Synthesis of diazepinoquinoxalines and imidazolobenzopteridines

Diazepinoquinoxalines 3, 4 and imidazolobenzopteridines 5, 6a-d, 7a-d, 8, 9 were synthesized from 3-allylamino-6,7-dimethyl-2-quinoxalinecarboxamide ( 1 ) and 2-allylamino-6,7-dimethyl-3,4-dihydrobenzo[g]pteridin-4-one ( 2 ) by the intramolecular cyclization using phenylselenenyl chloride.     

RECENT PROGRESS OF NANO-MECHANICAL MAPPING

 Nano-mechanical mapping by atomic force microscopy has been developed as an useful application to measure mechanical properties of soft materials at nanometer scale. To date, the Hertzian theory was used for analyzing force-distance curves as the simplest model among several contact mechanics between elastic bodies. However, the preexisting methods based on this theory do not consider the adhesive interaction in principle, which cannot be neglected in the ambient condition. A new analytical method was introduced to estimate the elasticity and the adhesive energy simultaneously by means of the JKR theory, describing adhesive contact between elastic materials. Poly(dimethylsiloxane) (PDMS) and isobutylene-co-isoprene rubber (IIR) were analyzed to verify the applicable limit of the JKR analysis. For elastic samples such as PDMS, the force-deformation plots obtained experimentally were consistent with JKR theoretical curves. Meanwhile, for viscoelastic samples, especially for IIR, the experimental plots revealed large deviations from JKR curves depending on scanning velocity and maximum loading force. Some nano-rheological arguments were employed based on the difference between these specimens.     

Optical rotary dispersion of nitrobenzene derivatives—IV : Absolute conformation of twisted nitrobenzen derivatives and its control through conformational transmission

The origin of Cotton effect shown by o-nitrobenzoyl esters is discussed. The Cotton effect observed for 1-(?)-methyl ester of 3-nitrophalic acid and 4-nitrohemimellitic acid (6 and 12), indicated that the favoured twisting direction of the nitrobenzene moiety is determined by the asymmetric menthyl group through the intervening carboxyl groups. This provides a new concept in conformational analysis of aromatic compounds. Extending the concept of conformational transmission to 2,2′-dinitrobipenhyl derivatives with known ab twisted nitrobenzene was related to the sign of the Cotton effect at 330 nm in accordance with the result of X-ray crystal analysis 1-(?)-menthyl 4-bromo-2-nitrobenzoate (1)     

Sequence-dependent conformational energy of DNA derived from molecular dynamics simulations: toward understanding the indirect readout mechanism in protein-DNA recognition

Sequence dependence of DNA conformation plays a crucial role in its recognition by proteins and ligands. To clarify the relationship between sequence and conformation, it is necessary to quantify the conformational energy and specificity of DNA. Here, we make a systematic analysis of dodecamer DNA structures including all the 136 unique tetranucleotide sequences at the center by molecular dynamics simulations. Using a simplified conformational model with six parameters to describe the geometry of adjacent base pairs and harmonic potentials along these coordinates, we estimated the equilibrium conformational parameters and the harmonic potentials of mean force for the central base-pair steps from many trajectories of the simulations. This enabled us to estimate the conformational energy and the specificity for any given DNA sequence and structure. We tested our method by using sequence-structure threading to estimate the conformational energy and the Z-score as a measure of specificity for many B-DNA and A-DNA crystal structures. The average Z-scores were negative for both kinds of structures, indicating that the potential of mean force from the simulation is capable of predicting sequence specificity for the crystal structures and that it may be used to study the sequence specificity of both types of DNA. We also estimated the positional distribution of conformational energy and Z-score within DNA and showed that they are strongly position dependent. This analysis enabled us to identify particular conformations responsible for the specificity. The presented results will provide an insight into the mechanisms of DNA sequence recognition by proteins and ligands.     

An unusual twist conformation of 2-O-methyl-1,3,4,5-tetrakis-O-tert-butyldiphenylsilyl-myo-inositol

The ring conformation of 2-O-methyl-1,3,4,5-tetrakis-O-tert-butyldiphenylsilyl-myo-inositol was in a twist form both in solid state and in solution. This is the first observation of a stable twist conformer induced by the introduction of bulky silyl protecting groups.     

Water soluble cyclodextrin polymers: Their interaction with drugs

The complex forming ability of a water-soluble -cyclodextrin epichlorohydrin, polymer (CDPS) and its different molecular weight fractions was studied and compared with the complexing properties of -cyclodextrin (CD) and dimethyl-CD (DM-CD). CDPS was separated into two main fractions. CDPS and its fractions formed well soluble inclusion compounds with the studied drugs. The low molecular weight fraction formed rather stable complexes with small guest molecules, the high molecular weight fraction was found to be more efficient in binding larger substrates. Structural studies of furosemide-CD complexes were attempted by NMR spectroscopy.Presented at the Fourth International Symposium on Inclusion Phenomena and the Third International Symposium on Cyclodextrins, Lancaster, U.K., 20–25 July 1986.     

The inclusion complex of piromidic acid with dimethyl-β-cyclodextrin in aqueous solution and in the solid state

Inclusion complex formation of piromidic acid (PA) with dimethyl--cyclodextrin (DM--CD) in aqueous solution and in the solid state was confirmed by the solubility method, differential scanning calorimetry (DSC) and proton nuclear magnetic resonance (¹H-NMR) spectroscopy. The apparent stability constant,K _c , of the complex was estimated to be 244 M^–1. The stoichiometry of the complex was given as the ratio 1:2 of PA to DM--CD. The dissolution rate of the PA/DM--CD complex was much greater than that of intact PA.Presented at the Fourth International Symposium on Inclusion Phenomena and the Third International Symposium on Cyclodextrins, Lancaster, U.K., 20–25 July 1986.     

Photodestruction of fluorophores and optimum conditions for trace DNA detection by automated DNA sequencer.

Although automated DNA sequencers are becoming popular, their sensitivity in detecting DNA bands is still around 10(-17) mole/band. The sensitivity of a system depends on the laser power, labeling fluorophore, and the fluorescence-collecting yield. The emission and photodestruction cross-sections of the fluorophores are critical in optimizing the irradiated laser power and the migration speeds of DNA fragments to achieve high sensitivity. We investigated photodestruction cross-sections of various fluorophores to optimize the irradiation laser power. In addition, we used a cylindrical lens system to improve the fluorescence-collecting yield of a DNA sequencer using side entry laser irradiation. Fluoresceine isothiocyanate (FITC) commonly used in fluorescence studies, is very photo-destructive, the cross-section of the destruction being about 3.8 x 10(-20) cm2 in buffer solution while that of Texas Red is 1.5 x 10(-21) cm2. When the time for DNA fragments to transit through the irradiated region is 11 s, the optimum laser powers are 0.9 mW, with an Ar laser (488 nm) for FITC-DNA, and 18 mW, with an He-Ne laser (594 nm) for Texas Red DNA. We have developed a DNA sequencer, with a cylindrical lens system which improves the fluorescence-collecting efficiency by a factor of 4, and an He-Ne laser (5 mW). Although the sequencer uses a slab gel, an ultra-high sensitivity of 5 x 10(-20) mole/band (S/N-4) was achieved under optimized conditions.     

Physicochemical properties and stability in the acidic solution of a new macrolide antibiotic, clarithromycin, in comparison with erythromycin.

Clarithromycin (6-O-methylerythromycin), a new 14-membered macrolide antibiotic, has been studied to clarify its physicochemical properties and stability in acidic solution, as compared with erythromycin (EM). The solubility of clarithromycin (CAM) in distilled water was lower than that of EM and decreased with increasing temperature. The solubilities of CAM and EM in the phosphate buffer solution at 37 degrees C decreased with an increasing pH and kept constant above pH 9. From pH-solubility profiles, the dissociation constants of CAM and EM were determined to be 8.76 and 8.36, respectively. The partition coefficient of CAM took a higher value than that of EM and increased with an increasing pH. In the acidic solution, the decomposition of CAM and EM obeyed the pseudo-first order kinetics. From the decomposition rate constants, the half life (T1/2) of CAM and EM were determined. In pH 1.39, CAM degraded with a T1/2 of 17 min while EM kinetics corresponded to a T1/2 of 3 s. Therefore, CAM was 340-fold more stable in pH 1.39 and markedly more stable in the acidic solution than EM.