NMR study on the photoresponsive DNA tethering an azobenzene. Assignment of the absolute configuration of two diastereomers and structure determination of their duplexes in the trans-form

Two diastereomers of a photoresponsive oligodeoxyribonucleotide tethering a trans-azobenzene, based on the chirality of the central carbon of a diol linker, were separated by reversed-phase HPLC. On the basis of 2D NMR analysis, absolute configurations of the diastereomers alpha and beta (tentatively designated from differences in their retention time) were determined as R- and S-forms, respectively. For both diastereomers, their NMR-determined duplex structure showed that trans-azobenzene intercalates between base pairs, because distinct NOEs were observed between the protons of azobenzene and those of the adjacent base pairs, such as with the imino protons and methyl protons of thymine. The melting temperatures of both duplexes were higher than that of the corresponding native duplex, which contained no azobenzene residue, due to the intercalated trans-azobenzene stabilizing the duplex by a stacking interaction. Between these two diastereomers, differences in T(m) were also found: the melting temperature of the R-form duplex (alpha-isomer) was higher than that of the S-form (beta-isomer). On the basis of the NMR-determined structure, this difference was attributed to the fact that the S-form (beta isomer) causes more stress forming the duplex than does the R-form (alpha isomer) due to disturbances of the right-hand helix.     

Skeletal diversity by allylation/RCM on Ugi four-component coupling reaction products

Here, we report a diversity-oriented synthetic approach toward skeletally diverse, cyclized peptidomimetics with diverse appendages. Starting from α-(N-acylamino)amides with various appendages, 12 to 16-membered lactams with defined olefin geometry were synthesized by a common synthetic sequence. We also synthesized the macrocycle in a liquid phase directed toward a construction of the peptidomimetics library.     

Synthesis and characterization of three novel perfluoro-oligothiophenes ranging in length from the trimer to the pentamer

In this Article, we report on the synthesis and full characterization of three perfluorinated oligothiophenes, ranging in length from the trimer to the pentamer (PF-nT, with n = 3, 4, or 5). The differential pulse voltammetry (DPV) analysis of the compounds showed that they can be both oxidized and reduced (i.e., they display a dual or amphoteric electrochemical behavior), with the reduction peaks positively shifted relative to those of the corresponding unsubstituted oligothiophenes. The electrochemically determined energy gaps are in agreement with those measured from the UV-vis-NIR absorption spectra in solution. The conjugational properties have been investigated by means of FT-Raman spectroscopy, both as pure solids and as dilute solutes in CH(2)Cl(2), revealing that: (i) pi-conjugation does not still reach saturation with chain length for the longest oligomer, and (ii) conformational distortions from a nearly coplanar arrangement of the successive thiophene units upon solution are not too large. DFT and TDDFT quantum chemical calculations have been performed, at the B3LYP/6-31G level, to assess information about the optimized molecular structure, equilibrium atomic charges distribution, energies and topologies of the frontier molecular orbitals (MO) around the gap, vibrational normal modes associated with the most outstanding Raman scatterings, and vertical one-electron excitations that give rise to the main optical absorptions.     

2-Oxo-1,3-dioxoles as specific substrates for measurement of arylesterase activity

Various 4-arylthiomethyl-2-oxo-1,3-dioxole derivatives IIIa-o were synthesized. Their hydrolysis rates by arylesterase (EC 3.1.1.2) and cholinesterase (EC 3.1.1.8) in human serum were evaluated. Some of them were not hydrolyzed by cholinesterase, but were hydrolyzed easily by arylesterase. Among the substrates, sodium 4-((5-methyl-2-oxo-1,3-dioxol-4-yl)methylthio)benzenesulfonate (IIIg) was selected for its substrate reactivity toward arylesterase and its good water solubility. In addition, neither aliesterase (EC 3.1.1.1), acetylesterase (EC 3.1.1.6) nor cholesterol esterase (EC 3.1.1.13) hydrolyzed the compound. IIIg is thus concluded to be a specific substrate for arylesterase. Our assay system for serum arylesterase using IIIg can be readily applied to an automatic analyzer in the diagnosis of liver cirrhosis.     

Photochemical study of [3(3)](1,3,5)cyclophane and emission spectral properties of [3n]cyclophanes (n = 2-6)

Thephotochemical reaction of [3(3)](1,3,5)cyclophane 2, which is a photoprecursor for the formation of propella[3(3)]prismane 18, was studied using a sterilizing lamp (254 nm). Upon photolysis in dry and wet CH2Cl2 or MeOH in the presence of 2 mol/L aqueous HCl solution, the cyclophane 2 afforded novel cage compounds comprised of new skeletons, tetracyclo[6.3.1.0.(2,7)0(4,11)]dodeca-5,9-diene 43, hexacyclo[6.4.0.0.(2,6)0.(4,11)0.(5,10)0(9,12)]dodecane 44, and pentacyclo[6.4.0.0.(2,6)0.(4,11)0(5,10)]dodecane 45. All of these products were confirmed by the X-ray structural analyses. A possible mechanism for the formation of these photoproducts via the hexaprismane derivative 18 is proposed. The photophysical properties in the excited state of the [3n]cyclophanes ([3n]CP, n = 2-6) were investigated by measuring the emission spectra and determining the quantum yields and lifetimes of the fluorescence. All [3n]CPs show excimeric fluorescence without a monomeric one. The lifetime of the excimer fluorescence becomes gradually longer with the increasing number of the trimethylene bridges. The [3n]CPs also shows excimeric phosphorescence spectra without vibrational structures for n = 2, 4, and 5, while phosphorescence is absent for n = 3 and 6. With an increase in symmetry of the benzene skeleton in the [3(3)]- and [3(6)]CPs, the probability of the radiation (phosphorescence) process from the lowest triplet state may drastically decrease.     

Modern microscopy methods for the structural study of porous materials

This article describes a number of important recent microscopy tools and their application in particular to the study of porous inorganic materials. The authors believe that these new techniques are on the threshold of delivering enormous new power in the chemist's arsenal for understanding new and complex behaviour in multi-component, hierarchical or composite materials. In particular we consider the contribution of electron crystallography, three-dimensional electron tomography, ultra-high resolution scanning electron microscopy as well as the combined application of high-resolution electron microscopy and atomic force microscopy to the study of surfaces and crystal growth. Much of this work has taken on a particular significance owing to the ground breaking work of scientists at Mobil and in Japan 10 years ago in the successful synthesis of materials with porosity on many length scales achieved through the cooperative self-assembly between inorganic and organic phases. This resulted in a series of materials known as M41S of which MCM-41 and MCM-48 were two of the first and most important structures to be synthesised. This has led to a wealth of new porous structures with order over many length scales and has presented new problems in characterisation. Microscopy methods properly executed are particularly important in the study of this new class of material.     

Motor protein nano-biomachine powered by self-supplying ATP

A new nano-biomachine has been created from microtubules (MTs) and hetero-bifunctional polymer particles bearing pyruvate kinase, which is propelled on glass surfaces coated with kinesin by use of self-supplying ATP.     

NOx-Sorbing Metal Oxides, MnOx–CeO2. Oxidative NO Adsorption and NOx–H2 Reaction

(n)MnO_x–(1?n)CeO₂ binary oxides have been studied for the sorptive NO removal and subsequent reduction of NO_x sorbed to N₂ at low temperatures (≤150 °C). The solid solution with a fluorite-type structure was found to be effective for oxidative NO adsorption, which yielded nitrate (NO^? ₃) and/or nitrite (NO^? ₂) species on the surface depending on temperature, O₂ concentration in the gas feed, and composition of the binary oxide (n). A surface reaction model was derived on the basis of XPS, TPD, and DRIFTS analyses. Redox of Mn accompanied by simultaneous oxygen equilibration between the surface and the gas phase promoted the oxidative NO adsorption. The reactivity of the adsorbed NO_x toward H₂ was examined for MnO_x–CeO₂ impregnated with Pd, which is known as a nonselective catalyst toward NO–H₂ reaction in the presence of excess oxygen. The Pd/MnO_x–CeO₂ catalyst after saturated by the NO uptake could be regenerated by micropulse injections of H₂ at 150 °C. Evidence was presented to show that the role of Pd is to generate reactive hydrogen atoms, which spillover onto the MnO_x–CeO₂ surface and reduce nitrite/nitrate adsorbing thereon. Because of the lower reducibility of nitrate and the competitive H₂–O₂ combustion, H₂–NO reaction was suppressed to a certain extent in the presence of O₂. Nevertheless, Pd/MnO_x–CeO₂ attained 65% NO-conversion in a steady stream of 0.08% NO, 2% H₂, and 6% O₂ in He at as low as 150 °C, compared to ca. 30% conversion for Pd/γ–Al₂O₃ at the same temperature. The combination of NO_x-sorbing materials and H₂-activation catalysts is expected to pave the way to development of novel NO_x-sorbing catalysts for selective deNO_x at very low temperatures.     

1,2,4-Triazines, 9. The synthesis of novel 4-amino-1,6-dihydro-1,2,4-triazinones

3-Alkylthio-4-amino-1,6-dihydro-1,2,4-triazin-5(4H)-ones were synthesized by the reduction of 3-thio-4-amino-1,2,4-triazine-3,5(2.H,4H)-diones and successive S-alkylation. The regiospecific alkylation on the N-1 position or the exo amino group leads to a variety of 1,6-dihydro-1,2,4-triazin-5(4H)-one derivatives. An alternative synthesis of 3-thio-4-amino-1,6-dihydro-1,2,4-triazine-3,5(2H,4H)-diones was accomplished through the cyclization of 1-thiocarbohydrazidoacetamide derivatives.