Characterization of a Nudix hydrolase from <Emphasis Type="Italic">Deinococcus radiodurans</Emphasis> with a marked specificity for (deoxy)ribonucleoside 5'-diphosphates

Background  

Nudix hydrolases form a protein family whose function is to hydrolyse intracellular nucleotides and so regulate their levels and eliminate potentially toxic derivatives. The genome of the radioresistant bacterium Deinococcus radiodurans encodes 25 nudix hydrolases, an unexpectedly large number. These may contribute to radioresistance by removing mutagenic oxidised and otherwise damaged nucleotides. Characterisation of these hydrolases is necessary to understand the reason for their presence. Here, we report the cloning and characterisation of the DR0975 gene product, a nudix hydrolase that appears to be unique to this organism.     

Stereoselective acid-catalyzed homoallylic rearrangement of cyclopropylsilylmethanols: an efficient route to Z-homoallyl derivatives

Treatment of cyclopropylsilylmethanols derived from cyclopropyl silyl ketones with acid catalyst gives the corresponding silyl-substituted homoallyl derivatives in high yields with good stereoselectivity, independent of the substituents on the cyclopropyl ring. Cyclopropylsilylmethanols having a n-, s-butyl or phenyl group on the carbinyl carbon react to afford the E-homoallyl derivatives selectively. On the other hand, the reaction of cyclopropylsilylmethanols having a tert-butyl group gives Z-isomers exclusively. The following protiodesilylation of the resulting homoallyl derivatives proceeds with retention of configuration.     

Elucidation of solid-state complexation in ground mixtures of cholic acid and guest compounds

The solid-state complexation between cholic acid (CA) and either methyl p-hydroxybenzoate (MPB) or ibuprofen (IBP) was investigated. Powder X-ray diffractometry, IR spectroscopy and thermal analysis suggested the complex formation between CA and MPB as well as between CA and IBP by co-grinding method. The stoichiometry of CA-MPB was 1 : 1 while that of CA-IBP was 2 : 1, reflecting the effect of guest size on complex formation. The guest compounds were assumed to be included in the channel of complexes formed by hydrogen bonds among CA molecules.     

Sensitive measurement of methylene blue active substances by attenuated total reflection spectrometry with a trimethylsilane-modified glass slab optical waveguide

Attenuated total reflection spectrometry with a slab optical waveguide (SOWG) was explored for the simple, rapid and sensitive measurement of total anionic surfactants by the methylene blue active substance (MBAS) method. A fused-silica sheet used as a guiding layer was modified with trimethylsilane (TMS) to extract and concentrate the MBASs on the SOWG surface. Based on preliminary studies of the adsorption behavior and visible ATR spectrum of MB on the modified silica surface, a detection wavelength of 600 nm was chosen for the sensitive measurement of anionic surfactants. When the concentration of MB was set at 10 microM in the final measurement solution, the calibration curve for a typical anionic surfactant (sodium dodecylbenzenesulfonate) was linear up to 0.6 microM and the detection limit was 0.07 microM. The proposed method was applied to the determination of total anionic surfactants in river water.     

Voltammetric investigation of avidin-biotin complex formation using an electroactive bisbiotinyl compound

Formation of avidin-biotin complex was investigated using bisbiotinyl thionine (BBT) by means of voltammetric techniques. Thionine is an electroactive compound and has two amino groups that are necessary for the reaction with a biotinylation reagent. The biotinylation of thionine produces a new reagent with two biotin moieties at each end of thionine. Three BBTs of different lengths of the spacer that connects the biotin moiety to the thionine moiety were prepared. The avidin-biotin binding assay was achieved by measuring the electrode response of the thionine moiety in BBT. The binding affinity and the conformation of complex, which depended on the length of spacer, are discussed. BBT in which the spacer is shortest (BBT-S, distance between carbonyl group of the two biotin moieties: 11 Å) binds with only one avidin molecule. BBT with medium length of spacer (BBT-M, 28.8 Å) forms the complex with two avidin molecules. BBT with the longest spacer (BBT-L, 46.6 Å) allows binding with two avidin molecules as well as intramolecular binding within one avidin molecule. The affinity constants of BBT-S, BBT-M and BBT-L for avidin were estimated to be 7.0 × 10¹² M⁻¹, 3.2 × 10¹² M⁻¹ and 4.0 × 10¹² M⁻¹, respectively.     

Theoretical study of the thermal interconversion mechanism between the norbornadiene and quadricyclane radical cations

Geometry optimizations at the UHF/6-31G^* and UMP2/6-31G^* levels of theory were performed to find the transition state in the interconversion between norbornadiene (N) and quadricyclane (Q) radical cations. Two transition structures, TS^+·₁ and TS^+·₂, were obtained which have C₁ and C₂ symmetry, respectively. Vibrational analysis at the UHF and UMP2 levels of theory and IRC calculation showed that TS^+·₁ is the true transition state connecting N^+· and Q^+·, while TS^+·₂ is a second order saddle point.     

Effects of electron beam preirradiation on the γ radiolysis of polyethylene

The γ radiolysis of polyethylene preirradiated with electron beams to 3 Mrad was carried out at 30–100°C in vacuo with a dose rate of 6.35 × 10⁵ rad/hr. The hydrogen formation in the γ radiolysis was little affected by the preirradiation of electron beams, whereas the formation of trans-vinylene unsaturation and gel was somewhat retarded. The rates of the formation of hydrogen and trans-vinylene unsaturation were described by the zero-order formation kinetics with respect to each concentration combined with the first-order disappearance. The apparent rate constants and activation energies for the formation and disappearance of hydrogen and trans-vinylene unsaturation were almost independent of the preirradiation. The gel fraction was analyzed by using the Charlesby–Pinner equation. The G values of crosslinking and main chain scission were increased by the preirradiation, whereas their activation energies remained unaltered. On the basis of these results the effects of preirradiation on the reactions induced by γ rays in polyethylene were discussed.     

Valency states of radioactive antimony in hydrochloric acid solutions. Preparation and stability of antimony tracer for radioanalytical use

Variations of¹²⁵Sb valency states in HCl solutions were investigated by the use of the N-benzoyl-N-phenyl-hydroxylamine (BPHA) extraction method.¹²⁵Sb(V) is completely reduced to Sb(III) by one hour refluxing in conc. HCl.¹²⁵Sb(III) is gradually oxidized to Sb(V) in solutions of low HCl concentrations by the effects of their own radiations. Natural light promotes such oxidation reactions. By utilizing such oxidation-reduction effects¹²⁵Sb(V) can be easily prepared from¹²⁵Sb(III) and also¹²⁵Sb(III) can be prepared by the reduction of Cl _aq ⁻ . Their valency states were stable on keeping them in brown-colored bottles at 6M HCl concentrations.     

Optimal control of ultrafast cis-trans photoisomerization of retinal in rhodopsin via a conical intersection

Optimal control simulation is applied to the cis-trans photoisomerization of retinal in rhodopsin within a two-dimensional, two-electronic-state model with a conical intersection [S. Hahn and G. Stock, J. Phys. Chem. B 104, 1146 (2000)]. For this case study, we investigate coherent control mechanisms, in which laser pulses work cooperatively with a conical intersection that acts as a "wave-packet cannon." Optimally designed pulses largely consist of shaping subpulses that prepare a wave packet, which is localized along a reaction coordinate and has little energy in the coupling mode, through multiple electronic transitions. This shaping process is shown to be essential for achieving a high target yield although the envelopes of the calculated pulses depend on the local topography of the potential-energy surfaces around the conical intersection and the choice of target. The control mechanisms are analyzed by considering the motion of reduced wave packets in a nuclear configuration space as well as by snapshots of probability current-density maps.     

Crystal structure of cobalt molybdate hydrate CoMoO4·nH2O

We have determined the crystal structure of the title compound, which has a triclinic cell with cell parameters of , , , α=76.617°, β=84.188°, γ=74.510° and space group . The crystal structure suggests the chemical formula CoMoO₄·3/4H₂O. The structure consists of MoO₄ tetrahedra and CoO₆ octahedra, confirming the earlier X-ray absorption near-edge spectroscopic (XANES) investigation on the hydrate. The comparison of the crystal structures of the hydrate and the α-,β-, and hp-phases shows that the hydrate exhibits metal cation coordinations similar to those of the β-phase, but had arrangements of CoO₆ and MoO_n polyhedra similar to those of the hp-phase.