Structure and ethanol complexation of cyclic tetrasaccharide in aqueous solution studied by NMR and molecular mechanics

The structure and ethanol complexation of a cyclic tetrasaccharide (CTS) in aqueous solution were investigated by proton NMR spectroscopy and molecular mechanics calculations. Two glucose units, A and B, of CTS are alternatively bonded by alpha-1,3 and alpha-1,6 linkages. The overlapped signals of protons A5, A6S, A6R, B3, B6S and B6R were resolved by spectral simulations to determine their chemical shifts and vicinal coupling constants. All vicinal coupling constants except for the A5-A6 spin system are consistent with the dihedral angles in the X-ray crystal structure. Each of protons A5, A6S, and A6R in the two units of A is equivalent with respect to the chemical shift. The vicinal coupling constants of (3)J(5-6S) and (3)J(5-6R) for unit A are close to the average of two rotamers that are present in crystals. The intensities of cross-peaks in the rotating frame nuclear Overhauser effect spectroscopy (ROESY) spectrum were rather well correlated with the effective distances calculated for the X-ray structure and molecular mechanics structures calculated in vacuo and water, although they are slightly better correlated with molecular mechanics structure in vacuo than with the other structures. From the changes of the chemical shifts of several CTS protons with increasing ethanol concentration, it was suggested that adsorption sites of ethanol on the plate structure of CTS are protons B2 and B4 (site B) in the concave face side and protons A1 and A2 (site A) in the convex back side. The binding constants for sites A and B are 0.0061 and 0.0176 M(-1), respectively. These binding constants are much smaller than a value of 4.1 M(-1) for the ethanol-alpha-cyclodextrin complex.     

Concise synthesis of anti-HIV-1 active (+)-inophyllum B and (+)-calanolide A by application of (-)-quinine-catalyzed intramolecular oxo-Michael addition

(-)-Quinine-catalyzed intramolecular oxo-Michael addition (IMA) of 7-hydroxy-5-methoxy-8-tigloylcoumarins was developed for the enantioselective construction of 2,3-dimethyl-4-chromanone systems in the context of the asymmetric synthesis of anti-HIV-1 active Calophyllum coumarins. Combination of the IMA and MgI(2)-assisted demethylation of the 5-methoxy group along with isomerization of the formed chromanone systems as key steps successfully led to the concise synthesis of (+)-inophyllum B and (+)-calanolide A, possible candidates for AIDS drugs. Further examination of the asymmetric IMA with cinchona alkaloids lacking a methoxy group on the quinoline skeleton suggested the influence of the methoxy substituent on stereoselectivity at the stereogenic centers of the chromanone systems.     

Intramolecular catalytic Friedel-Crafts reactions with allenyl cations for the synthesis of quinolines and their analogues

[reaction: see text] This paper describes a novel method to synthesize a quinoline backbone by incorporating allenyl cations into a catalytic intramolecular Friedel-Crafts reaction. The initial products were isomerized and aromatized upon treatment with acid and base, respectively, to give quinolines. The basic concept also proved to be promising for 1-benzazepine, 1-benzazocine, or isoquinoline synthesis.     

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.     

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.     

Synthesis of hydroxylated oligoarene-type phosphines by a repetitive two-step method

Hydroxylated oligoarene-type phosphines with various substitution patterns were synthesized. Such phosphines have potential as ligands for transition metal-catalyzed reactions. A successful route, which includes a repetitive Suzuki-Miyaura coupling-triflation sequence, reduction, and salt formation, was established starting from 2-bromophenyldicyclohexylphosphine oxide. Other key aspects of the method are the use of suitable triflation reagents and the formation of phosphines as HBF₄ salts. Interesting information was obtained from careful analysis of the byproducts in the triflation and reduction steps, and the mechanisms for their formation were proposed.     

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.