Estimation of activation energies from differential thermal analysis curves

An average activation energy ΔE3 of 31.7 ± 10.0 kcal/mole was calculated from exothermic peaks of urea nitrate differential thermal analysis (DTA) curves using the Murray and White equation and various other reaction rate equations developed by the authors. An average enthalpy of activation, ΔH3 of 30.8 ±9.7 kcal/mole was calculated from the same results. The values of ΔE3 and ΔH3 differed by a fraction of a kcal/mole indicating that ΔE3 <ΔH3 cannot be differentiated experimentally in our study. Application of the Kissinger method of calculating ΔE3 and ΔH3 produced respectively 21.6 ±7.9 and 20.7 ±8.0 kcal/mole, which are quite low. The values of ΔE3 and ΔH3 calculated thermogravimetrically were 28.1, ± 1.1 kcal/mole and 27.6 ± 1.2 kcal/mole which are close to those obtained from the Murray and White approach and the authors' approach to treatment of the DTA data. These results illustrate the pronounced effect of self heating on calculation of activation energies. The Kissinger method of calculating the reaction order developed for endothermic DTA peaks produced good results when applied to the present DTA study.     

Measurement of reaction kinetics by a pressure rise method

Decomposition of urea nitrate in an initially evacuated system gave sigmoidal pressurevs. time curves. The experimental kinetic data fit the growing nuclei model with a measured enthalpy of activation of 142±12.5 kJ/mole as compared to 115±11.3 kJ/mole obtained thermogravimetrically. This higher value ofH is explained on the basis of two factors: 1) the inhibitory effect of the product gases and 2) self heating, whose extent increasedH by about 12.5 kJ/mole.

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Zusammenfassung Die Zersetzung von Harnstoffnitrat in einem anfanglich evakuierten System ergab sigmoide Druck-Zeit Kurven. Die kinetischen Versuchsangaben können einem Kernwachstums-Modell einer gemessenen Aktivierungsenthalpie von 142±12,5 kJ/mol angepaßt werden, im Vergleich zu den auf thermogravimetrischen Weg ermittelten Wert von 115±11.3 kJ/Mol. Dieser hohe Wert vonH, wird auf Grund zweier Faktoren erklärt: 1) der Hemmungseffekt der Produktgase und 2) Selbsterhitzung, deren AusmaßH um etwa 12.5 kJ/Mol erhöhte.

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Résumé La décomposition du nitrate d'urée dans un système initialement mis sous vide, donne des courbes sigmoïdales de pression en fonction du temps. Les données cinétiques expérimentales peuvent être ajustées à un modèle de grossissement de germes, avec une enthalpie d'activation mesurée de 142±12.5 kJ/mole, comparée à 115±11.3 kJ/mole obtenue par thermogravimétrie. Cette valeur plus élevée deH s'explique sur la base de deux facteurs: 1) l' effet inhibiteur des gaz produits et 2) phénomène d'autoéchauffement qui augmente la valeur deH d'environ 12.5 kJ/mole.

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. , 142+-12.5 / 115 + 11.3 /, . H : 1) 2) , 12.5 /.

     

C-terminal processing of yeast Spt7 occurs in the absence of functional SAGA complex

Background  

Spt7 is an integral component of the multi-subunit SAGA complex that is required for the expression of ~10% of yeast genes. Two forms of Spt7 have been identified, the second of which is truncated at its C-terminus and found in the SAGA-like (SLIK) complex.     

Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4

Summary AutoDock 2.4 predicts the bound conformations of a small, flexible ligand to a nonflexible macromolecular target of known structure. The technique combines simulated annealing for conformation searching with a rapid grid-based method of energy evaluation based on the AMBER force field. AutoDock has been optimized in performance without sacrificing accuracy; it incorporates many enhancements and additions, including an intuitive interface. We have developed a set of tools for launching and analyzing many independent docking jobs in parallel on a heterogeneous network of UNIX-based workstations. This paper describes the current release, and the results of a suite of diverse test systems. We also present the results of a systematic investigation into the effects of varying simulated-annealing parameters on molecular docking. We show that even for ligands with a large number of degrees of freedom, root-mean-square deviations of less than 1 Å from the crystallographic conformation are obtained for the lowest-energy dockings, although fewer dockings find the crystallographic conformation when there are more degrees of freedom.The AutoDock 2.4 suite is written in ANSI C, and is supplied with Makefiles for the following platforms: Convex, DEC Alpha OSF/1, Hewlett-Packard Precision Architecture, Silicon Graphics, and Sun. The AutoDock suite of programs is freely available to the noncommercial scientific community and to educational establishments. Further information, including additional figures and MPEG animations showing all docked conformations for each test system, can be found at the following URL: http://www.scripps.edu/pub/olson-web/doc/autodock.     

Multiplex digital PCR: breaking the one target per color barrier of quantitative PCR

Quantitative polymerase chain reactions (qPCR) based on real-time PCR constitute a powerful and sensitive method for the analysis of nucleic acids. However, in qPCR, the ability to multiplex targets using differently colored fluorescent probes is typically limited to 4-fold by the spectral overlap of the fluorophores. Furthermore, multiplexing qPCR assays requires expensive instrumentation and most often lengthy assay development cycles. Digital PCR (dPCR), which is based on the amplification of single target DNA molecules in many separate reactions, is an attractive alternative to qPCR. Here we report a novel and easy method for multiplexing dPCR in picolitre droplets within emulsions-generated and read out in microfluidic devices-that takes advantage of both the very high numbers of reactions possible within emulsions (>10(6)) as well as the high likelihood that the amplification of only a single target DNA molecule will initiate within each droplet. By varying the concentration of different fluorogenic probes of the same color, it is possible to identify the different probes on the basis of fluorescence intensity. Adding multiple colors increases the number of possible reactions geometrically, rather than linearly as with qPCR. Accurate and precise copy numbers of up to sixteen per cell were measured using a model system. A 5-plex assay for spinal muscular atrophy was demonstrated with just two fluorophores to simultaneously measure the copy number of two genes (SMN1 and SMN2) and to genotype a single nucleotide polymorphism (c.815A>G, SMN1). Results of a pilot study with SMA patients are presented.     

Characterization of VX on concrete using ion trap secondary ionization mass spectrometry

The nerve agent VX (O-ethyl S-2-diisopropylaminoethyl methyl phosphonothiolate) was analyzed on the surface of concrete samples using an ion trap secondary ion mass spectrometer (IT-SIMS). It was found that VX could be detected down to an absolute quantity of 5 ng on a concrete chip, or to a surface coverage of 0.0004 monolayers on crushed concrete. To achieve these levels of detection, the m/z 268-->128 ion fragmentation was measured using MS2, where m/z 268 corresponds to [VX + H]+, and 128 corresponds to a diisopropylvinylammonium isomer, that is formed by the elimination of the phosphonothiolate moiety. Detection at these levels was accomplished by analyzing samples that had been recently exposed to VX, i.e., within an hour. When the VX-exposed concrete samples were aged, the SIMS signature for intact VX had disappeared, which signaled the degradation of the compound on the concrete surface. The VX signature was replaced by ions which are interpreted in terms of VX degradation products, which appear to be somewhat long lived on the concrete surface. These compounds include ethylmethylphosphonic acid (EMPA), diisopropyl taurine (DIPT), diisopropylaminoethanethiol (DESH), bis(diisopropylaminoethane) disulfide [(DES)2], and a particularly tenacious compound that may correspond to diisopropylvinylamine (DIVA), or an isomer thereof. It was found that the thiolamine-derived degradation products DIPT, DESH, and (DES)2 were removed with isopropyl alcohol extraction. However, the DIVA-related degradation product was observed to strongly adhere to the concrete surface for longer than one week. Although quantitation was not possible in this set of experiments, the results clearly show the rapid degradation of VX on concrete, as well as the surface sensitivity of the IT-SIMS for intact VX and its adsorptive degradation products.     

Spectroscopic study of (two-dimensional) molecule-based magnets: [M(II)(TCNE)(NCMe)2][SbF6] (M = Fe, Mn, Ni)

The M-[TCNE] (M = 3d metal; TCNE = tetracyanoethylene) system is one of the most interesting classes of molecule-based magnets, exhibiting a plethora of compositions and structures (inorganic polymer chains, 2D layers, 3D networks, and amorphous solids) with a wide range of magnetic ordering temperatures (up to 400 K). A systematic study of vibrational (both infrared and, for the first time, Raman) properties of the family of new TCNE-based magnets of M(II)(TCNE) (NCMe)(2)[SbF(6)] [M = Mn, Fe, Ni] composition is discussed in conjunction with their magnetic behavior and newly reso-lved crystal structures. The vibrational properties of the isolated TCNE(●-) anion in the paramagnetic Bu(4)N [TCNE(●-)] salt and recently characterized 2D layered magnet Fe(II)(TCNE)(NCMe)(2)[FeCl(4)] are also reported for comparison. Additionally, a linear correlation between ν(C=C) (a(g)) frequency of the TCNE ligand and its formal charge Z (the spin density on the π* orbital), Z = [1571 - ν(C=C) (a(g))]/154.5 [e], is presented. It is shown that monitoring Z by Raman spectroscopy is of great use in providing information that allows understanding the peculiarity of the superexchange interaction in M-[TCNE] magnets and establishing the structure-magnetic properties correlations in this class of magnetic material.     

Assessment of high-resolution methods for numerical simulations of compressible turbulence with shock waves

Flows in which shock waves and turbulence are present and interact dynamically occur in a wide range of applications, including inertial confinement fusion, supernovae explosion, and scramjet propulsion. Accurate simulations of such problems are challenging because of the contradictory requirements of numerical methods used to simulate turbulence, which must minimize any numerical dissipation that would otherwise overwhelm the small scales, and shock-capturing schemes, which introduce numerical dissipation to stabilize the solution. The objective of the present work is to evaluate the performance of several numerical methods capable of simultaneously handling turbulence and shock waves. A comprehensive range of high-resolution methods (WENO, hybrid WENO/central difference, artificial diffusivity, adaptive characteristic-based filter, and shock fitting) and suite of test cases (Taylor–Green vortex, Shu–Osher problem, shock-vorticity/entropy wave interaction, Noh problem, compressible isotropic turbulence) relevant to problems with shocks and turbulence are considered. The results indicate that the WENO methods provide sharp shock profiles, but overwhelm the physical dissipation. The hybrid method is minimally dissipative and leads to sharp shocks and well-resolved broadband turbulence, but relies on an appropriate shock sensor. Artificial diffusivity methods in which the artificial bulk viscosity is based on the magnitude of the strain-rate tensor resolve vortical structures well but damp dilatational modes in compressible turbulence; dilatation-based artificial bulk viscosity methods significantly improve this behavior. For well-defined shocks, the shock fitting approach yields good results.