of N2ase. In particular, the 226cm(-1) band is assigned as a potential 'promoting vibration' in the H-atom transfer (or proton-coupled electron transfer) processes that are an essential feature of N2ase catalysis. The results demonstrate that high-quality room-temperature solution data can be obtained on the MoFe protein by the FPPS technique and that these data provide added insight to the motions and possible operation of this protein and its catalytic prosthetic group.

Docking and migration of carbon monoxide in nitrogenase: the case for gated pockets from infrared spectroscopy and molecular dynamics

Evidence of a CO docking site near the FeMo cofactor in nitrogenase has been obtained by Fourier transform infrared spectroscopy-monitored low-temperature photolysis. We investigated the possible migration paths for CO from this docking site using molecular dynamics calculations. The simulations support the notion of a gas channel with multiple internal pockets from the active site to the protein exterior. Travel between pockets is gated by the motion of protein residues. Implications for the mechanism of nitrogenase reactions with CO and N2 are discussed.

Structural characterization of CO-inhibited Mo-nitrogenase by combined application of nuclear resonance vibrational spectroscopy, extended X-ray absorption fine structure, and density functional theory: new insights into the effects of CO binding and the role of the interstitial atom

The properties of CO-inhibited Azotobacter vinelandii (Av) Mo-nitrogenase (N2ase) have been examined by the combined application of nuclear resonance vibrational spectroscopy (NRVS), extended X-ray absorption fine structure (EXAFS), and density functional theory (DFT). Dramatic changes in the NRVS are seen under high-CO conditions, especially in a 188 cm(-1) mode associated with symmetric breathing of the central cage of the FeMo-cofactor. Similar changes are reproduced with the α-H195Q N2ase variant. In the frequency region above 450 cm(-1), additional features are seen that are assigned to Fe-CO bending and stretching modes (confirmed by (13)CO isotope shifts). The EXAFS for wild-type N2ase shows evidence for a significant cluster distortion under high-CO conditions, most dramatically in the splitting of the interaction between Mo and the shell of Fe atoms originally at 5.08 Å in the resting enzyme. A DFT model with both a terminal -CO and a partially reduced -CHO ligand bound to adjacent Fe sites is consistent with both earlier FT-IR experiments, and the present EXAFS and NRVS observations for the wild-type enzyme. Another DFT model with two terminal CO ligands on the adjacent Fe atoms yields Fe-CO bands consistent with the α-H195Q variant NRVS. The calculations also shed light on the vibrational "shake" modes of the interstitial atom inside the central cage, and their interaction with the Fe-CO modes. Implications for the CO and N2 reactivity of N2ase are discussed.

Ligand binding to the FeMo-cofactor: structures of CO-bound and reactivated nitrogenase

The mechanism of nitrogenase remains enigmatic, with a major unresolved issue concerning how inhibitors and substrates bind to the active site. We report a crystal structure of carbon monoxide (CO)-inhibited nitrogenase molybdenum-iron (MoFe)-protein at 1.50 angstrom resolution, which reveals a CO molecule bridging Fe2 and Fe6 of the FeMo-cofactor. The μ2 binding geometry is achieved by replacing a belt-sulfur atom (S2B) and highlights the generation of a reactive iron species uncovered by the displacement of sulfur. The CO inhibition is fully reversible as established by regain of enzyme activity and reappearance of S2B in the 1.43 angstrom resolution structure of the reactivated enzyme. The substantial and reversible reorganization of the FeMo-cofactor accompanying CO binding was unanticipated and provides insights into a catalytically competent state of nitrogenase.

A CO-derived iron dicarbyne that releases olefin upon hydrogenation

An iron diphosphineborane platform that was previously reported to facilitate a high degree of N2 functionalization is herein shown to effect reductive CO coupling. Disilylation of an iron dicarbonyl precursor furnishes a structurally unprecedented iron dicarbyne complex. Several complexes related to this process are also characterized which allows for a comparative analysis of their respective Fe-B and Fe-C bonding. Facile hydrogenation of the iron dicarbyne at ambient temperature and 1 atm H2 results in release of a CO-derived olefin.

Structure and spectroscopy of a bidentate bis-homocitrate dioxo-molybdenum(VI) complex: insights relevant to the structure and properties of the FeMo-cofactor in nitrogenase

Direct reaction of potassium molybdate (with natural abundance Mo or enriched with (92)Mo or (100)Mo) with excess hydrolyzed homocitric acid-γ-lactone in acidic solution resulted in the isolation of a cis-dioxo bis-homocitrato molybdenum(VI) complex, K(2)[*MoO(2)(R,S-H(2)homocit)(2)]·2H(2)O (1) (*Mo=Mo, 1; (92)Mo, 2; (100)Mo, 3; H(4)homocit=homocitric acid-γ-lactone·H(2)O) and K(2)[MoO(2)((18)O-R,S-H(2)homocit)(2)]·2H(2)O (4). The complex has been characterized by elemental analysis, FT-IR, solid and solution (13)C NMR, and single crystal x-ray diffraction analysis. The molybdenum atom in (1) is quasi-octahedrally coordinated by two cis oxo groups and two bidentate homocitrate ligands. The latter coordinates via its α-alkoxy and α-carboxy groups, while the β- and γ-carboxylic acid groups remain uncomplexed, similar to the coordination mode of homocitrate in the Mo-cofactor of nitrogenase. In the IR spectra, the MoO stretching modes near 900 cm(-1) show 2-3 cm(-1) red- and blue-shifts for the (92)Mo-complex (2) and (100)Mo-complex (3) respectively compared with the natural abundance version (1). At lower frequencies, bands at 553 and 540 cm(-1) are assigned to ν(Mo-O) vibrations involving the alkoxide ligand. At higher frequencies, bands in the 1700-1730 cm(-1) region are assigned to stretching modes of protonated carboxylates. In addition, a band at 1675 cm(-1) was observed that may be analogous to a band seen at 1677 cm(-1) in nitrogenase photolysis studies. The solution behavior of (1) in D(2)O was probed with (1)H and (13)C NMR spectra. An obvious dissociation of homocitrate was found, even though bound to the high valent Mo(VI). This suggests the likely lability of coordinated homocitrate in the FeMo-cofactor with its lower valence Mo(IV).

IR-monitored photolysis of CO-inhibited nitrogenase: a major EPR-silent species with coupled terminal CO ligands

Fourier transform infrared spectroscopy (FTIR) was used to observe the photolysis and recombination of a new EPR-silent CO-inhibited form of α-H195Q nitrogenase from Azotobacter vinelandii. Photolysis at 4 K reveals a strong negative IR difference band at nu = 1938 cm(-1), along with a weaker negative feature at 1911 cm(-1). These bands and the associated chemical species have both been assigned the label "Hi-3". A positive band at nu = 1921 cm(-1) was assigned to the "Lo-3" photoproduct. By using an isotopic mixture of (12)C (16)O and (13)C (18)O, we show that the Hi-3 bands arise from coupling of two similar CO oscillators with one uncoupled frequency at approximately nu = 1917 cm(-1). Although in previous studies Lo-3 was not observed to recombine, by extending the observation range to 200-240 K, we found that recombination to Hi-3 does indeed occur, with an activation energy of approximately 6.5 kJ mol(-1). The frequencies of the Hi-3 bands suggest terminal CO ligation. This hypothesis was tested with DFT calculations on models with terminal CO ligands on Fe2 and Fe6 of the FeMo-cofactor. An S = 0 model with both CO ligands in exo positions predicts symmetric and asymmetric stretches at nu = 1938 and 1909 cm(-1), respectively, with relative band intensities of about 3.5:1, which is in good agreement with experiment. From the observed IR intensities, Hi-3 was found to be present at a concentration about equal to that of the EPR-active Hi-1 species. The relevance of Hi-3 to the nitrogenase catalytic mechanism and its recently discovered Fischer-Tropsch chemistry is discussed.