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| 2. |
- Bulut, N., et al.
(author)
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Gas phase Elemental abundances in Molecular cloudS (GEMS): III. Unlocking the CS chemistry: The CS+O reaction
- 2021
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 646
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Journal article (peer-reviewed)abstract
- Context. Carbon monosulphide (CS) is among the most abundant gas-phase S-bearing molecules in cold dark molecular clouds. It is easily observable with several transitions in the millimeter wavelength range, and has been widely used as a tracer of the gas density in the interstellar medium in our Galaxy and external galaxies. However, chemical models fail to account for the observed CS abundances when assuming the cosmic value for the elemental abundance of sulfur. Aims. The CS+O → CO + S reaction has been proposed as a relevant CS destruction mechanism at low temperatures, and could explain the discrepancy between models and observations. Its reaction rate has been experimentally measured at temperatures of 150-400 K, but the extrapolation to lower temperatures is doubtful. Our goal is to calculate the CS+O reaction rate at temperatures <150 K which are prevailing in the interstellar medium. Methods. We performed ab initio calculations to obtain the three lowest potential energy surfaces (PES) of the CS+O system. These PESs are used to study the reaction dynamics, using several methods (classical, quantum, and semiclassical) to eventually calculate the CS + O thermal reaction rates. In order to check the accuracy of our calculations, we compare the results of our theoretical calculations for T ~ 150-400 K with those obtained in the laboratory. Results. Our detailed theoretical study on the CS+O reaction, which is in agreement with the experimental data obtained at 150-400 K, demonstrates the reliability of our approach. After a careful analysis at lower temperatures, we find that the rate constant at 10 K is negligible, below 10-15 cm s-1, which is consistent with the extrapolation of experimental data using the Arrhenius expression. Conclusions. We use the updated chemical network to model the sulfur chemistry in Taurus Molecular Cloud 1 (TMC 1) based on molecular abundances determined from Gas phase Elemental abundances in Molecular CloudS (GEMS) project observations. In our model, we take into account the expected decrease of the cosmic ray ionization rate, ζH2, along the cloud. The abundance of CS is still overestimated when assuming the cosmic value for the sulfur abundance.
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| 3. |
- Navarro-Almaida, D., et al.
(author)
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Gas phase Elemental abundances in Molecular cloudS (GEMS): II. On the quest for the sulphur reservoir in molecular clouds: the H2S case
- 2020
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 637
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Journal article (peer-reviewed)abstract
- Context. Sulphur is one of the most abundant elements in the Universe. Surprisingly, sulphuretted molecules are not as abundant as expected in the interstellar medium and the identity of the main sulphur reservoir is still an open question. Aims. Our goal is to investigate the H2S chemistry in dark clouds, as this stable molecule is a potential sulphur reservoir. Methods. Using millimeter observations of CS, SO, H2S, and their isotopologues, we determine the physical conditions and H2S abundances along the cores TMC 1-C, TMC 1-CP, and Barnard 1b. The gas-grain model NAUTILUS is used to model the sulphur chemistry and explore the impact of photo-desorption and chemical desorption on the H2S abundance. Results. Our modeling shows that chemical desorption is the main source of gas-phase H2S in dark cores. The measured H2S abundance can only be fitted if we assume that the chemical desorption rate decreases by more than a factor of 10 when n(H) > 2 x 10(4). This change in the desorption rate is consistent with the formation of thick H2O and CO ice mantles on grain surfaces. The observed SO and H2S abundances are in good agreement with our predictions adopting an undepleted value of the sulphur abundance. However, the CS abundance is overestimated by a factor of 5-10. Along the three cores, atomic S is predicted to be the main sulphur reservoir. Conclusions. The gaseous H2S abundance is well reproduced, assuming undepleted sulphur abundance and chemical desorption as the main source of H2S. The behavior of the observed H2S abundance suggests a changing desorption efficiency, which would probe the snowline in these cold cores. Our model, however, highly overestimates the observed gas-phase CS abundance. Given the uncertainty in the sulphur chemistry, we can only conclude that our data are consistent with a cosmic elemental S abundance with an uncertainty of a factor of 10.
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| 4. |
- Rodríguez-Baras, M., et al.
(author)
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Gas phase Elemental abundances in Molecular cloudS (GEMS): IV. Observational results and statistical trends
- 2021
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 648
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Journal article (peer-reviewed)abstract
- Gas phase Elemental abundances in Molecular CloudS (GEMS) is an IRAM 30 m Large Program designed to provide estimates of the S, 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 basis for estimating X(e-) and the C, O, N, and S depletions through chemical modeling. We observed and derived the abundances of 14 species (13CO, C18O, HCO+, H13CO+, HC18O+, HCN, H13CN, HNC, HCS+, CS, SO, 34SO, H2S, and OCS) in 244 positions, covering the AV ~3 to ~100 mag, n(H2) ~ a few 103 to 106 cm-3, and Tk ~10 to ~30 K ranges in these clouds, and avoiding protostars, HII regions, and bipolar outflows. A statistical analysis is carried out in order to identify general trends between different species and with physical parameters. Relations between molecules reveal strong linear correlations which define three different families of species: (1) 13CO and C18O isotopologs; (2) H13CO+, HC18O+, H13 CN, and HNC; and (3) the S-bearing molecules. The abundances of the CO isotopologs increase with the gas kinetic temperature until TK ~ 15 K. For higher temperatures, the abundance remains constant with a scatter of a factor of ~3. The abundances of H13 CO+, HC18 O+, H13 CN, and HNC are well correlated with each other, and all of them decrease with molecular hydrogen density, following the law ∝ n(H2)-0.8 ± 0.2. The abundances of S-bearing species also decrease with molecular hydrogen density at a rate of (S-bearing/H)gas ∝ n(H2)-0.6 ± 0.1. The abundances of molecules belonging to groups 2 and 3 do not present any clear trend with gas temperature. At scales of molecular clouds, the C18O abundance is the quantity that better correlates with the cloud mass. We discuss the utility of the 13CO/C18O, HCO+/H13CO+, and H13 CO+/H13CN abundance ratios as chemical diagnostics of star formation in external galaxies.
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| 5. |
- Fuente, A., et al.
(author)
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Gas phase Elemental abundances in Molecular cloudS (GEMS) I. The prototypical dark cloud TMC 1
- 2019
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 624
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Journal article (peer-reviewed)abstract
- GEMS is an IRAM 30 m Large Program whose aim is determining the elemental depletions and the ionization fraction in a set of prototypical star-forming regions. This paper presents the first results from the prototypical dark cloud Taurus molecular cloud (TMC) 1. Extensive millimeter observations have been carried out with the IRAM 30 m telescope (3 and 2mm) and the 40 m Yebes telescope (1.3 cm and 7 mm) to determine the fractional abundances of CO, HCO+, HCN, CS, SO, HCS+, and N2H+ in three cuts which intersect the dense filament at the well-known positions TMC 1-CP, TMC 1-NH3, and TMC 1-C, covering a visual extinction range from A(v) similar to 3 to similar to 20 mag. Two phases with differentiated chemistry can be distinguished: (i) the translucent envelope with molecular hydrogen densities of 1-5 x 10(3) cm(-3); and (ii) the dense phase, located at A(v) > 10 mag, with molecular hydrogen densities >10(4) cm(-3). Observations and modeling show that the gas phase abundances of C and O progressively decrease along the C+/C/CO transition zone (A(v) similar to 3 mag) where C/H similar to 8 x 10(-5) and C/O similar to 0.8-1, until the beginning of the dense phase at A(v) similar to 10 mag. This is consistent with the grain temperatures being below the CO evaporation temperature in this region. In the case of sulfur, a strong depletion should occur before the translucent phase where we estimate an S/H similar to (0.4-2.2) x 10(-6), an abundance similar to 7-40 times lower than the solar value. A second strong depletion must be present during the formation of the thick icy mantles to achieve the values of S/H measured in the dense cold cores (S/H similar to 8 x 10(-8)). Based on our chemical modeling, we constrain the value of zeta(H2) to similar to(0.5-1.8) x 10(-16) s(-1) in the translucent cloud.
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| 6. |
- Wakelam, V., et al.
(author)
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A KINETIC DATABASE FOR ASTROCHEMISTRY (KIDA)
- 2012
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In: Astrophysical Journal Supplement Series. - : American Astronomical Society. - 0067-0049 .- 1538-4365. ; 199:1, s. 21-
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Journal article (peer-reviewed)abstract
- We present a novel chemical database for gas-phase astrochemistry. Named the KInetic Database for Astrochemistry (KIDA), this database consists of gas-phase reactions with rate coefficients and uncertainties that will be vetted to the greatest extent possible. Submissions of measured and calculated rate coefficients are welcome, and will be studied by experts before inclusion into the database. Besides providing kinetic information for the interstellar medium, KIDA is planned to contain such data for planetary atmospheres and for circumstellar envelopes. Each year, a subset of the reactions in the database (kida.uva) will be provided as a network for the simulation of the chemistry of dense interstellar clouds with temperatures between 10 K and 300 K. We also provide a code, named Nahoon, to study the time-dependent gas-phase chemistry of zero-dimensional and one-dimensional interstellar sources.
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| 7. |
- Wakelam, V., et al.
(author)
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The 2014 KIDA Network for Interstellar Chemistry
- 2015
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In: Astrophysical Journal Supplement Series. - : American Astronomical Society. - 0067-0049 .- 1538-4365. ; 217:2
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Journal article (peer-reviewed)abstract
- Chemical models used to study the chemical composition of the gas and the ices in the interstellar medium are based on a network of chemical reactions and associated rate coefficients. These reactions and rate coefficients are partially compiled from data in the literature, when available. We present in this paper kida.uva.2014, a new updated version of the kida.uva public gas-phase network first released in 2012. In addition to a description of the many specific updates, we illustrate changes in the predicted abundances of molecules for cold dense cloud conditions as compared with the results of the previous version of our network, kida.uva.2011.
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| 8. |
- Manigand, S., et al.
(author)
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The ALMA-PILS survey: First detection of the unsaturated 3-carbon molecules Propenal (C2H3CHO) and Propylene (C3H6) towards IRAS 16293-2422 B
- 2021
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In: Astronomy and Astrophysics. - : EDP Sciences. - 0004-6361 .- 1432-0746. ; 645
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Journal article (peer-reviewed)abstract
- Context. Complex organic molecules with three carbon atoms are found in the earliest stages of star formation. In particular, propenal (C2H3CHO) is a species of interest due to its implication in the formation of more complex species and even biotic molecules. Aims. This study aims to search for the presence of C2H3CHO and other three-carbon species such as propylene (C3H6) in the hot corino region of the low-mass protostellar binary IRAS 16293-2422 to understand their formation pathways. Methods. We use ALMA observations in Band 6 and 7 from various surveys to search for the presence of C3H6 and C2H3CHO towards the protostar IRAS 16293-2422 B (IRAS 16293B). The identification of the species and the estimates of the column densities and excitation temperatures are carried out by modeling the observed spectrum under the assumption of local thermodynamical equilibrium. Results. We report the detection of both C3H6 and C2H3CHO towards IRAS 16293B, however, no unblended lines were found towards the other component of the binary system, IRAS 16293A. We derive column density upper limits for C3H8, HCCCHO, n-C3H7OH, i-C3H7OH, C3O, and cis-HC(O)CHO towards IRAS 16293B. We then use a three-phase chemical model to simulate the formation of these species in a typical prestellar environment followed by its hydrodynamical collapse until the birth of the central protostar. Different formation paths, such as successive hydrogenation and radical-radical additions on grain surfaces, are tested and compared to the observational results in a number of different simulations, to assess which are the dominant formation mechanisms in the most embedded region of the protostar. Conclusions. The simulations reproduce the abundances within one order of magnitude from those observed towards IRAS 16293B, with the best agreement found for a rate of 10-12 cm3 s-1 for the gas-phase reaction C3 + O → C2 + CO. Successive hydrogenations of C3, HC(O)CHO, and CH3OCHO on grain surfaces are a major and crucial formation route of complex organics molecules, whereas both successive hydrogenation pathways and radical-radical addition reactions contribute to the formation of C2H5CHO.
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| 9. |
- Wakelam, V., et al.
(author)
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Reaction Networks for Interstellar Chemical Modelling : Improvements and Challenges
- 2010
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In: Space Science Reviews. - : Springer Science and Business Media LLC. - 0038-6308 .- 1572-9672. ; 156:04-jan, s. 13-72
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Research review (peer-reviewed)abstract
- We survey the current situation regarding chemical modelling of the synthesis of molecules in the interstellar medium. The present state of knowledge concerning the rate coefficients and their uncertainties for the major gas-phase processes-ion-neutral reactions, neutral-neutral reactions, radiative association, and dissociative recombination-is reviewed. Emphasis is placed on those key reactions that have been identified, by sensitivity analyses, as 'crucial' in determining the predicted abundances of the species observed in the interstellar medium. These sensitivity analyses have been carried out for gas-phase models of three representative, molecule-rich, astronomical sources: the cold dense molecular clouds TMC-1 and L134N, and the expanding circumstellar envelope IRC +10216. Our review has led to the proposal of new values and uncertainties for the rate coefficients of many of the key reactions. The impact of these new data on the predicted abundances in TMC-1 and L134N is reported. Interstellar dust particles also influence the observed abundances of molecules in the interstellar medium. Their role is included in gas-grain, as distinct from gas-phase only, models. We review the methods for incorporating both accretion onto, and reactions on, the surfaces of grains in such models, as well as describing some recent experimental efforts to simulate and examine relevant processes in the laboratory. These efforts include experiments on the surface-catalyzed recombination of hydrogen atoms, on chemical processing on and in the ices that are known to exist on the surface of interstellar grains, and on desorption processes, which may enable species formed on grains to return to the gas-phase.
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| 10. |
- Botan, Alexandru, et al.
(author)
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Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions
- 2015
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In: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 119:49, s. 15075-15088
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Journal article (peer-reviewed)abstract
- Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR. experiments in terms of the highly structurally sensitive C-H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P-N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using nmrlipids.blogspot.fi as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files (https://zenodo.org/collection/user-nmrlipids) has become the most extensive publicly available collection of molecular dynamics simulation trajectories of lipid bilayers.
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