A model for dinitrogen binding in the E4 state of nitrogenase

Understanding non-reducible N2 in the mechanism of Mo-nitrogenase

In my proposed mechanism of Mo-nitrogenase there are two roles for separate N2 molecules. One N2 diffuses into the reaction zone between Fe2 and Fe6 where a strategic gallery of H atoms can capture N2 to form the Fe-bound HNNH intermediate which is then progressively hydrogenated through intermediates containing HNNH2, NH and NH2 entities and then two NH3 in sequence. The second N2 can be parked in an N2-pocket about 3.2 Å from Fe2 or bind end-on at the exo coordination site of Fe2. This second N2 is outside the reaction zone, not exposed to H atom donors, and so is 'non-reducible'. Here density functional calculations using a 485+ atom model describe the thermodynamics for non-reducible N2 moving between the N2-pocket and the exo-Fe2 position, for the resting state and 19 intermediates in the mechanism. The entropy component is estimated and included. The result is that for all intermediates with ligation by H or NHx at the endo-Fe2 position the free energy for association of non-reducible N2 at exo-Fe2 is negative. There remains some uncertainty about the status of exo-Fe2-N2 during the step in which H2 exchanges with the incoming reducible N2, where at least two unbound molecules are present. At Fe2 it is evident that attainment of octahedral coordination stereochemistry dominates the binding thermodynamics for non-reducible N2. Possibilities for experimental support of these computational conclusions are discussed.

Investigating the Molybdenum Nitrogenase Mechanistic Cycle Using Spectroelectrochemistry

Molybdenum nitrogenase plays a crucial role in the biological nitrogen cycle by catalyzing the reduction of dinitrogen (N2) to ammonia (NH3) under ambient conditions. However, the underlying mechanisms of nitrogenase catalysis, including electron and proton transfer dynamics, remain only partially understood. In this study, we covalently attached molybdenum nitrogenase (MoFe) to gold electrodes and utilized surface-enhanced infrared absorption spectroscopy (SEIRA) coupled with electrochemistry techniques to investigate its catalytic mechanism. Our biohybrid system enabled electron transfer via a mild mediator, likely mimicking the natural electron flow through the P-cluster to FeMoco, the enzyme's active site. For the first time, we experimentally observed both terminal and bridging S-H stretching frequencies, resulting from the protonation of bridging sulfides in FeMoco during turnover conditions providing direct evidence of their role in catalysis. These experimental observations are further supported by QM/MM calculations. Additionally, we investigated CO inhibition, demonstrating both CO binding and unbinding dynamics under electrochemical conditions. These insights not only advance our understanding of the mechanistic cycle of molybdenum nitrogenase but also establish a foundation for studying alternative nitrogenases, including vanadium and iron nitrogenases.

Probing the performance of DFT in the structural characterization of [FeFe] hydrogenase models

In this work, a series of DFT and DFT-D methods is combined with double-ζ basis sets to benchmark their performance in predicting the structures of five newly synthesized hexacarbonyl diiron complexes with a bridging ligand featuring a μ-S2C3 motif in a ring-containing unit functionalized with aromatic groups. Such complexes have been considered as [FeFe] hydrogenase catalytic site models with potential for eco-friendly energetic applications. According to this assessment, r2SCAN is identified as the density functional recommended for the reliable description of the molecular and crystal structures of the herein studied models. However, the butterfly (μ-S)2Fe2 core of the models demonstrates a minor deformation of its optimized geometry obtained from both molecular and periodic calculations. The FeFe bond length is slightly underestimated while the FeS bonds tend to be too long. Adding the D3(BJ) correction to r2SCAN does not lead to any improvement in the calculated structures.

The mechanism of Mo-nitrogenase: from N2 capture to first release of NH3

Mo-nitrogenase hydrogenates N2 to NH3. This report continues from the previous paper [I. Dance, Dalton Trans., 2024, 53, 14193-14211] that described how the active site FeMo-co of the enzyme is uniquely able to capture and activate N2, forming a key intermediate with Fe-bound HNNH. Density functional simulations with a 485+ atom model of the active site and its surroundings are used to describe here the further reactions of this HNNH intermediate. The first step is hydrogenation to form HNNH2 bridging Fe2 and Fe6. Then a single-step reaction breaks the N-N bond, generating an Fe2-NH-Fe6 bridge and forming NH3 bound to Fe6. Then NH3 dissociates from Fe6. Reaction potential energies and kinetic barriers for all steps are reported for the most favourable electronic states of the system. The steps that follow the Fe2-NH-Fe6 intermediate, forming and dissociating the second NH3, and regenerating the resting state of the enzyme, are outlined. These results provide an interpretation of the recent steady-state kinetics data and analysis by Harris et al., [Biochemistry, 2022, 61, 2131-2137] who found a slow step after the formation of the HNNH intermediate. The calculated potential energy barriers for the HNNH2 → NH + NH3 reaction (30-36 kcal mol-1) are larger than the potential energy barriers for the N2 → HNNH reaction (19-29 kcal mol-1). I propose that the post-HNNH slow step identified kinetically is the key HNNH2 → NH + NH3 reaction described here. This step and the N2-capture step are the most difficult in the conversion of N2 to 2NH3. The steps in the complete mechanism still to be computationally detailed are relatively straightforward.

Atomic-level design of biomimetic iron-sulfur clusters for biocatalysis

Designing biomimetic materials with high activity and customized biological functions by mimicking the central structure of biomolecules has become an important avenue for the development of medical materials. As an essential electron carrier, the iron-sulfur (Fe-S) clusters have the advantages of simple structure and high electron transport capacity. To rationally design and accurately construct functional materials, it is crucial to clarify the electronic structure and conformational relationships of Fe-S clusters. However, due to the complex catalytic mechanism and synthetic process in vitro, it is hard to reveal the structure-activity relationship of Fe-S clusters accurately. This review introduces the main structural types of Fe-S clusters and their catalytic mechanisms first. Then, several typical structural design strategies of biomimetic Fe-S clusters are systematically introduced. Furthermore, the development of Fe-S clusters in the biocatalytic field is enumerated, including tumor treatment, antibacterial, virus inhibition and plant photoprotection. Finally, the problems and development directions of Fe-S clusters are summarized. This review aims to guide people to accurately understand and regulate the electronic structure of Fe-S at the atomic level, which is of great significance for designing biomimetic materials with specific functions and expanding their applications in biocatalysis.

The activating capture of N2 at the active site of Mo-nitrogenase

Dinitrogen is inherently inert. This report describes detailed density functional calculations (with a 485+ atom model) of mechanistic steps by which the enzyme nitrogenase activates unreactive N2 at the intact active site FeMo-co, to form a key intermediate with bound HNNH. This mechanism does not bind N2 first and then add H atoms, but rather captures N2 ('N2-ready') that diffuses in through the substrate channel and enters a strategic gallery of H atom donors in the reaction zone, between Fe2 and Fe6. This occurs at the E4 stage of the complete mechanism. Exploration of possible reactions of N2 in this space leads to the conclusion that the first reaction step is transfer of H on Fe7 to one end of N2-ready, soon followed by Fe-N bond formation, and then a second H transfer from bridging S2BH to the other N. Two H-N bonds and one or two N-Fe bonds are formed, in some cases with a single transition state. The variable positions and orientations of N2-ready lead to various reaction trajectories and products. The favourable products resulting from this capture, judged by the criteria of reaction energies, reaction barriers, and mechanistic competence for further hydrogenation reactions in the nitrogenase cycle, have Fe2-NH-NH bonding. The trajectory of one N2 capture reaction is described in detail, and calculations that separate the H atom component and the 'heavy atom' components of the classical activation energy are described, in the context of possible H atom tunneling in the activation of N2-ready. I present arguments for the activation of N2 by the pathway of concerted hydrogenation and binding of N2-ready, alternative to the commonly assumed pathway of binding N2 first, with subsequent hydrogenation. The active site of nitrogenase is well primed for the thermodynamic and kinetic advantages of N2 capture.

Reaction Mechanism for CO Reduction by Mo-Nitrogenase Studied by QM/MM

We have studied the conversion of two molecules of carbon monoxide to ethylene catalyzed by nitrogenase. We start from a recent crystal structure showing the binding of two carbon monoxide molecules to nitrogenase and employ the combined quantum mechanics and molecular mechanics approach. Our results indicate that the reaction is possible only if S2B dissociates as H2S (i.e., the charge of the FeMo cluster remains the same as in the E0 state, indicating that the Fe ions are formally reduced two steps when CO binds). Eight electrons and protons are needed for the reaction, and our mechanism suggests that the first four bind alternatively to the two carbon atoms. The C-C bond formation takes place already after the first protonation (in the E3 state). The next two protons bind to the same O atom, which then dissociates as water. In the same state (E8), the second C-O bond is cleaved, forming the ethylene product. The last two electrons and protons are used to form a water molecule that can be exchanged by S2B or by two CO molecules to start a new reaction cycle.

Putative reaction mechanism of nitrogenase with a half-dissociated S2B ligand

We have studied whether dissociation of the S2B sulfide ligand from one of its two coordinating Fe ions may affect the later parts of the reaction mechanism of nitrogenase. Such dissociation has been shown to be favourable for the E2-E4 states in the reaction mechanism, but previous studies have assumed that S2B either remains bridging or has fully dissociated from the active-site FeMo cluster. We employ combined quantum mechanical and molecular mechanical (QM/MM) calculations with two density-functional theory methods, r2SCAN and TPSSh. To make dissociation of S2B possible, we have added a proton to this group throughout the reaction. We study the reaction starting from the E4 state with N2H2 bound to the cluster. Our results indicate that half-dissociation of S2B is unfavourable in most steps of the reaction mechanism. We observe favourable half-dissociation of S2B only when NH or NH2 is bound to the cluster, bridging Fe2 and Fe6. However, the former state is most likely not involved in the reaction mechanism and the latter state is only an intermittent intermediate of the E7 state. Therefore, half-dissociation of S2B seems to play only a minor role in the later parts of the reaction mechanism of nitrogenase. Our suggested mechanism with a protonated S2B is alternating (the two N atoms of the substrate is protonated in an alternating manner) and the substrate prefers to bind to Fe2, in contrast to the preferred binding to Fe6 observed when S2B is unprotonated and bridging Fe2 and Fe6.

CO Oxidation Mechanism of Silver-Substituted Mo/Cu CO-Dehydrogenase - Analogies and Differences to the Native Enzyme

The aerobic oxidation of carbon monoxide to carbon dioxide is catalysed by the Mo/Cu-containing CO-dehydrogenase enzyme in the soil bacterium Oligotropha carboxidovorans, enabling the organism to grow on the small gas molecule as carbon and energy source. It was shown experimentally that silver can be substituted for copper in the active site of Mo/Cu CODH to yield a functional enzyme. In this study, we employed QM/MM calculations to investigate whether the reaction mechanism of the silver-substituted enzyme is similar to that of the native enzyme. Our results suggest that the Ag-substituted enzyme can oxidize CO and release CO2 following the same reaction steps as the native enzyme, with a computed rate-limiting step of 10.4 kcal/mol, consistent with experimental findings. Surprisingly, lower activation energies for C-O bond formation have been found in the presence of silver. Furthermore, comparison of rate constants for reduction of copper- and silver-containing enzymes suggests a discrepancy in the transition state stabilization upon silver substitution. We also evaluated the effects that differences in the water-active site interaction may exert on the overall energy profile of catalysis. Finally, the formation of a thiocarbonate intermediate along the catalytic pathway was found to be energetically unfavorable for the Ag-substituted enzyme. This finding aligns with the hypothesis proposed for the wild-type form, suggesting that the creation of such species may not be necessary for the enzymatic catalysis of CO oxidation.

H2 formation from the E2-E4 states of nitrogenase

Nitrogenase is the only enzyme that can cleave the strong triple bond in N2, making nitrogen available for biological lifeforms. The active site is a MoFe7S9C cluster (the FeMo cluster) that binds eight electrons and protons during one catalytic cycle, giving rise to eight intermediate states E0-E7. It is experimentally known that N2 binds to the E4 state and that H2 is a compulsory byproduct of the reaction. However, formation of H2 is also an unproductive side reaction that should be avoided, especially in the early steps of the reaction mechanism (E2 and E3). Here, we study the formation of H2 for various structural interpretations of the E2-E4 states using combined quantum mechanical and molecular mechanical (QM/MM) calculations and four different density-functional theory methods. We find large differences in the predictions of the different methods. B3LYP strongly favours protonation of the central carbide ion and H2 cannot form from such structures. On the other hand, with TPSS, r2SCAN and TPSSh, H2 formation is strongly exothermic for all structures and En and therefore need strict kinetic control to be avoided. For the E2 state, the kinetic barriers for the low-energy structures are high enough to avoid H2 formation. However, for both the E3 and E4 states, all three methods predict that the best structure has two hydride ions bridging the same pair of Fe ions (Fe2 and Fe6) and these two ions can combine to form H2 with an activation barrier of only 29-57 kJ mol-1, corresponding to rates of 7 × 102 to 5 × 107 s-1, i.e. much faster than the turnover rate of the enzyme (1-5 s-1). We have also studied H-atom movements within the FeMo cluster, showing that the various protonation states can quite freely be interconverted (activation barriers of 12-69 kJ mol-1).

Multireference Protonation Energetics of a Dimeric Model of Nitrogenase Iron-Sulfur Clusters

Characterizing the electronic structure of the iron-sulfur clusters in nitrogenase is necessary to understand their role in the nitrogen fixation process. One challenging task is to determine the protonation state of the intermediates in the nitrogen fixing cycle. Here, we use a dimeric iron-sulfur model to study relative energies of protonation at C, S, or Fe. Using a composite method based on coupled cluster and density matrix renormalization group energetics, we converge the relative energies of four protonated configurations with respect to basis set and correlation level. We find that accurate relative energies require large basis sets as well as a proper treatment of multireference and relativistic effects. We have also tested ten density functional approximations for these systems. Most of them give large errors in their relative energies. The best performing functional in this system is B3LYP, which gives mean absolute and maximum deviations of only 10 and 13 kJ/mol with respect to our correlated wave function estimates, respectively, comparable to the uncertainty in our correlated estimates. Our work provides benchmark results for the calibration of new approximate electronic structure methods and density functionals for these problems.

Multiscale QM/MM modelling of catalytic systems with ChemShell

Hybrid quantum mechanical/molecular mechanical (QM/MM) methods are a powerful computational tool for the investigation of all forms of catalysis, as they allow for an accurate description of reactions occurring at catalytic sites in the context of a complicated electrostatic environment. The scriptable computational chemistry environment ChemShell is a leading software package for QM/MM calculations, providing a flexible, high performance framework for modelling both biomolecular and materials catalysis. We present an overview of recent applications of ChemShell to problems in catalysis and review new functionality introduced into the redeveloped Python-based version of ChemShell to support catalytic modelling. These include a fully guided workflow for biomolecular QM/MM modelling, starting from an experimental structure, a periodic QM/MM embedding scheme to support modelling of metallic materials, and a comprehensive set of tutorials for biomolecular and materials modelling.

The E3 state of FeMoco: one hydride, two hydrides or dihydrogen?

Hydrides are present in the reduced states of the iron-molybdenum cofactor (FeMoco) of Mo nitrogenase and are believed to play a key mechanistic role in the dinitrogen reduction reaction catalyzed by the enzyme. Two hydrides are present in the E4 state according to 1H ENDOR and there is likely a single hydride in the E2 redox state. The 2-hydride E4 state has been experimentally observed to bind N2 and it has been speculated that E3 may bind N2 as well. However, the E3 state has not been directly observed and very little is known about its molecular and electronic structure or reactivity. In recent computational studies, we have explored the energy surfaces of the E2 and E4 by QM/MM modelling, and found that the most stable hydride isomers contain bridging or partially bridging hydrides with an open protonated belt sulfide-bridge. In this work we systematically explore the energy surface of the E3 redox state, comparing single hydride and two-hydride isomers with varying coordination and bridging vs. terminal sulfhydryl groups. We also include a model featuring a triply protonated carbide. The results are only mildly dependent on the QM-region size. The three most stable E3 isomers at the r2SCAN level of theory have in common: an open belt sulfide-bridge (terminal sulfhydryl group on Fe6) and either 2 bridging hydrides (between Fe2 and Fe6), 1 bridging-1-terminal hydride (around Fe2 and Fe6) or a dihydrogen ligand bound at the Fe2 site. Analyzing the functional dependency of the results, we find that functionals previously found to predict accurate structures of spin-coupled Fe/Mo dimers and FeMoco (TPSSh, B97-D3, r2SCAN, and B3LYP*) are in generally good agreement about the stability of these 3 E3 isomers. However, B3LYP*, similar to its parent B3LYP method, predicts a triply protonated carbide isomer as the most stable isomer, an unlikely scenario in view of the lack of experimental evidence for carbide protonation occurring in reduced FeMoco states. Distinguishing further between the 3 hydride isomers is difficult and this flexible coordination nature of hydrides suggests that multiple hydride isomers could be present during experimental conditions. N2 binding was explored and resulted in geometries with 2 bridging hydrides and N2 bound to either Fe2 or Fe6 with a local low-spin state on the Fe. N2 binding is predicted to be mildly endothermic, similar to the E2 state, and it seems unlikely that the E3 state is capable of binding N2.

Assessment of DFT functionals for a minimal nitrogenase [Fe(SH)4H]- model employing state-of-the-art ab initio methods

We have designed a [Fe(SH)4H]- model with the fifth proton binding either to Fe or S. We show that the energy difference between these two isomers (∆E) is hard to estimate with quantum-mechanical (QM) methods. For example, different density functional theory (DFT) methods give ∆E estimates that vary by almost 140 kJ/mol, mainly depending on the amount of exact Hartree-Fock included (0%-54%). The model is so small that it can be treated by many high-level QM methods, including coupled-cluster (CC) and multiconfigurational perturbation theory approaches. With extrapolated CC series (up to fully connected coupled-cluster calculations with singles, doubles, and triples) and semistochastic heat-bath configuration interaction methods, we obtain results that seem to be converged to full configuration interaction results within 5 kJ/mol. Our best result for ∆E is 101 kJ/mol. With this reference, we show that M06 and B3LYP-D3 give the best results among 35 DFT methods tested for this system. Brueckner doubles coupled cluster with perturbaitve triples seems to be the most accurate coupled-cluster approach with approximate triples. CCSD(T) with Kohn-Sham orbitals gives results within 4-11 kJ/mol of the extrapolated CC results, depending on the DFT method. Single-reference CC calculations seem to be reasonably accurate (giving an error of ∼5 kJ/mol compared to multireference methods), even if the D1 diagnostic is quite high (0.25) for one of the two isomers.

The binding of reducible N2 in the reaction domain of nitrogenase

The binding of N₂ to FeMo-co, the catalytic site of the enzyme nitrogenase, is central to the conversion to NH₃, but also has a separate role in promoting the N₂-dependent HD reaction (D₂ + 2H⁺ + 2e^- → 2HD). The protein surrounding FeMo-co contains a clear channel for ingress of N₂, directly towards the exo-coordination position of Fe2, a position which is outside the catalytic reaction domain. This led to the hypothesis [I. Dance, Dalton Trans., 2022, 51, 12717] of 'promotional' N₂ bound at exo-Fe2, and a second 'reducible' N₂ bound in the reaction domain, specifically the endo-coordination position of Fe2 or Fe6. The range of possibilities for the binding of reducible N₂ in the presence of bound promotional N₂ is described here, using density functional simulations with a 486 atom model of the active site and surrounding protein. The pathway for ingress of the second N₂ through protein, past the first N₂ at exo-Fe2, and tumbling into the binding domain between Fe2 and Fe6, is described. The calculations explore 24 structures involving 6 different forms of hydrogenated FeMo-co, including structures with S2BH unhooked from Fe2 but tethered to Fe6. The calculations use the most probable electronic states. End-on (η¹) binding of N₂ at the endo position of either Fe2 or Fe6 is almost invariably exothermic, with binding potential energies ranging up to -18 kcal mol^-1. Many structures have binding energies in the range -6 to -14 kcal mol^-1. The relevant entropic penalty for N₂ binding from a diffusible position within the protein is estimated to be 4 kcal mol^-1, and so the binding free energies for reducible N₂ are suitably negative. N₂ binding at endo-Fe2 is stronger than at endo-Fe6 in three of the six structure categories. In many cases the reaction domain containing reducible N₂ is expanded. These results inform computational simulation of the subsequent steps in which surrounding H atoms transfer to reducible N₂.

Sulfur-Ligated [2Fe-2C] Clusters as Synthetic Model Systems for Nitrogenase

Metal clusters featuring carbon and sulfur donors have coordination environments comparable to the active site of nitrogenase enzymes. Here, we report a series of di-iron clusters supported by the dianionic yldiide ligands, in which the Fe sites are bridged by two μ2-C atoms and four pendant S donors.The [L2Fe2] (L = {[Ph2P(S)]2C}2-) cluster is isolable in two oxidation levels, all-ferrous Fe2II and mixed-valence FeIIFeIII. The mixed-valence cluster displays two peaks in the Mössbauer spectra, indicating slow electron transfer between the two sites. The addition of the Lewis base 4-dimethylaminopyridine to the Fe2II cluster results in coordination with only one of the two Fe sites, even in the presence of an excess base. Conversely, the cluster reacts with 8 equiv of isocyanide tBuNC to give a monometallic complex featuring a new C-C bond between the ligand backbone and the isocyanide. The electronic structure descriptions of these complexes are further supported by X-ray absorption and resonant X-ray emission spectroscopies.

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 Km 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.

QM/MM Study of Partial Dissociation of S2B for the E2 Intermediate of Nitrogenase

Nitrogenase is the only enzyme that can cleave the triple bond in N2, making nitrogen available for all lifeforms. Previous computational studies have given widely diverging results regarding the reaction mechanism of the enzyme. For example, some recent studies have suggested that one of the μ2-bridging sulfide ligands (S2B) may dissociate from one of the Fe ions when protonated in the doubly reduced and protonated E2 state, whereas other studies indicated that such half-dissociated states are unfavorable. We have examined how the relative energies of 26 structures of the E2 state depend on details of combined quantum mechanical and molecular mechanical (QM/MM) calculations. We show that the selection of the broken-symmetry state, the basis set, relativistic effects, the size of the QM system, relaxation of the surroundings, and the conformations of the bound protons may affect the relative energies of the various structures by up to 12, 22, 9, 20, 37, and 33 kJ/mol, respectively. However, they do not change the preferred type of structures. On the other hand, the choice of the DFT functional strongly affects the preferences. The hybrid B3LYP functional strongly prefers doubly protonation of the central carbide ion, but such a structure is not consistent with experimental EPR data. Other functionals suggest structures with a hydride ion, in agreement with the experiments, and show that the ion bridges between Fe2 and Fe6. Moreover, there are two structures of the same type that are degenerate within 1-5 kJ/mol, in agreement with the observation of two EPR signals. However, the pure generalized gradient approximation (GGA) functional TPSS favors structures with a protonated S2B also bridging Fe2 and Fe6, whereas r2SCAN (meta-GGA) and TPSSh (hybrid) prefer structures with S2B dissociated from Fe2 (but remaining bound to Fe6). The energy difference between the two types of structure is so small (7-18 kJ/mol) that both types need to be considered in future investigations of the mechanism of nitrogenase.

Terminal N2 Dissociation in [(PNN)Fe(N2 )]2 (μ-N2 ) Leads to Local Spin-State Changes and Augmented Bridging N2 Activation

Nitrogen fixation at iron centres is a fundamental catalytic step for N₂ utilisation, relevant to biological (nitrogenase) and industrial (Haber-Bosch) processes. This step is coupled with important electronic structure changes which are currently poorly understood. We show here for the first time that terminal dinitrogen dissociation from iron complexes that coordinate N₂ in a terminal and bridging fashion leaves the Fe-N₂ -Fe unit intact but significantly enhances the degree of N₂ activation (Δν≈180 cm^-1 , Raman spectroscopy) through charge redistribution. The transformation proceeds with local spin state change at the iron centre (S= 1 / 2 ${{ 1/2 }}$ →S=³ /₂ ). Further dissociation of the bridging N₂ can be induced under thermolytic conditions, triggering a disproportionation reaction, from which the tetrahedral (PNN)₂ Fe could be isolated. This work shows that dinitrogen activation can be induced in the absence of external chemical stimuli such as reducing agents or Lewis acids.

13C ENDOR Characterization of the Central Carbon within the Nitrogenase Catalytic Cofactor Indicates That the CFe6 Core Is a Stabilizing "Heart of Steel"

Substrates and inhibitors of Mo-dependent nitrogenase bind and react at Fe ions of the active-site FeMo-cofactor [7Fe-9S-C-Mo-homocitrate] contained within the MoFe protein α-subunit. The cofactor contains a CFe6 core, a carbon centered within a trigonal prism of six Fe, whose role in catalysis is unknown. Targeted 13C labeling of the carbon enables electron-nuclear double resonance (ENDOR) spectroscopy to sensitively monitor the electronic properties of the Fe-C bonds and the spin-coupling scheme adopted by the FeMo-cofactor metal ions. This report compares 13CFe6 ENDOR measurements for (i) the wild-type protein resting state (E0; α-Val70) to those of (ii) α-Ile70, (iii) α-Ala70-substituted proteins; (iv) crystallographically characterized CO-inhibited "hi-CO" state; (v) E4(4H) Janus intermediate, activated for N2 binding/reduction by accumulation of 4[e-/H+]; (vi) E4(2H)* state containing a doubly reduced FeMo-cofactor without Fe-bound substrates; and (vii) propargyl alcohol reduction intermediate having allyl alcohol bound as a ferracycle to FeMo-cofactor Fe6. All states examined, both S = 1/2 and 3/2 exhibited near-zero 13C isotropic hyperfine coupling constants, Ca = [-1.3 ↔ +2.7] MHz. Density functional theory computations and natural bond orbital analysis of the Fe-C bonds show that this occurs because a (3 spin-up/3 spin-down) spin-exchange configuration of CFe6 Fe-ion spins produces cancellation of large spin-transfers to carbon in each Fe-C bond. Previous X-ray diffraction and DFT both indicate that trigonal-prismatic geometry around carbon is maintained with high precision in all these states. The persistent structure and Fe-C bonding of the CFe6 core indicate that it does not provide a functionally dynamic (hemilabile) "beating heart"─instead it acts as "a heart of steel", stabilizing the structure of the FeMo-cofactor-active site during nitrogenase catalysis.

Understanding the tethered unhooking and rehooking of S2B in the reaction domain of FeMo-co, the active site of nitrogenase

The active site of the nitrogen fixing enzyme nitrogenase is an Fe₇MoS₉C cluster, and investigations of the enigmatic chemical mechanism of the enzyme have focussed on a pair of Fe atoms, Fe2 and Fe6, and the S2B atom that bridges them. There are three proposals for the status of the Fe2-S2B-Fe6 bridge during the catalytic cycle: one that it remains intact, another that it is completely labile and absent during catalysis, and a third that S2B is hemilabile, unhooking one of its bonds to Fe2 or Fe6. This report examines the tethered unhooking of S2B and factors that affect it, using DFT calculations of 50 geometric/electronic possibilities with a 485 atom model including all relevant parts of surrounding protein. The outcomes are: (a) unhooking the S2B-Fe2 bond is feasible and favourable, but alternative unhooking of the S2B-Fe6 bond is unlikely for steric reasons, (b) energy differences between hooked and unhooked isomers are generally <10 kcal mol^-1, usually with unhooked more stable, (c) ligation at the exo-Fe6 position inhibits unhooking, (d) unhooking of hydrogenated S2B is more favourable than that of bare S2B, (e) hydrogen bonding from the NεH function of His195 to S2B occurs in hooked and unhooked forms, and possibly stabilises unhooking, (f) unhooking is reversible with kinetic barriers ranging 10-13 kcal mol^-1. The conclusion is that energetically accessible reversible unhooking of S2B or S2BH, as an intrinsic property of FeMo-co, needs to be considered in the formulation of mechanisms for the reactions of nitrogenase.

Calculating the chemical mechanism of nitrogenase: new working hypotheses

The enzyme nitrogenase converts N₂ to NH₃ with stoichiometry N₂ + 8H⁺ + 8e^- → 2NH₃ + H₂. The mechanism is chemically complex with multiple steps that must be consistent with much accumulated experimental information, including exchange of H₂ and N₂ and the N₂-dependent hydrogenation of D₂ to HD. Previous investigations have developed a collection of working hypotheses that guide ongoing density functional investigations of mechanistic steps and sequences. These include (i) hypotheses about the serial provision of protons and their conversion to H atoms bonded to S and Fe atoms of the FeMo-co catalytic site, (ii) the migration of H atoms over the surface of FeMo-co, (iii) the roles of His195, (iv) identification of three protein channels, one for the ingress of N₂, a separate pathway for the passage of exogenous H₂ (D₂) and product H₂ (HD), and a hydrophilic pathway for egress of product NH₃. Two additional working hypotheses are described in this paper. N₂ passing along the N₂ channel approaches and binds end-on to the exo coordination position of Fe2, with favourable energetics when FeMo-co is pre-hydrogenated. This exo-Fe2-N₂ is apparently not reduced but has a promotional role by expanding the reaction zone. A second N₂ can enter via the N₂ ingress channel and bind at the endo-Fe6 position, where it is surrounded by H atom donors suitable for the N₂ → NH₃ conversion. It is proposed that this endo-Fe6 position is also the binding site for H₂ (generated or exogenous), accounting for the competitive inhibition of N₂ reduction by H₂. The HD reaction occurs at the endo-Fe6 site, promoted by N₂ at the exo-Fe2 site. The second hypothesis concerns the most stable electronic states of FeMo-co with ligands bound at Fe2 and Fe6, and provides a protocol for management of electronic states in mechanism calculations.

Review on the QM/MM Methodologies and Their Application to Metalloproteins

The multiscaling quantum mechanics/molecular mechanics (QM/MM) approach was introduced in 1976, while the extensive acceptance of this methodology started in the 1990s. The combination of QM/MM approach with molecular dynamics (MD) simulation, otherwise known as the QM/MM/MD approach, is a powerful and promising tool for the investigation of chemical reactions’ mechanism of complex molecular systems, drug delivery, properties of molecular devices, organic electronics, etc. In the present review, the main methodologies in the multiscaling approaches, i.e., density functional theory (DFT), semiempirical methodologies (SE), MD simulations, MM, and their new advances are discussed in short. Then, a review on calculations and reactions on metalloproteins is presented, where particular attention is given to nitrogenase that catalyzes the conversion of atmospheric nitrogen molecules N₂ into NH₃ through the process known as nitrogen fixation and the FeMo-cofactor.

Analysis of the Geometric and Electronic Structure of Spin-Coupled Iron-Sulfur Dimers with Broken-Symmetry DFT: Implications for FeMoco

The open-shell electronic structure of iron-sulfur clusters presents considerable challenges to quantum chemistry, with the complex iron-molybdenum cofactor (FeMoco) of nitrogenase representing perhaps the ultimate challenge for either wavefunction or density functional theory. While broken-symmetry density functional theory has seen some success in describing the electronic structure of such cofactors, there is a large exchange-correlation functional dependence in calculations that is not fully understood. In this work, we present a geometric benchmarking test set, FeMoD11, of synthetic spin-coupled Fe-Fe and Mo-Fe dimers, with relevance to the molecular and electronic structure of the Mo-nitrogenase FeMo cofactor. The reference data consists of high-resolution crystal structures of metal dimer compounds in different oxidation states. Multiple density functionals are tested on their ability to reproduce the local geometry, specifically the Fe-Fe/Mo-Fe distance, for both antiferromagnetically coupled and ferromagnetically coupled dimers via the broken-symmetry approach. The metal-metal distance is revealed not only to be highly sensitive to the amount of exact exchange in the functional but also to the specific exchange and correlation functionals. For the antiferromagnetically coupled dimers, the calculated metal-metal distance correlates well with the covalency of the bridging metal-ligand bonds, as revealed via the corresponding orbital analysis, Hirshfeld S/Fe charges, and Fe-S Mayer bond order. Superexchange via bridging ligands is expected to be the dominant interaction in these dimers, and our results suggest that functionals that predict accurate Fe-Fe and Mo-Fe distances describe the overall metal-ligand covalency more accurately and in turn the superexchange of these systems. The best performing density functionals of the 16 tested for the FeMoD11 test set are revealed to be either the nonhybrid functionals r2SCAN and B97-D3 or hybrid functionals with 10-15% exact exchange: TPSSh and B3LYP*. These same four functionals are furthermore found to reproduce the high-resolution X-ray structure of FeMoco well according to quantum mechanics/molecular mechanics (QM/MM) calculations. Almost all nonhybrid functionals systematically underestimate Fe-Fe and Mo-Fe distances (with r2SCAN and B97-D3 being the sole exceptions), while hybrid functionals with >15% exact exchange (including range-separated hybrid functionals) overestimate them. The results overall suggest r2SCAN, B97-D3, TPSSh, and B3LYP* as accurate density functionals for describing the electronic structure of iron-sulfur clusters in general, including the complex FeMoco cluster of nitrogenase.

Thermodynamically Favourable States in the Reaction of Nitrogenase without Dissociation of any Sulfide Ligand

We have used combined quantum mechanical and molecular mechanical (QM/MM) calculations to study the reaction mechanism of nitrogenase, assuming that none of the sulfide ligands dissociates. To avoid the problem that there is no consensus regarding the structure and protonation of the E₄ state, we start from a state where N₂ is bound to the cluster and is protonated to N₂H₂, after dissociation of H₂. We show that the reaction follows an alternating mechanism with HNNH (possibly protonated to HNNH₂) and H₂NNH₂ as intermediates and the two NH₃ products dissociate at the E₇ and E₈ levels. For all intermediates, coordination to Fe6 is preferred, but for the E₄ and E₈ intermediates, binding to Fe2 is competitive. For the E₄, E₅ and E₇ intermediates we find that the substrate may abstract a proton from the hydroxy group of the homocitrate ligand of the FeMo cluster, thereby forming HNNH₂, H₂NNH₂ and NH₃ intermediates. This may explain why homocitrate is a mandatory component of nitrogenase. All steps in the suggested reaction mechanism are thermodynamically favourable compared to protonation of the nearby His‐195 group and in all cases, protonation of the NE2 atom of the latter group is preferred.

Iron Complexes of a Proton-Responsive SCS Pincer Ligand with a Sensitive Electronic Structure

Sulfur/carbon/sulfur pincer ligands have an interesting combination of strong-field and weak-field donors, a coordination environment that is also present in the nitrogenase active site. Here, we explore the electronic structures of iron(II) and iron(III) complexes with such a pincer ligand, bearing a monodentate phosphine, thiolate S donor, amide N donor, ammonia, or CO. The ligand scaffold features a proton-responsive thioamide site, and the protonation state of the ligand greatly influences the reduction potential of iron in the phosphine complex. The N-H bond dissociation free energy, derived from the Bordwell equation, is 56 ± 2 kcal/mol. Electron paramagnetic resonance (EPR) spectroscopy and superconducting quantum interference device (SQUID) magnetometry measurements show that the iron(III) complexes with S and N as the fourth donors have an intermediate spin (S = 3/2) ground state with a large zero field splitting, and X-ray absorption spectra show a high Fe-S covalency. The Mössbauer spectrum changes drastically with the position of a nearby alkali metal cation in the iron(III) amido complex, and density functional theory calculations explain this phenomenon through a change between having the doubly occupied orbital as dz2 or dyz, as the former is more influenced by the nearby positive charge.

Comparisons of bond valences and distances for CO- and N2-bound clusters of FeMo-cofactors

By comparisons of N2 and isoelectronic substrate CO bound FeMo-cofactors (FeMo-cos) in nitrogenases, we have used a classical bond valence method to calculate the oxidation states of the iron and molybdenum atoms in FeMo-cos.

Structures and reaction dynamics of N2 and H2 binding at FeMo-co, the active site of nitrogenase

The chemical reactions occurring at the Fe₇MoS₉C(homocitrate) cluster, FeMo-co, the active site of the enzyme nitrogenase (N₂ → NH₃), are enigmatic. Experimental information collected over a long period reveals aspects of the roles of N₂ and H₂, each with more than one type of reactivity. This paper reports investigations of the binding of H₂ and N₂ at intact FeMo-co, using density functional simulations of a large 486 atom relevant portion of the protein, resulting in 27 new structures containing H₂ and/or N₂ bound at the exo and endo coordination sites of the participating Fe atoms, Fe2 and Fe6. Binding energies and transition states for association/dissociation are determined, and trajectories for the approach, binding and separation of H₂/N₂ are described, including diffusion of these small molecules through proximal protein. Influences of surrounding amino acids are identified. FeMo-co deforms geometrically when binding H₂ or N₂, and a procedure for calculating the energy cost involved, the adaptation energy, is introduced here. Adaptation energies, which range from 7 to 36 kcal mol^-1 for the reported structures, are influenced by the protonation state of the His195 side chain. Seven N₂ structures and three H₂ structures have negative binding free energies, which include the estimated entropy penalties for binding of N₂, H₂ from proximal protein. These favoured structures have N₂ bound end-on at exo-Fe2, exo-Fe6 and endo-Fe2 positions of FeMo-co, and H₂ bound at the endo-Fe2 position. Various postulated structures with N₂ bridging Fe2 and Fe6 revert to end-on-N₂ at endo positions. The structures are also assessed via the calculated potential energy barriers for association and dissociation. Barriers to the binding of H₂ range from 1 to 20 kcal mol^-1 and barriers to dissociation of H₂ range from 3 to 18 kcal mol^-1. Barriers to the binding of N₂, in either side-on or end-on mode, range from 2 to 18 kcal mol^-1, while dissociation of bound N₂ encounters barriers of 3 to 8 kcal mol^-1 for side-on bonding and 7 to 18 kcal mol^-1 for end-on bonding. These results allow formulation of mechanisms for the H₂/N₂ exchange reaction, and three feasible mechanisms for associative exchange and three for dissociative exchange are identified. Consistent electronic structures and potential energy surfaces are maintained throughout. Changes in the spin populations of Fe2 and Fe6 connected with cluster deformation and with metal-ligand bond formation are identified.

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.

Sulfide and transition metals - A partnership for life

Sulfide and transition metals often came together in Biology. The variety of possible structural combinations enabled living organisms to evolve an array of highly versatile metal-sulfide centers to fulfill different physiological roles. The ubiquitous iron‑sulfur centers, with their structural, redox, and functional diversity, are certainly the best-known partners, but other metal-sulfide centers, involving copper, nickel, molybdenum or tungsten, are equally crucial for Life. This review provides a concise overview of the exclusive sulfide properties as a metal ligand, with emphasis on the structural aspects and biosynthesis. Sulfide as catalyst and as a substrate is discussed. Different enzymes are considered, including xanthine oxidase, formate dehydrogenases, nitrogenases and carbon monoxide dehydrogenases. The sulfide effect on the activity and function of iron‑sulfur, heme and zinc proteins is also addressed.

The E2 state of FeMoco: Hydride Formation versus Fe Reduction and a Mechanism for H2 Evolution

The iron‐molybdenum cofactor (FeMoco) is responsible for dinitrogen reduction in Mo nitrogenase. Unlike the resting state, E₀, reduced states of FeMoco are much less well characterized. The E₂ state has been proposed to contain a hydride but direct spectroscopic evidence is still lacking. The E₂ state can, however, relax back the E₀ state via a H₂ side‐reaction, implying a hydride intermediate prior to H₂ formation. This E₂→E₀ pathway is one of the primary mechanisms for H₂ formation under low‐electron flux conditions. In this study we present an exploration of the energy surface of the E₂ state. Utilizing both cluster‐continuum and QM/MM calculations, we explore various classes of E₂ models: including terminal hydrides, bridging hydrides with a closed or open sulfide‐bridge, as well as models without. Importantly, we find the hemilability of a protonated belt‐sulfide to strongly influence the stability of hydrides. Surprisingly, non‐hydride models are found to be almost equally favorable as hydride models. While the cluster‐continuum calculations suggest multiple possibilities, QM/MM suggests only two models as contenders for the E₂ state. These models feature either i) a bridging hydride between Fe₂ and Fe₆ and an open sulfide‐bridge with terminal SH on Fe₆ (E₂‐hyd) or ii) a double belt‐sulfide protonated, reduced cofactor without a hydride (E₂‐nonhyd). We suggest both models as contenders for the E₂ redox state and further calculate a mechanism for H₂ evolution. The changes in electronic structure of FeMoco during the proposed redox‐state cycle, E₀→E₁→E₂→E₀, are discussed.

Quantitative Account of the Bonding Properties of a Rubredoxin Model Complex [Fe(SCH3)4]q, q = -2, -1, +2, +3

Iron-sulfur clusters play important roles in biology as parts of electron-transfer chains and catalytic cofactors. Here, we report a detailed computational analysis of a structural model of the simplest natural iron-sulfur cluster of rubredoxin and its cationic counterparts. Specifically, we investigated adiabatic reduction energies, dissociation energies, and bonding properties of the low-lying electronic states of the complexes [Fe(SCH₃)₄]^2-/1-/2+/3+ using multireference (CASSCF, MRCISD), and coupled cluster [CCSD(T)] methodologies. We show that the nature of the Fe-S chemical bond and the magnitude of the ionization potentials in the anionic and cationic [Fe(SCH₃)₄] complexes offer a physical rationale for the relative stabilization, structure, and speciation of these complexes. Anionic and cationic complexes present different types of chemical bonds: prevalently ionic in [Fe(SCH₃)₄]^2-/1- complexes and covalent in [Fe(SCH₃)₄]^2+/3+ complexes. The ionic bonds result in an energy gain for the transition [Fe(SCH₃)₄]^2- → [Fe(SCH₃)₄]^- (i.e., Fe^II → Fe^III) of 1.5 eV, while the covalent bonds result in an energy loss for the transition [Fe(SCH₃)₄]²⁺ → [Fe(SCH₃)₄]³⁺ of 16.6 eV, almost half of the ionization potential of Fe²⁺. The ionic versus covalent bond character influences the Fe-S bond strength and length, that is, ionic Fe-S bonds are longer than covalent ones by about 0.2 Å (for Fe^II) and 0.04 Å (for Fe^II). Finally, the average Fe-S heterolytic bond strength is 6.7 eV (Fe^II) and 14.6 eV (Fe^III) at the RCCSD(T) level of theory.

On the Use of Normalized Metrics for Density Sensitivity Analysis in DFT

In the past years, there has been a discussion about how the errors in density functional theory might be related to errors in the self-consistent densities obtained from different density functional approximations. This, in turn, brings up the discussion about the different ways in which we can measure such errors and develop metrics that assess the sensitivity of calculated energies to changes in the density. It is important to realize that there cannot be a unique metric in order to look at this density sensitivity, simultaneously needing size-extensive and size-intensive metrics. In this study, we report two metrics that are widely applicable to any density functional approximation. We also show how they can be used to classify different chemical systems of interest with respect to their sensitivity to small variations in the density.

The active E4 structure of nitrogenase studied with different DFT functionals

The present study concerns the technical aspects of obtaining the energetics for the E4 state of nitrogenase, the enzyme that fixes N₂ in nature. EPR experiments have shown that the critical E4 structure that activates N₂ should contain two bridging hydrides in the FeMo-cofactor. It is furthermore in equilibrium with a structure where the two hydrides have been released and N₂ binds. These observations led to the suggestion that E4 should have two bridging hydrides and two protonated sulfides. It is important to note that the structure for E4 has not been determined, but only suggested. For a long time, no DFT study led to the suggested structure, independent of which functional was used. However, in two recent DFT studies a good agreement with the experimental suggestion was claimed to have been obtained. In one of them the TPSS functional was used. That was the first out of 11 functionals tried that led to the experimentally suggested structure. In the second of the recent DFT studies, a similar conclusion was reached using the TPSSh functional. The conclusions in the recent studies have here been studied in detail, by calculating a critical energetic value strongly implied by the same EPR experiments. Both the TPSS and TPSSh functionals have been used. The present calculations suggest that those DFT functionals would not lead to agreement with the experimental EPR results either.

Electron Redistribution within the Nitrogenase Active Site FeMo-Cofactor During Reductive Elimination of H2 to Achieve N≡N Triple-Bond Activation

Nitrogen fixation by nitrogenase begins with the accumulation of four reducing equivalents at the active-site FeMo-cofactor (FeMo-co), generating a state (denoted E₄(4H)) with two [Fe-H-Fe] bridging hydrides. Recently, photolytic reductive elimination (re) of the E₄(4H) hydrides showed that enzymatic re of E₄(4H) hydride yields an H₂-bound complex (E₄(H₂,2H)), in a process corresponding to a formal 2-electron reduction of the metal-ion core of FeMo-co. The resulting electron-density redistribution from Fe-H bonds to the metal ions themselves enables N₂ to bind with concomitant H₂ release, a process illuminated here by QM/MM molecular dynamics simulations. What is the nature of this redistribution? Although E₄(H₂,2H) has not been trapped, cryogenic photolysis of E₄(4H) provides a means to address this question. Photolysis of E₄(4H) causes hydride-re with release of H₂, generating doubly reduced FeMo-co (denoted E₄(2H)*), the extreme limit of the electron-density redistribution upon formation of E₄(H₂,2H). Here we examine the doubly reduced FeMo-co core of the E₄(2H)* limiting-state by ¹H, ⁵⁷Fe, and ⁹⁵Mo ENDOR to illuminate the partial electron-density redistribution upon E₄(H₂,2H) formation during catalysis, complementing these results with corresponding DFT computations. Inferences from the E₄(2H)* ENDOR results as extended by DFT computations include (i) the Mo-site participates negligibly, and overall it is unlikely that Mo changes valency throughout the catalytic cycle; and (ii) two distinctive E₄(4H) ⁵⁷Fe signals are suggested as associated with structurally identified "anchors" of one bridging hydride, two others with identified anchors of the second, with NBO-analysis further identifying one anchor of each hydride as a major recipient of electrons released upon breaking Fe-H bonds.

Assignment of protonated R-homocitrate in extracted FeMo-cofactor of nitrogenase via vibrational circular dichroism spectroscopies

Protonation of FeMo-cofactor is important for the process of substrate hydrogenation. Its structure has been clarified as Δ-Mo*Fe₇S₉C(R-homocit*)(cys)(Hhis) for the efforts of nearly 30 years, while it remains controversial whether FeMo-cofactor is protonated or deprotonated with chelated ≡C-O(H) homocitrate. We have used protonated molybdenum(V) lactates 1 and its enantiomer as model compounds for R-homocitrate in FeMo-cofactor of nitrogenase. Vibrational circular dichroism (VCD) spectrum of 1 at 1051 cm^-1 is attributed to ≡C-O_H vibration, and molybdenum(VI) R-lactate at 1086 cm^-1 is assigned as ≡C-O _α-alkoxy vibration. These vibrations set up labels for the protonation state of coordinated α-hydroxycarboxylates. The characteristic VCD band of NMF-extracted FeMo-cofactor is assigned to ν(C-O_H), which is based on the comparison of molybdenum(VI) R-homocitrate. Density Functional Theory calculations are in consistent with these assignments. To the best of our knowledge, this is the first time that protonated R-homocitrate in FeMo-cofactor is confirmed by VCD spectra.

Quantum Mechanics/Molecular Mechanics Study of Resting-State Vanadium Nitrogenase: Molecular and Electronic Structure of the Iron-Vanadium Cofactor

The nitrogenase enzymes are responsible for all biological nitrogen reduction. How this is accomplished at the atomic level, however, has still not been established. The molybdenum-dependent nitrogenase has been extensively studied and is the most active catalyst for dinitrogen reduction of the nitrogenase enzymes. The vanadium-dependent form, on the other hand, displays different reactivity, being capable of CO and CO2 reduction to hydrocarbons. Only recently did a crystal structure of the VFe protein of vanadium nitrogenase become available, paving the way for detailed theoretical studies of the iron-vanadium cofactor (FeVco) within the protein matrix. The crystal structure revealed a bridging 4-atom ligand between two Fe atoms, proposed to be either a CO32- or NO3- ligand. Using a quantum mechanics/molecular mechanics model of the VFe protein, starting from the 1.35 Å crystal structure, we have systematically explored multiple computational models for FeVco, considering either a CO32- or NO3- ligand, three different redox states, and multiple broken-symmetry states. We find that only a [VFe7S8C(CO3)]2- model for FeVco reproduces the crystal structure of FeVco well, as seen in a comparison of the Fe-Fe and V-Fe distances in the computed models. Furthermore, a broken-symmetry solution with Fe2, Fe3, and Fe5 spin-down (BS7-235) is energetically preferred. The electronic structure of the [VFe7S8C(CO3)]2- BS7-235 model is compared to our [MoFe7S9C]- BS7-235 model of FeMoco via localized orbital analysis and is discussed in terms of local oxidation states and different degrees of delocalization. As previously found from Fe X-ray absorption spectroscopy studies, the Fe part of FeVco is reduced compared to FeMoco, and the calculations reveal Fe5 as locally ferrous. This suggests resting-state FeVco to be analogous to an unprotonated E1 state of FeMoco. Furthermore, V-Fe interactions in FeVco are not as strong compared to Mo-Fe interactions in FeMoco. These clear differences in the electronic structures of otherwise similar cofactors suggest an explanation for distinct differences in reactivity.

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.

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.

Bond-valence analyses of the crystal structures of FeMo/V cofactors in FeMo/V proteins

The bond-valence method has been used for valence calculations of FeMo/V cofactors in FeMo/V proteins using 51 crystallographic data sets of FeMo/V proteins from the Protein Data Bank. The calculations show molybdenum(III) to be present in MoFe₇S₉C(Cys)(HHis)[R-(H)homocit] (where H₄homocit is homocitric acid, HCys is cysteine and HHis is histidine) in FeMo cofactors, while vanadium(III) with a more reduced iron complement is obtained for FeV cofactors. Using an error analysis of the calculated valences, it was found that in FeMo cofactors Fe1, Fe6 and Fe7 can be unambiguously assigned as iron(III), while Fe2, Fe3, Fe4 and Fe5 show different degrees of mixed valences for the individual Fe atoms. For the FeV cofactors in PDB entry 5n6y, Fe4, Fe5 and Fe6 correspond to iron(II), iron(II) and iron(III), respectively, while Fe1, Fe2, Fe3 and Fe7 exhibit strongly mixed valences. Special situations such as CO-bound and selenium-substituted FeMo cofactors and O(N)H-bridged FeV cofactors are also discussed and suggest rearrangement of the electron configuration on the substitution of the bridging S atoms.

Mimicking the Constrained Geometry of a Nitrogen-Fixation Intermediate

Both biological and industrial nitrogen reduction catalysts activate N₂ at multinuclear binding sites with constrained Fe-Fe distances. This contrasts with molecular diiron systems, which routinely form linear N₂ bridges to minimize steric interactions. Model compounds that capture the salient geometric features of N₂ binding by the nitrogenase enzymes and Mittasch catalysts would contribute to understanding their high N₂-reduction activity. It is shown in the present study that use of a geometrically flexible, dinucleating macrocycle allows for the formation of a bridging N₂ ligand with an unusual Fe-Ct_N2-Fe angle of 150° (Ct_N2 = centroid of N₂), a geometry that approximates the α-N₂ binding mode on Fe(111) surfaces that precedes N₂ bond cleavage. The cavity size of the macrocycle prevents the formation of a linear Fe-N₂-Fe unit and leads to orbital interactions that are distinct from those available to the linear configuration.

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.

The influences of carbon donor ligands on biomimetic multi-iron complexes for N2 reduction

The active site clusters of nitrogenase enzymes possess the only examples of carbides in biology. These are the only biological FeS clusters that are capable of reducing N₂ to NH₄⁺, implicating the central carbon and its interaction with Fe as important in the mechanism of N₂ reduction. This biological question motivates study of the influence of carbon donors on the electronic structure and reactivity of unsaturated, high-spin iron centers. Here, we present functional and structural models that test the impacts of carbon donors and sulfide donors in simpler iron compounds. We report the first example of a diiron complex that is bridged by an alkylidene and a sulfide, which serves as a high-fidelity structural and spectroscopic model of a two-iron portion of the active-site cluster (FeMoco) in the resting state of Mo-nitrogenase. The model complexes have antiferromagnetically coupled pairs of high-spin iron centers, and sulfur K-edge X-ray absorption spectroscopy shows comparable covalency of the sulfide for C and S bridged species. The sulfur-bridged compound does not interact with N₂ even upon reduction, but upon removal of the sulfide it becomes capable of reducing N₂ to NH₄⁺ with the addition of protons and electrons. This provides synthetic support for sulfide extrusion in the activation of nitrogenase cofactors.

High-spin diiron alkylidenes give insight into the electronic structure and functional relevance of carbon in the FeMoco active site of nitrogenase.