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.     

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.     

Ultrafast Electron Transfer Kinetics of Graphene Grown by Chemical Vapor Deposition

High electrochemical reactivity is required for various energy and sensing applications of graphene grown by chemical vapor deposition (CVD). Herein, we report that heterogeneous electron transfer can be remarkably fast at CVD‐grown graphene electrodes that are fabricated without using the conventional poly(methyl methacrylate) (PMMA) for graphene transfer from a growth substrate. We use nanogap voltammetry based on scanning electrochemical microscopy to obtain very high standard rate constants k⁰≥25 cm s^?1 for ferrocenemethanol oxidation at polystyrene‐supported graphene. The rate constants are at least 2–3 orders of magnitude higher than those at PMMA‐transferred graphene, which demonstrates an anomalously weak dependence of electron‐transfer rates on the potential. Slow kinetics at PMMA‐transferred graphene is attributed to the presence of residual PMMA. This unprecedentedly high reactivity of PMMA‐free CVD‐grown graphene electrodes is fundamentally and practically important.     

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.     

Highly clear and transparent nanoemulsion preparation under surfactant-free conditions using tandem acoustic emulsification

A new technique for the preparation of a highly clear and transparent emulsified aqueous solution containing immiscible monomer droplets with diameters of a few tens of nanometres under surfactant-free conditions using tandem acoustic emulsification is described. Highly conductive transparent polymer films were successfully prepared from such an emulsified solution.     

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.