Chemical alteration of nucleic acids and their components—XIII: Reaction of nucleosides with diacyl peroxides

Diacyl peroxides reacted at room tempt with cytidine and adenosine. The former gave 4-acyl and 3-oxido derivatives and the latter gave 6-acyl and 1-oxido derivatives. At 90°, diacetyl peroxide reacted with guanosine, adenosine, cytidine, and uridine by a homolytic process to give their C-methylated derivatives. The latter reaction was accelerated by the presence of a ferrous ion.     

Development of a cooled He*(23S) beam source for measurements of state-resolved collision energy dependence of Penning ionization cross sections: Evidence for a stereospecific attractive well around methyl group in CH3CN

A low-temperature discharge nozzle source with a liquid-N(2) circulator for He*(2(3)S) metastable atoms has been developed in order to obtain the state-resolved collision energy dependence of Penning ionization cross sections in a low collision energy range from 20 to 80 meV. By controlling the discharge condition, we have made it possible to measure the collision energy dependence of partial ionization cross sections (CEDPICS) for a well-studied system of CH(3)CN+He*(2(3)S) in a wide energy range from 20 to 350 meV. The anisotropic interaction potential energy surface for the present system was obtained starting from an ab initio model potential via an optimization procedure based on classical trajectory calculations for the observed CEDPICS. A dominant attractive well depth was found to be 423 meV (ca. 10 kcal/mol) at a distance of 3.20 A from the center of mass of CH(3)CN in the N-atom side along the CCN axis. In addition, a weak attractive well (ca. 0.9 kcal/mol) surrounding the methyl group (-CH(3)) has been found and ascribed to the interaction between an unoccupied molecular orbital of CH(3)CN and 2s atomic orbital of He*(2(3)S).     

Chiral recognition in NMR spectroscopy using crown ethers and their ytterbium(III) complexes

Chiral crown ethers 1 and 5 are useful enantiomeric discriminating agents in ¹H NMR spectroscopy for neutral and protonated primary amines, amino acids, and amino alcohols. The presence of the carboxylic acid groups in 1 and 5 provide sites at which ytterbium(III) can bind. Adding ytterbium(III) nitrate to crown–substrate mixtures in methanol-d₄ causes shifts in the spectra of substrates and often enhances the chiral discrimination in the ¹H NMR spectrum. The enhancement in enantiomeric discrimination that occurs in the presence of ytterbium(III) allows lower concentrations of the crown ether to be used in chiral recognition studies. Several amide derivatives of 1 were prepared and evaluated as chiral NMR discriminating agents, although except for 1e, these were less effective than 1.     

Power-free poly(dimethylsiloxane) microfluidic devices for gold nanoparticle-based DNA analysis

An extremely simple, power-free pumping method for poly(dimethylsiloxane)(PDMS) microfluidic devices is presented. By exploiting the high gas solubility of PDMS, the energy for the pumping is pre-stored in the degassed bulk PDMS, therefore no additional structures other than channels and reservoirs are required. In a Y-shaped microchannel with cross section of 100 microm width x 25 microm height, this method has provided flow rate of 0.5-2 nL s(-1), corresponding to linear velocity of 0.2-0.8 mm s(-1), with good reproducibility. As an application of the power-free pumping, gold nanoparticle-based DNA analysis, which does not rely on the cross-linking mechanism between nanoparticles, has been implemented in a microchannel with three inlets. Target 15mer DNA has been easily and unambiguously discriminated from its single-base substituted mutant. Instead of colorimetric detection in a conventional microtube, an alternative detection technique suitable for microdevices has been discovered-observation of deposition on the PDMS surfaces. The channel layout enabled two simultaneous DNA analyses at the two interfaces between the three laminar streams.     

Measurement of density distributions for colloidal beta-FeOOH rods in suspensions exhibiting phase separation: the role of long-range forces in smectic ordering

We prepared monodisperse colloidal beta-FeOOH rods with length-to-width ratios L/W of 3.6-7.0 (L=210-330 nm and W=40-58 nm). Density gradients of the rods occurred in the suspensions by gravity, inducing a phase separation. The denser phase showed smectic (Sm) liquid crystalline structures exhibiting iridescent colors in a wide range of pH from 1.2 (at which the rods interact attractively) to 4.7 (repulsively). The lower density phase was disordered, but frequently emitted diffuse colors locally (at pH>2.6), implying the occurrence of short-range order. The nematic phase was not observed in the beta-FeOOH systems, being consistent with theoretical predictions. The particle density distributions were measured over the whole region of the suspensions (separated into two phases) at various pH values using a rapid freezing method. A phase diagram was determined thereby, where the critical (minimal) packing fraction of the particles for the Sm phase showed a nonlinear decrease from 0.43 to 0.12 with increasing pH. Rod-rod spacings in the Sm phase estimated experimentally at various pH were well explained using Derjaguin-Landau-Verwey-Overbeek (DLVO) type pair potentials. It is suggested that Sm ordering can be induced by attractive minima at pH<2.2, while driven by soft repulsions at pH>2.6. The former Sm ordering is expected to be the condensation-type phase transition and the latter the disorder-order transition.     

Modes of conformational changes of proteins adsorbed on a planar hydrophobic polymer surface reflecting their adsorption behaviors

Infrared spectra of hen egg white lysozyme and bovine serum albumin (BSA) adsorbed on a solid poly tris(trimethylsiloxy)silylstyrene (pTSS) surface in D2O solution were measured using attenuated total reflection (ATR) Fourier transform infrared spectroscopy. From the area and shape of the amide I' band of each spectrum, the adsorption amount and the secondary structure were determined simultaneously, as a function of adsorption time. We could show that the average conformation for all the adsorbed lysozyme molecules was solely determined by the adsorption time, and independent of the bulk concentration, while the adsorption amount increased with the bulk concentration as well as the adsorption time. These results suggest that lysozyme molecules form discrete assemblies on the surface, and that the surface assemblies grow over several hours to have a definite architecture independent of the adsorption amount. As for BSA, the extent of the conformational change was solely determined by the adsorption amount, regardless of the bulk concentration and the adsorption time. These differences in the adsorption properties of lysozyme and BSA may reflect differences in their conformational stabilities.     

Computational study of the aminolysis of esters. The reaction of methylformate with ammonia

The aminolysis of esters is a basic organic reaction considered as a model for the interaction of carbonyl group with nucleophiles. In the present computational study the different possible mechanistic pathways of the reaction are reinvestigated by applying higher level electronic structure theory, examining the general base catalysis by the nucleophile, and a more comprehensive study the solvent effect. Both the ab initio QCISD/6-31(d,p) method and density functional theory at the B3LYP/6-31G(d) level were employed to calculate the reaction pathways for the simplest model aminolysis reaction between methylformate and ammonia. Solvent effects were assessed by the PCM method. The results show that in the case of noncatalyzed aminolysis the addition/elimination stepwise mechanism involving two transition states and the concerted mechanism have very similar activation energies. However, in the case of catalyzed aminolysis by a second ammonia molecule the stepwise mechanism has a distinctly lower activation energy. All transition states in the catalyzed aminolysis are 10-17 kcal/mol lower than those for the uncatalyzed process.     

Broad spectrum and mode of action of an antibiotic produced byScytonema sp. TISTR 8208 in a seaweed-type bioreactor

A photobioreactor was constructed using anchored polyurethane foam strips (1 x 1 x 40 cm) fixed onto a stainless-steel ring to prevent flotation, as a biomass support material (BSM). This type of reactor was named a seaweed-type bioreactor. A filamentous cyanobacterium, Scytonema sp. TISTR 8208, which produces a novel cyclic dodecapeptide antibiotic, was immobilized in seaweed-type photobioreactor and cultivated with air containing 5% CO₂ sparged at a gas flow rate of 250 mL/min under illumination at a light intensity of 200 μmol photon m^-2s^-1. The antibiotic produced in the seaweed-type photobioreactor was purified by HPLC and examined regarding its spectrum and mode of action. The antibiotic effectively inhibited the growth of Gram-positive bacteria, pathogenic yeasts, and filamentous fungi, but it had only a weak effect on Gram-negative bacteria. Scanning electron micrograph analysis showed that the most characteristic change was swelling of the cells after exposure to the antibiotic. The antibiotic seems to alter the conformation of the microbial cell membrane, thereby changing its permeability, leading to osmotic shock.     

Response characteristics of the glucose-sensitive field-effect transistor. Computer simulation of the effect of gluconolactonase coimmobilization in a glucose oxidase membrane

The bienzyme system consisting of glucose oxidase and gluconolactonase was investigated using a conventional diffusion-kinetics model for an enzyme-modified field-effect transistor (FET) to clarify the effect of gluconolactonase coimmobilization in a glucose oxidase membrane on the steady-state response amplitude of a glucose sensor based on a FET. The model includes spontaneous and enzymatic hydrolysis reactions of d-glucono-δ-lactone and it elucidated the following experimental results: a glucose sensor with a membrane (about 1 μm in thickness) coimmobilizing these enzymes showed a sufficient response amplitude, whereas without coimmobilization of gluconolactonase no detectable response was observed up to 3 mM glucose; and the response amplitude depended strongly on the amount of lactonase in the membrane. The model also predicted an optimum enzyme ratio for coimmobilization in a membrane.     

Meerwein-Ponndorf-Verley alkynylation of aldehydes: essential modification of aluminium alkoxides for rate acceleration and asymmetric synthesis

A novel carbonyl alkynylation has been accomplished based on utilization of the Meerwein-Ponndorf-Verley (MPV) reaction system. The success of the MPV alkynylation crucially depends on the discovery of the remarkable ligand acceleration effect of 2,2'-biphenol. For example, the alkynylation of chloral (2c) with the aluminium alkoxide 6(R = Ph), prepared in situ from Me(3)Al, 2,2'-biphenol and 2-methyl-4-phenyl-3-butyn-2-ol (1a) as an alkynyl source, proceeded smoothly in CH(2)Cl(2) at room temperature to give the desired propargyl alcohol 3ca in almost quantitative yield after 5 h stirring. The characteristic feature of this new transformation involving no metal alkynides can be visualized by the fact that the alkynyl group bearing keto carbonyl was transferred successfully to aldehyde carbonyl without any side reactions on keto carbonyl. Although the use of (S)-1,1[prime or minute]-bi-2-naphthol and its simple analogues was found to be unsuitable for inducing asymmetry in this reaction, design of new chiral biphenols bearing a certain flexibility of the biphenyl axis led to satisfactory results in terms of enantioselectivity as well as reactivity.