Metal-complex assemblies constructed from the flexible hinge-like ligand H2bhnq: structural versatility and dynamic behavior in the solid state

Novel metal-complex assemblies constructed from the flexible hinge-like ligand H(2)bhnq (H(2)bhnq=2,2'-bi(3-hydroxy-1,4-naphthoquinone)) have been synthesized. The X-ray crystal structures of these compounds reveal that four types of architectures are accessible by variation of the metal ions. In copper(II) compounds 1-3, the chelating bhnq(2-) ions bridge copper(II) centers to form one-dimensional zigzag chains. The chains of 1-3 are arranged by hydrogen-bonding interactions and stacking interactions to produce porous structures. Cobalt(II) and zinc(II) compounds 4 and 5 form one-dimensional helical chains. In 4 and 5, the crystal packing induces spontaneous resolution of the helical chains with chiral cavities formed perpendicular to the helices. Nickel(II) compounds 6 and 7 form cyclic tetramers. The fourth architecture, a dimer (compound 8), is obtained by the reaction of zinc(II) and bhnq(2-) in MeOH. In these compounds, changes of the dihedral angles and the metal-coordination mode of the bhnq(2-) ion induce the structural versatility. The assemblies of the zigzag chains of the copper(II) compounds exhibit reversible vapochromic behavior. UV/Vis, powder X-ray diffraction, EPR, and adsorption isotherm measurements indicate that this vapochromic behavior is based on the hinge-like flexibility of the bhnq(2-) ion.     

Molecular structure of glucopyranosylamide lipid and nanotube morphology

A series of glucopyranosylamide lipids, N-(X-octadecenoyl)-beta-D-glucopyranosylamine [X = 13-cis (1), 11-cis (2), 9-cis (3), 6-cis (4), and 9-cis,12-cis (5)] and their saturated homologue N-octadecanoyl-beta-d-glucopyranosylamine (6), which differ in the position of a cis double bond in the C18 hydrocarbon chains, have been synthesized. The effect of the cis double bond position on the chiral self-assembly of each glycolipid has been examined by scanning electron microscopy, transmission electron microscopy, X-ray diffraction, UV, and circular dichroism (CD). The 11-cis derivative 2 was observed to self-assemble in water to form a uniform hollow cylinder structure with about 200-nm outer diameters in >98% yields. The obtained nanotubes from 2 showed the narrowest distribution of outer diameters and also gave a negative CD band around 234-236 nm, showing the largest CD intensity among the glycolipids investigated. Thus, we found that the position of a cis double bond significantly influences the homogeneity of the outer diameters as well as growth behavior of the self-assembled nanotube structures. Chiral molecular packing driven by a possible bending structure of the unsaturated glycolipids is playing a critical role in determining tubular morphology through molecular self-assembly.     

Preparation and Crystal Structures of 4-(4′-Pyridylthio)-1-methylpyridinium Salts: Assembly of a Donor-Acceptor-Type Molecule Containing a Sulfide Bridge

A series of ionic 4-(4′-pyridylthio)-1-methylpyridinium salts with different counteranions (1, I⁻; 2, BF⁻₄; 3, PF⁻₆; and 4, OTf⁻, where OTf=trifluoromethanesulfonate) have been prepared. Structural analysis reveals that the cation exhibits a variety of stacking structures dependent on the anion. Compound 1 crystallizes in space group P2_1/n (#14), with a=10.764(3) Å, b=9.601(5) Å, c=13.105(3) Å, β=108.35(2), V=1285.4(8) ų, and Z=4. In this compound, each cation moiety is stacked in a helical arrangement along the c-axis. Compound 2, which is isomorphous to 1, has space group P2_1/n (#14), with a=11.647(2) Å, b=9.203(3) Å, c=13.232(2) Å, β=108.42(2), V=1345.6(5) ų, and Z=4. Compound 3 crystallizes in space group P2_1/n (#14), with a=8.06(1) Å, b=17.43(1) Å, c=10.30(1) Å, β=103.0(1), V=1410(3) ų, and Z=4. In this salt, the cation molecules assume a head-to-tail stacking arrangement, forming a polar pseudo 1-D chain. Compound 4 crystallizes in space group Pb? (#2), with a=7.585(4) Å, b=15.443(7) Å, c=6.775(4) Å, α=99.33(4), β=108.35(2)^o, γ=98.37(4), V=756.6(7) ų, and Z=2. The structure of 4 consists of a columnar stacking of pyridine moieties, with the cation moieties surrounded by the counteranions. Calculations show that the 4-(4′-pyridylthio)-1-methylpyridinium cation may be a good building block for second harmonic generation (SHG) materials, even though salts 1-4 crystallized in centrosymmetric structures and were SHG inactive.     

Modes of conformational changes of proteins adsorbed on a planar hydrophobic polymer surface reflecting their adsorption behaviors

Infrared spectra of hen egg white lysozyme and bovine serum albumin (BSA) adsorbed on a solid poly tris(trimethylsiloxy)silylstyrene (pTSS) surface in D2O solution were measured using attenuated total reflection (ATR) Fourier transform infrared spectroscopy. From the area and shape of the amide I' band of each spectrum, the adsorption amount and the secondary structure were determined simultaneously, as a function of adsorption time. We could show that the average conformation for all the adsorbed lysozyme molecules was solely determined by the adsorption time, and independent of the bulk concentration, while the adsorption amount increased with the bulk concentration as well as the adsorption time. These results suggest that lysozyme molecules form discrete assemblies on the surface, and that the surface assemblies grow over several hours to have a definite architecture independent of the adsorption amount. As for BSA, the extent of the conformational change was solely determined by the adsorption amount, regardless of the bulk concentration and the adsorption time. These differences in the adsorption properties of lysozyme and BSA may reflect differences in their conformational stabilities.     

Small angle X-ray scattering from lamellar phase for β-3,7-dimethyloctylglucoside/water system: comparison with β-n-alkylglucosides

Small angle X-ray scattering (SAXS) is measured for the lamellar phase in aqueous systems of 1-o-β-3,7-dimethyoctyl-D-glucopyranoside (β-Glc(Ger)), which has recently been prepared by us, 1-o-β-decyl-D-glucopyranoside (β-GlcC₁₀), and 1-o-β-octyl-D-glucopyranoside (β-GlcC₈). The repeat distance d obtained from the position of the diffraction peak does not follow the swelling law d = 2δ_hc/_hc, where δ_hc and _hc are the thickness and the volume fraction of the hydrophobic layer, respectively. This may result from the fact that δ_hc increases and, equivalently, the surface area per surfactant molecule (a_s) decreases with increasing concentration. So we calculate δ_hc and a_s from the observed d value at each concentration using the above swelling law. The half-thickness δ_hc increases in the order β-GlcC₈ < β-Glc(Ger) < β-GlcC₁₀ at a fixed concentration. On the other hand, the data on a_s for β-GlcC₁₀ and β-GlcC₈ lie on the same line and the data for β-Glc(Ger) lies above this line. These results suggest that the cross-sectional area of the geranyl chain is larger than that of the glucose headgroup. Existence of water filled defects in bilayer sheets is also discussed based on the SAXS pattern and the concentration dependence of d.     

Asymmetric Hydroformylation of Vinylfurans Catalyzed by {(11bS)‐4‐{[(1R)‐2′‐Phosphino[1,1′‐binaphthalen]‐2‐yl]oxy}dinaphtho[2,1‐d:1′,2′‐f]‐ [1,3,2]dioxaphosphepin}rhodium(I) [RhI{(R,S)‐binaphos}] Derivatives

The asymmetric hydroformylation of 2‐ and 3‐vinylfurans ( 2a and 2b , resp.) was investigated by using [Rh{(R,S)‐binaphos}] complexes as catalysts ((R,S)‐binaphos = (11bS)‐4‐{[1R)‐2′‐phosphino[1,1′‐binaphthalen]‐2‐yl]oxy}dinaphtho[2,1‐d:1′,2′‐f][1,3,2]dioxaphosphepin; 1 ). Hydroformylation of 2 gave isoaldehydes 3 in high regio‐ and enantioselectivities (Scheme 2 and Table). Reduction of the aldehydes 3 with NaBH₄ successfully afforded the corresponding alcohols 5 without loss of enantiomeric purity (Scheme 3).     

Single-Round DNA Aptamer Selection by Combined Use of Capillary Electrophoresis and Next Generation Sequencing: An Aptaomics Approach for Identifying Unique Functional Protein-Binding DNA Aptamers

In DNA aptamer selection, existing methods do not discriminate aptamer sequences based on their binding affinity and function and the reproducibility of the selection is often poor, even for the selection of well-known aptamers like those that bind the commonly used model protein thrombin. In the present study, a novel single-round selection method (SR-CE selection) was developed by combining capillary electrophoresis (CE) with next generation sequencing. Using SR-CE selection, a successful semi-quantitative and semi-comprehensive aptamer selection for thrombin was demonstrated with high reproducibility for the first time. Selection rules based on dissociation equilibria and kinetics were devised to obtain families of analogous sequences. Selected sequences of the same family were shown to bind thrombin with high affinity. Furthermore, data acquired from SR-CE selection was mined by creating sub-libraries that were categorized by the functionality of the aptamers (e. g., pre-organized aptamers versus structure-induced aptamers). Using this approach, a novel fluorescent molecular recognition sensor for thrombin with nanomolar detection limits was discovered. Thus, in this proof-of-concept report, we have demonstrated the potential of a “DNA Aptaomics” approach to systematically design functional aptamers as well as to obtain high affinity aptamers.     

Polymerization-induced self-assembly of amino-acid-based nano-objects by reversible addition–fragmentation chain-transfer dispersion polymerization

A series of amino-acid-based amphiphilic diblock copolymer nano-objects having different morphologies were developed by reversible addition–fragmentation chain-transfer (RAFT) dispersion polymerization of styrene (St) in methanol. This was mediated by six different hydrophilic poly(N-acryloyl amino acid) macro-chain transfer agents (CTAs), including three carboxylic-acid-containing ones, poly(N-acryloyl-l -proline) (PAProOH), poly(N-acryloyl-4-trans-hydroxy-l -proline) (PAHypOH), and poly(N-acryloyl-l -threonine) (PAThrOH) prepared by RAFT polymerization, and their methyl ester forms, PAProOMe, PAHypOMe, and PAThrOMe. The effects of polymerization conditions on RAFT dispersion polymerization of St using a dithiocarbamate-terminated PAProOH was investigated. A systematic study of the effects of monomer conversion and concentration afforded the formation of various morphologies (i.e., spheres, worms, and vesicles). The effects of hydrogen-bonding and ionic interactions of the macro-CTAs on the assembled structures of the nano-objects were evaluated using six different macro-CTAs. Transforming the products from methanol to water via dialysis produced amino-acid-based block copolymer nano-objects, exhibiting pH-responsive morphological change, in aqueous solution.     

Design of a tripartite network for the prediction of drug targets

Drug-target networks have aided in many target prediction studies aiming at drug repurposing or the analysis of side effects. Conventional drug-target networks are bipartite. They contain two different types of nodes representing drugs and targets, respectively, and edges indicating pairwise drug-target interactions. In this work, we introduce a tripartite network consisting of drugs, other bioactive compounds, and targets from different sources. On the basis of analog relationships captured in the network and so-called neighbor targets of drugs, new drug targets can be inferred. The tripartite network was found to have a stable structure and simulated network growth was accompanied by a steady increase in assortativity, reflecting increasing correlation between degrees of connected nodes leading to even network connectivity. Local drug environments in the tripartite network typically contained neighbor targets and revealed interesting drug-compound-target relationships for further analysis. Candidate targets were prioritized. The tripartite network design extends standard drug-target networks and provides additional opportunities for drug target prediction.