Protonation of Homocitrate and the E1 State of Fe-Nitrogenase Studied by QM/MM Calculations

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.

Spiers Memorial Lecture: Quantum chemistry, classical heuristics, and quantum advantage

We describe the problems of quantum chemistry, the intuition behind classical heuristic methods used to solve them, a conjectured form of the classical complexity of quantum chemistry problems, and the subsequent opportunities for quantum advantage. This article is written for both quantum chemists and quantum information theorists. In particular, we attempt to summarize the domain of quantum chemistry problems as well as the chemical intuition that is applied to solve them within concrete statements (such as a classical heuristic cost conjecture) in the hope that this may stimulate future analysis.

Quantum refinement in real and reciprocal space using the Phenix and ORCA software

X-ray and neutron crystallography, as well as cryogenic electron microscopy (cryo-EM), are the most common methods to obtain atomic structures of biological macromolecules. A feature they all have in common is that, at typical resolutions, the experimental data need to be supplemented by empirical restraints, ensuring that the final structure is chemically reasonable. The restraints are accurate for amino acids and nucleic acids, but often less accurate for substrates, inhibitors, small-molecule ligands and metal sites, for which experimental data are scarce or empirical potentials are harder to formulate. This can be solved using quantum mechanical calculations for a small but interesting part of the structure. Such an approach, called quantum refinement, has been shown to improve structures locally, allow the determination of the protonation and oxidation states of ligands and metals, and discriminate between different interpretations of the structure. Here, we present a new implementation of quantum refinement interfacing the widely used structure-refinement software Phenix and the freely available quantum mechanical software ORCA. Through application to manganese superoxide dismutase and V- and Fe-nitrogenase, we show that the approach works effectively for X-ray and neutron crystal structures, that old results can be reproduced and structural discrimination can be performed. We discuss how the weight factor between the experimental data and the empirical restraints should be selected and how quantum mechanical quality measures such as strain energies should be calculated. We also present an application of quantum refinement to cryo-EM data for particulate methane monooxygenase and show that this may be the method of choice for metal sites in such structures because no accurate empirical restraints are currently available for metals.

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).