Theory of chemical bonds in metalloenzymes XI

Full geometry optimization and vibration analysis of porphyrin iron-oxo species

Mitsuo Shoji, Hiroshi Isobe, Toru Saito, Yasutaka Kitagawa, Shusuke Yamanaka, Takashi Kawakami, Mitsutaka Okumura, Kizashi Yamaguchi

Research output: Contribution to journalArticle

5 Citations (Scopus)

Abstract

Physiochemical properties of compound I and II intermediate states for heme enzymes (catalase, peroxidase, P450) and inorganic models are investigated by hybrid density functional theory. Used theoretical models are composed of an oxoferryl porphyrin and an axial ligand, which are cresol, methylimidazole, methylthiol, and chloride for catalase, peroxidase, P450, and inorganic models, respectively. The oxoferryl bonds are characterized in terms of bond lengths and vibration frequencies. It is found that the oxoferryl bond lengths (the stretching frequency) are shorter (higher) than those of the X-ray crystal structures of enzymes, on the other hand for inorganic models, they are comparable with the experimental values. Spin density distributions showed that radical state at the compound I can be classified into two types: (1) porphyrin radical state and (2) axial ligand radical state. Peroxidase and inorganic model are in the former case and Catalase and P450 are in the later case at the present calculation models. Magnetic interactions between oxoferryl and ligand radical moieties are analyzed by the natural orbital analysis and it is showed that the effective exchange integral (j) values are strongly related to the radical spin density distributions: axial ligand radical tends to increase the antiferromagnetic interaction. Mössbauer shift parameters are also evaluated and it is shown that iron charge states are similar for these models.

Original languageEnglish
Pages (from-to)2950-2965
Number of pages16
JournalInternational Journal of Quantum Chemistry
Volume108
Issue number15
DOIs
Publication statusPublished - 2008
Externally publishedYes

Fingerprint

Chemical bonds
Porphyrins
Vibration analysis
chemical bonds
porphyrins
Iron
iron
vibration
optimization
Geometry
catalase
geometry
Catalase
Peroxidase
Ligands
ligands
cresol
Bond length
density distribution
enzymes

Keywords

  • Compound I
  • Density functional theory
  • Natural orbital
  • Oxoferryl

ASJC Scopus subject areas

  • Condensed Matter Physics
  • Atomic and Molecular Physics, and Optics
  • Physical and Theoretical Chemistry

Cite this

Theory of chemical bonds in metalloenzymes XI : Full geometry optimization and vibration analysis of porphyrin iron-oxo species. / Shoji, Mitsuo; Isobe, Hiroshi; Saito, Toru; Kitagawa, Yasutaka; Yamanaka, Shusuke; Kawakami, Takashi; Okumura, Mitsutaka; Yamaguchi, Kizashi.

In: International Journal of Quantum Chemistry, Vol. 108, No. 15, 2008, p. 2950-2965.

Research output: Contribution to journalArticle

Shoji, Mitsuo ; Isobe, Hiroshi ; Saito, Toru ; Kitagawa, Yasutaka ; Yamanaka, Shusuke ; Kawakami, Takashi ; Okumura, Mitsutaka ; Yamaguchi, Kizashi. / Theory of chemical bonds in metalloenzymes XI : Full geometry optimization and vibration analysis of porphyrin iron-oxo species. In: International Journal of Quantum Chemistry. 2008 ; Vol. 108, No. 15. pp. 2950-2965.
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