An Isotope‐Coded Fluorogenic Cross‐Linker for High‐Performance Target Identification Based on Photoaffinity Labeling

A photoaffinity labeling (PAL)‐based method for the rapid identification of target proteins is presented in which a high‐performance chemical tag, an isotope‐coded fluorescent tag (IsoFT), can be attached to the interacting site by irradiation. Labeled peptides can be easily distinguished among numerous proteolytic digests by sequential detection with highly sensitive fluorescence spectroscopy and mass spectrometry. Subsequent MS/MS analysis provides amino acid sequence information with a higher depth of coverage. The combination of PAL and heterogeneous target‐selecting techniques significantly reduces the amount of time and protein required for identification. An additional photocleavable moiety successfully accelerated proteomic analysis using cell lysate. This method is a widely applicable approach for the rapid and accurate identification of interacting proteins.     

Emission Control by Molecular Manipulation of Double‐Paddled Binuclear PtII Complexes at the Air‐Water Interface

Molecular functions depend on conformations and motions of the corresponding molecular species. An air–water interface is a suitable asymmetric field for the control of molecular conformations and motions under a small applied force. In this work, double‐paddled binuclear Pt^II complexes containing pyrazole rings linked by alkyl spacers were synthesized and their orientations and emission properties dynamically manipulated at the air–water interface. The complexes emerge from water with concurrent variation of interface orientation of the planes of the Pt^II complexes from perpendicular to parallel during mechanical compression suggesting a unique ‘submarine emission‘. Phosphorescence of the complexes is quenched at the air–water interface prior to monolayer formation with intensities subsequently rapidly increasing during monolayer compression. These results indicate that asymmetric reactions and motions might be controlled by applying mechanical force at the air–water interface.     

A new set of atomic radii for accurate estimation of solvation free energy by Poisson–Boltzmann solvent model

The Poisson–Boltzmann implicit solvent (PB) is widely used to estimate the solvation free energies of biomolecules in molecular simulations. An optimized set of atomic radii (PB radii) is an important parameter for PB calculations, which determines the distribution of dielectric constants around the solute. We here present new PB radii for the AMBER protein force field to accurately reproduce the solvation free energies obtained from explicit solvent simulations. The presented PB radii were optimized using results from explicit solvent simulations of the large systems. In addition, we discriminated PB radii for N‐ and C‐terminal residues from those for nonterminal residues. The performances using our PB radii showed high accuracy for the estimation of solvation free energies at the level of the molecular fragment. The obtained PB radii are effective for the detailed analysis of the solvation effects of biomolecules. © 2014 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Spontaneous racemization and epimerization behavior in solution of chiral nitroxides

[reaction: see text] Enantiomerically enriched samples of chiral cyclic nitroxides with a 4-hydroxyphenyl group on the stereogenic center bearing the NO radical group undergo unprecedented spontaneous racemization and/or epimerization in aprotic solvents, which can be well accounted for by the multistep equilibrations involving planar quinoid intermediates.     

Development of a miniature double-pass cylindrical mirror electron energy analyzer (DPCMA), and its application to Auger photoelectron coincidence spectroscopy (APECS)

We have developed a miniature double-pass cylindrical mirror electron energy analyzer (DPCMA) with an outer diameter of 26 mm. The DPCMA consists of a shield for the electric field, inner and outer cylinders, two pinholes with a diameter of 2.0 mm, and an electron multiplier. By assembling the DPCMA in a coaxially symmetric mirror electron energy analyzer (ASMA) coaxially and confocally we developed an analyzer for Auger photoelectron coincidence spectroscopy (APECS). The performance was estimated by measuring the Si-LVV-Auger Si-1s-photoelectron coincidence spectra of clean Si(1 1 1). The electron-energy resolution of the DPCMA was estimated to be E/ΔE = 20. This value is better than that of the miniature single-pass CMA (E/ΔE = 12) that was used in the previous APECS analyzer.     

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.     

Diagonal composite order in a two-channel Kondo lattice

A novel type of symmetry breaking is reported for the two-channel Kondo lattice where conduction electrons have spin and orbital (channel) degrees of freedom. Using the continuous-time quantum Monte?Carlo and the dynamical mean-field theory, a spontaneous breaking of the orbital symmetry is observed. The tiny breakdown of orbital occupation number, however, vanishes if the conduction electrons have the particle-hole symmetry. The proper order parameter instead is identified as a composite quantity representing the orbital-selective Kondo effect. The single-particle spectrum of the selected orbital shows insulating property, while the other orbital behaves as a Fermi liquid. This composite order is the first example of odd-frequency order other than off-diagonal order (superconductivity), and is a candidate of hidden order in f-electron systems.     

Catalytic Mannich-type reaction of phosphorylimidates

Phosphorylimidates reacted with N-Boc imines in the presence of a catalytic amount of potassium hexamethyldisilazide, to afford the corresponding Mannich-type adducts in high yields. It was shown that, like sulfonylimidates, phosphorylimidates can function as ester equivalents. In contrast to sulfonylimidates however, phosphorylimidates exhibited high anti-selectivity even in low polar solvents. An explanation for the anti-selectivity is given.     

The IR modulator utilizing light scattering effect with ferroelectric liquid crystal for gas analysis

Experimental infrared modulator elements have been fabricated utilizing the transient light scattering effect of ferroelectric liquid crystal with asymmetric waveform voltage drive. The new elements perform 80% modulation degrees at the 632.8nm. We have also achieved 30% modulation degrees in the 4 to 5µ m region where the strongest CO₂ absorption bands exist. A new type of analyzer which monitors ambient air quality has been developed. This analyzer uses non-dispersive infrared absorption method and composes of a double-beam, a single detector and a pair of liquid crystal light modulator as the IR chopper. The detection has achieved 10ppm noise equivalent concentration.