Gas phase Elemental abundances in Molecular cloudS (GEMS). IV. Observational results and statistical trends
M. Rodríguez-Baras, A. Fuente, P. Riviére-Marichalar, D. Navarro-Almaida, P. Caselli, M. Gerin, C. Kramer, E. Roueff, V. Wakelam, G. Esplugues, S. García-Burillo, R. Le Gal, S. Spezzano, T. Alonso-Albi, R. Bachiller, S. Cazaux, B. Commercon, J.R. Goicoechea, J.C. Loison, S.P. Treviño-Morales, O. Roncero, I. Jiménez-Serra, J. Laas, A. Hacar, J. Kirk, V. Lattanzi, R. Martín-Doménech, G. Muñoz-Caro, J.E. Pineda, B. Tercero, D. Ward-Thompson, M. Tafalla, N. Marcelino, J. Malinen, R. Friesen, B.M. Giuliano
AAstronomy & Astrophysics manuscript no. 40112corr © ESO 2021March 1, 2021
Gas phase Elemental abundances in Molecular cloudS (GEMS)
IV. Observational results and statistical trends
M. Rodríguez-Baras , A. Fuente , P. Riviére-Marichalar D. Navarro-Almaida , P. Caselli , M. Gerin , C. Kramer ,E. Roue ff , V. Wakelam , G. Esplugues , S. García-Burillo , R. Le Gal , S. Spezzano , T. Alonso-Albi ,R. Bachiller , S. Cazaux , B. Commercon , J. R. Goicoechea , J. C. Loison , S. P. Treviño-Morales , O. Roncero ,I. Jiménez-Serra , J. Laas , A. Hacar , J. Kirk , V. Lattanzi , R. Martín-Doménech G. Muñoz-Caro , J. E. Pineda ,B. Tercero , , D. Ward-Thompson , M. Tafalla , N. Marcelino , J. Malinen , , R. Friesen , and B. M. Giuliano Observatorio Astronómico Nacional (OAN), Alfonso XII, 3, 28014, Madrid, Spain Centre for Astrochemical Studies, Max-Planck-Institute for Extraterrestrial Physics, Giessenbachstrasse 1, 85748, Garching, Ger-many Observatoire de Paris, PSL Research University, CNRS, École Normale Supérieure, Sorbonne Universités, UPMC Univ. Paris 06,75005, Paris, France Institut de Radioastronomie Millimétrique, 300 rue de la Piscine, Domaine Universitaire, 38406 Saint Martin d’Hères, France LERMA, Observatoire de PARIS, PSL Research University, CNRS, Sorbonne Université, 92190 Meudon, France Laboratoire d’astrophysique de Bordeaux, Univ. Bordeaux, CNRS, B18N, allée Geo ff roy Saint-Hilaire, 33615 Pessac, France Harvard-Smithsonian Center for Astrophysics, 60 Garden St., Cambridge, MA 02138, USA Faculty of Aerospace Engineering, Delft University of Technology, Delft, The Netherlands ; University of Leiden, P.O. Box 9513,NL, 2300 RA, Leiden, The Netherlands École Normale Supérieure de Lyon, CRAL, UMR CNRS 5574, Université Lyon I, 46 Allée d’Italie, 69364, Lyon Cedex 07, France Instituto de Física Fundamental (CSIC), Calle Serrano 123, 28006, Madrid, Spain Institut des Sciences Moléculaires (ISM), CNRS, Univ. Bordeaux, 351 cours de la Libération, F-33400, Talence, France Chalmers University of Technology, Department of Space, Earth and Environment, SE-412 93 Gothenburg, Sweden Centro de Astrobiología (CSIC-INTA), Ctra. de Ajalvir, km 4, Torrejón de Ardoz, 28850, Madrid, Spain University of Vienna, Department of Astrophysics, Tuerkenschanzstrasse 17, 1180, Vienna Jeremiah Horrocks Institute, University of Central Lancashire, Preston PR1 2HE, UK Observatorio de Yebes (IGN). Cerro de la Palera s / n, 19141 Yebes, Spain Department of Physics, University of Helsinki, PO Box 64, 00014 Helsinki, Finland Institute of Physics I, University of Cologne, Cologne, Germany National Radio Astronomy Observatory, 520 Edgemont Rd., Charlottesville VA 22901, USAMarch 1, 2021
ABSTRACT
Gas phase Elemental abundances in Molecular CloudS (GEMS) is an IRAM 30m Large Program designed to provide estimates of theS, C, N, and O depletions and gas ionization degree, X(e − ), in a selected set of star-forming filaments of Taurus, Perseus, and Orion.Our immediate goal is to build up a complete and large database of molecular abundances that can serve as an observational basisfor estimating X(e − ) and the C, O, N, and S depletions through chemical modeling. We observed and derived the abundances of 14species ( CO, C O, HCO + , H CO + , HC O + , HCN, H CN, HNC, HCS + , CS, SO, SO, H S, and OCS) in 244 positions, coveringthe A V ∼ ∼
100 mag, n ( H ) ∼ a few 10 to 10 cm − , and T k ∼
10 to ∼
30 K ranges in these clouds, and avoiding protostars, HIIregions, and bipolar outflows. A statistical analysis is carried out in order to identify general trends between di ff erent species and withphysical parameters. Relations between molecules reveal strong linear correlations which define three di ff erent families of species:(1) CO and C O isotopologs; (2) H CO + , HC O + , H CN, and HNC; and (3) the S-bearing molecules. The abundances of theCO isotopologs increase with the gas kinetic temperature until T K ∼
15 K. For higher temperatures, the abundance remains constantwith a scatter of a factor of ∼
3. The abundances of H CO + , HC O + , H CN, and HNC are well correlated with each other, and all ofthem decrease with molecular hydrogen density, following the law ∝ n ( H ) − . ± . . The abundances of S-bearing species also decreasewith molecular hydrogen density at a rate of (S-bearing / H) gas ∝ n ( H ) − . ± . . The abundances of molecules belonging to groups 2 and3 do not present any clear trend with gas temperature. At scales of molecular clouds, the C O abundance is the quantity that bettercorrelates with the cloud mass. We discuss the utility of the CO / C O, HCO + / H CO + , and H CO + / H CN abundance ratios aschemical diagnostics of star formation in external galaxies.
Key words.
Astrochemistry – ISM: abundances – ISM: molecules – ISM: clouds – stars: formation – galaxies: ISM
1. Introduction
Gas chemistry plays a key role in the star formation processby regulating fundamental parameters such as the gas cooling rate and ionization fraction. Molecular clouds can contract andfragment because molecules cool the gas, thus diminishing thethermal support relative to self-gravity. The ionization fraction
Article number, page 1 of 28 a r X i v : . [ a s t r o - ph . GA ] F e b & A proofs: manuscript no. 40112corr controls the coupling of magnetic fields with the gas, drivingthe dissipation of turbulence and angular momentum transfer,and therefore plays a crucial role in cloud collapse (isolated vs.clustered star formation) and the dynamics of accretion disks(see Zhao et al., 2016; Padovani et al., 2013). In the absence ofother ionization agents (X-rays, UV photons, J-type shocks), thesteady state ionization fraction is proportional to (cid:112) ζ H / n , where n is the molecular hydrogen density and ζ H is the cosmic-rayionization rate for H molecules, which becomes the key param-eter in the molecular cloud evolution (Oppenheimer & Dalgarno,1974; McKee, 1989; Caselli et al., 2002). The gas ionizationfraction, X(e − ) = n(e − ) / n H , and molecular abundances depend onthe elemental depletion factors (Caselli et al., 1998). In particu-lar, carbon (C) is the main donor of electrons in the cloud surfaceregion (A V < ∼ − / or icy mantles. Knowledge of elemental depletionscan therefore be valuable in studying the changes in the dustgrain composition across the cloud. Surface chemistry and theinterchange of molecules between the solid and gas phases havea leading role in the chemical evolution of gas from the di ff usecloud to the prestellar core phase.GEMS Gas phase Elemental abundances in MolecularCloudS (GEMS) is an IRAM 30m Large Program, the aim ofwhich is to estimate the S, C, N, and O depletions and X(e − )as a function of visual extinction in a selected set of prototyp-ical star-forming filaments. Regions with di ff erent illuminationare included in the sample in order to investigate the influenceof UV radiation (photodissociation, ionization, photodesorption)and turbulence on these parameters, and eventually in the starformation history of the cloud. The depletion factor is definedas the ratio between the total (dust + gas) abundance of a givenelement and its abundance as observed in the gas phase. The de-termination of the depletion factor of a given element can onlybeen done directly through high-sensitivity observations of themain molecular reservoirs of each element and detailed chemi-cal modeling of the secondary reservoirs (Fuente et al. 2019; seea simple scheme in Fig. 1).The first step to derive the elemental gas abundance of C, O,N, and S is to determine the abundances of the main reservoirs ofthe elements in the gas phase. Essentially, most of the carbon islocked in CO in dense cores and the C depletion is derived fromthe study of CO and its isotopologs. A significant fraction ofC may be atomic (C, C + ) in the molecular gas surrounding thecores. The gas ionization fraction, X(e − ), can be derived fromthe [HCO + ] / [CO] ratio, which can help to constrain the C deple-tion values through comparison with chemical models. The mainreservoirs of nitrogen are supposed to be atomic nitrogen (N) andmolecular nitrogen (N ) which are not observable. The nitrogenabundance can be derived by applying a chemical model to fitthe observed abundances of nitriles (HCN, HNC, CN) (Agúndez& Wakelam 2013; Le Gal et al. 2014). The HCN abundance isalso dependent on the amount of atomic C in gas phase, mainlyon the C / O ratio (Loison et al. 2014; Fuente et al. 2016). Themost abundant oxygenated molecules, O , H O, and OH, are dif-ficult to observe in the millimeter domain and the oxygen deple- tion factor has to be derived indirectly from the C / O ratio. TheCS / SO abundance ratio has been used as a proxy for the C / O ra-tio in di ff erent environments (Fuente et al. 2016; Semenov et al.2018). The abundances of other species such as HCN and C Hare also very sensitive to the C / O gas-phase ratio (Loison et al.2014; Miotello et al. 2019).Determining sulfur depletion is challenging. Sulfur is oneof the most abundant elements in the Universe (S / H ∼ × − )(Asplund et al. 2009) and plays a crucial role in biological sys-tems on Earth, and so it is important to follow its chemical his-tory in space (i.e., toward precursors of Solar System analogs).Surprisingly, S-bearing molecules are not as abundant as ex-pected in the interstellar medium. Sulfur is thought to be de-pleted in molecular clouds by a factor up to 1000 compared to itsestimated cosmic abundance (Ru ffl e et al. 1999; Wakelam et al.2004). Because of the high hydrogen abundances and the mobil-ity of hydrogen in the ice matrix, sulfur atoms in interstellar icemantles are expected to preferentially form H S. There are onlyupper limits to the solid H S abundance (e.g., Jiménez-Escobar& Muñoz Caro 2011), and OCS is the only S-bearing moleculeunambiguously detected in ice mantles because of its large bandstrength in the infrared (Geballe et al. 1985; Palumbo et al.1995) along with, tentatively, SO (Boogert et al. 1997). Onepossibility is that most of the sulfur is locked in atomic sulfurin the gas phase. Also, sulfur could be in refractory allotropes,mainly S , as found theoretically by Shingledecker et al. (2020),and previously observed in the laboratory by Jiménez-Escobaret al. (2012; 2014). The detection of sulfur allotropes in comets(Calmonte et al. 2016) and of S H in gas phase (Fuente et al.2017) testify to the importance of these compounds. Unfortu-nately, sulfur allotropes cannot be directly observed in the in-terstellar medium. Direct observation of the S atom is also dif-ficult and, until now, S has only been detected in some bipolaroutflows using the infrared space telescope Spitzer (Andersonet al. 2013). Our project includes a wide set of S-bearing species(CS, SO, H S, HCS + , SO , OCS, and H CS) that are going tobe used to constrain the sulfur depletion in our sample. To ourknowledge, this will constitute the most complete database ofS-bearing molecules in dark clouds so far.A detailed presentation of the project with a list of speciesand isotopologs observed was included in Fuente et al. (2019).This paper presents the abundances of CO, C O, CS, C S, CS, H S, SO, SO, HCO + , H CO + , HC O + , HCN, H CN,HNC, HCS + , and OCS towards the whole sample. Our goal is toinvestigate the statistical trends of these molecular abundancesand their dependency on the local physical conditions as a firststep toward understanding the chemical evolution of dark clouds.Detailed chemical modeling of each region, which constitutesan imperative step toward deriving elemental abundances (seeFig. 1), will be carried out in a future paper. The observationsof N H + will also be presented elsewhere since, as discussed byFuente et al. (2019), they require a more sophisticated modeling.We do not include H CS, because it has only been detected in asmall fraction of the observed positions, preventing a statisticalanalysis.
2. Sample selection
Our project focuses on the nearby star forming regions Taurus,Perseus, and Orion. These molecular cloud complexes were ob-served with Herschel and SCUBA as part of the Gould Belt Sur-vey (André et al. 2010), and accurate visual extinction (A V ) anddust temperature (T d ) maps are available (Malinen et al. 2012;Hatchell et al. 2005; Lombardi et al. 2014; Zari et al. 2016). The Article number, page 2 of 28. Rodríguez-Baras et al.: Gas phase Elemental abundances in Molecular cloudS (GEMS)
Fig. 1.
Block diagram of the GEMS project. angular resolution of the A V -T d maps ( ∼ (cid:48)(cid:48) ) is similar to thatprovided by the 30m telescope at 3mm allowing direct compari-son of continuum and spectroscopic data. Throughout this paperwe adopt A V ≈ N(H ) × − mag (Bohlin et al. 1978).These regions are characterized as having di ff erent star for-mation activity and therefore di ff erent illumination. This allowsus to investigate the influence of UV radiation on the gas com-position. Our strategy is to observe several starless cores withineach filament. By comparing the cores in the same filament, wewill be able to investigate the e ff ect of time evolution on thechemistry of dark cores (see, e.g., Frau et al. 2012). By compar-ing cores in di ff erent regions, we explore the e ff ect of the envi-ronment on the chemistry therein. The list of selected cores isshown in Table 1.Within the pilot project, we observed three cuts in TMC1 andone in Barnard 1b whose data have been partially published inFuente et al. (2019) and Navarro-Almaida et al. (2020). The datafrom these cuts are included in this paper for completeness.In total, our project includes observations towards 305 posi-tions distributed in 27 cuts roughly perpendicular to the selectedfilaments. The cuts are designed to intersect the filament alongone of the selected starless cores, avoiding the position of knownprotostars, HII regions, and bipolar outflows. They cover visualextinctions from A V ∼ V ∼
200 mag in the line ofsight towards the giant molecular cloud Orion A. The separa-tion between one position and another in a given cut is selectedto sample the visual extinction range in regular intervals of A V .However, this is not always possible, specially for A V >
10 mag,where the surface density gradient is steeper. At low visual ex-tinctions, not all the lines are detected. In this paper, we onlyconsider 244 positions for which we are able to determine thegas density from the CS and its isotopolog observations (seeSect. 4). In the following, we describe the observed positionsin more detail: – Taurus: TMC 1, B213 / L1495.
The Taurus molecular cloud(TMC), at a distance of 145 pc (Yan et al. 2019), is consid-ered an archetypal low-mass star-forming region. It has beenthe target of several cloud evolution and star formation stud-ies (Ungerechts & Thaddeus 1987; Mizuno et al. 1995; Gold-smith et al. 2008), being extensively mapped in CO (Cer-nicharo & Guelin 1987; Onishi et al. 1996; Narayanan et al.2008) and visual extinction (Cambrésy 1999; Padoan et al.2002; Schmalzl et al. 2010).In the pilot project we centered on the filament TMC 1,which has been the target of numerous chemical studies. Inparticular, the positions TMC 1-CP and TMC 1-NH3 (thecyanopolyynes and ammonia emission peaks) are generallyadopted as templates to compare with chemical codes (e.g.,Fehér et al. 2016; Gratier et al. 2016; Agúndez & Wake-lam 2013). Less studied from a chemical point of view,TMC 1-C has been identified as an accreting starless core (Schnee et al. 2007; 2010). Within GEMS, we observed threecuts across the TMC1-CP, TMC1-NH3, and TMC1-C (seeFig. 2). Fuente et al. (2019) carried out a complete analysisof these data to derive the gas ionization degree and elemen-tal abundances.In this work, we use the H column density and dust tem-perature maps of TMC 1 created following the process de-scribed in Kirk et al. (2013) and Fuente et al. (2019) on thebasis of Herschel (Poglitsch et al. 2010; Gri ffi n et al. 2010)data taken as part of the Herschel Gould Belt Survey (Andréet al. 2010) and Planck data (c.f. Bernard et al. 2010). Thedata were convolved to the resolution of the longest wave-length, 500 µ m (36 arcsec). The typical uncertainty on thefitted dust temperature was 0.3-0.4 K. The uncertainty on thecolumn density was typically 10% and reflects the assumedcalibration error of the Herschel maps.B213 / L1495 is a prominent filament in Taurus that has re-ceived a lot of recent observational attention (Palmeirim et al.2013; Hacar et al. 2013; Marsh et al. 2014; Tafalla & Hacar2015; Bracco et al. 2017; Shimajiri et al. 2019a). A pop-ulation of dense cores previously studied in emission linesof high-dipole-moment species, such as NH , H CO + , andN H + , are embedded in this filament (Benson & Myers 1989;Onishi et al. 2002; Tatematsu et al. 2004; Hacar et al. 2013;Punanova et al. 2018). Some of these dense cores are star-less, while others are associated with young stellar objects(YSOs) of di ff erent ages. This population of YSOs has beenthe subject of a number of dedicated studies, most recentlyby Luhman et al. (2009) and Rebull et al. (2010), and by thededicated outflow search by Davis et al. (2010). Interestingly,the density of stars decreases from north to south suggestinga di ff erent dynamical and chemical age along the filament.The morphology of the map with striations perpendicularto the filament suggests that the filament is accreting mate-rial from its surroundings (Goldsmith et al. 2008; Palmeirimet al. 2013). Shimajiri et al. (2019b) proposed that this ac-tive star-forming filament was initially formed by large-scalecompression of HI gas and is now growing in mass due to thegravitational accretion of molecular gas from ambient cloud.We observed nine cuts along clumps column density and dust temper-ature maps of B213 (see Fig. 3) obtained by Palmeirim et al.(2013) on the basis of the Herschel Gould Belt Survey (An-dré et al. 2010) and Planck data (c.f. Bernard et al. 2010) atan angular resolution of 18.2”. – Perseus: Barnard 1, NGC 1333, IC348, L1448, B5. ThePerseus molecular cloud is a well-known star-forming cloudin the Galaxy, at a distance of 310 pc (Ortiz-León et al.2018). The cloud was extensively studied using molecularline emission (Warin et al. 1996; Ridge et al. 2006; Curtis &Richer 2011; Pineda et al. 2008; 2010; 2015; Friesen et al.2017; Hacar et al. 2017b), star count extinction (Bachiller& Cernicharo 1984), and dust continuum emission (Hatchellet al. 2005; Kirk et al. 2006; Enoch et al. 2006; Zari et al.2016). The molecular cloud complex is associated with twoclusters containing pre-main-sequence stars: IC 348, with anestimated age of 2 Myr (Luhman et al. 2003); NGC 1333,which is younger than 1 Myr in age (Lada et al. 1996; Wilk-ing et al. 2004); and the Per 0B2 association, which containsa B0.5 star (Steenbrugge et al. 2003).Perseus is the prototype low- and intermediate-mass star-forming region. The molecular cloud itself contains numer-
Article number, page 3 of 28 & A proofs: manuscript no. 40112corr
Fig. 2.
TMC1 visual extinction map (Kirk et al., in prep). Positions ob-served with the 30m telescope are indicated with circles. Black circlesmark positions observed only with the 30m telescope, while yellow cir-cles indicate positions also observed with the Yebes 40m telescope. ous protostars and dense cores. Hatchell et al. (2005) pre-sented a survey of dense cores in the Perseus molecular cloudusing continuum maps at 850 and 450 µ m with SCUBA atthe JCMT. They detected a total of 91 protostars and starlesscores (Hatchell et al. 2007b). Later, Hatchell et al. (2007a)surveyed the outflow activity in the region to characterizethe populations of protostars. In contrast with Taurus, a sig-nificant fraction of these protostars are associated in proto-clusters, unveiling a di ff erent star formation regime. WithinGEMS, we observed 11 cuts along starless cores distributedin Barnard 1, IC348, L1448, NGC 1333, and B5 (see Fig. 4).The group of cores in IC348 and NGC 1333 are close tothe clusters and therefore immersed in a harsh environment,while Barnard 1 and L1448 are located in a quiescent region.We use the dust opacity and dust-temperature maps reportedby Zari et al. (2016) in our analysis (see Fig. 4). In orderto derive the molecular hydrogen column density from thedust opacity at 850 µ m ( τ ), we used expression (7) of Zariet al. (2016) and A V = A K / V <
10 mag) but may un-derestimate their value towards the extinction peaks. In therange of values considered in Perseus, A V ∼ −
30 mag, theuncertainty in the values of A V is a factor of two. – Orion A. The Orion star-forming region is the most massiveand most active star-forming complex in the local neighbor-hood (e.g., Maddalena et al. 1986; Brown et al. 1995; Bally2008; Lombardi et al. 2011; Kainulainen et al. 2017; Friesenet al. 2017; Monsch et al. 2018; Getman et al. 2019; Kar-nath et al. 2020; Tobin et al. 2020; Hacar et al. 2020). Itcontains the nearest massive star-forming cluster to Earth, the Trapezium cluster (e.g., Hillenbrand 1997; Lada et al.2000; Muench et al. 2002; Da Rio et al. 2012; Robberto et al.2013; Zari et al. 2019), at a distance of 388 pc (Kounkel et al.2017). Traditionally, the “Orion nebula” refers to the visiblepart of the region, the HII region, powered by the ionizing ra-diation of the Trapezium OB association. It is part of a muchlarger complex, referred to as the Orion molecular cloud(OMC), itself formed by two giant molecular clouds: OrionA hosting the Orion nebula and the more quiescent OrionB (see, e.g., Pety et al. 2017), both lying at the border of theEridanis super bubble (see e.g., Bally 2008; Ochsendorf et al.2015; Pon et al. 2016).Orion A has been extensively mapped in molecular lines us-ing single-dish telescopes (Hacar et al. 2017a; Goicoecheaet al. 2019; Nakamura et al. 2019; Tanabe et al. 2019; Ishiiet al. 2019; Hacar et al. 2020) and large millimeter arrays(Kirk et al. 2017; Hacar et al. 2018; Monsch et al. 2018;Suri et al. 2019; Kong et al. 2019). Di ff erent clouds havebeen identified within Orion A based on millimeter, submil-limeter, and infrared observations. Orion molecular cloud 1(OMC 1) was identified as a dense gas directly associatedwith Orion KL (Wilson et al. 1970; Zuckerman 1973; Lisztet al. 1974), then OMC 2 (Gatley et al. 1974) and OMC 3(Kutner et al. 1976) were detected as subsequent clumpsin CO emission located about 15 (cid:48) and 25 (cid:48) to the north ofOMC 1. The CO (J = →
0) observations by Bally et al.(1987) revealed that these clouds consist of the integral-shaped filament (ISF) of molecular gas, itself part of a largerfilamentary structure extending from north to south over 4 ◦ .After that, the SCUBA maps at 450 µ m and 850 µ m pre-sented concentrations of submillimeter continuum emissionin the southern part of the integral-shaped filament, whichare now referred to as OMC 4 (Johnstone & Bally 1999) andOMC 5 (Johnstone & Bally 2006).Three cuts along OMC-2 (ORI-C3), OMC-3 (ORI-C1), andOMC-4 (ORI-C2) were observed within GEMS (see Fig. 5).These cuts avoid the protostars and stars in this active star-forming region, probing di ff erent environments because oftheir di ff erent distance from the Orion nebula. In our anal-ysis, we use the dust opacity and dust temperatures mapsreported by Lombardi et al. (2014). Dust temperatures alongORI-C3 are higher than towards ORI-C1 and ORI-C2 withvalues always >
30 K. The values of the molecular hydrogencolumn density are derived from the dust opacity at 850 µ musing expression A K = × τ + .
012 of Lombardi et al.(2014) and A V = A K /
3. Observations
The 3 mm and 2 mm observations were carried out using theIRAM 30-m telescope at Pico Veleta (Spain) during three ob-serving periods in July 2017, August 2017, and February 2018.The observing mode was frequency switching with a frequencythrow of 6 MHz well adapted to removing standing waves be-tween the secondary mirror and the receivers. The Eight MIxerReceivers (EMIR) and the Fast Fourier Transform Spectrometers(FTS) with a spectral resolution of 49 kHz were used for theseobservations. The intensity scale is T MB , which is related to T ∗ A by T MB = ( F e f f / B e f f ) T ∗ A (see Table B.1 in Fuente et al. 2019).The di ff erence between T ∗ A and T MB is ≈
17 % at 86 GHz and27% at 145 GHz. The uncertainty in the source size is includedin the line intensity errors, which are assumed to be ∼ Article number, page 4 of 28. Rodríguez-Baras et al.: Gas phase Elemental abundances in Molecular cloudS (GEMS)
Fig. 3.
B213 molecular hydrogen column density maps as derived by Palmeirim et al. (2013), reconstructed at an angular resolution of 18.2”.General view of the region is represented at the center, and main regions of interest are enlarged. Contours are (3, 6, 9,12, 15, 20, and 25) × cm − . Positions observed by GEMS with the 30m telescope are indicated with triangles. Green triangles represent the position of the starless cores.Labels in red indicate the cut IDs. See Table 1 for further details. Fig. 4.
Perseus filaments (from left to right and top to bottom: NGC 1333, Barnard 1, IC348, L1448, and B5) dust opacity maps at 850 µ m by Zariet al. (2016), convolved at an angular resolution of 36”. Contours are (0.056, 0.13, 0.24, 0.56, 1.01, and 1.6) × − , which according to expression(7) from Zari et al. (2016) corresponds to visual extinctions of ∼
5, 7.5, 10, 15, 20, and 25 mag, respectively. Positions observed with the 30mtelescope are indicated with triangles. Blue triangles represent the positions of the starless cores.
For TMC 1 and Barnard 1, we use observations of the CS1 → ∼ ∼ ∼
38 kHz. Detailed information about the setups observed in theIRAM 30m and Yebes 40m telescopes and the telescopes param-eters were presented in Fuente et al. (2019).
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Table 1.
Cores included in the GEMS sample and observation cuts associated to them and shown in Fig. 2, Fig. 3, Fig. 4, and Fig. 5. N o indicatesthe total number of points observed in the corresponding cut. N v indicates the number of points where the molecular hydrogen density could bederived (see Sect. 4). Cloud Core Coordinates Other names Cut N o N v ID RA (J2000) Dec (J2000)TMC1 CP 04:41:41.90 + + + + + − C2 9 7 + + + + + − C12 9 6 + − C16 9 9 + + + + + C3 17 11 + + + + +
1b 03:33:20.80 + + + + + − − − B213 core IDs are from Hacar et al. (2013). IDs indicated in "Other names" column are from Onishi et al. (2002). Perseus core IDs (L 1448, NGC 1333, Barnard 1, Barnard 5, IC348) are from Hatchell et al. (2007b). NGC 1333 core IDs indicated in "Other names" column are from Sandell & Knee (2001).
4. Physical conditions: molecular hydrogen density
In order to derive the gas physical conditions, we use the line in-tensities of the observed CS, C S, and CS lines. CS has beenwidely used as a density and column density tracer in the in-terstellar medium (Linke & Goldsmith 1980; Zhou et al. 1989;Tatematsu et al. 1993; Zinchenko et al. 1995; Anglada et al.1996; Bronfman et al. 1996; Launhardt et al. 1998; Shirley et al.2003; Bayet et al. 2009; Wu et al. 2010; Zhang et al. 2014; Scour-field et al. 2020). We fit the lines using the molecular excitationand radiative transfer code RADEX (van der Tak et al. 2007),which do not consider local thermodynamic equilibrium (LTE),and the collisional coe ffi cients calculated by Denis-Alpizar et al.(2018). During the fitting process, we fix the ratios C / C = S / S = S at early time because of the S + + CS reaction but not at the characteristic times of dense clouds,which justifies the use of a fixed C S / CS ratio to derive molec-ular hydrogen densities and abundances (Loison et al. 2019b).More controversial is the CS / CS ratio; the adopted value is consistent with the results of Gratier et al. (2016) in TMC 1 andAgúndez et al. (2019) in L 483. This value is also consistentwith chemical predictions for typical conditions in dark cloudsand evolutionary times of approximately a few hundred thou-sand years (Colzi et al. 2020; Loison et al. 2020). We assume abeam-filling factor of 1 for all transitions (the emission is moreextended than the beam size).In addition, we assume that gas and dust are thermalized, thatis, that the kinetic temperature T k is equal to the dust temperaturederived from far-infrared and millimeter observations (TMC 1:Fuente et al. 2019; B 213: Palmeirim et al. 2013; Perseus: Zariet al. 2016; Orion: Lombardi et al. 2014). This assumption mightunderestimate the gas temperature at the low extinctions wherethe gas can be heated by the photoelectric e ff ect to temperatureshigher than the dust temperature (see, e.g., Okada et al. 2013).In order to test the reliability of this assumption we carried outthermal-balance calculations for three representative cases. Fig-ure 6 shows the dust and the gas temperatures calculated usingthe Meudon PDR (1.5.4) (Le Petit et al. 2006; Goicoechea &Le Bourlot 2007; Gonzalez Garcia et al. 2008; Le Bourlot et al.2012). The three panels show the output for three models that are Article number, page 6 of 28. Rodríguez-Baras et al.: Gas phase Elemental abundances in Molecular cloudS (GEMS)
Fig. 5.
Orion dust opacity map at 850 µ m by Lombardi et al. (2014),convolved at an angular resolution of 36". Contours are (0.056, 0.24,0.56, 1.36, and 1.61) × − , which according to Lombardi et al. (2014)correspond to visual extinctions of ∼ representative of the physical conditions in Taurus (Fuente et al.2019; Navarro-Almaida et al. 2020), Perseus (Navarro-Almaidaet al. 2020), and Orion. For Orion, we adopt χ UV ∼
60, whichis the incident Draine field estimated in the Horsehead nebula(Pety et al. 2005; Goicoechea et al. 2006; 2009a;b; Guzmán et al.2011; 2012a;b; 2013; Le Gal et al. 2017; Rivière-Marichalaret al. 2019). In every case the value of the cosmic ray ioniza-tion rate is set to ζ (H ) = × − s − . For all cases it could beobserved that T g ∼ T d within ∼ V > g ∼ T d would be ∼ V ∼ g ∼ T d + g ∼ T d +
10 K in Perseo, and T g ∼ T d +
15 K in Orion.Most of our points are located in the region > CO + , HC O + , H CN, HCS + , and OCS are onlydetected towards A V > ) and N(CS) vary as free pa-rameters and explore their parameter space following the MonteCarlo Markov Chain (MCMC) methodology with a Bayesian in-ference approach. In particular, we used the emcee (Foreman-Mackey et al. 2012) implementation of the Invariant MCMCEnsemble sampler methods by Goodman & Weare (2010). Thismethod was already used in Rivière-Marichalar et al. (2019) andNavarro-Almaida et al. (2020), and allowed us to estimate thedensity as long as the two transitions of CS, J = →
1, and 3 → = → → = → V = = → = → ) ∼ cm − or larger.In Fig. 7 we plot the derived molecular hydrogen densities asa function of the visual extinction, with colours indicating thedi ff erent observed filaments. As mentioned above, densities < × cm − are only measured in TMC 1 and Barnard 1b asa consequence of our methodology and the limitations of ourdataset. There is a clear trend of increasing hydrogen densitywith visual extinction, with higher densities in the inner layersof the clouds. However, the dispersion is large, with values ofthe molecular hydrogen density varying by a factor of >
30 for agiven visual extinction. This dispersion remains even if only thepoints of a given cloud are considered, which suggests that it isnot the result of mixing clouds in di ff erent environments but theconsequence of a complex density structure with di ff erent gaslayers along the line of sight.The distribution of the molecular hydrogen densities and gasthermal pressures ( n ( H ) × T K ) obtained for the 244 points isrepresented in the top row of Fig. 8, color-coded according tothe molecular cloud that they belong to, with legends indicat-ing the mean, median, and standard deviation values of theircorresponding distributions in logarithmic units. The densitiesin Taurus show a peaky distribution with a low mean densityvalue, as expected for low-mass star-forming regions. Perseushas higher values of densities and pressures, with a wider dis-tribution. The highest values of density and pressure and themost flattened distribution is observed in Orion. In order to ex-plore the origin of the wide distribution in Perseus, we madethe density and pressure histograms di ff erentiating the individ-ual clouds of this region (middle row in Fig. 8). NGC 1333 andIC 348, with higher temperatures and extinctions, have densityand pressure values closer to those of Orion, while low temper-ature regions such as Barnard 1b, L 1448, and Barnard 5 showvalues more similar to those obtained in Taurus. The wide dis-tribution shown by Perseus therefore seems to be produced bythe di ff erent contributions of its five observed regions, compris-ing a certain range of physical parameters. We carried out thesame analysis in Orion, although we only observed three cutswithout statistical significance. The three peaks observed in thepressure distribution of Orion (bottom row of Fig. 8) indeed cor-respond to the three observed cuts. As one would expect, the cutlocated closer to the Orion nebula (cut 3) is the one with the high-est pressure. The cut with the lowest pressure, that is, the mostsimilar to low-mass star forming regions, is the one in OMC 4(cut 2). The cut in OMC 3 presents intermediate conditions. Thisplot suggests that the range of physical conditions in high-massand intermediate-mass star forming regions is wider than the oneobserved in the low-mass star forming regions, which is surelyrelated to the feedback of the recently formed intermediate- andhigh-mass stars in the environment.
5. Molecular column densities
The fitting of the CS (and its isotopologs C S and CS) linesdescribed in Sect. 4 allows us to accurately determine the CS col-umn density values, and therefore its molecular abundances, foreach of the 244 points where the MCMC method can be applied.Considering the derived molecular hydrogen densities, we canalso determine the molecular column densities and the molecu-lar abundances for a set of species for which only one line is ob-
Article number, page 7 of 28 & A proofs: manuscript no. 40112corr
Fig. 6.
Dust and gas temperature derived using the Meudon PDR 1.5.4 code for a plane-parallel isobaric cloud illuminated from only one side.The plotted dust temperature is a weighted average of the dust temperatures calculated for di ff erent grain sizes, assuming a grain size distribution, n gr ∝ a − . (Mathis et al. 1977), where n gr is the number of grains with size a , and the minimum and maximum grain sizes are given by a = − cmand 3 × − cm, respectively. The incident UV flux and thermal pressure of each calculation are indicated in the panels. The values have beenselected to represent the physical conditions in Taurus ( χ UV ∼ χ UV ∼ χ UV ∼ χ UV is the incident UV field inunits of the Draine field (Draine 1978). Fig. 7.
Relation between derived molecular hydrogen densities and vi-sual extinctions for the sample used in this study. Colors indicate the dif-ferent observed regions as shown in the plot legend. Densities < × cm − are only measured in TMC 1 and Barnard 1b as a consequence ofour methodology and the limitations of our dataset, which is incompletefor the rest of the regions (see text). This value is marked with a dottedhorizontal line. served: CO, C O, HCO + , H CO + , HC O + , H CN, HNC,HCS + , SO, SO, H S, and OCS. We use the RADEX code andthe collisional coe ffi cients included in Table 2. Uncertainties arecalculated taking into account the errors in the measurement ofthe integrated line intensities as well as the systematic errors of10%-20% due to the flux calibration.In the following, we investigate the relationship between theobtained molecular abundances and the molecular cloud phys-ical parameters: kinetic temperature, extinction, and molecularhydrogen density, considering each molecular cloud separatelyand the statistical trends observed for the complete dataset. As afirst approach, in this section we analyze the correlations andtrends that can be observed in the corresponding figures in aqualitative way. A quantitative discussion based on numericalvalues of correlation coe ffi cients is provided in Sect. 6. It is im-portant to note that in the particular case of the CS, we obtainthe molecular abundance by fitting CS and its isotopologs C Sand CS simultaneously, which implies that we are already tak-
Table 2.
References for the collisional rate coe ffi cients used for the vol-ume density estimates. Molecule ReferenceCS Denis-Alpizar et al. (2013) CO Yang et al. (2010)C O Yang et al. (2010)HCO + Yazidi et al. (2014)H CO + Yazidi et al. (2014)HC O + Flower (1999)HCS + Flower (1999)H CN Vera et al. (2014); Hernández Vera et al. (2017)SO Lique & Spielfiedel (2007) SO Lique & Spielfiedel (2007)HNC Dumouchel et al. (2011)Vera et al. (2014)OCS Green & Chapman (1978)o-H S Dagdigian (2020)ing into account the influence of line opacity. We also assumethat the CS, C S, and CS line emission comes from the sameregion. The method applied for the other species is di ff erent, asmentioned above, and this should be considered in the interpre-tation of the results. This is a diatomic molecule with well-known collisional coe ffi -cients (Denis-Alpizar et al. 2013) and, as already mentioned inSect. 4, is widely used as a density and column density tracer inthe interstellar medium. In our Galaxy, CS is the most ubiquitoussulfur compound, the only one that is commonly detected in pho-todissociation regions (PDRs; Goicoechea et al. 2016; Rivière-Marichalar et al. 2019) and protoplanetary disks (Dutrey et al.1997; Fuente et al. 2010; Dutrey et al. 2011; Guilloteau et al.2016; Teague et al. 2018; Phuong et al. 2018; Le Gal et al. 2019).Therefore, a complete understanding of its chemistry would beof great value for estimating the physical conditions of the gasand sulfur depletion in many astrophysical environments. In thefollowing, we investigate the behavior of CS abundance in theGEMS sample. Article number, page 8 of 28. Rodríguez-Baras et al.: Gas phase Elemental abundances in Molecular cloudS (GEMS)
Fig. 8.
Histograms of the derived molecular hydrogen densities (left column) and corresponding pressures (right column). Histograms comprisevalues for the whole sample indicating the corresponding molecular complexes (top row), clouds in Perseus (middle row), and cuts of the Orioncloud (bottom row). In the middle and bottom rows, white histograms show the distribution for the molecular cloud complex to facilitate thecomparison. Statistical parameters of the di ff erent distributions are indicated in each histogram legend. Article number, page 9 of 28 & A proofs: manuscript no. 40112corr
The relationships between the derived CS molecular abun-dances and the main physical parameters of the clouds (kinetictemperature, extinction, and molecular hydrogen density) arerepresented in Fig. 9. The rows of the figure represent the samerelations but classifying the data following di ff erent criteria: first,the molecular cloud to which the points belong, and then divid-ing the dataset considering bins of temperature, extinction, ordensity. These divisions allow us to study the possible influenceof the variation of these parameters in the whole sample, beyondthe particular environment of each cloud. We consider bins oftemperature with limits of 15 K and 20 K, which approximatelydescribe di ff erent trends observed in the plots. Bins of extinctionare established below 8 magnitudes (translucent cloud), between8 and 20 magnitudes (dense core in low-mass star forming re-gions), and above 20 magnitudes (dense cores in intermediateand massive star-forming regions). Bins of molecular hydrogendensity are considered with limits of 4 and 5 in logarithmic scale,which describe the range of values that we observe in our data.The decreasing linear relation between CS molecular abun-dance and molecular hydrogen density is very clear. This trend,the linear fitting of which for the whole dataset is included inthe top-right panel of Fig. 9, is common to the three molecularclouds, although each cloud presents di ff erentiated physical con-ditions. Moreover, albeit with a dispersion by a factor of three,this trend remains for almost three orders of magnitude. There-fore, this parameter is the main driver of the changes in the CSabundance in our sample.In Fig. 9, we also show X(CS) as a function of the gas ki-netic temperature. A possible correlation is observed betweenX(CS) and T k up to ∼
14 K. Afterwards the abundance decreaseswith temperature in the range T k ∼ −
20 K. Beyond this point,T k >
20 K, the scatter increases and no clear trend is observed. In-terestingly enough, the classification of points according to theirmolecular cloud precisely reproduces this behavior: points withT k <
14 K belong to Taurus and the low-temperature regions ofPerseus, L1448 and B1B. In these cuts, X(CS) is increasing withT k . It should be noted that density and T k are anti-correlated inthese regions, with the lowest values of T k being associated withthe highest densities. This trend with T k is then related with theoverall trend of X(CS) decreasing with n(H ). On the other hand,most of the Perseus points show the decreasing relation between15 K and 20 K. We interpret this behavior as the consequence ofthe CS photodissociation at the illuminated cloud edge. We re-mind that G is higher in star forming regions of Perseus than inTaurus (Navarro-Almaida et al. 2020) and in our sample of star-less cores, the highest temperatures are found at the lowest visualextinctions. Lastly, points belonging to Orion show a high scat-ter and no clear trend with temperature. Interestingly, the Orionpoints follow the general anti-correlation between X(CS) and gasdensity quite well, confirming density as the dominant parameterof the CS chemistry.The depletion of CS has been widely studied in starlesscores, and the X(CS) / X(N H + ) abundance ratio has been pro-posed as an evolutionary diagnostic for these objects (Tafallaet al. 2002; 2004; Tafalla & Santiago 2004; Hirota & Yamamoto2006; Heithausen et al. 2008; Kim et al. 2020). Our data showthat the CS abundance decreases almost linearly with the den-sity for almost three orders of magnitude. Moreover, this trendremains valid for regions regardless of the star formation activityof the region, providing a tool with which to predict density andto subsequently interpret molecular observations in large scalesurveys. However, we must keep in mind that our cuts avoidprotostars and the hot cores or hot corinos, bipolar outflows, andHII regions formed around them. The binding energy of CS is estimated to be ∼ ±
960 K (Wakelam et al. 2017), and there-fore thermal evaporation is expected to be e ffi cient when the dusttemperature is >
50 K. Sputtering is also e ffi cient as a mecha-nism to release molecules to the gas phase for shock velocities >
10 km s − (Jiménez-Serra et al. 2008). Therefore, high CS abun-dances are expected in hot cores / corinos and bipolar outflowswhere the icy mantles are eroded (Bachiller & Pérez Gutiérrez1997; Jiménez-Serra et al. 2008; Esplugues et al. 2014; Crockettet al. 2014). + , H CO + , HC O + We derived the molecular abundances of HCO + , H CO + , andHC O + from the observations of their J = → C / C and O / O fractionation has been predictedunder the physical conditions prevailing in molecular clouds forHCO + (Roue ff et al. 2015; Loison et al. 2019b; Colzi et al. 2020;Loison et al. 2020). For this reason, we prefer to independentlyfit the three isotopologs. The number of detections depends onthe abundance of each isotopolog. The number of positions withA V < + → CO + → O + → V > ff erent regions of thecloud.We explore the possible (anti-)correlations of the abundancesof these ions with kinetic temperature, extinction, and molecu-lar hydrogen density in Fig. 10. The abundance of the main iso-topolog, X(HCO + ), seems to increase with temperature. This ap-parent correlation is the consequence of the fact that the HCO + → τ ∼
1, and ourcalculations only provide a lower limit to the real HCO + abun-dance. Moreover, this line is self-absorbed in many positions,especially in Taurus (Fuente et al. 2019). This apparent correla-tion disappears for the less abundant isotopologs, H CO + andHC O + , whose emission is expected to be optically thin. Theseisotopologs can be used as proxies for HCO + . Figure 10 showsthe decrease in the abundance of these molecular ions with den-sity. This anti-correlation is particularly clear for HC O + , thatis, for the inner layers of the gas, as we only detect this moleculefor A V > + ) / N(H CO + ) andN(H CO + ) / N(HC O + ) as derived from their J = → CO + ) / N(HC O + ) ≈ −
25, which isconsistent with our assumption that the emission of thesespecies is optically thin. It should be noted that the valuesof N(H CO + ) / N(HC O + ) are higher than approximately 10for most positions, with an average value of about 15. Thisvalue is higher than that expected when taking into accountthe adopted C / C and O / O isotopic ratios. One reasonis the presence of several velocity components at many of theobserved positions. Only the most intense of these componentsis detected in N(HC O + ), which introduces uncertainties of afactor of two in the measured N(H CO + ) / N(HC O + ) ratio.Carbon isotopic fractionation could also explain the high valuesof the N(H CO + ) / N(HC O + ) ratio. Chemical models predictthat the HCO + / H CO + abundance ratio varies during cloudevolution and could be <
60 for ages of a few 0.1 to ∼ ff et al. 2015; Colzi et al.2020; Loison et al. 2020). The overabundance of H CO + couldpush the N(H CO + ) / N(HC O + ) to values around > + ) / N(H CO + ) ratio correlates with the gas tem-perature and is lower than the C / C isotopic ratio at all po-
Article number, page 10 of 28. Rodríguez-Baras et al.: Gas phase Elemental abundances in Molecular cloudS (GEMS)
Fig. 9.
Relation of the CS molecular abundance to cloud physical parameters: kinetic temperature (left column), extinction (middle column), andmolecular hydrogen density (right column). From top to bottom, the dataset is color-coded according to the molecular cloud of the points (firstrow), bins of kinetic temperature (second row), bins of extinction (third row), and bins of molecular hydrogen density (last row), as indicated inthe corresponding legends. The black line in the top right plot shows the linear correlation between X(CS) and n(H ) for the whole sample, withthe correlation parameters indicated in the legend. sitions except a few points in Orion and Perseus. This stronglysupports the interpretation that the HCO + → CO + is detected. The ob-tained values of N(HCO + ) are only reliable at low visual ex-tinction (A V < + ) ∼ − − × − . The HCO + abundance in the dif-fuse medium has been estimated to be N(HCO + ) / N(H ) = × − (Liszt et al. 2010; Liszt & Gerin 2016), which is coincident withthe upper end of our range. Article number, page 11 of 28 & A proofs: manuscript no. 40112corr
The abundance ratio N(HCO + ) / N(CO) is traditionally usedto estimate the ionization degree, X(e − ), in molecular clouds(Wootten et al. 1979; Guelin et al. 1982; Caselli et al. 1998;Zinchenko et al. 2009; Fuente et al. 2016; 2019). For regionswhere CO is not heavily depleted (constant CO abundance),X(HCO + ) ∝ ζ ( H ) n ( H ) X ( e − ) (see e.g., Caselli et al. 1998). If we as-sume that the cosmic ray molecular hydrogen ionization rate, ζ ( H ), remains constant for the visual extinctions A V > O + data, the correlation found betweenHC O + and n(H ) is consistent with X ( e − ) ∝ n − . , which agreeswith chemical predictions for starless cores (Caselli et al. 1998).However, it should be noted that the Orion points lie systemat-ically below the straight line fitted in Fig. 10 while positionsin Taurus are systematically above this line. Although sugges-tive of a di ff erent X(e − ), a multitransition study of HCO + andits isotopologs and chemical modeling are required to estab-lish firm conclusions. A combination of uncertainties in n(H )in the low-density positions in Taurus and opacity e ff ects due tothe higher extinction towards the high-density positions towardsOrion could also produce this e ff ect. CN, HNC
The isomers hydrogen cyanide (HCN) and hydrogen isocyanide(HNC) are widely observed in the interstellar medium. Theyhave been detected in di ff use clouds (Liszt & Lucas 2001),translucent molecular clouds (Turner et al. 1997), dark cloudcores (Hirota et al. 1998; Hily-Blant et al. 2010), and in low-mass and massive star-forming regions (Colzi et al. 2018;Goicoechea et al. 2019; Hacar et al. 2020; Le Gal et al. 2020).Understanding their chemical behavior in all these environmentsis crucial for the correct interpretation of molecular observations.Figure 12 shows the relationships between HCN and H CNmolecular abundances and the physical parameters of the gas,classifying the data as a function of the hosting molecular cloud.The HCN column density was derived from the total area of the1 → → V > ff ects, we pre-fer to trace the behavior of this molecule using its isotopolog,H CN. We are aware that fractionation might be important forHCN and that the HCN / H CN ratio can vary by a factor ofabout two (Roue ff et al. 2015; Zeng et al. 2017; Loison et al.2019a; Colzi et al. 2020; Loison et al. 2020). Thus, H CN isa good proxy for HCN with an uncertainty of a factor of two.The H CN 1 → V > density, with less scatterthan in the case of H CO + and HC O + . The trend is commonto the three molecular clouds, and remains for around two or-ders of magnitude in density. This similarity between HCO + andHCN isotopologs suggests a related chemistry in dark clouds.The recombination of protonated compound HCNH + is the mostimportant formation mechanism for HCN and HNC in cold darkclouds (Loison et al. 2014). The radical CN is also a productof this recombination which itself can react with H + to pro- duce HCN + which is rapidly recycled to HCNH + by reactionswith H . The abundance of these isomers is therefore sensi-tive to variations in the gas ionization degree and H + abun-dance, similarly to the case of the molecular ions H CO + andHC O + . Zinchenko et al. (2009) carried out a survey of HN Cand H CN in massive star forming regions, and found an anti-correlation between the HN C abundance and the gas ioniza-tion degree. However, they did not obtain the same result forH CN. In contrast to HNC, the HCN abundance is boosted inthe shocked gas associated to bipolar outflows and the hot coresin the early stages of massive star formation (Schilke et al. 1992;Schöier et al. 2002; Rol ff s et al. 2011; James et al. 2020; Hacaret al. 2020). Our data show that the H CN abundance decreaseswith n(H ) in the quiescent gas. Hily-Blant et al. (2010) stud-ied the chemistry of HCN, HNC, and CN in starless cores, de-riving X(H CN) ∼ − towards the millimeter emission peaks.These values are in good agreement with the values we obtainedfor densities n(H ) > cm − , in the lower end of the observedrange of H CN fractional abundances.It is interesting to compare the behavior of X(H CN) withthat of X(HNC), whose relationships with cloud physical param-eters are also plotted in Fig. 12. X(HNC) also presents a decreas-ing abundance with molecular hydrogen density, but with a shal-lower power law of slope ∼ − ) correlation.The HCN / HNC line ratio has been proposed as a direct probeof the gas kinetic temperature (e.g., Goldsmith et al. 1981; 1986;Baan et al. 2008; Hacar et al. 2020), with increasing values ofthis ratio probing warmer material, which could lead to it beingused as a new chemical thermometer of the molecular interstellarmedium. In order to explore this proposal, Fig. 13 shows the re-lationships between the HCN / HNC and H CN / HNC line ratioswith kinetic temperature. In our case, the lack of reliability ofderived HCN abundances due to the mentioned self-absorptione ff ects in Taurus and partially in Perseus prevents a reliable anal-ysis of the trends found in these clouds. On the other hand, Orionpoints indeed show slight increase in this line ratio with temper-ature, in good agreement with results by Hacar et al. (2020), butthe number of points is not high enough to give a statistically ro-bust conclusion. The observed trend for Orion points disappearswhen considering the H CN / HNC line ratio. Indeed, consider-ing all the points (Taurus, Perseus and Orion), the H CN / HNCratio seems to decrease. Again, we think that this is not real,and is the e ff ect of the high optical depths of the HNC J = → CN and HN C are re-quired to constrain the X(HCN) / X(HNC) ratio. A deeper analy-sis based on chemical models and 3D radiative transfer calcula-tions should be carried out in order to determine the behavior ofthis abundance ratio with kinetic temperature. S Knowledge of the H S molecule is key to understanding sulfurchemistry. Sulfur is one of the most abundant elements in theuniverse, and its presence in the interstellar medium has beenwidely studied. Sulfur atoms in interstellar ice mantles are ex-pected to preferentially form H S because of the high hydro-gen abundances and the mobility of hydrogen in the ice matrix.Therefore, studying H S abundance in the gas phase is essential
Article number, page 12 of 28. Rodríguez-Baras et al.: Gas phase Elemental abundances in Molecular cloudS (GEMS)
Fig. 10.
Relation of the HCO + (top row), H CO + (middle row), and HC O + (bottom row) molecular abundances to cloud physical parameters:kinetic temperature (left column), extinction (middle column), and molecular hydrogen density (right column). The dataset is color-coded accord-ing to the molecular cloud of the points, as indicated in the legends. The black lines show the linear correlations between molecular abundancesand molecular hydrogen density for the corresponding whole samples, with the correlation parameters indicated in the legends. to our understanding of the chemical processes that lead to sul-fur depletion in these environments. Of particular importance,this molecule was the subject of a previous paper of the GEMSseries, where the H S observations of TMC 1-C and Barnard1b were analyzed (Navarro-Almaida et al. 2020). In Navarro-Almaida et al. (2020) we estimated the o-H S abundance us-ing the ortho-H O collisional coe ffi cients calculated by Duber-net et al. (2009), scaled to ortho-H S. Here we use the specifico-H S collisional coe ffi cients with o-H and p-H recently cal-culated by Dagdigian (2020). The di ff erence between these twosets of collisional coe ffi cients is of a factor of ∼ , which implies that the re-estimated ortho-H S column densities in TMC 1 and B1b are a factor of ∼ ff ect any of the conclusions of thispaper. The ortho-H S abundances derived from the observationsof the J K , K = , → , line are shown in Fig. 14. These abun-dances are represented as a function of the gas physical param-eters, and the points are classified according to their molecu-lar clouds. We also observe in this case a strong anti-correlationbetween H S abundance and molecular hydrogen density, span- ning over around three orders of magnitude. Interestingly, wedo observe a displacement between the trend of the points be-longing to Taurus and that shown by the warmer Perseus andOrion. This behavior was already observed by Navarro-Almaidaet al. (2020) based on the analysis of the data towards TMC 1-C and Barnard B1b. The analysis of the whole sample confirmsand extends this behavior, with the observed positions in Taurusfollowing a steeper law with density than those in Perseus andOrion. Navarro-Almaida et al. (2020) explained this behavior asthe consequence of the di ff erent chemical desorption e ffi ciencyin bare and ice-coated grains.Simultaneously with H S, we observed the H SJ K , K = , → , line with very few detections, whichproves the low optical depth of the same line of the mainisotopolog. Optical depth e ff ects are therefore not expected tobias the (anti-)correlation with density. SO One of the most abundant and easily observable species is SOwhich, along with CS, is the most abundant S-bearing molecule
Article number, page 13 of 28 & A proofs: manuscript no. 40112corr
Fig. 11.
Relation of the HCO + / H CO + (top row) and H CO + / HC O + (bottom row) molecular abundance ratios to cloud physical parameters:kinetic temperature (left), extinction (middle), and molecular hydrogen density (right). The dataset is color-coded according to the molecular cloudof the points, as indicated in the legend. in the gas phase. Within GEMS, we observed the SO J N = → , 2 → , 3 → , 3 → , and 4 → lines, allow-ing a multi-transition study. However, in most positions we onlydetected one or two of the observed lines. In order to apply auniform analysis method to all the positions included in this sta-tistical analysis, we estimated the SO column density based onthe intensities of the SO J N → line, assuming the molecularhydrogen density estimated from CS. In addition to the main iso-topolog, we observed the J N = → line of the rarer isotopolog SO which can provide important information with which toconstrain the SO abundance in the most obscured regions.The relations between SO and SO molecular abundancesand gas physical parameters are shown in Fig. 15, with pointsclassified as a function of their molecular clouds. As in previouscases, a linear decreasing relation with molecular hydrogen den-sity is found in both cases, but for SO isotopologs the relationseems to be weaker and with a wider scatter. In order to explorethe origin of this scatter, we plot the relationship between SOmolecular abundance and n(H ) in Fig. 16, with points classi-fied according to bins of extinction, and the corresponding linearrelations existing for each case. We observe that the slope is sim-ilar for all ranges of extinction, but the intercept changes, beinglower for A V < / N( SO) ( > S / S. Therefore, we discuss some ob-servational uncertainties. First of all, many positions of the cutOri-C2-1 present two velocity components in the SO line. Onlythe most intense of these components are detected in SO. Aswe did not carry out a di ff erentiated study for each velocity com- ponent, N(SO) / N( SO) is expected to be overestimated towardsthese positions. However, it is di ffi cult to justify N(SO) / N( SO) >
50 based only on this e ff ect. We recall that we assume the samephysical conditions for SO and SO. A steep gradient in tem-perature and density along the line of sight could also induceanomalously high N(SO) / N( SO) ratios. + , OCS The S-bearing species HCS + and OCS are detected only in afraction of the observed positions, meaning lower statistical sig-nificance. Nevertheless, we consider that it is interesting to in-clude them in our study. Figure 17 shows the relation betweenthe HCS + and OCS molecular abundances and the physical pa-rameters of the clouds. Both species are only detected for ex-tinctions greater than ∼ < × − in Ori-C1-2, X(OCS) < × − in Ori-C2-2, and X(OCS) < × − in Ori-C1-3, which are the extinctionpeaks of the three cuts observed in Orion. These upper limitsare in the range of OCS abundances derived in Perseus and Tau-rus. Therefore, the nondetection might be the consequence of thelimited sensitivity of the Orion observations.HCS + is the protonated species of CS and its precursor in dif-fuse clouds and the external layers of the photon-dissociation re-gion (Sternberg & Dalgarno 1995; Lucas & Liszt 2002; Rivière-Marichalar et al. 2019). Contrary to HCO + , deeper into themolecular cloud HCS + is rapidly destroyed by reaction with O,and CS is formed by neutral–neutral reactions such as SO + C → CS + O. In agreement with its origin in the outer layers of molec-ular clouds, in Fig. 17 we observe a steep decrease of the HCS + with visual extinction. In fact, contrary to most of the species Article number, page 14 of 28. Rodríguez-Baras et al.: Gas phase Elemental abundances in Molecular cloudS (GEMS)
Fig. 12.
Relation of the HCN (top row), H CN (middle row), and HNC (bottom row) molecular abundances to cloud physical parameters: kinetictemperature (left), extinction (middle), and molecular hydrogen density (right). The dataset is color-coded according to the molecular cloud of thepoints, as indicated in the legend. Black lines show the linear correlations between molecular abundances and molecular hydrogen density for thecorresponding whole samples, with the correlation parameters indicated in the legends. studied, the (anti-)correlation of X(HCS + ) with A V presents lessscattering than its relationship with gas density. In the case ofOCS, we do not find any clear relation between its abundanceand the physical conditions of the clouds. This is most likely dueto the small number of detections, which does not allow us toproperly cover the parameter space of our study. CO, C O We derived the CO and C O abundances from the observa-tions of their J = → ff ects in the studied linesand the assumption that gas and dust share the same tempera-ture. Assuming a standard CO abundance, X(CO) ∼ × − , andthe same isotopic ratios as in previous sections, the CO 1 → O 1 → V < −
10 mag and A V < −
100 mag respectively. Therefore the es-timated C O abundances are reliable in almost the entire rangeof visual extinctions considered in our study, with the excep-tion of a few positions with A V >
60 mag that have been re-moved from the plots and are not considered in this section here- after. The second approximation is our assumption that T d = T gas .As mentioned in Sect. 4, this approximation is reasonable forwell-shielded regions of molecular clouds, A V > ff et al. 2020), where the CO 1 → ffi ciently than the dustby the photoelectric ejection of electrons from grains and poly-cyclic aromatic hydrocarbons (PAHs). Caution should be takenin sources bathed in enhanced UV fields, like Orion and IC 348,where the gas temperature is ∼
15 K higher than the dust temper-ature in the cloud surface. In order to estimate the error due tothe uncertainty in the gas temperature in these regions, we car-ried out a simple calculation assuming typical physical values ofn(H ) = cm − and N( CO) ∼ a few 10 cm − . The di ff erencein the derived N( CO) assuming temperatures of between 15 Kand 30 K is of ∼ < ff erent panels. Points belonging to Taurus show clear Article number, page 15 of 28 & A proofs: manuscript no. 40112corr
Fig. 13.
Relation of the HCN / HNC (top) and H CN / HNC (bottom) lineratios to kinetic temperature. The dataset is color-coded considering themolecular cloud of the points, as indicated in the legend. trends with temperature and visual extinction, and a poorer cor-relation with density. The CO abundance increases with vi-sual extinction until A V ∼ V > COabundance is decreasing with visual extinction. As mentionedabove, the CO line is expected to be optically thick for A V > CO abundance could be underesti-mated. For A V > O isotopolog is a better proxyfor CO. The abundance peak of C O is found at A V ∼ CO) peak.For A V > Oabundance with visual extinction, although the scatter is widerthan in CO. The shift between the abundance peak of COand C O is not due to optical depth e ff ects but to an increaseof the N( CO) / N(C O) ratio at A V < ff set be-tween the two isotopologs was already observed by Cernicharo& Guelin (1987) and Fuente et al. (2019), and was interpretedas a consequence of the selective photodissociation and isotopicfractionation (Fuente et al. 2019).There is a tight correlation between X( CO) and X(C O)with temperature in Taurus. We observe an increasing relationbetween the abundances of these species with the gas kinetictemperature until T K ∼
14 K for CO and until T K ∼ −
13K in the case of C O, and a decrease in the abundances forhigher temperatures. In Taurus, the positions with T K >
14 Kcorrespond to the outer layers of the cloud, where the molecules are photo-dissociated.We measure X(C O) = (1 − × − in thecoldest cores.In Perseus we observe the same trends as in Taurus but with awider scatter. Peaks of the observed distributions for both COand C O are found at larger extinctions than in the case of Tau-rus (A V ∼ CO and A V ∼
10 mag for C O), whichis expected because the ambient UV field in Perseus is higherthan in Taurus. Indeed, based on the Herschel dust temperatureand extinction maps, Navarro-Almaida et al. (2020) estimated χ UV ∼
24 for Barnard 1b, which is located in a moderately activestar-forming region in Perseus (Hatchell et al. 2007b;a).We do not detect any clear trend in the Orion positions.It should be noted that dust temperatures are >
15 K towardsall positions in Orion. Nevertheless, the X(C O) < − towardssome positions, supporting the interpretation that part of the COmight remain locked in grains for warmer temperatures. Cazauxet al. (2017) analyzed the CO depletion from a microscopic pointof view, finding that the CO molecules depleted on grain sur-faces show a wide range of binding energies, from 300 to 830 K(T evap ∼ −
30 K), depending on the conditions (monolayer ormultilayer regime) in which CO has been deposited. Low abun-dances of C O have also been found in the dense and warm in-ner regions of protostellar envelopes Yıldız et al. (2010); Fuenteet al. (2012); Anderl et al. (2016), where complex organic chem-istry is going on. In general, we observe larger scatter in the cor-relations of X( CO) and X(C O) with the physical parametersin Orion than in Taurus and Perseus. The complex structure ofthis giant molecular cloud and the fact that it is located furtherthan Perseus and Taurus produce a mix of regions with di ff er-ent physical conditions along the line of sight and within thebeam of the 30m, increasing the scattering in the estimated abun-dances. Moreover, our approximation of deriving the molecularabundances assuming a single density and temperature is moreuncertain.Figure 19 represents the relations betweenN( CO) / N(C O) and the gas physical parameters. In ac-cordance with discussions above, we observe a decreasingrelation between this ratio and extinction in the case of Tauruspoints, which can be understood as the consequence of anincrease in the CO 1 → CO) / N(C O) are 10.9 ± ± ±
6. Statistical correlations
In this section, we analyze the statistical trends shown in thedataset in a quantitative and uniform way. In order to assess thedegree of correlation observed between di ff erent parameters, weuse the Pearson, Spearman, and Kendall correlation coe ffi cientsfor the relations between the di ff erent parameters considered.These coe ffi cients vary between values of + ± ffi cient is the most widely used correlation parameter tomeasure the degree of linear relationship between variables. Onthe other hand, Spearman and Kendall coe ffi cients measure theexistence of a monotonic, not necessarily linear, relationship be-tween variables. The Kendall coe ffi cient is usually more robustand is the most used in the case of small samples, but both are Article number, page 16 of 28. Rodríguez-Baras et al.: Gas phase Elemental abundances in Molecular cloudS (GEMS)
Fig. 14.
Relation of the H S molecular abundance to cloud physical parameters: kinetic temperature (left), extinction (middle), and molecularhydrogen density (right). The dataset is color-coded according to the molecular cloud of the points, as indicated in the legend. Lines in the rightplot show the linear correlations between X(H S) and n(H ) for the whole sample, in black, and for each one of the molecular clouds, color-codedas in the points. The corresponding correlation parameters are indicated in the legend. Fig. 15.
Relation of the SO (top row) and SO (bottom row) molecular abundances to cloud physical parameters: kinetic temperature (left),extinction (middle), and molecular hydrogen density (right). The dataset is color-coded according to the molecular cloud of the points, as indicatedin the legend. Black lines show the linear correlations between molecular abundances and molecular hydrogen density for the corresponding wholesamples, with the correlation parameters indicated in the legends. based on the same assumptions and provide useful information.Along with the coe ffi cient value, the probability of the null hy-pothesis (no relation between variables) is also computed, indi-cating the strength of the result provided by the coe ffi cient. Val-ues for the probability of the null hypothesis higher than 0.001are considered to indicate no relation at all. We consider the ex-istence of a linear correlation between the corresponding mag-nitudes when the Pearson correlation coe ffi cient is greater thanor similar to ∼ ∼ ffi cients as a further test: in the case of a linear re- lation, the Pearson and Spearman coe ffi cients are similar and ingood agreement with the Kendall coe ffi cient, although the latteris systematically smaller in absolute value. Furthermore, a sig-nificantly greater value of the Spearman coe ffi cient with respectto the Pearson coe ffi cient in a particular case may indicate, if ingood agreement with the corresponding Kendall coe ffi cient, theexistence of a nonlinear correlation. We explore the existence of behavioral similarities between thestudied molecules by analyzing the relations between their de-
Article number, page 17 of 28 & A proofs: manuscript no. 40112corr
Fig. 16.
Relation of the SO molecular abundance to the molecular hy-drogen density. The dataset is color-coded considering bins of extinc-tion, as indicated in the legend. Lines show the linear correlations be-tween molecular abundances and molecular hydrogen density for eachextinction bin, with the correlation parameters indicated in the legend. rived molecular abundances. Figure 20 includes the computedPearson coe ffi cients for these relations. In this case, we do notinclude the Spearman and Kendall coe ffi cients because the ob-tained relations are all linear and these coe ffi cients do not sig-nificantly deviate from the Pearson coe ffi cient value, and there-fore do not provide additional information. Some strong corre-lations between groups of molecules are observed, as indicatedin Fig. 20. In the first place, there is an almost complete corre-lation between H CO + and HC O + , which is the expected be-havior for isotopologs and confirms the results observed in Fig.11. These molecular ions also correlate with H CN and HNC,and to a lesser extent with CS and HCS + . It should be noted thatHCN is not strongly correlated with H CN, which is a conse-quence of the high optical depth and the strong self-absorptionfeatures in the HCN 1 → + andHCS + are rapidly destroyed by recombination with electrons togive back the neutral species, CO and CS. On the other hand,the neutral compound HCN is e ffi ciently formed in dark cloudsby the dissociative recombination of HCNH + . These three latterionic species are sensitive to the depletion on the grain surfacesof the neutral compounds, CO, CS, and HCN, respectively, butalso to variations in X(e − ). In the absence of shocks and UVphotons, cosmic rays are the main ionization agent. Cosmic raysare attenuated with N H within the molecular cloud following apower law whose index is dependent on the propagation mech-anism, which itself depends on the turbulence and ion densityalong the cloud (see, e.g., recent review by Padovani et al. 2020).A strong grid of correlations is also observed between CS,SO, SO, H S, and OCS, that is, all the S-bearing moleculeswith the exception of HCS + . The chemistry leading to CS andHCS + is thought to be initiated by reactions of S + and neutralcompounds in the external layers of the cloud. However, in darkmolecular clouds the formation of SO and OCS is initiated by re-actions of atomic S with O and OH, while CS is partly formed by the reaction C + SO → CS + O (Bulut et al. 2021). The de-crease of CS, SO, SO, and OCS with density is more likelyrelated with the adsorption of sulfur atoms on the grains surface(Vidal et al. 2017; Laas & Caselli 2019; Navarro-Almaida et al.2020). In order to estimate how sulfur depletion changes withdensity, we added the abundances of CS, SO, H S, and OCS,and found that X(S-bearing) decreases with density followingthe power law X(S-bearing) ∝ n − . ± . . As the abundances ofthese species correlate almost linearly with the gas-phase ele-mental sulfur abundance (see e.g., Vidal et al. 2017), this wouldimply that sulfur depletion from the gas phase increases by afactor of ∼
100 in the n(H ) = − cm − range. k and A V The Pearson, Spearman, and Kendall correlation coe ffi cients forthe relations of molecular abundances and a set of selected abun-dance ratios with the cloud physical parameters (kinetic temper-ature, extinction, and molecular hydrogen density) are includedin Fig. 21. The three first columns of Fig. 21 show the de-gree of correlation existing between the molecular abundancesand the gas kinetic temperature. Correlation coe ffi cients indi-cate a positive relation between the molecular abundances of CO and HCO + and T k . The Spearman coe ffi cient is largerthan the Pearson one in both cases, pointing to a nonlinear rela-tionship between parameters. This possible correlation becomesweaker for C O and completely disappears for H CO + andHC O + . This suggests that the correlation of the abundance of CO and HCO + with T k is not real, but it is an artifact pro-duced by the large opacity of the observed lines in most posi-tions. This could also partially explain the good correlation ofX( CO) / X(C O) with gas kinetic temperature. However, it isknown that this abundance ratio increases with the local UVfield, which is known to be correlated with the dust tempera-ture (see e.g., Bron et al. 2018; Fuente et al. 2019). This is cor-roborated by our observations, from which we obtain that theX( CO) / X(C O) ratio is higher in Orion than in Perseus, andis higher in Perseus than in Taurus, when comparing positionslocated at the same visual extinction, even for A V <
10 mag (seecentral panel of Fig. 19).For several other molecules (H CO + , HC O + , H CN,HNC, CS, HCS + , SO, SO) the correlation coe ffi cients in Fig.21 indicate the existence of a weak anti-correlation betweenmolecular abundance and T k . Confirmation of this trend requiresa more detailed analysis. Finally, we do detect significant anti-correlation between H CO + / CO and HC O + / C O and thegas temperature. This e ff ect is also shown in Fig. 10, where thepositions belonging to Orion present lower H CO + and HC O + abundances than those in Perseus, and the positions belongingto Perseus present lower H CO + and HC O + abundances thanthose in Taurus. Indeed, this anti-correlation reflects the di ff erentmean abundances of these ions in Taurus, Perseus, and Orion.Figure 21 reveals that there are no clear relations between thecomplete datasets of molecular abundances and the extinction.The specific analysis of some molecules in Sect. 5 shows thatextinction has indeed an influence in some particular aspects ofthe molecular abundance behavior, as is seen in the case of SO, SO (Sect. 5.5), and mainly CO, C O (Sect. 5.7). However,this influence does not follow a monotonic law. We would liketo recall the dependence of the CO and C O abundances onvisual extinction in Taurus. The correlation is positive for lowvisual extinctions and negative for high visual extinctions (seeFig. 18), thus preventing a clean result when considering thewhole dataset.
Article number, page 18 of 28. Rodríguez-Baras et al.: Gas phase Elemental abundances in Molecular cloudS (GEMS)
Fig. 17.
Relation of the HCS + (top row) and OCS (bottom row) molecular abundances to cloud physical parameters: kinetic temperature (left),extinction (middle), and molecular hydrogen density (right). The dataset is color-coded according to the molecular cloud of the points, as indicatedin the legend. ) The qualitative analysis of the relations between the molecularabundances of the studied species and the gas physical param-eters carried out in Sect. 5 already indicated that the molecularhydrogen density is the main driver of the abundance evolutionwithin molecular clouds. This is confirmed by the correlation co-e ffi cients in Fig. 21, pointing to clear anti-correlations betweenmost of the molecular abundances and the molecular hydrogendensity. Pearson coe ffi cients are greater than or similar to 0.5in absolute value for HCO + , H CO + , HC O + , H CN, HNC,CS, H S, SO, and SO, and the anti-correlation is particularlystrong for HC O + , H CN, CS, and H S, with Pearson coe ffi -cients greater than or similar to 0.7. The extremely low valuesof the probability of the null hypothesis obtained for all thesecoe ffi cients (at least smaller than 1.0 × − ) testify to the relia-bility of our results. The correlation stands for densities rangingfrom n(H ) ∼ cm − to ∼ cm − , i.e., over three orders ofmagnitude.In order to gain deeper insight into these relations, we ex-plored the possible dependence of these anti-correlations on vi-sual extinction and star formation activity. The Pearson coe ffi -cients of the relations between molecular abundances and n(H )considering each one of the clouds, as well as dividing the wholesample applying extinction bins of A V <
8, 8 −
20 mag, and > ζ ( H ). Perseus and Orion show weaker anti-correlations with H density, with smaller correlation parameters. However, we do re- cover strong anti-correlations with density for bins with 8 − >
20 mag in Orion. In these deep layers ofthe Perseus and Orion molecular clouds the gas chemistry is de-termined by the molecular hydrogen density, as in Taurus. Thisis a chemical footprint of the existence of a dark region in theseclouds, where the cosmic ray flux and the molecular depletionare driving the chemistry as in Taurus. This dark region is lo-cated at a di ff erent visual extinction depending on the star for-mation activity in the neighborhood. In particular, our data showthat this dark region is located at A V > V >
20 mag in Orion.
7. Limitations of our study
We were not able to carry out a multi-transition study of everyspecies. For some species, we only observed one line, preclud-ing any molecular excitation study (see Table B.2 in Fuente et al.2019). Even for the species for which we observed several tran-sitions, such as SO and H CS, we only detected one transition inmany positions. In the case of H CS, its lines have only been de-tected in a few positions (those close to the extinction peaks) andwe did not consider this species here. In order to calculate molec-ular column densities and abundances in a uniform way and in alarge number of positions, we calculated molecular abundancesassuming the density derived from the multi-transition study ofCS. The sensitivity of the estimated molecular abundances to theassumed gas density depends on the critical density of the transi-tion used in the calculation. For densities higher than the criticaldensity, T ex ≈ T k , and the molecular column density no longerdepends on the density. This is the case for the CO and C OJ = → ff ected by possible uncertainties in the adopted densities. How- Article number, page 19 of 28 & A proofs: manuscript no. 40112corr
Fig. 18.
Relation of the CO (blue) and C O (green, multiplied by a factor of ten) molecular abundances to cloud physical parameters: kinetictemperature (left), extinction (middle), and molecular hydrogen density (right), for the three observed molecular clouds, Taurus (top row), Perseus(middle row), and Orion (bottom row).
Fig. 19.
Relation of the CO / C O molecular abundance ratio to cloud physical parameters: kinetic temperature (left), extinction (middle), andmolecular hydrogen density (right). The dataset is color-coded considering the molecular cloud of the points, as indicated in the right-hand box. ever, for most of the studied lines the critical density is higherthan those measured in our positions (see Table 3). Under theseconditions, the lines are subthermally excited and T ex ∝ n(H ) × N X . An error in the molecular hydrogen density therefore trans- lates to an error of approximately the same order in the molecularcolumn density.To further test the reliability of the assumed densities, weindependently estimated the gas densities in 28 positions froma multi-transition study of SO and H CS. These positions cor-
Article number, page 20 of 28. Rodríguez-Baras et al.: Gas phase Elemental abundances in Molecular cloudS (GEMS)
Fig. 20.
Pearson correlation coe ffi cients of the relations between the molecular abundances of the studied species. Numbers in brackets correspondto the null hypothesis probability in each case, i.e. probability of no relation between variables, where a value higher than 0.001 is considered toindicate no ralation at all. Black rectangles indicate groups of molecules with strong correlations (see text). respond to high visual extinction peaks where several SO andH CS lines are detected. Our results show that the densitiesderived from CS (and C S, CS), SO ( SO), and H CS arein agreement within a factor of approximately five. Therefore,we consider that column densities towards the positions withn(H ) < n crit are reliable within this same factor.An important assumption in our calculations is that the gasalong the line of sight presents uniform physical and chemi-cal conditions. This assumption is reasonable at the layers withA V < −
10 mag, where the gas kinetic temperature and densitygradients are shallow, but it might not apply to the positionsclose to the extinction peaks. In order to discuss the possibleimpact of this assumption, we consider a toy model with twophases, "Phase 1" corresponding to a dense core with n(H ) = cm − , and "Phase 2" corresponding to a moderate density enve-lope with n(H ) = cm − . In this simple model, the observedbrightness temperature would be T b = T × exp ( − τ ) + J ν ( T ex , ) × (1 − exp ( − τ )) , (1)where T is T = J ν ( T ex , ) × (1 − exp ( − τ )), with T ex , and τ being the excitation temperature and line opacity of the densephase. Similarly, T ex , and τ are the excitation temperature andline opacity of "Phase 2". If we have high values of τ and lowvalues of T ex , , which is the case for the millimeter lines of molecules with a high dipole moment, the flux emergent fromthe cloud would be ∼ T × exp( − τ ), producing self-absorbedprofiles. This kind of self-absorbed profile is observed in theJ = → + , HCN, andHNC (see examples of spectra in Fuente et al. 2019). In thecase of the rarer isotopologs H CO + , HC O + , H CN, C S, CS, and SO, the lines are expected to be optically thin, andT b = T ex , × τ + T ex , × τ , which is proportional to the sum ofthe column densities weighted by the excitation temperatures. Inthis case, our one-phase model is giving an averaged excitationtemperature and column density along the line of sight. This ap-proximation is reasonable as long as the molecular abundancesdo not greatly di ff er between the two phases. In the most pes-simistic case of one species that is only abundant in one phase,the derived molecular abundance would be wrong by a factor often, which is the di ff erence between the Phase 1 and 2 densities.All the studied species are abundant in the translucent part ofthe cloud, as demonstrated in TMC 1 by Fuente et al. (2019).Although di ff erent species and transitions are probing di ff erentregions within the cloud, the observed transitions have similarE u and n crit to those of CS, and therefore are expected to comefrom the same gas layer.To further check our result, in Fig. 22 we show the relationsbetween density and molecular abundances in di ff erent bins ofvisual extinction and density. The similarity in the correlation Article number, page 21 of 28 & A proofs: manuscript no. 40112corr
Fig. 21.
Pearson, Spearman, and Kendall correlation parameters of the relations between the molecular abundances of the studied species (andtheir ratios) and the molecular cloud physical parameters: kinetic temperature, extinction, and molecular hydrogen density. Numbers in bracketscorrespond to the null hypothesis probability in each case, i.e. probability of no relation between variables, where a value higher than 0.001 isconsidered to indicate no ralation at all.
Table 3.
Critical densities
Molecule Transition A i j C i j n crit (s − ) (T k =
10 K) (cm − )CS 2 → × − × − × C O 1 → × − × − × H CO + → × − × − × HCS + → × − × − × H CN 1 → × − × − × SO 3 → × − × − × HNC 1 → × − × − × OCS 7 → × − × − × H S 1 → × − × − × coe ffi cients found for all the bins supports the reliability of ourresults.
8. Comparison between Taurus, Perseus, and Orion
The C O column density is widely used as a tracer of the gasmass in our galaxy and other galaxies. The reliability of thistracer is based on presenting a relatively uniform fractional abun-dance in interstellar molecular clouds. Based on our data, weestimated the mean C O abundances in Taurus, Perseus, andOrion. The obtained values are: X(C O) = (1.4 ± × − forTaurus, X(C O) = (2.1 ± × − for Perseus, and X(C O) = (1.6 ± × − for Orion. These values are in good agree-ment with those obtained by previous works, as Frerking et al.(1989) in Taurus, Treviño-Morales et al. (2019) in MonocerosR2, and Roue ff et al. (2020) in Orion B. Therefore, our resultscorroborate the idea that the abundance of C O is quite stableat scales of molecular clouds, and is therefore a good gas masstracer for large-scale surveys and extragalactic research.We derived the mean values of the CO / C O abundanceratio for the three star-forming regions, obtaining values of CO / C O = ± CO / C O = ± Article number, page 22 of 28. Rodríguez-Baras et al.: Gas phase Elemental abundances in Molecular cloudS (GEMS)
Fig. 22.
Pearson correlation coe ffi cients of the relations between molecular abundances and molecular hydrogen density, considering the totalsample (first column), the molecular cloud of the points (second, third, and fourth columns), the extinction bins (fifth, sixth, and seventh columns)and the density bins (eighth, ninth, and tenth columns). Numbers in brackets correspond to the null hypothesis probability in each case, i.e.probability of no relation between variables, where a value higher than 0.001 is considered to indicate no ralation at all. Perseus, and CO / C O = ± CO / C O = − C / C = − O / O = −
600 (Gerin et al. 2015; Langer & Pen-zias 1990; Wilson & Rood 1994). As mentioned in Sect. 5.7,the CO / C O abundance ratio increases in regions of enhancedUV field (Shimajiri et al. 2014; Ishii et al. 2019; Areal et al.2018). This variation is interpreted in terms of the selective pho-todissociation and isotopic fractionation (see Bron et al. 2018;Fuente et al. 2019). This e ff ect is produced because the moreabundant CO isotopolog shields itself from the e ff ect of UV pho-tons more e ffi ciently than less abundant isotopologs (Stark et al.2014; Visser et al. 2009). Our data confirm this trend in Orion,although the observed positions are located at a distance > O), which presents uniform abundance in the threeregions, the mean CO abundance is a factor of approximatelytwo higher in Orion than in Taurus. One interesting question per-tains to whether the observed variation in the CO abundance isrelated to a variation in the CO / CO ratio (Roue ff et al. 2015;Colzi et al. 2020) or is revealing variations for a higher CO abundance in Orion. Because of the higher gas temperature andincident UV field in Orion, selective photodissociation wouldwork in the direction of increasing N( CO) / N( CO) in Orionwith respect to Taurus. Therefore, a higher CO abundance inOrion stands as the most likely explanation. Our results are basedon significant approximations (one single phase, gas-dust ther-malization), and therefore a detailed multi-transition study ofthese compounds is required to confirm this result.Apart from CO, C O, and H S, the abundances of all thestudied species decrease following the sequence Taurus, Perseus,and Orion. This might be interpreted considering the observedrelations between the molecular abundances and the molecularhydrogen density, and the di ff erent density distributions of thepositions observed in Taurus, Perseus, and Orion (see Fig. 8). Itshould be noted that the relation between CS abundance and den-sity does not present significant di ff erences between molecularclouds. However, the abundances of the protonated compoundsHCO + (and isotopologs) and HCS + are systematically lower inOrion than in Taurus and Perseus for similar values of the molec-ular hydrogen density and visual extinction. To a lesser extent,this behavior is also observed in H CN. A detailed modeling of
Article number, page 23 of 28 & A proofs: manuscript no. 40112corr the chemistry including all the species is required to discern thecause of this di ff erence.
9. The extragalactic connection
Our data provide a comprehensive view of the abundance be-havior of the most commonly observed species in molecularclouds, and it is interesting to compare them with extragalacticchemical studies. In most cases, the spatial resolution of currenttelescopes does not allow molecular clouds in external galaxiesto be resolved, and therefore millimeter observations are usedto measure cloud-weighted molecular abundances. To comparewith external galaxies we computed mean values of observedmolecular column densities and abundances in Taurus, Perseus,and Orion (Table 4). We caution that these mean values werecomputed using only detections. The majority of the detectionscorrespond to dense gas (n(H ) > cm − ) located in regionswith A V > ff erences between the abundances mea-sured in Taurus, Perseus, and Orion. The greatest di ff erences be-tween these averaged values are found for the N( CO) / N(C O)( R COC O ) and the N(HCO + ) / N(H CO + ) ( R HCO + HC O + ) ratios. Both R COC O and R HCO + HC O + increase with star formation activity follow-ing the sequence Taurus, Perseus, and Orion. This progressiveincrease is related to the di ff erent density distribution, averagegas and dust temperatures, and incident UV field.In Table 4, we compare the mean column densities in Taurus,Perseus, and Orion with those observed in a sample of galaxiesincluding the starburst galaxies M 83, M 82, and NGC 253, thegalaxies hosting an active galactic nucleus (AGN) M 51, NGC1068, and NGC 7469, and the ultra-luminous infrared galaxies(ULIRGs) Arp 220 and Mrk 231. Aladro et al. (2015) carried outa molecular survey of this sample at λ = CO + towardsNGC 1068. We used the data reported by Usero et al. (2004)to estimate N(HCO + ) and N(H CO + ) by assuming the samesource size and using the same methodology as Aladro et al.(2015) (LTE and T rot =
10 K). The obtained values are shown inTable 4.The values of R COC O are lower in the sample of galax-ies considered than in GEMS sample. Moreover, we do notobserve any increase with star formation activity. Instead,N( CO) / N(C O) ∼ − ∼ R COC O is not determined by the star formation activitybut by optical depth e ff ects and variations in the carbon andoxygen isotopic ratio because of stellar nucleosynthesis (Henkelet al. 1993; 1998; Wang et al. 2004). Jiménez-Donaire et al.(2017) carried out a survey of CO and C O in a sample ofnine nearby spiral galaxies. These latter authors found an aver-age value of R COC O = ± R COC O = ± R COC O seems to be anti-correlated with star formation activity.These same authors, using higher spatial resolution ALMA ob-servations (beam ∼ <
400 pc) of NGC 3351, NGC 3627, andNGC 4321, observed that when zooming into the central regions, R COC O increases in a narrow ring at R ∼
500 pc. As the authors dis- cussed, this increase in R COC O might be related to the enhancedstar formation in these regions, which are fed by gas flows alongthe bars. Thus, the R COC O could be a diagnostic of star forma-tion at scales comparable to the size of a giant molecular cloud,namely approximately a few hundred parsecs, but fails at scalesof the whole galaxy. Moreover, accurate determination of the lo-cal C / C and O / O isotopic ratios is required for the correctcomparison with galactic patterns and chemical models.In the GEMS sample, the N(HCO + ) / N(H CO + ) ratio is cor-related with local star formation activity. Despite the limitationsof our comparison, we observe the same trend in the galax-ies sample. In M 83, R HCO + HC O + is similar to those measured inTaurus and Perseus, suggesting that the J = → R HCO + HC O + >
10, suggesting that the emission could be dominatedby massive star forming regions. In Taurus, the low estimatedvalue of the N(HCO + ) / N(H CO + ) ratio is not a chemical ef-fect, but the consequence of a thick absorbing envelope thatleads to a systematic underestimation of the HCO + abundancewhen using one-phase models and the optically thick J = → + ) / N(H CO + ) in Orion and those in starburst might bethe consequence of the cloud properties in these regions wherethe ambient UV field is expected to be higher than in our galaxy(see, e.g., Fuente et al. 2005; 2006; 2008). The same trend isobserved in N(HCN / N(H CN).It is interesting to discuss the N(H CO + ) / N(H CN) (orN(HCO + )) / N(HCN)) ratio, which is commonly used to dif-ferentiate between starburst- and AGN-dominated chemistry(see, e.g., García-Burillo et al. 2008). Indeed, the abundance ofH CO + is highest in the M 82 galaxy which is considered as theprototype of evolved starburst with a photon-dominated chem-istry in the nuclear region (Fuente et al. 2005; 2006; 2008). Incontrast, H CN is especially abundant in the active galaxy NGC1068 and the ULIRGS Arp 220 and Mrk 231. The extraordinaryabundance of HCN in these galaxies have been widely discussedby several authors that proposed mechanical heating, shocks, andX-rays as physical agents to boost the abundance of HCN (Useroet al. 2004; García-Burillo et al. 2008; Pérez-Beaupuits et al.2009; García-Burillo et al. 2014; Viti et al. 2014). We do notsee a clear variation of the N(H CO + ) / N(H CN) in the GEMSsample. We recall that GEMS positions were selected to avoidprotostars, HII regions, and bipolar outflows. The di ff erence be-tween the N(H CO + ) / N(H CN) ratios in GEMS clouds andthose towards AGNs and ULIRGS supports the interpretationthat the emission of H CN in these galaxies is dominated by thegas associated with XDRs and shocks.Viti (2017) analyzed grids of time-dependent chemical mod-els, varying in gas density, temperature, cosmic ray ionizationrate, and radiation field to calculate abundances and line intensi-ties in order to compare with molecular observations in externalgalaxies. This latter study found that line intensities and line ra-tios from di ff erent chemical models can be very similar, leadingto a large degeneracy. This degeneracy can be partially removedif chemical abundances and abundance ratios are used insteadfor the comparison. We provide tables of chemical abundancesfor three Galactic prototypical star forming regions that could beuseful to interpret molecular data in external galaxies even if ourdata are not representative of the whole molecular cloud. Article number, page 24 of 28. Rodríguez-Baras et al.: Gas phase Elemental abundances in Molecular cloudS (GEMS)
Table 4.
Mean column densities obtained in this work for Taurus, Perseus, and Orion and column densities observed in a sample of nearby galaxies.The galaxy sample data are obtained from Aladro et al. (2015) (upper limits are shown for undetected species), with the exception of the HCO + and H CO + column densities in NGC 1068, obtained from Usero et al. (2004). Star formation rates of the comparison galaxies are obtained fromWalter et al. (2008) for M 83; Strickland et al. (2004) for NGC 253 and M 82; Schuster et al. (2007) for M 51; Esquej et al. (2014) for NGC 1068;Genzel et al. (1995) for NGC 7469; Anantharamaiah et al. (2000) for Arp 220; Taylor et al. (1999) for Mrk 231. This parameter is only meant togive a rough idea of the activity, as it was calculated for di ff erent volumes in each galaxy. Star formation rate in galactic molecular clouds are takenfrom Lada et al. (2010). Molecule Taurus Perseus Orion M 83 NGC 253 M 82 M 51 NGC 1068 NGC 7469 Arp 220 Mrk 231SFR (M (cid:12) yr − ) 715 · − · − · − CO 1.1 · · · · · · · · · · · C O 1.4 · · · · · · · · · · · HCO + · · · · · · · · · · · H CO + · · · · · · ≤ · · ≤ · · ≤ · HC O + · · · · · · · · · · · · · · · · H CN 4.7 · · · · · · · · ≤ · · · HNC 1.3 · · · · · · · · · · · HCS + · · · · · · · · · · · · · · SO 2.0 · · · · · · · · ≤ · ≤ · ≤ · SO 1.8 · · · S 2.4 · · · · · ≤ · · ≤ · ≤ · ≤ · ≤ · ≤ · ≤ · CO / C O (1) + / H CO + (1) >
20 27 > > / H CN (1) / SO 5.4 4.1 3.2 2.8 2.4 3.2 1.6 3.4 1.2 > > CO + / CO 1.5 · − · − · − · − · − · − < · − · − < · − < · − HC O + / C O 9.8 · − · − · − · − · − HCO + / HCN 0.14 0.19 0.24 0.53 0.50 0.88 0.29 0.37 0.71 0.24 0.39H CO + / H CN 0.69 0.68 0.83 0.46 1.38 0.25 0.14 < CO + ) 1.3 · − · − · − · − · − · − < · − · − < · − · − < · − X(H CN) 2.9 · − · − · − · − · − · − · − · − < · − · − · − X(CS) 6.3 · − · − · − · − · − · − · − · − · − · − · − X(SO) 1.8 · − · − · − · − · − · − X( SO) 1.3 · − · − · − (1) We would like to reiterate that the low values of the HCO + / H CO + in Taurus and Perseus are mainly due to the proliferation ofself-absorbed profiles in the HCO + ff ect is also a ff ecting the HCN / H CN and CO / C O ratios.
10. Summary and conclusions
We present the molecular database of the GEMS project. Thisprogram is focused on the observation of starless cores in fila-ments of the nearby star-forming regions Taurus, Perseus, andOrion. These regions have di ff erent degrees of star formationactivity, and therefore di ff erent physical conditions, providinga possibility to explore the e ff ect of environment on gas chem-istry. The project includes observations towards 305 positionsdistributed in 27 cuts that have been selected to avoid recentlyformed stars and their associated bipolar outflows. The gaschemistry in these positions is therefore not a ff ected by theshocks produced by these energetic phenomena and / or the UVradiation coming from internal sources. Our project is character-izing the molecular cloud chemistry during the pre-stellar phase.The number of positions allows an unprecedented analysis of thestatistical trends shown by the molecular abundances in a widerange of physical conditions.We carried out a multi-transition analysis of the CS moleculeand its isotopologs C S and CS to derive the gas physicalconditions, applying the MCMC methodology with a Bayesianinference approach, and using the RADEX code. We derivedthe molecular hydrogen abundance for 244 positions. Assum-ing the molecular hydrogen densities derived from the CS multi-transition fitting and using the RADEX code, we determined the molecular abundances for the following species: CO, C O,HCO + , H CO + , HC O + , H CN, HNC, HCS + , SO, SO, H S,and OCS. We estimated the o-H S abundances using the spe-cific collisional rates recently calculated by Dagdigian (2020).We analyzed the relation between the molecular abundances andthe gas physical parameters (kinetic temperature, extinction, andmolecular hydrogen density), exploring the degree of correlationbetween parameters by the computation of the Pearson, Spear-man, and Kendall correlation coe ffi cients. Our main results areas follows: – Taurus shows the lowest mean density, with a peaky distribu-tion at n(H ) ∼ × cm − Higher density values, and widerdensity distributions are found in Perseus and Orion, withmean values of n(H ) ∼ × cm − and ∼ × cm − , respec-tively. The wider density distribution in Perseus and Orion isthe consequence of the superposition of regions with di ff er-ent environmental conditions resulting from the feedback ofrecently formed stars. – Relations between molecules themselves reveal strong linearcorrelations that define three families of species: (i) the COisotopologs CO, C O; (ii) H CO + , HC O + , H CN, andHNC; and (iii) the S-bearing molecules CS, SO, SO, H S,and OCS. – Only CO and C O show a correlation with gas kinetictemperature. In the shielded gas, we observe an increasing
Article number, page 25 of 28 & A proofs: manuscript no. 40112corr relation between the abundances of these species with thegas kinetic temperature, until T K ∼
15 K. Beyond this value,the abundance remains constant with a large scatter. TheX( CO) / X(C O) increases in the cloud border as the conse-quence of selective photodissociation and isotopic fractiona-tion. – The abundances of H CO + , HC O + , H CN, and HNC arewell correlated and all of them decrease with molecular hy-drogen density, which seems to be one of the main factorsdetermining their abundances in starless cores. This anti-correlation spans over around three orders of magnitude indensity, from n(H ) ∼ cm − to n(H ) ∼ cm − . – Strong linear correlations are also found between abun-dances of the S-bearing species CS, SO, SO, H S, andOCS, which is very likely caused by the decrease of sulfurin gas phase. Under the reasonable assumption that the S / Hin gas phase, (S / H) gas , is correlated with the abundances ofthese species, we obtain that (S / H) gas ∝ n − . in the n(H ) ∼ − cm − density range. – The observed anti-correlation of the studied molecular abun-dances with density is always stronger in the case of the Tau-rus cloud. Perseus and Orion show weaker anti-correlationswith H density with smaller correlation parameters. How-ever, we do recover strong anti-correlations with density forbins of 8 −
20 mag in Perseus and >
20 mag in Orion. Thisshows that the dark region is located at a di ff erent visual ex-tinction depending on the star formation activity.In addition to the statistical analysis, we computed mean val-ues of molecular column densities and abundances in Taurus,Perseus, and Orion in order to compare with extragalactic stud-ies. The C O abundance is quite uniform in the three clouds,suggesting that its column density is a good gas mass tracer.However, the abundance of most species decreases, followingthe sequence Taurus, Perseus, and Orion, as a consequence ofdensity distributions in these clouds.The GEMS project provides an unprecedented database withwhich to investigate the gas chemistry in molecular clouds andstarless cores. This database is also useful to compare withmolecular observations in external galaxies. A complete anal-ysis of the chemical processes involved in the detected relationsrequires the comparison of observational data with predictionsof chemical models, which will be carried out in a forthcomingpaper.
Acknowledgements.
We thank the Spanish the Spanish Ministerio de Cien-cia e Innovación for funding support through AYA2016-75066-C2-1 / / AEI / FEDER,UE) and PID2019-106027GA-C44. JRG acknowledges support through grants AYA2017-85111-P andPID2019-106110GB-I00. I.J.-S. has received partial support from the Span-ish FEDER (project number ESP2017-86582-C4-1-R) and the State ResearchAgency (AEI; project number PID2019-105552RB-C41). SPTM acknowledgesto the European Union’s Horizon 2020 research and innovation program forfunding support given under grant agreement No 639459 (PROMISE). We thankthe anonymous referee for valuable comments that improved the manuscript.
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