Experimental characterization of the weakly anisotropic CN X 2Σ+ + Ne potential from IR-UV double resonance studies of the CN-Ne complex

IR-UV double resonance spectroscopy has been used to characterize hindered internal rotor states (n(K) = 0(0), 1(1), and 1(0)) of the CN-Ne complex in its ground electronic state with various degrees of CN stretch (ν(CN)) excitation. Rotationally resolved infrared overtone spectra of the CN-Ne complex exhibit perturbations arising from Coriolis coupling between the closely spaced hindered rotor states (1(1) and 1(0)) with two quanta of CN stretch (ν(CN) = 2). A deperturbation analysis is used to obtain accurate rotational constants and associated average CN center-of-mass to Ne separation distances as well as the coupling strength. The energetic ordering and spacings of the hindered internal rotor states provide a direct reflection of the weakly anisotropic intermolecular potential between CN X (2)Σ(+) and Ne, with only an 8 cm(-1) barrier to CN internal rotation, from which radially averaged anisotropy parameters (V(10) and V(20)) are extracted that are consistent for ν(CN) = 0-3. Complementary ab initio calculation of the CN X (2)Σ(+) + Ne potential using MRCI+Q extrapolated to the complete one-electron basis set limit is compared with the experimentally derived anisotropy by optimizing the radial potential at each angle. Experiment and theory are in excellent accord, both indicating a bent minimum energy configuration and nearly free rotor behavior. Analogous experimental and theoretical studies of the CN-Ne complex upon electronic excitation to the CN B (2)Σ(+) state indicate a slightly more anisotropic potential with a linear CN-Ne minimum energy configuration. The results from these IR-UV double resonance studies are compared with prior electronic spectroscopy and theoretical studies of the CN-Ne system.     

Nano‐emulsion use for the synthesis of polyaniline nano‐grains or nano‐fibers

We report that nano‐emulsions can be creatively used as a morphology selective synthesis method to prepare not only nano‐grains but also nano‐fibers with high selectivity. Synthesis of the two different morphological materials was demonstrated using polyaniline synthesis as a model case. Polyaniline nano‐grains were synthesized from aniline molecules in nano‐size aqueous droplets as polymerization sites whose droplets were generated by inverse water‐in‐oil nano‐emulsion use, and polyaniline nano‐fibers were synthesized from aniline in aqueous nano‐dimensional channels as polymerization sites whose channels were generated by direct oil‐in‐water nano‐emulsion use containing high population of oil droplets. Using the approaches, we successfully synthesized nano‐fibers of 60 nm diameter with 0.5 µm length and also nano‐grains having diameter of 60–80 nm. The two different polymerization sites of nano‐scale dimension were made by changing the ratio among surfactant, aqueous aniline/HCl solution, and oil, i.e. organic solvent. We found the nano‐fibers synthesized from the channels formed by the direct oil‐in‐water nano‐emulsion have higher bulk electrical conductivity than the nano‐grains which were synthesized from the droplets formed by the inverse water‐in‐oil emulsion. We also found that the emulsion use allows us to use a room temperature synthesis unlike conventional synthesis methods which require to use ice bath temperature. Physical properties of both nano‐fibers and nano‐grains synthesized were characterized by Fourier transform infrared (FTIR), UV–Vis spectra, scanning electron microscopy (SEM), and four probes conductivity measurement. Copyright © 2009 John Wiley & Sons, Ltd.     

Electron Capture,Collision-Induced,and Electron Capture-Collision Induced Dissociation in Q-TOF

Recently, we demonstrated that a radio-frequency-free electromagnetostatic (rf-free EMS) cell could be retrofitted into a triple quad mass spectrometer to allow electron-capture dissociation (ECD) without the aid of cooling gas or phase-specific electron injection into the cell (Voinov et al., Rapid Commun Mass Spectrom 22, 3087–3088, 2008; Voinov et al., Anal Chem 81, 1238–1243, 2009). Subsequently, we used our rf-free EMS cell in the same instrument platform to demonstrate ECD occurring in the same space and at the same time with collision-induced dissociation (CID) to produce golden pairs and even triplets from peptides (Voinov et al., Rapid Commun Mass Spectrom 23, 3028–3030, 2009). In this report, we demonstrate that ECD and CID product-ion mass spectra can be recorded at high resolution with flexible control of fragmentation processes using a newly designed cell installed in a hybrid Q-TOF tandem mass spectrometer.     

Lung assist device technology with physiologic blood flow developed on a tissue engineered scaffold platform

There is no technology available to support failing lung function for patients outside the hospital. An implantable lung assist device would augment lung function as a bridge to transplant or possible destination therapy. Utilizing biomimetic design principles, a microfluidic vascular network was developed for blood inflow from the pulmonary artery and blood return to the left atrium. Computational fluid dynamics analysis was used to optimize blood flow within the vascular network. A micro milled variable depth mold with 3D features was created to achieve both physiologic blood flow and shear stress. Gas exchange occurs across a thin silicone membrane between the vascular network and adjacent alveolar chamber with flowing oxygen. The device had a surface area of 23.1 cm(2) and respiratory membrane thickness of 8.7 ± 1.2 μm. Carbon dioxide transfer within the device was 156 ml min(-1) m(-2) and the oxygen transfer was 34 ml min(-1) m(-2). A lung assist device based on tissue engineering architecture achieves gas exchange comparable to hollow fiber oxygenators yet does so while maintaining physiologic blood flow. This device may be scaled up to create an implantable ambulatory lung assist device.     

Synthesis of novel PPARα/γ dual agonists as potential drugs for the treatment of the metabolic syndrome and diabetes type II designed using a new de novo design program PROTOBUILD

Peroxisome proliferator activated receptors (PPARs) have been shown to have critical roles in fatty acid oxidation, triglyceride synthesis, and lipid metabolism - making them an important target in drug discovery. Here we describe the in silico design, synthesis and in vitro characterisation of a novel series of 2,5-disubstituted indoles as PPARα/γ dual agonists. PPAR activation assays are performed with known agonists diazabenzene (WY14.643), aminopyridine (BRL49653) and bisaryl (L165.041), as positive controls. All the indole compounds synthesized are found to be active PPARα and PPARγ agonists, with particular efficacy from those with 2-naphthylmethyl substitution. This is a useful demonstration of a new de novo design methodology implemented by the protobuild program and its ability to rapidly produce novel modulators for a well characterized drug target.     

Information-theoretic approaches to SVM feature selection for metagenome read classification

Analysis of DNA sequences isolated directly from the environment, known as metagenomics, produces a large quantity of genome fragments that need to be classified into specific taxa. Most composition-based classification methods use all features instead of a subset of features that may maximize classifier accuracy. We show that feature selection methods can boost performance of taxonomic classifiers. This work proposes three different filter-based feature selection methods that stem from information theory: (1) a technique that combines Kullback-Leibler, Mutual Information, and distance information, (2) a text mining technique, TF-IDF, and (3) minimum redundancy-maximum-relevance (mRMR). The feature selection methods are compared by how well they improve support vector machine classification of genomic reads. Overall, the 6mer mRMR method performs well, especially on the phyla-level. If the number of total features is very large, feature selection becomes difficult because a small subset of features that captures a majority of the data variance is less likely to exist. Therefore, we conclude that there is a trade-off between feature set size and feature selection method to optimize classification performance. For larger feature set sizes, TF-IDF works better for finer-resolutions while mRMR performs the best out of any method for N=6 for all taxonomic levels.     

Modification of the magnetic properties of a heterometallic wheel by inclusion of a Jahn-Teller distorted Cu(II) ion

An investigation into the physical consequences of including a Jahn-Teller distorted Cu(II) ion within an antiferromagnetically coupled ring, [R(2)NH(2)][Cr(7)CuF(8)((O(2)C(t)Bu)(16))] is reported. Inelastic neutron scattering (INS) and electron paramagnetic resonance (EPR) spectroscopic data are simulated using a microscopic spin Hamiltonian, and show that the two Cr-Cu exchange interactions must be inequivalent. One Cr-Cu exchange is found to be antiferromagnetic and the other ferromagnetic. The geometry of the Jahn-Teller elongation is deduced from these results, and shows that a Jahn-Teller elongation axis must lie in the plane of the Cr(7)Cu wheel; the elongation is not observed by X-ray crystallography, due to positional disorder of the Cu site within the wheel. An electronic structure calculation confirms the structural distortion of the Cu site.     

Effect of terminal N-substitution in 2-oxo-1,2-dihydroquinoline-3-carbaldehyde thiosemicarbazones on the mode of coordination, structure, interaction with protein, radical scavenging and cytotoxic activity of copper(II) complexes

Four 2-oxo-1,2-dihydroquinoline-3-carbaldehyde N-substituted thiosemicarbazone ligands (H(2)-OQtsc-R, where R = H, Me, Et or Ph) and their corresponding new copper(II) complexes [CuCl(2)(H(2)-OQtsc-H)]·2H(2)O (1), [CuCl(2)(H(2)-OQtsc-Me)]·2H(2)O (2), [CuCl(2)(H(2)-OQtsc-Et)(CH(3)OH)]Cl (3) and [CuCl(H-OQtsc-Ph)]·CH(3)OH (4) have been synthesized in order to correlate the effect of terminal N-substitution on coordination behaviour, structure and biological activity. Single crystal X-ray diffraction studies revealed that the complexes 1, 2 and 3 have square pyramidal geometry around the central metal ion. In the complexes 1 and 2, the copper ion is coordinated by the ligand with ONS donor atoms, one chloride ion in apical position and the other chloride in the basal plane. Complex 3 consists of [CuCl(2)(H(2)-OQtsc-Et)(CH(3)OH)](+) cation and a chloride as counter ion. The copper ion is coordinated by the ligand with ONS donor atoms and by one chloride ion in the basal plane. One methanol molecule is bonded through its neutral oxygen in the apical position. Complex 4 is square planar with the ligand coordinating through uni-negative tridentate ONS(-) and by one chloride ion in the basal plane. The binding of complexes with lysozyme protein was carried out by fluorescence spectroscopy. Investigations of antioxidation properties showed that all the copper(II) complexes have strong radical scavenging properties. The cytotoxicity of the complexes 3 and 4 against NIH 3T3 and HeLa cell lines showed that synergy between the metal and ligands results in a significant enhancement in the cell death with IC(50) of ~10-40 μM. A size dependence of substitution at terminal N in the thiosemicarbazones on the biological activities of the complexes has been observed.     

Glycomimetic building blocks: a divergent synthesis of epimers of shikimic acid

A divergent synthesis of (-)-4-epi-shikimic acid was developed. This route features a one-pot zinc-mediated reductive ring opening of an arabinofuranose followed by a Barbier reaction and culminates in a ring-closing metathesis. Functionalization of (-)-4-epi-shikimic acid via conjugate addition of a thiol occurs in high diastereoselectivity to afford a product with the features of fucosylated glycans.     

ThermoData Engine (TDE): software implementation of the dynamic data evaluation concept. 5. Experiment planning and product design

ThermoData Engine (TDE) is the first full-scale software implementation of the dynamic data evaluation concept, as reported recently in this journal. In the present paper, we describe development of an algorithmic approach to assist experiment planning through assessment of the existing body of knowledge, including availability of experimental thermophysical property data, variable ranges studied, associated uncertainties, state of prediction methods, and parameters for deployment of prediction methods and how these parameters can be obtained using targeted measurements, etc., and, indeed, how the intended measurement may address the underlying scientific or engineering problem under consideration. A second new feature described here is the application of the software capabilities for aid in the design of chemical products through identification of chemical systems possessing desired values of thermophysical properties within defined ranges of tolerance. The algorithms and their software implementation to achieve this are described. Finally, implementation of a new data validation and weighting system is described for vapor-liquid equilibrium (VLE) data, and directions for future enhancements are outlined.