Cavity search: An algorithm for the isolation and display of cavity-like binding regions

Summary A set of algorithms designed to enhance the display of protein binding cavities is presented. These algorithms, collectively entitled CAVITY SEARCH, allow the user to isolate and fully define the extent of a particular cavity. Solid modeling techniques are employed to produce a detailed cast of the active site region, which can then be color-coded to show electrostatic and steric interactions between the protein cavity and a bound ligand.     

Poly(dimethylsiloxane) microchip for precolumn reaction and micellar electrokinetic chromatography of biogenic amines

We have demonstrated that precolumn derivatization and capillary electrophoresis separation on a poly(dimethylsiloxane) (PDMS) microchip can be realized as efficient as those on glass microchips. In an optimized condition of micellar electrokinetic chromatography (MEKC), using 25 mM sodium borate buffer (pH 10.0) with 25 mM sodium dodecyl sulfate (SDS) and 5% v/v methanol, the electroosmotic flow in an oxidized PDMS microchip is stabilized within 3% for days. By employing a fluorometric derivatization with o-phthaldialdehyde (OPA) in an optimally designed reaction chamber, four most important biogenic amines occurring in foods, histamine, tyramine, putrescine, and tryptamine, are quantitatively determined in less than 1 min at the levels applicable to real samples. The migration behaviors of anionic OPA-derivatized biogenic amines under the MEKC conditions are analyzed, and it has been found that under our separation conditions, the electrophoretic mobility of the SDS micelles is significantly greater than those of the anions in the aqueous phase. The channel manifold in a PDMS substrate is fabricated using replica molding against a thick photoresist, SU-8, pattern generated by photolithography. The plate with the microchannel pattern is strongly, irreversibly bonded to another PDMS plate by using a new bonding technique, which employs surface oxidation by corona discharge generated from a cheap, handy source, Tesla coil.     

A novel synthetic method for 2-arylmethyl substituted imidazolines and imidazoles from 2-aryl-1,1-dibromoethenes

Various 2-arylmethylimidazolines were prepared by treating readily available 2-aryl-1,1-dibromoethenes with ethylenediamine under mild conditions and further converted into the corresponding imidazoles smoothly with Swern oxidation.     

Feature based fuzzy matching of 2D gel electrophoresis images

Automatic alignment (matching) of two-dimensional gel electrophoresis images is of primary interest in the evolving field of proteomics. In the present study, feature-based matching techniques, in their classical and robust versions, are described, and an automatic method of fuzzy alignment (FA) is introduced. This method allows automatic matching of two gel images with different numbers of features with unknown correspondence. Performance of FA is tested on simulated and real data sets.     

Characterization of the short-chain branches in poly(vinyl chloride)s by γ irradiation of the reduced polymers

The volatile products from the γ irradiation of samples of poly(vinyl chloride) prepared under different conditions and reduced to the corresponding polyethylenes have been measured quantitatively and compared with those for low- and high-density polyethylenes and copolymers of ethylene with small amounts of α-olefins. The presence of methyl branches is clearly demonstrated and there is also evidence for ethyl and butyl branches, although these had not been considered significant in previous [¹³C] NMR studies. The method is shown to be extremely sensitive to small quantities of residual trialkyl tin hydride reductant occluded in, and possibly also reacted with, the polymer, and to residual chlorine (<0.5%). The yields of alkanes are higher than expected from the branch frequencies determined by i.r. and [¹³C] NMR and results for ethylene-α-olefin copolymers. This difference is apparently due to sensitisation of the radiation degradation by residual chlorine and reductant. Quantitative determinations of branch frequencies by the radiolytic method are unlikely to be obtained until these problems are overcome.     

Relaxation of the optical Kerr effect of anisotropic molecules in mixed liquids

The relaxation time of the Kerr effect of nitrobenzene and m-nitrotoluene in various mixtures with carbon tetrachloride and various alcohols was determined by measuring the kinetics of the Kerr effect using picosecond laser techniques. These measurements yield information on the rotational motion of molecules in liquids. The relaxation time data are interpreted in terms of an effective local viscosity effect, pair correlation, and coupling of rotational motion with shear modes.     

Asymmetric Diels-Alder Reactions of Chiral Menthyl α-Sulfinylacrylates

Introducing two chiral auxiliaries, sulfoxide and menthol, into an acrylate would have either matched or mismatched pair systems. The presence of chiral menthol in α-sulfinylacrylates can change the diastereoselectivity from 24% d.e. to a single diastereomer by manipulation of the double asymmetric strategy.     

Conformation and chiroptical properties of mandelic acids

Using CD data (solution, solid state, various temperatures), X-ray data and MO calculations for a number of substituted mandelic acids (phenylglycolic acids) an attempt was made to explain the different results for the relation between sign of the ¹L_b CD band and substitution pattern as described in the literature for various types of aromatic compounds. Moreover the reported sector rule has been reconsidered taking into account the sign and magnitude of the spectroscopic moments. It has been found that in any explanation of the signs of the ¹L_b CD bands of substituted aromatic compounds both the conformational behaviour and the spectroscopic moments should be taken into account.     

Efficient oxidation of benzylic alcohols with [hydroxy(tosyloxy)iodo]benzene under microwave irradiation

An efficient method for the oxidation of benzylic alcohols with [hydroxy(tosyloxy)iodo]benzene under solvent-free microwave irradiation conditions is described.     

The Photochemistry of Diazomethane the Reactions of Methylene with Toluene and P-Xylene in Liquid Phase (I)

The photochemistry of diazomethane in toluene and p-xylene solutions was investigated. The reactions of methylene with toluene gave eight products. In the diazomethane p-xylene solution, p-ethyltoluene, 1,2,4-trimethylbenzene, 1,4-dimethylcyclohepatriene-1,3,5 and three unidentified compounds were found as products of the reaction of methylene with p-xylene. The relative rates of addition and insertion reaction of methylene with toluene and p-xylene have been calculated.