An insight into iTRAQ: where do we stand now?

The iTRAQ (isobaric tags for relative and absolute quantification) technique is widely employed in proteomic workflows requiring relative quantification. Here, we review the iTRAQ literature; in particular, we focus on iTRAQ usage in relation to other commonly used quantitative techniques e.g. stable isotope labelling in culture (SILAC), label-free methods and selected reaction monitoring (SRM). As a result, we identify several issues arising with respect to iTRAQ. Perhaps frustratingly, iTRAQ's attractiveness has been undermined by a number of technical and analytical limitations: it may not be truly quantitative, as the changes in abundance reported will generally be underestimated. We discuss weaknesses and strengths of iTRAQ as a methodology for relative quantification in the light of this and other technical issues. We focus on technical developments targeted at iTRAQ accuracy and precision, use of 4-plex over 8-plex reagents and application of iTRAQ to post-translational modification (PTM) workflows. We also discuss iTRAQ in relation to label-free approaches, to which iTRAQ is losing ground.     

Intermediates and kinetics for phenol gasification in supercritical water

We processed phenol with supercritical water in a series of experiments, which systematically varied the temperature, water density, reactant concentration, and reaction time. Both the gas and liquid phases were analyzed post-reaction using gas chromatographic techniques, which identified and quantified the reaction intermediates and products, including H(2), CO, CH(4), and CO(2) in the gas phase and twenty different compounds--mainly polycyclic aromatic hydrocarbons--in the liquid phase. Many of these liquid phase compounds were identified for the first time and could pose environmental risks. Higher temperatures promoted gasification and resulted in a product gas rich in H(2) and CH(4) (33% and 29%, respectively, at 700 °C), but char yields increased as well. We implicated dibenzofuran and other identified phenolic dimers as precursor molecules for char formation pathways, which can be driven by free radical polymerization at high temperatures. Examination of the trends in conversion as a function of initial water and phenol concentrations revealed competing effects, and these informed the kinetic modeling of phenol disappearance. Two different reaction pathways emerged from the kinetic modeling: one in which rate ∝ [phenol](1.73)[water](-16.60) and the other in which rate ∝ [phenol](0.92)[water](1.39). These pathways may correspond to pyrolysis, which dominates when there is abundant phenol and little water, and hydrothermal reactions, which dominate in excess water. This result confirms that supercritical water gasification of phenol does not simply follow first-order kinetics, as previous efforts to model phenol disappearance had assumed.     

Kinetic model for supercritical water gasification of algae

The article reports the first quantitative kinetics model for supercritical water gasification (SCWG) of real biomass (algae) that describes the formation of the individual gaseous products. The phenomenological model is based on a set of reaction pathways that includes two types of compounds being intermediate between the algal biomass and the final gaseous products. To best correlate the experimental gas yields obtained at 450, 500 and 550 °C, the model allowed one type of intermediate to react to gases more quickly than the other type of intermediate. The model parameters indicate that gas yields increase with temperature because higher temperatures favor production of the more easily gasified intermediate and the production of gas at the expense of char. The model can accurately predict the qualitative influence of the biomass loading and water density on the gas yields. Sensitivity analysis and reaction rate analysis indicate that steam reforming of intermediates is an important source of H(2), whereas direct decomposition of the intermediate species is the main source of CO, CO(2) and CH(4).     

Reactions of triflate esters and triflamides with an organic neutral super-electron-donor

The bis-pyridinylidene 13 converts aliphatic and aryl triflate esters to the corresponding alcohols and phenols respectively, using DMF as solvent, generally in excellent yields. While the deprotection of aryl triflates has been seen with other reagents and by more than one mechanism, the deprotection of alkyl triflates is a new reaction. Studies with (18)O labelled DMF indicate that the C-O bond stays intact and hence it is the S-O bond that cleaves, underlining that the cleavage results from the extraordinary electron donor capability of 13. Trifluoromethanesulfonamides are converted to the parent amines in like manner, representing the first cleavage of such substrates by a ground-state organic reducing reagent.     

Diruthenium(II,III) tetramidates as a new class of oxygenation catalysts

Two new diruthenium(II,III) tetramidate compounds, Ru(2)(NHOCC(CH(3))(2))(4)Cl (1) and Ru(2)(NHOCCH(2)CH(3))(4)Cl (2) have been prepared and structurally characterized by X-ray crystallography. The activity of promoting sulfide oxygenation using simple oxidants such as hydrogen peroxide (H(2)O(2)) and tert-butyl hydroperoxide (TBHP) was studied. A UV-kinetics study indicated that the initial rates of 1 and 2 are comparable to the previously studied diruthenium tetracarboxylates in promoting TBHP oxygenation of methyl phenyl sulfide (MPS). Using excess oxidant and CH(3)CN as the solvent, organic sulfides MPS and diphenyl sulfide (PPS) were oxidized using 1 mol% of the catalytic species. Compound 1 is more effective than 2 in converting sulfides to sulfoxide under the same conditions. Fast conversion was achieved when the reactions were carried out in the solvent-free conditions, and the major oxidation product was the sulfoxide. The electronic structure of the title compounds was studied with DFT calculations to gain an understanding of the activation of peroxy reagents.     

Layered inorganic-organic frameworks based on the 2,2-dimethylsuccinate ligand: structural diversity and its effect on nanosheet exfoliation and magnetic properties

The structures of four new 2,2-dimethylsuccinate frameworks suitable for exfoliation into nanosheets using ultrasonication are reported. These hybrid compounds contain either monovalent (Li(+)) or divalent (Co(2+) and Zn(2+)) cations, and they all feature hydrophobically capped covalently bonded layers that only interact with each other via weak van der Waals forces. Critically this shows that the use of this dicarboxylate ligand generally yields two dimensional compounds suitable for simple and affordable nanosheet exfoliation. This extends the range of frameworks that can be exfoliated and highlights the 2,2-dimethylsuccinate ligand as an excellent versatile platform for the production of nanosheets. The topologies of the layers in each framework were found to vary significantly and this appears to have a significant effect on the relative size of the nanosheets produced; increased space between methyl groups and more extensive inorganic connectivity appears to favour the formation of thin nanosheets with larger lateral dimensions. Additionally the magnetic properties of two of these frameworks were examined, and it was found that both exhibit strong low dimensional antiferromagnetic coupling despite their well-separated layers preventing three dimensional magnetic order.     

Synthesis of U(IV) imidos from Tp*2U(CH2Ph) (Tp* = hydrotris(3,5-dimethylpyrazolyl)borate) by extrusion of bibenzyl

Addition of organic azides, N(3)R (R = 2,4,6-trimethylphenyl (Mes), phenyl (Ph), 1-adamantyl (Ad)), to a solution of the uranium(III) alkyl complex, Tp*(2)U(CH(2)Ph) (Tp* = hydrotris(3,5-dimethylpyrazolyl)borate) (1), results in the formation of a family of uranium(iv) imido derivatives, Tp*(2)U(NR) (2-R). Notably, these complexes were synthesized in high yields by coupling of the benzyl groups to form bibenzyl. The uranium(IV) imido derivatives, 2-Mes, 2-Ph, and 2-Ad, were all characterized by both (1)H NMR and IR spectroscopy, and 2-Mes and 2-Ad were also characterized by X-ray crystallography. In the molecular structure of 2-Mes, typical κ(3)-coordination of the Tp* ligands was observed; however in the case of 2-Ad, one pyrazole ring of a Tp* ligand has rotated away from the metal centre, forcing a κ(2)-coordination of the pyrazoles. This results in a uranium-hydrogen interaction with the Tp* B-H. Treating these imido complexes with para-tolualdehyde results in multiple bond metathesis, forming the terminal uranium(IV) oxo complex, Tp*(2)U(O), and the corresponding imine.     

Analysis of Basic Drugs: A Comparison of Two Different Strong Cation Exchange-Modified LC Packings

Evidence in the literature of systematic investigation of retention mechanisms on strong cation-exchange (SCX) modified silica LC packings is lacking. In this study, the retention behaviour of selected basic drugs using a propylbenzenesulfonic acid-modified packing (Nucleosil 100SA) were compared, under similar conditions, with previous findings from a propylsulfonic acid-modified packing (Waters Spherisorb S5SCX). Eluent ionic strength, apparent pH, and solvent composition were investigated. Good efficiency (70,000 plates m^?1) and peak symmetry (<1.5) were observed using the Nucleosil 100SA packing. The use of different alkyl ‘spacer’ moieties in each packing influenced retention, with hydrophobic partitioning of analytes more evident for the Nucleosil packing compared with Spherisorb, particularly when water-containing eluents were used. On Nucleosil 100SA, non ion-exchange interactions accounted for up to 61% of retention. Despite some correlation with analyte LogP on Nucleosil 100SA, and the environment surrounding basic nitrogen moieties, retention on both SCX packings was unrelated to analyte pK _a.     

Chermak–Delgado Lattice Extension Theorems

If G is a finite group with subgroup H, then the Chermak–Delgado measure of H (in G) is defined as |H||C _G (H)|. The Chermak–Delgado lattice of G, denoted 𝒞𝒟(G), is the set of all subgroups with maximal Chermak–Delgado measure; this set is a moduar sublattice within the subgroup lattice of G. In this paper we provide an example of a p-group P, for any prime p, where 𝒞𝒟(P) is lattice isomorphic to 2 copies of ?₂ (a quasiantichain of width 2) that are adjoined maximum-to-minimum. We introduce terminology to describe this structure, called a 2-string of 2-diamonds, and we also give two constructions for generalizing the example. The first generalization results in a p-group with Chermak–Delgado lattice that, for any positive integers n and l, is a 2l-string of n-dimensional cubes adjoined maximum-to-minimum and the second generalization gives a construction for a p-group with Chermak–Delgado lattice that is a 2l-string of ? _p+1 (quasiantichains, each of width p + 1) adjoined maximum-to-minimum.