Tripodal borate ligands from tris(dimethylamino)borane: the first synthesis of a chiral tris(methimazolyl)borate ligand, and the crystal structure of a single diastereomer pseudo-C3-symmetric Ru(II) complex

The activation of tris(dimethylamino)borane towards reaction with a chiral methimazole by N-methylimidazole has been used to prepare the first example of a chiral tris(methimazolyl)borate ligand. Coordination of this neutral ligand to Ru(II) has been achieved by reaction with [(p-cymene)RuCl(2)](2) to provide a single diastereomer complex in which the chirality of the methimazolyl substituents dictate the chirality of the bicyclo[3.3.3]cage formed by the ligand on coordination to the metal. The alternative approach to chiral tris(methimazolyl)borate ligands involving the introduction of a chiral group onto the boron atom has been explored by replacing N-methylimidazole in the above reaction by chiral oxazolines as activating bases in reaction with simple methimazole. However, although the B(NMe(2))(3) is activated to reaction with methimazole by these oxazolines, an intramolecular oxazoline ring-opening by a coordinated methimazolyl sulfur occurs and prevents the successful synthesis of these ligands.     

Improved short-lived nuclide activation analysis

A novel technique has been developed to increase the sensitivity, precision and accuracy of short-lived nuclide activation analysis and especially of delayed fission neutron counting, by improving the counting statistics. This has been achieved by approaching the irradiated sample to the detector during the counting period in order to compensate for the rapid radioactive decay by variation of the counting efficiency, permitting prolongation of the counting period with constant count rate. The sample holder movement with approximately exponentially decreasing velocity is implemented by a variable DC motor with a rotary to linear movement converter, which is being replaced by a more reliable stepping motor.     

Highly efficient synthesis of linear pyrrole oligomers by twofold Heck reactions

The twofold Heck reaction of the vinylpyrroles 3a and 3b with the iodobenzenes 4a-c led to the linear pyrrole oligomers 5, 6, and 7. The synthesis of both symmetrical and unsymmetrical oligomers, such as 10a and 10b, was also accomplished by a Heck reaction of 8 and 9 and by a Heck reaction of 3a and 11 followed by a Wittig reaction and a second Heck reaction with 8. The pentacyclic oligomers 14 and 19 were prepared by a twofold Heck reaction of 13 with 4 and by a twofold Heck reaction of 15 with 16 followed by a Wittig reaction and a twofold Heck reaction with 8.     

Chemical modification of the surface of a sulfonated membrane by formation of a sulfonamide bond

This paper describes a novel approach for the surface modification of a cation-exchange membrane, bearing sulfonate groups, by a cationic layer. The modification procedure involved the chlorosulfonation of the sulfonate groups of the base membrane with thionyl chloride, followed by a reaction with a diamine to yield a sulfonamide bond and a terminal amine. The latter could be quaternized by reaction with methyl iodide or protonated by soaking in acidic media. The membranes were characterized in detail by attenuated total reflectance Fourier transform infrared and X-ray photoelectron spectroscopies as well as elemental analysis to confirm that the above reactions occurred. The selectivity of these membranes toward the electrochemically assisted transport of protons versus Zn2+ metallic cations was determined during an electrodialysis in a two-compartment electrochemical cell. The data indicate a significant decrease of the transport of the metallic cations following modification of the membrane with the cationic layer. The later allows for the transport of protons from the catholyte to the anolyte compartment with much improved selectivity since the divalent cations are excluded from the membrane due to the electrostatic barrier of the cationic layer.     

Electron-triggered motions in technomimetic molecules

Technomimetic molecules are molecules designed to imitate macroscopic objects at the molecular level, also transposing the motions that these objects are able to undergo. This article focuses on technomimetic molecules with motions triggered by electrons. The first part is devoted to our work in the field of molecular switches: after having demonstrated the possibility of controlling an intramolecular electron transfer by photoisomerisation, we are now trying to control the isomerisation, either by electrochemistry, or by embedding the photochromic compound in a self-assembled monolayer and testing the electrical conduction with a STM tip. In a second part, we present our strategy on controlling the rotation in a molecular rotary motor and the family of ruthenium complexes designed to perform such a task. The molecules have a piano-stool structure with a "stator" meant to be grafted on an oxide surface, and a "rotor" bearing redox-active groups, so that addressing the molecule with nano-electrodes would trigger rotation. The electrical control of the charge state of a molecule by a STM tip is developed in a final part.     

Photochemical micropatterning of carbohydrates on a surface

In this report, we demonstrate a versatile method for the immobilization and patterning of unmodified carbohydrates onto glass substrates. The method employs a novel self-assembled monolayer to present photoactive phthalimide chromophores at the air-monolayer interface. Upon exposure to UV radiation, the phthalimide end-groups graft to surface-adsorbed carbohydrates, presumably by a hydrogen abstraction mechanism followed by radical recombination to form a covalent bond. Immobilized carbohydrate thin films are evidenced by fluorescence, ellipsometry and contact-angle measurements. Surface micropatterns of mono-, oligo-, and polysaccharides are generated by exposure through a contact photomask and are visualized by condensing water onto the surface. The efficiency of covalent coupling is dependent on the thermodynamic state of the surface. The amount of surface-grafted carbohydrate is enhanced when carbohydrate surface interactions are increased by the incorporation of amine-terminated molecules into the monolayer. Glass substrates modified with mixed monolayers of this nature are used to construct carbohydrate microarrays by spotting the carbohydrates with a robot and subsequently illuminating them with UV light to covalently link the carbohydrates. Surface-immobilized polysaccharides display well-defined antigenic determinants for antibody recognition. We demonstrate, therefore, that this novel technology combines the ability to create carbohydrate microarrays using the current state-of-the-art technology of robotic microspotting and the ability to control the shape of immobilized carbohydrate patterns with a spatial resolution defined by the UV wavelength and a shape defined by a photomask.     

On the shape of a hydrostatic meniscus attached to a corrugated plate or wavy cylinder

The shape of a hydrostatic meniscus attached at a fixed contact angle to a vertical plate or circular cylinder with periodic corrugations is studied by analytical and numerical methods, and the effect of wall irregularities on the shape of the contact line and vertical component of the capillary force is discussed. An asymptotic analysis for a plate with small-amplitude sinusoidal corrugations is carried out to first order with respect to the corrugation amplitude, and a boundary-value problem is formulated and solved by a shooting method to determine the meniscus shape and elevation of the contact line. The meniscus attached to a corrugated plate with rounded corners produced by a Schwarz-Christoffel mapping function for a triangular wave is considered by numerical methods. The Laplace-Young equation determining the meniscus shape is solved in orthogonal curvilinear coordinates generated by conformal mapping using a finite-difference method. The numerical results are successfully compared with the predictions of the perturbation expansion for small amplitudes and discussed with reference to the rise of a meniscus inside a dihedral angle for large amplitudes. A companion asymptotic analysis is presented for a meniscus outside a vertical circular cylinder with small-amplitude sinusoidal corrugations. The analytical predictions are successfully compared with numerical solutions of the Laplace-Young equation for a meniscus outside an elliptical cylinder with aspect ratio near unity, regarded as a deformed circle.     

Cationic oligonucleotide-peptide conjugates with aggregating properties enter efficiently into cells while maintaining hybridization properties and enzymatic recognition

Oligonucleotide delivery is a crucial issue for therapeutical purposes and is often addressed by conjugation to short cationic peptides although with controversial results. To further examine this mechanism, a 15-mer anionic oligonucleotide was conjugated to a cationic peptide in order to obtain a diblock compound with an overall positive charge with aggregation properties. These microaggregates were efficiently internalized in cells via the expeditious pathway used by commercial gene delivery systems. Moreover, stability of the duplex formed with the complementary sequence increased without inhibiting oligonucleotide enzyme recognition as shown by the properties of the conjugate to prime chain elongation by Taq DNA polymerase in a linear amplification/sequencing process.     

Models for Oscillating Polymerization: Activation by Product in a System with Flow

In this work, four polymerization mechanisms with flow are proposed where sustained oscillation can be present: (1) Polyaddition initiated by radicals produced by initiator decomposition, which is catalyzed by the polymer, first‐order termination, a polymer disappears by a reaction with a third substance and by leaving the system in the exit flow. (2) Polycondensation where the polymer has catalytic activity upon H to produce a monomer, first‐order termination and a monomer disappears by a reaction with a third substance, and there is exit flow for all the species. (3) Polycondensation with catalytic activity of the polymer upon A to produce a monomer, first‐order termination, conformational transitions of the polymers, one of the polymer conformations disappears by a reaction with a monomer and exit flow for all the species. (4) Polycondensation combined with polyaddition where the polycondensation polymer product has catalytic activity on the monomer, first‐order termination and exit flow of all the species.     

Simulation-aided design and synthesis of hierarchically porous membranes

Free-standing silica membranes with hierarchical porosity (ca. 300 nm macropores surrounded by 6-8 nm mesopores) and controllable mesopore architecture were prepared by a dual-templating method, with the structural design aided by mesoscale simulation. To create a two-dimensional, hexagonal macropore array, polymeric colloidal hemisphere arrays were synthesized by a two-step annealing process starting with non-close-packed polystyrene sphere arrays on silicon coated with a sacrificial alumina layer. A silica precursor containing a poly(ethylene) oxide-poly(propylene oxide)-poly(ethylene) oxide (PEO-PPO-PEO) triblock-copolymer surfactant as template for mesopore creation was spin-coated onto the support and aged and then converted into the free-standing membranes by dissolving both templates and the alumina layer. To test the hypothesis that the mesopore architecture may be influenced by confinement of the surfactant-containing precursor solution in the colloidal array and by its interactions with the polymeric colloids, the system was studied theoretically by dissipative particle dynamics (DPD) simulations and experimentally by examining the pore structures of silica membranes via electron microscopy. The DPD simulations demonstrated that, while only tilted columnar structure can be formed through tuning the interaction with the substrate, perfect alignment of 2D hexagonal micelles perpendicular to the plane of the membrane is achievable by confinement between parallel walls that interact preferentially with the hydrophilic components (PEO blocks, silicate, and solvent). The simulations predicted that this alignment could be maintained across a span of up to 10 columns of micelles, the same length scale defined by the colloidal array. In the actual membranes, we manipulated the mesopore alignment by tuning the solvent polarity relative to the polar surface characteristics of the colloidal hemispheres. With methanol as a solvent, columnar mesopores parallel to the substrate were observed; with a methanol-water mixed solvent, individual spherical mesopores were present; and with water as the only solvent, twisted columnar structures were seen.     

Role of binding entropy in the refinement of protein-ligand docking predictions: analysis based on the use of 11 scoring functions

We present results of testing the ability of eleven popular scoring functions to predict native docked positions using a recently developed method (Ruvinsky and Kozintsev, J Comput Chem 2005, 26, 1089) for estimation the entropy contributions of relative motions to protein-ligand binding affinity. The method is based on the integration of the configurational integral over clusters obtained from multiple docked positions. We use a test set of 100 PDB protein-ligand complexes and ensembles of 101 docked positions generated by (Wang et al. J Med Chem 2003, 46, 2287) for each ligand in the test set. To test the suggested method we compared the averaged root-mean square deviations (RMSD) of the top-scored ligand docked positions, accounting and not accounting for entropy contributions, relative to the experimentally determined positions. We demonstrate that the method increases docking accuracy by 10-21% when used in conjunction with the AutoDock scoring function, by 2-25% with G-Score, by 7-41% with D-Score, by 0-8% with LigScore, by 1-6% with PLP, by 0-12% with LUDI, by 2-8% with F-Score, by 7-29% with ChemScore, by 0-9% with X-Score, by 2-19% with PMF, and by 1-7% with DrugScore. We also compared the performance of the suggested method with the method based on ranking by cluster occupancy only. We analyze how the choice of a clustering-RMSD and a low bound of dense clusters impacts on docking accuracy of the scoring methods. We derive optimal intervals of the clustering-RMSD for 11 scoring functions.     

Integration of capillary isoelectric focusing with monolithic immobilized pH gradient,immobilized trypsin microreactor and capillary zone electrophoresis for on‐line protein analysis

An integrated platform consisting of protein separation by CIEF with monolithic immobilized pH gradient (M‐IPG), on‐line digestion by trypsin‐based immobilized enzyme microreactor (trypsin‐IMER), and peptide separation by CZE was established. In such a platform, a tee unit was used not only to connect M‐IPG CIEF column and trypsin‐IMER, but also to supply adjustment buffer to improve the compatibility of protein separation and digestion. Another interface was made by a Teflon tube with a nick to couple IMER and CZE via a short capillary, which was immerged in a centrifuge tube filled with 20 mmol/L glutamic acid, to exchange protein digests buffer and keep electric contact for peptide separation. By such a platform, under the optimal conditions, a mixture of ribonuclease A, myoglobin and BSA was separated into 12 fractions by M‐IPG CIEF, followed by on‐line digestion by trypsin‐IMER and peptide separation by CZE. Many peaks of tryptic peptides, corresponding to different proteins, were observed with high UV signals, indicating the excellent performance of such an integrated system. We hope that the CE‐based on‐line platform developed herein would provide another powerful alternative for an integrated analysis of proteins.     

Enhanced melanin fluorescence by stepwise three-photon excitation

The fluorescence of eumelanin (from Sepia officinalis and black human hair) was activated and enhanced by almost three orders of magnitude by exposure to near-infrared radiation. No activation or enhanced emission was observed when the samples were heated up to 100°C. The near-infrared irradiation caused obvious changes to the eumelanin and could be seen by fluorescence and bright field imaging. The area of enhanced emission appeared to originate from a region with changes in the morphology of the eumelanin's granule and increased with exposure time. At least two different components with enhanced fluorescence were activated and could be distinguished by their excitation properties. One component could be excited efficiently with wavelengths in the visible region and exhibited linear absorption dependence with respect to the laser power level. The second component could be excited efficiently using near-infrared wavelengths by a nonlinear process and exhibited a third-order dependence on the excitation. The third-order dependence is explained by a step-wise excited-state absorption process since the same third-order dependence was present when either continuous wave or femtosecond pulsed laser, with similar average-power levels, was used.     

Use of ionic polymers as stationary and pseudo-stationary phases in the separation of ions by capillary electrophoresis and capillary electrochromatography

One of the problems with capillary electrophoresis is a lack of versatility regarding manipulation of the separation selectivity. A new and potentially universal concept is to introduce an ion-exchange component into a separation so that the migration of analyte ions is influenced by both their electrophoretic mobilities and their chromatographic properties. This may be accomplished by use of capillaries filled with or coated with solid ion-exchange polymers, or by addition of a soluble ionic polymer to the background electrolyte to create a pseudo-stationary phase. While each of these methods achieves the same result, they are not competitive, but rather complementary as the problems associated by one approach are overcome by the others. Recent highlights in the field are used to illustrate the flexibility that this approach provides to electrophoretic separation of ions.     

Conversion of a metastable superhydrophobic surface to an ultraphobic surface

Superhydrophobic surfaces in Wenzel and metastable wetting state were prepared and the conversion of such surfaces to ultraphobic surfaces was reported by the application of a fine-scale roughness. Silicon nitride substrates with hexagonally arranged pillars were prepared by micromachining. The two-scale roughness was achieved by coating these substrates with 60 nm silica nanoparticles. The surface was made hydrophobic by silanization with octadecytrichlorosilane (OTS). Wettability studies of the silicon nitride flat surface, silicon nitride pillars, and the surfaces with two-scale roughness showed that a two-scale roughness can effectively improve the hydrophobicity of surfaces with a higher apparent contact angle and reduced contact angle hysteresis when the original rough surface was in a metastable or Wenzel state. This study shows the pathway of converting a metastable hydrophobic surface to an ultraphobic surface by the introduction of a fine-scale roughness, which adds to the literature a new aspect of fine-scale roughness effect.     

Development of high-temperature pulsed slit nozzle and its application to supersonic jet absorption spectrometry

A high-temperature pulsed slit nozzle, consisting of a circular pulsed nozzle and an interface to convert a circular flow into a slit flow has been constructed. The absorption spectrum is measured by scanning the wavelength of the monochromator equipped with a xenon arc lamp and by detecting the transmitted light through a jet with a photomultiplier. A rotationally cooled spectrum is clearly observed for aniline only when a long slit nozzle is employed. The absorptivity increases proportionally to the slit length at least up to 6 cm. The time for recording a spectrum is 3.5 min, which is reduced to several seconds by transmitting a white light through a jet and by measuring the spectrum with an optical multichannel analyzer. The detection limit is estimated to a partial vapor pressure of 0.4 torr for aniline. The present system can be conveniently used in routine analysis, because of a wide spectral coverage of the lamp source.     

Gold(I)-catalyzed intramolecular [4+2] cycloadditions of arylalkynes or 1,3-enynes with alkenes: scope and mechanism

The cyclizations of enynes substituted at the alkyne gives products of formal [4+2] cyclization with Au(I) catalysts. 1,8-Dien-3-ynes cyclize by a 5-exo-dig pathway to form hydrindanes. 1,6-Enynes with an aryl ring at the alkyne give 2,3,9,9a-tetrahydro-1H-cyclopenta[b]naphthalenes by a 5-exo-dig cyclization followed by a Friedel-Crafts-type ring expansion. A 6-endo-dig cyclization is also observed in some cases as a minor process, although in a few cases, this is the major cyclization pathway. In addition to cationic gold complexes bearing bulky biphenyl phosphines, a gold complex with tris(2,6-di-tert-butylphenyl)phosphite is exceptionally reactive as a catalyst for this reaction. This cyclization can also be carried out very efficiently with heating under microwave irradiation. DFT calculations support a stepwise mechanism for the cycloaddition by the initial formation of an anti-cyclopropyl gold(I)-carbene, followed by its opening to form a carbocation stabilized by a pi interaction with the aryl ring, which undergoes a Friedel-Crafts-type reaction.     

Construction of ssDNA-Attached LR-Chimera Involving Z-DNA for ZBP1 Binding Analysis

The binding of proteins to Z-DNA is hard to analyze, especially for short non-modified DNA, because it is easily transferred to B-DNA. Here, by the hybridization of a larger circular single-stranded DNA (ssDNA) with a smaller one, an LR-chimera (involving a left-handed part and a right-handed one) with an ssDNA loop is produced. The circular ssDNAs are prepared by the hybridization of two ssDNA fragments to form two nicks, followed by nick sealing with T4 DNA ligase. No splint (a scaffold DNA for circularizing ssDNA) is required, and no polymeric byproducts are produced. The ssDNA loop on the LR-chimera can be used to attach it with other molecules by hybridization with another ssDNA. The gel shift binding assay with Z-DNA specific binding antibody (Z22) or Z-DNA binding protein 1 (ZBP1) shows that stable Z-DNA can form under physiological ionic conditions even when the extra ssDNA part is present. Concretely, a 5′-terminal biotin-modified DNA oligonucleotide complementary to the ssDNA loop on the LR-chimera is used to attach it on the surface of a biosensor inlaid with streptavidin molecules, and the binding constant of ZBP1 with Z-DNA is analyzed by BLI (bio-layer interferometry). This approach is convenient for quantitatively analyzing the binding dynamics of Z-DNA with other molecules.     

Divergent Synthesis of Molecular Winch Prototypes

We report the synthesis of conceptually new prototypes of molecular winches with the ultimate aim to investigate the work performed by a single ruthenium-based molecular motor anchored on a surface by probing its ability to pull a load upon electrically-driven directional rotation. According to a technomimetic design, the motor was embedded in a winch structure, with a long flexible polyethylene glycol chain terminated by an azide hook to connect a variety of molecular loads. The structure of the motor was first derivatized by means of two sequential cross-coupling reactions involving a penta(4-halogenophenyl)cyclopentadienyl hydrotris(indazolyl)borate ruthenium(II) precursor and the resulting benzylamine derivative was next exploited as key intermediate in the divergent synthesis of a family of nanowinch prototypes. A one-pot method involving sequential peptide coupling and Cu-catalyzed azide-alkyne cycloaddition was developed to yield four loaded nanowinches, with load fragments encompassing triptycene, fullerene and porphyrin moieties.     

Determination of the space-charge field amplitude in polymeric photorefractive polymers

The space-charge field built in a polymeric photorefractive polymer was calculated by a simple method based on the oriented gas model. When anisotropic chromophores in a photorefractive polymer were exposed to an external field, they oriented preferentially to exhibit a birefringence. Then, under illumination of two coherent beams and an external field, they reoriented to form a photorefractive grating. During the formation of the grating, the chromophores were reoriented by the space-charge field as well as by the external applied field. The birefringence induced in the material by an external electric field was determined by measuring the transmittance of the sample which is placed between crossed polarizers, where birefringence depicts the orientation of the chromophores. By measuring the diffraction efficiency with a modified degenerate four-wave mixing setup, the index amplitude of the grating was determined. Finally, the space-charge field was determined by comparing the diffraction efficiency with the birefringence with respect to the applied electric field. In our study, the space-charge field was about 20% of the external applied field, which coincided with previous results obtained from our laboratory.