A novel polyacrylamide gel system for proteomic use offering controllable pore expansion by crosslinker cleavage

SDS‐PAGE is still one of the most widespread separation techniques in proteomic research and usually coupled to subsequent MS measurement for protein identification. The proteins are digested while embedded in the gel matrix. The resultant peptides are eluted out of the gel and finally analyzed. The in‐gel digestion process suffers from several drawbacks which influence the experimental outcome with respect to protein sequence coverage and detection sensitivity. Limited accessibility of the protease to the substrate protein and insufficient peptide extraction represent the two major problems. To specifically target these issues, we established a novel partly reversible gel system, in which the gel matrix can be conditionally cleaved to increase the pore diameters. By using a crosslinker mixture consisting of Bis and ethylene‐glycol‐diacrylate the acrylamide filament interconnections can be partly hydrolyzed in alkaline solution. The new hybrid gels have been tested to be compatible with a variety of acidic staining techniques. They exhibit similar electrophoretic performance compared with regular solely Bis‐based gels, but yield significantly better MS results. Thus, the Bis/ethylene‐glycol‐diacrylate SDS‐PAGE gel system is a promising alternative for MS‐based in‐gel workflows and might be transferred to other gel‐electrophoretic applications.     

Simultaneous determination of nine endogenous steroids in human urine by polymeric-mixed micelle capillary electrophoresis

A new CE system based on the use of polymeric-mixed micelles (cholic acid, SDS and the poloxamine Tetronic(?) 1107) was developed for the simultaneous determination of nine steroids in human urine. This method allows the baseline separation and quantitation of cortisol, androstenedione, estriol, dehydroepiandrosterone sulfate, testosterone, dehydroepiandrosterone, estrone, progesterone and estradiol in less than 25 min showing to be sensitive enough to detect low concentrations of these steroids in urine samples (5-45 ng/mL). The optimized electrophoretic conditions were performed using a 50 cm × 75 μm capillary, 18 kV, 25°C, with 44 mM cholic acid, 10 mM SDS, 0.05% w/v tetronic(?) 1107, 2.5% v/v methanol, 2.5% v/v tetrahydrofuran in 5 mM borate - 5 mM phosphate buffer (pH=8.0) as a background electrolyte and a dual 210/254 UV-detection. The method can simultaneously determine 0.1-120 μg/mL, which corresponds to 5-6000 ng/mL of steroids in 2 mL urine. The recoveries ranged between 82.4 and 101.5%. Due to its simplicity, speed, accuracy and reliability, the proposed method could be a potential alternative to the traditional methodologies used with clinical purposes.     

Pd complexes of iminophosphine ligands: A homogeneous molecular catalyst for Suzuki–Miyaura cross-coupling reactions under mild conditions

The complexes formed by combining Pd(OAc)₂ and iminophosphine ligands (P^N) are active catalysts in Suzuki–Miyaura cross-coupling reactions under mild conditions. Aryl bromides and iodides, as well as benzyl chlorides give the corresponding coupled products in high yields at low temperatures (25–50 °C) using these catalysts. Iminophosphines containing the most sterically demanding groups attached to the N-imino moiety were the most effective ligands. New divalent Pd complexes of known iminophosphines were synthesised and their activity was compared with the in situ generated catalyst system. The complex resulting from the oxidative addition of 4-bromo anisole [Pd(4-CH₃OC₆H₄)Br(P^N)] was more active than the in situ generated system. However, palladacycles containing the iminophosphine ligand (e.g., {[C₆H₄CH(Me)₂St-Bu]Pd(P^N)}⁺PF₆⁻) were less active than the in situ generated catalyst due to the greater stability of the complexes that involve two bidentate ligands. Poisoning tests demonstrated that homogeneous mononuclear palladium species containing the iminophsophine ligand were responsible for the catalytic activity.     

Measurement of PAHs in environmental matrices: results from an interlaboratory comparison on the different steps of the measurement procedure

Proficiency testing (PT) is becoming a feature of laboratory accreditation and the PT results are used to assess the technical competence of the participating laboratories. ISPRA (former APAT) plays an important role in supporting the Italian laboratories belonging to the network of the Regional Environmental Agencies to improve the quality of their analytical measurements. As a consequence, ISPRA organized an interlaboratory comparison to assess the performance of the laboratories on PAH measurement procedure. The interlaboratory comparison was drawn separating the different steps of the measurement (from the extraction to the instrumental measurement). Two matrix reference materials: (1) a polluted soil and (2) an extract reference material of the same polluted soil and a “blind” PAH mixture standard stock solution were distributed to 59 Italian laboratories. The results of interlaboratory comparison showed a significant dispersion of the PAH measurements that masks the effects of the different extraction and cleanup procedures used, but it is consistent with the results of other European interlaboratory comparisons.     

Role of structural order and excess energy on ultrafast free charge generation in hybrid polythiophene/Si photovoltaics probed in real time by near-infrared broadband transient absorption

Despite the central role of light absorption and the subsequent generation of free charge carriers in organic and hybrid organic-inorganic photovoltaics, the precise process of this initial photoconversion is still debated. We employ a novel broadband (UV-Vis-NIR) transient absorption spectroscopy setup to probe charge generation and recombination in the thin films of the recently suggested hybrid material combination poly(3-hexylthiophene)/silicon (P3HT/Si) with 40 fs time resolution. Our approach allows for monitoring the time evolution of the relevant transient species under various excitation intensities and excitation wavelengths. Both in regioregular (RR) and regiorandom (RRa) P3HT, we observe an instant (<40 fs) creation of singlet excitons, which subsequently dissociate to form polarons in 140 fs. The quantum yield of polaron formation through dissociation of delocalized excitons is significantly enhanced by adding Si as an electron acceptor, revealing ultrafast electron transfer from P3HT to Si. P3HT/Si films with aggregated RR-P3HT are found to provide free charge carriers in planar as well as in bulk heterojunctions, and losses are due to nongeminate recombination. In contrast for RRa-P3HT/Si, geminate recombination of bound carriers is observed as the dominant loss mechanism. Site-selective excitation by variation of pump wavelength uncovers an energy transfer from P3HT coils to aggregates with a 1/e transfer time of 3 ps and reveals a factor of 2 more efficient polaron formation using aggregated RR-P3HT compared to disordered RRa-P3HT. Therefore, we find that polymer structural order rather than excess energy is the key criterion for free charge generation in hybrid P3HT/Si solar cells.     

Pyochelin enantiomers and their outer-membrane siderophore transporters in fluorescent pseudomonads: structural bases for unique enantiospecific recognition

Pyochelin (Pch) and enantiopyochelin (EPch) are enantiomeric siderophores, with three chiral centers, produced under iron limitation conditions by Pseudomonas aeruginosa and Pseudomonas fluorescens , respectively. After iron chelation in the extracellular medium, Pch-Fe and EPch-Fe are recognized and transported by their specific outer-membrane transporters: FptA in P. aeruginosa and FetA in P. fluorescens . Structural analysis of FetA-EPch-Fe and FptA-Pch-Fe, combined with mutagenesis and docking studies revealed the structural basis of the stereospecific recognition of these enantiomers by their respective transporters. Whereas FetA and FptA have a low sequence identity but high structural homology, the Pch and EPch binding pockets do not share any structural homology, but display similar physicochemical properties. The stereospecific recognition of both enantiomers by their corresponding transporters is imposed by the configuration of the siderophore's C4' and C2' chiral centers. This recognition involves specific hydrogen bonds between the Arg91 guanidinium group and EPch-Fe for FetA and between the Leu117-Leu116 main chain and Pch-Fe for FptA. FetA and FptA are the first membrane receptors to be structurally described with opposite binding enantioselectivities for their ligands, giving insights into the structural basis of their enantiospecificity.     

Two‐Dimensional Infrared Spectroscopy Reveals the Structure of an Evans Auxiliary Derivative and Its SnCl4 Lewis Acid Complex

Determining the structure of reactive intermediates is the key to understanding reaction mechanisms. To access these structures, a method combining structural sensitivity and high time resolution is required. Here ultrafast polarization‐dependent two‐dimensional infrared (P2D‐IR) spectroscopy is shown to be an excellent complement to commonly used methods such as one‐dimensional IR and multidimensional NMR spectroscopy for investigating intermediates. P2D‐IR spectroscopy allows structure determination by measuring the angles between vibrational transition dipole moments. The high time resolution makes P2D‐IR spectroscopy an attractive method for structure determination in the presence of fast exchange and for short‐lived intermediates. The ubiquity of vibrations in molecules ensures broad applicability of the method, particularly in cases in which NMR spectroscopy is challenging due to a low density of active nuclei. Here we illustrate the strengths of P2D‐IR by determining the conformation of a Diels–Alder dienophile that carries the Evans auxiliary and its conformational change induced by the complexation with the Lewis acid SnCl₄, which is a catalyst for stereoselective Diels–Alder reactions. We show that P2D‐IR in combination with DFT computations can discriminate between the various conformers of the free dienophile N‐crotonyloxazolidinone that have been debated before, proving antiperiplanar orientation of the carbonyl groups and s‐cis conformation of the crotonyl moiety. P2D‐IR unequivocally identifies the coordination and conformation in the catalyst–substrate complex with SnCl₄, even in the presence of exchange that is fast on the NMR time scale. It resolves a chelate with the carbonyl orientation flipped to synperiplanar and s‐cis crotonyl configuration as the main species. This work sets the stage for future studies of other catalyst–substrate complexes and intermediates using a combination of P2D‐IR spectroscopy and DFT computations.     

Identification and quantification of six major α-dicarbonyl process contaminants in high-fructose corn syrup

High-fructose corn syrup (HFCS) is a widely used liquid sweetener produced from corn starch by hydrolysis and partial isomerization of glucose to fructose. During these processing steps, sugars can be considerably degraded, leading, for example, to the formation of reactive α-dicarbonyl compounds (α-DCs). The present study performed targeted screening to identify the major α-DCs in HFCS. For this purpose, α-DCs were selectively converted with o-phenylendiamine to the corresponding quinoxaline derivatives, which were analyzed by liquid chromatography with hyphenated diode array-tandem mass spectrometry (LC-DAD-MS/MS) detection. 3-Deoxy-D-erythro-hexos-2-ulose (3-deoxyglucosone), D-lyxo-hexos-2-ulose (glucosone), 3-deoxy-D-threo-hexos-2-ulose (3-deoxygalactosone), 1-deoxy-D-erythro-hexos-2,3-diulose (1-deoxyglucosone), 3,4-dideoxyglucosone-3-ene, methylglyoxal, and glyoxal were identified by enhanced mass spectra as well as MS/MS product ion spectra using the synthesized standards as reference. Addition of diethylene triamine pentaacetic acid and adjustment of the derivatization conditions ensured complete derivatization without de novo formation for all identified α-DCs in HFCS matrix except for glyoxal. Subsequently, a ultra-high performance LC-DAD-MS/MS method was established to quantify 3-deoxyglucosone, glucosone, 3-deoxygalactosone, 1-deoxyglucosone, 3,4-dideoxyglucosone-3-ene, and methylglyoxal in HFCS. Depending on the α-DC compound and concentration, the recovery ranged between 89.2% and 105.8% with a relative standard deviation between 1.9% and 6.5%. Subsequently, the α-DC profiles of 14 commercial HFCS samples were recorded. 3-Deoxyglucosone was identified as the major α-DC with concentrations up to 730 μg/mL HFCS. The total α-DC content ranged from 293 μg/mL to 1,130 μg/mL HFCS. Significantly different α-DC levels were not detected between different HFCS specifications, but between samples of various manufacturers indicating that the α-DC load is influenced by the production procedures.     

Reflectometric interference spectroscopy (RIfS) as a new tool to measure in the complex matrix milk at low analyte concentration

Measurements in complex matrices like milk still present a challenge in biosensor development. This is especially important when using a label-free detection method or when measuring low analyte concentrations. The direct optical method reflectometric interference spectroscopy (RIfS) was used for investigating matrix effects in immunoassay development. Furthermore, approaches to reduce these effects have been established. As a model system, the hormone testosterone has been chosen because this immunoassay has been well characterized in buffer. In a first step, the immunoassay for the detection of testosterone in buffer was improved beyond former published results. Therefore, the sensor surface was optimized, resulting in a fivefold lower limit of detection (70.2 ng L⁻¹) and limit of quantification (130.0 ng L⁻¹). Additionally, the assay time could be reduced to 15 min. Consequently, we used this improved assay to investigate matrix effects of whole pasteurized bovine milk. To minimize these effects, the surface chemistry was adapted and a suitable evaluation method was established, reducing the effects of Tyndall scattering and nonspecific binding to the sensor surface. These improvements allow for very reliable quantitative measurements in milk. The assay developed required no sample pretreatment and allowed for the regeneration of the sensor surface so that calibration could be performed on one chip. The calibration in milk (3.5% fat) resulted in a limit of detection of 94.4 ng L⁻¹ and a limit of quantification of 229.3 ng L⁻¹. Furthermore, recovery rates between 70% and 120% could be obtained. Thus, for the first time, an analyte in the matrix milk was successfully quantified with RIfS at low concentrations.