Redox functionality mediated by adsorbed oxygen on a Pd-oxide film over a Pd(100) thin structure: A first-principles study

Stable oxygen sites on a PdO film over a Pd(100) thin structures with a (sqrt{5} times sqrt{5}) R27^circ surface-unit cell are determined using the first-principles electronic structure calculations with the generalized gradient approximation. The adsorbed monatomic oxygen goes to a site bridging two 2-fold-coordinated Pd atoms or to a site bridging a 2-fold-coordinated Pd atom and a 4-fold-coordinated Pd atom. Estimated reaction energies of CO oxidation by reduction of the oxidized PdO film and N_2O reduction mediated by oxidation of the PdO film are exothermic. Motion of the adsorbed oxygen atom between the two stable sites is evaluated using the nudged elastic band method, where an energy barrier for a translational motion of the adsorbed oxygen may become sim 0.45 eV, which is low enough to allow fluxionality of the surface oxygen at high temperatures. The oxygen fluxionality is allowed by existence of 2-fold-coordinated Pd atoms on the PdO film, whose local structure has similarity to that of Pd catalysts for the Suzuki-Miyaura cross coupling. Although NO_x (including NO_2 and NO) reduction is not always catalyzed only by the PdO film, we conclude that there may happen continual redox reactions mediated by oxygen-adsorbed PdO films over a Pd surface structure, when the influx of NO_x and CO continues, and when the reaction cycle is kept on a well-designed oxygen surface.Comment: 15 pages, 6 figures, submitted to J. Phys. Condens. Matte

[2,2′-Imino­diethano­lato(2−)-κ3 O,N,O′][4-(meth­oxy­carbonyl­meth­yl)phen­yl]boron

The title compound, C13H18BNO4, was readily obtained from the reaction of methyl 4-boronobenzene acetate with ethano­lamine. A combination of inter­molecular N—H⋯O hydrogen bonds and C—H⋯π inter­actions leads to the pairwise association of mol­ecules

First examples of functionalisation of meso-aryl tetrabenzotriazaporphyrins (TBTAPs) through cross-coupling reactions

Recent synthetic advances have given convenient access to tetrabenzotriazaporphyrins (TBTAPs) functionalised with meso-aryl substituents. In this paper we report the first examples of further functionalization of the meso-sites through Suzuki-Miyaura and copper-free Sonagashira cross-coupling reactions of the meso-(bromophenyl)TBTAPs, demonstrating the breadth of new materials design now possible in the hybrid macrocycles

Structure, Photophysics and the Order-Disorder Transition to the Beta Phase in Poly(9,9-(di -n,n-octyl)fluorene)

X-ray diffraction, UV-vis absorption and photoluminescence (PL) spectroscopy have been used to study the well-known order-disorder transition (ODT) to the beta phase in poly(9,9-(di n,n-octyl)fluorene)) (PF8) thin film samples through combination of time-dependent and temperature-dependent measurements. The ODT is well described by a simple Avrami picture of one-dimensional nucleation and growth but crystallization, on cooling, proceeds only after molecular-level conformational relaxation to the so called beta phase. Rapid thermal quenching is employed for PF8 studies of pure alpha phase samples while extended low-temperature annealing is used for improved beta phase formation. Low temperature PL studies reveal sharp Franck-Condon type emission bands and, in the beta phase, two distinguishable vibronic sub-bands with energies of approximately 199 and 158 meV at 25 K. This improved molecular level structural order leads to a more complete analysis of the higher-order vibronic bands. A net Huang-Rhys coupling parameter of just under 0.7 is typically observed but the relative contributions by the two distinguishable vibronic sub-bands exhibit an anomalous temperature dependence. The PL studies also identify strongly correlated behavior between the relative beta phase 0-0 PL peak position and peak width. This relationship is modeled under the assumption that emission represents excitons in thermodynamic equilibrium from states at the bottom of a quasi-one-dimensional exciton band. The crystalline phase, as observed in annealed thin-film samples, has scattering peaks which are incompatible with a simple hexagonal packing of the PF8 chains.Comment: Submitted to PRB, 12 files; 1 tex, 1 bbl, 10 eps figure

Computer-Aided Lead Optimization: Improved Small-Molecule Inhibitor of the Zinc Endopeptidase of Botulinum Neurotoxin Serotype A

Optimization of a serotype-selective, small-molecule inhibitor of botulinum neurotoxin serotype A (BoNTA) endopeptidase is a formidable challenge because the enzyme-substrate interface is unusually large and the endopeptidase itself is a large, zinc-binding protein with a complex fold that is difficult to simulate computationally. We conducted multiple molecular dynamics simulations of the endopeptidase in complex with a previously described inhibitor (Kiapp of 7±2.4 µM) using the cationic dummy atom approach. Based on our computational results, we hypothesized that introducing a hydroxyl group to the inhibitor could improve its potency. Synthesis and testing of the hydroxyl-containing analog as a BoNTA endopeptidase inhibitor showed a twofold improvement in inhibitory potency (Kiapp of 3.8±0.8 µM) with a relatively small increase in molecular weight (16 Da). The results offer an improved template for further optimization of BoNTA endopeptidase inhibitors and demonstrate the effectiveness of the cationic dummy atom approach in the design and optimization of zinc protease inhibitors

Synthesis and fluorescence emission properties of 1,3,6,8-tetraarylpyrenes

This paper was accepted for publication in the Journal of Molecular Structure and the definitive version can be found at: http://dx.doi.org/10.1016/j.molstruc.2013.04.07

Design and Synthesis of Heterocyclic Cations for Specific DNA Recognition: From AT-Rich to Mixed-Base-Pair DNA Sequences

The compounds synthesized in this research were designed with the goal of establishing a new paradigm for mixed-base-pair DNA sequence-specific recognition. The design scheme starts with a cell-permeable heterocyclic cation that binds to AT base pair sites in the DNA minor groove. Modifications were introduced in the original compound to include an Hbond accepting group to specifically recognize the G-NH that projects into the minor groove. Therefore, a series of heterocyclic cations substituted with an azabenzimidazole ring has been designed and synthesized for mixed-base-pair DNA recognition. The most successful compound, 12a, had an azabenzimidazole to recognize G and additional modifications for general minor groove interactions. It binds to the DNA site −AAAGTTT− more strongly than the −AAATTT− site without GC and indicates the design success. Structural modifications of 12a generally weakened binding. The interactions of the new compound with a variety of DNA sequences with and without GC base pairs were evaluated by thermal melting analysis, circular dichroism, fluorescence emission spectroscopy, surface plasmon resonance, and molecular modeling