Isolation and Immobilization of Influenza Virus-Specific N-SA-α-2,3-Gal Receptors Using Magnetic Nanoparticles Coated with Chitosan and Maackia amurensis Lectin

Avian influenza viruses preferentially bind to sialic acid alpha-2,3-galactose (N-SA-α-2,3-Gal) receptors on epithelial cells. Herein, we describe a procedure we have developed for isolation of N-SA-α-2,3-Gal receptors from porcine trachea using magnetic nanoparticles (NPs) coated with chitosan (NP-Ch) and functionalized with Maackia amurensis lectin (NP-lectin). Magnetic nanoparticles were coated with chitosan in a one-step co-precipitation, and then M. amurensis lectin was immobilized covalently using glutaraldehyde. Lectin coated nanoparticles were incubated with sialic acid enriched fraction of tracheal homogenate, and N-SA-α-2,3-Gal receptor was extracted under magnetic field in two cycles. The presence of 66.4 kDa protein was determined by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The interaction of immobilized receptor (NP-Ch-R) with M. amurensis lectin (NP-Ch-R-L) was demonstrated by Fourier transform infrared spectrometry (FTIR) and thermogravimetric analysis (TGA).     

Synthesis of polypyrrole nanoparticles by batch and semicontinuous heterophase polymerizations

Nanoparticles of semiconducting polypyrrole (PPy) were synthesized by batch heterophase (BHP) and semicontinuous heterophase polymerization (SHP) using ferric chloride (FeCl₃), potassium persulfate (KPS), or ammonium persulfate (APS) as the oxidizing agent, sodium dodecyl sulfate (SDS) as surfactant, and ethanol (EtOH) or iso-pentyl alcohol (iC₅OH) as co-surfactants. In all cases, the molar ratios of monomer/oxidizing agent were 1/1. Pyrrol polymerization by BHP and SHP allowed using much lower percentages of surfactant than those employed in microemulsion polymerization of this monomer. The effects of temperature, oxidizing agent, and co-surfactant on conductivity were studied. The polymers were analyzed by transmission electron microscopy (TEM), UV/Visible and Fourier transform infrared (FTIR) spectroscopies, and cyclic voltammetry. Higher PPy conductivities were obtained by polymerizing at 0 °C with FeCl₃ as the oxidizing agent, in the presence of iC₅OH as co-surfactant. When the reaction was carried out by SHP with low reaction times, smaller particles with similar conductivities were obtained compared to those obtained by BHP; the conductivity of PPy decreases with increasing polymerization time, which can be explained by PPy overoxidation.     

Switchable dielectric permittivity with temperature and Dc-bias in a semifluorinated azobenzene derivative

The thermodynamic, optical, structural, and dynamic properties of the semifluorinated (E)-1-(4-octylphenyl)-2-(4-(perfluorooctyl)phenyl)diazene (4) and the corresponding (E)-1,2-bis(4-octylphenyl)diazene (5) have been studied with differential scanning calorimetry, polarizing optical microscopy, X-ray diffraction, and dielectric spectroscopy. 4 combines the azobenzene properties with the fluorophobic effect and gives rise to a responsive material with a temperature and dc-bias-driven switchable dielectric permittivity within the narrower nematic phase. This is caused by the nematic potential that inevitably brings some fluorocarbon chains in proximity to the hydrocarbon chains from adjacent molecules. Frustration is alleviated by reducing the nematic-to-isotropic transition temperature and by increasing the crystalline-to-nematic transition temperature, thus limiting the stability of the nematic phase. Unlike the normal isotropic phase of compound 5, the isotropic phase of compound 4 contains dipoles with short-range orientation correlations. Optimizing the type of interactions may result in materials with applications as molecular switches and electrooptic devices.     

Electro-Mechanochemical Atom Transfer Radical Cyclizations using Piezoelectric BaTiO3

The formation and regeneration of active Cu^I species is a fundamental mechanistic step in copper-catalyzed atom transfer radical cyclizations (ATRC). Typically, the presence of the catalytically active Cu^I species in the reaction mixture is secured by using high Cu^I catalyst loadings or the addition of complementary reducing agents. In this study it is demonstrated how the piezoelectric properties of barium titanate (BaTiO₃) can be harnessed by mechanical ball milling to induce electrical polarization in the strained piezomaterial. This strategy enables the conversion of mechanical energy into electrical energy, leading to the reduction of a Cu^II precatalyst into the active Cu^I species in copper-catalyzed mechanochemical solvent-free ATRC reactions.     

On-Surface Synthesis of Cumulene-Containing Polymers via Two-Step Dehalogenative Homocoupling of Dibromomethylene-Functionalized Tribenzoazulene

Cumulene compounds are notoriously difficult to prepare and study because their reactivity increases dramatically with the increasing number of consecutive double bonds. In this respect, the emerging field of on-surface synthesis provides exceptional opportunities because it relies on reactions on clean metal substrates under well-controlled ultrahigh-vacuum conditions. Here we report the on-surface synthesis of a polymer linked by cumulene-like bonds on a Au(111) surface via sequential thermally activated dehalogenative C−C coupling of a tribenzoazulene precursor equipped with two dibromomethylene groups. The structure and electronic properties of the resulting polymer with cumulene-like pentagon–pentagon and heptagon–heptagon connections have been investigated by means of scanning probe microscopy and spectroscopy methods and X-ray photoelectron spectroscopy, complemented by density functional theory calculations. Our results provide perspectives for the on-surface synthesis of cumulene-containing compounds, as well as protocols relevant to the stepwise fabrication of carbon–carbon bonds on surfaces.     

Tandem Photoredox Catalysis: Enabling Carbonylative Amidation of Aryl and Alkylhalides

We report a new visible-light-mediated carbonylative amidation of aryl, heteroaryl, and alkyl halides. A tandem catalytic cycle of [Ir(ppy)₂(dtb-bpy)]⁺ generates a potent iridium photoreductant through a second catalytic cycle in the presence of DIPEA, which productively engages aryl bromides, iodides, and even chlorides as well as primary, secondary, and tertiary alkyl iodides. The versatile in situ generated catalyst is compatible with aliphatic and aromatic amines, shows high functional-group tolerance, and enables the late-stage amidation of complex natural products.     

Direct Derivation of Free Energies of Membrane Deformation and Other Solvent Density Variations From Enhanced Sampling Molecular Dynamics

We report a methodology to calculate the free energy of a shape transformation in a lipid membrane directly from a molecular dynamics simulation. The bilayer need not be homogeneous or symmetric and can be atomically detailed or coarse grained. The method is based on a collective variable that quantifies the similarity between the membrane and a set of predefined density distributions. Enhanced sampling of this “Multi-Map” variable re-shapes the bilayer and permits the derivation of the corresponding potential of mean force. Calculated energies thus reflect the dynamic interplay of atoms and molecules, rather than postulated effects. Evaluation of deformations of different shape, amplitude, and range demonstrates that the macroscopic bending modulus assumed by the Helfrich–Canham model is increasingly unsuitable below the 100-Å scale. In this range of major biological significance, direct free-energy calculations reveal a much greater plasticity. We also quantify the stiffening effect of cholesterol on bilayers of different composition and compare with experiments. Lastly, we illustrate how this approach facilitates analysis of other solvent reorganization processes, such as hydrophobic hydration. Published 2019. This article is a U.S. Government work and is in the public domain in the USA.     

Distributed and multicore QuBiLS-MIDAS software v2.0: Computing chiral,fuzzy, weighted and truncated geometrical molecular descriptors based on tensor algebra

Advances to the distributed, multi-core and fully cross-platform QuBiLS-MIDAS software v2.0 ( http://tomocomd.com/qubils-midas ) are reported in this article since the v1.0 release. The QuBiLS-MIDAS software is the only one that computes atom-pair and alignment-free geometrical MDs (3D-MDs) from several distance metrics other than the Euclidean distance, as well as alignment-free 3D-MDs that codify structural information regarding the relations among three and four atoms of a molecule. The most recent features added to the QuBiLS-MIDAS software v2.0 are related (a) to the calculation of atomic weightings from indices based on the vertex-degree invariant (e.g., Alikhanidi index); (b) to consider central chirality during the molecular encoding; (c) to use measures based on clustering methods and statistical functions to codify structural information among more than two atoms; (d) to the use of a novel method based on fuzzy membership functions to spherically truncate inter-atomic relations; and (e) to the use of weighted and fuzzy aggregation operators to compute global 3D-MDs according to the importance and/or interrelation of the atoms of a molecule during the molecular encoding. Moreover, a novel module to compute QuBiLS-MIDAS 3D-MDs from their headings was also developed. This module can be used either by the graphical user interface or by means of the software library. By using the library, both the predictive models built with the QuBiLS-MIDAS 3D-MDs and the QuBiLS-MIDAS 3D-MDs calculation can be embedded in other tools. A set of predefined QuBiLS-MIDAS 3D-MDs with high information content and low redundancy on a set comprised of 20,469 compounds is also provided to be employed in further cheminformatics tasks. This set of predefined 3D-MDs evidenced better performance than all the universe of Dragon (v5.5) and PaDEL 0D-to-3D MDs in variability studies, whereas a linear independence study proved that these QuBiLS-MIDAS 3D-MDs codify chemical information orthogonal to the Dragon 0D-to-3D MDs. This set of predefined 3D-MDs would be periodically updated as long as new results be achieved. In general, this report highlights our continued efforts to provide a better tool for a most suitable characterization of compounds, and in this way, to contribute to obtaining better outcomes in future applications.     

On the strength of hydrogen bonding within water clusters on the coordination limit

Hydrogen bonds (HB) are arguably the most important noncovalent interactions in chemistry. We study herein how differences in connectivity alter the strength of HBs within water clusters of different sizes. We used for this purpose the interacting quantum atoms energy partition, which allows for the quantification of HB formation energies within a molecular cluster. We could expand our previously reported hierarchy of HB strength in these systems (Phys. Chem. Chem. Phys., 2016, 18 , 19557) to include tetracoordinated monomers. Surprisingly, the HBs between tetracoordinated water molecules are not the strongest HBs despite the widespread occurrence of these motifs (e.g., in ice I_h). The strongest HBs within H₂O clusters involve tricoordinated monomers. Nonetheless, HB tetracoordination is preferred in large water clusters because (a) it reduces HB anticooperativity associated with double HB donors and acceptors and (b) it results in a larger number of favorable interactions in the system. Finally, we also discuss (a) the importance of exchange-correlation to discriminate among the different examined types of HBs within H₂O clusters, (b) the use of the above-mentioned scale to quickly assess the relative stability of different isomers of a given water cluster, and (c) how the findings of this research can be exploited to indagate about the formation of polymorphs in crystallography. Overall, we expect that this investigation will provide valuable insights into the subtle interplay of tri- and tetracoordination in HB donors and acceptors as well as the ensuing interaction energies within H₂O clusters.