Comparison of topological, shape, and docking methods in virtual screening

Virtual screening benchmarking studies were carried out on 11 targets to evaluate the performance of three commonly used approaches: 2D ligand similarity (Daylight, TOPOSIM), 3D ligand similarity (SQW, ROCS), and protein structure-based docking (FLOG, FRED, Glide). Active and decoy compound sets were assembled from both the MDDR and the Merck compound databases. Averaged over multiple targets, ligand-based methods outperformed docking algorithms. This was true for 3D ligand-based methods only when chemical typing was included. Using mean enrichment factor as a performance metric, Glide appears to be the best docking method among the three with FRED a close second. Results for all virtual screening methods are database dependent and can vary greatly for particular targets.     

Structure Analysis of PVC Nanocomposites

In this paper poly(vinyl chloride)/clay nanocomposites were prepared by melt intercalation using a single screw extruder. Problems with thermal stability of these nanocomposites during compounding were largely eliminated by pre-treatment of the organoclay with plasticizer (dioctyl phthalate), which created a barrier between polymer and quaternary amine. These nanocomposite materials were analyzed with respect to their morphology. The intercalation, exfoliation, nano-phase dispersion and orientation were investigated using Transmission Electron Microscopy (TEM), Scanning Electron Microscopy (SEM), Atomic Force Microscopy (AFM) and X-ray diffraction (XRD). Moreover, different types of sample preparation for these techniques were tested as well. It was found that partially intercalated and disordered structure arose in poly (vinyl chloride) composites containing sodium type of montmorillonite, while a fine dispersion of partial to nearly full exfoliation of individual montmorillonite layers in poly (vinyl chloride) matrix was observed when this clay was organically modified. Finally, the influence of different mixing time (in extruder) on nano-phase morphology was surveyed.     

Modeling Very Oscillating Signals. Application to Image Processing

This article is a companion paper of a previous work where we have developed the numerical analysis of a variational model first introduced by Rudin et al. and revisited by Meyer for removing the noise and capturing textures in an image. The basic idea in this model is to decompose an image f into two components (u + v) and then to search for (u,v) as a minimizer of an energy functional. The first component u belongs to BV and contains geometrical information, while the second one v is sought in a space G which contains signals with large oscillations, i.e. noise and textures. In Meyer carried out his study in the whole ² and his approach is rather built on harmonic analysis tools. We place ourselves in the case of a bounded set of ² which is the proper setting for image processing and our approach is based upon functional analysis arguments. We define in this context the space G, give some of its properties, and then study in this continuous setting the energy functional which allows us to recover the components u and v. We present some numerical experiments to show the relevance of the model for image decomposition and for image denoising.     

TOF-GISANS investigation of polymer infiltration in mesoporous TiO2 films for photovoltaic applications

The structure of porous TiO₂ films and TiO₂:poly(N-vinylcarbazole) (PVK) composite films is investigated with time-of-flight grazing incidence small-angle neutron scattering (TOF-GISANS). The TiO₂ films have been prepared by application of a sol–gel process with a diblock copolymer as structure directing agent, and the conductive polymer PVK is infiltrated in the porous network by spin coating and solution casting. The films show a hierarchical pore structure with mesopores 52 nm in size and additional large macropores with a diameter of about 180 nm. By matching the scattering contrast of the TiO₂ with the polymer information about the penetration of the polymer in the pores is determined. Whereas in the PVK film prepared by solution casting the pores are filled to a high degree; in the spin coated film, PVK wets only the TiO₂ pore walls and forms a solid overlying layer. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 1628–1635, 2010     

HIV-1 integrase inhibition of biscoumarin analogues

Nineteen biscoumarins bearing free and modified hydroxyl substituents at benzoyloxyphenyl linker have been synthesized by multiple step synthesis. Among these biscoumarins, thirteen were found to be active molecules against HIV-1 integrase (HIV-1 IN). The structure-activity relationship of the nineteen compounds on HIV IN may be useful for the design of potent therapeutic agents.     

Fast and Exact Simulation of Complex-Valued Stationary Gaussian Processes Through Embedding Circulant Matrix

This article is concerned with the study of the embedding circulant matrix method to simulate stationary complex-valued Gaussian sequences. The method is, in particular, shown to be well-suited to generate circularly symmetric stationary Gaussian processes. We provide simple conditions on the complex covariance function ensuring the theoretical validity of the minimal embedding circulant matrix method. We show that these conditions are satisfied by many examples and illustrate the simulation algorithm. In particular, we present a simulation study involving the circularly symmetric fractional Gaussian noise, a model introduced in this article. Supplementary material for this article is available online.     

Synthesis of Isobrassilexin,a Biologically Active Isomer of Brassilexin,a Cruciferac Phytoalexin

The synthesis of isobrassilexin 2, a hitherto non natural indoloisothiazole is reported (two steps, 43% yield). This substance, an isomer of brassilexin 1 has shown important biological properties in vitro.     

Qualitative By-Product Identification of Plasma-Assisted TCE Abatement by Mass Spectrometry and Fourier-Transform Infrared Spectroscopy

In this study, the formation of by-products resulting from the decomposition of trichloroethylene with a negative DC glow discharge has been investigated. By combining the qualitative data from mass spectrometry and Fourier-transform infrared spectroscopy, the formation of phosgene, dichloroacetylchloride and trichloroacetaldehyde have been confirmed as incomplete oxidation products. Hydrogen chloride, chlorine, carbon monoxide and carbon dioxide were also detected. Also, formation of ozone was found in the outlet stream. Based on this information, it is possible to chose an appropriate catalyst to combine with non thermal plasma. In this way emission of harmful, incomplete oxidation products can be further reduced at a lower energy cost.     

Phase transitions of an ionic liquid self-assembled monolayer on Au

The properties of a surface modified with an ionic liquid self-assembled monolayer (IL-SAM) can be tuned by simply changing the deposition temperature. Mid-IR, SERS, and molecular modelling demonstrated that 1-(12-mercaptododecyl)-3-methylimidazolium bromide (MDMIBr) exhibited a crystalline monolayer for deposition temperatures below 25 °C. Above 25 °C, the aliphatic chain collapsed into a disordered conformation. At 40 °C, another phase transition occurs due to the imidazolium group tilting parallel to the surface. Consequently, the wettability of IL-SAM was tuned over a broad range of contact angle (from 20° to nearly 40°) by varying the deposition temperature. Permeation of redox mediators to a Au electrode coated with MDMIBr strongly depends on the net charge of the redox mediator. Electron transfer was excellent for neutral and negatively charged redox mediators on electrodes coated with IL-SAM regardless of deposition temperature.     

Predicting variability in the dynamic failure strength of brittle materials considering pre-existing flaws

We perform two-dimensional dynamic fracture simulations of a specimen in biaxial tension, incorporating various distributions of pre-existing microcracks. The simulations consider the spatial distribution of flaws while modeling the discrete failure processes of crack interactions and coalescence, and predict the macroscopic variability in failure strength. The model quantitatively predicts the effect (on the dynamic failure strength) of different shapes of the flaw size distribution function, the random spatial distribution of flaws, and the random local resistance to crack growth (i.e. strength) associated with each flaw. The effect of changing material volumes on the variability in failure strengths is also examined in relation to the flaw size distribution. The effect of loading rate on the variability in failure strengths is presented in a form that will enable improved constitutive modeling using non-local formulations at the continuum scale.