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Volumn 113, Issue 19, 2009, Pages 6866-6872

Significant change in electronic structures of heme upon reduction by strong coulomb repulsion between Fe d electrons

Author keywords

[No Author keywords available]

Indexed keywords

DENSITY FUNCTIONAL THEORY; ELECTRONIC STRUCTURE; ELECTRONS; HEMOGLOBIN;

EID: 67650069446     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp809405s     Document Type: Article
Times cited : (6)

References (43)
  • 26
    • 84906375775 scopus 로고    scopus 로고
    • The RCSB Protein Data Bank (PDB: http://www.pdb.org/), PDB ID 2eij.
    • (b) The RCSB Protein Data Bank (PDB: http://www.pdb.org/), PDB ID 2eij.
  • 27
    • 84906404437 scopus 로고    scopus 로고
    • Codes used in the present work are based on Tokyo Ab initio Program Package (TAPP);
    • (a) Codes used in the present work are based on Tokyo Ab initio Program Package (TAPP);
  • 36
    • 84906389709 scopus 로고    scopus 로고
    • These DFT calculations have been conducted by using the CarrParrinello Molecular Dynamics code (CPMD, Copyright IBM Corp. 1990-2006, Copyright MPI fur Festkörperforschung Stuttgart 1997-2001.).
    • These DFT calculations have been conducted by using the CarrParrinello Molecular Dynamics code (CPMD, Copyright IBM Corp. 1990-2006, Copyright MPI fur Festkörperforschung Stuttgart 1997-2001.).
  • 38
    • 84906389710 scopus 로고    scopus 로고
    • 2, and NFeO. The differences between our calculated results and the experimental and/or theoretical available data are 0.1 - 1.3%, assuring required accuracy in the present calculations.
    • 2, and NFeO. The differences between our calculated results and the experimental and/or theoretical available data are 0.1 - 1.3%, assuring required accuracy in the present calculations.
  • 39
    • 84906389711 scopus 로고    scopus 로고
    • The positions of five terminal H atoms and the H in the hydroxyl group have been kept fixed, according to the CcO crystal structure
    • The positions of five terminal H atoms and the H in the hydroxyl group have been kept fixed, according to the CcO crystal structure.
  • 40
    • 84906389708 scopus 로고    scopus 로고
    • The geometry optimization has been performed until the forces become less than 5.1 × 10-2 eV/Å. During the calculations, the positions of the Cα atom and four terminal H atoms of the imidazole ligands and the C and H atoms in the hydroxyl group have been kept fixed, in accordance with the CcO X-ray structure, 37 The present heme b model has been constructed on the basis of the X-ray structure of the bovine cytochrome b 538 in a similar manner as in the case of the heme a. An orthorhombic supercell was obtained with the following sizes: a, 16.75 Å, b, 17.23 Å, and c, 20.53 Å. The DFT calculations have been performed in the plane-wave basis set with a cutoff energy of 80 Ry by using the PBE exchange-correlation functional and Troullier-Martins norm-conserving pseudopotentials
    • 38 in a similar manner as in the case of the heme a. An orthorhombic supercell was obtained with the following sizes: a ) 16.75 Å, b ) 17.23 Å, and c ) 20.53 Å. The DFT calculations have been performed in the plane-wave basis set with a cutoff energy of 80 Ry by using the PBE exchange-correlation functional and Troullier-Martins norm-conserving pseudopotentials.
  • 42
    • 84906375774 scopus 로고    scopus 로고
    • The PDB ID is 1cyo
    • (b) The PDB ID is 1cyo.
  • 43
    • 84906404436 scopus 로고    scopus 로고
    • 20 of the porphyrin (in accordance with 1-24 IUPAC numbering nomenclature) in heme b, whereas they are perpendicular each other in heme a.
    • 20 of the porphyrin (in accordance with 1-24 IUPAC numbering nomenclature) in heme b, whereas they are perpendicular each other in heme a.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.