Molecular Recognition of Nucleic Acid Bases in Water by Hydrogen Bonding of Poly(vinyldiaminotriazine)

Poly(2-vinyl-4,6-diamino-1,3,5-triazine) efficiently binds nucleic acid bases and nucleosides in water by using complementary hydrogen bonding. The binding activity decreases in the order: U, T > A C, G. The corresponding monomer shows virtually no activity, indicating a predominant role of polymer effect for the molecular recognition in water.     

Synthesis of disubstituted cucurbit[6]uril and its rotaxane derivative

Synthesis of diphenyl cucurbit[6]uril (CB[6]) has been achieved via co-oligomerization of diphenyl glycoluril and unsubstituted glycoluril. The unsymmetrically substituted CB[6], Ph(2)CB[6], was further converted to a rotaxane incorporating bis(dinitrophenyl)spermine. [reaction: see text]     

γ-Radiolysis of 5-fluorouracil and 5-fluorouridine derivatives having sulfur-containing substituents

γ-Radiolysis reactions of eight 5-fluorouracil (5-FU) derivatives having sulfonyl group-containing substituents at the 1-position and five 5-fluorouridine (5-FUR) derivatives having thioureido group-containing substituents were studied under the conditions where hydrated electron (e_aq^?) and hydroxyl radical (HO·) become the principal reactive species. The 5-FU and 5-FUR derivatives were radiolyzed to give 5-FU and 5-FUR, respectively. The efficiency of the reactions depended upon the nature of reactive species and also upon the nature of substituents. The reactivity features of the γ-radiolysis reactions are discussed.     

Second-order perturbational treatment of normal coordinates in the string model for the hydration reaction of formaldehyde

A perturbation theory for normal coordinates of nonadiabatic solvation is presented by means of the “string model” of chemical reactions. The dynamic normal coordinate is introduced for the perturbational treatment of the “intrinsic” normal coordinates that are orthogonal to the reaction path. The reaction is defined as the intrinsic reaction coordinate (IRC ) that is treated as a string. The string is thrown in the external force field that acts as a nonadiabatic source of perturbation. As an application of the present treatment, the effect of a water molecule for hydration reaction of formaldehyde is calculated. A second-order perturbation effect for the enhancement of the reaction rate is found.     

Reactivity of cobaloxime bound to polystyrene chain by carbon–cobalt σ bond

The (alkyl)-bis(dimethylglyoximato)pyridinecobalt attached to polychloromethylstyrene by a cobalt–carbon bond was prepared by the reaction of Co(II)(DH)₂Py with polychloromethylstyrene in benzene. The fraction of p-vinylbenzyl·Co(DH)₂Py introduced to the polymer was 8.1 and 2.1 mole %. The photodecomposition of the polymer-bonded cobaloxime was investigated by following the change of the visible spectrum. The rate constant k_dec of the polymer-bonded cobaloxime was 1.1 × 10^?2 sec^?1 in benzene; it is one-fourth of that of its monomeric analog, benzyl·Co(DH)₂Py. The k_dec values of the cobaloximes were also measured in benzene–dimethyl sulfoxide mixed solvents, and the polymer effects were discussed. The dependence of the photodecomposition on energy of the irradiation light was investigated, and it was found that the absorption band near 470 nm is important for the photodecomposition of the cobalt–carbon bond. Spectroscopic measurements of the ligand exchange reaction of polymer-bonded cobaloxime with pyridine in dimethyl sulfoxide gave a larger equilibrium constant (1.2 × 10⁴ liter/mole) than that of benzyl·Co(DH)₂Py (9.4 × 10² liter/mole). The kinetic data of the ligand exchange reaction indicated that the larger equilibrium constant for the polymeric system is due to the smaller rate constant of the reverse reaction. The thermodynamic parameters were also obtained.     

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.     

First asymmetric total synthesis of tetrodotoxin

Tetrodotoxin, a toxic principle of puffer fish poisoning, is one of the most famous marine natural products because of the complex structure having many functional groups and its potent biological activity leading to death. Since the structure elucidation in 1964, this toxin has been recognized as a formidable target molecule for total synthesis. We have recently achieved the first asymmetric total synthesis from 2-acetoxy-tri-O-acetyl-d-glucal as a chiral starting material. The highly hydroxylated cyclohexane ring was constructed by Claisen rearrangement and regioselective hydroxylations of an acetone moiety and an intramolecular directed aldol condensation of the precursor having methyl ketone with dihydroxyacetone, which was synthesized through Sonogashira coupling. Installation of nitrogen functionality was unsuccessful through an attempted Overman rearrangement. We, therefore, employed a new intramolecular conjugate addition strategy between the carbamate and unsaturated ester groups. The alpha-hydroxyl lactone moiety was synthesized through an intramolecular epoxide opening by the Z-enolate of aldehyde, which was followed by oxidation-reduction of the resulting cyclic vinyl ether. The lactone was then converted to a protected ortho ester, and then gunanidinylation was followed by cleavage of the 1,2-glycol to give the fully protected tetrodotoxin. Selection of the protective groups has finally led us to accomplish the total synthesis of tetrodotoxin in an enantiomerically pure form. All the stereogenic centers were controlled with high selectivity, and the hydroxyl groups were differently protected to discriminate for the future analogue synthesis of a bioorganic program. The synthetic tetrodotoxin was purified by ion exchange chromatography and characterized to be identical with the natural compound.     

Distributed computing and NMR constraint-based high-resolution structure determination: applied for bioactive Peptide endothelin-1 to determine C-terminal folding

Distributed computing has been implemented to the solution structure determination of endothelin-1 to evaluate efficiency of the method for NMR constraint-based structure calculations. A key target of the investigation was determination of the C-terminal folding of the peptide, which had been dispersed in previous studies of NMR, despite its pharmacological significances. With use of tens of thousands of random initial structures to explore the conformational space comprehensively, we determined high-resolution structures with good convergences of C-terminal as well as previously defined N-terminal structures. The previous studies had missed the C-terminal convergence because of initial structure dependencies trapped in localized folding of the N-terminal region, which are strongly constricted by two disulfide bonds.     

Conductive characteristics of radical‐bearing polythiophenes using a microcomb‐shaped electrode

The electric conductivity of π‐conjugated and radical‐bearing polymers, i.e., polythiophenes bearing pendant galvinoxyl and phenoxyl radical groups, was measured using a microcomb‐shaped electrode. The electric conductivity was found to be enhanced by the radical content in the polymer. The infrared (IR) and Raman spectroscopies suggested a structural change from an aromatic form to a quinoid one in the polythiophene backbone by the phenoxyl radical generation. The effect of the pendant galvinoxyl radical's unpaired electron on the electric conductivity of the polythiophene was discussed by comparing the conductivity of a radical‐bearing polystyrene and a polythiophene mixed with low‐molecular radical molecules. Copyright © 2007 John Wiley & Sons, Ltd.