Jump to main content
Jump to site search

Issue 5, 2019
Previous Article Next Article

Extremely large differences in DFT energies for nitrogenase models

Author affiliations

Abstract

Nitrogenase is the only enzyme that can cleave the triple bond in N2, making nitrogen avaiable for other organisms. It contains a complicated MoFe7S9C(homocitrate) cluster in its active site. Many computational studies with density-functional theory (DFT) of the nitrogenase enzyme have been presented, but they do not show any consensus – they do not even agree where the first four protons should be added, forming the central intermediate E4. We show that the prime reason for this is that different DFT methods give relative energies that differ by almost 600 kJ mol−1 for different protonation states. This is 4–30 times more than what is observed for other systems. The reason for this is that in some structures, the hydrogens bind to sulfide or carbide ions as protons, whereas in other structures they bind to the metals as hydride ions, changing the oxidation state of the metals, as well as the Fe–C, Fe–S and Fe–Fe distances. The energies correlate with the amount of Hartree–Fock exchange in the method, indicating a variation in the amount of static correlation in the structures. It is currently unclear which DFT method gives the best results for nitrogenase. We show that non-hybrid DFT functionals and TPSSh give the most accurate structures of the resting active site, whereas B3LYP and PBE0 give the best H2 dissociation energies. However, no DFT method indicates that a structure of E4 with two bridging hydride ions is lowest in energy, as spectroscopic experiments indicate.

Graphical abstract: Extremely large differences in DFT energies for nitrogenase models

Back to tab navigation

Supplementary files

Publication details

The article was received on 08 Nov 2018, accepted on 20 Dec 2018 and first published on 21 Dec 2018


Article type: Paper
DOI: 10.1039/C8CP06930A
Phys. Chem. Chem. Phys., 2019,21, 2480-2488
  • Open access: Creative Commons BY license
  •   Request permissions

    Extremely large differences in DFT energies for nitrogenase models

    L. Cao and U. Ryde, Phys. Chem. Chem. Phys., 2019, 21, 2480
    DOI: 10.1039/C8CP06930A

    This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. Material from this article can be used in other publications provided that the correct acknowledgement is given with the reproduced material.

    Reproduced material should be attributed as follows:

    • For reproduction of material from NJC:
      [Original citation] - Published by The Royal Society of Chemistry (RSC) on behalf of the Centre National de la Recherche Scientifique (CNRS) and the RSC.
    • For reproduction of material from PCCP:
      [Original citation] - Published by the PCCP Owner Societies.
    • For reproduction of material from PPS:
      [Original citation] - Published by The Royal Society of Chemistry (RSC) on behalf of the European Society for Photobiology, the European Photochemistry Association, and RSC.
    • For reproduction of material from all other RSC journals:
      [Original citation] - Published by The Royal Society of Chemistry.

    Information about reproducing material from RSC articles with different licences is available on our Permission Requests page.

Search articles by author

Spotlight

Advertisements