An efficient and selective conversion of sorbitol in ionic liquids: Use of ion exchange resin as a solid acid catalyst

Sorbitol was readily converted by heating in hydrophobic ionic liquids by the presence of ion exchange resins. Chemoseletivity of the dehydration depended on the choice of ion exchange resin; Nafion selectively produced isosorbide while Amberlite gave 1,5-anhydrosorbitol along with unreacted sorbitol. Ionic liquids used in the reaction were readily recovered by simple extraction procedure. With these procedures, we succeeded to prepare isosorbide in pure form, not contaminated with either ionic liquids or acid catalyst, by simple experimental procedure.     

PIDA-mediated synthesis of oxazoles through oxidative cycloisomerization of propargylamides

PIDA [phenyliodine(III) diacetate] in AcOH or AcOH-HFIP (hexafluoroisopropanol) efficiently promotes the formation of 2,5-disubstituted oxazoles via the oxidative cycloisomerization of propargylamide derivatives.     

Detecting coupled collective motions in protein by independent subspace analysis

Protein dynamics evolves in a high-dimensional space, comprising aharmonic, strongly correlated motional modes. Such correlation often plays an important role in analyzing protein function. In order to identify significantly correlated collective motions, here we employ independent subspace analysis based on the subspace joint approximate diagonalization of eigenmatrices algorithm for the analysis of molecular dynamics (MD) simulation trajectories. From the 100 ns MD simulation of T4 lysozyme, we extract several independent subspaces in each of which collective modes are significantly correlated, and identify the other modes as independent. This method successfully detects the modes along which long-tailed non-Gaussian probability distributions are obtained. Based on the time cross-correlation analysis, we identified a series of events among domain motions and more localized motions in the protein, indicating the connection between the functionally relevant phenomena which have been independently revealed by experiments.     

Spectral variations in background light emission of surface-enhanced resonance hyper Raman scattering coupled with plasma resonance of individual silver nanoaggregates

We demonstrate the origin of spectral variations in background light emission of surface enhanced resonance hyper Raman scattering (SERHRS) from single Ag nanoaggregates. Ag nanoaggregate-by-nanoaggregate variations in background light emission spectra are related to plasma (plasmon) resonance spectra. Temporal variations in background light emission spectra with temporal blueshifts in plasma resonance spectra are also observed under continuous laser excitation. Both types of the variations in background light emission are reproduced by multiplying background light emission spectra measured from a Ag microaggregate by Lorentz function spectra derived from plasma resonance spectra. The reproduction reveals that second electromagnetic (EM) enhancement by plasma resonance is the origin of the variations. Additionally, spectral variations in background light emission of SERHRS are similar to that of surface enhanced resonance Raman scattering (SERRS). The similarity indicates that both types of background light emission commonly obtain second EM enhancement from identical plasma resonance.     

Grignard allylic substitution catalyzed by imidazol-2-ylidene- and imidazol-4-ylidene-magnesium complexes

In the presence of a catalytic amount of 1,2-disubstituted or 1,2,3-trisubstituted imidazolium salts, γ-substituted allyl chlorides reacted with alkyl Grignard reagents to undergo substitution reactions in an S_N2′-selective fashion, where the magnesium ate complexes [(N-heterocyclic carbene-MgR₃)⁻(MgX)⁺] of imidazol-2-ylidenes or imidazol-4-ylidenes, generated in situ, were postulated as the active species. It was observed that the reactions with imidazol-4-ylidene catalysts were faster than those with imidazol-2-ylidenes. Enantioselective catalysis using a chiral imidazolium salt was preliminarily investigated.     

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.     

Ion-pair structure of vaporized ionic liquid studied by matrix-isolation FTIR spectroscopy with DFT calculations: a case of 1-ethyl-3-methylimidazolium trifluoromethanesulfonate

The matrix-isolation infrared spectrum of a thermally evaporated ionic liquid, 1-ethyl-3-methylimidazolium trifluoromethanesulfonate ([Emim][OTf]), was measured by FTIR spectroscopy and analyzed with the aid of DFT calculations. The main chemical species in the observed IR spectrum was mainly identified as the 1:1 cation-anion pair, which corresponds to the second stable ion-pair structure bonded through five hydrogen bonds between three O atoms of the anion side and four H atoms of the cation.     

Counter-current chromatographic separation of nucleic acid constituents with a hydrophilic solvent system

Nucleic acid constituents such as nucleobases, nucleosides and nucleotides were separated by counter-current chromatography using type J coil planet centrifuge. The separation was performed with a hydrophilic solvent system composed of 1-propanol/800 mM potassium phosphate buffer (pH 7.4) (1:1, v/v) by eluting the lower aqueous phase at a flow-rate of 0.5 ml/min. Eight selected nucleic acid constituents (4.0 mg, 0.5 mg of each), uridine monophosphate (UMP), adenosine monophosphate (AMP), deoxyadenosine monophosphate (dAMP), uridine, urasile, deoxy uridine, adenosine and adenine were well resolved within 160 min.     

Precise and global identification of phospholipid molecular species by an Orbitrap mass spectrometer and automated search engine Lipid Search

In the present research, we have established a new lipidomics approach for the comprehensive and precise identification of molecular species in a crude lipid mixture using a LTQ Orbitrap mass spectrometer (MS) and reverse-phase liquid chromatography (RPLC) combination with our newly developed lipid search engine “Lipid Search”. LTQ Orbitrap provides high mass accuracy MS spectra by Fourier-transform (FT) mass spectrometer mode and can perform rapid MSⁿ by ion trap (IT) mass spectrometer mode. In this study, the negative ion mode was selected to detect fragment ions from phospholipids, such as fatty acid anions, by MS2 or MS3. We selected the specific detection approach by neutral loss survey-dependent MS3, for the identification of molecular species of phosphatidylcholine, sphingomyelin and phosphatidylserine. Identification of molecular species was performed by using both the high mass accuracy of the mass spectrometric data obtained from FT mode and structural data obtained from fragments in IT mode. Some alkylacyl and alkenylacyl species have the same m/z value as molecular-related ions and fragment ions, thus, direct acid hydrolysis analysis was performed to identify alkylacyl and alkenylacyl species, and then the RPLC–LTQ Orbitrap method was applied. As a result, 290 species from mouse liver and 248 species from mouse brain were identified within six different classes of phospholipid, only those in manually detected and confirmed. Most of all manually detected mass peaks were also automatically detected by “Lipid Search”. Adding to differences in molecular species in different classes of phospholipids, many characteristic differences in molecular species were detected in mouse liver and brain. More variable number of saturated and monounsaturated fatty acid-containing molecular species were detected in mouse brain than liver.     

3D atomic imaging by internal-detector electron holography

A method of internal-detector electron holography is the time-reversed version of photoelectron holography. Using an energy-dispersive x-ray detector, an electron gun, and a computer-controllable sample stage, we measured a multiple-energy hologram of the atomic arrangement around the Ti atom in SrTiO3 by recording the characteristic Ti Kα x-ray spectra for different electron beam angles and wavelengths. A real-space image was obtained by using a fitting-based reconstruction algorithm. 3D atomic images of the elements Sr, Ti, and O in SrTiO3 were clearly visualized. The present work reveals that internal-detector electron holography has great potential for reproducing 3D atomic arrangements, even for light elements.