Evaluation of docking/scoring approaches: A comparative study based on MMP3 inhibitors

An increasing number of docking/scoring programs are available that use different sampling and scoring algorithms. A reliable scoring function is the crucial element of such approaches. Comparative studies are needed to evaluate their current capabilities. DOCK4 with force field and PMF scoring as well as FlexX were used to evaluate the predictive power of these docking/scoring approaches to identify the correct binding mode of 61 MMP-3 inhibitors in a crystal structure of stromelysin and also to rank them according to their different binding affinities. It was found that DOCK4/PMF scoring performs significantly better than FlexX and DOCK4/FF in both ranking ligands and predicting their binding modes. Most notably, DOCK4/PMF was the only scoring/docking approach that found a significant correlation between binding affinity and predicted score of the docked inhibitors. However, comparing only those cases where the correct binding mode was identified (scoring highest among sampled poses), FlexX showed the best `fine tuning' (lowest rmsd) in predicted binding modes. The results suggest that not so much the sampling procedure but rather the scoring function is the crucial element of a docking program.     

Semi-industrial isolation of salicin and amygdalin from plant extracts using slow rotary counter-current chromatography

Salicin in the bark extract of Salix alba and amygdalin in the fruit extract of Semen armeniacae were each separated by slow rotary counter-current chromatography (SRCCC). The apparatus was equipped with a 40-L column made of 17 mm i.d. convoluted Teflon tubing. A 500g amount of crude extract containing salicin at 13.5% was separated yielding 63.5 g of salicin at 95.3% purity in 20h using methyl tert-butyl ether-l-butanol (1:3) saturated by methanol-water (1:5) as a stationary phase and methanol-water (1:5) saturated by methyl tert-butyl ether-1-butanol (1:3) as a mobile phase. A 400g amount of crude extract containing amygdalin at 55.3% was isolated to yield 221.2g of amygdalin at 94.1% purity in 19h using ethyl acetate-1-butanol (1:2) saturated by water as a stationary phase and water saturated by ethyl acetate-1-butanol (1:2) as a mobile phase. The flow rate of the mobile phase was 50 ml/min. The results show that industrial SRCCC separation of salicin and amygdalin is feasible using a larger column at a higher flow rate of the mobile phase.     

Synthesis of N,N-diethyldithiocarbamate functionalized 1,4-polyisoprene, from natural rubber and synthetic 1,4-polyisoprene

N,N-Diethyldithiocarbamate functionnalized 1,4-polyisoprenes were prepared from 1,4-polyisoprenes (natural or synthetic). The syntheses were performed by nucleophilic addition of N,N-diethyldithiocarbamate salts upon oxirane rings of epoxidized units according to a SN2 mechanism with ring opening. Studies on model molecules of epoxidized 1,4-polyisoprene units (1,2-epoxy-1-methylcyclohexane and 4,5-epoxy-4-methyloctane) were previously achieved to develop the procedure. The best yields were obtained at low temperature in polar medium, and more especially in water with sodium N,N-diethyldithiocarbamate (DEDT-Na) as reagent. A diastereospecific addition was noted when reaction was performed in water with DEDT-Na. Afterwards, the developed procedure was successfully generalized to epoxidized synthetic polyisoprenes and epoxidized natural rubber (in THF, then in latex medium). Excellent results were obtained in latex medium with epoxidized natural rubber (ENR) latices. As with the models, a diastereospecific addition of sodium N,N-diethyldithiocarbamate trihydrate onto epoxidized 1,4-polyisoprene units of ENR was observed at the condition to bring the latex medium to pH 8 before introduction of DEDT-Na. Influence of temperature, drc, and DEDT-Na concentration were successively examined to determine the best conditions of the addition on ENR latices.     

DNA-templated self-assembly of protein and nanoparticle linear arrays

Self-assembling DNA tiling lattices represent a versatile system for nanoscale construction. Self-assembled DNA arrays provide an excellent template for spatially positioning other molecules with increased relative precision and programmability. Here we report an experiment using a linear array of DNA triple crossover tiles to controllably template the self-assembly of single-layer or double-layer linear arrays of streptavidin molecules and streptavidin-conjugated nanogold particles through biotin-streptavidin interaction. The organization of streptavidin and its conjugated gold nanoparticles into periodic arrays was visualized by atomic force microscopy and scanning electron microscopy.     

Structural tuning of coordination polymers by 4-connecting metal node and secondary building process

Due to variation in ligand's conformation, metal node's connecting geometry, and secondary building process by anions, bat-like, dumbell-like, diamondoid, or pillar-layer topologies are achieved.     

A Theoretical Study of Complex Formation between Formaldehyde and Lithium

Ab initio SCF and CI calculations on the cationic and neutral complexes of formaldehyde and lithium are reported. For the cationic complex CH₂O/Li⁺, the stabilization energy of 41.7 kcal/mol obtained from the SCF calculation increases to 51.6 kcal/mol if a configuration interaction is introduced. For the neutral complex CH₂O^?/Li⁺, the C_2v-conformer of the ²A₁-state with the equilibrium bond distances of d(C? O) = 1.23 Å and d (O? Li) = 1.90 Å is calculated to be more stable than the ₂B₁-state with d (C? O) = 1.34 Å, and d (O? Li) = 1.65 Å. Charge transfer and polarization effects upon complex formation are discussed.     

Determination of Cr(III) and Cr(VI) in environmental waters by derivative flame atomic absorption spectrometry using flow injection on-line preconcentration with double-microcolumn adsorption

The species of Cr(III) and Cr(VI) in water samples were determined by flow injection on-line preconcentration and separation on two-microcolumn system-derivative flame atomic absorption spectrometry during a collaborative analysis for certification. The Cr(III) and Cr(VI) in water samples were retained on two microcolumns with ion exchange resin and were eluted directly to nebulizer by 15% HNO³ and 8% NH⁴NO³, respectively. The characteristic concentration (at the sensitivity grade of 2 mV min^?1 for 1 min of preconcentration time) for Cr(III) and Cr(VI) were 0.130 and 0.0985 μg l^?1, in the order which were 332- and 431-fold better than those of FAAS, and 45- and 47-fold better than those of FI-FAAS, respectively. The relative standard deviations were 3.27% and 3.66% with corresponding detection limits (3σ) of 0.244 and 0.235 μg l^?1, respectively. The linear ranges of determinations for Cr(III) and Cr(VI) were 0～100 μgm l^?1 with correlation coefficients of 0.9984 to 0.9996. The satisfactory recovery of 94.4%～106% for Cr(III) and Cr(VI) could be obtained from water samples.