Chemical synthesis of the 5-́half molecule of E.coli tRNA2GLY

A tritriacontanucleotide which has the sequence of the 5$\text{-}\text{?}$half molecule of E.coli glycine tRNA₂, was synthesized by the phosphotriester method involving p-anisidate protection for the 3$\text{-}\text{?}$phosphate ends. Di- and trinucleotide units were prepared from 5$\text{-}\text{?}$dimethoxytrityl-2$\text{-}\text{?}$O-tetrahydrofuranyl-3?-O-(o-chlorophenyl)phosphoryl derivatives of uridine, N-benzoylcytidine, N-benzolyadenosine and N-iso-butyrylguanosine by condensation with 3$\text{,}\text{?}$5$\text{-}\text{?}$unprotected nucleosides followed by phosphorylation to give 3$\text{-}\text{?}$phosphodiester blocks. The 3$\text{-}\text{?}$terminal dimers and trimers were synthesized by using 3$\text{-}\text{?}$(o- chlorophenyl)phosphoro-p-anisidates instead of 3?,5?-unprotected nucleosides. The 3?-phosphodiesters of oligonucleotides with a chain length of larger than 5 were obtained by removal of the 3?-phosphoro-p-anisidate with isoamyl nitrite. The 5$\text{-}\text{?}$dimethoxytrityl group was removed by treatment with zinc bromide under anhydrous conditions. Fragments were designed to use common dimer blocks and to reduce the step for 5$\text{-}\text{?}$deblocking of larger fragments. Finally a 3$\text{-}\text{?}$phosphodiester block with a chain length of 20 was condensed with a 5$\text{-}\text{?}$OH component (tridecanucleotide). The fully protected 33 mer was deblocked and purified by chromatography. The structural integrity of the product was confirmed by mobility shift analysis and complete digestion with RNase T2.     

Membrane-based microchannel device for continuous quantitative extraction of dissolved free sulfide from water and from oil

Underground fluids are important natural sources of drinking water, geothermal energy, and oil-based fuels. To facilitate the surveying of such underground fluids, a novel microchannel extraction device was investigated for in-line continuous analysis and flow injection analysis of sulfide levels in water and in oil. Of the four designs investigated, the honeycomb-patterned microchannel extraction (HMCE) device was found to offer the most effective liquid–liquid extraction. In the HMCE device, a thin silicone membrane was sandwiched between two polydimethylsiloxane plates in which honeycomb-patterned microchannels had been fabricated. The identical patterns on the two plates were accurately aligned. The extracted sulfide was detected by quenching monitoring of fluorescein mercuric acetate (FMA). The sulfide extraction efficiencies from water and oil samples of the HMCE device and of three other designs (two annular and one rectangular channel) were examined theoretically and experimentally. The best performance was obtained with the HMCE device because of its thin sample layer (small diffusion distance) and large interface area. Quantitative extraction from both water and oil could be obtained using the HMCE device. The estimated limit of detection for continuous monitoring was 0.05 μM, and sulfide concentrations in the range of 0.15–10 μM could be determined when the acceptor was 5 μM FMA alkaline solution. The method was applied to natural water analysis using flow injection mode, and the data agreed with those obtained using headspace gas chromatography-flame photometric detection. The analysis of hydrogen sulfide levels in prepared oil samples was also performed. The proposed device is expected to be used for real time survey of oil wells and groundwater wells.     

Synthesis of Star-Shaped Polymers via Coordination of Bipyridyl-Terminated Polyoxyethylene with Metal Ions

Abstract

This paper describes the synthesis of various star-shaped polymers by means of complexation of bipyridyl-terminated polyoxyethylene with Ru(II) ion. Three kinds of bipyridyl-terminated polyoxyethylenes of different molecular weights were prepared from the corresponding polyoxyethylene monomethyl ethers with narrow molecular weight distributions. Bipyridyl was found to be introduced quantitatively at the end of the polymers based on the results of UV spectra. The formation of a star-shaped polymer was carried out by the reaction of RuCl₃ with three equivalents of bipyridyl-terminated polyoxyethylene. The UV spectrum of the star-shaped polymer obtained supported the formation of a typical Ru(II) tris(bipyridyl) complex. From the results of GPC, the star-shaped polymer obtained had a higher molecular weight than the pre-polymer and showed a narrow molecular weight distribution. In the case of a Ni(II) or a Co(II) complex, however, the star-shaped polymer was found to be dissociated into three linear prepolymers under the conditions of GPC measurement.     

Synthesis of Substituted Phenyl Esters of Amino Acids and Polycondensation in Langmuirblodgett Films

Long-alkyl-chain phenyl esters of β-alanine, glycine, and L-valine were prepared, and their monolayer properties were correlated with their molecular structures. These compounds formed stable monolayers on acidic subphases. In particular, the p-hexadecylphenyl esters of β-alanine and glycine were remarkably stable, and their monolayers could be deposited on calcium fluoride plates as Y-type film by Blodgett's technique. The polycondensation of multilayers under an atmosphere saturated with triethylamine was investigated by changes in the IR spectra. It was determined that the polycondensation proceeded by a first-order reaction mechanism in the initial stage and that the rate in multilayers was faster than that in the bulk crystalline powder. These results suggest that the polycondensation is accelerated by a regular arrangement of the monomer in the multilayers, where the active sites are concentrated and located better for the polycondensation. In the case of the polycondensation in multilayers of the glycine ester, two kinds of condensation proceeded to afford poly(glycine) and 2,5-piperazinedione.     

Generation of 3-Carbanion Species from 3-Phenylsulfinyl- and 3-Phenylsulfonyl Propionic Acids

During the course of studies on butenolide synthesis¹ we have investigated the utilities of 3-sulfur-functionalized propionic acid derivatives. We report the results with 3-carbanion species obtained from 3-phenylsulfiny1- and 3-phenylsulfonylpropionic acids (1) and (2). These compounds were easily prepared from 3-phenylthiopropionic acid.     

Structural Elucidation of an Elicitor-Active Oligosaccharide,LN-3, Prepared from Algal Laminaran

Abstract

The primary structure of an elicitor-active oligosaccharide, LN-3, prepared from partially hydrolyzed algal laminaran was determined by means of the analyses of glycosyl-linkage, fragments by acetolysis, and glycosyl-sequence. The elicitor-active oligosaccharide, LN-3, is a pyridylaminated hepta-β-d-glucoside which was shown to have the following linear structure: β-d-Glcp(1→6)-β-d-Glcp(1→3)-β-d-Glcp(1→3)-β-d-Glcp(1→3)-β-d-Glcp(1→6)-β-d-Glcp(1→3)-Glc-PA.     

Application of plug–plug technique to ACE experiments for discovery of peptides binding to a larger target protein: A model study of calmodulin‐binding fragments selected from a digested mixture of reduced BSA

To discover peptide ligands that bind to a target protein with a higher molecular mass, a concise screening methodology has been established, by applying a “plug–plug” technique to ACE experiments. Exploratory experiments using three mixed peptides, mastoparan‐X, β‐endorphin, and oxytocin, as candidates for calmodulin‐binding ligands, revealed that the technique not only reduces the consumption of the protein sample, but also increases the flexibility of the experimental conditions, by allowing the use of MS detection in the ACE experiments. With the plug–plug technique, the ACE–MS screening methodology successfully selected calmodulin‐binding peptides from a random library with diverse constituents, such as protease digests of BSA. Three peptides with K_d values between 8–147 μM for calmodulin were obtained from a Glu‐C endoprotease digest of reduced BSA, although the digest showed more than 70 peaks in its ACE–MS electropherogram. The method established here will be quite useful for the screening of peptide ligands, which have only low affinities due to their flexible chain structures but could potentially provide primary information for designing inhibitors against the target protein.     

Neomacrophorin I,II, and III,novel drimenyl cyclohexanes with hydroxylated butanoates from Trichoderma sp. 1212-03

Neomacrophorins I (1), II (2), and III (3) were isolated from the culture broth of Trichoderma sp. 1212-03, which was collected at Shirakami Mountainous area in Japan. Structural analyses disclosed that these resemble known macrophorins but possess axial-hydroxy group at C3 as well as different side chains at C7′. These are diastereomeric forms of macrophorins for 5′,6′-epoxide functionality. The NMR analyses suggested their relative configurational relationship between the C1–C15 drimene and C1′–C7′ epoxyquinone moieties. ECD spectral discussions verified them particularly for C5′,C6′-epoxyquinone (1), C5′,C6′-epoxysemiquinone (2 and 3), and 2″,3″-dihydroxybutanoate moiety in 1 and 2. The configuration of C3″-stereocenter of 3 was determined by chiral GC–MS after converting into methyl (S)-3″-hydroxybutanoate by basic of 3 methanolysis. Biological assays disclosed that 1 induces hyphal branching of Cochliobolus miyabeanus as well as cytotoxicity against human colorectal cancer COLO 201.     

Rate constant measurements for initial addition reactions of radicals at the propagation step of photo‐polymerization as studied by pulsed EPR spectroscopy

Pulsed EPR spectroscopy was employed to determine reaction rate constants at an early stage of addition reactions in radical polymerizations triggered by four initiator radicals, which were generated by photodissociation of four parent molecules. Two monomers (tert‐butylacrylate and tert‐butylmethacrylate) were examined as reactant. Stern–Volmer analysis on the measured decay time of electron spin echo intensity of reacting radicals provides rate constants for addition reactions. We focused on rate constants for the second step reaction between monomer and adduct radical that is produced by the first step addition reaction between initiator radical and monomer. The rate constant measured by pulsed EPR was evaluated by theoretical calculations in the light of (1) enthalpy difference between product radical and reactants and (2) charge transfer interaction between reacting radical and monomer. Copyright © 2016 John Wiley & Sons, Ltd.