Atomic and molecular analysis highlights the biophysics of unprotonated and protonated retinal in UV and scotopic vision.

During the photoreaction of rhodopsin, retinal isomerizes, rotating the C11[double bond, length as m-dash]C12 π-bond from cis to an all-trans configuration. Unprotonated (UR) or protonated (PR) retinal in the Schiff's base (SB) is related to UV and light vision. Because the UR and PR have important differences in their physicochemical reactivities, we compared the atomic and molecular properties of these molecules using DFT calculations. The C10-C11[double bond, length as m-dash]C12-C13 dihedral angle was rotated from 0° to 180° in 45° steps, giving five conformers, and the following were calculated from them: atomic orbital (AO) contributions to the HOMO and LUMO, atomic charges, bond length, bond order, HOMO, LUMO, hardness, electronegativity, polarizability, electrostatic potential, UV-vis spectra and dipole moment (DM). Similarly, the following were analyzed: the energy profile, hybridization, pyramidalization and the hydrogen-out-of-plane (HOOP) wagging from the H11-C11[double bond, length as m-dash]C12-H12 dihedral angle. In addition, retinal with a water H-bond (HR) in the SB was included for comparison. Interestingly, in the PR, C11 and C12 are totally the LUMO and the HOMO, respectively, and have a large electronegativity difference, which predicts an electron jump in these atoms during photoexcitation. At the same time, the PR showed a longer bond length and lower bond order, with a larger DM, lower HOMO-LUMO gap, lower hardness and higher electronegativity. In addition, the AOs of -45° and -90° conformers changed significantly, from pz to py, during the rotation concomitantly with marked hybridization, smooth pyramidalization and lower HOOP activity. Clearly, the atomic and molecular differences between the UR and PR are overwhelming, including the rotational energy profile and light absorption spectra, which indicates that light absorption of UR and PR is already determined by the retinal characteristics of the SB protonation. The HR-model compared with UR shows a lower energy barrier and a discreet bathochromic effect in the UV region.

Kinetics of amide and peptide cleavage by alkaline hydrogen peroxide.

The hydroperoxide anion cleaves unactivated amides and peptides although it is completely unreactive toward ethyl esters. The cleavage by HO2(-) proceeds faster than by OH(-) and involves additional routes with general acid assistance by H2O2 and general base assistance by OH(-) and HO2(-). Cleavage of polypeptides occurs at the N-terminal peptide bond. [reaction: see text]

Metal-catalyzed hydroxylaminolysis of unactivated amide and peptide bonds.

Kinetics of the hydroxylaminolysis of acetamide, glycinamide, glycylglycine and triglycine have been studied in the range of temperatures 37-60 degrees C as a function of pH and hydroxylamine concentration. Rate constants for specific acid, general-acid and general-base catalyzed pathways have been determined for all substrates (for glycine derivatives rate constants for different protonation forms were obtained). Testing different metal ions as possible reaction catalysts revealed a significant catalytic effect of Zn(II) on the hydroxylaminolysis of glycine substrates, but not acetamide. On the basis of the kinetic results, a mechanism of Zn(II) catalysis is proposed, which involves the coordination of the metal ion to the alpha-amino group of the substrate and the base-assisted nucleophilic attack of hydroxylamine on the bound substrate. The product analysis by proton NMR shows that the primary reaction product in the catalytic reaction is glycine hydroxamic acid, which undergoes further Zn(II)-catalyzed hydrolysis to glycine. Thus the final result of the Zn(II)-catalyzed treatment of peptides by hydroxylamine is hydrolytic cleavage.