DNA polymerase template interactions probed by degenerate isosteric nucleobase analogs

The development of novel artificial nucleobases and detailed X-ray crystal structures for primer/template/DNA polymerase complexes provide opportunities to assess DNA-protein interactions that dictate specificity. Recent results have shown that base pair shape recognition in the context of DNA polymerase must be considered a significant component. The isosteric azole carboxamide nucleobases (compounds 1-5; ) differ only in the number and placement of nitrogen atoms within a common shape and therefore present unique electronic distributions that are shown to dictate the selectivity of template-directed nucleotide incorporation by DNA polymerases. The results demonstrate how nucleoside triphosphate substrate selection by DNA polymerase is a complex phenomenon involving electrostatic interactions in addition to hydrogen bonding and shape recognition. These azole nucleobase analogs offer unique molecular tools for probing nonbonded interactions dictating substrate selection and fidelity of DNA polymerases.     

Synthesis of 2-amino-4,4-bis(trifluoromethyl)-3-cyano-1,4-dihydrobenzo[h]-quinoline

Conclusions The reactions of -naphthylamine with 2,2-bis(trifluororaethyl)-1,1-dicyanoethylene leads to the formation of 2-amino-4,4-bis(trifluoromethyl)-3-cyano-1,4-dihydrobenzo[h]quinoline. The structure of this product was established by x-ray diffraction structural analysis.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 8, pp. 1917–1920, August, 1988.     

Comprehensive DFT and MO studies on glyoxilic acid oxime and related ions in gas phase and solution: Conformations,basicities and acidities

Density functional (BLYP, B3LYP and BHLYP) and highly correlated MP2 and CCSD(T) calculations have been performed to investigate conformers, energy barriers, intramolecular H-bond strength, gas-phase basicity and deprotonation energies of glyoxilic acid oxime (gao) and related ions in gas phase and in aqueous solution (SCRF-PCM method). BHLYP/6-311G(d,p) and B3LYP/6-31++G(d) predictions for the global minimum conformer of gao were consistent with experiment. BLYP level overestimated the H-bond and stabilized incorrectly the H-bonded conformer. The calculations in solution indicated destabilization of H-bonded conformers due to the small polarizability and weaken of the H-bond. The same global minimum structures in gas phase and aqueous solution were found for gao-neutral (ectt) and gao-dianion (e⁻²), whereas they were different for gao-anion because of the strong decrease of the conformational energies in solution. The global minimum structures of the neutral, anion and dianion of gao, obtained in solution, are in agreement with experiment. The gas-phase basicity (GB) and molecular electrostatic potential (MEP) calculations revealed the same sites for electrophilic attack, supported by the nature of HOMO: the carbonylic oxygen for the neutral, the carboxylic oxygen for the anion and the oxime nitrogen for the dianion. MEP results in gas phase and in solution suggested a region between the two atoms, but not on one atom in accordance with bidentate binding of gao ions to a metal. The BHLYP/6-31++G(d,p) molecular properties of gao were in best consistent with CCSD(T) results. The thermodynamical properties (GB and bond deprotonation energy) of gao were better estimated at B3LYP level.     

Cleavage of α-oxides by trimethyliodosilane

Conclusions The cleavage of the ethylene and propylene oxides by trimethyliodosilane proceeds easily to give trimethyl(2-iodoethoxy)silane and a mixture of trimethyl(2-iodopropoxy) silane and trimethyl(1-iodoisopropoxy)silane in a 12.5 ratio.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 11, pp. 2623–2624, November, 1978.     

X-Ray Powder Diffraction Studies of Polyhydrates of Cross-Linked Tetraisoamylammonium Polyacrylates

X-ray powder diffraction studies were performed of the polyhydrates, formed at positive temperature in swelled grains of carboxylic cation-exchange resins in the form of tetraisoamylammonium (cross-linked tetraisoamylammonium polyacrylates, differing in the degree of cross-linking: 1, 2 and 3%). It was shown that the polyhydrates exist as the crystalline phase under specific conditions, determined earlier by DTA technique. Diffraction patterns of the samples, recorded at the temperature +3 ± 1 °C, indicate that the polyhydrates crystallize in hexagonal symmetry, the unit cell parameters are close to a=12.25 Å, c=12.72 Å and do not depend significantly upon the degree of cross-linking. The suppositions were made concerning the size of hydrate crystallites, formed in the swelled grains of the studied resins.This revised version was published online in July 2005 with a corrected issue number.     

Molecular structures of inorganic compounds of low volatility : Part II. Metaborates of alkali metals

The molecular structures of caesium, rubidium and thallium metaborates have been studied in the gas phase by electron diffraction. Results indicate that alkali metal metaborate molecules have the bent configuration, with linear BO₂ groups. Parameters of the potential function for angle deformation are discussed.     

Cleavage of di- and trioxacyclohexanes by trimethyliodosilane

Conclusions The reaction of Me₃SiI with 1,4-dioxane gives 1,2-diiodoethane, 1,2-bis(trimethylsiloxy)ethane, and hexamethyldisiloxane, while reaction with 1,3,5-trioxane and 2,4,6-trimethyl-1,3-5-trioxane respectively gives the,-diiodomethyl and ethyl ethers and HMDS.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 6, pp. 1391–1392, June, 1981.     

Syntheses and Crystal Structures of Some CCo3 Clusters Containing PPh3 or dppm Ligands

Molecular structural determinations are reported for six Co₃C carbonyl cluster complexes containing tertiary phosphines, which have been isolated as by-products from a variety of reactions. Structural features are similar to those of related complexes already reported. Some discussion of apparent orientational preferences of the CH₂ group of dppm ligands, which appear to enter into H-bonding interactions with amido or carboxylate substituents, is given. Appropriate comparisons are made with unsubstituted analogues.     

Distribution of CdSe quantum dots within swollen polystyrene microgel particles using confocal microscopy

CdSe quantum dots (QDs) are semiconducting nanoparticles that fluoresce when stimulated by visible light. This property has been exploited in their use as tracer particles in biomedical applications. In this study, confocal microscopy has been used to determine the distribution of QDs within polystyrene microgel particles, dispersed in an organic solvent. It was found that the extent of microgel swelling affected the penetration of the QDs into the particles. Only when the microgel particles were swollen to their maximum extent were the QDs able to penetrate into the central core region of the particles.