Chemical shifts in nucleic acids studied by density functional theory calculations and comparison with experiment

NMR chemical shifts are highly sensitive probes of local molecular conformation and environment and form an important source of structural information. In this study, the relationship between the NMR chemical shifts of nucleic acids and the glycosidic torsion angle, χ, has been investigated for the two commonly occurring sugar conformations. We have calculated by means of DFT the chemical shifts of all atoms in the eight DNA and RNA mono-nucleosides as a function of these two variables. From the DFT calculations, structures and potential energy surfaces were determined by using constrained geometry optimizations at the BP86/TZ2P level of theory. The NMR parameters were subsequently calculated by single-point calculations at the SAOP/TZ2P level of theory. Comparison of the (1) H and (13) C?NMR shifts calculated for the mono-nucleosides with the shifts determined by NMR spectroscopy for nucleic acids demonstrates that the theoretical shifts are valuable for the characterization of nucleic acid conformation. For example, a clear distinction can be made between χ angles in the anti and syn domains. Furthermore, a quantitative determination of the χ angle in the syn domain is possible, in particular when (13) C and (1) H chemical shift data are combined. The approximate linear dependence of the C1' shift on the χ angle in the anti domain provides a good estimate of the angle in this region. It is also possible to derive the sugar conformation from the chemical shift information. The DFT calculations reported herein were performed on mono-nucleosides, but examples are also provided to estimate intramolecularly induced shifts as a result of hydrogen bonding, polarization effects, or ring-current effects.     

Synthesis of quinolines via Friedländer reaction catalyzed by CuBTC metal-organic-framework

Friedl?nder condensation between 2-aminoaryl ketones and different carbonyl compounds, catalyzed by CuBTC was investigated by a combination of various experimental techniques and by density functional theory based modelling. CuBTC exhibiting hard Lewis acid character showed highly improved catalytic activity when compared with other molecular sieves showing high concentraion of Lewis acid sites, e.g. in BEA and (Al)SBA-15. Polysubstituted quinolines were synthesized via a Friedl?nder reaction catalyzed by CuBTC under the solvent-free conditions. High concentration of active sites in CuBTC together with the concerted effect of a pair of adjacent Cu(2+) coordinatively unsaturated active sites are behind a very high quinoline yield reached within a short reaction time. Results reported here make CuBTC a promising catalyst for other Lewis acid-promoted condensations, including those leading to biologically active compounds with a particular relevance for the pharmaceutical industry. The mechanism of a catalyzed Friedl?nder reaction investigated computationally is also reported.     

Photoinduced decarboxylation of 9‐oxo‐6,9‐dihydro[1,2,5]selenadiazolo[3,4‐f]quinoline‐8‐carboxylic acid

Photoinduced reactions of 9‐oxo‐6,9‐dihydro[1,2,5]selenadiazolo[3,4‐f]quinoline‐8‐carboxylic acid (SeQCA) were investigated in alkaline media (aqueous NaOH solutions) by electron paramagnetic resonance (EPR) spectroscopy, following the in situ formation of paramagnetic species. According to UV–Vis and nuclear magnetic resonance investigations, protonation (pH ≈ 11) and deprotonation (pH ≈ 13) of the imino hydrogen of the 4‐pyridone moiety has to be considered, reflected also in the different EPR spectra observed upon irradiation. Photoinduced generation of radicals was found only for carboxylate substituted SeQCA; other studied selenadiazoloquinolone derivatives, together with those substituted at the C(8) position (R = H, COOCH₂CH₃, COOCH₃, COCH₃ or CN), did not generate paramagnetic species during exposure. Consequently, photodecarboxylation was suggested as the decisive step, accompanied by the decomposition of the selenadiazole ring, resulting in the formation of ortho‐hydroxylate anions. EPR parameters elucidated from experimental EPR spectra obtained at pH ≈ 11 and pH ≈ 13 indicate the formation of oxygen‐centered radicals at the decarboxylated 4‐pyridone ring. EPR spin trapping experiments with nitromethane confirmed a very effective photoinduced electron transfer from all the selenadiazoloquinolones investigated. Copyright © 2011 John Wiley & Sons, Ltd.     

Thermoanalytical investigation and biological properties of zinc(II) 4-chloro- and 5-chlorosalicylates with N-donor ligands

New zinc(II) 4- and 5-chlorosalicylate complexes of general formula [Zn(X-sal)₂(L) _n (H₂O) _x ] (where X-sal?=?4-Clsalicylate, 5-Clsalicylate; L?=?N,N-diethylnicotinamide, isonicotinamide, theophylline; n?=?1, 2; x?=?0, 1, 2, 4) were prepared. The complexes were determined by elemental analysis and characterised by infrared spectroscopy. The thermal behaviour of the complexes was studied by simultaneous TG, DTG and DTA methods under dynamic air conditions. The thermal decomposition is a multi-step process. In the first step of the thermal decomposition, water is released in hydrated compounds. The anhydrous compounds start to decompose by the release of organic ligand, followed by chlorosalicylic acid, chlorophenol and carbon monoxide. The final solid product of the thermal decomposition is zinc oxide. The volatile products of the thermal decomposition were determined by mass spectrometry. The antimicrobial activities of the complexes were evaluated against selected pathogen and probiotic bacteria, yeasts and fungi strains. Bioactivities of the tested compounds are different against bacteria, yeasts and filamentous fungi. It was found that bacteria were more sensitive to the studied zinc(II) complex compounds than yeasts or filamentous fungi.     

Stimulatory action of cyclooxygenase inhibitors on hematopoiesis: a review

The presented review summarizes experimental data obtained with a mouse model when investigating the relationship between inhibition of prostaglandin production and hematopoiesis. While prostaglandin E₂ acts in a negative feedback control of myelopoiesis, inhibition of cyclooxygenases, responsible for its production, shifts the feedback to positive control. Based on these relationships, agents inhibiting cyclo-oxygenases, known as non-steroidal anti-inflammatory drugs (NSAIDs), can activate hematopoiesis and be protective or curative under myelosuppressive states. The effectiveness of therapeutic use of NSAIDs in these situations is expressive especially under the selective inhibition of cyclooxygenase-2 (COX-2), when undesirable side effects of cyclooxygenase-1 inhibition, like gastrointestinal damage, are absent. The effects of the clinically approved selective COX-2 inhibitor, meloxicam, were investigated and demonstrated significant hematopoiesis-stimulating and survival-enhancing actions of this drug in sublethally or lethally γ-irradiated mice. These effects were connected with the ability of meloxicam to increase serum levels of the granulocyte colony-stimulating factor. It can be inferred from these findings that selective COX-2 inhibitors might find their use in the treatment of myelosuppressions of various etiologies.     

Photoinduced Oxidation of Sterically Hindered Amines in Acetonitrile Solutions and Titania Suspensions (An EPR Study)

The reactions of sterically hindered amines (SHA) were investigated in acetonitrile solutions and TiO₂ suspensions upon exposure to monochromatic radiation, λ = 365 nm, by means of in situ EPR spectroscopy. The formation of singlet oxygen, as one of the possible oxidation agents for SHA, in these systems is affected significantly by solvent used and the experimental conditions. Experiments in homogeneous media evidenced alternative pathways for the SHA oxidation with a variety reactive oxygen species involved. In anhydrous acetonitrile solutions containing KO₂, the SHA oxidation was negligible not only in the dark but also on continuous exposure. However, the presence of water, even at low concentrations, led to the transformation of O₂^?? to singlet oxygen and hydrogen peroxide, which served as a source of hydroxyl radicals. These species participated in oxidation of SHA resulting in the generation of nitroxide radicals. To investigate the influence of different competitive reactions of SHA with other ROS formed upon TiO₂ photoexcitation, a series of experiments using different additives (e.g. KO₂, H₂O₂, NaN₃, dimethylsulfoxide, methanol as organic cosolvents) under air or argon were performed. The detailed analysis of paramagnetic intermediates formed upon the irradiation of the studied systems was accomplished using EPR spin trapping technique.     

Stereospecific Synthesis of D-Glycero-D-ido-oct-2-ulose

Summary.  D-Glycero-D-gulo-heptose reacted with 2,2-dimethoxypropane to give its 2,3:6,7-di-O-isopropylidene derivative. Its base-catalyzed addition to formaldehyde resulted in the formation of 2,3:6,7-di-O-isopropylidene-2-C-(hydroxymethyl)-D-glycero-D-gulo-heptofuranose. After acid hydrolysis of this aldolization product, a new branched-chain aldose, 2-C-(hydroxymethyl)-D-glycero-D-gulo-heptose, was obtained, which was stereospecifically rearranged under the catalytic action of molybdic acid to D-glycero-D-ido-oct-2-ulose. Received October 17, 2000. Accepted December 4, 2000     

Kinetics and Mechanism of the Autocatalytic Oxidation of Mn(II) by Bromine

The oxidation of Mn(II) by bromine is an autocatalytic reaction, which seems to be important for a detailed elucidation of chemical oscillators, based on manganese chemistry. With regard to the mechanism proposed previously, an alternative reaction mechanism is proposed, based on a micro-heterogeneous oxidation of Mn(II) ion, adsorbed on a surface of the MnO₂ colloid. This revised version was published online in June 2006 with corrections to the Cover Date.     

Vibrational Study (Raman,SERS, and IR) of Plant Gallnut Polyphenols Related to the Fabrication of Iron Gall Inks

FT-Raman, FTIR, and SERS spectra of the structurally related gallnut polyphenols tannic acid, gallic acid, pyrogallol, and syringic acid are reported in this work aiming at performing a comparative assignation of the bands and finding specific marker features that can identify these compounds in complex polyphenol mixtures. Tannic and gallic acids are the principal components in oak gallnuts, and they can be found in iron gall inks. The different functional groups existing in these molecules and their spatial distribution lead to slight changes of the vibrations. The Raman spectra are dominated by bands corresponding to the ring vibrations, but the substituents in the ring strongly affect these vibrations. In contrast, the FTIR spectra of these molecules are dominated by the peripheral oxygen-containing substituents of the aromatic ring and afford complementary information. SERS spectroscopy can be used to analyze trace amounts of these compounds, but the spectra of these polyphenols show strong changes in comparison with the Raman spectra, indicating a strong interaction with the metal. The most significant modification observed in the SERS spectra of these compounds is the weakening of the benzene 8a ring vibration and the subsequent intensification of the 19a mode of the benzene ring. This mode is also more intense in the FTIR spectra, and its intensification in the SERS spectra could be related to a drastic change in the molecular polarizability associated with the interaction of the polyphenol with the metal in Ag NPs.     

The CH–π Interaction in Protein–Carbohydrate Binding: Bioinformatics and In Vitro Quantification

The molecular recognition of carbohydrates by proteins plays a key role in many biological processes including immune response, pathogen entry into a cell, and cell–cell adhesion (e.g., in cancer metastasis). Carbohydrates interact with proteins mainly through hydrogen bonding, metal-ion-mediated interaction, and non-polar dispersion interactions. The role of dispersion-driven CH–π interactions (stacking) in protein–carbohydrate recognition has been underestimated for a long time considering the polar interactions to be the main forces for saccharide interactions. However, over the last few years it turns out that non-polar interactions are equally important. In this study, we analyzed the CH–π interactions employing bioinformatics (data mining, structural analysis), several experimental (isothermal titration calorimetry (ITC), X-ray crystallography), and computational techniques. The Protein Data Bank (PDB) has been used as a source of structural data. The PDB contains over 12 000 protein complexes with carbohydrates. Stacking interactions are very frequently present in such complexes (about 39 % of identified structures). The calculations and the ITC measurement results suggest that the CH–π stacking contribution to the overall binding energy ranges from 4 up to 8 kcal mol⁻¹. All the results show that the stacking CH–π interactions in protein–carbohydrate complexes can be considered to be a driving force of the binding in such complexes.