Putative reaction mechanism of nitrogenase after dissociation of a sulfide ligand

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Abstract

We have investigated the implications of the recent crystallographic findings that the m2-bridging S2B sulfide ligand may reversibly dissociate from the active-site FeMo cluster of nitrogenase. We show with combined quantum mechanical and molecular mechanical (QM/MM) calculations that once S2B has dis- sociated, N2 may bind in that position and can be protonated to two NH3 groups by thermodynamically favourable steps. The substrate forms hydrogen bonds with two protein ligands, Gln-191 and His-195. For all steps, we have studied three possible protonation states of His-195 (protonated on either ND1, NE2 or both). We find that the thermodynamically favoured path involves an end-on NNH2 structure, a mixed side-on/end-on H2NNH structure, a side-on H2NNH2 structure, a bridging NH2 structure and a bridging NH3 structure. In all cases, His-195 seems to be protonated on the NE2 atom. Dissociation of the NH3 pro- duct is often unfavourable and requires either further reduction or protonation of the cluster or rebinding of S2B. In conclusion, our calculations show that dissociation of S2B gives rise to a natural binding and reaction site for nitrogenase, between the Fe2 and Fe6 atoms, which can support an alternating reaction mechanism with favourable energetics.

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Subject classification (UKÄ) – MANDATORY

  • Theoretical Chemistry

Keywords

  • Nitrogenase, QM/MM, S2B dissociation, Nitrogen fixation, Alternating or distal reaction mechanism
Original languageEnglish
Pages (from-to)247–259
Number of pages13
JournalJournal of Catalysis
Volume391
Publication statusPublished - 2020 Sep 1
Publication categoryResearch
Peer-reviewedYes

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