ElectroShape: fast molecular similarity calculations incorporating shape,chirality and electrostatics

We present ElectroShape, a novel ligand-based virtual screening method, that combines shape and electrostatic information into a single, unified framework. Building on the ultra-fast shape recognition (USR) approach for fast non-superpositional shape-based virtual screening, it extends the method by representing partial charge information as a fourth dimension. It also incorporates the chiral shape recognition (CSR) method, which distinguishes enantiomers. It has been validated using release 2 of the Directory of useful decoys (DUD), and shows a near doubling in enrichment ratio at 1% over USR and CSR, and improvements as measured by Receiver Operating Characteristic curves. These improvements persisted even after taking into account the chemotype redundancy in the sets of active ligands in DUD. During the course of its development, ElectroShape revealed a difference in the charge allocation of the DUD ligand and decoy sets, leading to several new versions of DUD being generated as a result. ElectroShape provides a significant addition to the family of ultra-fast ligand-based virtual screening methods, and its higher-dimensional shape recognition approach has great potential for extension and generalisation.     

Electron capture dissociation mass spectrometry of metallo-supramolecular complexes

The electron capture dissociation (ECD) of metallo-supramolecular dinuclear triple-stranded helicate Fe₂L₃⁴⁺ ions was determined by Fourier transform ion cyclotron resonance mass spectrometry. Initial electron capture by the di-iron(II) triple helicate ions produces dinuclear double-stranded complexes analogous to those seen in solution with the monocationic metal centers Cu^I or Ag^I. The gas-phase fragmentation behavior [ECD, collision-induced dissociation (CID), and infrared multiphoton dissociation (IRMPD)] of the di-iron double-stranded complexes, (i.e., MS³ of the ECD product) was compared with the ECD, CID, and IRMPD of the Cu^I and Ag^I complexes generated from solution. The results suggest that iron-bound dimers may be of the form Fe₂^IL₂²⁺ and that ECD by metallo-complexes allows access, in the gas phase, to oxidation states and coordination chemistry that cannot be accessed in solution.     

Digital biomagnetism: Electrodeposited multilayer magnetic barcodes

A novel magnetic encoding technique for performing high-throughput biological assays is presented. Electrodeposited Ni/Cu and Co/Cu multilayer pillar structures with a diameter of 15 μm and a thickness up to 10 μm are presented as “magnetic barcodes”, where the number of unique codes possible increases exponentially with a linear increase in length. A gold cap facilitates the growth of self-assembled monolayers (SAMs), while microdrop printing allows efficient generation of large libraries of tagged probes. Coercivity-tuning techniques are used to exploit a non-proximity encoding methodology compatible with microfluidic flow.     

Time-resolved,stress-induced,and anisotropic phase transformation of a piezoelectric polymer

We investigate the time-dependent and anisotropic phase transformation of poly (vinylidene difluoride) (PVDF) under bending. Using combined techniques of an atomic force microscope and a Fourier transform infrared spectroscope, observation of surface morphology and phase transformation in time was made. Results showed that bending stress induces the transformation of amorphous, α,β, and γ crystalline phases. Specifically, the amorphous phase was transformed into the β phase when the bending force was applied. In addition, the transformation observed was time and direction dependent. The anisotropic behavior observed brings insights into the origin of the piezoelectricity of PVDF.     

Coulomb excitation of radioactive 20, 21Na

The low-energy structures of the radioactive nuclei ^{20, 21}Na have been examined using Coulomb excitation at the TRIUMF-ISAC radioactive ion beam facility. Beams of ～ 5×10⁶ ions/s were accelerated to 1.7MeV/A and Coulomb excited in a 0.5mg/cm^2 ^natTi target. Two TIGRESS HPGe clover detectors perpendicular to the beam axis were used for $ \gamma$ -ray detection, while scattered nuclei were observed by the Si detector BAMBINO. For ²¹Na , Coulomb excitation from the 3/2⁺ ground state to the first excited 5/2⁺ state was observed, while for ²⁰Na , Coulomb excitation was observed from the 2⁺ ground state to the first excited 3⁺ and 4⁺ states. For both beams, B ( $ \lambda$ L) values were determined using the 2⁺ $ \rightarrow$ 0⁺ de-excitation in ⁴⁸Ti as a reference. The resulting B(E2) ↓ value for ²¹Na is 137±9 e^2fm^4, while the resulting B( $ \lambda$ L) ↓ values for ²⁰Na are 55±6 e^2fm^4 for the 3⁺ $ \rightarrow$ 2⁺ , 35.7±5.7 e^2 fm^4 for the 4⁺ $ \rightarrow$ 2⁺ , and 0.154±0.030 μ_N^2 for the 4⁺ $ \rightarrow$ 3⁺ transitions. This analysis significantly improves the measurement of the ²¹Na B(E2) value, and provides the first experimental determination of B( $ \lambda$ L) values for the proton dripline nucleus ²⁰Na .-1     

Unique crystal morphologies of glycine grown from octanoic acid-in-water emulsions

We have obtained both porous and dendritic, intricate morphology crystals of beta-glycine by the novel and simple method of emulsion droplet adhesion and encapsulation. By using octanoic acid emulsified with nonionic surfactants, the adhesion of the emulsion droplets can be so strong that, remarkably, crystal growth often proceeds around the droplets, leading to their inclusion within the single crystals. Consequently, porous single crystals can be produced with the pore diameters ( approximately 10-25 mum) corresponding to the emulsion droplet sizes. Highly intricate, dendritic morphologies for glycine were obtained by increasing the surfactant concentration in the emulsions to 50%. In this case, partial droplet encapsulation results in crystal dendrites growing on either side of adsorbed droplets, with the complex morphologies developing due to the high density of dendritic branches that can occur. These intricate morphologies are in stark contrast to the facetted crystals that normally develop at these low supersaturations in the absence of octanoic acid droplets. This study demonstrates that complex architectures can be attained by using simple emulsion systems and tuning the degree of droplet adhesion.     

Intrinsic charge ladders of a monoclonal antibody in hydroxypropylcellulose-coated capillaries

Capillary zone electrophoresis (CZE) has been used to resolve the charge heterogeneity of an intact ( approximately 150 kDa) monoclonal IgG antibody (mAb). Although this microheterogeneity can also be observed by isoelectric focusing, CZE allows the net charge of each variant to be measured as a function of pH and other solution conditions. Separation was achieved in both borate and Tris run buffers using capillaries that had been statically coated with hydroxypropylcellulose (HPC). The HPC coating makes inadvertent chromatographic retention of the mAb undetectably small and decreases electroosmotic flow (EOF) to approximately 10(-5) cm(2) V(-1) s(-1), with reasonable stability over dozens of runs under the conditions tested (pH 8.5 and 9.0 for each buffer). We also describe a novel means of measuring small, positive EOF coefficients and larger, negative net mobilities in the same run. This allows determination of accurate electrophoretic mobilities despite variations in EOF. The resolved mAb charge variants (which most likely result from deamidation or partial truncation) constitute what we call an "intrinsic" charge ladder. As with conventional charge ladders formed by deliberate modification of a homogeneous protein, net charge is obtained by extrapolating a plot of electrophoretic mobility versus (assumed) incremental charge difference. At a given pH, the mAb is more negatively charged in borate than in Tris, reflecting specific binding of the B(OH)(4)(-) anion. We also report hydrodynamic radii calculated from the slopes of these plots.     

Novel Putative Positive Modulators of α4β2 nAChRs Potentiate Nicotine Reward-Related Behavior

The popular tobacco and e-cigarette chemical flavorant (−)-menthol acts as a nonselective, noncompetitive antagonist of nicotinic acetylcholine receptors (nAChRs), and contributes to multiple physiological effects that exacerbates nicotine addiction-related behavior. Menthol is classically known as a TRPM8 agonist; therefore, some have postulated that TRPM8 antagonists may be potential candidates for novel nicotine cessation pharmacotherapies. Here, we examine a novel class of TRPM8 antagonists for their ability to alter nicotine reward-related behavior in a mouse model of conditioned place preference. We found that these novel ligands enhanced nicotine reward-related behavior in a mouse model of conditioned place preference. To gain an understanding of the potential mechanism, we examined these ligands on mouse α4β2 nAChRs transiently transfected into neuroblastoma-2a cells. Using calcium flux assays, we determined that these ligands act as positive modulators (PMs) on α4β2 nAChRs. Due to α4β2 nAChRs’ important role in nicotine dependence, as well as various neurological disorders including Parkinson’s disease, the identification of these ligands as α4β2 nAChR PMs is an important finding, and they may serve as novel molecular tools for future nAChR-related investigations.     

Plasmonic enhancement of the two photon absorption cross section of an organic chromophore using polyelectrolyte-coated gold nanorods

The effect of plasmonic enhancement on the two-photon absorption cross section of organic chromophores attached to polyelectrolyte-coated gold nanorods was investigated. The magnitudes of such enhancements were confirmed using single and two photon excitations of the chromophore molecules bound to polyelectrolyte-coated gold nanorods. By synthesizing two-, four-, six-, and eight-polyelectrolyte layer coated nanorods of a particular aspect ratio, the distance dependence of the evanescent electromagnetic field on molecular two-photon absorption was observed. Enhancements of 40-fold were observed for the chromophores nearest to the surface.