A quantum chemical study of the catalysis for cytidine deaminase: contribution of the extra water molecule

Cytidine deaminase is known as an important enzyme responsible for the hydrolytic deamination of cytidine, which is applied as a key step to the conversion of the precursor of the cancer drug to an active form in the living body. Cytidine with water is efficiently converted to uridine with ammonia in the cleft of cytidine deaminase. In this work, the catalysis of cytidine deaminase for the hydrolytic deamination was examined using cytosine as a model of cytidine and the model molecules for the active site of cytidine deaminase by means of the quantum chemical method. We especially investigated the contribution of the water molecule from the solvent to the catalysis, because the X-ray diffraction analysis of a crystal structure has revealed the existence of the water molecule in the vicinity of the substrate bound to the active site inside the cleft. Our computations showed that the extra water molecule from the solvent has a possibility to support the catalysis of cytidine deaminase.     

Dimerization and double proton transfer-induced tautomerism of 4(3H)-pyrimidinone in solution studied by IR spectroscopy and quantum chemical calculations

The tautomerism and dimerization of 4(3H)-pyrimidinone (4(3H)Pyr) in carbon tetrachloride (CCl4) and chloroform (CHCl3) solutions were investigated using IR spectroscopy and quantum chemical calculations. The observed IR spectra in the NH and OH stretching regions clearly revealed the predominance of the keto tautomer in both solvent systems. The enol form only exists in a very small proportion in the CCl4 solution. The tautomeric constant for the two monomers KT[OH/NH] = 0.012 and DeltaE = 2.62 kcal/mol were estimated at 25 degrees C. This result was supported by the self-consistent reaction field/polarizable continuum (SCRF/PCM) calculation at the MP4(full, SDQ)/aug-cc-pVDZ level, which predicted DeltaE = 3.06 kcal/mol in CCl4. In the C=O stretching region, two bands were observed, suggesting the coexistence of two keto structures at equilibrium. The calculated IR spectra indicated that the bands at 1711 and 1675 cm(-1) arise from the keto monomer and keto-keto (KK) ring dimer, respectively. At elevated temperature, the populations of both the keto and enol monomers increased for the CCl4 solution. The present study revealed that the keto <--> enol tautomerization does not occur in the isolated monomer molecule. The double proton transfer (DPT) reaction in the KK ring dimer presumably plays a substantial role in the population increase of the enol monomer. To our knowledge, this may be the first observation of the tautomerization in a model base pair via the temperature-induced ground-state DPT reaction under a nonpolar liquid environment reported so far. This tautomerism can serve as a mimic circumstance for the spontaneous mutations induced by proton transfer in the DNA base pairs.     

Potential oscillations in galvanostatic electrooxidation of formic acid on platinum: a mathematical modeling and simulation

We have modeled temporal potential oscillations during the electrooxidation of formic acid on platinum on the basis of the experimental results obtained by time-resolved surface-enhanced infrared absorption spectroscopy (J. Phys. Chem. B 2005, 109, 23509). The model was constructed within the framework of the so-called dual-path mechanism; a direct path via a reactive intermediate and an indirect path via strongly bonded CO formed by dehydration of formic acid. The model differs from earlier ones in the intermediate in the direct path. The reactive intermediate in this model is formate, and the oxidation of formate to CO2 is rate-determining. The reaction rate of the latter process is represented by a second-order rate equation. Simulations using this model well reproduce the experimentally observed oscillation patterns and the temporal changes in the coverages of the adsorbed formate and CO. Most properties of the voltammetric behavior of formic acid, including the potential dependence of adsorbate coverages and a negative differential resistance, are also reproduced.     

Effect of oxygen deficiency on response of CR-39 on board scientific balloons

We should be careful about the effect of oxygen deficiency on polymeric track detectors even at balloon altitude. Results of balloon experiments and calibration experiments in a vacuum chamber at different pressures show that the effect of oxygen deficiency becomes serious at a pressure below 10 hPa.     

Sulfur-containing polymers. X. Aromatic poly(sulfenyl thiocarbonates)

Aromatic poly(sulfenyl thiocarbonates) have been synthesized by the interfacial polycondensation of bis(dithiocarbonyl chlorides) with bisphenols. Bisphenols having the hydroxyl groups on separate rings gave polymers in high yields. The inherent viscosities of the polymers ranged from 0.22 to 0.51. In general, they were soluble in chloroform, sym-tetrachloroethane, hexamethylphosphoramide, m-cresol, and dimethylformamide and formed transparent tough films on evaporation of chloroform solutions. Almost all of the polymers were amorphous and gave melt-spun fibers. The polymer films decomposed upon ultraviolet irradiation with liberation of carbonyl sulfide.     

Chemiluminescence study on the oxidation of several polyolefins—I. Thermal-induced degradation of additive-free polyolefins

Chemiluminescence (CL) has been applied to evaluate the oxidation susceptibility of various polyolefins: low-density polyethylene (LDPE), linear low-density polyethylene (LLDPE), high-density polyethylene (HDPE) and isotactic polypropylene (i-PP). The intensity of CL emission in inert atmosphere could be related to the previous oxidation level. The thermal stability at 170 °C of the hydroperoxides in LDPE seems to be lower than that in LLDPE or HDPE. The kinetic parameters of the oxidation at 170 °C in oxygen, calculated from CL data, suggest the following stability order: HDPE > LLDPE > LDPEi-PP. The intensity of CL emission was related to the CH₃ content as evaluated by Fourier transform infra-red spectroscopy.     

Sugar binding specificities of anti-H(O) lectins disclosed by use of fucose-containing human milk oligosaccharides as binding inhibitors

The binding to normal and sialidase-treated human erythrocytes of six 125I-labeled lectins [Ulex europeus lectin I (UEA-1) and II (UEA-II), Laburnum alpinum lectins I (LAA-I) and II (LAA-II), and Cytisus multiflorus lectins I (CMA-I) and II (CMA-II)], was studied in detail. Quantitative inhibition assays of the lectin binding to the cells were also performed with various human milk oligosaccharides as inhibitors. Based on a comparison of the inhibition constants of the inhibitors thus obtained with the association constants of the lectins to the cells, the relative activities of cell surface blood group antigens toward the lectins are discussed.     

Synthesis and anti-inflammatory activity of antioxidants, 4-alkylthio-o-anisidine derivatives.

In order to search for anti-inflammatory agents against autoimmune diseases, we synthesized 4-alkylthio-o-anisidine derivatives possessing antioxidant activity, and tested them for anti-inflammatory activity against the Arthus reaction in mice. Experimental inflammations, including the Arthus reaction, concanavalin A, phorbol ester and pyrophosphate-induced edemas in rats were inhibited by 4-propylthio-o-anisidine, which inhibited autoxidation of rat brain homogenate and suppressed the lipopolysaccharide-induced increase in the plasma malondialdehyde level in mice. An antioxidant may be an effective agent in immune complex type inflammation where active oxygen species play an important role.     

Synthesis of deuterium-labeled 16 alpha,19-dihydroxy C19 steroids as internal standards for gas chromatography-mass spectrometry.

[2 beta,7,7,16 beta-2H4]16 alpha,19-Dihydroxyandrost-4-ene-3,17-dione (14) and [7,7,16 beta-2H3]3 beta,16 alpha,19-trihydroxyandrost-5-en-17-one (16), with high isotopic purity, respectively, were synthesized from unlabeled 3 beta-(tert-butyldimethylsiloxy)-androst-5-ene-17 beta-yl acetate (1). The deuterium introduction at C-7 was carried out by reductive deoxygenation of the 7-keto compound 3 with dichloroaluminum deuteride and that at C-2 beta and/or C-16 beta by controlled alkaline hydrolysis of 16-bromo-17-ketone 11 or 12 with NaOD in D2O and pyridine. [7,7-2H2]3 beta-Hydroxyandrost-5-en-17-one (6), obtained from compound 1 by a five-step sequence, was converted to compound 14 or 16 by an eight-step or seven-step sequence, respectively. The labeled steroids 14 and 16 are useful as internal standards for gas chromatography-mass spectrometry analysis of the endogenous levels.