ArQiologist: an integrated decision support tool for lead optimization

This paper describes ArQiologist, a Web-based tool that integrates chemical, analytical, biological, and computational data to facilitate decision support for lead optimization at ArQule. It features an easy-to-use graphical query builder that allows queries to be saved, reused, and shared by researchers. Query results can be viewed with built-in data browsers or exported with structures to external applications such as Microsoft Excel or Spotfire for further analysis.     

Effect of Pr-Ca substitution on the transport and magnetic behavior of LaMnO3 perovskite

The effect of simultaneous substitution of a fluctuating cation and a divalent cation in LaMnO₃ perovskite modifies the properties of the material to exhibit large valence colossal magnetoresistance (CMR) effect. A good example of these properties is (La_1−2x Pr _x Ca _x )MnO₃ (LPCMO) type CMR material. In this communication it is reported that, with the increase in x (for x=0.1, 0.15, 0.2), the T _c varies between 100 and 120 K with improvisation in metal-insulator transition. Interestingly, resistance increases with x from few hundred ohms to few kilo ohms with corresponding decrease in the unit cell volume. The results of the studies using X-ray diffraction (XRD), electrical resistivity, magnetoresistance and ac susceptibility measurements on LPCMO samples for understanding the structural, transport and magnetic properties are discussed in detail.     

Stability of A15 type phases

Previous works dealing with the stability of the A15 phases are reviewed. Data for over 60 known A15 phases are used to develop criteria for stability which may be applied to hypothetical A15 phases. Occurrence of these phases is examined in terms of the valence bond concepts of the Engel-Brewer correlation and in its frequency with changes in electronic density of states. A15 is most favored when the “A” elements are V, Nb or Cr, when radii of the constituent atoms differ by no more than 8 per cent, at compositions determined by electron concentration, and at relatively low temperatures. Composition and temperature of formation are predicted for several likely hypothetical A15 phases.     

An examination of a density functional/molecular mechanical coupled potential

In this article we describe the coupling of a density functional (DF) Hamiltonian with the molecular mechanics (MM) potential function AMBER. We examine a series of test cases in which we compare the binding energies and geometries of the complexes predicted by this coupled potential with those predicted by other theoretical methods and experiment to establish the relative accuracy of the DF/MM coupled potential. We find that the DF/MM coupled potential performs well in most cases studied and, in general, outperforms the semiempirical/MM approach. The interaction energies and structures obtained using this method appear to be insensitive to the use of nonlocal (NL) corrections to the DF method. The is fortuitous because the NL treatment is significantly more computationally expensive than the local treatment. However, NL corrections may be required to predict accurately the shape of potential energy surfaces that involve bond breaking and formation. The DF/MM method has also been applied to the determination of the solvation free energy for a series of ions using free-energy perturbation methods. The results obtained are good and can be improved by a simple scaling of the Lennard-Jones parameters for the ion in question. © 1995 by John Wiley & Sons, Inc.     

Liquid chromatography/electrospray mass spectrometric analysis of metabolites from an inhibitory RNA duplex

Liquid chromatography/mass spectrometry (LC/MS) was used as a method for analyzing the metabolites of a model short interfering RNA (siRNA) duplex. The model siRNA duplex incorporated oligonucleotide stabilizing and protecting chemistries as these have been shown to increase the half-life of oligonucleotides. Two complementary 23 nucleotide single strands were joined to form the duplex. The intact duplex was analyzed using ion-pair reversed-phase chromatography coupled to electrospray ionization mass spectrometry (ESI-MS). The method used a hexafluoroisopropanol/triethylamine ion-pairing buffer with a methanol gradient to separate single-stranded oligonucleotide components from the duplex. This buffer system with ESI also preserved the duplex in the gas phase for analysis by a triple quadrupole mass spectrometer. Using this methodology, in vitro and in vivo metabolites from urine and rabbit ocular vitreous humor were determined and a pattern of duplex siRNA degradation was established. The masses of the metabolites were determined by ESI-MS and used with the known sequence of the siRNA duplex to identify the metabolites. Over the time course of the metabolism experiments it was shown that the breakdown products of the siRNA are consistent with the nuclease protection given by chemical modifications and that the duplex structure adds additional stability compared to the single strands alone. This study demonstrates that the ability of LC/MS to analyze duplex oligonucleotides has unique benefits for the study of siRNA metabolism.     

Cr(VI) Oxidation of Cholesterol—A Kinetic Study Using N-Cetylpicolinium Dichromates,A Class of Novel Phase Transfer Oxidants

Kinetics and Catalysis - Kinetic study of cholesterol oxidation has been studied using a series of N-cetylpicolinium dichromates (CPDC), a class of phase transfer oxidants, in acetic acid medium...     

Elastic properties of the Ta–V system: bcc Ta0.33V0.67 and C15 TaV2

Resonant ultrasound spectroscopy was used to measure the elastic constants of bcc Ta_0.33V_0.67 over the temperature range 3.5–300?K; the results were compared to earlier measurements on C15 TaV₂. The temperature dependence of the polycrystalline shear modulus is completely different in the two phases; that of the bcc phase decreases with temperature whereas that of the C15 phases increases in an anomalous fashion. This difference is consistent with a model involving doubly-degenerate levels at the X point of the Brillouin zone in the C15 phase with the Fermi level lying near the doubly degenerate level. This model accounted for the unusual behaviour of the C15 phase. Debye temperatures were determined from the ultrasonic measurements: 295?K for the C15 phase and 315?K for the bcc phase.     

Irradiation of a cone by a magnetic dipole

Th electromagnetic field produced by a magnetic dipole in thepresence of a perfectly conducting cone of arbitrary cross-sectionis determined. The solution is used to find out how a currenton the cone travelling towards the apex is reflected. Some valuesof the reflection coefficient are calculated. In particular,it is shown that there is a sort of resonance with the reflectionincreasing significantly as the cone approaches a plane.