Manipulation of protein fingerprints during on-column fluorescent labeling: protein fingerprinting of six Staphylococcus species by capillary electrophoresis

Bacterial proteomes were analyzed by use of electrophoretically mediated microanalysis (EMMA) and field-enhanced stacking. A water-soluble protein fraction was injected onto a capillary. Next, a fluorogenic reagent was injected and allowed to react with the protein mixture, producing fluorescent products that were separated by submicellar capillary electrophoresis and detected by laser-induced fluorescence. By use of a low-ionic strength sample buffer and a brief electrophoretic step, slow moving anionic proteins were stacked at the reagent-sample interface and were preferentially labeled. By reversing the order of sample injection and labeling reagent, fast moving cationic proteins were preferentially labeled. By adjustment of the sample buffer pH, proteins with different isoelectric points were selectively labeled. Electrophoresis fingerprints were generated for the water-soluble protein fraction from six Staphylococcus species. The protein patterns produced were species-specific and were used to construct a phylogenetic tree.     

A resonance Raman,surface-enhanced resonance Raman,IR, and ab initio vibrational spectroscopic study of nickel(II) tetraazaannulene complexes

The IR and resonance Raman spectra of the nickel(II) complexes of dibenzo[b,i][1,4,8,11]tetraaza[14]annulene (TAA) and 5,7,12,14-tetramethyldibenzo[b,i][1,4,8,11]tetraaza[14]annulene (TMTAA) have been measured and compared with ab initio calculations of the vibrational wavenumbers at the B3-LYP level using the LanL2DZ basis set. An excellent fit is found between the experimental and calculated data, enabling precise vibrational assignments to be made. Surface-enhanced resonance Raman spectra were obtained following adsorption on Ag electrodes, with potentials in the range -0.1 to -1.1 V vs Ag/AgCl. There is evidence for contributions from both the electromagnetic and charge transfer (CT) surface enhancement mechanisms. The data indicate that variations in band intensities with electrode potential can be interpreted in terms of the CT mechanism.     

Structural properties of ultra-small thorium and uranium dioxide nanoparticles embedded in a covalent organic framework

We report the structural properties of ultra-small ThO₂ and UO₂ nanoparticles (NPs), which were synthesized without strong binding surface ligands by employing a covalent organic framework (COF-5) as an inert template. The resultant NPs were used to observe how structural properties are affected by decreasing grain size within bulk actinide oxides, which has implications for understanding the behavior of nuclear fuel materials. Through a comprehensive characterization strategy, we gain insight regarding how structure at the NP surface differs from the interior. Characterization using electron microscopy and small-angle X-ray scattering indicates that growth of the ThO₂ and UO₂ NPs was confined by the pores of the COF template, resulting in sub-3 nm particles. X-ray absorption fine structure spectroscopy results indicate that the NPs are best described as ThO₂ and UO₂ materials with unpassivated surfaces. The surface layers of these particles compensate for high surface energy by exhibiting a broader distribution of Th–O and U–O bond distances despite retaining average bond lengths that are characteristic of bulk ThO₂ and UO₂. The combined synthesis and physical characterization efforts provide a detailed picture of actinide oxide structure at the nanoscale, which remains highly underexplored compared to transition metal counterparts.

ThO₂ and UO₂ nanoparticles synthesized using a COF-5 template exhibit unpassivated surfaces and provide insight into nanoscale properties of actinides.     

Mass spectrometry in structural and stereochemical problems. Part CLIII. Electron impact-promoted fragmentation of n-alkyl cyanides

In spite of previous extensive studies on the mass spectrometry of alkyl cyanides, no good mechanistic insight has as yet been gained into the behavior of straight chain alky1 cyanides. For this reason the possible origins for the principal ions in the mass spectrum of a typical alkyl cyanide (n-hexyl cyanide) have been determined using high resolution mass spectrometry anddeuterium labeling of every carbon atom. The results lead to the conclusion that most of the typical fragmentation processes of n-alkyl cyanides proceed through cyclic intermediates.     

Modeling Pb sorption to microporous amorphous oxides as discrete particles and coatings

Hydrous amorphous Al (HAO), Fe (HFO), and Mn (HMO) oxides are ubiquitous in the subsurface as both discrete particles and coatings and exhibit a high affinity for heavy metal contaminants. To assess risks associated with heavy metals, such as Pb, to the surrounding environment and manage remedial activities requires accurate mechanistic models with well-defined transport parameters that represent sorption processes. Experiments were conducted to evaluate Pb sorption to microporous Al, Fe, and Mn oxides, as well as to montmorillonite and HAO-coated montmorillonite. Intraparticle diffusion, a natural attenuating process, was observed to be the rate-limiting mechanism in the sorption process, where best-fit surface diffusivities ranged from 10(-18) to 10(-15) cm(2) s(-1). Specifically, diffusivities of Pb sorption to discrete aluminum oxide, aluminum oxide-coated montmorillonite, and montmorillonite indicated substrate surface characteristics influence metal mobility where diffusivity increased as affinity decreased. Furthermore, the diffusivity for aluminum oxide-coated montmorillonite was consistent with the concentrations of the individual minerals present and their associated particle size distributions. These results suggest that diffusivities for other coated systems can be predicted, and that oxide coatings and montmorillonite are effective sinks for heavy metal ions.     

Charge density analysis of two polymorphs of antimony(III) oxide

High-resolution X-ray diffraction data have been collected on the cubic polymorph of antimony(III) oxide (senarmontite) to determine the charge distribution in the crystal. The results are in quantitative agreement with crystal Hartree-Fock calculations for this polymorph, and have been compared with theoretical calculations on the orthorhombic polymorph (valentinite). Information about the nature of bonding and relative bond strengths in the two polymorphs has been extracted in a straightforward manner via topological analysis of the electron density. All the close contacts in both polymorphs are found to be similar in nature based on the value of the Laplacian, the magnitude of the electron density and the local energy density at the bond critical points, and these characterise the observed interactions as substantially polar covalent, similar to molecular calculation results on Si-O and Ge-O. Electrostatic potential isosurfaces reveal the octopolar nature of this function for senarmontite, and shed light on the observed packing arrangement of Sb4O6 molecules in the crystal.     

Chemical interactions in the surface-enhanced resonance Raman scattering of ruthenium polypyridyl complexes

Surface-enhanced resonance Raman scattering (SERRS) from the alpha-diimine complexes [Ru(bpm)(3)](2+) and [Ru(bpz)(3)](2+) is reported for the first time at a roughened silver electrode. In both cases, a possible adsorbate orientation has been proposed involving binding through nitrogen lone pair electrons to the silver surface, based on changes in band positions upon adsorption. The SERRS spectra of [Ru(bpm)(3)](2+) were found to change slightly with a change in applied potential. The relative intensity of the nu(C6C6') band was found to be dependent on both excitation wavelength and applied potential. This was ascribed to an active charge transfer (CT) mechanism operating synergistically with the electromagnetic mechanism. No such CT activity was observed in [Ru(bpz)(3)](2+). It is tentatively suggested that this behavior may arise from the different modes of adsorption of the two complexes.     

OptiDock: virtual HTS of combinatorial libraries by efficient sampling of binding modes in product space

Products from combinatorial libraries generally share a common core structure that can be exploited to improve the efficiency of virtual high-throughput screening (vHTS). In general, it is more efficient to find a method that scales with the total number of reagents (Sigma growth) rather with the number of products (Pi growth). The OptiDock methodology described herein entails selecting a diverse but representative subset of compounds that span the structural space encompassed by the full library. These compounds are docked individually using the FlexX program (Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. J. Mol. Biol. 1995, 251, 470-489) to define distinct docking modes in terms of reference placements for combinatorial core atoms. Thereafter, substituents in R-cores (consisting of the core structure substituted at a single variation site) are docked, keeping the core atoms fixed at the coordinates dictated by each reference placement. Interaction energies are calculated for each docked R-core with respect to the target protein, and energies for whole compounds are calculated by finding the reference core placement for which the sum of corresponding R-core energies is most negative. The use of diverse whole compounds to define binding modes is a key advantage of the protocol over other combinatorial docking programs. As a result, OptiDock returns better-scoring conformers than does serially applied FlexX. OptiDock is also better able to find a viable docked pose for each library member than are other combinatorial approaches.     

Toward the development of new photolabile protecting groups that can rapidly release bioactive compounds upon photolysis with visible light

The synthesis and characterization of a new photolabile protecting group (caging group) for carboxylic acids, the 2-(dimethylamino)-5-nitrophenyl (DANP) group, is described. This compound has a major absorption band in the visible wavelength region with a maximum near 400 nm (epsilon400 = 9077 M(-1) cm(-1) at pH 7.4 and 21 degrees C). The caging group is attached through an ester linkage to the carboxyl functionality of beta-alanine, which activates the inhibitory glycine receptor in the mammalian central nervous system. Such caged compounds play an important role in transient kinetic investigations of fast cellular processes. Upon photolysis of DANP-caged beta-alanine, the caging group is released within 5 micros. Quantum yields of 0.03 and 0.002 were obtained in the UV region (308 and 360 nm) and the visible region (450 nm), respectively. Laser-pulse photolysis experiments, using 337 or 360 nm light, were performed with the caged compound equilibrated with HEK 293 cells transiently transfected with cDNA encoding the alpha1 homomeric, wild-type glycine receptor. The experiments demonstrated that neither DANP-caged beta-alanine nor its byproducts inhibit or activate the glycine receptors on the cell surface. Under physiological conditions, the DANP-caged beta-alanine is water-soluble and stable and can be used for transient kinetic measurements.     

Coupling of an aldehyde or ketone to pyridine mediated by a tungsten imido complex

The reactivity of W(NPh)(o-(Me3SiN)2C6H4)(py)2 and W(NPh)(o-(Me3SiN)2C6H4)(pic)2 (py=pyridine; pic=4-picoline) with unsaturated substrates has been investigated. Treatment of W(NPh)(o-(Me3SiN)2C6H4)(py)2 with diphenylacetylene or 2,3-dimethyl-1,3-butadiene generates W(NPh)(o-(Me3SiN)2C6H4)(eta2-PhCCPh) and W(NPh)(o-(Me3SiN)2C6H4)(eta4-CH2=C(Me)C(Me)=CH2), respectively, while the addition of ethylene to W(NPh)(o-(Me3SiN)2C6H4)(py)2 generates the known metallacycle W(NPh)(o-(Me3SiN)2C6H4)(CH2CH2CH2CH2). The addition of 2 equiv of acetone to W(NPh)(o-(Me3SiN)2C6H4)(pic)2 provides the azaoxymetallacycle W(NPh)(o-(Me3SiN)2C6H4)(OCH(Me)2)(OC(Me)2-o-C5H3N-p-Me), the result of acetone insertion into the ortho C-H bond of picoline. Similarily, the addition of 2 equiv of RC(O)H [R=Ph, tBu] to W(NPh)(o-(Me3SiN)2C6H4)(py)2 generates W(NPh)(o-(Me3SiN)2C6H4)(OCH2R)(OCHR-o-C5H4N) [R=Ph, tBu,]. In contrast, reaction between W(NPh)(o-(Me3SiN)2C6H4)(py)2 and 2-pyridine carboxaldehyde yields the diolate W(NPh)(o-(Me3SiN)2C6H4)(OCH(C5H4N)CH(C5H4N)O). The synthesis of W(NPh)(o-(Me3SiN)2C6H4)(PMe3)(py)(eta2-OC(H)C6H4-p-Me), formed by the addition of p-tolualdehyde to a mixture of W(NPh)(o-(Me3SiN)2C6H4)(py)2 and PMe3, suggests that an eta2-aldehyde intermediate is involved in the formation of the azaoxymetallacycle, while the isolation of W(NPh)(o-(Me3SiN)2C6H4)(Cl)(OC(Me)(CMe3)-o-C5H4N), formed by the reaction of pinacolone with W(NPh)(o-(Me3SiN)2C6H4)(py)2, in the presence of adventitious CH2Cl2, suggests that the reaction proceeds via the hydride W(NPh)(o-(Me3SiN)2C6H4)(H)(OC(Me)(CMe3)-o-C5H4N).