Bulletin of the Chemical Society of Japan
Online ISSN : 1348-0634
Print ISSN : 0009-2673
ISSN-L : 0009-2673
Volume 82 , Issue 1
Showing 1-17 articles out of 17 articles from the selected issue
Award Accounts
The Chemical Society of Japan Award for Creative Work for 2007
  • Naoki Sugimoto
    2009 Volume 82 Issue 1 Pages 1-10
    Published: January 15, 2009
    Released: January 14, 2009
    JOURNALS FREE ACCESS
    DNA has many properties that cannot be attained with other molecules. The ability of DNA to form base pairing and its structural polymorphism allow the formation of distinct secondary and tertiary structures and may have further catalytic or aptamer function. It is also of great advantage that the base pairing of a short oligonucleotide sequence can be well predicted and designed with the thermodynamic parameters of Watson–Crick base pairs, mismatch pairs, and noncanonical base pairs based on the nearest-neighbor model. We have investigated the thermodynamics of various types of oligonucleotide structures, and obtained the nearest-neighbor parameters for Watson–Crick base pair formations and fundamental information regarding the nucleotide interactions. The data of the DNA interaction energy were also applied for molecular design of a DNA logic gate and DNA nanowire. I will further discuss the importance of quantitative data of DNA interaction energy toward the rational design of artificial DNAs carried out by our laboratory, such as base pair-mimic nucleosides and DNA containing bipyridine units, useful as nanobiodevices and nanobiomaterial.
    The quantitative data of DNA interaction energy can be applied to molecular design of functional DNAs which allow us to develop novel nanobiodevices and nanobiomaterial which are promising for in vitro and in vivo applications. Fullsize Image
The Chemical Society of Japan Award for Young Chemists for 2007
  • Akihiko Tsuda
    2009 Volume 82 Issue 1 Pages 11-28
    Published: January 15, 2009
    Released: January 14, 2009
    JOURNALS FREE ACCESS
    We have designed a variety of functional metalloporphyrin nanoclusters, connected via covalent or noncovalent linkages, since a discovery of fused bismetalloporphyrins [Ar3P]2(II) and [Ar3P]2(III) (Schemes 1–10 include symbols of the compounds), which have a strong π-electronic interaction over the bisporphyrin array. Among them, the following three topics are described in this review article. (1) Fused porphyrin nanoclusters: Directly fused oligoporphyrins, obtained through oxidative fused reactions of metalloporphyrins, show extremely strong π-electronic communications among the multiporphyrin components. (2) Self-assembled porphyrin nanoclusters: A zinc complex of meso–meso linked bisporphyrin [PyP]2(I) bearing 4-pyridyl substituents, which allow Zn–N coordination interaction, forms a homochiral box-shaped cyclic tetramer {[PyP]2(I)}4. Its rotamers upon insertion of an oligoalkynylene bridge between the two porphyrin components [PyP]2(≡)n (n = 1, 2, and 4) result in “conformational solvatochromism in nonpolar solvents” in n = 2 and “chiroptical sensing of asymmetric hydrocarbons” in n = 4, due to molecular recognition of solvents at the nanoscale cavity of box-shaped architecture. While a zinc porphyrin bearing a 3-pyridyl substituent (3-Py)P forms a cyclic tetramer with considerable structural distortion, its π-extended derivative (3-Py)P(≡)1 bearing a trimethylsilylethynyl group shows “supramolecular thermochromism” with a vivid color change, due to a temperature-dependent self-assembling event. A supramolecular polymer of J-aggregated zinc porphyrin dendrimer DP can visualize chiroptically a macroscopic chirality of vortex flows, generated by mechanical rotary stirring of a fluid. (3) Inorganic–organic nanocomposites: A giant ring-shaped polyoxomolybdate cluster MC having a large cavity with a diameter of approximately 2.3 nm accommodates up to three molecules of aminophenyl-substituted metalloporphyrins TAP via hydrogen-bonding interactions, resulting in formation of discrete inorganic/organic inclusion complexes. Template-assisted cofacial assembly of MC by an oligomeric p-phenylenebutadiynylene rigid rod molecule bearing ammonium ion pendants PBn allows formation of an inorganic/organic one-dimensional (1D) nano-object, having a polypseudorotaxane structure.
    Our designed functional metalloporphyrin nanoclusters, connected via covalent or noncovalent linkages, showed interesting properties and functions, originating from characteristic π-electronic features and molecular dynamics. We have successfully synthesized (1) fused oligoporphyrins, (2) self-assembled porphyrins, and (3) inorganic–organic nanocomposites. Fullsize Image
Accounts
  • Toshimichi Ohmura, Michinori Suginome
    2009 Volume 82 Issue 1 Pages 29-49
    Published: January 15, 2009
    Released: January 14, 2009
    JOURNALS FREE ACCESS
    New reactivities of silylboranes are described with their applications to organic synthesis. The silylboranes add to unsaturated organic compounds such as alkynes, alkenes, 1,3-dienes, and allenes in the presence of nickel, palladium, and platinum catalysts. Reactions with isocyanide proceed in the absence of catalysts, giving 1,1-addition products. The silaborations proceed in highly regio- and stereoselective manners, leading to the formation of organic compounds bearing silyl and boryl groups. Silaborations accompanied by regioselective C–C bond cleavage in three-membered rings take place in the reactions of methylenecyclopropane and vinylcyclopropane derivatives. Unsaturated organic molecules, e.g., 1,3-diene and aldehyde, undergo silaborative C–C coupling reactions in the presence of transition-metal catalysts. Enantioselective silaboration of terminal allenes and silaborative C–C cleavage of meso-methylenecyclopropanes have been achieved. Silaborations in which the stereochemical course, i.e., cis and trans stereoselectivities, is governed by the ligand have been established in platinum-catalyzed intramolecular silaborations of alkenes. Synthetic applications of the silaboration products through Suzuki–Miyaura coupling, one-carbon homologation, oxidation, allylation, and Rh-catalyzed conjugate addition are also described. Synthesis of silylboranes, including those having heteroatom functional groups at the silicon atoms, is summarized.
    Silylboranes react with a variety of unsaturated organic compounds in the presence of transition-metal catalysts, leading to regio-, stereo-, and enantioselective silaborations, silaborative C–C coupling reactions, silaborative C–C cleavage reactions, generation of a silylene equivalent, and intramolecular silaboration. Fullsize Image
BCSJ Award Article
  • Kohei Johmoto, Akiko Sekine, Hidehiro Uekusa, Yuji Ohashi
    2009 Volume 82 Issue 1 Pages 50-57
    Published: January 15, 2009
    Released: January 14, 2009
    JOURNALS FREE ACCESS
    The crystallization of N-3,5-di-tert-butylsalicylidene-3-carboxyaniline (1) from a methanol solution gave three crystal forms, , , and . The colorless and pale yellow turned red when they were irradiated with UV light whereas orange showed no color change. The lifetimes of the colored crystals were estimated to be 17 and 780 min at room temperature for and , respectively, from IR spectra. The structure of the colored crystal was analyzed by X-ray at 93 K. In addition to the original enol form of 1, the trans-keto form appeared on the difference electron density map with an occupancy factor of 0.117(2). This indicates that the color change was caused by the structural change from the enol to trans-keto form, which is the same as the color change previously reported in the crystal of N-3,5-di-tert-butylsalicylidene-3-nitroaniline (2) (lifetime, 1200 min). It was made clear from the structures of the trans-keto forms in the crystals of , , and 2 that the lifetime of the unstable colored form should be determined by the possibility and the strength of the intermolecular hydrogen bond formation of the N–H group of the trans-keto form to the neighboring molecules.
    Three crystal forms of N-3,5-di-tert-butylsalicylidene-3-carboxyaniline showed different photochromic character. X-ray analysis revealed the unstable colored species is the trans-keto form. The lifetime of the trans-keto form is strongly influenced by the intermolecular hydrogen bond formation of the trans-keto form. Fullsize Image
  • Toshiki Yamaji, Islam SM Saiful, Masaaki Baba, Seigo Yamauchi, Jun Yam ...
    2009 Volume 82 Issue 1 Pages 58-64
    Published: January 15, 2009
    Released: January 14, 2009
    JOURNALS RESTRICTED ACCESS
    We propose a novel formation model of an intermolecular hydrogen bond between radicals and a diamagnetic matrix in the condensed phase. W-band and multi-frequency ESR studies revealed that the polycrystalline radical sample generated from PbO2 oxidation of 2,6-di-tert-butyl-4-hydroxymethylphenol in toluene solution in vacuum at room temperature has an anomalously large 1H-hyperfine interaction. It was concluded that this interaction is attributed to hydrogen bonding between the which is a paramagnetic center in the molecular structure of the radicals and the para-OH or the phenolic OH of the primary phenol. Although the phenol shows interesting radical chemical reactions unlike other 2,6-di-tert-butylphenol derivatives, the generated radical species were successfully defined by the solution ESR investigations. This may be the first ESR observation of an anomalously large hyperfine doublet structure coming from a proton on an intermolecular hydrogen bond between a radical and a diamagnetic phenol.
  • Vitaly A. Ruchenin, Alexey V. Markin, Natalia N. Smirnova, Gennady V. ...
    2009 Volume 82 Issue 1 Pages 65-69
    Published: January 15, 2009
    Released: January 14, 2009
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    In this work, the temperature dependence of heat capacity of crystalline bis(η6-t-butylphenyl)chromium fulleride between T = 6 and 360 K was measured for the first time by precision adiabatic vacuum calorimetry. Also, for the first time, the temperature dependence of EPR signal parameters of bis(η6-t-butylphenyl)chromium fulleride in the range from 118 to 298 K was investigated by electron paramagnetic resonance. In the interval 170–210 K the reversible endothermic transformation was detected and its thermodynamic characteristics were estimated. This transformation was caused by dedimerization of fullerene fragments during heating. Based on the experimental data, the standard (p° = 0.1 MPa) thermodynamic functions, namely, the heat capacity, enthalpy, entropy, and Gibbs function of heating were calculated for dimeric fulleride in the interval from T → 0 to 170 K as well as for monomeric [Cr{η6-(t-BuPh)}2]+C60 complex between 210 and 360 K. The standard thermodynamic properties of tested fulleride and previously studied C60 fullerite and neutral dimer (C60)2 were compared.
  • Mitsutaka Kudoh, Takehiko Satoh, Hiroshi Ikeda, Tomoo Nakazawa, Tsutom ...
    2009 Volume 82 Issue 1 Pages 70-75
    Published: January 15, 2009
    Released: January 14, 2009
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    From both the experimental and computational perspectives, we examined the annulation effects of benzene rings on the ground-state dipole moment for two series of conjugated ketones. The first is a series of tropones (1), 4,5-benzotropone (2), 4,5-naphthotropone (3), 4,5-anthratropone (4), 4,5-tetracenotropone (5), and 4,5-pentacenotropone (6). The second is a series of 1,4-benzoquinones (7), 1,4-naphthoquinone (8), 1,4-anthraquinone (9), 1,4-tetracenequinone (10), 1,4-pentacenequinone (11), 1,4-hexacenequinone (12), and 5,12-tetracenequinone (13). Among these compounds, we determined the ground-state dipole moments of compounds 3, 9, 10, and 13 experimentally as 5.19, 2.07, 2.95, and 1.33 D, respectively. The ground-state dipole moments of the above two series were calculated by Hartree–Fock (HF), density functional theory (DFT), and Møller–Plesset second-order perturbation (MP2) methods. We examined the ground-state dipole moments of the two series to determine whether they converge to a limit. From the MP2 calculations, we estimated the converged dipole moments of annulated-tropones and 1,4-polyacenequinone, as 7.58 and 6.17 D, respectively.
  • Takuya Nagata, Kenta Yamamoto, Keisuke Yoshikiyo, Yoshihisa Matsui, Ta ...
    2009 Volume 82 Issue 1 Pages 76-80
    Published: January 15, 2009
    Released: January 14, 2009
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    α-Cyclodextrin (α-CD) and 6-O-α-D-glucopyranosyl-β-cyclodextrin (G1-β-CD) affected the rates of phenol release from a few dimethyl(nitrophenyl) phosphates and the corresponding thiophosphates in aqueous alkaline solutions. Curve-fitting analysis of changes in the rate constants with CD concentrations showed that both α-CD and G1-β-CD form not only 1:1 but also 2:1 (host:guest) complexes with the phosphates and thiophosphates. In 1:1 complexes, phenol release from the phosphates was mostly accelerated, and that from the thiophosphates was decelerated. In 2:1 complexes, the reactions both of the phosphates and thiophosphates were strongly retarded. Binding constants and rate constants determined showed significant host and substrate specificities.
  • Nanhai Singh, Akhilesh Prasad, Rohit K. Sinha
    2009 Volume 82 Issue 1 Pages 81-85
    Published: January 15, 2009
    Released: January 14, 2009
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    A series of new heterometallic complexes of the type [MM′(bzta)4] [M = Co2+, Pd2+, or 2Cu+; M′ = Ni2+; M = Fe3+ or Co3+; M′ = Cu+; bzta = benzothiazole-2-thiolate (C6H4NSCS)] and their I2-doped products have been synthesized. These have been characterized by elemental analyses, magnetic susceptibility measurement, IR and UV–visible spectroscopies, and solid-state electrical conductivity techniques. A significant observation is the ligand benzothiazole-2-thiolate mediated reduction of Cu2+ to Cu+ and subsequent oxidation of Co2+/Fe2+ to Co3+/Fe3+ in aqueous medium for some of the bimetallic complexes. Room-temperature solid-state electrical conductivities, σrt, ≈10−12 S m−1 and the increase in conductivity with increase in temperature in the 300–420 K range with activation energies, Ea = 0.20–0.68 eV show semiconducting properties of [CoNi(bzta)4], [NiPd(bzta)4], and [FeCu(bzta)4]. The σrt of I2-doped products of the complexes are increased 10–102 fold and show the behavior of semiconductors over the given temperature range.
  • Naoya Nishi, Akihito Suzuki, Takashi Kakiuchi
    2009 Volume 82 Issue 1 Pages 86-92
    Published: January 15, 2009
    Released: January 14, 2009
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    Ionic liquids (ILs) composed of perfluoroalkyltrifluoroborate ions (CnF2n+1BF3, n = 2, 3, 4, and 6) and highly hydrophobic cations are found to have properties suitable to the applications of ILs in IL–water (W) two-phase systems because of their high stability against hydrolysis, high hydrophobicity, and low melting points. The rate of hydrolysis of CnF2n+1BF3 is four orders of magnitude slower than that of BF4. The ion-transfer voltammograms for the transfer of CnF2n+1BF3 across the interface between nitrobenzene and W show that these CnF2n+1BF3 have hydrophobicity comparable to or higher than those of PF6 and bis(trifluoromethylsulfonyl)imide depending on n. The physicochemical properties (density, viscosity, conductivity, and solubility of ILs in W) of CnF2n+1BF3-based ILs are measured for the ILs having melting points lower than room temperature. The hydrophobicity of the CnF2n+1BF3 ions is well correlated with the solubility of the ILs in W and also with the width of the polarized potential window at the IL|W interface.
  • Shuichi Ishigure, Ayumi Okuda, Kaoru Fujii, Yuko Maki, Mamoru Nango, Y ...
    2009 Volume 82 Issue 1 Pages 93-95
    Published: January 15, 2009
    Released: January 14, 2009
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    Photoinduced hydrogen production via the photoreduction of methyl viologen (MV2+) using the sensitization of light-harvesting chlorophyll a/b–protein complex of photosystem II (LHCII) from spinach in the presence of platinum nanoparticles and NADH is developed.
  • Akiko Hori, Ayaka Shinohe, Shohei Takatani, Takeshi K. Miyamoto
    2009 Volume 82 Issue 1 Pages 96-98
    Published: January 15, 2009
    Released: January 14, 2009
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    Co2+, Ni2+, and Cu2+ complexes with bis(pentafluorobenzoyl)methanide (L, C6F5COCHCOC6F5) were prepared from [Al(L)3], which was directly synthesized from AlCl3, pentafluorobenzoyl chloride, and vinyl acetate under N2 atmosphere. The complexation of L with Co2+ and Ni2+ ions gave [M2(L)4(OH2)2] (M = Co and Ni) and that with Cu2+ ion gave [Cu(L)2].
  • Mingzhe Liu, Takuma Kagahara, Hiroshi Abe, Yoshihiro Ito
    2009 Volume 82 Issue 1 Pages 99-104
    Published: January 15, 2009
    Released: January 14, 2009
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    A novel hemin-binding DNA was synthesized using in vitro selection (SELEX) method. The selected DNA not only bound to the hemin, but also had peroxidase activity when complexed with hemin. A pool of 104-nt single-stranded DNA (ssDNA) molecules containing a randomized sequence of 60 nt was synthesized. The DNA pool having random sequences was incubated with a hemin-immobilized affinity column. Bound DNAs were eluted with hemin solution and amplified by PCR with biotin-labeled primers. ssDNAs were isolated from the biotin-labeled double-stranded DNA (dsDNA) molecules after each selection process. After four rounds of selection process, the selected DNAs were cloned and sequenced. Four DNA aptamers were chemically synthesized from the sequenced clones. Two aptamers exhibited binding affinity to hemin and peroxidase activity. A 21-nt oligonucleotide was designed from the aptamer sequence that formed a complex with hemin and exhibited high peroxidase activity.
  • Shinobu Oda, Kunio Isshiki, Shinichi Ohashi
    2009 Volume 82 Issue 1 Pages 105-109
    Published: January 15, 2009
    Released: January 14, 2009
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    This article may be the first report to describe the excellent regio- and stereoselective subterminal hydroxylations of n-alkane with microorganisms. Approximately 2000 fungal strains were screened for the regioselective hydroxylation of n-decane with a solid–liquid interface bioreactor, which is a microbial transformation device on an interface between an agar plate and an organic phase (n-decane). Although Beauveria bassiana ATCC 7159, a typical fungus having a strong and versatile hydroxylating ability, mainly produced a mixture of 2-, 3-, 4-, and 5-decanone regioisomers into a n-decane layer, Monilliela sp. NAP 00702 and Rhizopus oryzae R-38-8 typically accumulated 4- and 5-decanols into the n-decane layer, respectively. Although a small amount of 4- and 5-decanones were also produced, the regioselectivity at C-4 and C-5 positions of n-decane reached 99 and 90%, respectively. Furthermore, the hydroxylation of n-decane with Monilliela sp. NAP 00702 stereoselectively proceeded to afford almost 100% ee of (−)-4-decanol.
  • Takeshi Kubota, Shuji Ikeda, Akimitsu Okamoto
    2009 Volume 82 Issue 1 Pages 110-117
    Published: January 15, 2009
    Released: January 14, 2009
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    A hybridization-sensitive, quencher-free fluorescent probe for RNA detection has been designed using the concept of fluorescence quenching caused by the intramolecular excitonic interaction of fluorescence dyes. We synthesized a doubly thiazole orange-labeled nucleoside showing high fluorescence intensity for a hybrid with the target RNA and effective quenching for the single-stranded state. The probe was applied to living HeLa cells using microinjection to visualize intracellular mRNA localization. Immediately after injection of the probe into the cell, fluorescence from the probe hybridizing with the target RNA was observed. This fluorescence rapidly decreased upon addition of a competitor DNA. This probe realized a large, rapid, and reversible change in fluorescence intensity in sensitive response to the amount of target RNA, and facilitated spatiotemporal monitoring of the behavior of intracellular RNA.
  • Tomoko Kanda, Atsuya Momotake, Yoshihiro Shinohara, Tomoo Sato, Yoshin ...
    2009 Volume 82 Issue 1 Pages 118-120
    Published: January 15, 2009
    Released: January 14, 2009
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    2-(2′-Hydroxynaphthalenyl)benzoxazole (1) emits fluorescence with small Stokes shift from its excited tautomer (K*), produced by excited-state intramolecular proton transfer. Intramolecular hydrogen bonding may be responsible for this phenomenon on comparison with the results of 2-(2′-hydroxyphenyl)benzoxazole (HBO) and 2-(naphthalene-1-yl)benzoxazole (2) as a reference compound.
  • Makoto Ogawa, Kei Kato, Naoki Shimura
    2009 Volume 82 Issue 1 Pages 121-125
    Published: January 15, 2009
    Released: January 14, 2009
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    Spherical particles of nanoporous silica (with a diameter of 600 nm) containing mercaptopropylsilyl groups on the pore surface were synthesized by a modified Stöber method and subsequently silylated using (3-mercaptopropyl)trimethoxysilane. The spherical particles of organosilica formed an artificial opal structure by simply casting the suspension (water dimethylformamide mixture) on a mercaptopropylsilylated Si wafer.
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