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Putative reaction mechanism of nitrogenase with a half-dissociated S2B ligand

Jiang, Hao LU orcid and Ryde, Ulf LU orcid (2024) In Dalton Transactions 53(27). p.11500-11513
Abstract
We have studied whether dissociation of the S2B sulfide ligand from one of its two coordinating Fe ions may affect the later parts of the reaction mechanism of nitrogenase. Such dissociation has been shown to be favourable for the E2–E4 states in the reaction mechanism, but previous studies have assumed that S2B either remains bridging or has fully dissociated from the active-site FeMo cluster. We employ combined quantum mechanical and molecular mechanical (QM/MM) calculations with two density-functional theory methods, r2SCAN and TPSSh. To make dissociation of S2B possible, we have added a proton to this group throughout the reaction. We study the reaction starting from the E4 state with... (More)
We have studied whether dissociation of the S2B sulfide ligand from one of its two coordinating Fe ions may affect the later parts of the reaction mechanism of nitrogenase. Such dissociation has been shown to be favourable for the E2–E4 states in the reaction mechanism, but previous studies have assumed that S2B either remains bridging or has fully dissociated from the active-site FeMo cluster. We employ combined quantum mechanical and molecular mechanical (QM/MM) calculations with two density-functional theory methods, r2SCAN and TPSSh. To make dissociation of S2B possible, we have added a proton to this group throughout the reaction. We study the reaction starting from the E4 state with N2H2 bound to the cluster. Our results indicate that half-dissociation of S2B is unfavourable in most steps of the reaction mechanism. We observe favourable half-dissociation of S2B only when NH or NH2 is bound to the cluster, bridging Fe2 and Fe6. However, the former state is most likely not involved in the reaction mechanism and the latter state is only an intermittent intermediate of the E7 state. Therefore, half-dissociation of S2B seems to play only a minor role in the later parts of the reaction mechanism of nitrogenase. Our suggested mechanism with a protonated S2B is alternating (the two N atoms of the substrate is protonated in an alternating manner) and the substrate prefers to bind to Fe2, in contrast to the preferred binding to Fe6 observed when S2B is unprotonated and bridging Fe2 and Fe6. (Less)
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author
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type
Contribution to journal
publication status
published
subject
in
Dalton Transactions
volume
53
issue
27
pages
14 pages
publisher
Royal Society of Chemistry
ISSN
1477-9234
DOI
10.1039/D4DT00937A
language
English
LU publication?
yes
id
ae90264e-d759-4a99-8eef-43374b8500a5
date added to LUP
2024-07-11 09:01:46
date last changed
2024-08-08 11:19:25
@article{ae90264e-d759-4a99-8eef-43374b8500a5,
  abstract     = {{We have studied whether dissociation of the S2B sulfide ligand from one of its two coordinating Fe ions may affect the later parts of the reaction mechanism of nitrogenase. Such dissociation has been shown to be favourable for the E<sub>2</sub>–E<sub>4</sub> states in the reaction mechanism, but previous studies have assumed that S2B either remains bridging or has fully dissociated from the active-site FeMo cluster. We employ combined quantum mechanical and molecular mechanical (QM/MM) calculations with two density-functional theory methods, r<sup>2</sup>SCAN and TPSSh. To make dissociation of S2B possible, we have added a proton to this group throughout the reaction. We study the reaction starting from the E<sub>4</sub> state with N<sub>2</sub>H<sub>2</sub> bound to the cluster. Our results indicate that half-dissociation of S2B is unfavourable in most steps of the reaction mechanism. We observe favourable half-dissociation of S2B only when NH or NH<sub>2</sub> is bound to the cluster, bridging Fe2 and Fe6. However, the former state is most likely not involved in the reaction mechanism and the latter state is only an intermittent intermediate of the E<sub>7</sub> state. Therefore, half-dissociation of S2B seems to play only a minor role in the later parts of the reaction mechanism of nitrogenase. Our suggested mechanism with a protonated S2B is alternating (the two N atoms of the substrate is protonated in an alternating manner) and the substrate prefers to bind to Fe2, in contrast to the preferred binding to Fe6 observed when S2B is unprotonated and bridging Fe2 and Fe6.}},
  author       = {{Jiang, Hao and Ryde, Ulf}},
  issn         = {{1477-9234}},
  language     = {{eng}},
  month        = {{06}},
  number       = {{27}},
  pages        = {{11500--11513}},
  publisher    = {{Royal Society of Chemistry}},
  series       = {{Dalton Transactions}},
  title        = {{Putative reaction mechanism of nitrogenase with a half-dissociated S2B ligand}},
  url          = {{http://dx.doi.org/10.1039/D4DT00937A}},
  doi          = {{10.1039/D4DT00937A}},
  volume       = {{53}},
  year         = {{2024}},
}