Dual-core optofluidic chip for independent particle detection and tunable spectral filtering

We present the first integration of fluidically tunable filters with a separate particle detection channel on a single planar, optofluidic chip. Two optically connected, but fluidically isolated liquid-core antiresonant reflecting optical waveguide (ARROW) segments serve as analyte and spectral filter sections, respectively. Ultrasensitive detection of fluorescent nanobeads with high signal-to-noise ratio provided by a fluidically tuned excitation notch filter is demonstrated. In addition, reconfigurable filter response is demonstrated using both core index tuning and bulk liquid tuning. Notch filters with 43 dB rejection ratio and a record 90 nm tuning range are implemented by using different mixtures of ethylene glycol and water in the filter section. Moreover, absorber dyes and liquids with pH-dependent transmission in the filter channel provide additional spectral control independent of the waveguide response. Using both core index and pH control, independent filter tuning at multiple wavelengths is demonstrated for the first time. This extensive on-chip control over spectral filtering as one of the fundamental components of optical particle detection techniques offers significant advantages in terms of compactness, cost, and simplicity, and opens new opportunities for waveguide-based optofluidic analysis systems.     

Borylene transfer from an iron bis(borylene) complex: synthesis of 1,4-diboracyclohexadiene and 1,4-dibora-1,3-butadiene complexes

Diene to be made: By tuning the size of acetylenic substituents, 1,4-diboracyclohexadiene and unprecedented 1,4-dibora-1,3-butadiene complexes were generated in a controlled manner by borylene transfer from an iron bis(borylene) complex to alkynes (see scheme).     

Syntheses and PE-Spectroscopic Investigations of 2,6- and 3,5-Bridged 1,4-Dimethylidenecyclohexanes

Three 1,4-dimethylidenecyclohexanes, bridged in the 2,6- and 3,5-positions by two ethano ( 4 ), one ethano and one propano ( 5 ), and two propano bridges ( 6 ) have been synthesized. The interaction of the two exocyclic methylidene groups has been investigated by He(I) photoelectron (PE) spectroscopy. It revealed a slightly larger energy difference (0.8 eV) for 4 and 5 as compared to the parent 1,4-dimethylidenecyclohexane ( 7 ) (0.7 eV). The interpretation of the PE spectra was based on the comparison with PE data of related systems and with the results of semiempirical calculations on 4–6 .     

Substantial improvements in large-scale redocking and screening using the novel HYDE scoring function

The HYDE scoring function consistently describes hydrogen bonding, the hydrophobic effect and desolvation. It relies on HYdration and DEsolvation terms which are calibrated using octanol/water partition coefficients of small molecules. We do not use affinity data for calibration, therefore HYDE is generally applicable to all protein targets. HYDE reflects the Gibbs free energy of binding while only considering the essential interactions of protein-ligand complexes. The greatest benefit of HYDE is that it yields a very intuitive atom-based score, which can be mapped onto the ligand and protein atoms. This allows the direct visualization of the score and consequently facilitates analysis of protein-ligand complexes during the lead optimization process. In this study, we validated our new scoring function by applying it in large-scale docking experiments. We could successfully predict the correct binding mode in 93% of complexes in redocking calculations on the Astex diverse set, while our performance in virtual screening experiments using the DUD dataset showed significant enrichment values with a mean AUC of 0.77 across all protein targets with little or no structural defects. As part of these studies, we also carried out a very detailed analysis of the data that revealed interesting pitfalls, which we highlight here and which should be addressed in future benchmark datasets.     

Crystal structure and physical properties of the new one-dimensional metal Ba2Cu(7-x)Te6

The telluride Ba(2)Cu(7-x)Te(6) was synthesized from the elements in stoichiometric ratios, heated to 1073 K, followed by slow cooling to 873 K over 120 h. Ba(2)Cu(7-x)Te(6) crystallizes in space group P2(1)/m with lattice dimensions of a = 6.8591(7) ?, b = 12.1439(12) ?, c = 9.0198(9) ?, β = 110.7509(14)°, V = 702.58(12) ?(3), and Z = 2. The structure is comprised of Cu atoms forming a six-membered ring and triangles, interconnected to an infinite ribbon of Cu atoms. The ribbons are connected to each other via Cu-Te bonds to yield a three-dimensional structure, wherein each Cu atom is tetrahedrally coordinated by four Te atoms. A special feature of this telluride is the occurrence of a quasi-linear Te atom chain, which causes one-dimensional metallic properties, in accordance with electronic structure calculations and property measurements.     

Fluorescence-based active site probes for profiling deubiquitinating enzymes

Novel ubiquitin-based active site probes including a fluorescent tag have been developed and evaluated. A new, functionalizable electrophilic trap is utilized allowing for late stage diversification of the probe. Attachment of fluorescent dyes allowed direct detection of endogenous deubiquitinating enzyme (DUB) activities in cell extracts by in-gel fluorescence imaging.     

Rearrangement from the heteroantiaromatic borole to the heteroaromatic azaborine motif

Treatment of 9-chloro-9-borafluorene with N,O-bis(trimethylsilyl)hydroxylamine results in 10-trimethylsilyloxy-9-aza-10-boraphenanthrene 6b. NMR spectroscopy shows that the expected antiaromatic 9-(trimethylsilyloxyamino)-9-borafluorene 5b rearranges to the formally aromatic phenanthrene 6b at room temperature.     

FEW: A workflow tool for free energy calculations of ligand binding

In the later stages of drug design projects, accurately predicting relative binding affinities of chemically similar compounds to a biomolecular target is of utmost importance for making decisions based on the ranking of such compounds. So far, the extensive application of binding free energy approaches has been hampered by the complex and time‐consuming setup of such calculations. We introduce the free energy workflow (FEW) tool that facilitates setup and execution of binding free energy calculations with the AMBER suite for multiple ligands. FEW allows performing free energy calculations according to the implicit solvent molecular mechanics (MM‐PB(GB)SA), the linear interaction energy, and the thermodynamic integration approaches. We describe the tool's architecture and functionality and demonstrate in a show case study on Factor Xa inhibitors that the time needed for the preparation and analysis of free energy calculations is considerably reduced with FEW compared to a fully manual procedure. © 2013 Wiley Periodicals, Inc.