Conformation and chiral effects in α,β,α-tripeptides

Short α,β,α-tripeptides comprising a central chiral trisubstituted β(2,2,3)*-amino acid residue form unusual γ-turns and δ-turns in CDCl(3) and DMSO-d(6) solutions but do not form β-turns. Thermal coefficients of backbone amide protons, 2D-NMR spectra, and molecular modeling revealed that these motifs were strongly dependent on the configuration (chiral effect) of the central β-amino acid residue within the triad. Accordingly, SSS tripeptides adopted an intraresidual γ-turn like (C6) arrangement in the central β-amino acid, whereas SRS diastereomers preferred an extended δ-turn (C9) conformation. A different SRS-stabilizing bias was observed in the crystal structures of the same compounds, which shared the extended δ-turn (C9) found in solution, but incorporated an additional extended β-turn (C11) to form an overlapped double turn motif.     

Peptide binding to β-cyclodextrins: structure, dynamics, energetics, and electronic effects

Peptide-cyclodextrin and protein-cyclodextrin host-guest complexes are becoming more and more important for industrial applications, in particular in the fields of pharmaceutical and food chemistry. They have already deserved many experimental investigations although the effect of complex formation in terms of peptide (or protein) structure is not well-known yet. Theoretical calculations represent a unique tool to analyze such effects, and with this aim we have carried out in the present investigation molecular dynamics simulations and combined quantum mechanics-molecular mechanics calculations. We have studied complexes formed between the model Ace-Phe-Nme peptide and the β-cyclodextrin (β-CD) macromolecule, and our analysis focuses on the following points: (1) how is the peptide structure modified in going from bulk water to CD environment (backbone torsion angles), (2) which are the main peptide-CD interactions, in particular in terms of hydrogen bonds, (3) which relative peptide-CD orientation is preferred and which are the structural and energetic differences between them, and (4) how the electronic properties of the peptide changes under complex formation. Overall, our calculations show that in the most stable configuration, the backbone chain lies in the narrow rim of the CD. Strong hydrogen bonds form between the H atoms of the peptidic NH groups and oxygen atoms of the secondary OH groups in the CD. These and other (weaker) hydrogen bonds formed by the carbonyl groups reduce considerably the flexibility of the peptide structure, compared to bulk water, and produce a marked increase of the local dipole moment by favoring configurations in which the two C═O bonds point toward the same direction. This effect might have important consequences in terms of the peptide secondary structure, although this hypothesis needs to be tested using larger peptide models.     

Steric effects in the catalytic amination of γ-, δ-, and ε-glycols

The amination of butane-1,4-diol, isomeric dipropylene glycols, and cyclohexane-1,4-diyldimethanol in the presence of nickel/copper/chromium catalysts has been studied. The effect of the initial glycol structure on the reaction selectivity has been estimated.     

Semisynthetic, site-specific ubiquitin modification of α-synuclein reveals differential effects on aggregation

The process of neurodegeneration in Parkinson's Disease is intimately associated with the aggregation of the protein α-synuclein into toxic oligomers and fibrils. Interestingly, many of these protein aggregates are found to be post-translationally modified by ubiquitin at several different lysine residues. However, the inability to generate homogeneously ubiquitin modified α-synuclein at each site has prevented the understanding of the specific biochemical consequences. We have used protein semisynthesis to generate nine site-specifically ubiquitin modified α-synuclein derivatives and have demonstrated that different ubiquitination sites have differential effects on α-synuclein aggregation.     

Selectivity in DNA replication. Interplay of steric shape, hydrogen bonds, π-stacking and solvent effects

Our dispersion-corrected DFT computations reveal key factors behind the intrinsic affinity of a DNA template-primer complex to select the correct nucleotide.     

Micelle to vesicle transitions of N-dodecyl-1, ω-diaminoalkanes: effects of pH, temperature and salt

The self-assembly behavior of pH-sensitive amphiphiles N-dodecyl-1, 2-diaminoethane (C12N2N), N-dodecyl-1, 3-diaminopropane (C12N3N) and N-dodecyl-1, 4-diaminobutane (C12N4N) has been studied in aqueous solutions. Light scattering, viscosity and cryo-transmission electronic microscopy (cryo-TEM) results revealed that the aggregates transferred from spherical micelles to vesicles (MVT) via wormlike micelles as the pH was gradually varied from acidic to basic conditions. pH-dependent zeta potential and (1)H NMR studies confirmed these transitions. Interestingly, the formed wormlike micelles could transform into vesicles upon heating, which was studied by cryo-TEM, light scattering and viscosity techniques in detail. It is concluded that the pH and thermal MVT are a general phenomenon in all three amphiphiles investigated. Furthermore, NaCl induced a wormlike micelle to vesicle transition was also observed in C12N2N solution.     

γ-substituent effects on the oxidative cyclization of o-acyl β,γ-unsaturated hydroxamates

Bromine induced cyclization of O-acyl β,γ-unsaturated hydroxamates to β-lactams is compatible with a variety of γ-substitutents.     

“Adatom” sites,structure and mobility effects on the sers of cyanine

The origins of specific surface-enhanced Raman scattering (SERS) bands of 2,2′-cyanine in an electrochemical system using 488 nm excitation are discussed. Under special conditions of concentration and potential, using KI as supporting electrolyte, bands can be grouped according to their potential dependency. Experimental evidence shows that several cyanine bands are attributable to aggregated molecules. Some cyanine bands depend on the presence of different sites that can be enhanced by exposure to pulsed laser radiation; the temporal behavior of some bands indicates that different surface mobilities exist for some of the molecules.     

Substituent effects on the compounds CX1X2•− (X1, X2 = H, F, Cl, Br, I) from theoretical investigation

The electronic and molecular structures of mono- and dihalocarbene anions constructed by model CX¹X^2?? (X¹, X² = H, F, Cl, Br, I), as well as the corresponding carbenes CX¹X² and analogous silicon-anions SiX¹X^2??, have been studied in detail using the B3LYP, MP2, and QCISD(T) levels of theory. Our calculated findings suggest that stabilization of the compounds is associated with the size of the halogen substituent X, which is further confirmed by ionization energies, the spin density (S _d), and the second-order perturbative energies (E(2)). Besides, we have also explored the source of the anions’ proton affinity difference.     

Therapeutic effects of soy isoflavones on α-amylase activity, insulin deficiency, liver-kidney function and metabolic disorders in diabetic rats

Natural estrogens have demonstrated a wide variety of biological activities, which makes them a good candidate for the treatment of diabetes. In vitro, this study evidenced that isoflavones enhanced insulin secretion and inhibited α-amylase activity. In vivo, the findings indicated that soy isoflavones stimulated insulin secretion, increased the hepatic glycogen content and suppressed blood glucose level. The soy isoflavones were also protected hepatic-kidney functions showed by the significant increase in superoxide dismutase, catalase and glutathione peroxidase activities and the decrease in thiobarbituric acid reactive substances, total bilirubin, creatinine and transaminases content. Moreover, soy isoflavones induced a decrease in LDL-cholesterol and triglycerides and an increase in HDL-cholesterol in plasma and liver. Overall, the findings of the current study indicate that soy isoflavones exhibit attractive properties and can, therefore, be considered a promising candidate for future application as alternative therapeutic agents, particularly in the development of anti-diabetic and hypolipidaemic drugs.     

Substituent effects in infrared spectroscopy—carbonyl stretching frequency in substituted acetonaphthones,acetylfluorenes and acetylbiphenyls

The carbonyl stretching frequencies of several ring substituted acetonaphthones, acetylfluorenes and acetylbiphenyls have been measured in CCl₄/CHCl₃ solvent and correlated with the substituent constants. The data are also analysed by DSP equation to evaluate ϱ_I and ϱ_R. Compared to acetylfluorenes, acetylbiphenyls transmit substituent effects to a lesser extent, which is explained in terms of the noncoplanarity of the two phenyl rings in the later system.     

Chemical effects on Kβ/Kα X-ray intensity ratios of Mo,Ag, Cd,Ba, La,Ce compounds and total mass attenuation coefficients of Fe and Cu

The Kβ/Kα intensity ratios for pure Mo, Ag, Cd, Ba, La and Ce elements and for some of their compounds were investigated. The vacancies in the K shell were created by 59.5-keV γ-rays from a heavily filtered ²⁴¹Am radioactive source. K X-rays were measured using a Si(Li) detector with a resolution of 155 eV at 5.9 keV. We observed chemical effects on Kβ/Kα intensity ratios of Mo, Ag, Cd, Ba, La and Ce compounds. Detailed interpretation of data obtained from X-ray transmission measurements usually depends on the assumption that the contribution of each element is additive. This assumption yields the mixture rule for X-ray attenuation coefficients which is valid if molecular and chemical effects are negligible. We measured the total mass attenuation coefficients of Fe and Cu in various compounds. Self-absorption corrections were carried out on data for ligands in the different compounds. Our values were compared with the theoretical values for pure elements.     

Lead-nano-dopings effects on the structural,microstructural, vibrational and thermal properties of Bi2−xPbxSrV2O9 layered perovskite

The sample with in the general formula Bi_2-xPb_xSrV₂O₉, where x = 0.0, 0.05, 0.1, 0.2, 0.3, and 0.6 mol were synthesized by the high temperature solid state reaction and firing method. The X-ray diffractograms confirmed the formation of single phased layered perovskite in all samples. TGA and DTA thermal analyses on the green samples included steps of thermal analysis of strontium carbonate, bismuth carbonate, ammonium vanadate, lead oxide and finally on the high temperature solid state formation. The effect of lead dopings on the sintering, structural and micro-structure, properties of 212BiSrV-ceramics were investigated. The infrared absorption spectra show a series of vibrational modes within the range of 400–1600 cm^?1.     

Strong aphicidal activity of GlcNAc(β1→4)Glc disaccharides: synthesis, physiological effects, and chitinase inhibition

The synthesis of four GlcNAc(β1→4)Glc disaccharides containing 2-O-acetyl and/or 6-sulfate groups was performed in high yields with total 1,2-trans stereoselectivity. These disaccharides were evaluated as candidates for insect chitinase inhibition and aphicidal activity. All the compounds prepared displayed physiological effects on M. persicae aphids; however, the inhibition of chitinases of different sources (bacteria, fungus, and aphid) followed different patterns according to subtle structural characteristics.     

Dimerization of HNO in aqueous solution: an interplay of solvation effects, fast acid-base equilibria, and intramolecular hydrogen bonding?

The recent unraveling of the rather complex acid-base equilibrium of nitroxyl (HNO) has stimulated a renewed interest in the significance of HNO for biology and pharmacy. HNO plays an important role in enzymatic mechanisms and is discussed as a potential therapeutic agent against heart failure. A cumbersome property for studying HNO reactions, its fast dimerization leading to the rapid formation of N(2)O, is surprisingly far from being well understood. It prevents isolation and limits intermediate concentrations of nitroxyl in solution. In this study, a new mechanism for the HNO dimerization reaction in aqueous solution has been theoretically derived on the basis of DFT calculations. Detailed analysis of the initial reaction step suggests a reversal of the cis-trans isomer preference in solution compared to the corresponding gas phase reaction. In contrast to a gas phase derived model based on intramolecular rearrangement steps, an acid-base equilibrium model is in agreement with previous experimental findings and, moreover, explains the fundamental differences between the well studied gas phase reaction and the solvent reaction in terms of polarity, cis-trans isomerizations, and acidities of the intermediates. In the case of cis-hyponitrous acid, the calculated pK(a) values of the acid-base equilibria were found to be significantly different from the corresponding experimental value of the stable trans isomer. Under physiological conditions, N(2)O formation is dominated by the decomposition of the unstable monoanion cis-N(2)O(2)H(-) rather than that of the commonly stated cis-HONNOH.     

Unexpected nonadditivity effects in anion-π complexes

Several complexes of fluorine-substituted ethyne, ethene, butadiene, benzene, and [n]radialenes (n = 3-5) with two anions have been optimized at the RI-MP2/aug-cc-pVTZ level of theory. The additivity of the anion-π interaction was studied depending on the number of double bonds and fluorine atoms. Interesting nonadditivity effects were observed in the aromatic and antiaromatic complexes, which were analyzed by partitioning the total interaction energy into individual components, using Bader's theory of "atoms in molecules" and changes in the aromatic character of the ring upon complexation.     

Chemical effects on Lα/Lβ X-ray intensity ratios of Ba,La and Ce

Chemical effects on the Lα/Lβ X-ray intensity ratio of Ba, La and Ce were investigated. The vacancies in the L shell were created by 59.5 keV γ-rays from an Am-241 radioactive source and the L X-rays were measured using a Si(Li) detector with resolution 160 eV at 5.9 keV. The experimental values are given with the theoretical values of the pure elements.