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(Abridged) We explore the chemistry of the most abundant C, O, S, and N bearing species in molecular clouds, in the context of the IRAM 30 m Large Programme Gas phase Elemental abundances in Molecular Clouds (GEMS). In this work, we aim to assess the limitations introduced in the observational works when a uniform density is assumed along the line of sight for fitting the observations, developing a very simple numerical model of a turbulent box. We perform a MHD simulation in order to reproduce the turbulent steady-state of a turbulent box with properties typical of a molecular filament before collapse. We post-process the results of the MHD simulation with a chemical code to predict molecular abundances, and then post-process this cube with a radiative transfer code to create synthetic emission maps for a series of rotational transitions observed during the GEMS project. From the chemical point of view, we find that turbulence produces variations on the predicted abundances, but they are more or less critical depending on the chosen transition and the chemical age. When compared to real observations, the results from the turbulent simulation provides a better fit than when assuming a uniform gas distribution along the line of sight. In the view of our results, we conclude that taking into account turbulence when fitting observations might significantly improve the agreement with model predictions. This is especially important for sulfur bearing species that are very sensitive to the variations of density produced by turbulence at early times (0.1 Myr). The abundance of CO is also quite sensitive to turbulence when considering the evolution beyond a few 0.1 Myr., Comment: Published in Astronomy and Astrophysics

Within the project Evolution of Chemistry in the envelope of HOt corinoS (ECHOS), we present a study of sulphur chemistry in the envelope of the Class 0 source B335 through observations in the spectral range 7, 3, and 2 mm. We have modelled observations assuming LTE and LVG approximation. We have also used the code Nautilus to study the time evolution of sulphur species. We have detected 20 sulphur species with a total gas-phase S abundance similar to that found in the envelopes of other Class 0 objects, but with significant differences in the abundances between sulphur carbon chains and sulphur molecules containing oxygen and nitrogen. Our results highlight the nature of B335 as a source especially rich in sulphur carbon chains unlike other Class 0 sources. The low presence or absence of some molecules, such as SO and SO+, suggests a chemistry not particularly influenced by shocks. We, however, detect a large presence of HCS+ that, together with the low rotational temperatures obtained for all the S species (<15 K), reveals the moderate or low density of the envelope of B335. We also find that observations are better reproduced by models with a sulphur depletion factor of 10 with respect to the sulphur cosmic elemental abundance. The comparison between our model and observational results for B335 reveals an age of 10$^4$$<$t$<$10$^5$ yr, which highlights the particularly early evolutionary stage of this source. B335 presents a different chemistry compared to other young protostars that have formed in dense molecular clouds, which could be the result of accretion of surrounding material from the diffuse cloud onto the protostellar envelope of B335. In addition, the analysis of the SO2/C2S, SO/CS, and HCS+/CS ratios within a sample of prestellar cores and Class 0 objects show that they could be used as good chemical evolutionary indicators of the prestellar to protostellar transition.

HCN, HNC, and their isotopologues are ubiquitous molecules that can serve as chemical thermometers and evolutionary tracers to characterize star-forming regions. Despite their importance in carrying information that is vital to studies of the chemistry and evolution of star-forming regions, the collision rates of some of these molecules have not been available for rigorous studies in the past. We perform an up-to-date gas and dust chemical characterization of two different star-forming regions, TMC 1-C and NGC 1333-C7, using new collisional rates of HCN, HNC, and their isotopologues. We investigated the possible effects of the environment and stellar feedback in their chemistry and their evolution. With millimeter observations, we derived their column densities, the C and N isotopic fractions, the isomeric ratios, and the deuterium fractionation. The continuum data at 3 mm and 850 $\mu$m allowed us to compute the emissivity spectral index and look for grain growth as an evolutionary tracer. The H$^{13}$CN/HN$^{13}$C ratio is anticorrelated with the deuterium fraction of HCN, thus it can readily serve as a proxy for the temperature. The spectral index $(\beta\sim 1.34-2.09)$ shows a tentative anticorrelation with the H$^{13}$CN/HN$^{13}$C ratio, suggesting grain growth in the evolved, hotter, and less deuterated sources. Unlike TMC 1-C, the south-to-north gradient in dust temperature and spectral index observed in NGC 1333-C7 suggests feedback from the main NGC 1333 cloud. With this up-to-date characterization of two star-forming regions, we found that the chemistry and the physical properties are tightly related. The dust temperature, deuterium fraction, and the spectral index are complementary evolutionary tracers. The large-scale environmental factors may dominate the chemistry and evolution in clustered star-forming regions., Comment: 25 pages, 20 figures

Gas phase Elemental abundances in molecular CloudS (GEMS) is an IRAM 30m large program aimed at determining the elemental abundances of carbon (C), oxygen (O), nitrogen (N), and sulfur (S) in a selected set of prototypical star-forming filaments. In particular, the elemental abundance of S remains uncertain by several orders of magnitude and its determination is one of the most challenging goals of this program. We have carried out an extensive chemical modeling of the fractional abundances of CO, HCO$^+$, HCN, HNC, CS, SO, H$_2$S, OCS, and HCS$^+$ to determine the sulfur depletion toward the 244 positions in the GEMS database. These positions sample visual extinctions from A$_V$ $\sim$ 3 mag to $>$50 mag, molecular hydrogen densities ranging from a few 10$^3$~cm$^{-3}$ to 3$\times$10$^6$~cm$^{-3}$, and T$_k$ $\sim$ 10$-$35 K. Most of the positions in Taurus and Perseus are best fitted assuming early-time chemistry, t=0.1 Myr, $\zeta_{H_2}$$\sim$ (0.5$-$1)$\times$10$^{-16}$ s$^{-1}$, and [S/H]$\sim$1.5$\times$10$^{-6}$. On the contrary, most of the positions in Orion are fitted with t=1~Myr and $\zeta_{H_2}$$\sim$ 10$^{-17}$ s$^{-1}$. Moreover, $\sim$40% of the positions in Orion are best fitted assuming the undepleted sulfur abundance, [S/H]$\sim$1.5$\times$10$^{-5}$. Our results suggest that sulfur depletion depends on the environment. While the abundances of sulfur-bearing species are consistent with undepleted sulfur in Orion, a depletion factor of $\sim$20 is required to explain those observed in Taurus and Perseus. We propose that differences in the grain charge distribution in the envelopes of the studied clouds might explain these variations. The shocks associated with past and ongoing star formation could also contribute to enhance [S/H] in Orion., Comment: 22 pages, 15 figures, Astronomy and Astrophysics, in press

In the context of the IRAM 30m Large Program GEMS, we present a study of thioformaldehyde in several starless cores located in star-forming filaments of Taurus, Perseus, and Orion. We investigate the influence of the environmental conditions on the abundances of these molecules in the cores, and the effect of time evolution. We have modelled the observed lines of H2CS, HDCS, and D2CS using the radiative transfer code RADEX. We have also used the chemical code Nautilus to model the evolution of these species depending on the characteristics of the starless cores. We derive column densities and abundances for all the cores. We also derive deuterium fractionation ratios, Dfrac, to determine and compare the evolutionary stage between different parts of each star-forming region. Our results indicate that the north region of the B213 filament in Taurus is more evolved than the south, while the north-eastern part of Perseus presents an earlier evolutionary stage than the south-western zone. Model results also show that Dfrac decreases with the cosmic-ray ionisation rate, while it increases with density and with the degree of sulphur depletion. In particular, we only reproduce the observations when the initial sulphur abundance in the starless cores is at least one order of magnitude lower than the solar elemental sulphur abundance. The progressive increase in HDCS/H2CS and D2CS/H2CS with time makes these ratios powerful tools for deriving the chemical evolutionary stage of starless cores. However, they cannot be used to derive the temperature of these regions, since both ratios present a similar evolution at two different temperature ranges (7-11 K and 15-19 K). Regarding chemistry, (deuterated) thioformaldehyde is mainly formed through gas-phase reactions (double-replacement and neutral-neutral displacement reactions), while surface chemistry plays an important role as a destruction mechanism., Comment: 31 pages, 26 figures

Methanol, one of the simplest complex organic molecules in the Interstellar Medium (ISM), has been shown to be present and extended in cold environments such as starless cores. We aim at studying methanol emission across several starless cores and investigate the physical conditions at which methanol starts to be efficiently formed, as well as how the physical structure of the cores and their surrounding environment affect its distribution. Methanol and C$^{18}$O emission lines at 3 mm have been observed with the IRAM 30m telescope within the large program "Gas phase Elemental abundances in Molecular CloudS" (GEMS) towards 66 positions across 12 starless cores in the Taurus Molecular Cloud. A non-LTE radiative transfer code was used to compute the column densities in all positions. We then used state-of-the-art chemical models to reproduce our observations. We have computed N(CH$_3$OH)/N(C$^{18}$O) column density ratios for all the observed offsets, and two different behaviours can be recognised: the cores where the ratio peaks at the dust peak, and the cores where the ratio peaks with a slight offset with respect to the dust peak ($\sim $10000 AU). We suggest that the cause of this behaviour is the irradiation on the cores due to protostars nearby which accelerate energetic particles along their outflows. The chemical models, which do not take into account irradiation variations, can reproduce fairly well the overall observed column density of methanol, but cannot reproduce the two different radial profiles observed. We confirm the substantial effect of the environment onto the distribution of methanol in starless cores. We suggest that the clumpy medium generated by protostellar outflows might cause a more efficient penetration of the interstellar radiation field in the molecular cloud and have an impact on the distribution of methanol in starless cores., Comment: Accepted for publication in A&A

Gas phase Elemental abundances in Molecular CloudS (GEMS) is an IRAM 30m Large Program designed to estimate the S, C, N, and O depletions and gas ionization degree, X(e-), in a set of star-forming filaments of Taurus, Perseus and Orion. Our immediate goal is to build up a complete database of molecular abundances that can serve as an observational basis for estimating X(e-) and the C, O, N, and S depletions through chemical modeling. We observed and derived the abundances of 14 species (13CO, C18O, HCO+, H13CO+, HC18O+, HCN, H13CN, HNC, HCS+, CS, SO, 34SO, H2S, and OCS) in 244 positions, covering the AV 3 to 100 mag, n(H2) a few 10$^{3}$ to 10$^6$ cm$^{-3}$, and Tk 10 to 30 K ranges in these clouds, avoiding protostars, HII regions, and outflows. A statistical analysis is carried out to identify general trends between different species and with physical parameters. Relations between molecules reveal strong linear correlations which define three different families: (1) 13CO and C18O; (2) H13CO+, HC18O+, H13CN, and HNC; and (3) the S-bearing molecules. The abundances of the CO isotopologs increase with the gas kinetic temperature until TK 15 K. For higher temperatures, the abundance remains constant with a scatter of a factor of 3. The abundances of H13CO+, HC18O+, H13CN, and HNC are well correlated with each other, and all of them decrease with molecular hydrogen density, following the law n(H2)$^{-0.8\pm0.2}$. The abundances of S-bearing species also decrease with n(H2) at a rate of (S-bearing/H)gas n(H2)$^{-0.6\pm0.1}$. The abundances of molecules belonging to groups 2 and 3 do not present any clear trend with gas temperature. At scales of molecular clouds, the C18O abundance is the quantity that better correlates with the cloud mass. We discuss the utility of the 13CO/C18O, HCO+/H13CO+, and H13CO+/H13CN abundance ratios as chemical diagnostics of star formation in external galaxies., Comment: 28 pages, 22 figures. Accepted for publication in A&A

CS is among the most abundant gas-phase S-bearing molecules in cold dark molecular clouds. It is easily observable with several transitions in the millimeter wavelength range, and has been widely used as a tracer of the gas density in the interstellar medium in our Galaxy and external galaxies. Chemical models fail to account for the observed CS abundances when assuming the cosmic value for the elemental abundance of sulfur. The CS+O -> CO + S reaction has been proposed as a relevant CS destruction mechanism at low temperatures, and could explain the discrepancy between models and observations. Its reaction rate has been experimentally measured at temperatures of 150-400 K, but the extrapolation to lower temperatures is doubtful. Here we calculate the CS+O reaction rate at temperatures <150 K which are prevailing in the interstellar medium. We performed ab initio calculations to obtain the three lowest PES of the CS+O system. These PESs are used to study the reaction dynamics, using several methods to eventually calculate the CS+O thermal reaction rates. We compare the results of our theoretical calculations for 150-400 K with those obtained in the laboratory. Our detailed theoretical study on the CS+O reaction, which is in agreement with the experimental data obtained at 150-400 K, demonstrates the reliability of our approach. After a careful analysis at lower temperatures, we find that the rate constant at 10 K is negligible, which is consistent with the extrapolation of experimental data using the Arrhenius expression. We use the updated chemical network to model the sulfur chemistry in TMC1 based on molecular abundances determined from GEMS project observations. In our model, we take into account the expected decrease of the cosmic ray ionization rate along the cloud. The abundance of CS is still overestimated when assuming the cosmic value for the sulfur abundance., Comment: 11 pages, 10 figures, accepted in Astronomy & Astrophysics

A large effort has been made to detect warm gas in the planet formation zone of circumstellar discs using space and ground-based near infrared facilities. GV Tau N, the most obscured component of the GV Tau system, is an outstanding source, being one of the first targets detected in HCN and the only one detected in CH$_4$ so far. Although near infrared observations have shed light on its chemical content, the physical structure and kinematics of the circumstellar matter remained unknown. We use interferometric images of the HCN 3-2 and $^{13}$CO 3-2 lines, and far-IR observations of $^{13}$CO, HCN, CN and H$_2$O transitions to discern the morphology, kinematics, and chemistry of the dense gas close to the star. These observations constitute the first detection of H$_2$O towards GV Tau N. Moreover, ALMA high spatial resolution (~ 7 au) images of the continuum at 1.1 mm and the HCN 3-2 line resolve different gas components towards GV Tau N, a gaseous disc with R~25 au, an ionized jet, and one (or two) molecular outflows. The asymmetric morphology of the gaseous disc shows that it has been eroded by the jet. All observations can be explained if GV Tau N is binary, and the primary component has a highly inclined individual disc relative to the circumbinary disc. We discuss the origin of the water and the other molecules emission according to this scenario. In particular, we propose that the water emission would come from the disrupted gaseous disc and the molecular outflows., Comment: 12 pages, 8 figures. Accepted for publication in MNRAS

The HII regions are all studied employing the same general prescriptions, despite the possible influence of their environment in their star formation processes. Through the analysis of two samples of 725 inner and 671 outer disk HII region observed spectra, we explore possible systematic differences between their ionising clusters physical properties (metallicity, mass, and age), comparing observations and predictions by photoionisation models. Higher metallicities are confirmed for inner regions, although there are important discrepancies between the diagnostic diagrams. Calibrations based on the N2 index may underestimate inner regions O/H due to the [NII] saturation at solar metallicities. The degeneracy between the age and ionisation parameter affects O/H calibrations based on the O3N2 index. Innermost regions have enhanced N/O ratios, indicating an increase in the slope of the relation between N/O and O/H. Ionisation parameter calibrations based on the [SII]/H{\alpha} ratio are not valid for inner regions due to the bivalued behaviour of this ratio with O/H. Innermost regions have lower [OII]/[OIII] ratios than expected, indicating a possible non-linear relation between u and Z. Ionising and non-ionising populations are present in both inner and outer regions. Inner regions show larger ionising cluster masses that possibly compose star-forming complexes. Outer regions might be affected by stochastic effects. Equivalent widths indicate younger ages for outer regions, but degeneracy between evolution and underlying population effects prevent a quantitative determination. Inner regions have larger angular sizes, lower filling factors, and larger ionised hydrogen masses. The confirmed systematic differences between ionising clusters of inner and outer HII regions condition the validity and range of reliability of O/H and u calibrations commonly applied to the study of HII regions., Comment: Accepted for publication in A&A. 14 pages, 12 figures

Context. The knowledge of abundance distributions is central to understanding the formation and evolution of galaxies. Most of the relations employed for the derivation of gas abundances have so far been derived from observations of outer disk HII regions, despite the known differences between inner and outer regions. Aims. Using integral field spectroscopy (IFS) observations we aim to perform a systematic study and comparison of two inner and outer HII regions samples. The spatial resolution of the IFS, the number of objects and the homogeneity and coherence of the observations allow a complete characterization of the main observational properties and differences of the regions. Methods. We analyzed a sample of 725 inner HII regions and a sample of 671 outer HII regions, all of them detected and extracted from the observations of a sample of 263 nearby, isolated, spiral galaxies observed by the CALIFA survey. Results. We find that inner HII regions show smaller equivalent widths, greater extinction and luminosities, along with greater values of [NII]{\lambda}6583/H{\alpha} and [OII]{\lambda}3727/[OIII]{\lambda}5007 emission-line ratios, indicating higher metallicites and lower ionization parameters. Inner regions have also redder colors and higher photometric and ionizing masses, although Mion/Mphot is slighty higher for the outer regions. Conclusions. This work shows important observational differences between inner and outer HII regions in star forming galaxies not previously studied in detail. These differences indicate that inner regions have more evolved stellar populations and are in a later evolution state with respect to outer regions, which goes in line with the inside-out galaxy formation paradigm., Comment: 16 pages

The Stephan's Quintet (SQ) is a famous interacting compact group of galaxies in an important stage of dynamical evolution, but surprisingly very few spectroscopic studies are found in the literature. We present optical integral field spectroscopy (IFS) observations of the SQ from the PPAK IFS Nearby Galaxies Survey (PINGS), that provide a powerful way of studying with spatial resolution the physical characteristics of the ionized gas within the group. The nature of the gas emission is analysed using 2D maps of continuum-subtracted, pure emission-line intensities, stacked spectra, diagnostic diagrams, and photoionization model predictions. In the case of NGC 7319, we study the galaxy-wide high-velocity outflow emission by comparing the emission properties with theoretical shock and AGN models. We conclude that the excitation mechanism of the gas in this galaxy is a mixture of AGN photoionization and shocks with a photoionizing precursor. The emission spectra from the large scale shock front in the interacting pair NGC 7318A/B is analysed, confirming the presence of several kinematic components. Comparison with predictions from theoretical shock models suggests that the gas emission is consistent with shocks without a photoionizing precursor, low pre-shock density, and velocities in the range of 200 - 400 km s-1. The gas oxygen abundance for NGC 7318B is determined using an updated O3N2 calibration. Although NGC 7317 shows no significant gas emission, an ionizing cluster is found southwest of this galaxy, probably the result of tidal interaction. As a by-product, we analyse the gas emission of the foreground galaxy NGC 7320., Comment: 17 pages, 13 figures. To be published in Monthly Notices of the Royal Astronomical Society