JBIC Journal of Biological Inorganic Chemistry

, Volume 11, Issue 3, pp 286–306

Density functional study of the catalytic cycle of nickel–iron [NiFe] hydrogenases and the involvement of high-spin nickel(II)

  • Alejandro Pardo
  • Antonio L. De Lacey
  • Víctor M. Fernández
  • Hua-Jun Fan
  • Yubo Fan
  • Michael B. Hall
Original Paper


In light of recent experiments suggesting high-spin (HS) Ni(II) species in the catalytic cycle of [NiFe] hydrogenase, a series of models of the Ni(II) forms Ni-SI(I,II), SI-CO and Ni-R(I,II,III) were examined in their high-spin states via density functional calculations. Because of its importance in the catalytic cycle, the Ni–C form was also included in this study. Unlike the Ni(II) forms in previous studies, in which a low-spin (LS) state was assumed and a square–planar structure found, the optimized geometries of these HS Ni(II) forms resemble those observed in the crystal structures: a distorted tetrahedral to distorted pyramidal coordination for the NiS4. This resemblance is particularly significant because the LS state is 20–30 kcal/mol less stable than the HS state for the geometry of the crystal structure. If these Ni(II) forms in the enzyme are not high spin, a large change in geometry at the active site is required during the catalytic cycle. Furthermore, only the HS state for the CO-inhibited form SI-CO has CO stretching frequencies that match the experimental results. As in the previous work, these new results show that the heterolytic cleavage reaction of dihydrogen (where H2 is cleaved with the metal acting as a hydride acceptor and a cysteine as the proton acceptor) has a lower energy barrier and is more exothermic when the active site is oxidized to Ni(III). The enzyme models described here are supported by a calibrated correlation of the calculated and measured CO stretching frequencies of the forms of the enzyme. The correlation coefficient for the final set of models of the forms of [NiFe] hydrogenase is 0.8.


[NiFe] hydrogenases Density functional theory High-spin Ni(II) Catalytic cycle Quantum mechanics 

Supplementary material

775_2005_76_MOESM1_ESM.pdf (21 kb)
Supplementary material


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Copyright information

© SBIC 2006

Authors and Affiliations

  • Alejandro Pardo
    • 1
  • Antonio L. De Lacey
    • 1
  • Víctor M. Fernández
    • 1
  • Hua-Jun Fan
    • 2
  • Yubo Fan
    • 2
  • Michael B. Hall
    • 2
  1. 1.Instituto de Catalisis, CSICMadridSpain
  2. 2.Department of ChemistryTexas A&M UniversityCollege StationUSA

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