Critical computational analysis illuminates the reductive-elimination mechanism that activates nitrogenase for N 2 reduction

Raugei, Simone; Seefeldt, Lance C.; Hoffman, Brian M.

doi:10.1073/pnas.1810211115

Title: Critical computational analysis illuminates the reductive-elimination mechanism that activates nitrogenase for N ₂ reduction

Journal Article · Wed Oct 24 00:00:00 EDT 2018 · Proceedings of the National Academy of Sciences of the United States of America

DOI:https://doi.org/10.1073/pnas.1810211115· OSTI ID:1478700

Raugei, Simone ^[1]; Seefeldt, Lance C. ^[2];

^[3]

Physical and Computational Sciences Directorate, Pacific Northwestern National Laboratory, Richland, WA 99352,
Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322,
Department of Chemistry, Northwestern University, Evanston, IL 60208

Recent spectroscopic, kinetic, photophysical, and thermodynamic measurements show activation of nitrogenase for N₂→ 2NH₃ reduction involves the reductive elimination (re) of H₂from two [Fe–H–Fe] bridging hydrides bound to the catalytic [7Fe–9S–Mo–C–homocitrate] FeMo-cofactor (FeMo-co). These studies rationalize the Lowe–Thorneley kinetic scheme’s proposal of mechanistically obligatory formation of one H₂for each N₂reduced. They also provide an overall framework for understanding the mechanism of nitrogen fixation by nitrogenase. However, they directly pose fundamental questions addressed computationally here. We here report an extensive computational investigation of the structure and energetics of possible nitrogenase intermediates using structural models for the active site with a broad range in complexity, while evaluating a diverse set of density functional theory flavors. (i) This shows that to prevent spurious disruption of FeMo-co having accumulated 4[e^-/H⁺] it is necessary to include: all residues (and water molecules) interacting directly with FeMo-co via specific H-bond interactions; nonspecific local electrostatic interactions; and steric confinement. (ii) These calculations indicate an important role of sulfide hemilability in the overall conversion of E₀to a diazene-level intermediate. (iii) Perhaps most importantly, they explain (iiia) how the enzyme mechanistically couples exothermic H₂formation to endothermic cleavage of the N≡N triple bond in a nearly thermoneutral re/oxidative-addition equilibrium, (iiib) while preventing the “futile” generation of two H₂without N₂reduction: hydride re generates an H₂complex, but H₂is only lost when displaced by N₂, to form an end-on N₂complex that proceeds to a diazene-level intermediate.

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Research Organization:: Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH); National Science Foundation (NSF)

Grant/Contract Number:: AC05-76RL01830/FWP66476; SC0010687; AC05-76RL01830; 0/FWP66476; GM 111097; MCB 1515981

OSTI ID:: 1478700

Alternate ID(s):: OSTI ID: 1710224

Report Number(s):: PNNL-SA-130353

Journal Information:: Proceedings of the National Academy of Sciences of the United States of America, Journal Name: Proceedings of the National Academy of Sciences of the United States of America Vol. 115 Journal Issue: 45; ISSN 0027-8424

Publisher:: Proceedings of the National Academy of SciencesCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 88 works

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37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
nitrogenase
mechanism
DFT
computation

Title: Critical computational analysis illuminates the reductive-elimination mechanism that activates nitrogenase for N 2 reduction

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Title: Critical computational analysis illuminates the reductive-elimination mechanism that activates nitrogenase for N ₂ reduction