Skip to main content

Lund University Publications

LUND UNIVERSITY LIBRARIES

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

Jiang, Hao LU orcid and Ryde, Ulf LU orcid (2022) In Chemistry - A European Journal 28(14).
Abstract

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,... (More)

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.

(Less)
Please use this url to cite or link to this publication:
author
and
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
alternating mechanism, homocitrate, nitrogen fixation, nitrogenase, QM/MM
in
Chemistry - A European Journal
volume
28
issue
14
article number
e202103933
publisher
Wiley-Blackwell
external identifiers
  • scopus:85124164147
  • pmid:35006641
ISSN
0947-6539
DOI
10.1002/chem.202103933
language
English
LU publication?
yes
id
c8059d64-2830-4692-954e-babc3a2f3e2a
date added to LUP
2022-05-16 15:12:41
date last changed
2024-06-21 17:22:36
@article{c8059d64-2830-4692-954e-babc3a2f3e2a,
  abstract     = {{<p>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 E<sub>4</sub> state, we start from a state where N<sub>2</sub> is bound to the cluster and is protonated to N<sub>2</sub>H<sub>2</sub>, after dissociation of H<sub>2</sub>. We show that the reaction follows an alternating mechanism with HNNH (possibly protonated to HNNH<sub>2</sub>) and H<sub>2</sub>NNH<sub>2</sub> as intermediates and the two NH<sub>3</sub> products dissociate at the E<sub>7</sub> and E<sub>8</sub> levels. For all intermediates, coordination to Fe6 is preferred, but for the E<sub>4</sub> and E<sub>8</sub> intermediates, binding to Fe2 is competitive. For the E<sub>4</sub>, E<sub>5</sub> and E<sub>7</sub> intermediates we find that the substrate may abstract a proton from the hydroxy group of the homocitrate ligand of the FeMo cluster, thereby forming HNNH<sub>2</sub>, H<sub>2</sub>NNH<sub>2</sub> and NH<sub>3</sub> 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.</p>}},
  author       = {{Jiang, Hao and Ryde, Ulf}},
  issn         = {{0947-6539}},
  keywords     = {{alternating mechanism; homocitrate; nitrogen fixation; nitrogenase; QM/MM}},
  language     = {{eng}},
  month        = {{03}},
  number       = {{14}},
  publisher    = {{Wiley-Blackwell}},
  series       = {{Chemistry - A European Journal}},
  title        = {{Thermodynamically Favourable States in the Reaction of Nitrogenase without Dissociation of any Sulfide Ligand}},
  url          = {{http://dx.doi.org/10.1002/chem.202103933}},
  doi          = {{10.1002/chem.202103933}},
  volume       = {{28}},
  year         = {{2022}},
}