BaTiO3 and PbTiO3 perovskite as catalysts for methane combustion

Unsupported and γ-Al₂O₃-supported Ba and Pb titanate catalysts were prepared, characterized and studied in the combustion of methane, as a test reaction for VOCs’ catalytic combustion. They present good catalytic activities, and after dispersion (5%) on γ-Al₂O₃ the specific activity of the supported perovskite phase increased 25 and 30 times, respectively, compared with the unsupported samples. PbTiO₃/γ-Al₂O₃ shows the best catalytic properties among the tested samples.     

TRAJELIX: A Computational Tool for the Geometric Characterization of Protein Helices During Molecular Dynamics Simulations

Summary We have developed a computer program with the necessary mathematical formalism for the geometric characterization of distorted conformations of alpha-helices proteins, such as those that can potentially be sampled during typical molecular dynamics simulations. This formalism has been incorporated into TRAJELIX, a new module within the SIMULAID framework (http://inka.mssm.edu/~mezei/simulaid/) that is capable of monitoring distortions of alpha-helices in terms of their displacement, global and local tilting, rotation around their axes, compression/extension, winding/unwinding, and bending. Accurate evaluation of these global and local structural properties of the helix can help study possible intramolecular and intermolecular changes in the helix packing of alpha-helical membrane proteins, as shown here in an application to the interacting helical domains of rhodopsin dimers. Quantification of the dynamic structural behavior of alpha-helical membrane proteins is critical for our understanding of signal transduction, and may enable structure-based design of more specific and efficient drugs.     

Quantitation of the nearest-neighbour effects of amino acid side-chains that restrict conformational freedom of the polypeptide chain using reversed-phase liquid chromatography of synthetic model peptides with L- and D-amino acid substitutions

Side-chain backbone interactions (or "effects") between nearest neighbours may severely restrict the conformations accessible to a polypeptide chain and thus represent the first step in protein folding. We have quantified nearest-neighbour effects (i to i+1) in peptides through reversed-phase liquid chromatography (RP-HPLC) of model synthetic peptides, where L- and D-amino acids were substituted at the N-terminal end of the peptide sequence, adjacent to a L-Leu residue. These nearest-neighbour effects (expressed as the difference in retention times of L- and D-peptide diastereomers at pHs 2 and 7) were frequently dramatic, depending on the type of side-chain adjacent to the L-Leu residue, albeit such effects were independent of mobile phase conditions. No nearest-neighbour effects were observed when residue i is adjacent to a Gly residue. Calculation of minimum energy conformations of selected peptides supported the view that, whether a L- or D-amino acid is substituted adjacent to L-Leu, its orientation relative to this bulky Leu side-chain represents the most energetically favourable configuration. We believe that such energetically favourable, and different, configurations of L- and D-peptide diastereomers affect their respective interactions with a hydrophobic stationary phase, which are thus quantified by different RP-HPLC retention times. Side-chain hydrophilicity/hydrophobicity coefficients were generated in the presence of these nearest-neighbour effects and, despite the relative difference in such coefficients generated from peptides substituted with L- or D-amino acids, the relative difference in hydrophilicity/hydrophobicity between different amino acids in the L- or D-series is maintained. Overall, our results demonstrate that such nearest-neighbour effects can clearly restrict conformational space of an amino acid side-chain in a polypeptide chain.     

Single diastereomers of polyhydroxylated 9-oxa-1-azabicyclo[4.2.1]nonanes from intramolecular 1,3-dipolar cycloaddition of omega-unsaturated nitrones

8-Benzyloxymethyl-3,4,5-tribenzoyloxy-9-oxa-1-azabicyclo[4.2.1]nonane has been prepared as the single diastereoisomer 8 from an intramolecular 1,3-dipolar cycloaddition involving 2-(benzyloxy)acetaldehyde and omega-unsaturated hydroxylamine 7 derived from methyl alpha-D-glucopyranoside. The analogous 8-methoxycarbonyl 9-oxa-1-azabicyclo[4.2.1]nonane was afforded in a similar manner, from methyl D-galactopyranoside and methyl glyoxylate, as a 3:1 mixture of diastereoisomers 15 and 16. When conducted in achiral ionic liquid 17 this ratio increased to 8:1, and in chiral ionic liquid 18, compound 15 was formed exclusively.     

High-throughput genotyping of repeat polymorphism in the regulatory region of serotonin transporter gene by gel microchip electrophoresis.

Large-scale genotyping of the repeat polymorphism in the regulatory region of the serotonin transporter gene (5-HTTLPR) was attempted by polymerase chain reaction (PCR) amplification followed by gel microchip electrophoresis analysis. The multilane (96) format of the gel microchip system allowed parallel separation of a large number of samples. The separation and visualization of the PCR amplicons from either the 5-HTTLPR short allele (number of repeats are 14) or the 5-HTTLPR long form (16 repeats) was completed in a few minutes. Genotyping of healthy Caucasian individuals showed that the short allele had a somewhat lower frequency (0.42) than the long form (0.58), and the genotype frequencies fulfilled the criteria of the Hardy-Weinberg equilibrium (chi = 0.012, p = 0.994). Based on these results, gel microchip electrophoresis system proved to be a powerful tool for high throughput genotyping of repeat polymorphism.     

Dielectric response enhancement in the current carrying CDW state

The dc electric field dependence of the low frequency dielectric constant was investigated in the linear chain compound orthorhombic TaS₃. While the dielectric constant is barely effected by an applied dc field below the threshold field of the nonlinear conduction, in the current carrying state a large enhancement is observed. Inductive response at the narrow band noise frequency was also detected.     

Probing the influence of local coordination environment on the properties of Fe-type nitrile hydratase model complexes

A series of four structurally related cis-dithiolate-ligated Fe(III) complexes, [Fe(III)(DITpy)2]Cl (1), [Fe(III)(DITIm)2]Cl (2), [Fe(III)(ADIT)2]Cl (3), and [Fe(III)(AMIT)2]Cl (4), are described. The structural characterization of 3 as well as the spectroscopic properties of 3 and 4 has been previously reported. Crystal data for 1, 2, and 4 are as follows: 1.3H2O crystallizes in the orthorhombic space group Pca2(1) with a = 19.800(4) A, b = 18.450(4) A, c = 14.800(3) A, and Z = 8. 2.(1/2)EtOH.1/2H2O crystallizes in the monoclinic space group Cc with a = 24.792(4) A, b = 14.364(3) A, c = 17.527(3) A, beta = 124.91(2) degrees, and Z = 8. 4 crystallizes in the triclinic space group P1 with a = 8.0152(6) A, b = 10.0221(8) A, c = 11.8384(10) A, alpha = 73.460(3) degrees, beta = 71.451(5) degrees, gamma = 72.856(4) degrees, and Z = 2. Complexes 1-4 share a common S2N4 coordination environment that consists of two cis-thiolates, two trans-imines, and two cis-terminal nitrogen donors: Nterm = pyridine (1), imidazole (2), and primary amine (3 and 4). The crystallographically determined mean Fe-S bond distances in 1-4 range from 2.196 to 2.232 A and are characteristic of low-spin Fe(III)-thiolate complexes. The low-spin S = 1/2 ground state was confirmed by both EPR and magnetic susceptibility measurements. The electronic spectra of these complexes are characterized by broad absorption bands centered near approximately 700 nm that are consistent with ligand-to-metal charge-transfer (CT) bands. The complexes were further characterized by cyclic voltammetry measurements, and all possess highly negative Fe(III)/Fe(II) redox couples ( approximately -1 V vs SCE, saturated calomel electrode) indicating that alkyl thiolate donors are effective at stabilizing Fe(III) centers. Both the redox couple and the 700 nm band in the visible spectra show solvent-dependent shifts that are dependent upon the H-bonding ability of the solvent. The implications of these results with respect to the active site of the iron-containing nitrile hydratases are also discussed.     

Representing receptor flexibility in ligand docking through relevant normal modes

Inspired by the current representation of the ligand-receptor binding process, a normal-mode-based methodology is presented to incorporate receptor flexibility in ligand docking and virtual screening. However, the systematic representation of the deformation space grows geometrically with the number of modes, and furthermore, midscale loop rearrangements like those found in protein kinase binding pockets cannot be accounted for with the first lowest-frequency modes. We thus introduced a measure of relevance of normal modes on a given region of interest and showed that only very few modes in the low-frequency range are necessary and sufficient to describe loop flexibility in cAMP-dependent protein kinase. We used this approach to generate an ensemble of representative receptor backbone conformations by perturbing the structure along a combination of relevant modes. Each ensemble conformation is complexed with known non-native binders to optimize the position of the binding-pocket side chains through a full flexible docking procedure. The multiple receptor conformations thus obtained are used in a small-scale virtual screening using receptor ensemble docking. We evaluated this algorithm on holo and apo structures of cAMP-dependent protein kinase that exhibit backbone rearrangements on two independent loop regions close to the binding pocket. Docking accuracy is improved, since the ligands considered in the virtual screening docked within 1.5 A to at least one of the structures. The discrimination between binders and nonbinders is also enhanced, as shown by the improvement of the enrichment factor. This constitutes a new step toward the systematic integration of flexible ligand-flexible receptor docking tools in structure-based drug discovery.     

Die Bildung von [(tBu)2P]2P?P[P(tBu)2]2 aus LiP[P(tBu)2]2 und 1,2-Dibromethan. Die Thermolyse von tBu2P?PP(Br)tBu2

[(tBu)₂P]₂P? P[P(tBu)₂]₂ from LiP[P(tBu)₂]₂ and 1,2-Dibromomethane. Pyrolysis of tBu₂P? P?P(Br)tBu₂ All products of the reaction of [tBu₂P]₂PLi 1 with 1,2-dibromoethane 2 were investigated. Already at ?70°C tBu₂P? P?P(Br)tBu₂ 3 as main product and [tBu₂P]₂PBr 4 are formed. Only with an excess of 1 also [tBu₂P]P? P[P(tBu)₂]₂ 5 is obtained. Warming of a pure solution of 3 in toluene from ?70°C to ?30°C leads to 4 , and at 20°C tBu₂PBr and the cyclophosphanes P₄[P(tBu)₂]₄ and P₃[P(tBu)₂]₃ are observed. 5 does not result from 3 , it's rather a byproduct from the reaction of 1 with 4 . Also the ylide 3 and 1 yields 5 .