Calculation of affinities of peptides for proteins

Several methodologies were employed to calculate the Gibbs standard free energy of binding for a collection of protein-ligand complexes, where the ligand is a peptide and the protein is representative for various protein families. Almost 40 protein-ligand complexes were employed for a continuum approach, which considers the protein and the peptide at the atomic level, but includes solvent as a polarizable continuum. Five protein-ligand complexes were employed for an all-atom approach that relies on a combination of the double decoupling method with thermodynamic integration and molecular dynamics. These affinities were also computed by means of the linear interaction energy method. Although it generally proved rather difficult to predict the absolute free energies correctly, for some protein families the experimental ranking order was correctly reproduced by the continuum and all-atom approach. Considerable attention has also been given to correctly analyze the affinities of charged peptides, where it is required to judge the effect of one or more ions that are being decoupled in an all-atom approach to preserve electroneutrality. The various methods are further judged upon their merits.     

Determination of manganese in brain samples by slurry sampling graphite furnace atomic absorption spectrometry

A simple procedure for the determination of manganese in different sections of human brain samples by graphite furnace atomic absorption spectrometry has been developed. Brain sections included cerebellum, hypothalamus, frontal cortex, vermix and encephalic trunk. Two sample preparation procedures were evaluated, namely, slurry sampling and microwave-assisted acid digestion. Brain slurries (2% w/v) could be prepared in distilled, de-ionized water, with good stability for up to 30 min. Brain samples were also digested in a domestic microwave oven using 5 ml of concentrated HNO₃. A mixed palladium+magnesium nitrate chemical modifier was used for thermal stabilization of the analyte in the electrothermal atomizer up to pyrolysis temperatures of 1300 °C, irrespective of the matrix. Quantitation of manganese was conducted in both cases by means of aqueous standards calibration. The detection limits were 0.3 and 0.4 ng ml⁻¹ for the slurry and the digested samples, respectively. The accuracy of the procedure was checked by comparing the results obtained in the analysis of slurries and digested brain samples, and by analysis of the NIST Bovine Liver standard reference material (SRM 1577a). The ease of slurry preparation, together with the conventional set of analytical and instrumental conditions selected for the determination of manganese make such methodology suitable for routine clinical applications.     

Reversible colorimetric probes for mercury sensing

The selectivity and sensitivity of two colorimetric sensors based on the ruthenium complexes N719 [bis(2,2'-bipyridyl-4,4'-dicarboxylate)ruthenium(II) bis(tetrabutylammonium) bis(thiocyanate)] and N749 [(2,2':6',2' '-terpyridine-4,4',4' '-tricarboxylate)ruthenium(II) tris(tetrabutylammonium) tris(isothiocyanate)] are described. It was found that mercury ions coordinate reversibly to the sulfur atom of the dyes' NCS groups. This interaction induces a color change in the dyes at submicromolar concentrations of mercury. Furthermore, the color change of these dyes is selective for mercury(II) when compared with other ions such as lead(II), cadmium(II), zinc(II), or iron(II). The detection limit for mercury(II) ions--using UV-vis spectroscopy--in homogeneous aqueous solutions is estimated to be approximately 20 ppb for N719 and approximately 150 ppb for N749. Moreover, the sensor molecules can be adsorbed onto high-surface-area mesoporous metal oxide films, allowing reversible heterogeneous sensing of mercury ions in aqueous solution. The results shown herein have important implications in the development of new reversible colorimetric sensors for the fast, easy, and selective detection and monitoring of mercuric ions in aqueous solutions.     

Revealing structural effects: electrochemical reactions of butanols on platinum

Spectroelectrochemical studies on the reactivity of butanol isomers on Pt electrodes in perchloric acid medium led to the observation of structural effects that result from the different arrangements of atoms in the organic molecules. The use of differential electrochemical mass spectrometry (DEMS) to detect volatile products showed that all four isomers react on the electrode, though different product yields were observed for each compound. In spite of the differences in the electrochemical behaviour of the butanol isomers, a series of general processes accounts for the results obtained. The formation of strongly adsorbed residues by a dehydration process leading to the formation of a C=C bond was proposed for all isomers. Electroreduction of the adsorbates produces C(4) and C(3) alkanes, and the latter reveal the existence of a fragmentation process. The C(4) hydrocarbons can be formed by hydrogenation of these residues and by hydrogenolysis of alcohol molecules in the bulk solution which react at the electrode with adsorbed hydrogen. On the other hand, CO(2) is formed during electrooxidation of the adsorbed species. Partial-oxidation products containing a carbonyl group were detected from 0.2 M solutions of 1-butanol, isobutyl alcohol and sec-butyl alcohol. The tertiary alcohol tert-butyl alcohol only reacts in its adsorbed state.     

Screening and analytical confirmation of sulfonamide residues in milk by capillary electrophoresis-mass spectrometry

A new methodology is proposed to automate the monitoring of sulfonamide residues in milk samples. It combines a screening unit for the total amount of sulfonamide with capillary electrophoresis-mass spectrometry (CE-MS) equipment for processing the samples containing a detectable level of sulfonamide. The screening unit consists of continuous-flow system (CFS) to precipitate the proteins connected on-line to the CE-MS equipment, in which a common characteristic ion of all sulfonamides was monitored with the MS detector by flushing the sample through the capillary. The confirmatory method is based on the purification and preconcentration of sulfonamides in a CFS unit and posterior analysis by CE-MS. The sample treatment unit was also on-line connected to the CE-MS equipment. In order to increase sensitivity, the flow rate of the sheath liquid was diminished from 0.5 to 0.2 microL.min(-1) by increasing the content in water from 0 to 50% and the formic acid from 0.5 to 1.5% in this liquid and by applying an overimposed pressure of 5 mbar during the electrophoretic separation. The method allowed the analysis of 30 samples per hour.     

Carbon fiber cylindrical microelectrode-based detector for the determination of antithyroid drugs

An amperometric flow-injection method for the determination of antithyroid drugs such as 6-methyl-2-thiouracil (MTU) using a carbon fiber cylindrical microelectrode-based detector is reported. A home-made flow-cell specially adapted for working with cylindrical microelectrodes ranging between 4 and 10 mm in length was used for this purpose. Methanol containing 0.05 mol l(-1) tetrabutylammonium perchlorate as the supporting electrolyte was employed, and a potential of +1.6 V was selected for the amperometric detection of MTU. No cleaning or electrode surface regeneration of the fiber was necessary during the whole working day. A limit of detection of 2.6x10(-7) mol l(-1) (37 mug MTU l(-1)) was achieved. The method was applied to the determination of MTU in spiked feed samples (peas and corn flour), at the 142 mug g(-1) level. The procedure involved the extraction of the drug in methanol, a clean-up step using Florisil cartridges and the use of the standard additions method. Recoveries of 81+/-6 and 85+/-8% were obtained for peas and corn flour, respectively.     

Totally selective ring-opening of amino epoxides with ketones: a general entry to enantiopure (2R,3S)- and (2S,3S)-3-aminoalkano-1,2-diols

[Reaction: see text] Transformation of enantiopure diastereoisomers (2R,1'S)- and (2S,1'S)-2-(1-aminoalkyl)epoxides into the corresponding 4-(1-aminoalkyl)-1,3-dioxolanes is achieved by reaction with different ketones in the presence of BF3.Et2O. The conversion takes place in very high yields, total selectivity, and without epimerization. A mechanism to explain this transformation is proposed. The obtained 1,3-dioxolanes can be deprotected, and (2R,3S)- and (2S,3S)-3-aminoalkano-1,2-diols were isolated.     

Cycloaddition reactions of 5-deutero-1-phenyl-4-vinylpyrazole. Stereoselectivecis “ene” reaction and simplification of NMR spectra of mixtures of cycloadducts

Summary The reaction of methyl propiolate (MP) with 1-phenyl-4-vinylpyrazole deuterated in the five position has clarified the¹H NMR spectrum of the mixture of the adducts 1:2 which are obtained as a result of a Diels-Alder cycloaddition followed by a non-regioselective ene reaction. The deuterated substrate allowed at the same time to establish the stereochemistry of the ene reaction as a concertedcis process.

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Cycloadditionsreaktionen von 5-Deutero-1-phenyl-4-vinylpyrazol. Stereoselektivecis-en-Reaktion und Vereinfachung von NMR-Spektren von Mischungen der Cycloaddukte (Kurze Mitt.)

Zusammenfassung Die Reaktion von Methylpropiolat (MP) mit an der 5-Stellung deuteriertem 1-Phenyl-4-vinylpyrazol wurde zur vereinfachten Interpretation der¹H-NMR-Spektren einer 1:2 Mischung von Addukten aus der Diels-Alder-Cycloaddition mit nachfolgender nicht-regioselektiver en-Reaktion eingesetzt. Das deuterierte Substrat erlaubte zugleich auch die Bestimmung der Stereochemie der en-Reaktion als einen konzertiertencis-Prozeß.

     

Determination of lead in the urine of exposed and unexposed adults by extraction and flow-injection/atomic absorption spectrometry

Lead is extracted from urine with ammonium pyrrolidien dithiocrbamate into methyl isobutyl ketone, and 20 μl of the extract is injected into a water carrier stream in a flow-injection/atomic absorption system. The procedure is simple, quick, accurate and reproducible. Recoveries are 96–105%. The mean urine lead contents of 20 unexposed and 20 printing-press lead exposed workers was found to be 39.0 ± 8.3 and 71.7 ± 26.3 μg Pb l^?1, respectively.     

Structural characterization of single-walled carbon nanotube bundles by experiment and molecular simulation

A procedure, combining molecular simulation, Raman spectroscopy, and standard nitrogen adsorption, is developed for structural characterization of single-walled carbon nanotube (SWNT) samples. Grand canonical Monte Carlo simulations of nitrogen adsorption are performed on the external and internal adsorption sites of homogeneous arrays of SWNTs of diameters previously determined by Raman spectroscopy of the sample. The results show the importance of the peripheral grooves of a nanotube bundle at low relative pressure and the insensitivity of nanotube diameter toward adsorption on the external surface of the bundle at higher pressures. Simulations also reveal that samples containing thin nanotubes have less internal adsorption capacity that saturates at lower pressure than those comprising large diameter nanotubes. The fraction of open-ended nanotubes in a sample can be estimated by scaling the simulated internal adsorption inside nanotubes to obtain a near perfect fit between simulated and experimental isotherms. This procedure allows extrapolation of adsorption properties to conditions in which all nanotubes in the sample are open-ended.