Search

(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

The study of the chemical composition of the interstellar medium (ISM) requires a strong synergy between laboratory astrophysics, modeling, and observations. In particular, astrochemical models have been developed for decades now and include an increasing number of processes studied in the laboratory or theoretically. These models follow the chemistry both in the gas phase and at the surface of interstellar grains. Since 2012, we have provided complete gas-phase chemical networks for astrochemical codes that can be used to model various environments of the ISM. Our aim is to introduce the new up-to-date astrochemical network kida.uva.2024 together with the ice chemical network and the fortran code to compute time dependent compositions of the gas, the ice surface, and the ice mantles under physical conditions relevant for the ISM. The gas-phase chemical reactions, as well as associated rate coefficients, included in kida.uva.2024 were carefully selected from the KIDA online database and represent the most recent values. The model predictions for cold core conditions and for when considering only gas-phase processes were computed as a function of time and compared to the predictions obtained with the previous version, kida.uva.2014. In addition, key chemical reactions were identified. The model predictions, including both gas and surface processes, were compared to the molecular abundances as observed in the cold core TMC1-CP. Many gas-phase reactions were revised or added to produce kida.uva.2024. The new model predictions are different by several orders of magnitude for some species. The agreement of this new model with observations in TMC-1 (CP) is, however, similar to the one obtained with the previous network., Comment: Accepted for publication in A&A

Astrochemical models are important tools to interpret observations of molecular and atomic species in different environments. However, these models are time-consuming, precluding a thorough exploration of the parameter space, leading to uncertainties and biased results. Using neural networks to simulate the behavior of astrochemical models is a way to circumvent this problem, providing fast calculations that are based on real astrochemical models. In this paper, we present a fast neural emulator of the astrochemical code Nautilus based on conditional neural fields. The resulting model produces the abundance of 192 species for arbitrary times between 1 and 10$^7$ years. Uncertainties well below 0.2 dex are found for all species, while the computing time is of the order of 10$^4$ smaller than Nautilus. This will open up the possibility of performing much more complex forward models to better understand the physical properties of the interstellar medium. As an example of the power of these models, we ran a feature importance analysis on the electron abundance predicted by Nautilus. We found that the electron density is coupled to the initial sulphur abundance in a low density gas. Increasing the initial sulphur abundance from a depleted scenario to the cosmic abundance leads to an enhancement of an order of magnitude of the electron density. This enhancement can potentially influence the dynamics of the gas in star formation sites., Comment: 12 pages, 8 figures, accepted for publication in MNRAS

The first hydrostatic core (FHSC) phase is a brief stage in the protostellar evolution that is difficult to detect. Our goal is to characterize the chemical evolution of gas and dust during the formation of the FHSC. Moreover, we are interested in analyzing, for the first time with 3D magnetohydrodynamic (MHD) simulations, the role of grain growth in its chemistry. We postprocessed $2\times10^{5}$ tracer particles from a $\texttt{RAMSES}$ non-ideal MHD simulation using the codes $\texttt{NAUTILUS}$ and $\texttt{SHARK}$ to follow the chemistry and grain growth throughout the simulation. A great chemical inheritance is seen, as gas-phase abundances of most of the C, O, N, and S reservoirs in the hot corino at the end of the simulation match the ice-phase abundances from the prestellar phase. Additionally, interstellar complex organic molecules (iCOMs) such as methyl formate, acetaldehyde, and formamide are formed during the warm-up process. The typical grain size in the hot corino $(n_{\rm H}>10^{11}\ {\rm cm^{-3}})$ increases forty-fold during the last 30 kyr, with negligible effects on its chemical composition. At moderate densities $(10^{10}

Based on a novel laboratory method, 14 mm-wave lines of the molecular ion H$_2$CCCH$^+$ have been measured in high resolution, and the spectroscopic constants of this asymmetric rotor determined with high accuracy. Using the Yebes 40 m and IRAM 30 m radio telescopes, we detect four lines of H$_2$CCCH$^+$ towards the cold dense core TMC-1. With a dipole moment of about 0.55 Debye obtained from high-level ab initio calculations, we derive a column density of 5.4$\pm$1$\times$10$^{11}$ cm$^{-2}$ and 1.6$\pm$0.5$\times$10$^{11}$ cm$^{-2}$ for the ortho and para species, respectively, and an abundance ratio N(H$_2$CCC)/N(H$_2$CCCH$^+$)= 2.8$\pm$0.7. The chemistry of H$_2$CCCH$^+$ is modelled using the most recent chemical network for the reactions involving the formation of H$_2$CCCH$^+$. We find a reasonable agreement between model predictions and observations, and new insights into the chemistry of C$_3$ bearing species in TMC-1 are obtained.

Ice is ubiquitous in the interstellar medium. We model the formation of the main constituents of interstellar ices, including H2O, CO2 , CO, and CH3 OH. We strive to understand what physical or chemical parameters influence the final composition of the ice and how they benchmark to what has already been observed, with the aim of applying these models to the preparation and analysis of JWST observations. We used the Nautilus gas-grain model, which computes the gas and ice composition as a function of time for a set of physical conditions, starting from an initial gas phase composition. All important processes (gas-phase reactions, gas-grain interactions, and grain surface processes) are included and solved with the rate equation approximation. We first ran an astrochemical code for fixed conditions of temperature and density mapped in the cold core L429-C to benchmark the chemistry. One key parameter was revealed to be the dust temperature. When the dust temperature is higher than 12 K, CO2 will form efficiently at the expense of H2O, while at temperatures below 12 K, it will not form. Whatever hypothesis we assumed for the chemistry (within realistic conditions), the static simulations failed to reproduce the observed trends of interstellar ices in our target core. In a second step, we simulated the chemical evolution of parcels of gas undergoing different physical and chemical situations throughout the molecular cloud evolution and starting a few 1e7 yr prior to the core formation (dynamical simulations). Our dynamical simulations satisfactorily reproduce the main trends already observed for interstellar ices. Moreover, we predict that the apparent constant ratio of CO2/H2O observed to date is probably not true for regions of low AV , and that the history of the evolution of clouds plays an essential role, even prior to their formation., Comment: Accepted for publication in A&A

We present the detection of ethanol (C2H5OH), acetone (CH3COCH3), and propanal (C2H5CHO) toward the cyanopolyyne peak of TMC-1. These three O-bearing complex organic molecules are known to be present in warm interstellar clouds, but had never been observed in a starless core. The addition of these three new pieces to the puzzle of complex organic molecules in cold interstellar clouds stresses the rich chemical diversity of cold dense cores in stages prior to the onset of star formation. The detections of ethanol, acetone, and propanal were made in the framework of QUIJOTE, a deep line survey of TMC-1 in the Q band that is being carried out with the Yebes 40m telescope. We derive column densities of (1.1 +/- 0.3)e12 cm-2 for C2H5OH, (1.4 +/- 0.6)e11 cm-2 for CH3COCH3, and (1.9 +/- 0.7)e11 cm-2 for C2H5CHO. The formation of these three O-bearing complex organic molecules is investigated with the aid of a detailed chemical model which includes gas and ice chemistry. The calculated abundances at a time around 2e5 yr are in reasonable agreement with the values derived from the observations. The formation mechanisms of these molecules in our chemical model are as follows. Ethanol is formed on grains by addition of atomic carbon on methanol followed by hydrogenation and non-thermal desorption. Acetone and propanal are produced by the gas-phase reaction between atomic oxygen and two different isomers of the C3H7 radical, where the latter follows from the hydrogenation of C3 on grains followed by non-thermal desorption. A gas-phase route involving the formation of (CH3)2COH+ through several ion-neutral reactions followed by its dissociative recombination with electrons do also contribute to the formation of acetone., Comment: Accepted for publication in A&A

Cold cores are an early step of star formation, characterized by densities > 10$^4$ cm$^{-3}$, low temperatures (< 15 K), and very low external UV radiation. We investigate the physico-chemical processes at play to tracing the origin of molecules that are predominantly formed via reactions on dust grain surfaces. We observed the cold core LDN 429-C with the NOEMA interferometer and the IRAM 30m single dish telescope in order to obtain the gas-phase abundances of key species, including CO and CH$_3$OH. Comparing the observed gas phase of methanol to its solid phase previously observed with Spitzer allows us to put quantitative constraints on the efficiency of the non-thermal desorption of this species. With physical parameters determined from available Herschel data, we computed abundance maps of 11 detected molecules with a non-local thermal equilibrium radiative transfer model. These observations allowed us to probe the molecular abundances as a function of density and visual extinction, with the variation in temperature being restrained between 12 and 18 K. We then compared the observed abundances to the predictions of the Nautilus astrochemical model. We find that all molecules have lower abundances at high densities and visual extinctions with respect to lower density regions, except for methanol. Comparing these observations with a grid of chemical models based on the local physical conditions, we were able to reproduce these observations, allowing only the parameter time to vary. Comparing the observed gas-phase abundance of methanol with previous measurements of the methanol ice, we estimate a non-thermal desorption efficiency between 0.002% and 0.09%, increasing with density. The apparent increase in the desorption efficiency cannot be reproduced by our model unless the yield of cosmic-ray sputtering is altered due to the ice composition varying as a function of density.

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

The observational counterparts of theoretically predicted first hydrostatic cores (FHSC) have been searched for in the interstellar medium for nearly two decades now. Distinguishing them from other types of more evolved but still embedded objects remains a challenge because these objects have a short lifetime, are small, and embedded in a dense cocoon. One possible lead to finding them is the characterization of the outflows that are launched by these objects. We observed the L1451-mm FHSC candidate with the NOEMA interferometer in order to study the emission of several molecules. A nonlocal thermodynamic equilibrium analysis of the CH$_3$OH detected lines was performed to retrieve the physical conditions of the emitting region around the central source, together with the CH$_3$OH, SiO, CS, and H$_2$CO column densities. Of the targeted molecules, we detected lines of c-C$_3$H$_2$, CH$_3$OH, CS, C$^{34}$S, SO, DCN, DCO$^+$, H$_2$CO, HC$_3$N, HDCO, and SiO. One of the methanol lines appears to be a maser line. The detection of this class I maser and the SiO line in L1451-mm support the presence of a low-velocity and compact outflow. The excitation conditions of the thermal lines of methanol are also compatible with shocks (H$_2$ density of $\sim 3\times 10^6$~cm$^{-3}$ and a temperature higher than 40~K). Although these low-velocity outflows are theoretically predicted by some models of FHSC, these models also predict the shock temperature to be below 20~K, that is, not evaporating methanol. In addition, the predicted velocities would not erode the grains and release silicon in the gas phase. We therefore conclude that these new observations favor the hypothesis that L1451-mm would be at a very early protostellar stage, launching an outflow nearly on the plane of the sky with a higher velocity than is observed., Comment: Accepted for publication in A&A

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

Characterizing the molecular composition of solar-type protostars is useful for improving our understanding of the physico-chemical conditions under which the Sun and its planets formed. In this work, we analyzed the Atacama Large Millimeter/submillimeter Array (ALMA) data of the Protostellar Interferometric Line Survey (PILS), an unbiased spectral survey of the solar-type protostar IRAS~16293--2422, and we tentatively detected 3-hydroxypropenal (HOCHCHCHO) for the first time in the interstellar medium towards source B. Based on the observed line intensities and assuming local thermodynamic equilibrium, its column density is constrained to be $\sim$10$^{15}$ cm$^{-2}$, corresponding to an abundance of 10$^{-4}$ relative to methanol, CH$_3$OH. Additional spectroscopic studies are needed to constrain the excitation temperature of this molecule. We included HOCHCHCHO and five of its isomers in the chemical network presented in Manigand et al. (2021) and we predicted their chemical evolution with the Nautilus code. The model reproduces the abundance of HOCHCHCHO within the uncertainties. This species is mainly formed through the grain surface reaction CH$_2$CHO + HCO $\rightarrow$ HCOCH$_2$CHO, followed by the tautomerization of HCOCH$_2$CHO into HOCHCHCHO. Two isomers, CH$_3$COCHO and CH$_2$COHCHO, are predicted to be even more abundant than HOCHCHCHO. Spectroscopic studies of these molecules are essential in searching for them in IRAS~16293--2422 and other astrophysical sources., Comment: Accepted in A&A Letters

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

Silicon monosulfide is an important silicon bearing molecule detected in circumstellar envelopes and star forming regions. Its formation and destruction routes are not well understood, partially due to the lack of a detailed knowledge on the involved reactions and their rate coefficients. In this work we have calculated and modeled the potential energy surface (PES) of the HSiS system employing highly accurate multireference electronic structure methods. After obtaining an accurate analytic representation of the PES, which includes long-range energy terms in a realistic way via the DMBE method, we have calculated rate coefficients for the Si+SH$\rightarrow$SiS+H reaction over the temperature range of 25-1000K. This reaction is predicted to be fast, with a rate coefficient of $\sim 1\times 10^{-10}\rm cm^3\, s^{-1}$ at 200K, which substantially increases for lower temperatures (the temperature dependence can be described by a modified Arrhenius equation with $\alpha=0.770\times 10^{-10}\rm cm^3\,s^{-1}$, $\beta=-0.756$ and $\gamma=9.873\, \rm K$). An astrochemical gas-grain model of a shock region similar to L1157-B1 shows that the inclusion of the Si+SH reaction increases the SiS gas-phase abundance relative to \ce{H2} from $5\times 10^{-10}$ to $1.4\times 10^{-8}$, which perfectly matches the observed abundance of $\sim 2\times 10^{-8}$., Comment: 11 pages, 7 figures. Accepted for publication in The Astrophysical Journal

The chemical and physical evolution of starless and pre-stellar cores are of paramount importance to understanding the process of star formation. The Taurus Molecular Cloud cores TMC 1-C and TMC 1-CP share similar initial conditions and provide an excellent opportunity to understand the evolution of the pre-stellar core phase. We investigated the evolutionary stage of starless cores based on observations towards the prototypical dark cores TMC 1-C and TMC 1-CP, mapping them in the CS $3\rightarrow 2$, C$^{34}$S $3\rightarrow 2$, $^{13}$CS $2\rightarrow 1$, DCN $1\rightarrow 0$, DCN $2\rightarrow 1$, DNC $1\rightarrow 0$, DNC $2\rightarrow 1$, DN$^{13}$C $1\rightarrow 0$, DN$^{13}$C $2\rightarrow 1$, N$_2$H$^+$ $1\rightarrow 0$, and N$_2$D$^+$ $1\rightarrow 0$ transitions. We performed a multi-transitional study of CS and its isotopologs, DCN, and DNC lines to characterize the physical and chemical properties of these cores. We studied their chemistry using the state-of-the-art gas-grain chemical code Nautilus and pseudo time-dependent models to determine their evolutionary stage. Observational diagnostics seem to indicate that TMC 1-C is in a later evolutionary stage than TMC 1-CP, with a chemical age $\sim$1 Myr. TMC 1-C shows signs of being an evolved core at the onset of star formation, while TMC 1-CP appears to be in an earlier evolutionary stage due to a more recent formation or, alternatively, a collapse slowed down by a magnetic support., Comment: 26 pages, 10 figures

Under cold conditions in dense cores, gas-phase molecules and atoms are depleted from the gas-phase to the surface of interstellar grains. Considering the time scales and physical conditions within these cores, a portion of these molecules has to be brought back into the gas-phase to explain their observation by milimeter telescopes. We tested the respective efficiencies of the different mechanisms commonly included in the models. We also tested the addition of sputtering of ice grain mantles via a collision with cosmic rays in the electronic stopping power regime. The ice sputtering induced by cosmic rays has been added to the Nautilus gas-grain model while the other processes were already present. Each of these processes were tested on a 1D physical structure determined by observations in TMC1 cold cores. The resulting 1D chemical structure was also compared to methanol gas-phase abundances observed in these cores. We found that all species are not sensitive in the same way to the non-thermal desorption mechanisms, and the sensitivity also depends on the physical conditions. Thus, it is mandatory to include all of them. Chemical desorption seems to be essential in reproducing the observations for H densities smaller than $4\times 10^4$~cm$^{-3}$, whereas sputtering is essential above this density. The models are, however, systematically below the observed methanol abundances. A more efficient chemical desorption and a more efficient sputtering could better reproduce the observations. In conclusion, the sputtering of ices by cosmic-rays collisions may be the most efficient desorption mechanism at high density (a few $10^4$~cm$^{-3}$ under the conditions studied here) in cold cores, whereas chemical desorption is still required at smaller densities. Additional works are needed on both mechanisms to assess their efficiency with respect to the main ice composition., Comment: Accepted for publication in A&A

Grain surface chemistry is key to the composition of protoplanetary disks around young stars. The temperature of grains depends on their size. We evaluate the impact of this temperature dependence on the disk chemistry. We model a moderately massive disk with 16 different grain sizes. We use POLARIS to calculate the dust grain temperatures and the local UV flux. We model the chemistry using the 3-phase astrochemical code NAUTILUS. Photoprocesses are handled using frequency-dependent cross-sections, and a new method to account for self and mutual shielding. The multi-grain model outputs are compared to those of single-grain size models (0.1 $\mu$m), with two different assumptions for their equivalent temperature. We find that the Langmuir-Hinshelwood (LH) mechanism at equilibrium temperature is not efficient to form H$_2$ at 3-4 scale heights ($H$), and adopt a parametric fit to a stochastic method to model H$_2$ formation instead. We find the molecular layer composition (1-3 $H$) to depend on the amount of remaining H atoms. Differences in molecular surface densities between single and multi-grain models are mostly due to what occurs above 1.5 $H$. At 100 au, models with colder grains produce H$_2$O and CH$_4$ ices in the midplane, and warmer ones produce more CO$_2$ ices, both allowing efficient depletion of C and O as soon as CO sticks on grain surfaces. Complex organic molecules (COMs) production is enhanced by the presence of warmer grains in the multi-grain models. Using a single grain model mimicking grain growth and dust settling fails to reproduce the complexity of gas-grain chemistry. Chemical models with a single grain size are sensitive to the adopted grain temperature, and cannot account for all expected effects. A spatial spread of the snowlines is expected to result from the ranges in grain temperature. The amplitude of the effects will depend on the dust disk mass., Comment: 39 pages, 33 figures

Aims: Interstellar molecules form early in the evolutionary sequence of interstellar material that eventually forms stars and planets. To understand this evolutionary sequence, it is important to characterize the chemical composition of its first steps. Methods: In this paper, we present the result of a 2 and 3 mm survey of five cold clumps identified by the Planck mission. We carried out a radiative transfer analysis on the detected lines in order to put some constraints on the physical conditions within the cores and on the molecular column densities. We also performed chemical models to reproduce the observed abundances in each source using the gas-grain model Nautilus. Results: Twelve molecules were detected: H2CO, CS, SO, NO, HNO, HCO+, HCN, HNC, CN, CCH, CH3OH, and CO. Here, CCH is the only carbon chain we detected in two sources. Radiative transfer analyses of HCN, SO, CS, and CO were performed to constrain the physical conditions of each cloud with limited success. The sources have a density larger than $10^4$ cm$^{-3}$ and a temperature lower than 15 K. The derived species column densities are not very sensitive to the uncertainties in the physical conditions, within a factor of 2. The different sources seem to present significant chemical differences with species abundances spreading over one order of magnitude. The chemical composition of these clumps is poorer than the one of Taurus Molecular Cloud 1 Cyanopolyyne Peak (TMC-1 CP) cold core. Our chemical model reproduces the observational abundances and upper limits for 79 to 83\% of the species in our sources. The "best" times for our sources seem to be smaller than those of TMC-1, indicating that our sources may be less evolved and explaining the smaller abundances and the numerous non-detections. Also, CS and HCN are always overestimated by our models., 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

(Abridged) The aim of this study is to investigate the chemical evolution from the prestellar phase to the formation of the disk, and to determine the impact that the chemical composition of the cold and dense core has on the final composition of the disk. We performed 3D nonideal magneto-hydrodynamic (MHD) simulations of a dense core collapse using the adaptive-mesh-refinement RAMSES code. For each particle ending in the young rotationally supported disk, we ran chemical simulations with the three-phase gas-grain chemistry code Nautilus. Two different sets of initial abundances, which are characteristic of cold cores, were considered. The final distributions of the abundances of common species were compared to each other, as well as with the initial abundances of the cold core. We find that the spatial distributions of molecules reflect their sensitivity to the temperature distribution. The main carriers of the chemical elements in the disk are usually the same as the ones in the cold core, except for the S-bearing species, where HS is replaced by H$_2$S$_3$, and the P-bearing species, where atomic P leads to the formation of PO, PN, HCP, and CP. However, the abundances of less abundant species change over time. This is especially the case for "large" complex organic molecules (COMs) such as CH$_3$CHO, CH$_3$NH$_2$, CH$_3$OCH$_3$, and HCOOCH$_3$ which see their abundances significantly increase during the collapse. These COMs often present similar abundances in the disk despite significantly different abundances in the cold core. In contrast, the abundances of many radicals decrease with time. A significant number of species still show the same abundances in the cold core and the disk, which indicates efficient formation of these molecules in the cold core. This includes H$_2$O, H$_2$CO, HNCO, and "small" COMs such as CH$_3$OH, CH$_3$CN, and NH$_2$CHO., Comment: Accepted in Astronomy & Astrophysics, 44 pages, 36 figures

Measuring isotopic ratios is a sensitive technique used to obtain information on stellar nucleosynthesis and chemical evolution. We present measurements of the carbon and sulphur abundances in the interstellar medium of the central region of our Galaxy. The selected targets are the +50km/s Cloud and several l.o.s. clouds towards Sgr B2(N). Towards the +50km/s Cloud, we observed the J=2-1 rotational transitions of CS, C34S, 13CS, C33S, and 13C34S, and the J=3-2 transitions of CS and C34S with the IRAM-30m telescope, as well as the J=6-5 transitions of C34S and 13CS with the APEX 12m telescope, all in emission. The J=2-1 rotational transitions of CS, C34S, 13CS, and 13C34S were observed with ALMA in the envelope of Sgr B2(N), with those of CS and C34S also observed in the l.o.s. clouds towards Sgr B2(N), all in absorption. In the +50km/s Cloud we derive a 12C13C isotopic ratio of ~22.1, that leads, with the measured 13CS/C34S line intensity ratio, to a 32S/34S ratio of 16.3+3.0-2.4. We also derive the 32S/34S isotopic ratio more directly from the two isotopologues 13CS and 13C34S, which leads to an independent 32S/34S estimation of 16.3+2.1-1.7 and 17.9+-5.0 for the +50km/s Cloud and Sgr B2(N), respectively. We also obtain a 34S/33S ratio of ~4.3 in the +50 km/s Cloud. Previous studies observed a decreasing trend in the 32S/34S isotopic ratios when approaching the Galactic centre. Our result indicates a termination of this tendency at least at a galactocentric distance of 130-30+60 pc. This is at variance with findings based on 12C/13C, 14N/15N and 18O/17O isotope ratios, where the above-mentioned trend is observed to continue right to the central molecular zone. This can indicate a drop in the production of massive stars at the Galactic centre, in the same line as recent metallicity gradient studies, and opens the work towards a comparison with Galactic and stellar evolution models., Comment: 16 pages, 7 figures, accepted for publication by A&A

We present a study of the elemental depletion in the interstellar medium. We combined the results of a Galatic model describing the gas physical conditions during the formation of dense cores with a full-gas-grain chemical model. During the transition between diffuse and dense medium, the reservoirs of elements, initially atomic in the gas, are gradually depleted on dust grains (with a phase of neutralisation for those which are ions). This process becomes efficient when the density is larger than 100~cm$^{-3}$. If the dense material goes back into diffuse conditions, these elements are brought back in the gas-phase because of photo-dissociations of the molecules on the ices followed by thermal desorption from the grains. Nothing remains on the grains for densities below 10~cm$^{-3}$ or in the gas-phase in a molecular form. One exception is chlorine, which is efficiently converted at low density. Our current gas-grain chemical model is not able to reproduce the depletion of atoms observed in the diffuse medium except for Cl which gas abundance follows the observed one in medium with densities smaller than 10~cm$^{-3}$. This is an indication that crucial processes (involving maybe chemisorption and/or ice irradiation profoundly modifying the nature of the ices) are missing., Comment: Accepted for publication in MNRAS

The current generation of (sub)mm-telescopes has allowed molecular line emission to become a major tool for studying the physical, kinematic, and chemical properties of extragalactic systems, yet exploiting these observations requires a detailed understanding of where emission lines originate within the Milky Way. In this paper, we present 60$^{\prime\prime}$ ($\sim$3pc) resolution observations of many 3mm-band molecular lines across a large map of the W49 massive star-forming region ($\sim$100$\times$100pc at 11kpc), which were taken as part of the "LEGO" IRAM-30m large project. We find that the spatial extent or brightness of the molecular line transitions are not well correlated with their critical densities, highlighting abundance and optical depth must be considered when estimating line emission characteristics. We explore how the total emission and emission efficiency (i.e. line brightness per H$_{2}$ column density) of the line emission vary as a function of molecular hydrogen column density and dust temperature. We find that there is not a single region of this parameter space responsible for the brightest and most efficiently emitting gas for all species. For example, we find that the HCN transition shows high emission efficiency at high column density ($10^{22}$cm$^{-2}$) and moderate temperatures (35K), whilst e.g. N$_2$H$^+$ emits most efficiently towards lower temperatures ($10^{22}$cm$^{-2}$; <20K). We determine $X_{\mathrm{CO} (1-0)} \sim 0.3 \times 10^{20} \mathrm{cm^{-2}(Kkms^{-1})^{-1}}$, and $\alpha_{\mathrm{HCN} (1-0)} \sim 30\mathrm{M_\odot(Kkms^{-1}pc^2)^{-1}}$, which both differ significantly from the commonly adopted values. In all, these results suggest caution should be taken when interpreting molecular line emission., Comment: 33+2 pages, 17+3 figures, 4+4 tables. Tables available online in a machine-readable format. Accepted for publication in MNRAS

Complex organic molecules with three carbon atoms are found in the earliest stages of star formation. In particular, propenal (C$_2$H$_3$CHO) is a species of interest due to its implication in the formation of more complex species and even biotic molecules. This study aims to search for the presence of C$_2$H$_3$CHO and other three-carbon species such as propylene (C$_3$H$_6$) in the hot corino region of the low-mass protostellar binary IRAS 16293--2422 to understand their formation pathways. We use ALMA observations in Band 6 and 7 from various surveys to search for the presence of C$_3$H$_6$ and C$_2$H$_3$CHO towards the protostar IRAS 16293--2422 B (IRAS 16293B). We report the detection of both C$_3$H$_6$ and C$_2$H$_3$CHO towards IRAS 16293B, however, no unblended lines were found towards the other component of the binary system, IRAS 16293A. We derive column density upper limits for C$_3$H$_8$, HCCCHO, n-C$_3$H$_7$OH, i-C$_3$H$_7$OH, C$_3$O, and cis-HC(O)CHO towards IRAS 16293B. We then use a three-phase chemical model to simulate the formation of these species in a typical prestellar environment followed by its hydrodynamical collapse until the birth of the central protostar. Different formation paths, such as successive hydrogenation and radical-radical additions on grain surfaces, are tested and compared to the observational results. The simulations reproduce the abundances within one order of magnitude from those observed towards IRAS 16293B, with the best agreement found for a rate of $10^{-12}$ cm$^3$ s$^{-1}$ for the gas-phase reaction C$_3$ + O $\rightarrow$ C$_2$ + CO. Successive hydrogenations of C$_3$, HC(O)CHO, and CH$_3$OCHO on grain surfaces are a major and crucial formation route of complex organics molecules, whereas both successive hydrogenation pathways and radical-radical addition reactions contribute to the formation of C$_2$H$_5$CHO., Comment: Accepted for publication in A&A. 24 pages, 17 figures

Sulphur is one of the most abundant elements in the Universe. Surprisingly, sulphuretted molecules are not as abundant as expected in the interstellar medium, and the identity of the main sulphur reservoir is still an open question. Our goal is to investigate the H$_{2}$S chemistry in dark clouds, as this stable molecule is a potential sulphur reservoir. Using millimeter observations of CS, SO, H$_{2}$S, and their isotopologues, we determine the physical conditions and H$_{2}$S abundances along the cores TMC 1-C, TMC 1-CP, and Barnard 1b. The gas-grain model Nautilus is then used to model the sulphur chemistry and explore the impact of photo-desorption and chemical desorption on the H$_2$S abundance. Our model shows that chemical desorption is the main source of gas-phase H$_2$S in dark cores. The measured H$_{2}$S abundance can only be fitted if we assume that the chemical desorption rate decreases by more than a factor of 10 when $n_{\rm H}>2\times10^{4}$. This change in the desorption rate is consistent with the formation of thick H$_2$O and CO ice mantles on grain surfaces. The observed SO and H$_2$S abundances are in good agreement with our predictions adopting an undepleted value of the sulphur abundance. However, the CS abundance is overestimated by a factor of $5-10$. Along the three cores, atomic S is predicted to be the main sulphur reservoir. We conclude that the gaseous H$_2$S abundance is well reproduced, assuming undepleted sulphur abundance and chemical desorption as the main source of H$_2$S. The behavior of the observed H$_{2}$S abundance suggests a changing desorption efficiency, which would probe the snowline in these cores. Our model, however, overestimates the observed gas-phase CS abundance. Given the uncertainty in the sulphur chemistry, our data are consistent with a cosmic elemental S abundance with an uncertainty of a factor of 10., Comment: 23 pages, 16 figures

Aims. Our goal is to complete the inventory of S-bearing molecules and their abundances in the prototypical photodissociation region (PDR) the Horsehead nebula to gain insight into sulphur chemistry in UV irradiated regions. Based on the WHISPER millimeter (mm) line survey, our goal is to provide an improved and more accurate description of sulphur species and their abundances towards the core and PDR positions in the Horsehead. Methods. The Monte Carlo Markov chain (MCMC) methodology and the molecular excitation and radiative transfer code RADEX were used to explore the parameter space and determine physical conditions and beam-averaged molecular abundances. Results. A total of 13 S-bearing species (CS, SO, SO2, OCS, H2CS - both ortho and para - HDCS, C2S, HCS+, SO+, H2S, S2H, NS and NS+) have been detected in the two targeted positions. This is the first detection of SO+ in the Horsehead and the first detection of NS+ in any PDR. We find a differentiated chemical behaviour between C-S and O-S bearing species within the nebula. The C-S bearing species C2S and o-H2CS present fractional abundances a factor grater than two higher in the core than in the PDR. In contrast, the O-S bearing molecules SO, SO2, and OCS present similar abundances towards both positions. A few molecules, SO+, NS, and NS+, are more abundant towards the PDR than towards the core, and could be considered as PDR tracers. Conclusions. This is the first complete study of S-bearing species towards a PDR. Our study shows that CS, SO, and H2S are the most abundant S-bearing molecules in the PDR with abundances of a few 1E-9. We recall that SH, SH+, S, and S+ are not observable at the wavelengths covered by the WHISPER survey. At the spatial scale of our observations, the total abundance of S atoms locked in the detected species is < 1E-8, only ~0.1% of the cosmic sulphur abundance., Comment: 15 pages, 7 figures, 6 tables

Molecular oxygen has been the subject of many observational searches as chemical models predicted it to be a reservoir of oxygen. Although it has been detected in two regions of the interstellar medium, its rarity is a challenge for astrochemical models. In this paper, we have combined the physical conditions computed with smoothed particle hydrodynamics (SPH) simulations with our full gas-grain chemical model Nautilus, to study the predicted O2 abundance in interstellar material forming cold cores. We thus follow the chemical evolution of gas and ices in parcels of material from the diffuse interstellar conditions to the cold dense cores. Most of our predicted O2 abundances are below 1e-8 (with respect to the total proton density) and the predicted column densities in simulated cold cores is at maximum a few 1e14 cm-2, in agreement with the non detection limits. This low O2 abundance can be explained by the fact that, in a large fraction of the interstellar material, the atomic oxygen is depleted onto the grain surface (and hydrogenated to form H2O) before O2 can be formed in the gas-phase and protected from UV photo-dissociations. We could achieve this result only because we took into account the full history of the evolution of the physical conditions from the diffuse medium to the cold cores., Comment: Accepted for publication in MNRAS

Nitrogen oxides are thought to play a significant role as a nitrogen reservoir and to potentially participate in the formation of more complex species. Until now, only NO, N$_2$O and HNO have been detected in the interstellar medium. We report the first interstellar detection of nitrous acid (HONO). Twelve lines were identified towards component B of the low-mass protostellar binary IRAS~16293--2422 with the Atacama Large Millimeter/submillimeter Array, at the position where NO and N$_2$O have previously been seen. A local thermodynamic equilibrium model was used to derive the column density ($\sim$ 9 $\times$ 10$^{14}$ cm$^{-2}$ in a 0.5'' beam) and excitation temperature ($\sim$ 100 K) of this molecule. HNO, NO$_2$, NO$^+$, and HNO$_3$ were also searched for in the data, but not detected. We simulated the HONO formation using an updated version of the chemical code Nautilus and compared the results with the observations. The chemical model is able to reproduce satisfactorily the HONO, N$_2$O, and NO$_2$ abundances, but not the NO, HNO, and NH$_2$OH abundances. This could be due to some thermal desorption mechanisms being destructive and therefore limiting the amount of HNO and NH$_2$OH present in the gas phase. Other options are UV photodestruction of these species in ices or missing reactions potentially relevant at protostellar temperatures., Comment: Accepted in A&A Letters

Studying molecular species in protoplanetary disks is very useful to characterize the properties of these objects, which are the site of planet formation. We attempt to constrain the chemistry of S-bearing molecules in the cold parts of circumstellar disk of GG Tau A. We searched for H$_2$S, CS, SO, and SO$_2$ in the dense disk around GG Tau A with the NOrthem Extended Millimeter Array (NOEMA) interferometer. We detected H$_2$S emission from the dense and cold ring orbiting around GG Tau A. This is the first detection of H$_2$S in a protoplanetary disk. We also detected HCO$^+$, H$^{13}$CO$^+$, and DCO$^+$ in the disk. Upper limits for other molecules, CCS, SO$_2$, SO, HC$_3$N, and $c$-C$_3$H$_2$ are also obtained. The observed DCO$^+$/HCO$^+$ ratio is similar to those in other disks. The observed column densities, derived using our radiative transfer code DiskFit, are then compared with those from our chemical code Nautilus. The column densities are in reasonable agreement for DCO$^{+}$, CS, CCS, and SO$_2$. For H$_2$S and SO, our predicted vertical integrated column densities are more than a factor of 10 higher than the measured values. Our results reinforce the hypothesis that only a strong sulfur depletion may explain the low observed H$_2$S column density in the disk. The H$_2$S detection in GG Tau A is most likely linked to the much larger mass of this disk compared to that in other T Tauri systems., Comment: 6 pages, 7 figures, 3 tables

Ions and electrons play an important role in various stages of the star formation process. By following the magnetic field of their environment and interacting with neutral species, they slow down the gravitational collapse of the proto-star envelope. This process (known as ambipolar diffusion) depends on the ionisation degree, which can be derived from the \hco abundance. We present a study of \hco and its isotopologues (H$^{13}$CO$^+$, HC$^{18}$O$^+$, DCO$^+$, and H$^{13}$CO$^+$) in the low-mass proto-star IRAS16293$-$2422. The structure of this object is complex, and the HCO$^+$ emission arises from the contribution of a young NW-SE outflow, the proto-stellar envelope and the foreground cloud. We aim at constraining the physical parameters of these structures using all the observed transitions. For the young NW-SE outflow, we derive $T_{\rm kin}=180-220$ K and $n({\rm H_2})=(4-7)\times10^6$ cm$^{-3}$ with an HCO$^+$ abundance of $(3-5)\times10^{-9}$. Following previous studies, we demonstrate that the presence of a cold ($T_{\rm kin}$$\leqslant$30 K) and low density ($n({\rm H_2})\leqslant1\times10^4$ cm$^{-3}$) foreground cloud is also necessary to reproduce the observed line profiles. We have used the gas-grain chemical code \textsc{nautilus} to derive the HCO$^+$ abundance profile across the envelope and the external regions where X(HCO$^+$)$\gtrsim1\times10^{-9}$ dominate the envelope emission. From this, we derive an ionisation degree of $10^{-8.9}\,\lesssim\,x(e)\,\lesssim\,10^{-7.9}$. The ambipolar diffusion timescale is $\sim$5 times the free-fall timescale, indicating that the magnetic field starts to support the source against gravitational collapse and the magnetic field strength is estimated to be $6-46 \mu$G., Comment: 17 pages, 10 figures, accepted for publication in MNRAS

Aims. We study the effect of large scale dynamics on the molecular composition of the dense interstellar medium during the transition between diffuse to dense clouds. Methods. We followed the formation of dense clouds (on sub-parsec scales) through the dynamics of the interstellar medium at galac- tic scales. We used results from smoothed particle hydrodynamics (SPH) simulations from which we extracted physical parameters that are used as inputs for our full gas-grain chemical model. In these simulations, the evolution of the interstellar matter is followed for ~50 Myr. The warm low-density interstellar medium gas flows into spiral arms where orbit crowding produces the shock formation of dense clouds, which are held together temporarily by the external pressure. Results. We show that depending on the physical history of each SPH particle, the molecular composition of the modeled dense clouds presents a high dispersion in the computed abundances even if the local physical properties are similar. We find that carbon chains are the most affected species and show that these differences are directly connected to differences in (1) the electronic fraction, (2) the C/O ratio, and (3) the local physical conditions. We argue that differences in the dynamical evolution of the gas that formed dense clouds could account for the molecular diversity observed between and within these clouds. Conclusions. This study shows the importance of past physical conditions in establishing the chemical composition of the dense medium., Comment: 15 pages, 15 figures

Determining the gas density and temperature structures of protoplanetary disks is a fundamental task to constrain planet formation theories. This is a challenging procedure and most determinations are based on model-dependent assumptions. We attempt a direct determination of the radial and vertical temperature structure of the Flying Saucer disk, thanks to its favorable inclination of 90 degrees. We present a method based on the tomographic study of an edge-on disk. Using ALMA, we observe at 0.5$"$ resolution the Flying Saucer in CO J=2-1 and CS J=5-4. This edge-on disk appears in silhouette against the CO J=2-1 emission from background molecular clouds in $\rho$ Oph. The combination of velocity gradients due to the Keplerian rotation of the disk and intensity variations in the CO background as a function of velocity provide a direct measure of the gas temperature as a function of radius and height above the disk mid-plane. The overall thermal structure is consistent with model predictions, with a cold ($< 15-12 $~K), CO-depleted mid-plane, and a warmer disk atmosphere. However, we find evidence for CO gas along the mid-plane beyond a radius of about 200\,au, coincident with a change of grain properties. Such a behavior is expected in case of efficient rise of UV penetration re-heating the disk and thus allowing CO thermal desorption or favoring direct CO photo-desorption. CO is also detected up to 3-4 scale heights while CS is confined around 1 scale height above the mid-plane. The limits of the method due to finite spatial and spectral resolutions are also discussed. This method appears to be very promising to determine the gas structure of planet-forming disks, provided that the molecular data have an angular resolution which is high enough, of the order of $0.3 - 0.1"$ at the distance of the nearest star forming regions., Comment: 14 pages + 11 figures

Cyclic-C3HD (c-C3HD) is a singly deuterated isotopologue of c-C3H2, which is one of the most abundant and widespread molecules in our Galaxy. We observed IRAS 16293-2422 in the 3 mm band with a single frequency setup using the EMIR heterodyne 3 mm receiver of the IRAM 30m telescope. We observed seven lines of c-C3HD and three lines of c-C3H2. Observed abundances are compared with astrochemical simulations using the NAUTILUS gas-grain chemical model. Our results clearly show that c-C3HD can be used as an important supplement for studying chemistry and physical conditions for cold environments. Assuming that the size of the protostellar envelope is 3000 AU and same excitation temperatures for both c-C3H2 and c-C3HD, we obtain a deuterium fraction of $14_{-3}^{+4}\%$., Comment: Accepted for publication in MNRAS

Recent laboratory measurements have confirmed that chemical desorption (desorption of products due to exothermic surface reactions) can be an efficient process. The impact of including this process into gas-grain chemical models entirely depends on the formalism used and the associated parameters. Among these parameters, binding energies are probably the most uncertain ones for the moment. We propose a new model to compute binding energy of species to water ice surfaces. We have also compared the model results using either the new chemical desorption model proposed by Minissale et al. (2016) or the one of Garrod et al. (2007). The new binding energies have a strong impact on the formation of complex organic molecules. In addition, the new chemical desorption model from Minissale produces a much smaller desorption of these species and also of methanol. Combining the two effects, the abundances of CH3OH and COMs observed in cold cores cannot be reproduced by astrochemical models anymore.

Deuterated species are unique and powerful tools in astronomy since they can probe the physical conditions, chemistry, and ionization level of various astrophysical media. Recent observations of several deuterated species along with some of their spin isomeric forms have rekindled the interest for more accurate studies on deuterium fractionation. This paper presents the first publicly available chemical network of multiply deuterated species along with spin chemistry implemented on the latest state-of-the-art gas-grain chemical code `NAUTILUS'. D/H ratios for all deuterated species observed at different positions of TMC-1 are compared with the results of our model, which considers multiply deuterated species along with the spin chemistry of light hydrogen bearing species H2, H2+, H3+ and their isotopologues. We also show the differences in the modeled abundances of non-deuterated species after the inclusion of deuteration and spin chemistry in the model. Finally, we present a list of potentially observable deuterated species in TMC-1 awaiting detection., Comment: Accepted for publication in MNRAS on Dec. 22nd

Recent detections of complex organic molecules in dark clouds have rekindled interest in the astrochemical modeling of these environments. Because of its relative closeness and rich molecular complexity, TMC-1 has been extensively observed to study the chemical processes taking place in dark clouds. We use local thermodynamical equilibrium radiative transfer modeling coupled with a Bayesian statistical method which takes into account outliers to analyze the data from the Nobeyama spectral survey of TMC-1 between 8 and 50 GHz. We compute the abundance relative to molecular hydrogen of 57 molecules, including 19 isotopologues in TMC-1 along with their associated uncertainty. The new results are in general agreement with previous abundance determination from Ohishi & Kaifu and the values reported in the review from Agundez & Wakelam. However, in some cases, large opacity and low signal to noise effects allow only upper or lower limits to be derived, respectively., Comment: Accepted for publication in ApJS

Protoplanetary disks are the target of many chemical studies (both observational and theoretical) as they contain the building material for planets. Their large vertical and radial gradients in density and temperature make them challenging objects for chemical models. In the outer part of these disks, the large densities and low temperatures provide a particular environment where the binding of species onto the dust grains can be very efficient and can affect the gas-phase chemical composition. We attempt to quantify to what extent the vertical abundance profiles and the integrated column densities of molecules predicted by a detailed gas-grain code are affected by the treatment of the molecular hydrogen physisorption at the surface of the grains. We performed three different models using the Nautilus gas-grain code. One model uses a H2 binding energy on the surface of water (440 K) and produces strong sticking of H2. Another model uses a small binding energy of 23 K (as if there were already a monolayer of H2), and the sticking of H$_2$ is almost negligible. Finally, the remaining model is an intermediate solution known as the encounter desorption mechanism. We show that the efficiency of molecular hydrogen binding (and thus its abundance at the surface of the grains) can have a quantitative effect on the predicted column densities in the gas phase of major species such as CO, CS, CN, and HCN., Comment: Accepted for publication as a Research Note in A&A

(abridged) We used the IRAM 30-m to perform a sensitive wideband survey of 30 protoplanetary disks in the Taurus Auriga region. We simultaneously observed HCO$^+$(3-2), HCN(3-2), C$_2$H(3-2), CS(5-4), and two transitions of SO. We combine the results with a previous survey which observed $^{13}$CO (2-1), CN(2-1), two o-H$_2$CO lines and one of SO. We use available interferometric data to derive excitation temperatures of CN and C$_2$H in several sources. We determine characteristic sizes of the gas disks and column densities of all molecules using a parametric power-law disk model. Our study is mostly sensitive to molecules at 200-400 au from the stars. We compare the derived column densities to the predictions of an extensive gas-grain chemical disk model, under conditions representative of T Tauri disks. This survey provides 20 new detections of HCO$^+$ in disks, 18 in HCN, 11 in C$_2$H, 8 in CS and 4 in SO. HCO$^+$ is detected in almost all sources, and its J=3-2 line is essentially optically thick, providing good estimates of the disk radii. The other transitions are (at least partially) optically thin. Variations of the column density ratios do not correlate with any specific property of the star or disk. Disks around Herbig Ae stars appear less rich in molecules than those around T Tauri stars, although the sample remains small. SO is only found in the (presumably younger) embedded objects, perhaps reflecting an evolution of the S chemistry due to increasing depletion with time. Overall, the molecular column densities, and in particular the CN/HCN and CN/C$_2$H ratios, are well reproduced by gas-grain chemistry in cold disks. This study provides a census of simple molecules in disks of radii $> 200-300$ au. Extending that to smaller disks, or searching for less abundant or more complex molecules requires a much more sensitive facility, i.e. NOEMA and ALMA., Comment: To appear in Astronomy & Astrophysics

The first hydrostatic core, also called the first Larson core, is one of the first steps in low-mass star formation, as predicted by theory. With recent and future high performance telescopes, details of these first phases become accessible, and observations may confirm theory and even bring new challenges for theoreticians. In this context, we study from a theoretical point of view the chemical and physical evolution of the collapse of prestellar cores until the formation of the first Larson core, in order to better characterize this early phase in the star formation process. We couple a state-of-the-art hydrodynamical model with full gas-grain chemistry, using different assumptions on the magnetic field strength and orientation. We extract the different components of each collapsing core (i.e., the central core, the outflow, the disk, the pseudodisk, and the envelope) to highlight their specific physical and chemical characteristics. Each component often presents a specific physical history, as well as a specific chemical evolution. From some species, the components can clearly be differentiated. The different core models can also be chemically differentiated. Our simulation suggests some chemical species as tracers of the different components of a collapsing prestellar dense core, and as tracers of the magnetic field characteristics of the core. From this result, we pinpoint promising key chemical species to be observed., Comment: Accepted for publication in ApJ

The ketenyl radical (HCCO) has recently been discovered in two cold dense clouds with a non-negligible abundance of a few 1e-11 (compared to H2) (Agundez et al. 2015). Until now, no chemical network has been able to reproduce this observation. We propose here a chemical scheme that can reproduce HCCO abundances together with HCO, H2CCO and CH3CHO in the dark clouds Lupus-1A and L486. The main formation pathway for HCCO is the OH + CCH -> HCCO + H reaction as suggested by Agundez et al. (2015) but with a much larger rate coefficient than used in current models. Since this reaction has never been studied experimentally or theoretically, this larger value is based on a comparison with other similar systems.

Hereafter we describe the activities of the $Grand \, Sud-Ouest$ Data Centre operated for INSU/CNRS by the OMP-IRAP and the Universit\'e Paul Sabatier (Toulouse), in a collaboration with the OASU-LAB (Bordeaux) and OREME-LUPM (Montpellier)., Comment: To appear in the proceedings of SF2A 2015. (ov-gso.irap.omp.eu)

The gas mass of protoplanetary disks, and the gas-to-dust ratio, are two key elements driving the evolution of these disks and the formation of planetary system. We explore here to what extent CO (or its isotopologues) can be used as a tracer of gas mass. We use a detailed gas-grain chemical model and study the evolution of the disk composition, starting from a dense pre-stellar core composition. We explore a range of disk temperature profiles, cosmic rays ionization rates, and disk ages for a disk model representative of T Tauri stars. At the high densities that prevail in disks, we find that, due to fast reactions on grain surfaces, CO can be converted to less volatile forms (principally s-CO$_2$, and to a lesser extent s-CH$_4$) instead of being evaporated over a wide range of temperature. The canonical gas-phase abundance of 10$^{-4}$ is only reached above about 30-35 K. The dominant Carbon bearing entity depends on the temperature structure and age of the disk. The chemical evolution of CO is also sensitive to the cosmic rays ionization rate. Larger gas phase CO abundances are found in younger disks. Initial conditions, such as parent cloud age and density, have a limited impact. This study reveals that CO gas-phase abundance is heavily dependent on grain surface processes, which remain very incompletely understood so far. The strong dependence on dust temperature profile makes CO a poor tracer of the gas-phase content of disks., Comment: 11 pages, 9 figures, Accepted for publication in A&A

We attempt to determine the molecular composition of disks around young low-mass stars in the $\rho$ Oph region and to compare our results with a similar study performed in the Taurus-Auriga region. We used the IRAM 30 m telescope to perform a sensitive search for CN N=2-1 in 29 T Tauri stars located in the $\rho$ Oph and upper Scorpius regions. $^{13}$CO J=2-1 is observed simultaneously to provide an indication of the level of confusion with the surrounding molecular cloud. The bandpass also contains two transitions of ortho-H$_2$CO, one of SO, and the C$^{17}$O J=2-1 line, which provides complementary information on the nature of the emission. Contamination by molecular cloud in $^{13}$CO and even C$^{17}$O is ubiquitous. The CN detection rate appears to be lower than for the Taurus region, with only four sources being detected (three are attributable to disks). H$_2$CO emission is found more frequently, but appears in general to be due to the surrounding cloud. The weaker emission than in Taurus may suggest that the average disk size in the $\rho$ Oph region is smaller than in the Taurus cloud. Chemical modeling shows that the somewhat higher expected disk temperatures in $\rho$ Oph play a direct role in decreasing the CN abundance. Warmer dust temperatures contribute to convert CN into less volatile forms. In such a young region, CN is no longer a simple, sensitive tracer of disks, and observations with other tracers and at high enough resolution with ALMA are required to probe the gas disk population., Comment: 18 pages, 5 figures, accepted for publication in A&A

Chemical models used to study the chemical composition of the gas and the ices in the interstellar medium are based on a network of chemical reactions and associated rate coefficients. These reactions and rate coefficients are partially compiled from data in the literature, when available. We present in this paper kida.uva.2014, a new updated version of the kida.uva public gas-phase network first released in 2012. In addition to a description of the many specific updates, we illustrate changes in the predicted abundances of molecules for cold dense cloud conditions as compared with the results of the previous version of our network, kida.uva.2011., Comment: Accepted for publication in ApJS on February 26th, 2015

Recent observations have revealed the existence of Complex Organic Molecules (COMs) in cold dense cores and prestellar cores. The presence of these molecules in such cold conditions is not well understood and remains a matter of debate since the previously proposed "warm- up" scenario cannot explain these observations. In this article, we study the effect of Eley- Rideal and complex induced reaction mechanisms of gas-phase carbon atoms with the main ice components of dust grains on the formation of COMs in cold and dense regions. Based on recent experiments we use a low value for the chemical desorption efficiency (which was previously invoked to explain the observed COM abundances). We show that our introduced mechanisms are efficient enough to produce a large amount of complex organic molecules in the gas-phase at temperatures as low as 10K., Comment: 14 pages, 12 figures, 8 tables

The freezeout of gas-phase species onto cold dust grains can drastically alter the chemistry and the heating-cooling balance of protostellar material. In contrast to well-known species such as carbon monoxide (CO), the freezeout of various carriers of elements with abundances $<10^{-5}$ has not yet been well studied. Our aim here is to study the depletion of chlorine in the protostellar core, OMC-2 FIR 4. We observed transitions of HCl and H2Cl+ towards OMC-2 FIR 4 using the Herschel Space Observatory and Caltech Submillimeter Observatory facilities. Our analysis makes use of state of the art chlorine gas-grain chemical models and newly calculated HCl-H$_{2}$ hyperfine collisional excitation rate coefficients. A narrow emission component in the HCl lines traces the extended envelope, and a broad one traces a more compact central region. The gas-phase HCl abundance in FIR 4 is 9e-11, a factor of only 0.001 that of volatile elemental chlorine. The H2Cl+ lines are detected in absorption and trace a tenuous foreground cloud, where we find no depletion of volatile chlorine. Gas-phase HCl is the tip of the chlorine iceberg in protostellar cores. Using a gas-grain chemical model, we show that the hydrogenation of atomic chlorine on grain surfaces in the dark cloud stage sequesters at least 90% of the volatile chlorine into HCl ice, where it remains in the protostellar stage. About 10% of chlorine is in gaseous atomic form. Gas-phase HCl is a minor, but diagnostically key reservoir, with an abundance of <1e-10 in most of the protostellar core. We find the 35Cl/37Cl ratio in OMC-2 FIR 4 to be 3.2\pm0.1, consistent with the solar system value., Comment: 13 pages, 12 figures, accepted for publication in A&A