TargetATPsite: A template‐free method for ATP‐binding sites prediction with residue evolution image sparse representation and classifier ensemble

Understanding the interactions between proteins and ligands is critical for protein function annotations and drug discovery. We report a new sequence‐based template‐free predictor (TargetATPsite) to identify the Adenosine‐5′‐triphosphate (ATP) binding sites with machine‐learning approaches. Two steps are implemented in TargetATPsite: binding residues and pockets predictions, respectively. To predict the binding residues, a novel image sparse representation technique is proposed to encode residue evolution information treated as the input features. An ensemble classifier constructed based on support vector machines (SVM) from multiple random under‐samplings is used as the prediction model, which is effective for dealing with imbalance phenomenon between the positive and negative training samples. Compared with the existing ATP‐specific sequence‐based predictors, TargetATPsite is featured by the second step of possessing the capability of further identifying the binding pockets from the predicted binding residues through a spatial clustering algorithm. Experimental results on three benchmark datasets demonstrate the efficacy of TargetATPsite. © 2013 Wiley Periodicals, Inc.     

Euphorbiane: A Novel Triterpenoid with an Unprecedented Skeleton from Euphorbia tirucalli

Euphorbiane ( 1 ), a novel triterpenoid exhibiting a unique skeleton, together with seven known compounds were isolated from the 95% EtOH extract of the fresh stems of Euphorbia tirucalli. The structure of 1 and relative stereochemistry were elucidated by extensive NMR and a single‐crystal X‐ray crystallographic analysis.     

Encapsulating Sulfur into Hierarchically Ordered Porous Carbon as a High‐Performance Cathode for Lithium–Sulfur Batteries

A three‐dimensional (3D) hierarchical carbon–sulfur nanocomposite that is useful as a high‐performance cathode for rechargeable lithium–sulfur batteries is reported. The 3D hierarchically ordered porous carbon (HOPC) with mesoporous walls and interconnected macropores was prepared by in situ self‐assembly of colloidal polymer and silica spheres with sucrose as the carbon source. The obtained porous carbon possesses a large specific surface area and pore volume with narrow mesopore size distribution, and acts as a host and conducting framework to contain highly dispersed elemental sulfur. Electrochemical tests reveal that the HOPC/S nanocomposite with well‐defined nanostructure delivers a high initial specific capacity up to 1193 mAh g^?1 and a stable capacity of 884 mAh g^?1 after 50 cycles at 0.1 C. In addition, the HOPC/S nanocomposite exhibits high reversible capacity at high rates. The excellent electrochemical performance is attributed exclusively to the beneficial integration of the mesopores for the electrochemical reaction and macropores for ion transport. The mesoporous walls of the HOPC act as solvent‐restricted reactors for the redox reaction of sulfur and aid in suppressing the diffusion of polysulfide species into the electrolyte. The “open” ordered interconnected macropores and windows facilitate transportation of electrolyte and solvated lithium ions during the charge/discharge process. These results show that nanostructured carbon with hierarchical pore distribution could be a promising scaffold for encapsulating sulfur to approach high specific capacity and energy density with long cycling performance.     

Dielectric Relaxations in Plasma-Polymerized Hydrocarbons and Fluorocarbons

The dielectric behavior of plasma-polymerized ethylene (PPE), ethylene/acetylene (PPEA), ethane/vinyl chloride (PPEVC) and tetrafluoroethylene (PPTFE) was studied over a frequency range of 10² to 10⁵ Hz between -150 and 100°C. After exposure to the atmosphere, each of the polymers exhibited a pronounced loss peak. This relaxation process was designated as the γ_pprocess, and was attributed to the local mode motion of several molecular segments. The average activation energy for all four polymers was found to be 13.8 kcal/mole. It was proposed that oxidation introduces carbonyl groups into the nonpolar polymer chain. The added polar carbonyl groups then act as tracers to render the molecular motions observable by dielectric measurements. The presence of these carbonyl groups was confirmed by concomitant IR spectroscopic determinations. Comparison of the experimental data with the Kirkwood-Froelich theory was found to be satisfactory.     

Synthesis and characterization of poly(2‐methacryloyloxyethyl phosphorylcholine) onto graphene oxide

The polyzwitterionic brushes comprised of poly(2‐methacryloyloxyethyl phosphorylcholine) (pMPC) segments, which are used for surface modification of polymers and biocompatible coatings, were investigated. In this work, reverse surface‐initiated atom transfer radical polymerization (RATRP) of zwitterionic 2‐methacryloyloxyethyl phosphorylcholine (MPC) is employed to tailor the functionality of graphene oxide (GeneO) in a well‐controlled manner and produce a series of well‐defined hemocompatible hybrids (termed as GeneO‐g‐pMPC). The complexes were characterized by FT‐IR, XRD, and Raman. Results show that MPC has been coordinated on the graphene oxide sheet. Thermal stability of the nanocomposites in comparison with the neat copolymer is revealed by thermogravimetric analysis and differential thermal analysis. Scanning electron microscopy and transmission electron microscope images of the nanoconposite displays pMPC chains were capable of existing on GeneO sheet by RATRP. The biocompatibility properties were measured by plasma recalcification profile tests, hemolysis test, and MTT assays, respectively. The results confirm that the pMPC grafting can substantially enhance the hemocompatibility of the GeneO particles, and the GeneO‐g‐pMPC hybrids can be used as biomaterials without causing any hemolysis. With the versatility of RATRP and the excellent hemocompatibility of zwitterionic polymer chains, the GeneO‐g‐pMPC nanoparticles with desirable blood properties can be readily tailored to cater to various biomedical applications. Copyright © 2013 John Wiley & Sons, Ltd.     

Influence of fluorinated substituent and terminal length on phase behavior of mesogen‐jacketed liquid crystalline polymers with a biphenyl mesogen

A series of mesogen‐jacketed liquid crystalline polymers, poly{2,2,3,3,4,4,4‐heptafluorobutyl 4′‐hydroxy‐2‐vinylbiphenyl‐4‐carboxylate} (PF3Cm, where m is the number of carbon atoms in the alkoxy groups, and m = 1, 4, 6, and 8), the side chain of which contains a biphenyl core with a fluorocarbon substituent at one end and an alkoxy unit of varying length on the other end, were designed and successfully synthesized via atom transfer radical polymerization. For comparison, poly{butyl 4′‐hydroxy‐2‐vinylbiphenyl‐4‐carboxylate} (PC4Cm), similar to PF3Cm but with a butyl group instead of the fluorocarbon substituent, was also prepared. Differential scanning calorimetric results reveal that the glass transition temperatures (T_gs) of the two series of polymers decrease as m increases and T_gs of the fluorocarbon‐substituted polymers are higher than those of the corresponding butyl‐substituted polymers. Wide‐angle X‐ray diffraction measurements show that the mesophase structures of these polymers are dependent on the number of the carbon atoms in the fluorocarbon substituent and the property of the other terminal substituent. Polymers with fluorocarbon substituents enter into columnar nematic phases when m ≥ 4, whereas the polymer PF3C1 exhibits no liquid crystallinity. For polymers with butyl substituents, columnar nematic phases form when the number of carbon atoms at both ends of the side chain is not equal at high temperatures and disappear after the polymers are cooled to ambient temperature. However, when the polymer has the same number of carbon atoms at both ends of the side chain, a hexagonal columnar phase develops, and this phase remains after the polymer is cooled. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2013     

Oxidant Effect of H2O2 for the Syntheses of Quinoline Derivatives via One-Pot Reaction of Aniline and Aldehyde

A convenient one-pot method for the synthesis of substituted quinolines via the reaction of aniline and aldehyde in the presence of a Lewis acid (AlCl₃) and an oxidant (H₂O₂) has been developed. Hydrogen peroxide was found to promote the reaction by its function as a hydrogen hunter, hindering the formation of by-product N-alkylaniline. The effect of the oxidant on the yield and selectivity was studied. When the molar ratio of aniline, n-butyraldehyde, and H₂O₂ was 1:3:0.5 at 25 °C, the yield of 3-ethyl-2-propylquinoline was improved from 64% (reaction without H₂O₂) to 84% (with H₂O₂), and the quinoline selectivity was improved to almost 100%. Moreover, the reaction time was obviously reduced. The substituent effect was also investigated in this work.     

Diastereo‐ and Enantioselective Synthesis of Organometallic Bis(helicene)s by a Combination of C?H Activation and Dynamic Isomerization

Homochiral and heterochiral cis‐bis‐cycloplatinated‐[6]helicene derivatives 1 b^{1, 2} , as representative examples of platina[6]helicenes that share a common platinum center, have been prepared. A diastereo‐ and enantioselective synthesis, which combines CH activation and dynamic isomerization from heterochiral structure 1 b² into homochiral structure 1 b¹ , is also described. Overall, this isomerization process results in the transfer of chiral information from one helicene moiety to the other one. The chiroptical properties of homochiral (P)‐ and (M)‐ 1 b¹ were greatly modified upon oxidation into their corresponding (P)‐ and (M)‐diiodo‐Pt^IV complexes ( 5 ). The changes were also analyzed by performing theoretical calculations. C? H activation in the synthesis of organometallic helicenes is further demonstrated by the preparation of cis‐bis‐cycloplatinated‐[8]helicene 1 c .     

Theoretical Study on the Hydrogen Bonding Interactions in Complexes of 5‐Hydroxytryptamine with Water

The energies, geometries and harmonic vibrational frequencies of 1:1 5‐hydroxytryptamine‐water (5‐HT‐H₂O) complexes are studied at the MP2/6‐311++G(d,p) level. Natural bond orbital (NBO), quantum theory of atoms in molecules (QTAIM) analyses and the localized molecular orbital energy decomposition analysis (LMO‐EDA) were performed to explore the nature of the hydrogen‐bonding interactions in these complexes. Various types of hydrogen bonds (H‐bonds) are formed in these 5‐HT‐H₂O complexes. The intermolecular C4H5^5‐HT···O^w H‐bond in HTW3 is strengthened due to the cooperativity, whereas no such cooperativity is found in the other 5‐HT‐H₂O complexes. H‐bond in which nitrogen atom of amino in 5‐HT acted as proton donors was stronger than other H‐bonds. Our researches show that the hydrogen bonding interaction plays a vital role on the relative stabilities of 5‐HT‐H₂O complexes.