Lanthanide-assisted NMR evaluation of a dynamic ensemble of oligosaccharide conformations

A novel methodology is presented for evaluating a dynamic ensemble of oligosaccharide conformations by lanthanide-assisted NMR spectroscopy combined with molecular dynamics (MD) simulations. The results obtained using the GM3 trisaccharide demonstrated that pseudocontact shift measurements offer a valuable experimental tool for the validation of MD simulations of highly flexible biomolecules.     

Ruthenium-catalyzed hydrophosphinylative cyclization of 1,6-diynes. Stereoselective synthesis of exocyclic 1,3-dienylphosphine oxides

The first catalytic synthesis of exocyclic 1,3-dienylphosphine oxides was achieved by the ruthenium-catalyzed selective hydrophosphinylative cyclization of 1,6-diynes. A plausible mechanism involving a ruthenacyclopentatriene intermediate is proposed on the basis of the DFT calculations of model ruthenium complexes.     

Elucidation of the Active Conformation of Vancomycin Dimers with Antibacterial Activity against Vancomycin‐Resistant Bacteria

Covalently linked vancomycin dimers have attracted a great deal of attention among researchers because of their enhanced antibacterial activity against vancomycin‐resistant strains. However, the lack of a clear insight into the mechanisms of action of these dimers hampers rational optimization of their antibacterial potency. Here, we describe the synthesis and antibacterial activity of novel vancomycin dimers with a constrained molecular conformation achieved by two tethers between vancomycin units. Conformational restriction is a useful strategy for studying the relationship between the molecular topology and biological activity of compounds. In this study, two vancomycin units were linked at three distinct positions of the glycopeptide (vancosamine residue (V), C terminus (C), and N terminus (N)) to form two types of novel vancomycin cyclic dimers. Active NC‐VV‐linked dimers with a stable conformation as indicated by molecular mechanics calculations selectively suppressed the peptidoglycan polymerization reaction of vancomycin‐resistant Staphylococcus aureus in vitro. In addition, double‐disk diffusion tests indicated that the antibacterial activity of these dimers against vancomycin‐resistant enterococci might arise from the inhibition of enzymes responsible for peptidoglycan polymerization. These findings provide a new insight into the biological targets of vancomycin dimers and the conformational requirements for efficient antibacterial activity against vancomycin‐resistant strains.     

Determination of ethylenediaminetetraacetic acid in sea water by solid-phase extraction and high-performance liquid chromatography

The chelating agent EDTA is widely used, and as a result is showing up widely in the aquatic environment. Here we describe a preconcentration procedure for measuring EDTA concentration in sea water samples by HPLC. The procedure consists of forming an Fe(III) complex followed by solid-phase extraction using an activated carbon cartridge. After the preconcentration, EDTA was quantified by HPLC with ultraviolet detection (260 nm). The enrichment permitted the determination of EDTA at concentrations as low as 1 nM. Good recoveries were obtained for both brackish and full-strength sea water with high repeatability (RSD < 6%). The method was applied to sea water samples taken from near the mouth of the Oyabe River in Japan.     

Preparation,crystal structure,and spectroscopic,chemical, and electrochemical properties of (2E,4E)-1,4-di(3-guaiazulenyl)-1,3-butadiene compared with those of (E)-1,2-di(3-guaiazulenyl)ethylene

Wittig reaction of (E)-3-(3-guaiazulenyl)propenal (11) with (3-guaiazulenylmethyl)triphenylphosphonium bromide (9) in ethanol containing NaOEt at 25 °C for 24 h under argon gives the title new (2E,4E)-1,3-butadiene derivative 4, in 33% isolated yield, which upon treatment with hexafluorophosphoric acid (i.e., 65% HPF₆ aqueous solution) in tetrahydrofuran (=THF) at 25 °C for 1 h under aerobic conditions affords a new air (two-electron) oxidation product (E)-ethylene-1,2-bis(3-guaiazulenylmethylium) bis(hexafluorophosphate) (14), quantitatively, and further, zinc-reduction of 14 in trifluoroacetic acid (=CF₃COOH) at 0 °C for 1 h under argon reverts 4, quantitatively. Along with the above interesting results, our discovered another preparation method, spectroscopic properties, crystal structure, and electrochemical behavior of 4, which serves as a strong two-electron donor and acceptor, compared with those of the previously reported (E)-1,2-di(3-guaiazulenyl)ethylene (3) are documented in detail.     

Synthesis of 2,3-dihydro-1H-inden-1-one derivatives via Ni-catalyzed intramolecular hydroacylation

An efficient synthetic method for the formation of 2,3-dihydro-1H-inden-1-one derivatives through a Ni-catalyzed intramolecular hydroacylation of 2-(prop-2-ynyl)benzaldehydes has been developed. Examination of various nickel and other transition metal catalysts and phosphine ligands showed that the use of Ni(COD)₂ catalyst combined with P(i-Pr)₃ ligand was the best choice to the success of the present intramolecular hydroacylation. A wide range of functional groups were tolerated, affording the corresponding substituted α-lidene-2,3-dihydro-1H-inden-1-ones in good to high yields with a sole E-selectivity under present reaction conditions.     

Cascade cyclization of aryldiynes using iodine: synthesis of iodo-substituted benzo[b]naphtho[2,1-d]thiophene derivatives for dye-sensitized solar cells

A facile, efficient, and general synthetic method for iodo-substituted benzo[b]naphtho[2,1-d]thiophenes has been developed via a cascade cyclization of thioanisole-substituted aryldiynes using iodine. A new donor–π linker–acceptor (D–π–A) organic dye, G1, with the benzo[b]naphtho[2,1-d]thiophene moiety as an electron donor has been synthesized, and the performance of dye-sensitized solar cell based on G1 has been investigated.     

Mechanism of the alkali degradation of (6-4) photoproduct-containing DNA

The (6-4) photoproduct is one of the major damaged bases produced by ultraviolet light in DNA. This lesion is known to be alkali-labile, and strand breaks occur at its sites when UV-irradiated DNA is treated with hot alkali. We have analyzed the product obtained by the alkali treatment of a dinucleoside monophosphate containing the (6-4) photoproduct, by HPLC, NMR spectroscopy, and mass spectrometry. We previously found that the N3-C4 bond of the 5' component was hydrolyzed by a mild alkali treatment, and the present study revealed that the following reaction was the hydrolysis of the glycosidic bond at the 3' component. The sugar moiety of this component was lost, even when a 3'-flanking nucleotide was not present. Glycosidic bond hydrolysis was also observed for a dimer and a trimer containing 5-methyl-2-pyrimidinone, which was used as an analog of the 3' component of the (6-4) photoproduct, and its mechanism was elucidated. Finally, the alkali treatment of a tetramer, d(GT(6-4)TC), yielded 2'-deoxycytidine 5'-monophosphate, while 2'-deoxyguanosine 3'-monophosphate was not detected. This result demonstrated the hydrolysis of the glycosidic bond at the 3' component of the (6-4) photoproduct and the subsequent strand break by β-elimination. It was also shown that the glycosidic bond at the 3' component of the Dewar valence isomer was more alkali-labile than that of the (6-4) photoproduct.     

Auslander–Gorenstein resolution

We introduce the notion of Auslander–Gorenstein resolution and show that a Noetherian ring is an Auslander–Gorenstein ring if it admits an Auslander–Gorenstein resolution over another Auslander–Gorenstein ring.     

Gravitational compression dynamics of charged colloidal crystals

We examine the compression of charged colloidal crystals under the influence of gravitational force by monitoring the spatiotemporal variations of Bragg diffraction from the crystal lattice. We use the dilute aqueous dispersions of colloidal silica particles (diameter=216 nm, charge number=733, a particle volume fraction φ=0.06) in the presence of 5-15 μM sodium chloride. The sedimentation profiles of the colloidal crystals along the crystal height are determined by in situ fiber optics reflection spectroscopy. The time evolutions of the sedimentation profiles are calculated by numerical simulations based on a phenomenological continuum model that explicitly incorporates the electrostatic interparticle interactions. The simulation results correctly describe the experiments at sufficiently high ionic strength.