Fragmentation methods on the balance: unambiguous top–down mass spectrometric characterization of oxaliplatin–ubiquitin binding sites

The interaction between oxaliplatin and the model protein ubiquitin (Ub) was investigated in a top–down approach by means of high-resolution electrospray ionization mass spectrometry (ESI-MS) using diverse tandem mass spectrometric (MS/MS) techniques, including collision-induced dissociation (CID), higher-energy C-trap dissociation (HCD), and electron transfer dissociation (ETD). To the best of our knowledge, this is the first time that metallodrug–protein adducts were analyzed for the metal-binding site by ETD-MS/MS, which outperformed both CID and HCD in terms of number of identified metallated peptide fragments in the mass spectra and the localization of the binding sites. Only ETD allowed the simultaneous and exact determination of Met1 and His68 residues as binding partners for oxaliplatin. CID-MS/MS experiments were carried out on orbitrap and ion cyclotron resonance (ICR)-FT mass spectrometers and both instruments yielded similar results with respect to number of metallated fragments and the localization of the binding sites. A comparison of the protein secondary structure with the intensities of peptide fragments generated by collisional activation of the [Ub + Pt-(chxn)] adduct [chxn = (1R,2R)-cyclohexanediamine] revealed a correlation with cleavages in solution phase random coil areas, indicating that the N-terminal β-hairpin and α-helix structures are retained in the gas phase.     

TiO2-based photocatalysts impregnated with metallo-porphyrins employed for degradation of 4-nitrophenol in aqueous solutions: role of metal and macrocycle

Photodegradation of organic compounds in water solutions by means of economically advantageous and environment-friendly processes is a topic of growing interest. In recent years a great attention has been devoted to TiO₂-based photocatalysts for the oxidative degradation of various organic pollutants. In this context, we have prepared new photo-catalytic polycrystalline TiO₂ systems impregnated with sensitizers, i.e., copper, iron or manganese porphyrins, and investigated their photoactivity for 4-nitrophenol oxidation compared with that of bare TiO₂. A significant improvement of the photoreactivity was observed in the case of TiO₂ impregnated with copper porphyrin, while only a slight beneficial effect was observed in the case of iron porphyrin. In contrast, the presence of manganese porphyrin appeared to be detrimental.     

H/D isotopic recognition in hydrogen bonded systems: H/D isotopic self-organization effects in the IR spectra of the hydrogen bond in 2-methylimidazole crystals

Polarized IR spectra of H12(3)45 2-methylimidazole and of its H1D2(3)45, D1H2(3)45 and D12(3)45 deuterium derivative crystals are reported and interpreted within the limits of the "strong-coupling" theory. The spectra interpretation facilitated the recognition of the H/D isotopic "self-organization" phenomenon, which depends on a non-random distribution of protons and deuterons in the lattices of isotopically diluted crystal samples. The H/D isotopic "self-organization" mechanism engaged all four hydrogen bonds from each unit cell. These effects basically resulted from the dynamical co-operative interactions involving adjacent hydrogen bonds in each hydrogen bond chain. A weaker exciton coupling involved the closely spaced hydrogen bonds; each belonging to a different chain of associated 2-methylimidazole molecules. The high intensity of the narrow band at ca. 1880cm(-1) was interpreted as the result of coupling between the γ(N-H?N) proton bending "out of plane" vibration overtone and the ν(N-H) proton stretching vibration.     

Phase behavior of colloidal suspensions with critical solvents in terms of effective interactions

We study the phase behavior of colloidal suspensions the solvents of which are considered to be binary liquid mixtures undergoing phase segregation. We focus on the thermodynamic region close to the critical point of the accompanying miscibility gap. There, due to the colloidal particles acting as cavities in the critical medium, the spatial confinements of the critical fluctuations of the corresponding order parameter result in the effective, so-called critical Casimir forces between the colloids. Employing an approach in terms of effective, one-component colloidal systems, we explore the possibility of phase coexistence between two phases of colloidal suspensions, one being rich and the other being poor in colloidal particles. The reliability of this effective approach is discussed.     

Structural diversity in native cyclodextrins/folic acid complexes--from [2]-rotaxane to exclusion compound

The formation of different complexes of folic acid depending on the size of the host cyclodextrin resulting in either an exclusion compound (with the smallest α-cyclodextrin) or 2-rotaxane, where cyclodextrin is threaded over folic acid (with β- and γ-cyclodextrins), is presented. The formation is carried out in water which allows both possible application in pharmaceutical sciences and usage of environmentally friendly "green chemistry". The obtained compounds are thoroughly characterized using one and two dimensional NMR, mass spectrometry, differential scanning calorimetry and thermogravimetric analysis.     

Monitoring and analytics of semivolatile organic compounds (SVOCs) in indoor air

This paper reviews literature information on the behaviour of semivolatile organic compounds (SVOCs) in the indoor environment, as well as the most likely emission sources. The consecutive stages of analytical procedures used for monitoring SVOCs in indoor environments are described. The most common approaches used for collecting samples from the gas and particulate phases are mentioned. The paper discusses and compares various types of sorbents and filters applied in dynamic, passive and denudational techniques, as well as the techniques used to liberate the SVOCs, including Soxhlet, sonication and microwave extraction. The main advantages and disadvantages of each technique are discussed, together with possible future trends. The approaches commonly used during the final determination step, such as gas chromatography and liquid chromatography, are presented together with their possible drawbacks, and ways of eliminating them are suggested. The review makes brief reference to the effects of human exposure to SVOCs in house dust and discusses the main aspects of the analytical procedures used to monitor the presence of SVOCs in this medium.     

Characteristics of X-H···π interactions: ab initio and QTAIM studies

The MP2/6-311++G(d,p) calculations were performed on several hydrogen-bonded systems. Different complexes were taken into account to analyze various types of hydrogen bonds, possessing different types of proton donors and proton acceptors as well as characterized by the broad range of the interaction energy. The Quantum Theory of Atoms in Molecules is applied. The results of the hybrid variational-perturbational approach are discussed. The unique properties of hydrogen bonds, where π-electrons act as the proton acceptor (X-H···π), are analyzed, and these interactions are compared with the other types of hydrogen bonds, mainly with C-H···Y interactions. It is shown that for X-H···π systems the ellipticity at the bond critical point of the proton···acceptor interaction is much greater than for the other types of hydrogen bonds. However, both X-H···π and C-H···Y interactions are characterized by the dominance of the dispersive energy.     

Determination of total carbon and total organic carbon from volatile air pollutants. Part I

Summary A new method of collection of representative air samples for the determination of TC and TOC from volatile air pollutants has been developed. The organic substances undergo combustion and only the carbon dioxide produced is concentrated on molecular sieve 5 A at ambient temperature. The CO₂ is subsequently liberated by thermal desorption at ca. 380°C in a stream of purified gas. Atmospheric CO₂ must be removed first and this can be done (at the sample flow rate of 700 ml/min) by a layer of Ascarite heated at 90° C. Organic compounds passing through the layer are then combusted by a dynamic method utilizing Körbl catalyst and the CO₂ formed is concentrated on a molecular sieve 5 A, followed by thermal desorption and final determination. Organic acids are also retained by the first CO₂ absorber. A diffusion cell for preparation of the mixtures of purified air with vapours of organic compounds is described.

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Zusammenfassung Eine neue Anreicherungsmethode zur Gewinnung representativer Luftproben zur Bestimmung des Gesamtkohlenstoffgehaltes und des Gehaltes an organischem Kohlenstoff (TOC) aus flüchtigen Luftverunreinigungen wurde entwickelt. Während der Probenahme werden die flüchtigen Verunreinigungen verbrannt und nur das entstandene Kohlendioxid bei Zimmertemperatur am Molekularsieb 5A angereichert. Anschließend wird CO₂ bei ca. 380° C im gereinigten Gasstrom thermisch desorbiert. Bei der TOC-Bestimmung muß atmosphärisches CO₂ vorangehend aus dem Luftstrom entfernt werden und wird an einer auf 90° C erwärmten Ascariteschicht gebunden. Die durchfließenden organischen Verbindungen werden dann im dynamischen System am Körblkatalysator oxydiert, das entstandene CO₂ am Molekularsieb 5A angereichert, thermisch desorbiert und einer Endbestimmung zugeführt. Organische Säuren werden gleichfalls durch den ersten CO₂-Absorber gebunden. Eine Diffusionszelle zur Herstellung von Gemischen gereinigter Luft mit Dämpfen organischer Verbindungen wurde beschrieben.

     

Dielectric studies of two liquid crystalline benzoates with coupled and decoupled CN groups

The results of dielectric studies performed in a broad frequency range for two compounds, 4-cyanophenyl 4-n-heptylbenzoate (7BBCN) and 4-(4-cyanobutyloxy)phenyl 4- n-heptylbenzoate (7BB4CN), are compared. They have the same molecular core whereas the strongly polar CN group is attached to the benzene ring in 7BBCN or is separated from it by the butyloxy chain in 7BB4CN. 7BBCN has a nematic phase, whereas 7BB4CN exhibits a monotropic nematic and smectic A₂ polymorphism. Large differences in the dielectric properties of the two substances were found. The analysis of the results led to the conclusion that the antiparallel dipole-dipole associations are considerably stronger in the substance with a decoupled CN group.