Electronic Structure of Cytochrome f and Its Oxidation Potential

Abstract

The electronic structure of turnip cytochrome f has been investigated by CNDO method. The crystallographic coordinates were obtained from the Protein Data Bank at Brookhaven National Laboratory. The protein chain was truncated to separate the entity Cyt-f that retains the essential structural features of cytochrome f. Thus Cyt-f consists of the basic heme unit, one water molecule hydrogen bonded to a carboxylic acid substituent of the heme unit, and one tyrosine residue and one histidine residue along the axial positions on top and below the iron atom, respectively. The central metal atom's orbital angular momenta are found to be fully quenched. The HOMOs and the first few LUMOs are basically the π orbitals of the porphyrin macrocycle. Since the latter orbitals are quasi-degenerate, the Fe complex always has a high-spin ground state. Both heme and Cyt-f have pentet (2S + 1 = 5) ground states. The CNDO calculations indicate that the quartet (2S + 1 = 4) state is slightly more stable than the hextet (2S + 1 = 6) state for the oxidized forms of heme and Cyt-f; but the relative stability is so small that even the inclusion of only the monatomic exchange integrals would lead the spin hextets to clearly emerge as the ground states of respective cations. Hence the redox potentials were calculated with the pentet states of the reduced forms and the hextet states of the oxidized species. The reduction potential calculated for Cyt-f + in an aqueous solution at pH 7 is 0.295 V at 25 °C. This is in excellent agreement with the experimentally determined midpoint potential 0.365 V for the reduction of cytochrome f cation. The calculated potential for the species in the condensed phase of thylakoid is 0.398 V which agrees with the placement of cytochrome f in Z-scheme. Significant deviations in calculated potentials can be observed in the absence of histidine and tyrosine residues, which indicates the importance of these axial ligands in the evolution of the redox properties of cytochrome f.

Electronic Structure of a Rieske Iron−Sulfur Complex and the Calculation of Its Reduction Potential

“…In our previous work 8 we have shown that the change in free energy ∆G 1/2H2fH + (aq) calculated by the CNDO/2 method for the process is 5.133 eV at 298.15 K at pH 7. This value is in good agreement with the experimentally observed values and has been used throughout in our calculations.…”

“…[3][4][5]12 We relied on the CNDO calculation because of the reasons mentioned in our earlier work. 8 Our CNDO program had been modified for the estimation of medium polarization effects 12 in terms of the Born term and Onsager's energy correction due to the feedback field. We used the G92W software 13 to compute the Onsager radius.…”

“…The CNDO/2 and INDO methods yield good values of thermochemical properties. The INDO method is known to yield very accurate free energy changes, − but the CNDO method nevertheless yields reasonably good values. − , We relied on the CNDO calculation because of the reasons mentioned in our earlier work . Our CNDO program had been modified for the estimation of medium polarization effects 12 in terms of the Born term and Onsager's energy correction due to the feedback field.…”

“…As part of our ongoing investigations on the redox processes occurring in the Z-scheme, − we have calculated the redox potential of the Rieske iron−sulfur protein by using the CNDO/2 method. The crystallographic molecular structure selected for our quantum chemical investigation is described in section 2.…”

Excited-State Hydrogen Bonding Dynamics of Hydrogen-Bonded Clusters Formed by of Coumarin Derivatives in Aqueous Solution: A Time-Dependent Density Functional Theory Study

“…In the 1970s, Ab initio quantum-chemical calculations on hydrogen-bonded complexes were performed for the first time by Janet Del Bene et al [17][18][19], providing a first-principles basis for a description of the hydrogen bond. What's more, the semiempirical methods such as CNDO and INDO were also used widely to study excited-state hydrogen bonding in the past years, providing a wealth of important information about the nature of the hydrogen bond [20][21][22][23][24]. In very recent years, the changes of the hydrogen bonds between the molecules and the solvents upon photoexcitation have been figured out by a variety of theoretical and experimental methods [1,[10][11][12][13][14].…”