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

Abstract

Recent spectroscopic, kinetic, photophysical, and thermodynamic measurements show activation of nitrogenase for N 2 → 2NH 3 reduction involves the reductive elimination ( re ) of H 2 from 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 H 2 for each N 2 reduced. 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 E 0 to a diazene-level intermediate. ( iii ) Perhaps most importantly, they explainmore » ( iiia ) how the enzyme mechanistically couples exothermic H 2 formation 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 H 2 without N 2 reduction: hydride re generates an H 2 complex, but H 2 is only lost when displaced by N 2 , to form an end-on N 2 complex that proceeds to a diazene-level intermediate.« less

Authors:
; ; ORCiD logo
Publication Date:
Research Org.:
Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES); National Institutes of Health (NIH); National Science Foundation (NSF)
OSTI Identifier:
1478700
Alternate Identifier(s):
OSTI ID: 1710224
Report Number(s):
PNNL-SA-130353
Journal ID: ISSN 0027-8424; /pnas/115/45/E10521.atom
Grant/Contract Number:  
AC05-76RL01830/FWP66476; SC0010687; AC05-76RL01830; 0/FWP66476; GM 111097; MCB 1515981
Resource Type:
Journal Article: Published Article
Journal Name:
Proceedings of the National Academy of Sciences of the United States of America
Additional Journal Information:
Journal Name: Proceedings of the National Academy of Sciences of the United States of America Journal Volume: 115 Journal Issue: 45; Journal ID: ISSN 0027-8424
Publisher:
Proceedings of the National Academy of Sciences
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; nitrogenase; mechanism; DFT; computation

Citation Formats

Raugei, Simone, Seefeldt, Lance C., and Hoffman, Brian M.. Critical computational analysis illuminates the reductive-elimination mechanism that activates nitrogenase for N 2 reduction. United States: N. p., 2018. Web. doi:10.1073/pnas.1810211115.
Raugei, Simone, Seefeldt, Lance C., & Hoffman, Brian M.. Critical computational analysis illuminates the reductive-elimination mechanism that activates nitrogenase for N 2 reduction. United States. https://doi.org/10.1073/pnas.1810211115
Raugei, Simone, Seefeldt, Lance C., and Hoffman, Brian M.. 2018. "Critical computational analysis illuminates the reductive-elimination mechanism that activates nitrogenase for N 2 reduction". United States. https://doi.org/10.1073/pnas.1810211115.
@article{osti_1478700,
title = {Critical computational analysis illuminates the reductive-elimination mechanism that activates nitrogenase for N 2 reduction},
author = {Raugei, Simone and Seefeldt, Lance C. and Hoffman, Brian M.},
abstractNote = {Recent spectroscopic, kinetic, photophysical, and thermodynamic measurements show activation of nitrogenase for N 2 → 2NH 3 reduction involves the reductive elimination ( re ) of H 2 from 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 H 2 for each N 2 reduced. 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 E 0 to a diazene-level intermediate. ( iii ) Perhaps most importantly, they explain ( iiia ) how the enzyme mechanistically couples exothermic H 2 formation 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 H 2 without N 2 reduction: hydride re generates an H 2 complex, but H 2 is only lost when displaced by N 2 , to form an end-on N 2 complex that proceeds to a diazene-level intermediate.},
doi = {10.1073/pnas.1810211115},
url = {https://www.osti.gov/biblio/1478700}, journal = {Proceedings of the National Academy of Sciences of the United States of America},
issn = {0027-8424},
number = 45,
volume = 115,
place = {United States},
year = {2018},
month = {10}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at https://doi.org/10.1073/pnas.1810211115

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Cited by: 16 works
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Works referenced in this record:

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Works referencing / citing this record:

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journal, January 2019


The mechanism for nitrogenase including all steps
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Complete cleavage of the N≡N triple bond by Ta 2 N + via degenerate ligand exchange at ambient temperature: A perfect catalytic cycle
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A Systematic DFT Approach for Studying Mechanisms of Redox Active Enzymes
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