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Substrate Orientation (substrate + orientation)
Selected AbstractsAn Inverse Substrate Orientation for the Regioselective Acylation of 3,,5,-Diaminonucleosides Catalyzed by Candida antarctica lipase B?CHEMBIOCHEM, Issue 8 2005Iván Lavandera Dr. Abstract Candida antarctica lipase B (CAL-B) catalyzes the regioselective acylation of natural thymidine with oxime esters and also the regioselective acylation of an analogue, 3,,5,-diamino-3,,5,-dideoxythymidine with nonactivated esters. In both cases, acylation favors the less hindered 5,-position over the 3,-position by upto 80-fold. Computer modeling of phosphonate transition-state analogues for the acylation of thymidine suggests that CAL-B favors acylation of the 5,-position because this orientation allows the thymine ring to bind in a hydrophobic pocket and forms stronger key hydrogen bonds than acylation of the 3,-position. On the other hand, computer modeling of phosphonamidate analogues of the transition states for acylation of either the 3,- or 5,-amino groups in 3,,5,-diamino-3,,5,-dideoxythymidine shows similar orientations and hydrogen bonds and, thus, does not explain the high regioselectivity. However, computer modeling of inverse structures, in which the acyl chain binds in the nucleophile pocket and vice versa, does rationalize the observed regioselectivity. The inverse structures fit the 5,-, but not the 3,-intermediate thymine ring, into the hydrophobic pocket, and form a weak new hydrogen bond between the O-2 carbonyl atom of the thymine and the nucleophile amine only for the 5,-intermediate. A water molecule might transfer a proton from the ammonium group to the active-site histidine. As a test of this inverse orientation, we compared the acylation of thymidine and 3,,5,-diamino-3,,5,-dideoxythymidine with butyryl acyl donors and with isosteric methoxyacetyl acyl donors. Both acyl donors reacted at equal rates with thymidine, but the methoxyacetyl acyl donor reacted four times faster than the butyryl acyl donor with 3,,5,-diamino-3,,5,-dideoxythymidine. This faster rate is consistent with an inverse orientation for 3,,5,-diamino-3,,5,-dideoxythymidine, in which the ether oxygen atom of the methoxyacetyl group can form a similar hydrogen bond to the nucleophilic amine. This combination of modeling and experiments suggests that such lipase-catalyzed reactions of apparently close substrate analogues like alcohols and amines might follow different pathways. [source] Self-Assembled In-Plane Growth of Mg2SiO4 Nanowires on Si Substrates Catalyzed by Au NanoparticlesADVANCED FUNCTIONAL MATERIALS, Issue 15 2010Zhou Zhang Abstract In-plane growth of Mg2SiO4 nanowires on Si substrates is achieved by using a vapor transport method with Au nanoparticles as catalyst. The self-assembly of the as-grown nanowires shows dependence on the substrate orientation, i.e., they are along one, two, and three particular directions on Si (110), (100), and (111) substrates, respectively. Detailed electron microscopy studies suggest that the Si substrates participate in the formation of Mg2SiO4, and the epitaxial growth of the nanowires is confined along the Si <110> directions. This synthesis route is quite reliable, and the dimensions of the Mg2SiO4 nanowires can be well controlled by the experiment parameters. Furthermore, using these nanowires, a lithography-free method is demonstrated to fabricate nanowalls on Si substrates by controlled chemical etching. The Au nanoparticle catalyzed in-plane epitaxial growth of the Mg2SiO4 nanowires hinges on the intimate interactions between substrates, nanoparticles, and nanowires, and our study may help to advance the developments of novel nanomaterials and functional nanodevices. [source] Epitaxial Growth of AlN Layers on SiC Substrates in a Hot-Wall MOCVD SystemPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 1 2003A. Kakanakova-Georgieva Abstract In this study we report the successful growth of AlN and AlN/GaN on SiC substrates in a MOCVD process based on a hot-wall susceptor design. Different features of AlN growth are established depending on the total reactor pressure, temperature, off-cut SiC substrate orientation and V-to-III gas-flow ratio. The feasibility of the hot-wall MOCVD concept is demonstrated by the performance of AlN/GaN structures with state-of-the-art properties with strong potential for further optimization. A narrower X-ray rocking curve over the asymmetric 10.4 than the symmetric 00.2 reflection clearly underlines the high overall crystal quality of the GaN layers on AlN buffers grown in this type of MOCVD reactor. [source] Residues Asp164 and Glu165 at the substrate entryway function potently in substrate orientation of alanine racemase from E. coli: Enzymatic characterization with crystal structure analysisPROTEIN SCIENCE, Issue 6 2008Dalei Wu Abstract Alanine racemase (Alr) is an important enzyme that catalyzes the interconversion of L-alanine and D-alanine, an essential building block in the peptidoglycan biosynthesis. For the small size of the Alr active site, its conserved substrate entryway has been proposed as a potential choice for drug design. In this work, we fully analyzed the crystal structures of the native, the D-cycloserine-bound, and four mutants (P219A, E221A, E221K, and E221P) of biosynthetic Alr from Escherichia coli (EcAlr) and studied the potential roles in substrate orientation for the key residues involved in the substrate entryway in conjunction with the enzymatic assays. Structurally, it was discovered that EcAlr is similar to the Pseudomonas aeruginosa catabolic Alr in both overall and active site geometries. Mutation of the conserved negatively charged residue aspartate 164 or glutamate 165 at the substrate entryway could obviously reduce the binding affinity of enzyme against the substrate and decrease the turnover numbers in both D- to L-Ala and L- to D-Ala directions, especially when mutated to lysine with the opposite charge. However, mutation of Pro219 or Glu221 had only negligible or a small influence on the enzymatic activity. Together with the enzymatic and structural investigation results, we thus proposed that the negatively charged residues Asp164 and Glu165 around the substrate entryway play an important role in substrate orientation with cooperation of the positively charged Arg280 and Arg300 on the opposite monomer. Our findings are expected to provide some useful structural information for inhibitor design targeting the substrate entryway of Alr. [source] Structural characterization of tartrate dehydrogenase: a versatile enzyme catalyzing multiple reactionsACTA CRYSTALLOGRAPHICA SECTION D, Issue 6 2010Radhika Malik The first structure of an NAD-dependent tartrate dehydrogenase (TDH) has been solved to 2,Å resolution by single anomalous diffraction (SAD) phasing as a complex with the intermediate analog oxalate, Mg2+ and NADH. This TDH structure from Pseudomonas putida has a similar overall fold and domain organization to other structurally characterized members of the hydroxy-acid dehydrogenase family. However, there are considerable differences between TDH and these functionally related enzymes in the regions connecting the core secondary structure and in the relative positioning of important loops and helices. The active site in these complexes is highly ordered, allowing the identification of the substrate-binding and cofactor-binding groups and the ligands to the metal ions. Residues from the adjacent subunit are involved in both the substrate and divalent metal ion binding sites, establishing a dimer as the functional unit and providing structural support for an alternating-site reaction mechanism. The divalent metal ion plays a prominent role in substrate binding and orientation, together with several active-site arginines. Functional groups from both subunits form the cofactor-binding site and the ammonium ion aids in the orientation of the nicotinamide ring of the cofactor. A lysyl amino group (Lys192) is the base responsible for the water-mediated proton abstraction from the C2 hydroxyl group of the substrate that begins the catalytic reaction, followed by hydride transfer to NAD. A tyrosyl hydroxyl group (Tyr141) functions as a general acid to protonate the enolate intermediate. Each substrate undergoes the initial hydride transfer, but differences in substrate orientation are proposed to account for the different reactions catalyzed by TDH. [source] Optical gain and gain saturation of blue-green InGaN quantum wellsPHYSICA STATUS SOLIDI (A) APPLICATIONS AND MATERIALS SCIENCE, Issue 6 2010Dmitry Sizov Abstract Using varied stripe length method we systematically studied optical gain properties of blue-green 3,nm InGaN QWs grown on c -plane and (11,22) semipolar substrates. We determined that for such structures when the product of modal net gain at peak and stripe length exceeds factor 5 the gain saturation occurs due to depletion of pumped carriers. We then focused our attention on the gain in unsaturated conditions. We observed strong gain peak position blue shift with increase of pumping power for both substrate orientations due to quantum well state filling and for c -plane due to piezoelectric field screening. Thus in order to increase lasing wavelength, minimizing optical losses, and maximizing modal gain are essential. We then found that for the semipolar QWs the gain at ,500,nm was 2× higher with the stripe along [,1,123] direction despite the fact that at low pumping level the polarization switching of spontaneous emission resulted predominant E||[,1,123]. Finally we compared the semipolar and c -plane QWs and found that the gain increase with pumping power of c -plane QW is slower than that for semipolar QW in high gain direction while the transparency pumping power is lower for c -plane. [source] Polarization properties in deep-ultraviolet AlGaN quantum wells with various substrate orientationsPHYSICA STATUS SOLIDI (B) BASIC SOLID STATE PHYSICS, Issue 7 2010A. Atsushi Yamaguchi Abstract It is known that emission polarization in AlGaN quantum wells (QWs) on c-plane substrates switches from in-plane polarization to c -axis polarization with increasing Al composition. This behaviour is unfavourable for light extraction from c-plane based light emitting diodes (LEDs). Previously, we proposed theoretically that this unfavourable polarization can be changed into favourable in-plane polarization by decreasing well width and/or introduction of compressive strain in c-oriented AlGaN-QWs. In this work, we have investigated the substrate orientation dependence of polarization properties in such AlGaN QWs by numerical calculation using the 6,×,6 k·p Hamiltonian. It is shown that even small inclination of c-plane substrate makes a drastic change in the polarization characteristics and that the use of the vicinal substrates as well as semipolar and nonpolar substrates could be beneficial in improving optical device performance. [source] Laplace DLTS of molecular beam epitaxy GaAs grown on (100) and (211)B substratesPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 12 2009R. H. Mari Abstract Deep Level Transient Spectroscopy (DLTS) and Laplace DLTS (LDLTS) techniques have been employed to study defects in n-type GaAs grown by MBE on (100) and (211)B GaAs planes. The DLTS spectra were different for the two GaAs substrate orientations. Five and four defect states are found in samples grown on (100) and (211)B GaAs planes, respectively with activation energies ranging from 0.054 eV to 0.570 eV. For all of the traps observed in our samples we obtained small activation energies as compared to the previous data published in literature on n-GaAs samples grown by MBE. This can be explained by the fact that the emission of the carriers depends on the applied electric field and temperature dependence of the carrier concentration. These two phenomena seem to explain the small trap energies seen in our samples. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] | |||||||||||||