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Extremely large differences in DFT energies for nitrogenase models

Cao, Lili LU and Ryde, Ulf LU (2019) In Physical Chemistry Chemical Physics 21(5). p.2480-2488
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... (More)

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.

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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Physical Chemistry Chemical Physics
volume
21
issue
5
pages
9 pages
publisher
Royal Society of Chemistry
external identifiers
  • scopus:85060785641
ISSN
1463-9076
DOI
10.1039/c8cp06930a
language
English
LU publication?
yes
id
03a671db-f730-4482-8916-2f6bfdc0a8de
date added to LUP
2019-02-12 10:48:56
date last changed
2019-03-05 04:32:31
@article{03a671db-f730-4482-8916-2f6bfdc0a8de,
  abstract     = {<p>Nitrogenase is the only enzyme that can cleave the triple bond in N<sub>2</sub>, making nitrogen avaiable for other organisms. It contains a complicated MoFe<sub>7</sub>S<sub>9</sub>C(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 E<sub>4</sub>. We show that the prime reason for this is that different DFT methods give relative energies that differ by almost 600 kJ mol<sup>-1</sup> 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 H<sub>2</sub> dissociation energies. However, no DFT method indicates that a structure of E<sub>4</sub> with two bridging hydride ions is lowest in energy, as spectroscopic experiments indicate.</p>},
  author       = {Cao, Lili and Ryde, Ulf},
  issn         = {1463-9076},
  language     = {eng},
  number       = {5},
  pages        = {2480--2488},
  publisher    = {Royal Society of Chemistry},
  series       = {Physical Chemistry Chemical Physics},
  title        = {Extremely large differences in DFT energies for nitrogenase models},
  url          = {http://dx.doi.org/10.1039/c8cp06930a},
  volume       = {21},
  year         = {2019},
}