Galactic Bulge PNe:Carbon molecules in oxygen-rich environments

Galactic bulge planetary nebulae show evidence of mixed chemistry with emission from both silicate dust and PAHs. This mixed chemistry is unlikely to be related to carbon dredge up, as third dredge-up is not expected to occur in the low mass bulge stars. We show that the phenomenon is widespread, and is seen in 30 nebulae out of our sample of 40. A strong correlation is found between strength of the PAH bands and morphology, in particular, the presence of a dense torus. A chemical model is presented which shows that hydrocarbon chains can form within oxygen-rich gas through gas-phase chemical reactions. We conclude that the mixed chemistry phenomenon occurring in the galactic bulge planetary nebulae is best explained through hydrocarbon chemistry in an UV-irradiated, dense torus. © 2012 International Astronomical Union.

Immunomodulatory molecules of Fasciola hepatica:Candidates for both vaccine and immunotherapeutic development

The liver fluke, Fasciola hepatica, causes fascioliasis in domestic animals (sheep, cattle), a global disease that is also an important infection of humans. As soon as the parasite invades the gut wall its interaction with various host immune cells (e.g. dendritic cells, macrophages and mast cells) is complex. The parasite secretes a myriad of molecules that direct the immune response towards a favourable non-protective Th2-mediate/regulatory environment. These immunomodulatory molecules, such as cathepsin L peptidase (FhCL1), are under development as the first generation of fluke vaccines. However, this peptidase and other molecules, such as peroxiredoxin (FhPrx) and helminth defence molecule (FhHDM-1), exhibit various immunomodulatory properties that could be harnessed to help treat immune-related conditions in humans and animals.

Copper/TEMPO catalysed synthesis of nitriles from aldehydes or alcohols using aqueous ammonia and with air as the oxidant†‡

Copper/TEMPO catalysts can be used to prepare nitriles from aldehydes or alcohols using aqueous ammonia. Readily accessible methods were developed that enable standard glassware to be used with air as the source of O2. It was further shown that, at higher temperatures in a pressurised reactor under limiting oxygen conditions (8% O2), catalyst loadings of 1 mol% could be employed.

Adsorption of metal cations by hydrous aluminium(III) or iron(III) hydroxide precipitates: enhancement by EDTA and related chelate molecules

Stoichiometrically equivalent concentrations of ethylenediaminetetraacetate, EDTA, and of related chelating anions increase the adsorption of ca. millimolar concentrations heavy metal aqua-ions on amorphous precipitates of aluminium(III) or iron(III) hydroxide and, although higher concentrations decrease the adsorption, poly-EDTA, a polyelectrolyte containing EDTA functional groups, shows no such decrease.

Fixed Bed Study of Ammonia Removal from Aqueous Solutions Using Natural Zeolite

Purpose
– The purpose of this paper is to investigate the performance of natural Jordanian zeolite tuff to remove ammonia from aqueous solutions using a laboratory batch method and fixed-bed column apparatus. Equilibrium data were fitted to Langmuir and Freundlich models.

Design/methodology/approach
– Column experiments were conducted in packed bed column. The used apparatus consisted of a bench-mounted glass column of 2.5 cm inside diameter and 100 cm height (column volume = 490 cm3). The column was packed with a certain amount of zeolite to give the desired bed height. The feeding solution was supplied from a 30 liter plastic container at the beginning of each experiment and fed to the column down-flow through a glass flow meter having a working range of 10-280ml/min.

Findings
– Ammonium ion exchange by natural Jordanian zeolite data were fitted by Langmuir and Freundlich isotherms. Continuous sorption of ammonium ions by natural Jordanian zeolite tuff has proven to be effective in decreasing concentrations ranging from 15-50 mg NH4-N/L down to levels below 1 mg/l. Breakthrough time increased by increasing the bed depth as well as decreasing zeolite particle size, solution flow-rate, initial NH4+ concentration and pH. Sorption of ammonium by the zeolite under the tested conditions gave the sorption capacity of 28 mg NH4-N/L at 20°C, and 32 mg NH4-N/L at 30°C.

Originality/value
– This research investigates the performance of natural Jordanian zeolite tuff to remove ammonia from aqueous solutions using a laboratory batch method and fixed-bed column apparatus. The equilibrium data of the sorption of Ammonia were plotted by using the Langmuir and Freundlich isotherms, then the experimental data were compared to the predictions of the above equilibrium isotherm models. It is clear that the NH4+ ion exchange data fitted better with Langmuir isotherm than with Freundlich model and gave an adequate correlation coefficient value.

In situ FTIR studies on the effect of temperature on the electro-oxidation of small organic molecules at the Ru(0001) electrode

The adsorption and electro-oxidation of formaldehyde, formic acid and methanol at the Ru(0001) electrode in perchloric acid solution have been studied as a function of temperature, potential and time using in situ FTIR spectroscopy, and the results interpreted in terms of the surface chemistry of the Ru(0001) electrode and compared to those obtained during our previous studies on the adsorption of CO under the same conditions. It was found that no dissociative adsorption or electro-oxidation of methanol takes place at Ru(0001) at potentials 1000 mV, both the oxidation of formic acid to CO and the oxidation of formaldehyde to both CO and formic acid were significantly increased, and the oxidation of methanol to CO and methyl formate was observed, all of which were attributed to the formation of an active RuO phase on the Ru(0001) surface.

Cathelicidin-like Helminth Defence Molecules (HDMs):Absence of Cytotoxic, Anti-microbial and Anti-protozoan Activities Imply a Specific Adaptation to Immune Modulation

Host defence peptides (HDPs) are expressed throughout the animal and plant kingdoms. They have multifunctional roles in the defence against infectious agents of mammals, possessing both bactericidal and immune-modulatory activities. We have identified a novel family of molecules secreted by helminth parasites (helminth defence molecules; HDMs) that exhibit similar structural and biochemical characteristics to the HDPs. Here, we have analyzed the functional activities of four HDMs derived from Schistosoma mansoni and Fasciola hepatica and compared them to human, mouse, bovine and sheep HDPs. Unlike the mammalian HDPs the helminth-derived HDMs show no antimicrobial activity and are non-cytotoxic to mammalian cells (macrophages and red blood cells). However, both the mammalian- and helminth-derived peptides suppress the activation of macrophages by microbial stimuli and alter the response of B cells to cytokine stimulation. Therefore, we hypothesise that HDMs represent a novel family of HDPs that evolved to regulate the immune responses of their mammalian hosts by retaining potent immune modulatory properties without causing deleterious cytotoxic effects.

High energy resolution fluorescence detection XANES - an in situ method to study the interaction of adsorbed molecules with metal catalysts in the liquid phase

The change in the Pt electronic structure following the adsorption of an a,ß-unsaturated aldehyde and ketone was followed by in situ HERFD-XANES in the liquid phase. The resulting shift in the Pt Fermi energy is in good agreement with the molecule adsorption energy trends calculated by DFT and provides insight into the reaction selectivity.

Complex organic molecules in protoplanetary disks

Context. Protoplanetary disks are vital objects in star and planet formation, possessing all the material, gas and dust, which may form a planetary system orbiting the new star. Small, simple molecules have traditionally been detected in protoplanetary disks; however, in the ALMA era, we expect the molecular inventory of protoplanetary disks to significantly increase.

Aims. We investigate the synthesis of complex organic molecules (COMs) in protoplanetary disks to put constraints on the achievable chemical complexity and to predict species and transitions which may be observable with ALMA.

Methods. We have coupled a 2D steady-state physical model of a protoplanetary disk around a typical T Tauri star with a large gas-grain chemical network including COMs. We compare the resulting column densities with those derived from observations and perform ray-tracing calculations to predict line spectra. We compare the synthesised line intensities with current observations and determine those COMs which may be observable in nearby objects. We also compare the predicted grain-surface abundances with those derived from cometary comae observations.

Results. We find COMs are efficiently formed in the disk midplane via grain-surface chemical reactions, reaching peak grain-surface fractional abundances similar to 10(-6)-10(-4) that of the H nuclei number density. COMs formed on grain surfaces are returned to the gas phase via non-thermal desorption; however, gas-phase species reach lower fractional abundances than their grain-surface equivalents, similar to 10(-12)-10(-7). Including the irradiation of grain mantle material helps build further complexity in the ice through the replenishment of grain-surface radicals which take part in further grain-surface reactions. There is reasonable agreement with several line transitions of H2CO observed towards T Tauri star-disk systems. There is poor agreement with HC3(N) lines observed towards LkCa 15 and GO Tau and we discuss possible explanations for these discrepancies. The synthesised line intensities for CH3OH are consistent with upper limits determined towards all sources. Our models suggest CH3OH should be readily observable in nearby protoplanetary disks with ALMA; however, detection of more complex species may prove challenging, even with ALMA "Full Science" capabilities. Our grain-surface abundances are consistent with those derived from cometary comae observations providing additional evidence for the hypothesis that comets (and other planetesimals) formed via the coagulation of icy grains in the Sun's natal disk.

Complex organic molecules along the accretion flow in isolated and externally irradiated protoplanetary disks

(Abridged) The birth environment of the Sun will have influenced the conditions in the pre-solar nebula, including the attainable chemical complexity, important for prebiotic chemistry. The formation and distribution of complex organic molecules (COMs) in a disk around a T Tauri star is investigated for two scenarios: (i) an isolated disk, and (ii) a disk irradiated externally by a nearby massive star. The chemistry is calculated along the accretion flow from the outer disk inwards using a comprehensive network. Two simulations are performed, one beginning with complex ices and one with simple ices only. For the isolated disk, COMs are transported without major alteration into the inner disk where they thermally desorb into the gas reaching an abundance representative of the initial assumed ice abundance. For simple ices, COMs efficiently form on grain surfaces under the conditions in the outer disk. Gas-phase COMs are released into the molecular layer via photodesorption. For the irradiated disk, complex ices are also transported inwards; however, they undergo thermal processing caused by the warmer conditions in the irradiated disk which tends to reduce their abundance along the accretion flow. For simple ices, grain-surface chemistry cannot synthesise COMs in the outer disk because the necessary grain-surface radicals, which tend to be particularly volatile, are not sufficiently abundant on the grain surfaces. Gas-phase COMs are formed in the inner region of the irradiated disk via gas-phase chemistry induced by the desorption of strongly bound molecules such as methanol; hence, the abundances are not representative of the initial molecular abundances injected into the outer disk. These results suggest that the composition of comets formed in isolated disks may differ from those formed in externally irradiated disks with the latter composed of more simple ices.

A high resolution study of complex organic molecules in hot cores

We present the results of a line identification analysis using data from the IRAM Plateau de Bure Inferferometer, focusing on six massive star-forming hot cores: G31.41+0.31, G29.96-0.02, G19.61-0.23, G10.62-0.38, G24.78+0.08A1 and G24.78+0.08A2. We identify several transitions of vibrationally excited methyl formate (HCOOCH$_3$) for the first time in these objects as well as transitions of other complex molecules, including ethyl cyanide (C$_2$H$_5$CN), and isocyanic acid (HNCO). We also postulate a detection of one transition of glycolaldehyde (CH$_2$(OH)CHO) in two new hot cores. We find G29.96-0.02, G19.61-0.23, G24.78+0.08A1 and 24.78+0.08A2 to be chemically very similar. G31.41+0.31, however, is chemically different: it manifests a larger chemical inventory and has significantly larger column densities. We suggest that it may represent a different evolutionary stage to the other hot cores in the sample, or it may surround a star with a higher mass. We derive column densities for methyl formate in G31.41+0.31, using the rotation diagram method, of $\times$10$^{17}$ cm$^{-2}$ and a T$_{rot}$ of $\sim$170 K. For G29.96-0.02, G24.78+0.08A1 and G24.78+0.08A2, glycolaldehyde, methyl formate and methyl cyanide all seem to trace the same material and peak at roughly the same position towards the dust emission peak. For G31.41+0.31, however, glycolaldehyde shows a different distribution to methyl formate and methyl cyanide and seems to trace the densest, most compact inner part of hot cores.

Universal tight binding model for chemical reactions in solution and at surfaces. I. Organic molecules

As is now well established, a first order expansion of the Hohenberg-Kohn total energy density functional about a trial input density, namely, the Harris-Foulkes functional, can be used to rationalize a non self consistent tight binding model. If the expansion is taken to second order then the energy and electron density matrix need to be calculated self consistently and from this functional one can derive a charge self consistent tight binding theory. In this paper we have used this to describe a polarizable ion tight binding model which has the benefit of treating charge transfer in point multipoles. This admits a ready description of ionic polarizability and crystal field splitting. It is necessary in constructing such a model to find a number of parameters that mimic their more exact counterparts in the density functional theory. We describe in detail how this is done using a combination of intuition, exact analytical fitting, and a genetic optimization algorithm. Having obtained model parameters we show that this constitutes a transferable scheme that can be applied rather universally to small and medium sized organic molecules. We have shown that the model gives a good account of static structural and dynamic vibrational properties of a library of molecules, and finally we demonstrate the model's capability by showing a real time simulation of an enolization reaction in aqueous solution. In two subsequent papers, we show that the model is a great deal more general in that it will describe solvents and solid substrates and that therefore we have created a self consistent quantum mechanical scheme that may be applied to simulations in heterogeneous catalysis.

Microelectronic manufacturing of a microsensor based on polyaniline for ammonia gas sensing

The fabrication and operation of an ammonia chemoresistor is described. The sensor responds to changes in the resistance (impedance) of a thin layer of conductive polymer is due to changes in ammonia concentration. The polyaniline film was deposited by electroless plating (dipping) method on interdigitated array made by photolithographic technique. The PANI film was characterized by UV/VIS and IR Spectroscopy and respectively, Atomic Force Microscopy. Impedance Spectroscopy was used for sensor characterization