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.     

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.     

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.     

In Situ Processing of Nano Crystalline Oxide Particles/Polymer Hybrid

Nano sized crystalline particles/polymer hybrids were synthesized form designed metal-organic precursors. The newly developed method is composed of the synthesis of organic matrix by polymerization and the in situ nucleation and growth of crystalline oxide particles in the organic matrix below 100°C. The design of metal-organic precursor modified with polymerizable ligand and the selection of reaction conditions does influence the size and crystallinity of ceramic particles in organic matrix. The nano-sized magnetic particle/polymer hybrid exhibits the interesting feature of superparamagnetism and quantum size effect. The crystalline particles of BaTiO₃/, PbTiO₃/, and KNbO₃/polymer hybrids behave to be dielectric and show the typical electro-rheological behavior.     

Stereoselective syntheses of 4-hydroxy 4-substituted glutamic acids

The 4-hydroxy 4-substituted glutamic acid moiety is a common substructure of biologically important natural products such as monatin [(2S,4S)-2], lycoperdic acid (3), and dysiherbaine (4). To develop methodology for syntheses of these natural products, cycloadditions of nitrone 5 with 2-substituted 2-propen-1-ols 6 and 2-substituted acrylates 8 were investigated. Reactions of nitrone 5 with alcohols 6 in the presence of MgBr2OEt2 gave cycloadducts 7 in a highly stereoselective manner, whereas noncatalyzed reactions of 5 with acrylates 8 afforded adducts 9. Using the former reaction, syntheses of monatin [(2S,4S)-2], monatin derivative 18, and lycoperdic acid (3) were accomplished. The C4-epimer of monatin [(2S,4R)-2)] was also synthesized by employing the latter cycloaddition.     

Structures and ligand exchange of N-confused porphyrin dimer complexes with group 12 metals

N-confused 5,20-diphenylporphyrin (NCDPP, 1) formed 2:2 dimer complexes with group 12 metals both in the solid state and in solution. X-ray single-crystal analyses of the Zn(II) and Cd(II) complexes (7, 8) revealed that each metal ion is coordinated with three inner core nitrogens and a peripheral nitrogen of the other NCDPP in the pair. In the (1)H NMR spectra of 7, 8, and the Hg(II) complex (9), the outer alpha-H signals of the confused pyrrole ring appeared in the upfield region at 2.57, 3.44, and 3.60 ppm, respectively, due to the ring current effect by the coordinated porphyrins. In the case of the Cd(II) and Hg(II) complexes (8, 9), additional magnetic couplings with the metal nuclei of the partner rings were observed. The equilibrium constants (K) of the monomer exchange reaction at 25 degrees C were determined to be 2.5, 1.3, and 0.6 for the (Zn-Cd), (Cd-Hg), and (Zn-Hg) heterodimer complexes, respectively, from the (1)H NMR spectra of a solution containing two different dimers. Furthermore, a metal-transfer reaction from a Zn(II) NCP dimer complex to the free base porphyrin was demonstrated.     

Electronic structures of I2− and I4− ions in γ-irradiated rigid solutions

Radical-anions of iodine, bromine, and monoiodochloride are produced in γ-irradiated amorphous solids at 77 K, and their electronic and ESR spectra measured. On limited warming of the irradiated solution dimerization by the reaction I₂^? + I₂ → I₄^? occurs to produce the same species as reported by Fornier de Violet et al. The electronic structure of the dimeric anion is discussed in comparison with the monomeric anion.     

Thermal and palladium-catalyzed [3 + 2] synthesis of cyclopentadienone acetals from cyclopropenone acetals and acetylenes

[reaction: see text] Substituted cyclopentadienone acetals (CPDAs) were synthesized by a thermal or palladium-catalyzed [3 + 2] cycloaddition reaction of a substituted cyclopropenone acetal to an electron-deficient acetylene. The synthesis afforded di-, tri-, and tetra-substituted CPDAs of considerable structural varieties that undergo Diels-Alder reaction to produce bicyclo[2.2.1]heptenes.