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Understanding rubredoxin redox sites by density functional theory studies of analogues.

ABSTRACT: Determining the redox energetics of redox site analogues of metalloproteins is essential in unraveling the various contributions to electron transfer properties of these proteins. Since studies of the [4Fe-4S] analogues show that the energies are dependent on the ligand dihedral angles, broken symmetry density functional theory (BS-DFT) with the B3LYP functional and double-? basis sets calculations of optimized geometries and electron detachment energies of [1Fe] rubredoxin analogues are compared to crystal structures and gas-phase photoelectron spectroscopy data, respectively, for [Fe(SCH(3))(4)](0/1-/2-), [Fe(S(2)-o-xyl)(2)](0/1-/2-), and Na(+)[Fe(S(2)-o-xyl)(2)](1-/2-) in different conformations. In particular, the study of Na(+)[Fe(S(2)-o-xyl)(2)](1-/2-) is the only direct comparison of calculated and experimental gas phase detachment energies for the 1-/2- couple found in the rubredoxins. These results show that variations in the inner sphere energetics by up to ?0.4 eV can be caused by differences in the ligand dihedral angles in either or both redox states. Moreover, these results indicate that the protein stabilizes the conformation that favors reduction. In addition, the free energies and reorganization energies of oxidation and reduction as well as electrostatic potential charges are calculated, which can be used as estimates in continuum electrostatic calculations of electron transfer properties of [1Fe] proteins.

SUBMITTER: Luo Y

PROVIDER: S-EPMC3443601 | biostudies-literature | 2012 Sep

REPOSITORIES: biostudies-literature

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Understanding rubredoxin redox sites by density functional theory studies of analogues.

Luo Yan Y Niu Shuqiang S Ichiye Toshiko T

The journal of physical chemistry. A 20120827 35

Determining the redox energetics of redox site analogues of metalloproteins is essential in unraveling the various contributions to electron transfer properties of these proteins. Since studies of the [4Fe-4S] analogues show that the energies are dependent on the ligand dihedral angles, broken symmetry density functional theory (BS-DFT) with the B3LYP functional and double-ζ basis sets calculations of optimized geometries and electron detachment energies of [1Fe] rubredoxin analogues are compare ...[more]

PMID: 22881577

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Project description:This research investigated the thermodynamic favorability and resulting structures for chemical adsorption of trichloroethylene (TCE) to metallic iron using periodic density functional theory (DFT). Three initial TCE positions having the plane defined by HCC atoms parallel to the iron surface resulted in formation of three different chemisorption complexes between carbon atoms in TCE and the iron surface. The Cl-bridge initial configuration with the HCC plane of TCE perpendicular to the iron surface did not result in C-Fe bond formation. The most energetically favorable complex formed at the C-bridge site where the initial configuration had the C=C bond in TCE at a bridge site between adjacent iron atoms. In the C-bridge complex, one C atom formed two a bonds to different Fe atoms, while the second C atom formed a sigma bond with a second Fe atom. Surface complexation atthe C-bridge site resulted in scission of all three C-Cl bonds and also resulted in a shortening of the C==C bond to a distance intermediate between a double and a triple bond. Initial configurations with the C==C bond adsorbed at top or hollow sites on the iron surface resulted in formation of C-Fe a bonds between a single C and two adjacent Fe atoms, and the scission of only two C==Cl bonds. Bond angles and bond lengths indicated that there were no changes in bond order of the C==C bond for top and hollow adsorption. Chemisorption at the C-bridge site had an activation energy of 49 kJ/mol and an early transition state where all three C-CI bonds were activated. The early transition state and the loss of all three Cl atoms upon chemisorption are consistent with most experimental observations that TCE undergoes complete dechlorination in one interaction with the iron surface. The absence of chemisorption and scission of only two C--Cl bonds at the Cl-bridge site is consistent with experimental observations that trace amounts of chloroacetylene may also be produced from reactions of TCE with iron.

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Understanding rubredoxin redox sites by density functional theory studies of analogues.

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Understanding rubredoxin redox sites by density functional theory studies of analogues.

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