Novel sign-alternation rule for the triplet state in aromatic systems

Within the framework of the LCAO -MO theory, a novel sign-alternation rule has been found empirically for the lowest excited ππ* triplet state in the alternant aromatic system. This rule can be applied to identify the phosphorescent state.     

Generation and development of RNA ligase ribozymes with modular architecture through "design and selection"

In vitro selection with long random RNA libraries has been used as a powerful method to generate novel functional RNAs, although it often requires laborious structural analysis of isolated RNA molecules. Rational RNA design is an attractive alternative to avoid this laborious step, but rational design of catalytic modules is still a challenging task. A hybrid strategy of in vitro selection and rational design has been proposed. With this strategy termed "design and selection," new ribozymes can be generated through installation of catalytic modules onto RNA scaffolds with defined 3D structures. This approach, the concept of which was inspired by the modular architecture of naturally occurring ribozymes, allows prediction of the overall architectures of the resulting ribozymes, and the structural modularity of the resulting ribozymes allows modification of their structures and functions. In this review, we summarize the design, generation, properties, and engineering of four classes of ligase ribozyme generated by design and selection.     

Discrimination Between 8‐Oxo‐2′‐Deoxyguanosine and 2′‐Deoxyguanosine in DNA by the Single Nucleotide Primer Extension Reaction with Adap Triphosphate

The adenosine derivative of 2‐oxo‐1,3‐diazaphenoxazine (Adap) exhibits a superb ability to recognize and form base pairs with 8‐oxo‐2′‐deoxyguanosine (8‐oxo‐dG) in duplex DNA. In this study, the triphosphate of Adap (dAdapTP) was synthesized and tested for single nucleotide incorporation into primer strands using the Klenow Fragment. The efficiency of dAdapTP incorporation into 8‐oxo‐dG‐containing templates was more than 36‐fold higher than with dG‐containing templates, and provides better discrimination than does the incorporation of natural 2′‐deoxyadenosine triphosphate (dATP). The selective incorporation of dAdapTP into 8‐oxo‐dG templates was therefore applied to the detection of 8‐oxo‐dG in human telomeric DNA sequences extracted from H₂O₂‐treated HeLa cells. The enzymatic incorporation of dAdapTP into 8‐oxo‐dG‐containing templates may provide a novel basis for sequencing oxidative DNA damage in the genome.     

Switch in stereoselectivity caused by the isocyanide structure in the rhodium-catalyzed silylimination of alkynes

The reaction of terminal alkynes with hydrosilanes and tert-alkyl isocyanides in the presence of Rh(4)(CO)(12) gives (Z)-β-silyl-α,β-unsaturated imines in good yields. On the other hand, the use of aryl isocyanides in place of tert-alkyl isocyanides leads to the formation of E isomers.     

UV and IR spectroscopic studies of cold alkali metal ion-crown ether complexes in the gas phase

We report UV photodissociation (UVPD) and IR-UV double-resonance spectra of dibenzo-18-crown-6 (DB18C6) complexes with alkali metal ions (Li(+), Na(+), K(+), Rb(+), and Cs(+)) in a cold, 22-pole ion trap. All the complexes show a number of vibronically resolved UV bands in the 36,000-38,000 cm(-1) region. The Li(+) and Na(+) complexes each exhibit two stable conformations in the cold ion trap (as verified by IR-UV double resonance), whereas the K(+), Rb(+), and Cs(+) complexes exist in a single conformation. We analyze the structure of the conformers with the aid of density functional theory (DFT) calculations. In the Li(+) and Na(+) complexes, DB18C6 distorts the ether ring to fit the cavity size to the small diameter of Li(+) and Na(+). In the complexes with K(+), Rb(+), and Cs(+), DB18C6 adopts a boat-type (C(2v)) open conformation. The K(+) ion is captured in the cavity of the open conformer thanks to the optimum matching between the cavity size and the ion diameter. The Rb(+) and Cs(+) ions sit on top of the ether ring because they are too large to enter the cavity of the open conformer. According to time-dependent DFT calculations, complexes that are highly distorted to hold metal ions open the ether ring upon S(1)-S(0) excitation, and this is confirmed by extensive low-frequency progressions in the UVPD spectra.     

Structure of host-guest complexes between dibenzo-18-crown-6 and water, ammonia, methanol, and acetylene: evidence of molecular recognition on the complexation

Complexes of dibenzo-18-crown-6 (DB18C6, host) with water, ammonia, methanol, and acetylene (guest) in supersonic jets have been characterized by laser induced fluorescence (LIF), UV-UV hole-burning (UV-UV HB), and IR-UV double resonance (IR-UV DR) spectroscopy. Firstly, we reinvestigated the conformation of bare DB18C6 (species m1 and m2) and the structure of DB18C6-H(2)O (species a) [R. Kusaka, Y. Inokuchi, T. Ebata, Phys. Chem. Chem. Phys., 2008, 10, 6238] by measuring IR-UV DR spectra in the region of the methylene CH stretching vibrations. The IR spectral feature of the methylene CH stretch of DB18C6-H(2)O is clearly different from those of bare DB18C6 conformers, suggesting that DB18C6 changes its conformation when forming a complex with a water molecule. With the aid of Monte Carlo simulation for extensive conformational search and density functional calculations (M05-2X/6-31+G*), we reassigned species m1 and m2 to conformers having C(1) and C(2) symmetry, respectively. Also, we confirmed the DB18C6 part in species a of DB18C6-H(2)O to be "boat" conformation (C(2v)). Secondly, we identified nine, one, and two species for the DB18C6 complexes with ammonia, methanol, and acetylene, respectively, by the combination of LIF and UV-UV HB spectroscopy. From the IR spectroscopic measurement in the methylene CH stretching region, a similar conformational change was identified in the DB18C6-ammonia complexes, but not in the complexes with methanol or acetylene. The structures of all the complexes were determined by analyzing the electronic transition energies, exciton splitting, and IR spectra in the region of the OH, NH, and CH stretching vibrations. In DB18C6-ammonia complexes, an ammonia molecule is incorporated into the cavity of the boat conformation by forming "bifurcated" and "bidentate" hydrogen-bond (H-bond), similar to the case of the DB18C6-H(2)O complex. On the other hand, in the DB18C6-methanol and -acetylene complexes, methanol and acetylene molecules are simply attached to the C(1) and C(2) conformations, respectively. From the difference of the DB18C6 conformations depending on the type of the guest molecules, it is concluded that DB18C6 distinguishes water and ammonia from methanol and acetylene when it forms complexes, depending on whether guest molecules have an ability to form bidentate H-bonding.     

A comparative study on acute toxicity of methylarsonic acid,dimethylarsinic acid and trimethylarsine oxide in mice

The acute toxicity of methylarsonic acid, CH₃AsO(OH)₂ (MAA), dimethylarsininc acid, (CH₃)₂AsO(OH) (DMAA), and trimethylarsine oxide, (CH₃)₃AsO (TMAO), were examined in mice with oral administration. The LD₅₀ values of MAA, DMAA and TMAO were 1.8, 1.2 and 10.6 g kg^?1 respectively. The toxicity of MAA and DMAA was very much lower than that for inorganic arsenic compounds. It was shown that TMAO has a similar acute toxicity to arsenobetaine. On the other hand, when the mice were administered 14.4 g kg^?1 of TMAO once only orally, a garlic-like odor (trimethylarsine, (CH₃)₃As) was definitely detectable in the exhalation of the animals by the human olfactory sense within about a few minutes.     

Tunneling time based on the quantum diffusion process approach in multichannel and optical potential cases

We analyze the effects of inelastic scattering on the tunneling time theoretically, using generalized Nelson’s quantum mechanics. This generalization enables us to describe quantum system with channel couplings and optical potential in a real time stochastic approach, which seems to give us a new insight into quantum mechanics beyond Copenhagen interpretation     

Hydration profiles of aromatic amino acids: conformations and vibrations of L-phenylalanine-(H2O)n clusters

IR-UV double resonance spectroscopy and ab initio calculations were employed to investigate the structures and vibrations of the aromatic amino acid, L-phenylalanine-(H(2)O)(n) clusters formed in a supersonic free jet. Our results indicate that up to three water molecules are preferentially bound to both the carbonyl oxygen and the carboxyl hydrogen of L-phenylalanine (L-Phe) in a bridged hydrogen-bonded conformation. As the number of water molecules is increased, the bridge becomes longer. Two isomers are found for L-Phe-(H(2)O)(1), and both of them form a cyclic hydrogen-bond between the carboxyl group and the water molecule. In L-Phe-(H(2)O)(2), only one isomer was identified, in which two water molecules form extended cyclic hydrogen bonds with the carboxyl group. In the calculated structure of L-Phe-(H(2)O)(3) the bridge of water molecules becomes larger and exhibits an extended hydrogen-bond to the pi-system. Finally, in isolated L-Phe, the D conformer was found to be the most stable conformer by the experiment and by the ab initio calculation.     

Laser Spectroscopy and Lifetime Measurements of the S1 State of Tetracyanoquinodimethane (TCNQ) in a Cold Gas-Phase Free-Jet

The S₁ electronic state of 7,7,8,8-Tetracyanoquinodimethane (TCNQ) has been investigated by laser induced fluorescence (LIF), dispersed fluorescence (DF) spectroscopy, and lifetime measurements under jet-cooled conditions in the gas-phase. The LIF spectrum showed a weak origin band at 412.13 nm (24262 cm⁻¹) with prominent progression and combination bands involving vibrations of 327, 1098, and 2430 cm⁻¹. In addition, very strong bands appeared at ∼363.6 nm (3300 cm⁻¹ above the origin). Both the LIF and DF spectra indicate considerable geometric change in the S₁ state. The fluorescence lifetime of S₁ at zero-point level was obtained to be 220 ns. This lifetime is 40 times longer than the radiative lifetime estimated from the S₁−S₀ oscillator strength. Furthermore, the lifetimes of the vibronic bands exhibited drastic energy dependence, indicating a strong mixing with the triplet (T₁) or intramolecular charge-transfer (CT) state. This study is thought to disclose intrinsic nature of TCNQ, which has been well known as a component of organic semiconductors and a versatile p-type dopant.