Vibrational dynamics of DNA. II. Deuterium exchange effects and simulated IR absorption spectra

In Paper I, we studied vibrational properties of normal bases, base derivatives, Watson-Crick base pairs, and multiple layer base pair stacks in the frequency range of 1400-1800 cm(-1). However, typical IR absorption spectra of single- and double-stranded DNA have been measured in D(2)O solution. Consequently, the more relevant bases and base pairs are those with deuterium atoms in replacement with labile amino hydrogen atoms. Thus, we have carried out density functional theory vibrational analyses of properly deuterated bases, base pairs, and stacked base pair systems. In the frequency range of interest, both aromatic ring deformation modes and carbonyl stretching modes appear to be strongly IR active. Basis mode frequencies and vibrational coupling constants are newly determined and used to numerically simulate IR absorption spectra. It turns out that the hydration effects on vibrational spectra are important. The numerically simulated vibrational spectra are directly compared with experiments. Also, the (18)O-isotope exchange effect on the poly(dG):poly(dC) spectrum is quantitatively described. The present calculation results will be used to further simulate two-dimensional IR photon echo spectra of DNA oligomers in the companion Paper III.     

Tandem Diels-Alder cycloadditions of 2-pyrone-5-acrylates for the efficient synthesis of novel tetracyclolactones

Readily prepared from the regioselective Pd-catalyzed coupling reactions of 3,5-dibromo-2-pyrone, 3-bromo-2-pyrone-5-carboxylates undergo tandem uninterrupted sequential Diels-Alder cycloaddition reactions with allyl vinyl ethers in a highly regio- and stereoselective fashion to provide a series of novel tetracyclolactones in good yields.     

Theoretical prediction of heterogeneous molecular wires on the Si(001) surface

Using first-principles density-functional calculations, we propose a self-assembly technique for fabrication of the heterogeneous molecular wire on the dangling-bond wire generated on a H-passivated Si(001) surface. Here, we choose pyridine and borine as Lewis base and acid molecules, respectively, to demonstrate different behaviors in the chemical reactivity and selectivity on the dangling-bond wire, leading to formation of the heterogeneous pyridine-borine wire.     

Total synthesis of oxyfagaronine, phenolic benzo[c]phenanthridine and general synthetic way of 2,3,7,8- and 2,3,8,9-tetrasubstituted benzo[c]phenanthridine alkaloids

Benzo[c]phenanthridine alkaloids such as oxynitidine, oxysanguinarine, oxyavicine and phenolic oxyfagaronine were synthesized from easily available starting benzonitriles 5 and toluamides 6 using a lithiated toluamide-benzonitrile cycloaddition reaction. The coupling reaction provided 3-arylisoquinolinones that were transformed to the benzo[c]phenanthridones. This method is highly efficient and could be useful for preparing diverse substituted aromatic benzo[c]phenanthridine compounds on a multi gram scale.     

A rapid and sensitive liquid chromatography/positive ion tandem mass spectrometry method for the determination of cimetropium in human plasma by liquid-liquid extraction

We have developed and validated a simple detection system with high-performance liquid chromatography (HPLC) with positive ion electrospray ionization tandem mass spectrometry (ESI-MS/MS) for determining cimetropium levels in human plasma using scopolamine butyl bromide as an internal standard (I.S.). The acquisition was performed in the multiple reaction monitoring (MRM) mode, by monitoring the transitions: m/z 357.9 > 103.1 for cimetropium and m/z 359.9 > 103.1 for butyl-scopolamine. The method involves a simple single-step liquid-liquid extraction with dichloromethane. The analyte was chromatographed on an YMC C18 reversed-phase chromatographic column by isocratic elution with 10 mM ammonium formate buffer-methanol (19:81, v/v; adjusted to pH 4.0 with formic acid). The results were linear over the studied range (0.2-100 ng ml(-1)), with r2 = 1.0000, and the total analysis time for each run was 2 min. Intra- and interassay precisions were 0.70-8.54% and 1.08-4.85%, respectively, and intra- and interassay accuracies were 97.56-108.23% and 97.48-103.91%, respectively. The lower limit of quantification (LLOQ) was 0.2 ng ml(-1). At this concentration, mean intra- and interassay precisions were 8.54% and 4.85%, respectively, and mean intra- and interassay accuracies were 97.56% and 98.91%, respectively. The mean recovery ranged from 62.71 +/- 4.06 to 64.23 +/- 2.32%. Cimetropium was found to be stable in plasma samples under typical storage and processing conditions. The devised assay was successfully applied to a pharmacokinetic study of cimetropium bromide administered as a single oral dose (150 mg) to healthy volunteers.     

Variable temperature H and Si NMR of diastereomeric 1,3-dihydroxy-1,3-bis[(2-dimethylaminomethyl)phenyl]-1,3-divinyldisiloxanes

Variable temperature NMR experiments of diastereomeric 1,3-dihydroxy-1,3-bis[(2-dimethylaminomethyl)phenyl]-1,3-divinyldisiloxanes, meso-1 and rac-1 having intramolecular hydrogen bondings were carried out. As temperature increased, the ¹H NMRs of hydroxy groups of 1 resulted in a low frequency and their ²⁹Si NMRs were very slightly shifted to a low frequency. Interestingly, the ¹H NMR of two benzylic protons was split more widely as temperature increased.     

Sequential reaction intermediates in aliphatic C-H bond functionalization initiated by a bis(mu-oxo)dinickel(III) complex

The reaction of [Ni2(OH)2(Me2-tpa)2]2+ (1) (Me2-tpa = bis(6-methyl-2-pyridylmethyl)(2-pyridylmethyl)amine) with H2O2 causes oxidation of a methylene group on the Me2-tpa ligand to give an N-dealkylated ligand and oxidation of a methyl group to afford a ligand-based carboxylate and an alkoxide as the final oxidation products. A series of sequential reaction intermediates produced in the oxidation pathways, a bis(mu-oxo)dinickel(III) ([Ni2(O)2(Me2-tpa)2]2+ (2)), a bis(mu-superoxo)dinickel(II) ([Ni2(O2)2(Me2-tpa)2]2+ (3)), a (mu-hydroxo)(mu-alkylperoxo)dinickel(II) ([Ni2(OH)(Me2-tpa)(Me-tpa-CH2OO)]2+ (4)), and a bis(mu-alkylperoxo)dinickel(II) ([Ni2(Me-tpa-CH2OO)2]2+ (5)), was isolated and characterized by various physicochemical measurements including X-ray crystallography, and their oxidation pathways were investigated. Reaction of 1 with H2O2 in methanol at -40 degrees C generates 2, which is extremely reactive with H2O2, producing 3. Complex 2 was isolated only from disproportionation of the superoxo ligands in 3 in the absence of H2O2 at -40 degrees C. Thermal decomposition of 2 under N2 generated an N-dealkylated ligand Me-dpa ((6-methyl-2-pyridylmethyl)(2-pyridylmethyl)amine) and a ligand-coupling dimer (Me-tpa-CH2)2. The formation of (Me-tpa-CH2)2 suggests that a ligand-based radical Me-tpa-CH2* is generated as a reaction intermediate, probably produced by H-atom abstraction by the oxo group. An isotope-labeling experiment revealed that intramolecular coupling occurs for the formation of the coupling dimer. The results indicate that the rebound of oxygen to Me-tpa-CH2* is slower than that observed for various high-valence bis(mu-oxo)dimetal complexes. In contrast, the decomposition of 2 and 3 in the presence of O2 gave carboxylate and alkoxide ligands, respectively (Me-tpa-COO- and Me-tpa-CH2O-), instead of (Me-tpa-CH2)2, indicating that the reaction of Me-tpa-CH2* with O2 is faster than the coupling of Me-tpa-CH2* to generate ligand-based peroxyl radical Me-tpa-CH2OO*. Although there is a possibility that the Me-tpa-CH2OO* species could undergo various reactions, one of the possible reactive intermediates, 4, was isolated from the decomposition of 3 under O2 at -20 degrees C. The alkylperoxo ligands in 4 and 5 can be converted to a ligand-based aldehyde by either homolysis or heterolysis of the O-O bond, and disproportionation of the aldehyde gives a carboxylate and an alkoxide via the Cannizzaro reaction.     

Facile approach for diblock codendrimers by fusion between Fréchet dendrons and PAMAM dendrons

For the first time, a simple and facile approach for the synthesis of diblock codendrimers by fusion between the azide focal point functionalized Fréchet-type polyether and the propargyl focal point functionalized Tomalia-type PAMAM dendrons has been described based on click chemistry, i.e., the copper-catalyzed cycloaddition reaction between alkyne and azide.     

Cryopreservation of cultivated and wild potato varieties by droplet vitrification: effect of subculture of mother-plants and of preculture of shoot tips

In this paper, we studied the effect of subculture of mother-plants and of preculture of shoot tips of two potato varieties (Dejima, cultivated and STN13, wild) cryopreserved using the droplet-vitrification technique. The subculture conditions (light intensity, aeration and planting density) significantly affected survival of both non-cryopreserved and cryopreserved shoot-tips in both varieties. The subculture duration and the position of the shoot tips on the axis of the in vitro plantlets had a significant (P<0.0001) effect on survival of cryopreserved shoot tips. The optimal subculture duration was 7 and 5 weeks and the optimal size of shoot tips was 1.5-2.0 and 1.0-1.5 mm for var. Dejima and STN13, respectively. Survival of cryopreserved shoot tips was influenced by the sucrose concentration in the preculture medium and the preculture duration. The highest survival of cryopreserved shoot tips was observed after preculture with 0.3 M sucrose for 8 h followed by 0.7 M sucrose for 18 h. These results indicate that the parameters of the subculture of mother-plants and of preculture of shoot tips should be carefully optimized, especially in the case of wild species.     

Cryopreservation of garlic bulbil primordia by the droplet-vitrification procedure

The droplet-vitrification protocol, a combination of droplet-freezing and solution-based vitrification was applied for cryopreserving garlic bulbil primordia. The highest survival and regeneration percentages of cryopreserved primordia (90.1 to 95.0 percent and 82.7 to 85.0 percent, respectively) were achieved after preculture for 2-4 days at 10 degree C on solid medium with 0.1 - 0.3 M sucrose, loading for 50 minutes in liquid medium with 2 M glycerol + 0.5 M sucrose, dehydration with PVS3 vitrification solution for 90-150 min, cooling primordia in 5 microl droplets of PVS3 vitrification solution placed on aluminum foil strips by dipping these strips in liquid nitrogen, warming them by plunging the foil strips into pre-heated (40 degree C) 0.8 M sucrose solution for 30 s and further incubation in the same solution for 30 minutes. The optimized droplet-vitrification protocol was successfully applied to bulbil primordia of five garlic varieties originating from various countries and to immature bulbils of two vegetatively propagated Allium species, with regeneration percentages ranging between 77.4 - 95.4 percent.