H₂ formation from the E₂-E₄ states of nitrogenase

Area of Science:

• Biochemistry
• Computational Chemistry
• Enzymology

Background:

• Nitrogenase is the sole enzyme capable of N2 fixation, converting atmospheric nitrogen into biologically available forms.
• The enzyme's active site, the MoFe7S9C cluster (FeMo cluster), cycles through eight intermediate states (E0-E7) during catalysis.
• Nitrogen (N2) binding occurs at the E4 state, with hydrogen (H2) as a known byproduct, though its formation can be an unproductive side reaction.

Purpose of the Study:

• Investigate the formation of H2 as a side reaction in nitrogenase during the E2-E4 catalytic states.
• Evaluate different structural interpretations of the E2-E4 states using computational methods.
• Determine the kinetic feasibility of H2 formation and proton transfer within the FeMo cluster.

Main Methods:

• Employed combined quantum mechanical and molecular mechanical (QM/MM) calculations.
• Utilized four distinct density-functional theory (DFT) methods: B3LYP, TPSS, r2SCAN, and TPSSh.
• Analyzed various structural models for the E2-E4 intermediate states of the nitrogenase catalytic cycle.

Main Results:

• DFT methods showed significant variation in predicting H2 formation pathways.
• B3LYP calculations suggested H2 cannot form due to favored protonation of the central carbide.
• TPSS, r2SCAN, and TPSSh predicted exothermic H2 formation, particularly in E3 and E4 states, with low activation barriers (29-57 kJ mol-1) for two bridging hydrides.
• Proton transfer between different states of the FeMo cluster is facile, with low activation barriers (12-69 kJ mol-1).

Conclusions:

• H2 formation is kinetically feasible and potentially rapid in E3 and E4 states, exceeding the enzyme's turnover rate.
• The specific bridging hydride configuration in E3/E4 states facilitates rapid H2 formation.
• Efficient proton mobility within the FeMo cluster allows for rapid interconversion of protonation states, influencing reaction pathways.