Size‐matched alkyne‐conjugated cyanine fluorophores to identify differences in protein glycosylation

Currently, there are few methods to detect differences in posttranslational modifications (PTMs) in a specific manner from complex mixtures. Thus, we developed an approach that combines the sensitivity and specificity of click chemistry with the resolution capabilities of 2D‐DIGE. In “Click‐DIGE”, posttranslationally modified proteins are metabolically labeled with azido‐substrate analogs, then size‐ and charge‐matched alkyne‐Cy3 or alkyne‐Cy5 dyes are covalently attached to the azide of the PTM by click chemistry. The fluorescently‐tagged protein samples are then multiplexed for 2DE analysis. Whereas standard DIGE labels all proteins, Click‐DIGE focuses the analysis of protein differences to a targeted subset of posttranslationally modified proteins within a complex sample (i.e. specific labeling and analysis of azido glycoproteins within a cell lysate). Our data indicate that (i) Click‐DIGE specifically labels azido proteins, (ii) the resulting Cy‐protein conjugates are spectrally distinct, and (iii) the conjugates are size‐ and charge‐matched at the level of 2DE. We demonstrate the utility of this approach by detecting multiple differentially expressed glycoproteins between a mutant cell line defective in UDP‐galactose transport and the parental cell line. We anticipate that the diversity of azido substrates already available will enable Click‐DIGE to be compatible with analysis of a wide range of PTMs.     

Experimental, Theoretical and Biological Activity Study on the Acyl-Substituted Benzo-18-crown-6, Dibenzo-18-crown-6 and Dibenzo-24-crown-8

Hexadecanoyl, dihexadecanoyl, dioctadecaneoyl, di-10-undecenoyl, and dicis-9-octadecenoyl derivatives of benzo[18]crown-6, dibenzo[18]crown-6 and dibenzo[24]-8 were synthesized by the condensation of carboxylic acids (palmitic, stearic, oleic and undecenoic acid) with benzo and dibenzo crown ethers in the presence of zinc chloride. The extraction equilibrium constants of such macrocyclic ethers with long side chains were estimated using chloroform/water and dichloromethane/water membranes transfer of Na-PAR (4-(2-pyridylazo)-resorcinol mono sodium monohydrate) with UV–Vis spectroscopy. It was found that they were in the range of 10.88–11.71 in dichloromethane and 8.04–11.77 in chloroform. These results actually show that the Na+ binding effect of macrocyclic ethers depends on the type and the length of side chains. The geometrical properties of the molecules were studied employing semi-empirical calculations by simulated annealing technique. The frontier molecular orbital energies and dipole moments were also examined. The biological activity results showed that the synthesized crown ethers have no activity against the studied microorganisms.     

Electron-hole plasma in pulse photoexcited single quantum wells

We report photoluminescence studies of MOCVD grown, GaAsAl_xGa_1?xAs single quantum wells which were intensly excited with a pulse dye laser at T=2K. For a well width of d～40Å, the spectra are interpreted as due to the radiative recombination of a hot electron-hole plasma confined to the well. The density of charge carriers and their temperature depend upon the excitation intensity, and vary in the range of 10¹¹–10¹³ cm^?2 and 100–500K for an absorbed photon flux of 10¹³–10¹⁶ photons-cm^?2 per pulse, respectively. The observed spectral features are identified as the e1-hh1 and e1-lh1 transitions and two additional bands which are tentatively assigned to transitions involving virtual bound states of either the electron or the hole. The electron-hole plasma spectra of the d～40Å sample are strongly polarized perpendicular to the well quantization axis. For wider wells (d～80 and 150Å) smaller photoexcited carrier densities were observed for the same absorbed photon flux. It is thus concluded that the capture efficiency of the well is small.     

Novel heterotricyclic systems: 2,6-dioxa- and 2-oxa-6-thia-10-azatricyclo-[5.2.1.04,10] deeanes; 2,6-dioxa-11-azatricyclo[5.3.1.04,11] undecane; and 9,13-dioxa-14-azatetracyclo[6.5.1.02,7.011,14]tetradeca-2,4,6-triene

The acid-catalyzed condensation of 2-amino-1,3-propanediols and 1,4-diketones under water-azeotroping conditions has led to the first synthesis of the new tent-like, essentially strain-free heterotricyclic system, 2,6-dioxa-10-azatricyclo[5.2.1.0^4,10]decane. Over thirty new compounds containing this system are reported. In cases where the aminodiol is unsubstituted or bears a phenyl substituent a mixture of the tricycle and the isomeric pyrrole resulted. These observations indicate alternative pathways in the Knorr-Paal condensation which lead to one, or the other, or both of these products. A scheme postulating common intermediates is presented. Examples of three additional, related, novel heteropolycyclic systems synthesized in analogous fashion are also reported.     

Wave scattering effects in elastic percolation models

The study of the propagation of waves in randomly diluted models is presented. Porosity (crack-like) models are simulated by constructing typical elastic percolation networks with random microscopic heterogeneities in order to resemble rock media. Central and bond-bending forces (Born Hamiltonian) models are considered. For each experimental case, the elastic energy of the system is relaxed in equilibrium and then the model is excited by a pulse source in order to produce wave propagation. First, a review is presented of the well established velocity-porosity relationship from rock physics, which shows a linear trend from small porosities up to the critical porosity (percolation threshold) where the rocks fall apart. From the wave propagation analysis a general trend is observed for the attenuation of waves, from the small to the large porosity models, suggesting multiple scattering effects similar to those reported from effective-medium approximations of wave scattering due to random heterogeneities. Finally, the results are compared with those obtained from laboratory experiments on dry rocks with different porosities and different applied stress regimes.     

Anomalously soft dynamics of water in a nanotube: a revelation of nanoscale confinement

Quasi-one-dimensional water encapsulated inside single-walled carbon nanotubes, here referred to as nanotube water, was studied by neutron scattering. The results reveal an anomalously soft dynamics characterized by pliable hydrogen bonds, anharmonic intermolecular potentials, and large-amplitude motions in nanotube water. Molecular dynamics simulations consistently describe the observed phenomena and propose the structure of nanotube water, which comprises a square-ice sheet wrapped into a cylinder inside the carbon nanotube and interior molecules in a chainlike configuration.     

Thermodynamic analysis of pure and impurity doped pentaerythritol tetranitrate crystals grown at room temperature

Pentaerythritol tetranitrate (PETN) powders are used to initiate other explosives. During long-term storage, changes in powder properties can cause changes in the initiation performance. Changes in the morphology and surface area of aging powders are observed due to sublimation and growth of PETN crystals through coarsening mechanisms, (e.g. Ostwald ripening, sintering, etc.). In order to alleviate the sublimation of PETN crystals under service conditions, stabilization methods such as thermal cycling and doping with certain impurities during or after the crystallization of PETN have been proposed. In this report we present our work on the effect of impurities on the morphology and activation energy of the PETN crystals. The pure and impurity doped crystals of PETN were grown from supersaturated acetone solution by solvent evaporation technique at room temperature. The difference in the morphology of the impurity-doped PETN crystal compared to pure crystal was examined by optical microscopy. The changes in the activation energies and the evaporation rates are determined by thermogravimetry (TG). Our activation energies of evaporation agree with earlier reported enthalpies of vaporization. The morphology and activation energy of PETN crystals doped with Ca, Na, and Fe cations are similar to that for pure PETN crystal, whereas the Zn-ion-doped PETN crystals have different morphology and decreased activation energy.     

Sterically-crowded pyrroles

The syntheses in good yields of a considerable number of moderately to severely sterically-crowded 1,2,5-trisubstituted pyrroles by means of modifications of the Knorr-Paal condensation are described. Notwithstanding reports to the contrary, the classical procedure; succeeded in moderately sterically-crowded cases, e.g., R² = R⁵ = Me, R¹ = i-Pr, Me₂CHMeCH-, Me₂N-, Ph₂N-, 9-carbazolo, subst. 4-morpholino, 1-piperazino, 1-piperidino, etc. A product-water azeotroping procedure succeeded in more severely sterically-crowded cases e.g., R² = R⁵ = Et, R¹ = i-Pr; R² = R⁵ = Me, R¹ = Me₃CCH₂-, R² = R⁵ = i-Pr, R¹ = PhCH₂-. Highly sterically-crowded pyrroles, e.g., R² = R⁵ = Me, R¹ = t-Bu, adamantyl, PhCH₂CMe₂; R² = R⁵ = Et, R¹ = t-Bu; R¹ = R² = R⁵ = i-Pr; R² = R⁵ = t-Ru, R¹ = Me, Et, PhCH₂-, were obtained using titanium tetrachloride as a Lewis acid catalyst and as a water scavenger. Infrared spectra of the reacting mixtures provided evidence pertinent to the mechanism of the reaction, which is discussed.