Insights into the phosphoryl-transfer mechanism of cAMP-dependent protein kinase from quantum chemical calculations and molecular dynamics simulations

To investigate the molecular details of the phosphoryl-transfer mechanism catalyzed by cAMP-dependent protein kinase, we performed quantum mechanical (QM) calculations on a cluster model of the active site and molecular dynamics (MD) simulations of a ternary complex of the protein with Mg(2)ATP and a 20-residue peptide substrate. Overall, our theoretical results confirm the participation of the conserved aspartic acid, Asp(166), as an acid/base catalyst in the reaction mechanism catalyzed by protein kinases. The MD simulation shows that the contact between the nucleophilic serine side chain and the carboxylate group of Asp(166) is short and dynamically stable, whereas the QM study indicates that an Asp(166)-assisted pathway is structurally and energetically feasible and is in agreement with previous experimental results.     

On-line preconcentration of inorganic mercury and methylmercury in sea-water by sorbent-extraction and total mercury determination by cold vapour atomic absorption spectrometry

A comparative study of three mercury chelate forming reagents [diethyldithiocarbamate, pyrrolidin-1-yldithioformate and diphenylthiocarbazone (dithizone)] has been carried out for the preconcentration of ultratrace amounts of inorganic mercury and methylmercury in silica C(18) minicolumns as the solid sorbent. Sample flow injection in-line sorbent extraction was coupled with continuous cold vapour atomic absorption spectrometry (CVAAS) for detection. Results showed the superiority of the carbamate type reagents over the dithizone for the on-line formation and preconcentration of the corresponding mercury chelates. Using diethyldithiocarbamate (DDC) as reagent, aqueous sample volumes of 100 ml can be preconcentrated with 100% efficiency for both inorganic mercury and methylmercury. Quantitative release of the retained DDC chelates was obtained for volumes of eluent (ethanol) of 50 microl. Following the proposed procedure, detection limits of 16 ng/l. of mercury were achieved for sample volumes of 25 ml. The relative standard deviation was +/- 3.4% at 0.5 microg/l. Hg(II) levels. The method has been successfully applied to the determination of low levels of mercury in sea-water.     

Simultaneous spectrophotometric determination of La, Ho, Mn 5-Br-PADAP complexes using multivariate calibration with partial least-squares (PLS) data evaluation

A simple and fast analytical pocedure is proposed for the simultaneous spectrophotometric determination of lanthanum, holmium and manganese in synthetic ceramics, (La(0.8-x) Hox Sr0.2 MnO3), by using the partial least-squares (PLS) method. As chromogenic agent 5-Br-PADAP [2-(5-bromo-2-pyridylazo)-5-diethylaminophenol] was used, which form colored complexes with the three elements studied. To avoid metal hydrolysis, a mixture of ethanol and Triton X-100 at pH 9.5 was used for all experiments. A set of 17 calibration solutions measured throughout the 400-700 nm wavelength range was used in the calibration step. The concentration range for Mn(II) was 1-12 x 10(-6) mol L-1, while the range for the rare earth elements La(III) and Ho(III) was 2-8 x 10(-6) mol L-1. In order to demonstrate the applicability of the proposed method, a set of artificial samples containing the three analytes in variable proportions was prepared and analyzed. The analytical results obtained were quite acceptable with relative errors not greater than 7% in most cases.     

Synthese von 4H-Pyrano[2,3-d]pyrimidinen

Summary Good yields of substituted 5-(5R-2-furyl)-4H-pyrano[2,3-d]pyrimidines4 were obtained in the reaction of 2-ethoxymethyleneamino-3-cyano-4H-pyranes2 with ammonia. Compounds2 were prepared by the condensation of the starting 2-amino-5-acetyl-3-cyano-6-methyl-4H-pyranes1 with ethyl orthoformate. Spectral properties of the bicyclic system4 in relation to compounds3 are discussed.

     

Action spectroscopy and temperature diagnostics of H+ 3 by chemical probing

Infrared absorption spectroscopy of few hundred H+(3) ions trapped in a 22-pole ion trap is presented using chemical probing as a sensitive detection technique down to the single ion level. By exciting selected overtone transitions of the (v(1)=0,v(2) (l)=3(1))<--(0,0(0)) vibrational band using an external cavity diode laser an accurate diagnostics measurement of the effective translational and rotational temperatures of the trapped ions was performed. The absolute accuracy of the measured transition frequencies was improved by a factor of four compared to previous plasma spectroscopy measurements using velocity modulation [Ventrudo et al., J. Chem. Phys. 100, 6263 (1994)]. The observed buffer gas cooling conditions in the ion trap indicate how to cool trapped H+(3) ions into the lowest ortho and para rotational states. Future experiments will utilize such an internally cold ion ensemble for state-selected dissociative recombination experiments at the heavy ion storage ring Test Storage Ring (TSR).     

Determination of nonsteroidal anti-inflammatory drugs in biological fluids by automatic on-line integration of solid-phase extraction and capillary electrophoresis

A new, automatic method for the clean-up, preconcentration, separation, and quantitation of nonsteroidal anti-inflammatory drugs (NSAIDs) in biological samples (human urine and serum) using solid-phase extraction coupled on-line to capillary electrophoresis is proposed. Automatic pretreatment is carried out by using a continuous flow system operating simultaneously with the capillary electrophoresis equipment, to which it is linked via a laboratory-made mechanical arm. This integrated system is controlled by an electronic interface governed via a program developed in GWBasic. Capillary electrophoresis is conducted by using a separation buffer consisting of 20 mM NaHPO4, 20 mM beta-cyclodextrin and 50 mM SDS at pH 9.0, an applied potential of 20 kV and a temperature of 20 degrees C. The analysis time is 10 min and the detection limits were between 0.88 and 1.71 microg mL(-1). Automatic clean-up and preconcentration is accomplished by using a C-18 minicolumn and 75% methanol as eluent. The limit of detection of NSAIDs can be up to 400-fold improved when using sample clean-up. The extraction efficiency for these compounds is between 71.1 and 109.7 microg mL(-1) (RSD 2.0-7.7%) for urine samples and from 77.2 to 107.1 microg mL(-1) (RSD 3.5-7.1%) for serum samples.     

On-line preconcentration and determination of mercury in biological samples by flow injection vapour generation inductively coupled plasma atomic emission spectrometry

An FI-ICP-AES method for the determination of trace levels of mercury in biological samples has been described, which is based on the extraction of the mercury complex with 1,5-bis (di-2-pyridyl)methylene thiocarbonohydrazide (DPTH) on-line into isobuthyl-methyl ketone (IBMK). The organic phase (containing the complex) has been mixed on-line with SnCl₂ in N,N-dimethylformamide. Thus, mercury vapour can be generated directly from the organic phase and separated in a gas-liquid separation device. The detection limit for mercury is 4 ng/ml and the calibration curve is linear at least from 10 to 2500 ng/ml. The relative standard deviation for 10 replicate measurements is ±1% for 100 ng/ml of Hg(II). Results from the analysis of some certified biological reference materials are given.     

Quasi‐random integration in quantum chemistry: Efficiency,stability, and application to the study of small atoms and molecules constrained in spherical boxes

This project consists of two parts. In the first part, a series of test calculations is performed to verify that the integrals involved in the determination of atomic and molecular properties by standard self‐consistent field (SCF) methods can be obtained through Halton, Korobov, or Hammersley quasi‐random integration procedures. Through these calculations, we confirm that all three methods lead to results that meet the levels of precision required for their use in the calculation of properties of small atoms or molecules at least at a Hartree–Fock level. Moreover, we have ensured that the efficiency of quasi‐random integration methods that we have tested is Halton=Korobov>Hammersley?pseudo‐random. We also find that these results are comparable to those yielded by ordinary Monte Carlo (pseudo‐random) integration, with a calculation effort of two orders of smaller magnitude. The second part, which would not have been possible without the integration method previously analyzed, contains a first study of atoms constrained in spherical boxes through SCF calculations with basis functions adapted to the features of the problem: Slater‐type orbitals (STOs) trimmed by multiplying them by a function that yields 1 for 0 < r < (R‐δ), polynomial values for (R‐δ) < r < R and null for r > R, R being the radius of the box and δ a variationally determined interval. As a result, we obtain a equation of state for electrons of small systems, valid just in the limit of low temperatures, but fairly simple. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Direct electrochemical synthesis and characterization of copper(II), iron(II) and iron(III) complexes with 1- and 2-substituted pyridines

Summary The electrochemical oxidation of anodic metals (iron and copper) in MeCN solutions of 2-pyridinone (HOPy), 1-hydroxy-2-pyridinethione (HPT), 2-pyridinemethanethiol-1-oxide (HPMTO) or its dimer 2,2-dithiodimethyldipyridine-1,1-dioxide (PMTO)₂, gave the simple complexes Fe(OPy)₂ · H₂O, Cu(OPy)₂ · 3H₂O, Fe(PT)₂ · 3H₂O, Fe(PT)₃, Cu(PT)₂, Fe(PMTO)₂·3H₂O and Cu(PMTO)₂·H₂O, respectively. When 1,10-phenanthroline (phen) was added to the electrolytic phase, only two mixed complexes were obtained: Cu(OPy)₂phen·3H₂O and Fe(PT)₂phen·2H₂O. The possible molecular structures of the complexes were studied on the basis of their i.r. spectra and magnetic properties.     

Determination of lead in wines by hydride generation atomic absorption spectrometry.

The optimization of lead hydride generation in aqueous ethanolic media and the influence on its generation of the wine components, both white and red, have been studied. These interferences were overcome by careful control of the parameters affecting hydride generation and the procedure was applied to the determination of Pb in wines. The method is fast, accurate and sensitive and can be used to quantify 24 ppb of Pb in wines.