Synthesis of π‐conjugated oligomer that can form metallo polymers

An oligo(p‐phenylene vinylene) that contains terpyridine ligands has been synthesized. Upon addition of metal ions, a π‐conjugated metallo polymer is formed in which the well‐defined character of oligomers and the material properties of polymers are combined. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 40: 4020–4023, 2002     

Random and cooperative sequential adsorption on infinite ladders and strips

We analyze various processes where particles are added irreversibly and sequentially at the sites of infinite ladders or broader strips (i.e., on terraces) of adsorption sites. For sufficiently narrow strips or ladders, exact solution in closed form is possible for a variety of processes. Often this is most naturally achieved by mapping the process onto an equivalent one-dimensional process typically involvingcompetitive adsorption. We demonstrate this procedure for sequential adsorption with nearest-neighbor exclusion on a 2× square ladder. For other select processes on strips slightly too broad for exact solution, almost exact analysis is possible exploiting an empty-site shielding property. In this way, we determine a jamming coverage of 0.91556671 for random sequential adsorption of dimers on a 2× square ladder. For broader strips, we note that the complexity of these problems quickly approaches that for × lattices.     

Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®

We report the design and validation of a fast empirical function for scoring RNA-ligand interactions, and describe its implementation within RiboDock, a virtual screening system for automated flexible docking. Building on well-known protein-ligand scoring function foundations, features were added to describe the interactions of common RNA-binding functional groups that were not handled adequately by conventional terms, to disfavour non-complementary polar contacts, and to control non-specific charged interactions. The results of validation experiments against known structures of RNA-ligand complexes compare favourably with previously reported methods. Binding modes were well predicted in most cases and good discrimination was achieved between native and non-native ligands for each binding site, and between native and non-native binding sites for each ligand. Further evidence of the ability of the method to identify true RNA binders is provided by compound selection ('enrichment factor') experiments based around a series of HIV-1 TAR RNA-binding ligands. Significant enrichment in true binders was achieved amongst high scoring docking hits, even when selection was from a library of structurally related, positively charged molecules. Coupled with a semi-automated cavity detection algorithm for identification of putative ligand binding sites, also described here, the method is suitable for the screening of very large databases of molecules against RNA and RNA-protein interfaces, such as those presented by the bacterial ribosome.     

DNA tile based self-assembly: building complex nanoarchitectures.

DNA tile based self-assembly provides an attractive route to create nanoarchitectures of programmable patterns. It also offers excellent scaffolds for directed self-assembly of nanometer-scale materials, ranging from nanoparticles to proteins, with potential applications in constructing nanoelectronic/nanophotonic devices and protein/ligand nanoarrays. This Review first summarizes the currently available DNA tile toolboxes and further emphasizes recent developments toward self-assembling DNA nanostructures with increasing complexity. Exciting progress using DNA tiles for directed self-assembly of other nanometer scale components is also discussed.     

Fast Multi‐residue Screening for 84 Pesticides in Tea by Gas Chromatography with Dual‐tower Auto‐sampler,Dual‐column and Dual Detectors

A fast multi‐residue screening method for determining pesticides in tea is described. Pesticides are extracted from tea with acetone and methylene chloride, then enriched and cleaned up with solid phase extraction (SPE) prior to gas chromatographic determination. The fast screening is achieved by a gas chromatograph system equipped with dual‐column, dual‐tower auto‐sampler and both electron capture detector (ECD) and flame photometric detector (FPD). Optimal conditions are investigated for the prospective pesticides including column selection, detection mode, the retention behaviors, quantitative calibration, as well as the recoveries and repeatability of pesticides from tea samples. Under the optimal conditions, with the FPD‐P detector accompanied CP‐SIL 13CB column, 48 pesticides can be separated well and detected within 38 min; and with a DB‐5 column, 35 ECD‐detectable pesticides can be separated and detected within 46 min. The recoveries of 84 pesticides in tea samples are 65–120% with 0.34–16% RSD for spiking 0.02–3.0 mg/kg standard species. Because of the thermal instability of most pesticides, direct cold extraction of pesticides from a tea sample is recommended. The proposed method provided a very fast and efficient procedure to screen 84 pesticides from a complicated tea sample matrix.     

Structural regulation of a peptide-conjugated graft copolymer: a simple model for amyloid formation

The self-assembly of peptides and proteins into beta-sheet-rich high-order structures has attracted much attention as a result of the characteristic nanostructure of these assemblies and because of their association with neurodegenerative diseases. Here we report the structural and conformational properties of a peptide-conjugated graft copolymer, poly(gamma-methyl-L-glutamate) grafted polyallylamine (1) in a water-2,2,2-trifluoroethanol solution as a simple model for amyloid formation. Atomic force microscopy revealed that the globular peptide 1 self-assembles into nonbranching fibrils that are about 4 nm in height under certain conditions. These fibrils are rich in beta-sheets and, similar to authentic amyloid fibrils, bind the amyloidophilic dye Congo red. The secondary and quaternary structures of the peptide 1 can be controlled by manipulating the pH, solution composition, and salt concentration; this indicates that the three-dimensional packing arrangement of peptide chains is the key factor for such fibril formation. Furthermore, the addition of carboxylic acid-terminated poly(ethylene glycol), which interacts with both of amino groups of 1 and hydrophobic PMLG chains, was found to obviously inhibit the alpha-to-beta structural transition for non-assembled peptide 1 and to partially cause a beta-to-alpha structural transition against the 1-assembly in the beta-sheet form. These findings demonstrate that the amyloid fibril formation is not restricted to specific protein sequences but rather is a generic property of peptides. The ability to control the assembled structure of the peptide should provide useful information not only for understanding the amyloid fibril formation, but also for developing novel peptide-based material with well-defined nanostructures.     

Smart materials based on self-assembled hydrogen-bonded comb-shaped supramolecules

Block copolymer self-assembly and supramolecular chemistry can be combined most naturally to prepare smart polymer nanomaterials. An attractive route is based on comb-shaped supramolecules, obtained by attaching side chains to (co)polymers by physical (non-covalent) interactions. Hydrogen bonding is a key element of our approach. It combines an ease of synthesis with other important approach-specific elements, such as hierarchical self-assembly, strongly enhanced processability, swelling, and cleaving. Functional properties discussed include anisotropic proton conductivity, switching proton conductivity, electronically conducting nanowires, polarized luminance, dielectric stacks (optical reflectivity), functional membranes, and nano objects.     

Vibrational spectroscopic encoding of polystyrene-based resin beads: converting the encoding peaks into barcodes

A detailed approach is described for the vibrational spectroscopic encoding of polystyrene-based resin beads by converting the infrared absorption peaks suitable for encoding (encoding peaks) into barcodes. Based on combining the FT-IR measurements and the quantum-chemical computations, the vibrational characteristics of p-tert-butylstyrene monomer, polystyrene and poly(p-tert-butylstyrene) resin beads are analyzed, which are helpful for the selection of encoding peaks. The vibrational spectroscopic encoding of polystyrene-based resin beads could be obtained by converting the wavenumber, intensity and full width at half maximum (FWHM) of the encoding peaks into barcodes automatically through a computer program designed in our laboratory.     

Computational combinatorial ligand design: Application to human α-thrombin

Summary A new method is presented for computer-aided ligand design by combinatorial selection of fragments that bind favorably to a macromolecular target of known three-dimensional structure. Firstly, the multiple-copy simultaneous-search procedure (MCSS) is used to exhaustively search for optimal positions and orientations of functional groups on the surface of the macromolecule (enzyme or receptor fragment). The MCSS minima are then sorted according to an approximated binding free energy, whose solvation component is expressed as a sum of separate electrostatic and nonpolar contributions. The electrostatic solvation energy is calculated by the numerical solution of the linearized Poisson-Boltzmann equation, while the nonpolar contribution to the binding free energy is assumed to be proportional to the loss in solvent-accessible surface area. The program developed for computational combinatorial ligand design (CCLD) allows the fast and automatic generation of a multitude of highly diverse compounds, by connecting in a combinatorial fashion the functional groups in their minimized positions. The fragments are linked as two atoms may be either fused, or connected by a covalent bond or a small linker unit. To avoid the combinatorial explosion problem, pruning of the growing ligand is performed according to the average value of the approximated binding free energy of its fragments. The method is illustrated here by constructing candidate ligands for the active site of human -thrombin. The MCSS minima with favorable binding free energy reproduce the interaction patterns of known inhibitors. Starting from these fragments, CCLD generates a set of compounds that are closely related to high-affinity thrombin inhibitors. In addition, putative ligands with novel binding motifs are suggested. Probable implications of the MCSS-CCLD approach for the evolving scenario of drug discovery are discussed.     

Reversible anion exchanges between the layered organic-inorganic hybridized architectures: syntheses and structures of manganese(II) and copper(II) complexes containing novel tripodal ligands

Six noninterpenetrating organic-inorganic hybridized coordination complexes, [Mn(3)(2)(H(2)O)(2)](ClO(4))(2).2 H(2)O (5), [Mn(3)(2)(H(2)O)(2)](NO(3))(2) (6), [Mn(3)(2)(N(3))(2)].2 H(2)O (7), [Cu(3)(2)(H(2)O)(2)](ClO(4))(2) (8), [Mn(4)(2)(H(2)O)(SO(4))].CH(3)OH.5 H(2)O (9) and [Mn(4)(2)](ClO(4))(2) (10) were obtained through self-assembly of novel tripodal ligands, 1,3,5-tris(1-imidazolyl)benzene (3) and 1,3-bis(1-imidazolyl)-5-(imidazol-1-ylmethyl)benzene (4) with the corresponding metal salts, respectively. Their structures were determined by X-ray crystallography. The results of structural analysis of complexes 5, 6, 7, and 8 with rigid ligand 3 indicate that their structures are mainly dependant on the nature of the organic ligand and geometric need of the metal ions, but not influenced greatly by the anions and metal ions. While in complexes 9 and 10, which contain the flexible ligand 4, the counteranion plays an important role in the formation of the frameworks. Entirely different structures of complexes 5 and 10 indicate that the organic ligands greatly affect the structures of assemblies. Furthermore, in complexes 5 and 6, the counteranions located between the cationic layers can be exchanged by other anions. Reversible anion exchanges between complexes 5 and 6 without destruction of the frameworks demonstrate that 5 and 6 can act as cationic layered materials for anion exchange, as determined by IR spectroscopy, elemental analyses, and X-ray powder diffraction.