SOS films and interfaces: chemical aspects

The possible chemical reactions that take place during the growth of single crystal films of silicon on sapphire (SOS) are analyzed thermodynamically. The temperature for the growth of good quality epitaxial films is dependent on the extent of water vapor present in the carrier gas. The higher the water vapor content the higher the temperature needed to grow SOS films. Due to the interaction of silicon with sapphire at elevated temperatures, SOS films are doped with aluminum. The extent of doping is dependent on the conditions of film growth. The doping by aluminum from the substrate increases with increasing growth temperatures and decreasing growth rates. The equilibrium concentrations of aluminum at the silicon-sapphire interface are calculated as a function of deposition temperature, assuming that SiO2 or Al6Si2O13 are the products of reaction. It is most likely that the product could be a solid solutio n of Al2O3 in SiO2. The total amount of aluminum released due to the interaction between silicon and sapphire will account only for the formation of not more than one monolayer of reaction product unless the films are annealed long enough at elevated temperatures. This value is in good agreement with the recently reported observations employing high resolution transmission electron microscopy.

Combined Electron Transfer Dissociation-Collision-Induced Dissociation Fragmentation in the Mass Spectrometric Distinction of Leucine, Isoleucine, and Hydroxyproline Residues in Peptide Natural Products

Distinctions between isobaric residues have been a major challenge in mass spectrometric peptide sequencing. Here, we propose a methodology for distinction among isobaric leucine, isoleucine, and hydroxyproline, a commonly found post-translationally modified amino acid with a nominal mass of 113 Da, through a combined electron transfer dissociation-collision-induced dissociation approach. While the absence of c and z(center dot) ions, corresponding to the Yyy-Xxx (Xxx = Leu, Ile, or Hyp) segment, is indicative of the presence of hydroxyproline, loss of isopropyl (Delta m = 43 Da) or ethyl radicals (Delta m = 29 Da), through collisional activation of z(center dot) radical ions, are characteristic of leucine or isoleucine, respectively. Radical migration processes permit distinctions even in cases where the specific e ions, corresponding to the Yyy-Leu or -Ile segments, are absent or of low intensity. This tandem mass spectrometric (MSn) method has been successfully implemented in a liquid chromatography MSn platform to determine the identity of 23 different isobaric residues from a mixture of five different peptides. The approach is convenient for distinction of isobaric residues from any crude peptide mixture, typically encountered in natural peptide libraries or proteomic analysis.

Caryophyllene-Rich Essential Oil of Didymocarpus tomentosa: Chemical Composition and Cytotoxic Activity

The essential oil from the leaves of Didymocarpus tomentosa was extracted by hydrodistillation and analyzed by GC/FID and GC/MS. Twenty five constituents amounting to 81.6% of the oil were identified. The leaf oil contained 78.7% sesquiterpenes and 2.9% monoterpenes. The leaf essential oil of D. tomentosa is a unique caryophyllene-rich natural source containing beta-caryophyllene, caryophyllene oxide, alpha-humulene and humulene oxide. The cytotoxic activity of the oil was determined by the BSLT using shrimp larva and the MTT assay using HeLa tumor cell line. The oil showed significant cytotoxic activity with LC50 and IC50 values of 12.26 and 11.4 mu g/mL, respectively. This is the first report on the chemical composition and cytotoxic activity of the essential oil of D. tomentosa.

Naphthalene Carbohydrazone Based Dizinc(II) Chemosensor for a Pyrophosphate Ion and Its DNA Assessment Application in Polymerase Chain Reaction Products

A new naphthalene carbohydrazone based dizinc(II) complex has been synthesized and investigated to act as a highly selective fluorescence and visual sensor for a pyrophosphate ion with a quite low detection limit of 155 ppb; this has also been used to detect the pyrophosphate ion released from polymerase-chain-reaction.

Multivariate PLS Modeling of Apicomplexan FabD-Ligand Interaction Space for Mapping Target-Specific Chemical Space and Pharmacophore Fingerprints

Biomolecular recognition underlying drug-target interactions is determined by both binding affinity and specificity. Whilst, quantification of binding efficacy is possible, determining specificity remains a challenge, as it requires affinity data for multiple targets with the same ligand dataset. Thus, understanding the interaction space by mapping the target space to model its complementary chemical space through computational techniques are desirable. In this study, active site architecture of FabD drug target in two apicomplexan parasites viz. Plasmodium falciparum (PfFabD) and Toxoplasma gondii (TgFabD) is explored, followed by consensus docking calculations and identification of fifteen best hit compounds, most of which are found to be derivatives of natural products. Subsequently, machine learning techniques were applied on molecular descriptors of six FabD homologs and sixty ligands to induce distinct multivariate partial-least square models. The biological space of FabD mapped by the various chemical entities explain their interaction space in general. It also highlights the selective variations in FabD of apicomplexan parasites with that of the host. Furthermore, chemometric models revealed the principal chemical scaffolds in PfFabD and TgFabD as pyrrolidines and imidazoles, respectively, which render target specificity and improve binding affinity in combination with other functional descriptors conducive for the design and optimization of the leads.

High-Pressure Kinetics of Vinyl Polyperoxides

This is the first report on studies carried out in detail on high-pressure oxygen copolymerization (> 50 psi) of the vinyl monomers styrene and alpha-methylstyrene (AMS). The saturation pressure of oxygen for AMS oxidation, hitherto obscure, is found to be 300 psi. Whereas the ease of oxidation is more favorable for styrene, the rate and yield of polyperoxide formation are higher for AMS. This is explained on the basis of the reactivity of the corresponding alkyl and peroxy radicals. Below 50 degrees C, degradation of the poly(styrene peroxide) formed is about 2.5 times less than that observed above 50 degrees C, so much so that it gives a break in the rate curve, and thereafter the rate is lowered. Normal free radical kinetics is followed before the break point, after which the monomer and initiator exponents become unusually high. This is interpreted on the basis of chain transfer to the degradation products. The low molecular weight of polyperoxides has been attributed to the (i) low reactivity of RO(2)(.) toward the monomer, (ii) chain transfer to degradation products, (iii) facile cleavage of O-O bond, followed by unzipping to nonradical products, and (iv) higher stability of the reinitiating radicals. At lower temperatures, (i) predominates, whereas at higher temperatures, chiefly (ii)-(iv) are the case.

Growth and electron effective mass measurements of strained Si and Si0.94Ge0.06 on relaxed Si0.62Ge0.38 buffers grown by rapid thermal chemical vapor deposition

Abstract: We report the growth and the electron cyclotron resonance measurements of n-type Si/Si0.62Ge0.38 and Si0.94Ge0.06/Si0.62Ge0.38 modulation-doped heterostructures grown by rapid thermal chemical vapor deposition. The strained Si and Si0.94Ge0.06 channels were grown on relaxed Si0.62Ge0.38 buffer layers, which consist of 0.6 mu m uniform Si0.62Ge0.38 layers and 0.5 mu m compositionally graded relaxed SiGe layers from 0 to 38% Ge. The buffer layers were annealed at 800 degrees C for 1 h to obtain complete relaxation. A 75 Angstrom Si(SiGe) channel with a 100 Angstrom spacer and a 300 Angstrom 2 X 10(19) cm(-3) n-type supply layer was grown on the top of the buffer layers. The cross-sectional transmission electron microscope reveals that the dense dislocation network is confined to the buffer layer, and relatively few dislocations terminate on the surface. The plan-view image indicates the threading dislocation density is about 4 X 10(6) cm(-2). The far-infrared measurements of electron cyclotron resonance were performed at 4 K with the magnetic field of 4-8 T. The effective masses determined from the slope of the center frequency of the absorption peak versus applied magnetic field plot are 0.203m(0) and 0.193m(0) for the two dimensional electron gases in the Si and Si0.94Ge0.06 channels, respectively. The Si effective mass is very close to that of a two dimensional electron gas in an Si MOSFET (0.198m(0)). The electron effective mass of Si0.94Ge0.06 is reported for the first time and is about 5% lower than that of pure Si.

Surface chemical studies of Thiobacillus ferrooxidans with reference to copper tolerance

A strain of Thiobacillus ferrooxidans was adapted to grow at higher concentrations of copper by single step culturing in the presence of 20 g/L (0.314 mol/L) cupric ions added to 9K medium. Exposure to copper results in change in the surface chemistry of the microorganism. The isoelectric point of the adapted strain (pI=4.7) was observed to be at a higher pH than that of the wild unadapted strain(pI=2.0). Compared to the wild strain, the copper adapted strain was found to be more hydrophobic and showed enhanced attachment efficiency to the pyrite mineral. The copper adsorption ability of the adapted strain was also found to be higher than that of the wild strain. Fourier transform infrared spectroscopy of adapted cells suggested that a proteinaceous new cell surface component is synthesized by the adapted strain. Treatment of adapted cells with proteinase-K, resulted in complete loss of tolerance to copper, reduction in copper adsorption and hydrophobicity of the adapted cells. These observations strongly suggest a role played by cell surface modifications of Thiobacillus ferrooxidans in imparting the copper tolerance to the cells and bioleaching of sulphide minerals.

Surface chemical studies on mica and galena using dextrin

The interactions of dextrin with biotite mica and galena have been investigated through adsorption, flotation, and electrokinetic measurements. The adsorption densities of dextrin onto mica continuously increase with increase of pH, while those onto galena show a maximum at pH 11.5. It is observed that the adsorption density of dextrin onto galena is quite high compared to that on mica. Both the adsorption isotherms exhibit Langmuirian behavior. Electrokinetic measurements portray conformational rearrangements of macromolecules with the loading, resulting in a shift of the shear plane, further away from the interface. Dissolution experiments indicate release of the lattice metal ions from mica and galena. Coprecipitation tests confirm polymer-metal ion interaction in the bulk solution. Dextrin does not exhibit any depressant action toward mica, whereas, with galena, the flotation recovery is decreased with an increase in pH beyond 9, in the presence of dextrin, complementing the adsorption results. Differential flotation results on a synthetic mixture of mica and galena show that mica can be selectively separated from galena using dextrin as a depressant for galena above pH 10. Possible mechanisms of interaction between dextrin and mica/galena are discussed.

Synthesis, X-ray structures, and spectroscopic and electrochemical properties of (mu-oxo)bis(mu-carboxylato)diruthenium complexes having six imidazole bases as terminal ligands

Complexes [Ru2O(O2CR)(2)(1-MeIm)(6)](ClO4)(2) (la-c), [Ru2O(O2CR)(2)(ImH)(6)](ClO4)(2) (2a,b), and [Ru2O(O2CR)(2)(4-MeImH)(6)](ClO4)(2) (3a,b) with a (mu-oxo)bis(mu-carboxylato)diruthenium(III) core have been prepared by reacting Ru2Cl(O2CR)(4) with the corresponding imidazole base, viz. 1-methylimidazole (1-MeIm), imidazole (ImH), and 4-methylimidazole (4-MeImH) in methanol, followed by treatment with NaClO4 in water (R: Me, a; C6H4-p-OMe, b; C6H4-p-Me, c). Diruthenium(III,IV) complexes [Ru2O(O2CR)(2)(1-MeIm)(6)](ClO4)(3) (R: Me, 4a; C6H4-p-OMe, 4b; C6H4-p-Me, 4c) have been prepared by one-electron oxidation of 1 in MeCN with K2S2O8 in water. Complexes la, 2a . 3H(2)O, and 4a . 1.5H(2)O have been structurally characterized. Crystal data for the complexes are as follows: la, orthorhombic, P2(1)2(1)2(1), a = 7.659(3) Angstrom, b = 22.366(3) Angstrom, c = 23.688(2) Angstrom, V = 4058(2) Angstrom(3), Z = 4, R = 0.0475, and R-w = 0.0467 for 2669 reflections with F-o > 2 sigma(F-o); 2a . 3H(2)O, triclinic, , a = 13.735(3) Angstrom, b = 14.428(4) Angstrom, c = 20.515(8) Angstrom, alpha = 87.13(3)degrees, beta = 87.61(3)degrees, gamma = 63.92(2)degrees, V = 3646(2) Angstrom(3), Z = 4, R = 0.0485 and R-w = 0.0583 for 10 594 reflections with F-o > 6 sigma(F-o); 4a . 1.5H(2)O triclinic, , a = 11.969(3) Angstrom, b = 12.090(6) Angstrom, c = 17.421(3) Angstrom, alpha = 108.93(2)degrees, beta = 84.42(2)degrees, gamma = 105.97(2)degrees, V = 2292(1) Angstrom(3), Z = 2, R = 0.0567, and R-w = 0.0705 for 6775 reflections with F-o > 6 sigma(F-o). The complexes have a diruthenium unit held by an oxo and two carboxylate ligands, and the imidazole ligands occupy the terminal sites of the core. The Ru-Ru distance and the Ru-O-oxo-Ru angle in la and 2a . 3H(2)O are 3.266(1), 3.272(1) Angstrom and 122.4(4), 120.5(2)degrees, while in 4a . 1.5H(2)O these values are 3.327(1) Angstrom and 133.6(2)degrees. The diruthenium(III) complexes 1-3 are blue in color and they exhibit an intense visible band in the range 560-575 nm. The absorption is charge transfer in nature involving the Ru(III)-d pi and O-oxo-p pi orbitals. The diruthenium(III,IV) complexes are red in color and show an intense band near 500 nm. The diruthenium(III) core readily gets oxidized with K2S2O8 forming quantitatively the diruthenium(III,IV) complex. The visible spectral record of the conversion shows an isosbestic point at 545 nm for 1 and at 535 nm for 2 and 3. Protonation of the oxide bridge by HClO4 in methanol yields the [Ru-2(mu-OH)(mu-O2CR)(2)](3+) core. The hydroxo species shows a visible band al 550 nm. The pK(a) value for la is 2.45. The protonated species are unstable. The 1-MeIm species converts to the diruthenium(III,IV) core, while the imidazole complex converts to [Ru(ImH)(6)](3+) and some uncharacterized products. Complex [Ru(ImH)(6)](ClO4)(3) has been structurally characterized. The diruthenium(III) complexes are essentially diamagnetic and show characteristic H-1 NMR spectra indicating the presence of the dimeric structure in solution. The diruthenium(III,IV) complexes are paramagnetic and display rhombic EPR spectral features. Complexes 1-3 are redox active. Complex 1 shows the one-electron reversible Ru-2(III)/(RuRuIV)-Ru-III, one-electron quasireversible (RuRuIV)-Ru-III/Ru-2(IV), and two-electron quasireversible Ru-2(III)/Ru-2(II) couples near 0.4, 1.5, and -1.0 V vs SCE In MeCN-0.1 M TBAP, respectively, in the cyclic and differential pulse voltammetric studies. Complexes 2 and 3 exhibit only reversible Ru-2(III)/(RuRuIV)-Ru-III and the quasireversible (RuRuIV)-Ru-III/Ru-2(IV) couples near 0.4 and 1.6 V vs SCE, respectively, The observation of a quasireversible one-step two-electron transfer reduction process in 1 is significant considering its relevance to the rapid and reversible Fe-2(III)/Fe-2(II) redox process known for the tribridged diiron core in the oxy and deoxy forms of hemerythrin.

The role of lysine-41 in RNase A catalysis - A quantum chemical study on the active site ligand complex

Several mechanisms have been proposed to explain the action of enzymes at the atomic level. Among them, the recent proposals involving short hydrogen bonds as a step in catalysis by Gerlt and Gassman [1] and proton transfer through low barrier hydrogen bonds (LBHBs) [2, 3] have attracted attention. There are several limitations to experimentally testing such hypotheses, Recent developments in computational methods facilitate the study of active site-ligand complexes to high levels of accuracy, Our previous studies, which involved the docking of the dinucleotide substrate UpA to the active site of RNase A [4, 5], enabled us to obtain a realistic model of the ligand-bound active site of RNase A. From these studies, based on empirical potential functions, we were able to obtain the molecular dynamics averaged coordinates of RNase A, bound to the ligand UpA. A quantum mechanical study is required to investigate the catalytic process which involves the cleavage and formation of covalent bonds. In the present study, we have investigated the strengths of some of the hydrogen bonds between the active site residues of RNase A and UpA at the ab initio quantum chemical level using the molecular dynamics averaged coordinates as the starting point. The 49 atom system and other model systems were optimized at the 3-21G level and the energies of the optimized systems were obtained at the 6-31G* level. The results clearly indicate the strengthening of hydrogen bonds between neutral residues due to the presence of charged species at appropriate positions. Such a strengthening manifests itself in the form of short hydrogen bonds and a low barrier for proton transfer. In the present study, the proton transfer between the 2'-OH of ribose (from the substrate) and the imidazole group from the H12 of RNase A is influenced by K41, which plays a crucial role in strengthening the neutral hydrogen bond, reducing the barrier for proton transfer.

Time-temperature histories of spherical food products during bulk forced-air precooling

A general mathematical model for forced air precooling of spherical food products in bulk is developed. The food products are arranged inline to form a rectangular parallelepiped. Chilled air is blown along the height of the package. The governing equations for the transient two-dimensional conduction with internal heat generation in the product, simultaneous heat and mass transfer at the product-air interface and one-dimensional transient energy and species conservation equations for the moist air are solved numerically using finite difference methods. Results are presented in the form of time-temperature histories. Experiments are conducted with model foods in a laboratory scale air precooling tunnel. The agreement between the theoretical and experimental results is found to be good. In general, a single product analysis fails to predict the precooling characteristics of bulk loads of food products. In the range of values investigated, the respiration heat is found to have a negligible effect.

Dynamics of a dilute sheared inelastic fluid. II. The effect of correlations

The effect of correlations on the viscosity of a dilute sheared inelastic fluid is analyzed using the ring-kinetic equation for the two-particle correlation function. The leading-order contribution to the stress in an expansion in epsilon=(1-e)(1/2) is calculated, and it is shown that the leading-order viscosity is identical to that obtained from the Green-Kubo formula, provided the stress autocorrelation function in a sheared steady state is used in the Green-Kubo formula. A systemmatic extension of this to higher orders is also formulated, and the higher-order contributions to the stress from the ring-kinetic equation are determined in terms of the terms in the Chapman-Enskog solution for the Boltzmann equation. The series is resummed analytically to obtain a renormalized stress equation. The most dominant contributions to the two-particle correlation function are products of the eigenvectors of the conserved hydrodynamic modes of the two correlated particles. In Part I, it was shown that the long-time tails of the velocity autocorrelation function are not present in a sheared fluid. Using those results, we show that correlations do not cause a divergence in the transport coefficients; the viscosity is not divergent in two dimensions, and the Burnett coefficients are not divergent in three dimensions. The equations for three-particle and higher correlations are analyzed diagrammatically. It is found that the contributions due to the three-particle and higher correlation functions to the renormalized viscosity are smaller than those due to the two-particle distribution function in the limit epsilon -> 0. This implies that the most dominant correlation effects are due to the two-particle correlations.

Thermal Degradation Processes in Poly(xylylene sulfides) Investigated by Comparative Direct Pyrolysis MS and Flash Pyrolysis GC/MS Experiments

The thermal degradation processes of two sulfur polymers, poly(xylylene sulfide) (PXM) and poly(xylylene disulfide) (PXD), were investigated in parallel by direct pyrolysis mass spectrometry (DPMS) and flash pyrolysis GC/MS (Py-GC/MS). Thermogravimetric data showed that these polymers decompose with two separate steps in the temperature ranges of 250-280 and 600-650 degrees C, leaving a high amount of residue (about 50% at 800 degrees C). The pyrolysis products detected by DPMS in the first degradation step of PXM and PXD were terminated by three types of end groups, -CH3, -CH2SH, and -CH=S, originating from thermal cleavage reactions involving a series of homolytic chain scissions followed by hydrogen transfer reactions, generating several oligomers containing some intact xylylene sulfide repeating units. The presence of pyrolysis compounds containing some stilbene-like units in the first degradation step has also been observed. Their formation has been accounted for with a parallel cleavage involving the elimination of H2S from the PXM main chains. These unsaturated units can undergo cross-linking at higher temperatures, producing the high amount of char residue observed. The thermal degradation compounds detected by DPMS in the second decomposition step at about 600-650 degrees C were constituted of condensed aromatic molecules containing dihydrofenanthrene and fenanthrene units. These compounds might be generated from the polymer chains containing stilbene units, by isomerization and dehydrogenation reactions. The pyrolysis products obtained in the Py-GC/MS of PXM and PXD at 610 degrees C are almost identical. The relative abundance in the pyrolysate and the spectral properties of the main pyrolysis products were found to be in generally good agreement with those obtained by DPMS. Polycyclic aromatic hydrocarbons (PAHs) were also detected by Py-GC/MS but in minor amounts with respect to DPMS. This apparent discrepancy was due to the simultaneous detection of PAHs together with all pyrolysis products in the Py-GC/MS, whereas in DPMS they were detected in the second thermal degradation step without the greatest part of pyrolysis compounds generated in the first degradation step. The results obtained by DPMS and PSI-GC/MS experiments showed complementary data for the degradation of PXM and PXD and, therefore, allowed the unequivocal formulation of the thermal degradation mechanism for these sulfur-containing polymers.