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At least 1,657 records · Page 92Linked to original sources
PubMed1986

Conformations of cyclo(L-orD-Phe-L-Pro-Aca) and cyclo(L-Pro-L- or D-Phe-Aca). Cyclized dipeptide models for specific types of beta-bends.

Conformational analyses on four cyclic model peptides of the beta-bend, cyclo(L- or D-Phe-L-Pro-epsilon-aminocaproyl(Aca] and cyclo(L-Pro-L- or D-Phe-Aca), were carried out both experimentally and theoretically. Cyclo(D-Phe-L-Pro-Aca) was shown to exist as a single conformer taking the type II' beta-bend. The comparison of its CD spectra with those of cyclo(L-Ala-L-Ala-Aca) revealed that type I and II' beta-bends, both with alpha-helix-like CD spectra, can be distinguished. Cyclo(L-Phe-L-Pro-Aca) was shown to exist as a single conformer with a cis L-Phe-L-Pro peptide bond, taking the type VI beta-bend. Its CD spectrum has thus been observed for the first time for the bend containing a cis peptide bond. Cyclo(L-Pro-L-Phe-Aca) was shown to exist as a mixture of two conformers, the major one taking the type I beta-bend with a trans Aca-L-Pro peptide bond and the minor one with a cis Aca-L-Pro peptide bond. Cyclo(L-Pro-D-Phe-Aca) was suggested to exist as a mixture of two conformers, the major one taking the type II beta-bend with a trans Aca-L-Pro peptide bond and the minor one with a cis Aca-L-Pro peptide bond.

Dipeptides↗
PubMed2005

Photoisomerization as a trigger for Bergman cyclization: synthesis and reactivity of azoenediynes.

Cyclic enediynes 1a and 2a containing stable E-azo moiety (azoenediynes) have been synthesized. These compounds upon irradiation with long wavelength UV isomerize to the Z-compounds 1b and 2b, which can be thermally reisomerized to the Z compounds. Reactivity studies toward BC using DSC predictably indicate higher reactivity for the Z-isomers. Our studies may provide a novel way to modulate the reactivity of enediynes under thermal or photochemical conditions.

Amino Acids, Cyclic↗
PubMed2005

Cyclization of the substituted N-(ortho-cyclopropylphenyl)-N'-aryl ureas and thioureas in the gas phase and solution.

Electron ionization (EI), chemical ionization (CI), tandem mass spectrometry, high-resolution measurements, and labeling studies as well as quantum chemical calculations were used to understand the behavior of the molecular radical cations (EI) and protonated molecules (CI) of substituted N-(ortho-cyclopropylphenyl)-N'-aryl ureas and N-(ortho-cyclopropylphenyl)-N'-aryl thioureas in a mass spectrometer. Fragmentation schemes and possible mechanisms of primary isomerization were proposed. According to the fragmentation pattern, formation of the corresponding benzoxazines and benzothiazines was considered as the major process of isomerization of the original M(+.) and MH(+), although some portions of these ions definitely transformed into other structures. The treatment of N-(ortho-cyclopropylphenyl)-N'-phenyl urea and N-(ortho-cyclopropylphenyl)-N'-phenylthiourea in solution with strong acids formed predicted 4-ethyl-N-phenyl-4H-3,1-benzoxazin-2-amin and 4-ethyl-N-phenyl-4H-3,1-benzothiazin-2-amine as principal products.

Algorithms↗
PubMed1986

Stereoselective intramolecular cyclization in irradiated nucleic acids: R- and S-8,5'-cycloadenosine in polyadenylic acid.

The yields of R- and S-8,5'-cycloadenosines have been measured in poly A irradiated with gamma rays in the absence of oxygen. High performance liquid chromatographic analysis of the nucleoside analogues obtained by hydrolysis of the irradiated poly A shows that the R isomer predominates to the extent of 2.5-fold at doses of ionizing radiation in the range of 0-400 Gy.

Adenosine↗
PubMed2000

Multimerization-cyclization of DNA fragments as a method of conformational analysis.

Ligation of short DNA fragments results in the formation of linear and circular multimers of various lengths. The distribution of products in such a reaction is often used to evaluate fragment bending caused by specific chemical modification, by bound ligands or by the presence of irregular structural elements. We have developed a more rigorous quantitative approach to the analysis of such experimental data based on determination of j-factors for different multimers from the distribution of the reaction products. j-Factors define the effective concentration of one end of a linear chain in the vicinity of the other end. To extract j-factors we assumed that kinetics of the reaction is described by a system of differential equations where j-factors appear as coefficients. The assumption was confirmed by comparison with experimental data obtained here for DNA fragments containing A-tracts. At the second step of the analysis j-factors are used to determine conformational parameters of DNA fragments: the equilibrium bend angle, the bending rigidity of the fragment axis, and the total twist of the fragments. This procedure is based on empirical equations that connect the conformational parameters with the set of j-factors. To obtain the equations, we computed j-factors for a large array of conformational parameters that describe model fragments. The approach was tested on both simulated and actual experimental data for DNA fragments containing A-tracts. A-tract DNA bend angle determined here is in good agreement with previously published data. We have established a set of experimental conditions necessary for the data analysis to be successful.

Base Sequence↗
PubMed2001

Acid-catalyzed dehydrative cyclization of 4-(D-galacto -pentitol-1-yl)-2-phenyl-2H-1,2,3-triazole. synthesis and anomeric configuration of D-lyxo-C-nucleoside analogs.

Dehydration of 4-(D-galacto-pentitol-1-yl)-2-phenyl-2H-1,2,3-triazole with 20% methanolic sulfuric acid afforded the anomeric pairs of nucleosides, 4-(alpha-D-lyxopyranosyl)-2-phenyl-2H-1,2,3-triazole (major component) and its beta-anomer, as well as 4-(alpha-D-lyxofuranosyl)-2H-1,2,3-triazole and its beta-anomer. The four anomeric C-nucleosides were separated by chromatography, and their structure and anomeric configuration were determined by periodate oxidation, acylation, and NMR spectroscopy as well as mass spectrometry. The anomeric assignment from optical rotation was not in agreement with final structure assignment and represented a violation of the Hudson isorotation rules. NOE studies and X-ray diffraction measurements confirmed the anomeric configuration.

Catalysis↗
PubMed2003

Determination of the configuration of 3,6-anhydrogalactose and cyclizable alpha-galactose 6-sulfate units in red seaweed galactans.

A combination of two reported procedures was used in order to determine the configuration of the 3,6-anhydrogalactose present in red seaweed polysaccharides. A mild hydrolysis (to cleave only 3,6-anhydrogalactosyl linkages) was followed by a reductive amination with a chiral amine. Then, the total hydrolysis proceeded, followed by a new step of reductive amination. In this way, using (S)-alpha-methylbenzylamine as the chiral amine, it was possible to separate and quantitate both enantiomers of 3,6-AnGal and its 2-O-methyl ether as their diastereomeric acetylated aminoalditols. On the other hand, using (S)-1-amino-2-propanol, even though the derivatives of both enantiomers of 3,6-AnGal are not separated, the mixture can be safely quantitated with respect to galactose. Furthermore, a one-pot technique was developed to carry out an alkaline treatment of the polysaccharides, followed by the double hydrolysis-reductive amination procedure, which is useful to determine the proportions of both enantiomers of 6-sulfated 4-linked galactose units in the native polysaccharides. The unexpected presence of small amounts of units of this type belonging to the D-series in a porphyran sample is revealed by this novel procedure.

Amination↗