Vapor phase polymerization of EDOT from submicrometer scale oxidant patterned by dip-pen nanolithography

Some of the most exciting recent advances in conducting polymer synthesis have centered around the method of vapor phase polymerization (VPP) of thin films. However, it is not known whether the VPP process can proceed using significantly reduced volumes of oxidant and therefore be implemented as part of nanolithography approach. Here, we present a strategy for submicrometer scale patterning of the conducting polymer poly(3,4-ethylenedioxythiophene) (PEDOT) via in situ VPP. Attolitre (10(-18) L) volumes of oxidant "ink" are controllably deposited using dip-pen nanolithography (DPN). DPN patterning of the oxidant ink is facilitated by the incorporation of an amphiphilic block copolymer thickener, an additive that also assists with stabilization of the oxidant. When exposed to EDOT monomer in a VPP chamber, each deposited feature localizes the synthesis of conducting PEDOT structures of several micrometers down to 250 nm in width. PEDOT patterns are characterized by atomic force microscopy (AFM), conductive AFM, two probe electrical measurement, and micro-Raman spectroscopy, evidencing in situ vapor phase synthesis of conducting polymer at a scale (picogram) which is much smaller than that previously reported. Although the process of VPP on this scale was achieved, we highlight some of the challenges that need to be overcome to make this approach feasible in an applied setting.     

How Ubiquitin Unfolds after Transfer into the Gas Phase

The structural evolution of ubiquitin after transfer into the gas phase was studied by electron capture dissociation. Site-specific fragment yields show that ubiquitin’s solution fold is overall unstable in the gas phase, but unfolding caused by loss of solvent is slowest in regions stabilized by salt bridges.     

Procedural revision to the use-dilution methods: establishment of maximum log density value for test microbes on inoculated carriers

(Staphylococcus aureus) and 964.02 (Pseudomonas aeruginosa), were revised in 2009 to include a standardized procedure to measure the log density of the test microbe and to establish a minimum mean log density value of 6.0 (geometric mean of 1.0 x 10(6) CFU/carrier) to qualify the test results. This report proposes setting a maximum mean log density value of 7.0 (geometric mean of 1.0 x 10(7) CFU/carrier) to further standardize the procedure. The minimum value was based on carrier count data collected by four laboratories over an 8-year period (1999-2006). The data have been updated to include an additional 4 years' worth of data (2006-2010) collected by the same laboratories. A total of 512 tests were conducted on products bearing claims against P. aeruginosa and S. aureus with and without an organic soil load (OSL) added to the inoculum (as specified on the product label claim). Six carriers were assayed in each test, for a total of 3072 carriers. Mean log densities for each of the 512 tests were at least 6.0. With the exception of two tests, one for P. aeruginosa without OSL and one for S. aureus with OSL, the mean log densities did not exceed 7.5 (geometric mean of 3.2 x 10(7) CFU/carrier). Across microbes and OSL treatments, the mean log density (+/- SEM) was 6.80 (+/- 0.07) per carrier (a geometric mean of 6.32 x 10(6) CFUlcarrier) and acceptable repeatability (0.28) and reproducibility (0.31) SDs were exhibited. A maximum mean log density per carrier of 7.0 is being proposed here as a validity requirement for S. aureus and P. aeruginosa. A modification to the method to allow for dilution of the final test cultures to achieve carrier counts within 6.0-7.0 logs is also being proposed. Establishing a range of 6.0-7.0 logs will help improve the reliability of the method and should allow for more consistent results within and among laboratories.     

Novel carbon materials for thermal energy harvesting

To decrease the consumption of fossil fuels, research has been done on utilizing low grade heat, sourced from industrial waste streams. One promising thermoenergy conversion system is a thermogalvanic cell; it consists of two identical electrodes held at different temperatures that are placed in contact with a redox-based electrolyte [1, 2]. The temperature dependence of the direction of redox reactions allows power to be extracted from the cell [3, 4]. This study aims to increase the power conversion efficiency and reduce the cost of thermogalvanic cells by optimizing the electrolyte and utilizing a carbon based electromaterial, reduced graphene oxide, as electrodes. Thermal conductivity measurements of the K₃Fe(CN)₆/K₄Fe(CN)₆ solutions used, indicate that the thermal conductivity decreases from 0.591 to 0.547?W/m?K as the concentration is increased from 0.1 to 0.4?M. The lower thermal conductivity allowed a larger temperature gradient to be maintained in the cell. Increasing the electrolyte concentration also resulted in higher power densities, brought about by a decrease in the ohmic overpotential of the cell, which allowed higher values of short circuit current to be generated. The concentration of 0.4?M K₃Fe(CN)₆/K₄Fe(CN)₆ is optimal for thermal harvesting applications using R-GO electrodes due to the synergistic effect of the reduction in thermal flux across the cell and the enhancement of power output, on the overall power conversion efficiency. The maximum mass power density obtained using R-GO electrodes was 25.51?W/kg (three orders of magnitude higher than platinum) at a temperature difference of 60?°C and a K₃Fe(CN)₆/K₄Fe(CN)₆ concentration of 0.4?M.     

The feasibility of enzyme targeted activation for amino acid/dipeptide monoester prodrugs of floxuridine; cathepsin D as a potential targeted enzyme

The improvement of therapeutic efficacy for cancer agents has been a big challenge which includes the increase of tumor selectivity and the reduction of adverse effects at non-tumor sites. In order to achieve those goals, prodrug approaches have been extensively investigated. In this report, the potential activation enzymes for 5'-amino acid/dipeptide monoester floxuridine prodrugs in pancreatic cancer cells were selected and the feasibility of enzyme specific activation of prodrugs was evaluated. All prodrugs exhibited the range of 3.0-105.7 min of half life in Capan-2 cell homogenate with the presence and the absence of selective enzyme inhibitors. 5'-O-L-Phenylalanyl-L-tyrosyl-floxuridine exhibited longer half life only with the presence of pepstatin A. Human cathepsin B and D selectively hydrolized 5'-O-L-phenylalanyl-L-tyrosylfloxuridine and 5'-O-L-phenylalanyl-L-glycylfloxuridine compared to the other tested prodrugs. The wide range of growth inhibitory effect by floxuridine prodrugs in Capan-2 cells was observed due to the different affinities of prodrug promoieties to enzymes. In conclusion, it is feasible to design prodrugs which are activated by specific enzymes. Cathepsin D might be a good candidate as a target enzyme for prodrug activation and 5'-O-L-phenylalanyl-L-tyrosylfloxuridine may be the best candidate among the tested floxuridine prodrugs.     

Ab initio parametrized polarizable force field for rutile-type SnO<Subscript>2</Subscript>

We report a new, polarizable classical force field for the rutile-type phase of SnO₂, casserite. This force field has been parametrized using results from ab initio (density functional theory) calculations as a basis for fitting. The force field was found to provide structural, dynamical and thermodynamic properties of tin oxide that compare well with both ab initio and experimental results at ambient and high pressures.     

Physicochemical study of spiropyran-terthiophene derivatives: photochemistry and thermodynamics

The photochemistry and thermodynamics of two terthiophene (TTh) derivatives bearing benzospiropyran (BSP) moieties, 1-(3,3″-dimethylindoline-6'-nitrobenzospiropyranyl)-2-ethyl 4,4″-didecyloxy-2,2':5',2″-terthiophene-3'-acetate (BSP-2) and 1-(3,3″-dimethylindoline-6'-nitrobenzospiropyranyl)-2-ethyl 4,4″-didecyloxy-2,2':5',2″-terthiophene-3'-carboxylate (BSP-3), differing only by a single methylene spacer unit, have been studied. The kinetics of photogeneration of the equivalent merocyanine (MC) isomers (MC-2 and MC-3, respectively), the isomerisation properties of MC-2 and MC-3, and the thermodynamic parameters have been studied in acetonitrile, and compared to the parent, non-TTh-functionalised, benzospiropyran derivative, BSP-1. Despite the close structural similarity of BSP-2 and BSP-3, their physicochemical properties were found to differ significantly; examples include activation energies (E(a(MC-2)) = 75.05 kJ mol(-1), E(a(MC-3)) = 100.39 kJ mol(-1)) and entropies of activation (ΔS = 43.38 J K(-1) mol(-1), ΔS = 37.78 J K(-1) mol(-1)) for the thermal relaxation from MC to BSP, with the MC-3 value much closer to the unmodified MC-1 value (46.48 J K(-1) mol(-1)) for this latter quantity. The thermal relaxation kinetics and solvatochromic behaviour of the derivatives in a range of solvents of differing polarity (ethanol, dichloromethane, acetone, toluene and diethyl ether) are also presented. Differences in the estimated values of these thermodynamic and kinetic parameters are discussed with reference to the molecular structure of the derivatives.     

Architectures, mechanisms and molecular evolution of natural product methyltransferases

Covering: up to January 2012The addition of a methyl moiety to a small chemical is a common transformation in the biosynthesis of natural products across all three domains of life. These methylation reactions are most often catalysed by S-adenosyl-l-methionine (SAM)-dependent methyltransferases (MTs). MTs are categorized based on the electron-rich, methyl accepting atom, usually O, N, C, or S. SAM-dependent natural product MTs (NPMTs) are responsible for the modification of a wide array of structurally distinct substrates, including signalling and host defense compounds, pigments, prosthetic groups, cofactors, cell membrane and cell wall components, and xenobiotics. Most notably, methylation modulates the bioavailability, bioactivity, and reactivity of acceptor molecules, and thus exerts a central role on the functional output of many metabolic pathways. Our current understanding of the structural enzymology of NPMTs groups these phylogenetically diverse enzymes into two MT-superfamily fold classes (class I and class III). Structural biology has also shed light on the catalytic mechanisms and molecular bases for substrate specificity for over fifty NPMTs. These biophysical-based approaches have contributed to our understanding of NPMT evolution, demonstrating how a widespread protein fold evolved to accommodate chemically diverse methyl acceptors and to catalyse disparate mechanisms suited to the physiochemical properties of the target substrates. This evolutionary diversity suggests that NPMTs may serve as starting points for generating new biocatalysts.