The effect of ligand on the rate of propagation of Cu(0)‐wire catalyzed SET‐LRP of MA in DMSO at 25 °C

The effect of initial ligand concentration on the apparent rate constant of propagation of single‐electron transfer living radical polymerization (SET‐LRP) of MA in DMSO at 25 °C was examined using various lengths of Cu(0) wire as catalyst. It was determined that unlike other parameters such as initiator concentration, solvent concentration, and deactivator concentration, no simple external rate‐order for the ligand concentration could be determined. Rather, the response of the rate of SET‐LRP to initial ligand concentration is complex and is likely determined by a competition of ligand‐dependent extent of disproportionation as well as the role of ligand concentration in the surface mediated activation process. Results suggest that a minimum concentration of ligand is needed to achieve both acceptable reaction rate and reaction control, and therefore, ligand concentration must be considered in designing experimental conditions for SET‐LRP. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 5629–5638, 2009     

Fresnel incoherent correlation hologram—— a review （Invited Paper）

Holographic imaging offers a reliable and fast method to capture the complete three-dimensional （3D） information of the scene from a single perspective. We review our recently proposed single-channel optical system for generating digital Fresnel holograms of 3D real-existing objects illuminated by incoherent light. In this motionless holographic technique, light is reflected, or emitted from a 3D object, propagates through a spatial light modulator （SLM）, and is recorded by a digital camera. The SLM is used as a beamsplitter of the single-channel incoherent interferometer, such that each spherical beam originated from each object point is split into two spherical beams with two different curve radii. Incoherent sum of the entire interferences between all the couples of spherical beams creates the Fresnel hologram of the observed 3D object. When this hologram is reconstructed in the computer, the 3D properties of the object are revealed.     

Mimicking “nascent” Cu(0) mediated SET‐LRP of methyl acrylate in DMSO leads to complete conversion in several minutes

Cu(0) was prepared via disproportionation of Cu(I)Br in the presence of Me₆‐TREN in various solvents in a glove box. The resulting nanopowders were used as mimics of “nascent” Cu(0) catalyst in the single‐electron transfer living radical polymerization (SET‐LRP) of methyl acrylate (MA), providing faster polymerization than any commercial Cu(0) powder, Cu(0) wire, or Cu(I)Br and achieving 80% conversion in only 5 min reaction time. Despite the high rate, a living polymerization was observed with linear evolution of molecular weight, narrow polydispersity, no induction period, and high retention of chain‐end functionality. In addition to providing an unprecedentedly fast, yet controlled LRP of MA, these studies suggest that the very small “nascent” Cu(0) species formed via disproportionation in SET‐LRP are the most active catalysts. Thus, when bulk Cu(0) powder or wire may be the most abundant catalyst and dictates the overall kinetics, any Cu(0) produced via disproportionation will be rapidly consumed and contributes to the overall catalytic cycle. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 48: 403–409, 2010     

New efficient reaction media for SET‐LRP produced from binary mixtures of organic solvents and H2O

SET‐LRP is mediated by a combination of solvent and ligand that promotes disproportionation of Cu(I)X into Cu(0) and Cu(II)X₂. Therefore, the diversity of solvents suitable for SET‐LRP is limited. SET‐LRP of MA in a library of solvents with different equilibrium constants for disproportionation of Cu(I)X such as DMSO, DMF, DMAC, EC, PC, EtOH, MeOH, methoxyethanol, NMP, acetone and in their binary mixtures with H₂O was examined. H₂O exhibits the highest equilibrium constant for disproportionation of Cu(I)X. The apparent rate constant of the polymerization exhibits a linear increase with the addition of H₂O. This is consistent with higher equilibrium constants for disproportionation generated by addition of H₂O to organic solvents. Furthermore, with the exception of alcohols and carbonates, the rate constant of polymerization in binary mixtures could be correlated with the Dimroth‐Reichardt solvent polarity parameter. This is consistent with the single‐electron transfer mechanism proposed for SET‐LRP that involves a polar transition state. These experiments demonstrate that the use of binary mixtures of solvents with H₂O provides a new, simple and efficient method for the elaboration of a large diversity of reaction media that are suitable for SET‐LRP even when one of the two solvents does not mediate disproportionation of Cu(I)X. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 5577–5590, 2009     

Multi-funnel optimization using Gaussian underestimation

In several applications, underestimation of functions has proven to be a helpful tool for global optimization. In protein–ligand docking problems as well as in protein structure prediction, single convex quadratic underestimators have been used to approximate the location of the global minimum point. While this approach has been successful for basin-shaped functions, it is not suitable for energy functions with more than one distinct local minimum with a large magnitude. Such functions may contain several basin-shaped components and, thus, cannot be underfitted by a single convex underestimator. In this paper, we propose using an underestimator composed of several negative Gaussian functions. Such an underestimator can be computed by solving a nonlinear programming problem, which minimizes the error between the data points and the underestimator in the L ¹ norm. Numerical results for simulated and actual docking energy functions are presented.     

A substrate-free activity-based protein profiling screen for the discovery of selective PREPL inhibitors

Peptidases play vital roles in physiology through the biosynthesis, degradation, and regulation of peptides. Prolyl endopeptidase-like (PREPL) is a newly described member of the prolyl peptidase family, with significant homology to mammalian prolyl endopeptidase and the bacterial peptidase oligopeptidase B. The biochemistry and biology of PREPL are of fundamental interest due to this enzyme's homology to the biomedically important prolyl peptidases and its localization in the central nervous system. Furthermore, genetic studies of patients suffering from hypotonia-cystinuria syndrome (HCS) have revealed a deletion of a portion of the genome that includes the PREPL gene. HCS symptoms thought to be caused by lack of PREPL include neuromuscular and mild cognitive deficits. A number of complementary approaches, ranging from biochemistry to genetics, will be required to understand the biochemical, cellular, physiological, and pathological mechanisms regulated by PREPL. We are particularly interested in investigating physiological substrates and pathways controlled by PREPL. Here, we use a fluorescence polarization activity-based protein profiling (fluopol-ABPP) assay to discover selective small-molecule inhibitors of PREPL. Fluopol-ABPP is a substrate-free approach that is ideally suited for studying serine hydrolases for which no substrates are known, such as PREPL. After screening over 300,000 compounds using fluopol-ABPP, we employed a number of secondary assays to confirm assay hits and characterize a group of 3-oxo-1-phenyl-2,3,5,6,7,8-hexahydroisoquinoline-4-carbonitrile and 1-alkyl-3-oxo-3,5,6,7-tetrahydro-2H-cyclopenta[c]pyridine-4-carbonitrile PREPL inhibitors that are able to block PREPL activity in cells. Moreover, when administered to mice, 1-isobutyl-3-oxo-3,5,6,7-tetrahydro-2H-cyclopenta[c]pyridine-4-carbonitrile distributes to the brain, indicating that it may be useful for in vivo studies. The application of fluopol-ABPP has led to the first reported PREPL inhibitors, and these inhibitors will be of great value in studying the biochemistry of PREPL and in eventually understanding the link between PREPL and HCS.     

Transfer, amplification, and inversion of helical chirality mediated by concerted interactions of C3-supramolecular dendrimers

The synthesis, structural, and retrostructural analysis of two libraries containing 16 first and second generation C(3)-symmetric self-assembling dendrimers based on dendrons connected at their apex via trisesters and trisamides of 1,3,5-benzenetricarboxylic acid is reported. A combination of X-ray diffraction and CD/UV analysis methods demonstrated that their C(3)-symmetry modulates different degrees of packing on the periphery of supramolecular structures that are responsible for the formation of chiral helical supramolecular columns and spheres self-organizable in a diversity of three-dimensional (3D) columnar, tetragonal, and cubic lattices. Two of these periodic arrays, a 3D columnar hexagonal superlattice and a 3D columnar simple orthorhombic chiral lattice with P222(1) symmetry, are unprecedented for supramolecular dendrimers. A thermal-reversible inversion of chirality was discovered in helical supramolecular columns. This inversion is induced, on heating, by the change in symmetry from a 3D columnar simple orthorhombic chiral lattice to a 3D columnar hexagonal array and, on cooling, by the change in symmetry from a 2D hexagonal to a 2D centered rectangular lattice, both exhibiting intracolumnar order. A first-order transition from coupled columns with long helical pitch, to weakly or uncorrelated columns with short helical pitch that generates a molecular rotator, was also discovered. The torsion angles of the molecular rotator are proportional to the change in temperature, and this effect is amplified in the case of the C(3)-symmetric trisamide supramolecular dendrimers forming H-bonds along their column. The structural changes reported here can be used to design complex functions based on helical supramolecular dendrimers with different degree of packing on their periphery.     

Information-theoretic approaches to SVM feature selection for metagenome read classification

Analysis of DNA sequences isolated directly from the environment, known as metagenomics, produces a large quantity of genome fragments that need to be classified into specific taxa. Most composition-based classification methods use all features instead of a subset of features that may maximize classifier accuracy. We show that feature selection methods can boost performance of taxonomic classifiers. This work proposes three different filter-based feature selection methods that stem from information theory: (1) a technique that combines Kullback-Leibler, Mutual Information, and distance information, (2) a text mining technique, TF-IDF, and (3) minimum redundancy-maximum-relevance (mRMR). The feature selection methods are compared by how well they improve support vector machine classification of genomic reads. Overall, the 6mer mRMR method performs well, especially on the phyla-level. If the number of total features is very large, feature selection becomes difficult because a small subset of features that captures a majority of the data variance is less likely to exist. Therefore, we conclude that there is a trade-off between feature set size and feature selection method to optimize classification performance. For larger feature set sizes, TF-IDF works better for finer-resolutions while mRMR performs the best out of any method for N=6 for all taxonomic levels.