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 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.

A Stubbornly Large Mass of Cold Dust in the Ejecta of Supernova 1987A

We present new Herschel photometric and spectroscopic observations of Supernova 1987A, carried out in 2012. Our dedicated photometric measurements provide new 70 mu m data and improved imaging quality at 100 and 160 mu m compared to previous observations in 2010. Our Herschel spectra show only weak CO line emission, and provide an upper limit for the 63 mu m [O-I] line flux, eliminating the possibility that line contaminations distort the previously estimated dustmass. The far-infrared spectral energy distribution (SED) is well fitted by thermal emission from cold dust. The newly measured 70 mu m flux constrains the dust temperature, limiting it to nearly a single temperature. The far-infrared emission can be fitted by 0.5 +/- 0.1M(circle dot) of amorphous carbon, about a factor of two larger than the current nucleosynthetic mass prediction for carbon. The observation of SiO molecules at early and late phases suggests that silicates may also have formed and we could fit the SED with a combination of 0.3M(circle dot) of amorphous carbon and 0.5M(circle dot) of silicates, totalling 0.8M(circle dot) of dust. Our analysis thus supports the presence of a large dust reservoir in the ejecta of SN 1987A. The inferred dust mass suggests that supernovae can be an important source of dust in the interstellar medium, from local to high-redshift galaxies.

Sputtering of oxygen ice by low energy ions

Naturally occurring ices lie on both interstellar dust grains and on celestial objects, such as those in the outer Solar system. These ices are continuously subjected to irradiation by ions from the solar wind and/or cosmic rays, which modify their surfaces. As a result, new molecular species may form which can be sputtered off into space or planetary atmospheres. We determined the experimental values of sputtering yields for irradiation of oxygen ice at 10 K by singly (He+, C+, N+, O+ and Ar+) and doubly (C2 +, N2 + and O2 +) charged ions with 4 keV kinetic energy. In these laboratory experiments, oxygen ice was deposited and irradiated by ions in an ultra high vacuum chamber at low temperature to simulate the environment of space. The number of molecules removed by sputtering was observed by measurement of the ice thickness using laser interferometry. Preliminary mass spectra were taken of sputtered species and of molecules formed in the ice by temperature programmed desorption (TPD). We find that the experimental sputtering yields increase approximately linearly with the projectile ion mass (or momentum squared) for all ions studied. No difference was found between the sputtering yields for singly and doubly charged ions of the same atom within the experimental uncertainty, as expected for a process dominated by momentum transfer. The experimental sputter yields are in good agreement with values calculated using a theoretical model except in the case of oxygen ions. Preliminary studies have shown molecular oxygen as the dominant species sputtered and TPD measurements indicate ozone formation.

Early-type stars observed in the ESO UVES Paranal observatory project - IV. studies of CN, CH+ and CH in the interstellar medium

High spectral resolution (~80 000) and signal-to-noise observations from the Ultraviolet and Visual Echelle Spectrograph Paranal Observatory Project (UVES-POP) are used to study the interstellarmolecular lines CN (3874 Å), CH⁺ (3957, 4232 Å) and CH (3886, 4300 Å) towards 74 O- and B-type stellar sightlines. Additionally, archive data are presented for 140 ELODIE early-type stellar sightlines at R = 42 000, plus 25 FEROS at R = 48 000 and 3 UVES at R > 50 000, mainly in the CH⁺ (4232 Å) and CH (3886, 4300 Å) transitions. Detection rates are ~45 per cent for CN and ~67 per cent for the other lines in the POP sample, and ~10-15 per cent for CH⁺ and CH lines in the additional sample. CH and CH⁺ are well correlated between log[N(CH) cm^-2]~12-14, implying that these clouds are CH⁺-like CH and not CN-like CH. CH is also very well correlated with Na I D in the range log[N(Na I cm^-2]) ~12.2-14.2. A few sightlines show tentative velocity shifts of ~2 km s^-1 between CH and CH⁺, which appear to be caused by differences in component strength in blends, and hence do not provide firm evidence for shocks. Finally, we describe a search for ¹³CH⁺ in a sightline towards HD 76341. No ¹³CH⁺ is detected, placing a limit on the ¹³CH⁺ to ¹²CH⁺ ratio of ~0.01. If a formal fit is attempted, the equivalent width ratio in the two isotopes is a factor ~90 but with large errors. 

Early-type stars observed in the ESO UVES Paranal Observatory Project - V. Time-variable interstellar absorption

The structure and properties of the diffuse interstellar medium (ISM) on small scales, sub-au to 1 pc, are poorly understood. We compare interstellar absorption-lines, observed towards a selection of O- and B-type stars at two or more epochs, to search for variations over time caused by the transverse motion of each star combined with changes in the structure in the foreground ISM. Two sets of data were used: 83 VLT- UVES spectra with approximately 6 yr between epochs and 21 McDonald observatory 2.7m telescope echelle spectra with 6 - 20 yr between epochs, over a range of scales from 0 - 360 au. The interstellar absorption-lines observed at the two epochs were subtracted and searched for any residuals due to changes in the foreground ISM. Of the 104 sightlines investigated with typically five or more components in Na I D, possible temporal variation was identified in five UVES spectra (six components), in Ca II, Ca I and/or Na I absorption-lines. The variations detected range from 7\% to a factor of 3.6 in column density. No variation was found in any other interstellar species. Most sightlines show no variation, with 3{\sigma} upper limits to changes of the order 0.1 - 0.3 dex in Ca II and Na I. These variations observed imply that fine-scale structure is present in the ISM, but at the resolution available in this study, is not very common at visible wavelengths. A determination of the electron densities and lower limits to the total number density of a sample of the sightlines implies that there is no striking difference between these parameters in sightlines with, and sightlines without, varying components.

Astrochemistry

In the last 40 years a wide range of molecules, including neutrals, cations and anions, containing up to 13 atoms—in addition to detections of C₆₀ and C₇₀ — have been found in the harsh environment of the interstellar medium. The exquisite sensitivity and very high spectral and, more recently, spatial resolution, of modern telescopes has enabled the physics of star formation to be probed through rotational line emission. In this article, I review the basic properties of interstellar clouds and the processes that initiate the chemistry and generate chemical complexity, particularly in regions of star and planet formation. Our understanding of astrochemistry has evolved over the years. Before 1990, the general consensus was that molecules were formed in binary, gas-phase, or volume, reactions, most importantly ion-neutral reactions despite the very low ionization in clouds. Since then, observations have indicated unambiguously that there is also a contribution from surface processes, particularly on the icy mantles that form around refractory grain cores in cold, dense gas. The balance between these two processes depends on particular physical conditions and can vary during the life cycle of a particular volume of interstellar cloud.The complex chemistry that occurs in space is driven mostly through interaction of thegas with cosmic ray protons, a source of ionization that enables a rich ion-neutral chemistry. In addition, I show that the interaction between the gas and the dust in cold, dense regionsalso leads to additional chemical complexity through reactions that take place in ices at onlya few tens of degrees above absolute zero. Although densities are low compared to those in terrestrial environments, the extremely long life times of interstellar clouds and their enormous sizes, enable complex molecules to be synthesised and detected. I show that in some instances, particularly in reactions involving deuterium, the rotational populations of reactants, together with spin-selection rules, can determine the detailed abundances. Although the review is mainly focused on regions associated with star formation, I also consider chemistry in other interesting astronomical regions — in the early Universe and in the envelopes formed by mass loss during the final stages of stellar evolution.

Ultraluminous Supernovae as a New Probe of the Interstellar Medium in Distant Galaxies

We present the Pan-STARRS1 discovery and light curves, and follow-up MMT and Gemini spectroscopy of an ultraluminous supernova (ULSN; dubbed PS1-11bam) at a redshift of z = 1.566 with a peak brightness of M UV ≈ -22.3 mag. PS1-11bam is one of the highest redshift spectroscopically confirmed SNe known to date. The spectrum exhibits broad absorption features typical of previous ULSNe (e.g., C II, Si III), and strong and narrow Mg II and Fe II absorption lines from the interstellar medium (ISM) of the host galaxy, confirmed by an [O II]λ3727 emission line at the same redshift. The equivalent widths of the Fe II λ2600 and Mg II λ2803 lines are in the top quartile of the quasar intervening absorption system distribution, but are weaker than those of gamma-ray burst intrinsic absorbers (i.e., GRB host galaxies). We also detect the host galaxy in pre-explosion Pan-STARRS1 data and find that its UV spectral energy distribution is best fit with a young stellar population age of τ* ≈ 15-45 Myr and a stellar mass of M * ≈ (1.1-2.6) × 109 M ⊙ (for Z = 0.05-1 Z ⊙). The star formation rate inferred from the UV continuum and [O II]λ3727 emission line is ≈10 M ⊙ yr-1, higher than in previous ULSN hosts. PS1-11bam provides the first direct demonstration that ULSNe can serve as probes of the ISM in distant galaxies. The depth and red sensitivity of PS1 are uniquely suited to finding such events at cosmologically interesting redshifts (z ~ 1-2); the future combination of LSST and 30 m class telescopes promises to extend this technique to z ~ 4.

Information Gathering and Processing with Fluorescent Molecules

Molecular information gathering and processing – a young field of applied chemistry - is undergoing good growth. The progress is occurring both in terms of conceptual development and in terms of the strengthening of older concepts with new examples. This review critically surveys these two broad avenues. We consider some cases where molecules emulate one of the building blocks of electronic logic gates. We then examine molecular emulation of various Boolean logic gates carrying one, two or three inputs. Some single-input gates are popular information gathering devices. Special systems, such as ‘lab-on-a-molecule’ and molecular keypad locks, also receive attention. A situation deviating from the Boolean blueprint is also discussed. Some pointers are offered for maintaining the upward curve of the field.

Production of ultracold hydrogen and deuterium via Doppler-cooled Feshbach molecules

A counterintuitive scheme to produce ultracold hydrogen via fragmentation of laser cooled diatomic hydrides is presented where the final atomic H temperature is inversely proportional to the mass of the molecular parent. In addition, the critical density for formation of a Bose-Einstein condensate (BEC) at a fixed temperature is reduced by a factor (mH/mMH)3/2 over directly cooled hydrogen atoms. The narrow Feshbach resonances between a S01 atom and hydrogen are well suited to a tiny center of mass energy release necessary during fragmentation. With the support of ab initio quantum chemistry, it is demonstrated that BaH is an ideal diatomic precursor that can be laser cooled to a Doppler temperature of ∼26μK with just two rovibronic transitions, the simplest molecular cooling scheme identified to date. Preparation of a hydrogen atom gas below the critical BEC temperature Tc is feasible with present cooling technology, with optical pulse control of the condensation process.

Predicting solvent effects on the structure of porous organic molecules

A computational approach for the prediction of the open, metastable, conformations of porous organic molecules in the presence of solvent is developed.

The extracellular vesicles of the helminth pathogen, Fasciola hepatica: biogenesis pathways and cargo molecules involved in parasite pathogenesis.

Extracellular vesicles (EVs) released by parasites have important roles in establishing and maintaining infection. Analysis of the soluble and vesicular secretions of adult Fasciola hepatica has established a definitive characterisation of the total secretome of this zoonotic parasite. Fasciola secretes at least two sub-populations of EVs that differ according to size, cargo molecules and site of release from the parasite. The larger EVs are released from the specialised cells that line the parasite gastrodermus and contain the zymogen of the 37 kDa cathepsin L peptidase that performs a digestive function. The smaller exosome-like vesicle population originate from multivesicular bodies within the tegumental syncytium and carry many previously described immunomodulatory molecules that could be delivered into host cells. By integrating our proteomics data with recently available transcriptomic datasets we have detailed the pathways involved with EV biogenesis in F. hepatica and propose that the small exosome biogenesis occurs via ESCRT-dependent MVB formation in the tegumental syncytium before being shed from the apical plasma membrane. Furthermore, we found that the molecular machinery required for EV biogenesis is constitutively expressed across the intra-mammalian development stages of the parasite. By contrast, the cargo molecules packaged within the EVs are developmentally regulated, most likely to facilitate the parasites migration through host tissue and to counteract host immune attack.

IRS2 and PTEN are key molecules in controlling insulin sensitivity in podocytes

Insulin signaling to the glomerular podocyte is important for normal kidney function and is implicated in the pathogenesis of diabetic nephropathy (DN). This study determined the role of the insulin receptor substrate 2 (IRS2) in this system. Conditionally immortalized murine podocytes were generated from wild-type (WT) and insulin receptor substrate 2-deficient mice (Irs2−/−). Insulin signaling, glucose transport, cellular motility and cytoskeleton rearrangement were then analyzed. Within the glomerulus IRS2 is enriched in the podocyte and is preferentially phosphorylated by insulin in comparison to IRS1. Irs2−/− podocytes are significantly insulin resistant in respect to AKT signaling, insulin-stimulated GLUT4-mediated glucose uptake, filamentous actin (F-actin) cytoskeleton remodeling and cell motility. Mechanistically, we discovered that Irs2 deficiency causes insulin resistance through up-regulation of the phosphatase and tensin homolog (PTEN). Importantly, suppressing PTEN in Irs2−/− podocytes rescued insulin sensitivity. In conclusion, this study has identified for the first time IRS2 as a critical molecule for sensitizing the podocyte to insulin actions through its ability to modulate PTEN expression. This finding reveals two potential molecular targets in the podocyte for modulating insulin sensitivity and treating DN.