QM/MM Calculation of the Enzyme Catalytic Cycle Mechanism for Copper- and Zinc-Containing Superoxide Dismutase.

The entire enzyme catalytic mechanism including the electron and the proton transfers of the copper- and zinc-containing extracellular superoxide dismutase (SOD3) was investigated by using QM/MM method. In the first step, the electron transfer from O2·- to SOD3 occurred without the bond formation between the donor and the acceptor and formed the triplet oxygen molecule and reduced SOD3. In the reduced SOD3, the distorted tetrahedral structure of Cu(I) atom was maintained. The reduction of Cu(II) atom induced the protonation of His113, which bridges between the Cu(II) and Zn(II) atoms in the resting state. Since the protonation of His113 broke the bond between Cu(I) and His113, three-coordinated Cu(I) was formed. Further, we suggest the binding of O2·- formed hydrogen peroxide and the resting state after both the Cu reduction and the protonation of His113. The protonation of His113 caused the conformational change of Arg186 located at the entrance of the reactive site. The electrostatic potential surface around the reactive site showed that Arg186 plays an important role as electrostatic guidance for the negatively charged substrates only after the protonation of His113. The rotation of Arg186 switched the proton supply routes via Glu108 or Glu179 for transferring two protons from the bulk solvent.

DFT Study on Enzyme Turnover Including Proton and Electron Transfers of Copper-Containing Nitrite Reductase.

The reaction mechanism of copper-containing nitrite reductase (CuNiR) has been proposed to include two important events, an intramolecular electron transfer and a proton transfer. The two events have been suggested to be coupled, but the order of these events is currently under debate. We investigated the entire enzyme reaction mechanism of nitrite reduction at the T2 Cu site in thermophilic Geobacillus CuNiR from Geobacillus thermodenitrificans NG80-2 (GtNiR) using density functional theory calculations. We found significant conformational changes of His ligands coordinated to the T2 Cu site upon nitrite binding during the catalytic reaction. The reduction potentials and pKa values calculated for the relevant protonation and reduction states show two possible routes, A and B. Reduction of the T2 Cu site in the resting state is followed by endothermic nitrite binding in route A, while exothermic nitrite binding occurs prior to reduction of the T2 Cu site in route B. We concluded that our results support the random-sequential mechanism rather than the ordered mechanism.

DFT Study on Nitrite Reduction Mechanism in Copper-Containing Nitrite Reductase.

Dissimilatory reduction of nitrite by copper-containing nitrite reductase (CuNiR) is an important step in the geobiochemical nitrogen cycle. The proposed mechanisms for the reduction of nitrite by CuNiRs include intramolecular electron and proton transfers, and these two events are understood to couple. Proton-coupled electron transfer is one of the key processes in enzyme reactions. We investigated the geometric structure of bound nitrite and the mechanism of nitrite reduction on CuNiR using density functional theory calculations. Also, the proton transfer pathway, the key residues, and their roles in the reaction mechanism were clarified in this study. In our results, the reduction of T2 Cu site promotes the proton transfer, and the hydrogen bond network around the binding site has an important role not only to stabilize the nitrite binding but also to promote the proton transfer to nitrite.

Dynamic figure eight loop structure of meso-tetraaryl[32]octaphyrins(1.0.1.0.1.0.1.0).

3,3'-Diethyl substituents of the 2,2'-bipyrrole components in meso-tetraaryl[32]octaphyrins(1.0.1.0.1.0.1.0) affect the cavity shape through CH/pi interactions and remarkably accelerate syn-anti conformational change of the 2,2'-bipyrrole components leading to helicity change in the figure eight loop of [32]octaphyrins.

Direct determination of absolute configuration of carboxylic acids by cyclooctapyrrole.

Octaphyrin O1 has been found to be an effective sensor for the direct determination of absolute configuration of a variety of carboxylic acids at mM concentrations at room temperature based on CD exciton chirality method.

Supramolecular chirogenesis in zinc porphyrins: interaction with bidentate ligands, formation of tweezer structures, and the origin of enhanced optical activity.

The complexation behavior, binding properties, and spectral parameters of supramolecular chirality induction in the achiral host molecule, syn (face-to-face conformation) ethane-bridged bis(zinc porphyrin), upon interaction with chiral bidentate guests (diamines and amino alcohols) have been studied by means of UV-vis, CD, fluorescence, (1)H NMR, and ESI MS techniques. It was found that the guest structure plays a decisive role in the chirogenesis pathway. The majority of bidentate ligands (except those geometrically unsuitable) exhibit two major equilibria steps: the first guest ligation leading to formation of the 1:1 host-guest tweezer structure (K(1)) and the second guest molecule ligation (K(2)) forming the anti bis-ligated species (1:2). The second ligation is much weaker (K(1) >> K(2)) due to the optimal geometry and stability of the 1:1 tweezer complex. The enhanced conformational stability of the tweezer complex ensures an efficient chirality transfer from the chiral guest to the achiral host, consequently inducing a remarkably high optical activity in the bis-porphyrin.

Direct determination of absolute configuration of monoalcohols by bis(magnesium porphyrin).

Ethane bridged bis(Mg porphyrin) has been found to be an effective sensor for the direct determination of the absolute configuration of a variety of monoalcohols at millimolar concentrations and room temperature based on the CD exciton chirality method. Examination of a variety of synthetic and natural monoalcohols, including alpha-substituted aliphatic and aromatic alkanols with one chiral center, as well as alicyclic alcohols with 2-5 chiral centers, gave consistent results. In the case of alcohols with multiple chiral centers, the absolute configuration of the carbon alpha to OH is always read out.

Remarkable stability and enhanced optical activity of a chiral supramolecular bis-porphyrin tweezer in both solution and solid state.

Interaction of the achiral syn (face-to-face) conformer of the ethane-bridged bis(zinc octaethylporphyrin) with the enantiopure 1,2-diaminocyclohexane results in the exclusive formation of a supramolecular chiral tweezer. This 1:1 host-guest complex exhibits remarkable stability in both solution (even upon photoexcitation) and solid-state phases, with a high degree of optical activity arising from the two-point interaction mode and optimal spatial geometry.

Supramolecular chirogenesis in zinc porphyrins: equilibria, binding properties, and thermodynamics.

Complexation mechanism, binding properties and thermodynamic parameters of supramolecular chirality induction in the achiral host molecule, syn (face-to-face conformation) ethane-bridged bis(zinc porphyrin), upon interaction with chiral monoamine and monoalcohol guests have been studied by means of the UV-vis, CD, (1)H NMR, and ESI MS techniques. It was found that the chirogenesis process includes three major equilibria steps: the first guest ligation to a zinc porphyrin subunit of the host (K(1)), syn to anti conformational switching (K(S)), and further ligation by a second guest molecule to the remaining ligand-free zinc porphyrin subunit (K(2)), thus forming the final bis-ligated species possessing supramolecular chirality. The validity of this equilibria model is confirmed by the excellent match between the calculated and experimentally observed spectral parameters of the bis-ligated species. The second ligation proceeds in a cooperative manner as K(2) > K(1) for all supramolecular systems studied, regardless of the structure of the chiral ligand used. The binding properties are highly dependent on the nature of the functional group (amines are stronger binders than alcohols) and on the structure of the chiral guests (primary and aliphatic amines have overall binding constant values greater than those of secondary and aromatic amines, respectively).

Stoichiometry-controlled supramolecular chirality induction and inversion in bisporphyrin systems.

[reaction: see text] Stoichiometry is found to be an effective tool for controlling supramolecular chirality induction and inversion processes. Chirality induction in the achiral syn ethane-bridged bis(zinc octaethylporphyrin) is achieved upon interaction with the enantiopure (R,R)-1,2-diphenylethylenediamine at the low molar excess region, to yield the right-handed chiral 1:1 tweezer complex. Further increase of the ligand concentration results in chirality inversion as the equilibrium shifts toward the extended left-handed 1:2 anti complex as a result of switching of the complex helicity.