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

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.

Quantum Mechanical Calculations of Redox Potentials of the Metal Clusters in Nitrogenase

We have calculated redox potentials of the two metal clusters in Mo-nitrogenase with quantum mechanical (QM) calculations. We employ an approach calibrated for iron-sulfur clusters with 1-4 Fe ions, involving QM-cluster calculations in continuum solvent and large QM systems (400-500 atoms), based on structures from combined QM and molecular mechanics (QM/MM) geometry optimisations. Calculations on the P-cluster show that we can reproduce the experimental redox potentials within 0.33 V. This is similar to the accuracy obtained for the smaller clusters, although two of the redox reactions involve also proton transfer. The calculated P¹⁺/P^N redox potential is nearly the same independently of whether P¹⁺ is protonated or deprotonated, explaining why redox titrations do not show any pH dependence. For the FeMo cluster, the calculations clearly show that the formal oxidation state of the cluster in the resting E₀ state is MoIIIFe3IIFe4III , in agreement with previous experimental studies and QM calculations. Moreover, the redox potentials of the first five E₀-E₄ states are nearly constant, as is expected if the electrons are delivered by the same site (the P-cluster). However, the redox potentials are insensitive to the formal oxidation states of the Fe ion (i.e., whether the added protons bind to sulfide or Fe ions). Finally, we show that the later (E₄-E₈) states of the reaction mechanism have redox potential that are more positive (i.e., more exothermic) than that of the E₀/E₁ couple.

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.

Proton Transfer Pathways in Nitrogenase with and without Dissociated S2B

Nitrogenase is the only enzyme that can convert N₂ to NH₃ . Crystallographic structures have indicated that one of the sulfide ligands of the active-site FeMo cluster, S2B, can be replaced by an inhibitor, like CO and OH^- , and it has been suggested that it may be displaced also during the normal reaction. We have investigated possible proton transfer pathways within the FeMo cluster during the conversion of N₂ H₂ to two molecules of NH₃ , assuming that the protons enter the cluster at the S3B, S4B or S5A sulfide ions and are then transferred to the substrate. We use combined quantum mechanical and molecular mechanical (QM/MM) calculations with the TPSS and B3LYP functionals. The calculations indicate that the barriers for these reactions are reasonable if the S2B ligand remains bound to the cluster, but they become prohibitively high if S2B has dissociated. This suggests that it is unlikely that S2B reversibly dissociates during the normal reaction cycle.

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.