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Although the dinuclear center (DNC) of the resting oxidized "as-isolated" cytochrome c oxidase (CcO) is not a catalytically active state, its detailed structure, especially the nature of the bridging species between the Fea33+ and CuB2+ metal sites, is still both relevant and unsolved. Recent crystallographic work has shown an extended electron density for a peroxide type dioxygen species (O1-O2) bridging the Fea3 and CuB centers. In this paper, our density functional theory (DFT) calculations show that the observed peroxide type electron density between the two metal centers is most likely a mistaken analysis due to overlap of the electron density of a water molecule located at different positions between apparent O1 and O2 sites in DNCs of different CcO molecules with almost the same energy. Because the diffraction pattern and the resulting electron density map represent the effective long-range order averaged over many molecules and unit cells in the X-ray structure, this averaging can lead to an apparent observed superposition of different water positions between the Fea33+ and CuB2+ metal sites.

Although the dinuclear center (DNC) of the resting oxidized “as-isolated” cytochrome c oxidase (CcO) is not a catalytically active state, its detailed structure, especially the nature of the bridging species between the Fea33+ and CuB2+ metal sites, is still both relevant and unsolved. Recent crystallographic work has shown an extended electron density for a peroxide type dioxygen species (O1–O2) bridging the Fea3 and CuB centers. In this paper, our density functional theory (DFT) calculations show that the observed peroxide type electron density between the two metal centers is most likely a mistaken analysis due to overlap of the electron density of a water molecule located at different positions between apparent O1 and O2 sites in DNCs of different CcO molecules with almost the same energy. Because the diffraction pattern and the resulting electron density map represent the effective long-range order averaged over many molecules and unit cells in the X-ray structure, this averaging can lead to an apparent observed superposition of different water positions between the Fea33+ and CuB2+ metal sites., X-ray crystal structures have shown an extended electron density for a dioxygen species (O1−O2) bridging the Fea3 and CuB centers of the oxidized resting state of cytochrome c oxidase (CcO). Our current DFT calculations show that the observed peroxide type electron density is most likely an overlap of the electron density of a water molecule located at different positions between O1 and O2 in different CcO molecules with almost the same energy.

Broken-symmetry density functional calculations have been performed on the [Fea34+,CuB2+] state of the dinuclear center (DNC) for the PR → F part of the catalytic cycle of ba3 cytochrome c oxidase (CcO) from Thermus thermophilus (Tt), using the OLYP-D3-BJ functional. The calculations show that the movement of the H2O molecules in the DNC affects the pKa values of the residue side chains of Tyr237 and His376+, which are crucial for proton transfer/pumping in ba3 CcO from Tt. The calculated lowest energy structure of the DNC in the [Fea34+,CuB2+] state (state F) is of the form Fea34+═O2–···CuB2+, in which the H2O ligand that resulted from protonation of the OH– ligand in the PR state is dissociated from the CuB2+ site. The calculated Fea34+═O2– distance in F (1.68 A) is 0.03 A longer than that in PR (1.65 A), which can explain the different Fea34+═O2– stretching modes in P (804 cm–1) and F (785 cm–1) identified by resonance Raman experiments. In this F state, the CuB2+···O2– (ferryl–oxygen) distance is only...

Broken-symmetry density functional calculations have been performed on the [Fea34+, CuB2+] state of the dinuclear center (DNC) for the PR → F part of the catalytic cycle of ba3 cytochrome c oxidase (CcO) from Thermus thermophilus (Tt), using OLYP-D3-BJ functional. The calculations show that the movement of the H2O molecules in the DNC affects the pKa values of the residue side chains of Tyr237 and His376+, which are crucial for proton transfer/pumping in ba3 CcO from Tt. The calculated lowest energy structure of the DNC in the [Fea34+, CuB2+] state (state F) is of the form Fea34+=O2−⋯CuB2+, in which the H2O ligand that resulted from protonation of the OH− ligand in the PR state is dissociated from the CuB2+ site. The calculated Fea34+=O2− distance in F (1.68 Å) is by 0.03 Å longer than that in PR (1.65 Å), which can explain the different Fea34+=O2− stretching modes in P (804 cm−1) and F (785 cm−1) identified by resonance Raman experiments. In this F state, the CuB2+⋯O2− (ferryl-oxygen) distance is only around 2.4 Å. Hence the subsequent OH state [Fea33+-OH−-CuB2+] with a μ-hydroxo bridge can be easily formed as shown by our calculations.

After a summary of the problem of coupling electron and proton transfer to proton pumping in cytochrome c oxidase, we present the results of our earlier and recent density functional theory calculations for the dinuclear Fe-a3–CuB reaction center in this enzyme. A specific catalytic reaction wheel diagram is constructed from the calculations, based on the structures and relative energies of the intermediate states of the reaction cycle. A larger family of tautomers/protonation states is generated compared to our earlier work, and a new lowest-energy pathway is proposed. The entire reaction cycle is calculated for the new smaller model (about 185–190 atoms), and two selected arcs of the wheel are chosen for calculations using a larger model (about 205 atoms). We compare the structural and redox energetics and protonation calculations with available experimental data. The reaction cycle map that we have built is positioned for further improvement and testing against experiment., From density functional theory calculations on the dinuclear Fe-a3−CuB complex (DNC) in a type B bacterial cytochrome c oxidase, we construct a catalytic reaction wheel diagram for the full redox, O2 binding, and proton-transfer cycle. A new low-energy pathway is found. Strong shifts in the dipole moment direction/magnitude over the cycle and associated energy differences indicate that the DNC plays a major role not only in the chemical reaction cycle but also in proton pumping.

Hydrazine nitrosation of [Ru(NO)(py(si)S4)]Br.THF (1) (py(si)S4(2-) = 2,6-bis(3-triphenylsilyl-2-sulfanylphenylthiomethyl)pyridine2-) in methanol/DMF led to the formation of mononuclear ammine complex [Ru(NH3)(py(si)S4)] (2) and N2O, whereas the reaction performed in THF/CH2Cl2/toluene afforded thioether-bridged dinuclear ammine complex [(NH3)Ru(mu-py(si)S4)Ru(py(si)S4)] (3). Compound 2 dimerizes in solution at room temperature to form 3 and is regenerated upon treatment of 3 with NH3. A plausible mechanism for the hydrazine nitrosation of 1 has been proposed. The reaction of 1 with NH3 or N3- does not lead to a nucleophilic attack at the NO+ ligand but to a deprotonation that yields neutral nitrosyl complex [Ru(NO){py(si)S4(H+)}] (4), which is supported by density functional theory calculations.