Atmospheric molecular blobs shape up circumstellar envelopes of AGB stars.

During their thermally pulsing phase, asymptotic giant branch (AGB) stars eject material that forms extended dusty envelopes1. Visible polarimetric imaging found clumpy dust clouds within two stellar radii of several oxygen-rich stars2-6. Inhomogeneous molecular gas has also been observed in multiple emission lines within several stellar radii of different oxygen-rich stars, including W Hya and Mira7-10. At the stellar surface level, infrared images have shown intricate structures around the carbon semiregular variable R Scl and in the S-type star π1 Gru11,12. Infrared images have also shown clumpy dust structures within a few stellar radii of the prototypical carbon AGB star IRC+10°216 (refs. 13,14), and studies of molecular gas distribution beyond the dust formation zone have also shown complex circumstellar structures15. Because of the lack of sufficient spatial resolution, however, the distribution of molecular gas in the stellar atmosphere and the dust formation zone of AGB carbon stars is not known, nor is how it is subsequently expelled. Here we report observations with a resolution of one stellar radius of the recently formed dust and molecular gas in the atmosphere of IRC+10°216. Lines of HCN, SiS and SiC2 appear at different radii and in different clumps, which we interpret as large convective cells in the photosphere, as seen in Betelgeuse16. The convective cells coalesce with pulsation, causing anisotropies that, together with companions17,18, shape its circumstellar envelope.

Oxygen intercalation in PVD graphene grown on copper substrates: A decoupling approach.

We investigate the intercalation process of oxygen in-between a PVD-grown graphene layer and different copper substrates as a methodology for reducing the substrate-layer interaction. This growth method leads to an extended defect-free graphene layer that strongly couples with the substrate. We have found, by means of X-ray photoelectron spectroscopy, that after oxygen exposure at different temperatures, ranging from 280 °C to 550 °C, oxygen intercalates at the interface of graphene grown on Cu foil at an optimal temperature of 500 °C. The low energy electron diffraction technique confirms the adsorption of an atomic oxygen adlayer on top of the Cu surface and below graphene after oxygen exposure at elevated temperature, but no oxidation of the substrate is induced. The emergence of the 2D Raman peak, quenched by the large interaction with the substrate, reveals that the intercalation process induces a structural undoing. As suggested by atomic force microscopy, the oxygen intercalation does not change significantly the surface morphology. Moreover, theoretical simulations provide further insights into the electronic and structural undoing process. This protocol opens the door to an efficient methodology to weaken the graphene-substrate interaction for a more efficient transfer to arbitrary surfaces.

Direct visualization of the native structure of viroid RNAs at single-molecule resolution by atomic force microscopy.

Viroids are small infectious, non-protein-coding circular RNAs that replicate independently and, in some cases, incite diseases in plants. They are classified into two families: Pospiviroidae, composed of species that have a central conserved region (CCR) and replicate in the cell nucleus, and Avsunviroidae, containing species that lack a CCR and whose multimeric replicative intermediates of either polarity generated in plastids self-cleave through hammerhead ribozymes. The compact, rod-like or branched, secondary structures of viroid RNAs have been predicted by RNA folding algorithms and further examined using different in vitro and in vivo experimental techniques. However, direct data about their native tertiary structure remain scarce. Here we have applied atomic force microscopy (AFM) to image at single-molecule resolution different variant RNAs of three representative viroids: potato spindle tuber viroid (PSTVd, family Pospiviroidae), peach latent mosaic viroid and eggplant latent viroid (PLMVd and ELVd, family Avsunviroidae). Our results provide a direct visualization of their native, three-dimensional conformations at 0 and 4 mM Mg2+ and highlight the role that some elements of tertiary structure play in their stabilization. The AFM images show that addition of 4 mM Mg2+ to the folding buffer results in a size contraction in PSTVd and ELVd, as well as in PLMVd when the kissing-loop interaction that stabilizes its 3D structure is preserved.

Spectroscopic characterization of the on-surface induced (cyclo)dehydrogenation of a N-heteroaromatic compound on noble metal surfaces.

New nanoarchitectures can be built from polycyclic aromatic hydrocarbons (PAHs) by exploiting the capability of some metal surfaces for inducing cyclodehydrogenation reactions. This bottom-up approach allows the formation of nanostructures with a different dimensionality from the same precursor as a consequence of the diffusion and coupling of the PAHs adsorbed on the surface. In this work we present a thorough study, by means of a combination of X-ray photoemission spectroscopy, near-edge X-ray absorption fine structure and scanning tunneling microscopy with first principle calculations of the structural and chemical transformations undergone by pyridyl-substituted dibenzo[5]helicene on three coinage surfaces, namely Cu(110), Cu(111) and Au(111). Upon annealing, on-surface chemical reactions are promoted affecting the adsorbate/substrate and the molecule/molecule interactions. This thermally induced process favours the transformation from diffusing isolated molecules to polymeric nanographene chains and finally to N-doped graphene.

High-quality PVD graphene growth by fullerene decomposition on Cu foils.

We present a new protocol to grow large-area, high-quality single-layer graphene on Cu foils at relatively low temperatures. We use C60 molecules evaporated in ultra high vacuum conditions as carbon source. This clean environment results in a strong reduction of oxygen-containing groups as depicted by X-ray photoelectron spectroscopy (XPS). Unzipping of C60 is thermally promoted by annealing the substrate at 800ºC during evaporation. The graphene layer extends over areas larger than the Cu crystallite size, although it is changing its orientation with respect to the surface in the wrinkles and grain boundaries, producing a modulated ring in the low energy electron diffraction (LEED) pattern. This protocol is a self-limiting process leading exclusively to one single graphene layer. Raman spectroscopy confirms the high quality of the grown graphene. This layer exhibits an unperturbed Dirac-cone with a clear n-doping of 0.77 eV, which is caused by the interaction between graphene and substrate. Density functional theory (DFT) calculations show that this interaction can be induced by a coupling between graphene and substrate at specific points of the structure leading to a local sp3 configuration, which also contribute to the D-band in the Raman spectra.

Ortho and para hydrogen dimers on G/SiC(0001): combined STM and DFT study.

The hydrogen (H) dimer structures formed upon room-temperature H adsorption on single layer graphene (SLG) grown on SiC(0001) are addressed using a combined theoretical-experimental approach. Our study includes density functional theory (DFT) calculations for the full (6√3 × 6√3)R30° unit cell of the SLG/SiC(0001) substrate and atomically resolved scanning tunneling microscopy images determining simultaneously the graphene lattice and the internal structure of the H adsorbates. We show that H atoms normally group in chemisorbed coupled structures of different sizes and orientations. We make an atomic scale determination of the most stable experimental geometries, the small dimers and ellipsoid-shaped features, and we assign them to hydrogen adsorbed in para dimers and ortho dimers configuration, respectively, through comparison with the theory.

Adsorption and Coupling of 4-aminophenol on Pt(111) surfaces.

We have deposited 4-aminophenol on Pt(111) surfaces in ultra-high vacuum and studied the strength of its adsorption through a combination of STM, LEED, XPS and ab initio calculations. Although an ordered (2√3×2√3)R30° phase appears, we have observed that molecule-substrate interaction dominates the adsorption geometry and properties of the system. At RT the high catalytic activity of Pt induces aminophenol to lose the H atom from the hydroxyl group, and a proportion of the molecules lose the complete hydroxyl group. After annealing above 420K, all deposited aminophenol molecules have lost the OH moiety and some hydrogen atoms from the amino groups. At this temperature, short single-molecule oligomer chains can be observed. These chains are the product of a new reaction that proceeds via the coupling of radical species that is favoured by surface diffusion.

Ordered vacancy network induced by the growth of epitaxial graphene on Pt(111).

We have studied large areas of (√3×√3)R30° graphene commensurate with a Pt(111) substrate. A combination of experimental techniques with ab initio density functional theory indicates that this structure is related to a reconstruction at the Pt surface, consisting of an ordered vacancy network formed in the outermost Pt layer and a graphene layer covalently bound to the Pt substrate. The formation of this reconstruction is enhanced if low temperatures and polycyclic aromatic hydrocarbons are used as molecular precursors for epitaxial growth of the graphene layers.

Interplay between fast diffusion and molecular interaction in the formation of self-assembled nanostructures of S-cysteine on Au(111).

We have studied the first stages leading to the formation of self-assembled monolayers of S-cysteine molecules adsorbed on a Au(111) surface. Density functional theory (DFT) calculations for the adsorption of individual cysteine molecules on Au(111) at room temperature show low-energy barriers all over the 2D Au(111) unit cell. As a consequence, cysteine molecules diffuse freely on the Au(111) surface and they can be regarded as a 2D molecular gas. The balance between molecule-molecule and molecule-substrate interactions induces molecular condensation and evaporation from the morphological surface structures (steps, reconstruction edges, etc.) as revealed by scanning tunnelling microscopy (STM) images. These processes lead progressively to the formation of a number of stable arrangements, not previously reported, such as single-molecular rows, trimers, and 2D islands. The condensation of these structures is driven by the aggregation of new molecules, stabilized by the formation of electrostatic interactions between adjacent NH(3)(+) and COO(-) groups, together with adsorption at a slightly more favorable quasi-top site of the herringbone Au reconstruction.

Understanding atomic-resolved STM images on TiO2(110)-(1 x 1) surface by DFT calculations.

We present a combination of experimental STM images and DFT calculations to understand the atomic scale contrast of features found in high-resolution STM images. Simulating different plausible structural models for the tip, we have been able to reproduce various characteristics previously reported in experimental images on TiO(2)(110)-(1 x 1) under controlled UHV conditions. Our results allow us to determine the influence of different chemical and morphological tip terminations on the atomic-resolution STM images of the TiO(2)(110)-(1 x 1) surface. The commonest images have been properly explained using standard models for a W tip, either clean or with a single O atom located at the apex. Furthermore, a double transfer of oxygen atoms can account for different types of bizarre atomic-resolution features occasionally seen, and not conclusively interpreted before. Importantly, we discuss how typical point-defects are imaged on this surface by different tips, namely bridging O vacancies and adsorbed OH groups.

Chemical equilibrium in AGB atmospheres: Successes, failures, and prospects for small molecules, clusters, and condensates.

Chemical equilibrium has proven extremely useful for predicting the chemical composition of AGB atmospheres. Here we use a recently developed code and an updated thermochemical database that includes gaseous and condensed species involving 34 elements to compute the chemical equilibrium composition of AGB atmospheres of M-, S-, and C-type stars. We include for the first time Ti x C y clusters, with x = 1-4 and y = 1-4, and selected larger clusters ranging up to Ti13C22, for which thermochemical data are obtained from quantum-chemical calculations. Our main aims are to systematically survey the main reservoirs of each element in AGB atmospheres, review the successes and failures of chemical equilibrium by comparing it with the latest observational data, identify potentially detectable molecules that have not yet been observed, and diagnose the most likely gas-phase precursors of dust and determine which clusters might act as building blocks of dust grains. We find that in general, chemical equilibrium reproduces the observed abundances of parent molecules in circumstellar envelopes of AGB stars well. There are, however, severe discrepancies of several orders of magnitude for some parent molecules that are observed to be anomalously overabundant with respect to the predictions of chemical equilibrium. These are HCN, CS, NH3, and SO2 in M-type stars, H2O and NH3 in S-type stars, and the hydrides H2O, NH3, SiH4, and PH3 in C-type stars. Several molecules have not yet been observed in AGB atmospheres but are predicted with non-negligible abundances and are good candidates for detection with observatories such as ALMA. The most interesting ones are SiC5, SiNH, SiCl, PS, HBO, and the metal-containing molecules MgS, CaS, CaOH, CaCl, CaF, ScO, ZrO, VO, FeS, CoH, and NiS. In agreement with previous studies, the first condensates predicted to appear in C-rich atmospheres are found to be carbon, TiC, and SiC, while Al2O3 is the first major condensate expected in O-rich outflows. According to our chemical equilibrium calculations, the gas-phase precursors of carbon dust are probably acetylene, atomic carbon, and/or C3, while for silicon carbide dust, the most likely precursors are the molecules SiC2 and Si2C. In the case of titanium carbide dust, atomic Ti is the major reservoir of this element in the inner regions of AGB atmospheres, and therefore it is probably the main supplier of titanium during the formation of TiC dust. However, chemical equilibrium predicts that large titanium-carbon clusters such as Ti8C12 and Ti13C22 become the major reservoirs of titanium at the expense of atomic Ti in the region where condensation of TiC is expected to occur. This suggests that the assembly of large Ti x C y clusters might be related to the formation of the first condensation nuclei of TiC. In the case of Al2O3 dust, chemical equilibrium indicates that atomic Al and the carriers of Al-O bonds AlOH, AlO, and Al2O are the most likely gas-phase precursors.

Production of nanohole/nanodot patterns on Si(001) by ion beam sputtering with simultaneous metal incorporation.

We have established the conditions for which nanohole and nanodot patterns are produced on Si(001) surfaces by 1 keV Ar(+) ion beam sputtering (IBS) at normal incidence with an alternating cold cathode ion source (ACC-IS). Nanohole patterns are produced within a narrow IBS window for low ion fluxes (<100 µA cm(-2)) and relatively low ion fluences (<10(18) ions cm(-2)) whereas nanodot morphologies are produced above this window. The nanohole pattern is not stable after prolonged irradiation since it evolves to a nanodot morphology. Rutherford backscattering spectrometry (RBS) measurements show that nanohole patterns are produced when the metal content on the irradiated surfaces is higher (within (2.5-3.5 × 10(15)) atoms cm(-2)) than in the case of nanodots (<2.5 × 10(15) atoms cm(-2)). The different metal content is related to the ACC-IS operation, since the set-up provides simultaneous incorporation of Fe and Mo on the target surface from the erosion of the cathodes and sample holder, respectively. The role of metal incorporation on pattern selectivity has been corroborated qualitatively by extending the results obtained with the ACC-IS to a standard Kaufman-type source. In order to gain further information on the metal effects, chemical analysis of the surface has been performed to complement the compositional RBS results, showing for the first time the relevant participation of metal silicides. Further outlook and a discussion regarding the role of metal incorporation are also given.

Reversible Graphene decoupling by NaCl photo-dissociation.

We describe the reversible intercalation of Na under graphene on Ir(111) by photo-dissociation of a previously adsorbed NaCl overlayer. After room temperature evaporation, NaCl adsorbs on top of graphene forming a bilayer. With a combination of electron diffraction and photoemission techniques we demonstrate that the NaCl overlayer dissociates upon a short exposure to an X-ray beam. As a result, chlorine desorbs while sodium intercalates under the graphene, inducing an electronic decoupling from the underlying metal. Low energy electron diffraction shows the disappearance of the moiré pattern when Na intercalates between graphene and iridium. Analysis of the Na 2p core-level by X-ray photoelectron spectroscopy shows a chemical change from NaCl to metallic buried Na at the graphene/Ir interface. The intercalation-decoupling process leads to a n-doped graphene due to the charge transfer from the Na, as revealed by constant energy angle resolved X-ray photoemission maps. Moreover, the process is reversible by a mild annealing of the samples without damaging the graphene.

Broad band high resolution rotational spectroscopy for Laboratory Astrophysics.

We present a new experimental setup devoted to the study of gas phase molecules and processes using broad band high spectral resolution rotational spectroscopy. A reactor chamber has been equipped with radio receivers similar to those used by radio astronomers to search for molecular emission in space. The whole Q (31.5-50 GHz) and W bands (72-116.5 GHz) are available for rotational spectroscopy observations. The receivers are equipped with 16×2.5 GHz Fast Fourier Transform spectrometers with a spectral resolution of 38.14 kHz allowing the simultaneous observation of the complete Q band and one third of the W band. The whole W band can be observed in three settings in which the Q band is always observed. Species such as CH3CN, OCS, and SO2 are detected, together with many of their isotopologues and vibrationally excited states, in very short observing times. The system permits automatic overnight observations and integration times as long as 2.4×105 seconds have been reached. The chamber is equipped with a radiofrequency source to produce cold plasmas and with four ultraviolet lamps to study photochemical processes. Plasmas of CH4, N2, CH3CN, NH3, O2, and H2, among other species, have been generated and the molecular products easily identified by their rotational spectrum, and mass spectrometry and optical spectroscopy. Finally, the rotational spectrum of the lowest energy conformer of CH3CH2NHCHO (N-Ethylformamide), a molecule previously characterized in microwave rotational spectroscopy, has been measured up to 116.5 GHz allowing the accurate determination of its rotational and distortion constants and its search in space.

Precisely controlled fabrication, manipulation and in-situ analysis of Cu based nanoparticles.

The increasing demand for nanostructured materials is mainly motivated by their key role in a wide variety of technologically relevant fields such as biomedicine, green sustainable energy or catalysis. We have succeeded to scale-up a type of gas aggregation source, called a multiple ion cluster source, for the generation of complex, ultra-pure nanoparticles made of different materials. The high production rates achieved (tens of g/day) for this kind of gas aggregation sources, and the inherent ability to control the structure of the nanoparticles in a controlled environment, make this equipment appealing for industrial purposes, a highly coveted aspect since the introduction of this type of sources. Furthermore, our innovative UHV experimental station also includes in-flight manipulation and processing capabilities by annealing, acceleration, or interaction with background gases along with in-situ characterization of the clusters and nanoparticles fabricated. As an example to demonstrate some of the capabilities of this new equipment, herein we present the fabrication of copper nanoparticles and their processing, including the controlled oxidation (from Cu0 to CuO through Cu2O, and their mixtures) at different stages in the machine.

Circumstellar chemistry of Si-C bearing molecules in the C-rich AGB star IRC+10216.

Silicon carbide together with amorphous carbon are the main components of dust grains in the atmospheres of C-rich AGB stars. Small gaseous Si-C bearing molecules (such as SiC, SiCSi, and SiC2) are efficiently formed close to the stellar photosphere. They likely condense onto dust seeds owing to their highly refractory nature at the lower temperatures (i.e., below about 2500 K) in the dust growth zone which extends a few stellar radii from the photosphere. Beyond this region, the abundances of Si-C bearing molecules are expected to decrease until they are eventually reformed in the outer shells of the circumstellar envelope, owing to the interaction between the gas and the interstellar UV radiation field. Our goal is to understand the time-dependent chemical evolution of Si-C bond carriers probed by molecular spectral line emission in the circumstellar envelope of IRC+10216 at millimeter wavelengths.

Using radio astronomical receivers for molecular spectroscopic characterization in astrochemical laboratory simulations: A proof of concept.

We present a proof of concept on the coupling of radio astronomical receivers and spectrometers with chemical reactors and the performances of the resulting setup for spectroscopy and chemical simulations in laboratory astrophysics. Several experiments including cold plasma generation and UV photochemistry were performed in a 40 cm long gas cell placed in the beam path of the Aries 40 m radio telescope receivers operating in the 41-49 GHz frequency range interfaced with fast Fourier transform spectrometers providing 2 GHz bandwidth and 38 kHz resolution. The impedance matching of the cell windows has been studied using different materials. The choice of the material and its thickness was critical to obtain a sensitivity identical to that of standard radio astronomical observations. Spectroscopic signals arising from very low partial pressures of CH3OH, CH3CH2OH, HCOOH, OCS, CS, SO2 (<10-3 mbar) were detected in a few seconds. Fast data acquisition was achieved allowing for kinetic measurements in fragmentation experiments using electron impact or UV irradiation. Time evolution of chemical reactions involving OCS, O2 and CS2 was also observed demonstrating that reactive species, such as CS, can be maintained with high abundance in the gas phase during these experiments.

A DNA biosensor based on peptide nucleic acids on gold surfaces.

We present a DNA biosensor based on self-assembled monolayers (SAMs) of thiol-derivatized peptide nucleic acid (PNA) molecules adsorbed on gold surfaces. Previous works have shown that PNA molecules at an optimal concentration can be self-assembled with their molecular axes normal to the surface. In such structural configuration BioSAMs of PNAs maintain their capability for recognizing complementary DNA. We describe the combined use of PM-RAIRS and synchrotron radiation XPS for the detection and spectroscopic characterization of PNA-DNA hybridization process on gold surfaces. RAIRS and XPS are powerful techniques for surface characterization and molecular detection, which do not require a fluorescence labeling of the target. We present a characterization of the spectroscopic IR and XPS features, some of them associated to the phosphate groups of the DNA backbone, as an unambiguous signature of the PNA-DNA heteroduplex formation. The N(1s) XPS core level peak after DNA hybridization is decomposed in curves components, and every component assigned to different chemical species. Therefore, the results obtained by means of two complementary structural characterization techniques encourage the use of PNA-based biosensors for the detection of DNA molecules on natural samples.

The growth of carbon chains in IRC +10216 mapped with ALMA.

Linear carbon chains are common in various types of astronomical molecular sources. Possible formation mechanisms involve both bottom-up and top-down routes. We have carried out a combined observational and modeling study of the formation of carbon chains in the C-star envelope IRC +10216, where the polymerization of acetylene and hydrogen cyanide induced by ultraviolet photons can drive the formation of linear carbon chains of increasing length. We have used ALMA to map the emission of λ 3 mm rotational lines of the hydrocarbon radicals C2H, C4H, and C6H, and the CN-containing species CN, C3N, HC3N, and HC5N with an angular resolution of ~1″. The spatial distribution of all these species is a hollow, 5-10″ wide, spherical shell located at a radius of 10-20″ from the star, with no appreciable emission close to the star. Our observations resolve the broad shell of carbon chains into thinner sub-shells which are 1-2″ wide and not fully concentric, indicating that the mass loss process has been discontinuous and not fully isotropic. The radial distributions of the species mapped reveal subtle differences: while the hydrocarbon radicals have very similar radial distributions, the CN-containing species show more diverse distributions, with HC3N appearing earlier in the expansion and the radical CN extending later than the rest of the species. The observed morphology can be rationalized by a chemical model in which the growth of polyynes is mainly produced by rapid gas-phase chemical reactions of C2H and C4H radicals with unsaturated hydrocarbons, while cyanopolyynes are mainly formed from polyynes in gas-phase reactions with CN and C3N radicals.

Mimicking Martian dust: An in-vacuum dust deposition system for testing the ultraviolet sensors on the Curiosity rover.

We have designed and developed an in-vacuum dust deposition system specifically conceived to simulate and study the effect of accumulation of Martian dust on the electronic instruments of scientific planetary exploration missions. We have used this device to characterize the dust effect on the UV sensor of the Rover Environmental Monitoring Station in the Mars science Laboratory mission of NASA in similar conditions to those found on Mars surface. The UV sensor includes six photodiodes for measuring the radiation in all UV wavelengths (direct incidence and reflected); it is placed on the body of Curiosity rover and it is severely affected by the dust deposited on it. Our experimental setup can help to estimate the duration of reliable reading of this instrument during operation. We have used an analogous of the Martian dust in chemical composition (magnetic species), color, and density, which has been characterized by X-ray spectroscopy. To ensure a Brownian motion of the dust during its fall and a homogeneous coverage on the instrumentation, the operating conditions of the vacuum vessel, determined by partial pressures and temperature, have to be modified to account for the different gravities of Mars with respect to Earth. We propose that our designed device and operational protocol can be of interest to test optoelectronic instrumentation affected by the opacity of dust, as can be the degradation of UV photodiodes in planetary exploration.