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Volumn 47, Issue 13, 2008, Pages 6056-6071

Structural and electronic properties of the [FeFe] hydrogenase H-cluster in different redox and protonation states. A DFT investigation

Author keywords

[No Author keywords available]

Indexed keywords

HYDROGENASE; IRON SULFUR PROTEIN; PROTON;

EID: 47949116193     PISSN: 00201669     EISSN: None     Source Type: Journal    
DOI: 10.1021/ic8006298     Document Type: Article
Times cited : (50)

References (104)
  • 4
    • 47949123607 scopus 로고    scopus 로고
    • (d) Cammack, R. Nature 1999, 214, 397.
    • (1999) Nature , vol.214 , pp. 397
    • Cammack, R.1
  • 9
    • 0003723366 scopus 로고    scopus 로고
    • Cammack, R, Frey, M, Robson, R, Eds; London: Taylor and Francis
    • (i) Hydrogen as Fuel - Learning from Nature; Cammack, R., Frey, M., Robson, R., Eds; London: Taylor and Francis, 2001.
    • (2001) Hydrogen as Fuel - Learning from Nature
  • 80
    • 47949088041 scopus 로고    scopus 로고
    • 5- is negative and as large as -7.12 eV, indicating an unstable system. Nevertheless, such a redox state can be computed despite its tendency to lose an electron because of the finite nature of the basis set, which cannot represent the continuum electron and consequently confines electrons in a metastable state.
    • 5- is negative and as large as -7.12 eV, indicating an unstable system. Nevertheless, such a redox state can be computed despite its tendency to lose an electron because of the finite nature of the basis set, which cannot represent the continuum electron and consequently confines electrons in a metastable state.
  • 81
    • 47949090224 scopus 로고    scopus 로고
    • Calculations performed enclosing the H-cluster in a positively charged spherical cage, which produces a shift of all of the occupied orbital energies to negative values, without significantly affecting the molecular geometry and the electron distribution data not shown
    • Calculations performed enclosing the H-cluster in a positively charged spherical cage, which produces a shift of all of the occupied orbital energies to negative values, without significantly affecting the molecular geometry and the electron distribution (data not shown).
  • 85
    • 47949127217 scopus 로고    scopus 로고
    • COSMO has been shown to give accurate results when the quantum cluster charge and polarity is not too high. Again, we have to highlight that the large negative charge of the compounds investigated here is spread over a large due to the size of the molecule. In fact, the apparent surface charge (ASC) generated for each tessera of the cavity surface is even smaller than that generated for less-charged smaller anions data not shown
    • COSMO has been shown to give accurate results when the quantum cluster charge and polarity is not too high. Again, we have to highlight that the large negative charge of the compounds investigated here is spread over a large volume due to the size of the molecule. In fact, the apparent surface charge (ASC) generated for each tessera of the cavity surface is even smaller than that generated for less-charged smaller anions (data not shown).
  • 87
    • 47949114542 scopus 로고    scopus 로고
    • red form of the enzyme. The structure of ref 5 is not available in the PDB, and only the distances reported in Table 1 are given in the original publication. In parenthesis are the distances of the second non- crystallographically related molecule.
    • red form of the enzyme. The structure of ref 5 is not available in the PDB, and only the distances reported in Table 1 are given in the original publication. In parenthesis are the distances of the second non- crystallographically related molecule.
  • 88
    • 47949085664 scopus 로고    scopus 로고
    • The Fed coordination environment in me enzyme is square pyramidal, whereas a trigonal bypiramidal arrangement, with one sulfur atom of the PDT group and one CO ligand in axial positions, is observed in [Fe 6S6]b13, Supporting Information, This arrangement brings the CN ligand coordinated to the Fed atom in the plane defined by the two iron atoms and one sulfur atom of the PDT group, a position which differs significantly from that observed experimentally. A similar arrangement of the Fed(CO)2(CN) group is found in the binuclear complex [Fe2S2(H)]b1 1, in which the Fe4S4 cluster is replaced by the CH3SH group, whereas in the case of [Fe2S 2]b12- the coordination geometry of the Fed atom is more similar to the X-ray structure
    • 2- the coordination geometry of the Fed atom is more similar to the X-ray structure.
  • 89
    • 47949106424 scopus 로고    scopus 로고
    • The Fed atom in [Fe6S6]b 43- and in [Fe6S6]b 403, as well as in the binuclear model complexes [Fe 2S2(H)]b4-401- and [Fe 2S2]b4-402- assumes a square pyramidal configuration, with the CN ligand moving in the plane defined by the two sulfur atoms of PDT and the equatorial CO, as observed in the enzyme
    • 2- assumes a square pyramidal configuration, with the CN ligand moving in the plane defined by the two sulfur atoms of PDT and the equatorial CO, as observed in the enzyme.
  • 94
    • 47949121447 scopus 로고    scopus 로고
    • In fact, in addition to the two broad peaks in the region -6/-5 eV, assigned to the majority spin Fe(3d) orbitals, several other peaks at higher energies are observed. The peaks assigned to S(3p) orbitals are also distributed along the entire DOS profile. In particular, two intense peaks assigned to S* (3p) orbitals occur in the same region of the majority spin Fe(3d) orbitals, 6/-5 eV, whereas Scys(3p) orbitals mainly contribute to the energy levels in two regions centered at about -4.0 and -3.0 eV
    • cys(3p) orbitals mainly contribute to the energy levels in two regions centered at about -4.0 and -3.0 eV.
  • 96
    • 47949117516 scopus 로고    scopus 로고
    • 1 state.
    • 1 state.
  • 97
    • 47949125062 scopus 로고    scopus 로고
    • As discussed in Computational Details, BS states are not pure spin states. Correspondingly, the energy of a BS state does not correspond to the energy of the ground state of the molecule. However, the groundstate energy can be obtained by using spin-projection techniques
    • As discussed in Computational Details, BS states are not pure spin states. Correspondingly, the energy of a BS state does not correspond to the energy of the ground state of the molecule. However, the groundstate energy can be obtained by using spin-projection techniques.
  • 98
    • 47949101975 scopus 로고    scopus 로고
    • Also, the DOS profile of [Fe6S6]b4 4- clearly differs from that of [Fe6S6]b 43- in the region near the Fermi level. In fact, for the former, the DOS at the Fermi level is entirely assigned to the [2Fe]H cluster, whereas the contribution of Fe4S4 falls to zero part c of Figure 3, panels II and III, The opposite holds true for [Fe 6S6]b43, The DOS profile of the Fe4S4 cluster in [Fe6S6]b 44- differs from that of [Fe6S 6]b43- also at lower energies, probably due to its partial reduction
    • 3- also at lower energies, probably due to its partial reduction.
  • 99
    • 47949116643 scopus 로고    scopus 로고
    • The near degeneracy of highest occupied and lowest unoccupied orbitals may suggest that the triple state (S, 1) could be more stable than the singlet one S, 0, However, the calculated energy of the triplet state in its optimum geometry is larger than that of the singlet
    • The near degeneracy of highest occupied and lowest unoccupied orbitals may suggest that the triple state (S = 1) could be more stable than the singlet one (S = 0). However, the calculated energy of the triplet state in its optimum geometry is larger than that of the singlet.
  • 100
    • 47949107984 scopus 로고    scopus 로고
    • H moiety is in the oxidized state [Fe(I), Fe(II)], and the two unpaired electrons are antiferromagnetically coupled (data not shown).
    • H moiety is in the oxidized state [Fe(I), Fe(II)], and the two unpaired electrons are antiferromagnetically coupled (data not shown).
  • 101
    • 47949123606 scopus 로고    scopus 로고
    • For [Fe6S6]b45, the DOS profile of the [2Fe]H cluster (part e of Figure S1, panel III) is similar to that of [Fe6S6]B44- but shifted to lower energy with respect to the Fermi level. As expected by the change in the redox state, the DOS profile of the Fe4S4 cluster differs significantly from that of [Fe6S6]b 4- or [Fe6S6]b3, part e of Figure S1, panel II
    • 3- (part e of Figure S1, panel II).
  • 102
    • 47949098603 scopus 로고    scopus 로고
    • H cluster (manuscript in preparation).
    • H cluster (manuscript in preparation).
  • 103
    • 47949107985 scopus 로고    scopus 로고
    • The DOS profile of the Fe4S4 cluster is very similar to that calculated for [Fe6S6]b3, further indicating that in H2[Fe6S6]b 3- the electronic configuration of the Fe4S4 cluster is not affected by H2 binding. On the other hand, some differences are observed for the DOS of the [2Fe]H cluster. In particular, the orbital containing the unpaired electron rises in energy and becomes the highest occupied orbital
    • H cluster. In particular, the orbital containing the unpaired electron rises in energy and becomes the highest occupied orbital.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.