On the trimerization of cyanoacetylene: mechanism of formation of tricyanobenzene isomers and laboratory detection of their radio spectra

In support of a deeper understanding of the chemistry of cyanoacetylene--a known constituent of planetary atmospheres and interstellar space--theoretical and experimental studies address the chemical mechanism of dimerization and trimerization, and provide high-resolution rotational spectra of two of the trimeric products, 1,2,3- and 1,2,4-tricyanobenzene. Analysis of the rotational spectra is particularly challenging because of quadrupolar coupling from three (14)N nuclei. The laboratory rotational spectra provide the basis for future searches for these polar aromatic compounds in interstellar space by radio astronomy.     

Structural study of acetogenins by tandem mass spectrometry under high and low collision energy

Collision‐induced dissociation experiments of seven annonaceous acetogenins were carried out under high and low collision energy conditions. Each compound was studied as protonated or deprotonated and lithium‐ or sodium‐ cationized molecules, using ElectroSpray Ionisation (ESI) with a hybrid linear trap/orbitrap mass spectrometer (LTQ‐Orbitrap®). The same ion species were studied with a Matrix‐Assisted Laser Desorption Ionisation (MALDI) tandem mass spectrometer in a high collision energy regime (1 or 2 keV). Although each of the techniques showed some limitations in the detection of functional groups, unambiguous structural identification of the acetogenins was obtained. MALDI ToF‐ToF has the advantage over ESI‐based methods to provide mass spectra rich in informative fragments which allows the confirmation of some functional groups position. By contrast, ESI‐LTQ‐Orbitrap® analysis has the advantage over MALDI that the mass spectra are relatively simple with only fragments close to the functional groups. However, this technique needs to carry out experiments both in negative and positive ionization modes. Copyright © 2010 John Wiley & Sons, Ltd.     

Two-dimensional liquid chromatography/mass spectrometry/mass spectrometry separation of water-soluble metabolites

Off-line two-dimensional liquid chromatography with tandem mass spectrometry detection (2D-LC/MS-MS) was used to separate a set of metabolomic species. Water-soluble metabolites were extracted from Escherichia coli and Saccharomyces cerevisae cultures and were immediately analyzed using strong cation exchange (SCX)-hydrophilic interaction chromatography (HILIC). Metabolite mixtures are well-suited for multidimensional chromatography as the range of components varies widely with respect to polarity and chemical makeup. Some currently used methods employ two different separations for the detection of positively and negatively ionized metabolites by mass spectrometry. Here we developed a single set of chromatographic conditions for both ionization modes and were able to detect a total of 141 extracted metabolite species, with an overall peak capacity of ca. 2500. We show that a single two-dimensional separation method is sufficient and practical when a pair or more of unidimensional separations are used in metabolomics.     

Near-field optical characterization of interacting and non-interacting gold nanoparticles embedded in a silica thin film

By near-field optics, we characterized the local optical properties of clusters of gold nanoparticles randomly distributed under a 50 nm-thick SiO₂ thin film. A local field enhancement is visible above isolated clusters. A few hundred nanometers away from them, we observed a polarization-dependent pattern with elliptical lobes oriented in the incident polarization direction. A simple simulation shows that the observed near-field images can be represented by the sum of the field of an oscillating dipole and the incident field. When the cluster density is larger, the measured near-field images show numerous bright and dark spots. The position of the bright spots does not necessarily coincide with the gold clusters showing the presence of coupling effects between them.     

Coverage dependence of glycine adsorption on the Ge(100) − 2 × 1 surface

A combination of infrared spectroscopy, X-ray photoelectron spectroscopy and density functional theory has been used to investigate the adsorption behavior of glycine at the Ge(100) ? 2 × 1 surface under ultrahigh vacuum conditions. Comparison of experimental and simulated IR spectra indicates that at 310 K, glycine adsorbs on Ge(100) ? 2 × 1 via O–H dissociation, with some fraction of the products also forming an N dative bond to a neighboring germanium atom. O–Ge dative bonding is not observed. As coverage increases, the surface concentration of the monodentate O–H dissociated adduct increases, while that of the N dative-bonded species appears constant. XPS data support and clarify the IR findings and reveal new insights, including the presence at higher coverage of a minor product that has undergone dual O–H and N–H dissociation. These findings are supported by the calculated energy diagrams, which indicate that the reaction of a glycine molecule on the Ge(100) ? 2 × 1 surface via O–H dissociation and interdimer N dative bonding is both kinetically and thermodynamically favorable and that N–H dissociation of this adduct is feasible at room temperature given incomplete thermal accommodation along the reaction pathway.     

Highly efficient on-DNA amide couplings promoted by micelle forming surfactants for the synthesis of DNA encoded libraries

DNA encoded libraries (DELs) represent powerful new technology for finding small molecule ligands for proteins and are increasingly being applied to hit finding in medicinal chemistry. Crucial to the synthesis of high quality DELs is the identification of chemical reactions for their assembly that proceed with very high conversion across a range of different substrates, under conditions compatible with DNA-tagged substrates. Many current chemistries used in DEL synthesis do not meet this requirement, resulting in libraries of low fidelity. Amide couplings are the most commonly used reaction in synthesis of screening libraries and also in DELs. The ability to carry out highly efficient, widely applicable amide couplings in DEL synthesis would therefore be highly desirable. We report a method for amide coupling using micelle forming surfactants, promoted by a modified linker, that is broadly applicable across a wide range of substrates. Most significantly, this works exceptionally well for coupling of DNA-conjugated carboxylic acids (N-to-C) with amines in solution, a procedure that is currently very inefficient. The optimisation of separate procedures for coupling of DNA-conjugated acids and amines by reagent screening and statistically driven optimisation is described. The generality of the method is illustrated by the application to a wide range of examples with unprecedented levels of conversion. The utility of the (N-to-C) coupling of DNA-conjugated acids in DEL synthesis is illustrated by the three cycle synthesis of a fully DNA-encoded compound by two cycles of coupling of an aminoester, with intermediate ester hydrolysis, followed by capping with an amine. This methodology will be of great utility in the synthesis of high fidelity DELs.

Highly efficient forward and reverse on-DNA amide couplings were developed exploiting hydrophobic linkers in combination with the micelle forming surfactant TPGS-750M. The method is highly effective for a wide range of substrates in the synthesis of DNA-encoded libraries.     

FRET detection of Octamer-4 on a protein nanoarray made by size-dependent self-assembly

An alternative approach for fabricating a protein array at nanoscale is suggested with a capability of characterization and/or localization of multiple components on a nanoarray. Fluorescent micro- and nanobeads each conjugated with different antibodies are assembled by size-dependent self-assembly (SDSA) onto nanometer wells that were created on a polymethyl methacrylate (PMMA) substrate by electron beam lithography (EBL). Antibody-conjugated beads of different diameters are added serially and electrostatically attached to corresponding wells through electrostatic attraction between the charged beads (confirmed by zeta potential analysis) and exposed p-doped silicon substrate underneath the PMMA layer. This SDSA method is enhanced by vibrated-wire-guide manipulation of droplets on the PMMA surface containing nanometer wells. Saturation rates of antibody-conjugated beads to the nanometer patterns are up to 97% under one component and 58–70% under two components nanoarrays. High-density arrays (up to 40,000 wells) could be fabricated, which can also be multi-component. Target detection utilizes fluorescence resonance energy transfer (FRET) from fluorescent beads to fluorescent-tagged secondary antibodies to Octamer-4 (Oct4), which eliminates the need for multiple steps of rinsing. The 100 nm green beads are covalently conjugated with anti-Oct4 to capture Oct4 peptides (39 kDa); where the secondary anti-Oct4 and F(ab)₂ fragment of anti-gIgG tagged with phycoerythrin are then added to function as an indicator of Oct4 detection. FRET signals are detected through confocal microscopes, and further confirmed by Fluorolog3 spectrofluorometer. The success rates of detecting Oct4 are 32% and 14% of the beads in right place under one and two component nanoarrays, respectively. Ratiometric FRET is used to quantify the amount of Oct4 peptides per each bead, which is estimated about 2 molecules per bead.