Phenanthroline-derived ratiometric chemosensor for ureas

The syntheses of 1,10-phenanthroline fluorophore-based chemosensor 7 and its truncated analog 9 are reported. Interactions of these compounds with urea, thiourea, 1,3-dimethylurea, tetrahydropyrimidin-2(1H)-one, imidazolidin-2-one, and selected uronium salts were assessed by three-dimensional excitation-emission spectroscopy, UV-vis absorbance, and fluorescence titrations. Chemosensor 7 was found to be capable of distinguishing between neutral ureas and their salts, by producing a different optical response for each type of compounds. The complexation of urea by 7 was also studied by selective-NOE 1H NMR, 13C NMR (using 13C-labeled guest), and MALDI-TOF mass spectrometry. In addition, we performed DFT calculations (B3LYP 3-21g** level) for structures of complexes of 7 with urea, imidazolidin-2-one, and tetrahydropyrimidin-2(1H)-one. Development of chemosensor 7-type compounds in conjunction with differential excitation-emission spectroscopy represents an important step toward the development of novel tools for ureas and their salts analysis.     

Degenerate quasicrystal of hard triangular bipyramids

We report a degenerate quasicrystal in Monte Carlo simulations of hard triangular bipyramids each composed of two regular tetrahedra sharing a single face. The dodecagonal quasicrystal is similar to that recently reported for hard tetrahedra [Haji-Akbari et al., Nature (London) 462, 773 (2009)] but degenerate in the pairing of tetrahedra, and self-assembles at packing fractions above 54%. This notion of degeneracy differs from the degeneracy of a quasiperiodic random tiling arising through phason flips. Free energy calculations show that a triclinic crystal is preferred at high packing fractions.     

Kneelike structure in the spectrum of the heavy component of cosmic rays observed with KASCADE-Grande

We report the observation of a steepening in the cosmic ray energy spectrum of heavy primary particles at about 8×10(16) eV. This structure is also seen in the all-particle energy spectrum, but is less significant. Whereas the "knee" of the cosmic ray spectrum at 3-5×10(15) eV was assigned to light primary masses by the KASCADE experiment, the new structure found by the KASCADE-Grande experiment is caused by heavy primaries. The result is obtained by independent measurements of the charged particle and muon components of the secondary particles of extensive air showers in the primary energy range of 10(16) to 10(18) eV. The data are analyzed on a single-event basis taking into account also the correlation of the two observables.     

Nanofibers resulting from cooperative electrostatic and hydrophobic interactions between peptides and polyelectrolytes of opposite charge

We investigated whether cationic peptides that contain hydrophobic side chains were able to stabilize themselves via hydrophobic interactions between neighboring peptide molecules upon electrostatic binding to oppositely charged polyelectrolytes. The interaction mechanism was examined through a model system consisting of the anionic polyelectrolyte alginate and the cationic decapeptide ozarelix. The interaction resulted in the formation of highly ordered complexes that were noticeable upon visual inspection. These complexes were then investigated by microscopic techniques and shown to exhibit a branched network structure. Cryogenic-temperature transmission electron microscopy (cryo-TEM) and negative staining TEM revealed that the molecular interactions between alginate and ozarelix led to the formation of nanofibers. The rodlike nanofibers had a diameter distribution of 4-8 nm. Isothermal titration calorimetry was used to determine the thermodynamic parameters of the alginate-ozarelix interaction. The binding constant was found to be on the order of 10(6) M(-1), indicating a high binding affinity. The interaction of the peptide with the polyelectrolyte triggered profound changes in the conformation of ozarelix, which was confirmed by UV spectroscopy and circular dichroism. On the basis of these experimental results, a theoretical modeling study of the alginate-ozarelix interaction was conducted to gain a better molecular-level understanding of the complex structure. It revealed that, upon binding of ozarelix to alginate, new intermolecular and intramolecular aromatic interactions between the ozarelix molecules occurred. These interactions changed the conformation of the peptide, a modification in which the aromatic side chains played a major role. Our results indicate that the cationic peptides interact with the polyanions via electrostatic interactions, but are additionally stabilized via hydrophobic interactions. This binding mode may serve as a powerful tool to extend the duration of drug release in hydrogel drug delivery systems.     

Prior-predictive value from fast growth simulations

Building on a variant of the Jarzynski equation we propose a new method to numerically determine the prior-predictive value in a Bayesian inference problem. The method generalizes thermodynamic integration and is not hampered by equilibration problems. We demonstrate its operation by applying it to two simple examples and elucidate its performance. In the case of multi-modal posterior distributions the performance is superior to thermodynamic integration.     

Radio emission from extensive air showers as a method for cosmic-ray detection

At the present time, radio emission from extensive air showers (EASs) is being considered as a new promising method for detecting cosmic rays of energy in the region E ₀ > 5 × 10¹⁶ eV. Radio emission from an EAS whose development is simulated by the Monte Carlo method is calculated here. The field of radio emission from an EAS is calculated on the basis of two representations of a shower: that as a set of individual particles and that as a continuous set of currents. The sensitivity of radio emission to EAS parameters in the frequency range 10–100 MHz is investigated. The results can be used to analyze experiments that being presently performed (CODALEMA and LOPES) and those that are being planned for the future.     

Utility of Bioluminescent Homogeneous Nucleotide Detection Assays in Measuring Activities of Nucleotide-Sugar Dependent Glycosyltransferases and Studying Their Inhibitors

Traditional glycosyltransferase (GT) activity assays are not easily configured for rapid detection nor for high throughput screening because they rely on radioactive product isolation, the use of heterogeneous immunoassays or mass spectrometry. In a typical glycosyltransferase biochemical reaction, two products are generated, a glycosylated product and a nucleotide released from the sugar donor substrate. Therefore, an assay that detects the nucleotide could be universal to monitor the activity of diverse glycosyltransferases in vitro. Here we describe three homogeneous and bioluminescent glycosyltransferase activity assays based on UDP, GDP, CMP, and UMP detection. Each of these assays are performed in a one-step detection that relies on converting the nucleotide product to ATP, then to bioluminescence using firefly luciferase. These assays are highly sensitive, robust and resistant to chemical interference. Various applications of these assays are presented, including studies on the specificity of sugar transfer by diverse GTs and the characterization of acceptor substrate-dependent and independent nucleotide-sugar hydrolysis. Furthermore, their utility in screening for specific GT inhibitors and the study of their mode of action are described. We believe that the broad utility of these nucleotide assays will enable the investigation of a large number of GTs and may have a significant impact on diverse areas of Glycobiology research.