Thermodynamic analysis of duplex formation of the heterochiral DNA with L-deoxyadenosine.

An L-DNA, the mirror-image isomer of natural DNA, has extraordinary nuclease resistance, and thus the molecules should be promising reagents for many applications, such as antisense technology. However, little is known about the structural and thermodynamic properties of DNAs with this modified nucleotide. In this study, we prepared the L-nucleotide (L-dA) and introduced it into oligodeoxyribonucleotides to assess the ability of the L-nucleotide as a functional molecule for many applications based on the DNA hybridization. Two decamers with an L-dA at the center were synthesized and duplexes with the complementary DNA strand were applied to structural and thermodynamic analyses. The structural study by CD spectra showed that the structures of both modified "L/D-D" duplexes were the typical B-form. This result suggests that the global structure of DNA was not collapsed by the introduction of an L-DNA. Thermodynamic parameters (deltaH degrees, deltaS degrees, and deltaG degrees 37) of the duplex formation, determined by UV melting experiments, indicated that the both duplexes were destabilized at about 2.5 to 3.0 kcal mol(-1) by the introduced L-dA, mainly due to an unfavorable enthalpic effect. In conjunction with information by other researchers, these results suggest that the L-DNA affect on the duplex structure and the stability vary locally; thus, the thermodynamic stability of modified L/D-D duplexes should be predictable by the nearest-neighbor thermodynamic parameters.     

Donor–acceptor–acceptor-type near-infrared fluorophores that contain dithienophosphole oxide and boryl groups: effect of the boryl group on the nonradiative decay

The use of donor–π–acceptor (D–π–A) skeletons is an effective strategy for the design of fluorophores with red-shifted emission. In particular, the use of amino and boryl moieties as the electron-donating and -accepting groups, respectively, can produce dyes that exhibit high fluorescence and solvatochromism. Herein, we introduce a dithienophosphole P-oxide scaffold as an acceptor–spacer to produce a boryl- and amino-substituted donor–acceptor–acceptor (D–A–A) π-system. The thus obtained fluorophores exhibit emission in the near-infrared (NIR) region, while maintaining high fluorescence quantum yields even in polar solvents (e.g. λ_em = 704 nm and Φ_F = 0.69 in CH₃CN). A comparison of these compounds with their formyl- or cyano-substituted counterparts demonstrated the importance of the boryl group for generating intense emission. The differences among these electron-accepting substituents were examined in detail using theoretical calculations, which revealed the crucial role of the boryl group in lowering the nonradiative decay rate constant by decreasing the non-adiabatic coupling in the internal conversion process. The D–A–A framework was further fine-tuned to improve the photostability. One of these D–A–A dyes was successfully used in bioimaging to visualize the blood vessels of Japanese medaka larvae and mouse brain.

Combination of electron-accepting diarylboryl terminal groups and dithienophosphole oxide spacers with electron-donating triarylamine moieties produces donor–acceptor–acceptor type π-systems, which exhibit emissions in the near-infrared region.     

Peptide bond formation mediated by 4,5-dimethoxy-2-mercaptobenzylamine after periodate oxidation of the N-terminal serine residue

[reaction in text] A thiol linker-attached peptide was prepared from a nonprotected peptide via an N(alpha)()-alpha-oxoacyl peptide. Selective oxidation of the N-terminal serine with sodium periodate gave the N(alpha)-glyoxyloyl peptide, reductive amination of which with 4,5-dimethoxy-2-(triphenylmethylthio)benzylamine gave an N(alpha)-4,5-dimethoxy-2-mercaptobenzyl glycyl peptide after removal of the trityl group. The N(alpha)-4,5-dimethoxy-2-mercaptobenzyl peptide can be condensed with a peptide thioester, and the linker is removable. This strategy provides a useful method for the synthesis of peptides using recombinant proteins.     

Palladium(0)-catalyzed stereoselective cyclization of allenenes: divergent synthesis of pyrrolidines and 3-azabicyclo[3.1.0]hexanes from single allenenes

Two novel palladium(0)-catalyzed cyclizations of allenenes are described. Treatment of allenenes such as N-(1-alkyl-2,3-butadienyl)-N-allylsulfonamide with an aryl halide and K(2)CO(3) in the presence of a catalytic amount of Pd(PPh(3))(4) in dioxane affords 2,3-cis-pyrrolidines in a stereoselective manner. In sharp contrast, cyclization of the same allenenes using catalytic Pd(2)(dba)(3) x CHCl(3) in the presence of allyl methyl carbonate in CH(3)CN leads to stereoselective formation of a 3-azabicyclo[3.1.0]hexane framework in moderate yields.     

Photoreactive polyamides having m- or 1-type dimer moiety derived from 4-(3-oxo-3-phenyl-1-propenyl)benzoic acid derivatives

Photoreactive polyamides having m- or 1 -type cyclobutane moiety were prepared via a topochemical photodimerization of 4-(3-oxo-3-phenyl-1-propenyl)benzoic derivatives,⁴ followed by polycondensation of cyclobutane dicarboxylate derivatives with diamines. From the spectral studies of resulted polyamides compared with the corresponding reference diamides, it was concluded that both types of polyamides were depolymerized photochemically to give the same type of amide derivative having chalcone moiety with a small amount of undefined side reaction. The cyclobutane ring of the m-dimer from 4-(3-oxo-3-phenyl-1-propenyl)benzoic acid in crystal is severely twisted presumably because of the enhanced steric repulsions between two pairs of adjacent substituents. The higher quantum yield of the m-dimer for the photocleavege, compared with that of the 1 -dimer, has been interpreted in terms of such steric repulsions by the strained structure of the m-dimer.     

Selective determination of microbial cells by graphite electrode modified with adsorbed 4,4′-bipyridine

The concentrations of microbial cells in suspensions can be measured with a graphite electrode modifed with adsorbed 4,4′-bipyridine, by using cyclic volummetry or differential pulse volummetry. The relationship between the peak current and the cell concentration for Saccharomyces cerevisiae is linear over the range 0.03 × 10⁸—2.0 × 10⁸ cells ml^?1. Yeast, gram-positive bacteria and gram-negative bacteria gave different peak potentials, which may be useful for classification purposes. Electron transfer between the microbial cells and the 4,4′-bipyridine-modified electrode is mediated by coenzyme A in the cell wall.     

Asymmetric cyclization via memory of chirality: a concise access to cyclic amino acids with a quaternary stereocenter

N-(omega-Bromoalkyl)-amino acid derivatives, readily prepared from natural alpha-amino acids, gave cyclic amino acids with a quaternary stereocenter by treatment with potassium hexamethyldisilazaide in DMF. The chirality of parent amino acids was almost completely preserved during an enolate-formation and cyclization process, giving aza-cyclic amino acids in up to 98% ee in retention of configuration. This method is applicable to the asymmetric synthesis of azetidine, pyrrolidine, piperidine, and azepane derivatives. The asymmetric cyclization seems to proceed via an axially chiral enolate intermediate and not through a concerted SEi process.     

Chiral zirconium catalysts using multidentate BINOL derivatives for catalytic enantioselective Mannich-type reactions; ligand optimization and approaches to elucidation of the catalyst structure

Catalytic enantioselective Mannich-type reactions of silicon enolates with aldimines were investigated using chiral zirconium catalysts prepared from Zr(O(t)Bu)(4), N-methylimidazole, and newly designed multidentate BINOL derivatives. These new multidentate BINOL ligands were designed on the basis of an assumed transition state structure of a chiral zirconium catalyst derived from two molecules of (R)-6,6'-Br(2)-BINOL. Not only tetradentate BINOL 4 but also tridentate BINOL derivatives were found to be effective, and high enantioselectivities were attained. In a structural study of the most effective zirconium complex prepared from tridentate ligand 6e, several NMR experiments and DFT calculations were carried out. Consequently, the structure of an active catalyst and plausible mechanism of asymmetric induction were elucidated.     

Photophysical properties of porphyrin tapes

The novel fused Zn(II)porphyrin arrays (Tn, porphyrin tapes) in which the porphyrin macrocycles are triply linked at meso-meso, beta-beta, beta-beta positions have been investigated by steady-state and time-resolved spectroscopic measurements along with theoretical MO calculations. The absorption spectra of the porphyrin tapes show a systematic downshift to the IR region as the number of porphyrin pigments increases in the arrays. The fused porphyrin arrays exhibit a rapid formation of the lowest excited states (for T2, approximately 500 fs) via fast internal conversion processes upon photoexcitation at 400 nm (Soret bands), which is much faster than the internal conversion process of approximately 1.2 ps observed for a monomeric Zn(II)porphyrin. The relaxation dynamics of the lowest excited states of the porphyrin tapes were accelerated from approximately 4.5 ps for the T2 dimer to approximately 0.3 ps for the T6 hexamer as the number of porphyrin units increases, being explained well by the energy gap law. The overall photophysical properties of the porphyrin tapes were observed to be in a sharp contrast to those of the orthogonal porphyrin arrays. The PPP-SCI calculated charge-transfer probability indicates that the lowest excited state of the porphyrin tapes (Tn) resembles a Wannier-type exciton closely, whereas the lowest excited state of the directly linked porphyrin arrays can be considered as a Frenkel-type exciton. Conclusively, these unique photophysical properties of the porphyrin tapes have aroused much interest in the fundamental photophysics of large flat organic molecules as well as in the possible applications as electric wires, IR sensors, and nonlinear optical materials.