Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach

Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. The success of ensemble docking often requires the careful selection of complementary protein conformations, through docking and scoring of known co-crystallized ligands. False positives, in which a ligand in a wrong pose achieves a better docking score than that of native pose, arise as additional protein conformations are added. In the current study, we developed a new ligand-biased ensemble receptor docking method and composite scoring function which combine the use of ligand-based atomic property field (APF) method with receptor structure-based docking. This method helps us to correctly dock 30 out of 36 ligands presented by the D3R docking challenge. For the six mis-docked ligands, the cognate receptor structures prove to be too different from the 40 available experimental Pocketome conformations used for docking and could be identified only by receptor sampling beyond experimentally explored conformational subspace.     

A general powder dusting method for latent fingerprint development based on AIEgens

Powder dusting method is the most practically useful approach for latent fingerprint development in the crime scene. Herein, a general powder dusting method has been explored for latent fingerprint development based on aggregation-induced emission luminogens (AIEgens). A series of tetraphenylethene (TPE) derivatives with multiple diphenylamine (DPA), namely, TPE-DPA, TPE-2DPA and TPE-4DPA, were selected as candidates to dope with magnetic powders and applied for latent fingerprint development. After screening, the magnetic powder 3 doped with TPE-4DPA proves to be the best, in terms of fluorescent intensity, resolution and adhesiveness. Afterwards, the magnetic powder 3 was applied for visualization of latent fingerprint on various smooth and porous substrates, including glass, stainless steel, leaf, ceram, plastic bag, lime wall, wood and paper money. Specific details, such as island, core, termination and bifurcation, can be clearly observed for the fluorescent fingerprint images.     

In Situ Monitoring of RAFT Polymerization by Tetraphenylethylene‐Containing Agents with Aggregation‐Induced Emission Characteristics

A facile and efficient approach is demonstrated to visualize the polymerization in situ. A group of tetraphenylethylene (TPE)‐containing dithiocarbamates were synthesized and screened as agents for reversible addition fragmentation chain transfer (RAFT) polymerizations. The spatial‐temporal control characteristics of photochemistry enabled the RAFT polymerizations to be ON and OFF on demand under alternating visible light irradiation. The emission of TPE is sensitive to the local viscosity change owing to its aggregation‐induced emission characteristic. Quantitative information could be easily acquired by the naked eye without destroying the reaction system. Furthermore, the versatility of such a technique was well demonstrated by 12 different polymerization systems. The present approach thus demonstrated a powerful platform for understanding the controlled living radical polymerization process.     

Noiseless independent signal and power amplification

We present a noiseless optical amplifier comprising a signal-amplifying feed-forward loop and a power-amplifying injection-locked laser. We demonstrate that the signal amplifier can attain a signal-transfer coefficient limited solely by the quantum efficiency of our in-loop photodetector and that we can independently amplify the optical power while leaving the normalized intensity-noise spectral density of the input field unchanged.     

The effect of the secondary structure on dissociation of peptide radical cations: fragmentation of angiotensin III and its analogues

Fragmentation of protonated RVYIHPF and RVYIHPF-OMe and the corresponding radical cations was studied using time- and collision energy-resolved surface-induced dissociation (SID) in a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) specially equipped to perform SID experiments. Peptide radical cations were produced by gas-phase fragmentation of Co (III)(salen)-peptide complexes. Both the energetics and the mechanisms of dissociation of even-electron and odd-electron angiotensin III ions are quite different. Protonated molecules are much more stable toward fragmentation than the corresponding radical cations. RRKM modeling of the experimental data suggests that this stability is largely attributed to differences in threshold energies for dissociation, while activation entropies are very similar. Detailed analysis of the experimental data obtained for radical cations demonstrated the presence of two distinct structures separated by a high free-energy barrier. The two families of structures were ascribed to the canonical and zwitterionic forms of the radical cations produced in our experiments.     

Highly sensitive restriction enzyme assay and analysis: a review

Biological assays at the single molecule level are crucial to fundamental studies of DNA-protein mechanisms. In order to cater for high throughput applications, one area of immense research potential is single-molecule bioassays where miniaturized devices are developed to perform rapid and effective biological reactions and analyses. With the success of various emerging technologies for engineering miniaturized structures down to the nanoscale level, supported by specialized equipment for detection, many investigations in the field of life science that were once thought impossible can now be actively explored. In this review, the significance of downscaling to the single-molecule level is firstly presented in selected examples, with the focus placed on restriction enzyme assays. To determine the effectiveness of single-molecule restriction enzyme reactions, simple and direct analytical methods based on DNA stretching have often been reliably employed. DNA stretching can be realized based on a number of working principles related to the physical forces exerted on the DNA samples. We then discuss two examples of a nanochannel system and a microchamber system where single-molecule restriction enzyme digestion and DNA stretching have been integrated, which possess prospective capabilities of developing into highly sensitive and high-throughput restriction enzyme assays. Finally, we take a brief look at the general trends in technological development in this field by comparing the advantages and disadvantages of performing assays at bulk, microscale and single-molecule levels. Figure Minaturization of Restriction Enzyme Assays and DNA Stretching     

Cyclic bandwidth with an edge added

B_c(G) denotes the cyclic bandwidth of graph G. In this paper, we obtain the maximum cyclic bandwidth of graphs of order p with adding an edge as follows:

     

An efficient solid-phase synthesis of 3-substituted and 3,3-disubstituted 1,2-dialkylpyrazolidine-3,5-diones

An efficient and regioselective procedure for the synthesis of di-, tri- and fully-substituted pyrazolidine-3,5-diones on a solid-phase format is described. Microwave irradiation provided significant rate enhancement in this protocol. To demonstrate the versatility of this chemistry, a representative set of 25 compounds was prepared.     

Thermal decomposition of methyl butanoate: ab initio study of a biodiesel fuel surrogate

In this paper, we report a detailed analysis of the breakdown kinetic mechanism for methyl butanoate (MB) using theoretical approaches. Electronic structures and structure-related molecular properties of reactants, intermediates, products, and transition states were explored at the BH&HLYP/cc-pVTZ level of theory. Rate constants for the unimolecular and bimolecular reactions in the temperature range of 300-2500 K were calculated using Rice-Ramsperger-Kassel-Marcus and transition state theories, respectively. Thirteen pathways were identified leading to the formation of small compounds such as CH(3), C(2)H(3), CO, CO(2), and H(2)CO. For the initial formation of MB radicals, H, CH(3), and OH were considered as reactive radicals participating in hydrogen abstraction reactions. Kinetic simulation results for a high temperature pyrolysis environment show that MB radicals are mainly produced through hydrogen abstraction reactions by H atoms. In addition, the C(O)OCH(3) = CO + CH(3)O reaction is found to be the main source of CO formation. The newly computed kinetic sub-model for MB breakdown is recommended as a core component to study the combustion of oxygenated species.