Front initiation on microdesigned composite catalysts

We first briefly review the subject of spatiotemporal pattern formation on microdesigned composite catalysts. One of the most significant interaction mechanisms between different reacting domains (consisting of different metal catalysts such as Pt and Rh, coupled through surface diffusion) is the initiation of reaction fronts at the interface between them. We then explore in some detail the effect of two-dimensional composite geometry on this basic building block of composite catalyst dynamics. (c) 2002 American Institute of Physics.     

Real time imaging of catalytic reactions on surfaces: Past,present and future

Simple surface reactions like the CO-oxidation on single crystal platinum surfaces show a rich scenario of non-linear behavior under specific reaction parameters. Gerhard Ertl started in the late 1980s a new research group focusing on imaging of surface reactions to discover possible spatio-temporal pattern formation. Necessarily we conceived several unique imaging methods, which are discussed in the first part of the paper. An unexpected wealth of adsorbate patterns during the CO-oxidation on Pt was soon discovered and can be modeled by a reconstruction model. But the interaction of a multitude of micrometer scale concentration waves and fronts on the surface complicate our understanding of the underlying mechanisms for such patterns. We tackled those complications by constraining pattern formation within inactive or active boundaries formed by different metals evaporated onto the Pt single crystal, thereby isolating individual features of reaction diffusion systems (for example single pulses). Since 2001 we have been able to dynamically change the surface catalytic activity in real time and space by focusing an addressable laser beam to differentially heat a single crystal surface. Combining fixed microstructures made with different catalytic activities and the local heating of the surface opens new avenues of controlling pattern formation. In contrast to these approaches, varying one of the control parameters in time creates a globally coupled system, with the choice between direct forcing or a feedback experiment. In the last part temperature effects arising from the reaction heat are discussed, which become dominant at higher partial pressures for the reactants or on ultra thin samples where the reaction heat cannot be effectively dissipated into the bulk.     

XTOR-2F: A fully implicit Newton–Krylov solver applied to nonlinear 3D extended MHD in tokamaks

XTOR-2F solves a set of extended magnetohydrodynamic (MHD) equations in toroidal tokamak geometry. In the original XTOR code, the time stepping is handled by a semi-implicit method 1, 2 and 3. Moderate changes were necessary to transform it into a fully implicit one using the NITSOL library with Newton–Krylov methods of solution for nonlinear system of equations [4]. After addressing the sensitive issue of preconditioning and time step tuning, the performances of the semi-implicit and the implicit methods are compared for the nonlinear simulation of an internal kink mode test case within the framework of resistive MHD including anisotropic thermal transport. A convergence study comparing the semi-implicit and the implicit schemes is presented. Our main conclusion is that on one hand the Newton–Krylov implicit method, when applied to basic one fluid MHD is more computationally costly than the semi-implicit one by a factor 3 for a given numerical accuracy. But on the other hand, the implicit method allows to address challenging issues beyond MHD. By testing the Newton–Krylov method with diamagnetic modifications on the dynamics of the internal kink, some numerical issues, to be addressed further, are emphasized.     

Structural basis for engineering of retinoic acid receptor isotype-selective agonists and antagonists.

BACKGROUND: Many synthetic retinoids have been generated that exhibit a distinct pattern of agonist/antagonist activities with the three retinoic acid receptors (RARalpha, RARbeta and RARgamma). Because these retinoids are selective tools with which to dissect the pleiotropic functions of the natural pan-agonist, retinoic acid, and might constitute new therapeutic drugs, we have determined the structural basis of their receptor specificity and compared their activities in animal and yeast cells. RESULTS: There are only three divergent amino acid residues in the ligand binding pockets (LBPs) of RARalpha, RARbeta and RARgamma. We demonstrate here that the ability of monospecific (class I) retinoid agonists and antagonists to bind to and induce or inhibit transactivation by a given isotype is directly linked to the nature of these residues. The agonist/antagonist potential of class II retinoids, which bind to all three RARs but depending on the RAR isotype have the potential to act as agonists or antagonists, was also largely determined by the three divergent LBP residues. These mutational studies were complemented by modelling, on the basis of the three-dimensional structures of the RAR ligand-binding domains, and a comparison of the retinoid agonist/antagonist activities in animal and yeast cells. CONCLUSIONS: Our results reveal the rational basis of RAR isotype selectivity, explain the existence of class I and II retinoids, and provide a structural concept of ligand-mediated antagonism. Interestingly, the agonist/antagonist characteristics of retinoids are not conserved in yeast cells, suggesting that yeast co-regulators interact with RARs in a different way than the animal cell homologues do.     

Chlorine oxide radicals ClOx (x = 1-4) studied by matrix isolation spectroscopy

Low pressure flash thermolysis of different precursor molecules containing-ClO, -ClO3 or -OClO3 yield, when highly diluted in Ne or O2 and subsequent quenching of the products in a matrix at 5 or 15 K, ClOx (x = 1, 3, 4) radicals, respectively. If Ne or O2 gas is directed over solid ClO2 at -120 degrees C and the resulting gas mixtures are immediately deposited as a matrix, a high fraction of (OClO)2 is trapped. This enables recording of IR and UV spectra of weakly bonded (OClO)2 dimers and detailed studying of their photochemistry. For Ne or O2 matrix isolated ClO radicals the vibrational wavenumbers and electronic transitions are only slightly affected compared with the gas phase. In this study strong evidence is found for long lived ClO in the electronically excited 2 [symbol: see text] 1/2 state. A comprehensive IR study of Ne matrix isolated ClO3 (fundamentals at 1081, 905, 567, 476 cm-1) yield i) a reliable force field; ii) a OClO bond angle of alpha e = 113.8 +/- 1 degrees and iii) a ClO bond length of 148.5 +/- 2 pm in agreement with predicted data from quantum chemical calculations. The UV/Vis spectrum of ClO3 isolated in a Ne matrix (lambda max at 32,100 and 23,150 cm-1) agrees well with the photoelectron spectrum of ClO3- and theoretical predictions. The origin of the structured high energy absorption is at 22,696 cm-1 and three fundamentals (794, 498, 280 cm-1) are detected in the C2E state. By photolysis of ClO3 with visible light the complex ClO.O2 with ClO in the 2 [symbol: see text] 1/2 state is formed. In an extended spectroscopic study of the elusive ClO4 radical, isolated in a Ne or O2 matrix, three additional IR bands, a complete UV spectrum and a strong interaction with O2 are found. This leads to the conclusion that ClO4 exhibits C2v or Cs symmetry with a shallow potential minimum and forms with O2 the previously unknown peroxy radical O3ClO-O2. All these results are discussed in the context of recent developments in the chemistry and spectroscopy of the important and interesting ClOx (x = 1-4) family of radicals.     

Retinoid X receptor-antagonistic diazepinylbenzoic acids

Several dibenzodiazepine derivatives were identified as novel retinoid X receptor (RXR) antagonists on the basis of inhibitory activity on retinoid-induced cell differentiation of human promyelocytic leukemia cells HL-60 and transactivation assay using retinoic acid receptors (RARs) and RXRs in COS-1 cells. 4-(5H-2,3-(2,5-Dimethyl-2,5-hexano)-5-n- propyldibenzo[b,e][1,4]diazepin-11-yl)benzoic acid (HX603, 6c) is an N-n-propyl derivative of an RXR pan-agonist HX600 (6a), and exhibited RXR-selective antagonistic activity. Similar RXR-antagonistic activities were observed with 4-(5H-2,3-(2,5-dimethyl-2,5-hexano)-5-methyl- 8-nitrodibenzo[b,e][1,4]diazepin-11-yl)benzoic acid (HX531, 7a) and 4-(5H-10,11-dihydro-5,10-dimethyl-2,3-(2,5-dimethyl- 2,5-hexano)-dibenzo[b,e][1,4]diazepin-11-yl)benzoic acid (HX711, 8b), which also inhibited transactivation of RARs induced by an RAR agonist, Am80. These compounds inhibited HL-60 cell differentiation induced by the combination of a low concentration of the retinoid agonist Am80 with an RXR agonist (a retinoid synergist, HX600). These results indicated that HX603 (6c), and the related RXR antagonists inhibit the activation of RAR-RXR heterodimers as well as RXR homodimers, which is a distinct characteristic different from that of the known RXR antagonist, LG100754 (9).     

Directed evolution of O6-alkylguanine-DNA alkyltransferase for efficient labeling of fusion proteins with small molecules in vivo

We report here the generation of mutants of the human O(6)-alkylguanine-DNA alkyltransferase (hAGT) for the efficient in vivo labeling of fusion proteins with synthetic reporter molecules. Libraries of hAGT were displayed on phage, and mutants capable of efficiently reacting with the inhibitor O(6)-benzylguanine were selected based on their ability to irreversibly transfer the benzyl group to a reactive cysteine residue. Using synthetic O(6)-benzylguanine derivatives, the selected mutant proteins allow for a highly efficient covalent labeling of hAGT fusion proteins in vivo and in vitro with small molecules and therefore should become important tools for studying protein function in living cells. In addition to various applications in proteomics, the selected mutants also yield insight into the interaction of the DNA repair protein hAGT with its inhibitor O(6)-benzylguanine.     

Highlights in Colloid Science.Edited by D. Platikanov and D. Exerowa.

Wiley‐VCH, Weinheim 2009. 306 pp., hardcover, 129.00 €.—ISBN 978‐3527320370