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Photo Kristoffer Lundgren

Kristoffer Lundgren

Doctoral student

Photo Kristoffer Lundgren

Protonation of Homocitrate and the E1 State of Fe-Nitrogenase Studied by QM/MM Calculations

Author

  • Hao Jiang
  • Kristoffer j. m. Lundgren
  • Ulf Ryde

Summary, in English

Nitrogenase is the only enzyme that can cleave the strong triple bond in N2, making nitrogen available for biological life. There are three isozymes of nitrogenase, differing in the composition of the active site, viz., Mo, V, and Fe-nitrogenase. Recently, the first crystal structure of Fe-nitrogenase was presented. We have performed the first combined quantum mechanical and molecular mechanical (QM/MM) study of Fe-nitrogenase. We show with QM/MM and quantum-refinement calculations that the homocitrate ligand is most likely protonated on the alcohol oxygen in the resting E0 state. The most stable broken-symmetry (BS) states are the same as for Mo-nitrogenase, i.e., the three Noodleman BS7-type states (with a surplus of β spin on the eighth Fe ion), which maximize the number of nearby antiferromagnetically coupled Fe–Fe pairs. For the E1 state, we find that protonation of the S2B μ2 belt sulfide ion is most favorable, 14–117 kJ/mol more stable than structures with a Fe-bound hydride ion (the best has a hydride ion on the Fe2 ion) calculated with four different density-functional theory methods. This is similar to what was found for Mo-nitrogenase, but it does not explain the recent EPR observation that the E1 state of Fe-nitrogenase should contain a photolyzable hydride ion. For the E1 state, many BS states are close in energy, and the preferred BS state differs depending on the position of the extra proton and which density functional is used.

Department/s

  • Computational Chemistry
  • eSSENCE: The e-Science Collaboration

Publishing year

2023-11-21

Language

English

Pages

19433-19445

Publication/Series

Inorganic Chemistry

Volume

62

Issue

48

Document type

Journal article

Publisher

The American Chemical Society (ACS)

Topic

  • Theoretical Chemistry (including Computational Chemistry)
  • Inorganic Chemistry

Status

Published

ISBN/ISSN/Other

  • ISSN: 1520-510X