The chemistry of dense interstellar regions was analyzed using a time-dependent gas-grain astrochemical simulation and a new chemical network that incorporates deuterated chemistry taking into account nuclear spin-states for the hydrogen chemistry and its deuterated isotopologues. With this new network, the utility of the [HCO$^+$]/[DCO$^+$] abundance ratio as a probe of the cosmic ray ionization rate has been reexamined, with special attention paid to the effect of the initial value of the molecular hydrogen ortho-to-para ratio (OPR). After discussing the use of the probe for cold cores, we then compare our results with previous theoretical and observational results for a molecular cloud close to the supernova remnant W51C, which is thought to have an enhanced cosmic ray ionization rate $ζ$ caused by the nearby $γ$-ray source. In addition, we attempt to use our approach to estimate the cosmic ray ionization rate for L1174, a dense core with an embedded star. Beyond the previously known sensitivity of [HCO$^+$]/[DCO$^+$] to $ζ$, we demonstrate its additional dependence on the initial OPR and, secondarily, on the age of the source, its temperature, and its density. We conclude that the usefulness of the [HCO$^+$]/[DCO$^+$] abundance ratio to constrain the cosmic ray ionization rate in dense regions increases with source age and ionization rate as the ratio becomes far less sensitive to the initial value of the OPR.
The widespread rings and gaps seen in the dust continuum in protoplanetary disks are sometimes accompanied by similar substructures seen in molecular line emission. One example is the outer gap at 100 au in AS 209, which shows that the H$_{13}$CO$^+$ and C$_{18}$O emission intensities decrease along with the continuum in the gap, while the DCO$^+$ emission increases inside the gap. We aim to study the behavior of DCO$^+$/H$_{13}$CO$^+$ and DCO$^+$/HCO$^+$ ratios in protoplanetary disk gaps assuming the two scenarios: the gas depletion follows the dust depletion and only the dust is depleted. W…
The physical and chemical properties of cold and dense molecular clouds are key to understanding how stars form. Using the IRAM 30 m and NRO 45 m telescopes, we carried out a Multiwavelength line-Imaging survey of the 70 $μ$m dark and bright clOuds (MIAO). At a linear resolution of 0.1--0.5 pc, this work presents a detailed study of parsec-scale CO depletion and $\rm HCO^+$ deuterium (D-) fractionation toward four sources (G11.38+0.81, G15.22-0.43, G14.49-0.13, and G34.74-0.12) included in our full sample. In each source with $\rm T<20$ K and $n_{\rm H}\rm\sim10^4$--$\rm 10^5 cm^{-3}$, we comp…
The water snowline in circumstellar disks is a crucial component in planet formation, but direct observational constraints on its location remain sparse due to the difficulty of observing water in both young embedded and mature protoplanetary disks. Chemical imaging provides an alternative route to locate the snowline, and HCO$^+$ isotopologues have been shown to be good tracers in protostellar envelopes and Herbig disks. Here we present $\sim$0.5$^{\prime\prime}$ resolution ($\sim$35 au radius) Atacama Large Millimeter/submillimeter Array (ALMA) observations of HCO$^+$ $J=4-3$ and H$^{13}$CO$…
We have conducted the first extensive observational survey of several deuterated species in 16 Class 0/I proto-brown dwarfs (proto-BDs) and 4 Class Flat/Class II brown dwarfs. Observations were obtained with the IRAM 30m telescope in the DCO$^{+}$ (3-2), DCN (3-2), DNC (3-2), and N$_{2}$D$^{+}$ (3-2) lines. The DCO$^{+}$/H$^{13}$CO$^{+}$, DCN/H$^{13}$CN, and DNC/HN$^{13}$C ratios are comparatively higher and show a narrower range than the DCO$^{+}$/HCO$^{+}$, DCN/HCN, and DNC/HNC ratios, respectively. The mean D/H ratios for the proto-BDs derived from these molecules are in the range of $\sim$…
We observed HCO$^+$ $J=1-0$ and H$^{13}$CO$^+$ $J=1-0$ emission towards the five protoplanetary disks around IM Lup, GM Aur, AS 209, HD 163296, and MWC 480 as part of the MAPS project. HCO$^+$ is detected and mapped at 0.3\arcsec\,resolution in all five disks, while H$^{13}$CO$^+$ is detected (SNR$>6 σ$) towards GM Aur and HD 163296 and tentatively detected (SNR$>3 σ$) towards the other disks by a matched filter analysis. Inside a radius of $R\sim 100$ au, the HCO$^+$ column density is flat or shows a central dip. At outer radii ($\gtrsim 100$ au), the HCO$^+$ column density decreases outwards…
The Cygnus Allscale Survey of Chemistry and Dynamical Environments: CASCADE III. The large scale distribution of DCO+, DNC and DCN in the DR21 filament
Studying molecular species in protoplanetary disks is very useful to characterize the properties of these objects, which are the site of planet formation. We attempt to constrain the chemistry of S-bearing molecules in the cold parts of circumstellar disk of GG Tau A. We searched for H$_2$S, CS, SO, and SO$_2$ in the dense disk around GG Tau A with the NOrthem Extended Millimeter Array (NOEMA) interferometer. We detected H$_2$S emission from the dense and cold ring orbiting around GG Tau A. This is the first detection of H$_2$S in a protoplanetary disk. We also detected HCO$^+$, H$^{13}$CO$^+$…
Ions and electrons play an important role in various stages of the star formation process. By following the magnetic field of their environment and interacting with neutral species, they slow down the gravitational collapse of the proto-star envelope. This process (known as ambipolar diffusion) depends on the ionisation degree, which can be derived from the \hco abundance. We present a study of \hco and its isotopologues (H$^{13}$CO$^+$, HC$^{18}$O$^+$, DCO$^+$, and H$^{13}$CO$^+$) in the low-mass proto-star IRAS16293$-$2422. The structure of this object is complex, and the HCO$^+$ emission ar…
Galactic supernova remnants (SNRs) and their environments provide the nearest laboratories to study SN feedback. We performed molecular observations toward SNR W49B, the most luminous Galactic SNR in the X-ray band, aiming to explore signs of multiple feedback channels of SNRs on nearby molecular clouds (MCs). We found very broad HCO+ lines with widths of dv = 48--75 km/s in the SNR southwest, providing strong evidence that W49B is perturbing MCs at a systemic velocity of $V_{LSR}=61$--65 km/s, and placing W49B at a distance of $7.9\pm 0.6$ kpc. We observed unusually high-intensity ratios of H…
Predicting HCN, HCO$^+$, multi-transition CO, and dust emission of star-forming galaxies -- Extension to luminous infrared galaxies and the role of cosmic ray ionization
We investigate deuterium chemistry coupled with the nuclear spin-state chemistry of H$_2$ and H$_3^+$ in protoplanetary disks. Multiple paths of deuterium fractionation are found; exchange reactions with D atoms, such as HCO$^+$ + D, are effective in addition to those with HD. In a disk model with grain sizes appropriate for dark clouds, the freeze-out of molecules is severe in the outer midplane, while the disk surface is shielded from UV radiation. Gaseous molecules, including DCO$^+$, thus become abundant at the disk surface, which tends to make their column density distribution relatively …
The lines of HOC$^+$, HCO and CO$^+$ are considered good tracers of photon-dominated regions (PDRs) and X-ray dominated regions. We study these tracers towards regions of the Sgr B2 cloud selected to be affected by different heating mechanisms. We find the lowest values of the column density ratios of HCO$^+$ versus HOC$^+$, HCO and CO$^+$ in dense HII gas, where UV photons dominate the heating and chemistry of gas. HOC$^+$, HCO and CO$^+$ abundances and the above ratios are compared with those of chemical modeling, finding that high temperature chemistry, a cosmic-ray ionization rate of 10$^{…
The ionization fraction plays a key role in the physics and chemistry of the neutral interstellar medium, from controlling the coupling of the gas to the magnetic field to allowing fast ion-neutral reactions that drive interstellar chemistry. Most estimations of the ionization fraction have relied on deuterated species such as DCO+, whose detection is limited to dense cores representing an extremely small fraction of the volume of the giant molecular clouds they are part of. As large field-of-view hyperspectral maps become available, new tracers may be found. We search for the best observable …
Cosmic rays are an essential ingredient in the evolution of the interstellar medium, as they dominate the ionisation of the dense molecular gas, where stars and planets form. However, since they are efficiently scattered by the galactic magnetic fields, many questions remain open, such as where exactly they are accelerated, what is their original energy spectrum, and how they propagate into molecular clouds. In this work we present new observations and discuss in detail a method that allows us to measure the cosmic ray ionisation rate towards the molecular clouds close to the W28 supernova rem…
Although surveys of infall motions in dense cores have been carried out for years, few surveys have focused on mapping infall across cores using multiple spectral line observations. To fill this gap, we present IRAM 30-m Telescope maps of N2H+(1-0), DCO+(2-1), DCO+(3-2), and HCO+(3-2) emission towards two prestellar cores (L492 and L694-2) and one protostellar core (L1521F). We find that the measured infall velocity varies with position across each core and choice of molecular line, likely as a result of radial variations in core chemistry and dynamics. Line-of-sight infall speeds estimated fr…
Molecular abundances are sensitive to UV-photon flux and cosmic-ray ionization rate. In starburst environments, the effects of high-energy photons and particles are expected to be stronger. We examine these astrochemical signatures through multiple transitions of HCO$^+$ and its metastable isomer HOC$^+$ in the center of the starburst galaxy NGC 253 using data from the ALMA large program ALCHEMI. The distribution of the HOC$^+$(1-0) integrated intensity shows its association with "superbubbles", cavities created either by supernovae or expanding HII regions. The observed HCO$^+$/HOC$^+$ abunda…
The aim of this study is to investigate systematic chemical differentiation of molecules in regions of high mass star formation. We observed five prominent sites of high mass star formation in HCN, HNC, HCO+, their isotopes, C18O, C34S and some other molecular lines, for some sources both at 3 and 1.3 mm and in continuum at 1.3 mm. Taking into account earlier obtained data for N2H+ we derive molecular abundances and physical parameters of the sources (mass, density, ionization fraction, etc.). The kinetic temperature is estimated from CH3C2H observations. Then we analyze correlations between m…
We present a summary of our previous investigations of the physical and chemical structure of the Horsehead nebula, and discuss how these studies led to advances on the understanding of the impact of FUV radiation on the structure of dense interstellar clouds. Specific molecular tracers can be used to isolate different environments, that are more sensitive to changes in the FUV radiation or density than the classical tracers of molecular gas : the CO isotopologues or the dust (sub)millimeter continuum emission. They include the HCO or CCH radicals for the FUV illuminated interfaces, or the mol…
The early stages of low-mass star formation are likely to be subject to intense ionization by protostellar energetic MeV particles. As a result, the surrounding gas is enriched in molecular ions, such as HCO$^{+}$ and N$_{2}$H$^{+}$. Nonetheless, this phenomenon remains poorly understood for Class 0 objects. Recently, based on Herschel observations taken as part of the key program Chemical HErschel Surveys of Star forming regions (CHESS), a very low HCO$^{+}$/N$_{2}$H$^{+}$ abundance ratio of about 3-4, has been reported toward the protocluster OMC-2 FIR4. This finding suggests a cosmic-ray io…
The transition between atomic and molecular hydrogen is associated with important changes in the structure of interstellar clouds, and marks the beginning of interstellar chemistry. Because of the relatively simple networks controlling their abundances, molecular ions are usually good probes of the underlying physical conditions including for instance the fraction of gas in molecular form or the fractional ionization. In this paper we focus on three possible probes of the molecular hydrogen column density, HCO+, HOC+, and CF+. We presented high sensitivity ALMA absorption data toward a sample …
We compare observations of HI from the Very Large Array (VLA) and the Arecibo Observatory and observations of HCO$^+$ from the Atacama Large Millimeter/submillimeter Array (ALMA) and the Northern Extended Millimeter Array (NOEMA) in the diffuse ($A_V\lesssim1$) interstellar medium (ISM) to predictions from a photodissociation region (PDR) chemical model and multi-phase ISM simulations. Using a coarse grid of PDR models, we estimate the density, FUV radiation field, and cosmic ray ionization rate (CRIR) for each structure identified in HCO$^+$ and HI absorption. These structures fall into two c…
We investigate the impact of photochemistry and X-ray ionization on the molecular composition of, and ionization fraction in, a protoplanetary disk surrounding a typical T Tauri star. We use a sophisticated physical model, which includes a robust treatment of the radiative transfer of UV and X-ray radiation, and calculate the time-dependent chemical structure using a comprehensive chemical network. In previous work, we approximated the photochemistry and X-ray ionization, here, we recalculate the photoreaction rates using the explicit UV wavelength spectrum and wavelength-dependent reaction cr…
Ions (e.g., H$_3^+$, H$_2$O$^+$) have been used extensively to quantify the cosmic-ray ionization rate (CRIR) in diffuse sightlines. However, measurements of CRIR in low-to-intermediate density gas environments are rare, especially when background stars are absent. In this work, we combine molecular line observations of CO, OH, CH, and HCO$^+$ in the star-forming cloud IC~348, and chemical models to constrain the value of CRIR and study the response of the chemical abundances distribution. The cloud boundary is found to have an $A_{\rm V}$ of approximately 4 mag. From the interior to the exter…
The cosmic ray ionization rate (CRIR) is a key parameter in understanding the physical and chemical processes in the interstellar medium. Cosmic rays are a significant source of energy in star formation regions, which impacts the physical and chemical processes which drive the formation of stars. Previous studies of the circum-molecular zone (CMZ) of the starburst galaxy NGC 253 have found evidence for a high CRIR value; $10^3-10^6$ times the average cosmic ray ionization rate within the Milky Way. This is a broad constraint and one goal of this study is to determine this value with much highe…
Ultracompact (UC) HII regions constitute one of the earliest phases in the formation of a massive star and are characterized by extreme physical conditions (Go>10^5 Habing field and n>10^6 cm^-3). The UC HII Mon R2 is the closest one and therefore an excellent target to study the chemistry in these complex regions. We carried out a 3mm and 1mm spectral survey using the IRAM 30-m telescope towards three positions that represent different physical environments in Mon R2: (i) the ionization front (IF) at (0",0"); two peaks in the molecular cloud (ii) MP1 at the offset (+15",-15") and (iii) MP2 at…
We perform a complete census of molecular ions with an abundance larger than 1e-10 in the protostellar shock L1157-B1 by means of an unbiased high-sensitivity survey obtained with the IRAM-30m and Herschel/HIFI. By means of an LVG radiative transfer code the gas physical conditions and fractional abundances of molecular ions are derived. The latter are compared with estimates of steady-state abundances in the cloud and their evolution in the shock calculated with the chemical model Astrochem. We detect emission from HCO+, H13CO+, N2H+, HCS+, and, for the first time in a shock, from HOCO+, and …
Context: Observations of small carbon-bearing molecules such as CCH, C4H, c-C3H2, and HCO in the Horsehead Nebula have shown these species to have higher abundances towards the edge of the source than towards the center. Aims: Given the determination of a wide range of values for zeta (s-1), the total ionization rate of hydrogen atoms, and the proposal of a column-dependent zeta(N_H), where N_H is the total column of hydrogen nuclei, we desire to determine if the effects of zeta(N_H) in a single object with spatial variation can be observable. We chose the Horsehead Nebula because of its geome…
Within a few parsecs around the central Black Hole Sgr A*, chemistry in the dense molecular cloud material of the circumnuclear disk (CND) can be affected by many energetic phenomena such as high UV-flux from the massive central star cluster, X-rays from Sgr A*, shock waves, and an enhanced cosmic-ray flux. Recently, spectroscopic surveys with the IRAM 30 meter and the APEX 12 meter telescopes of substantial parts of the 80--500 GHz frequency range were made toward selected positions in and near the CND. These datasets contain lines from the molecules HCN, HCO$^+$, HNC, CS, SO, SiO, CN, H$_2$C…
This is the second in a series of papers based on data from DISCS, a Submillimeter Array observing program aimed at spatially and spectrally resolving the chemical composition of 12 protoplanetary disks. We present data on six Southern sky sources - IM Lup, SAO 206462 (HD 135344b), HD 142527, AS 209, AS 205 and V4046 Sgr - which complement the six sources in the Taurus star forming region reported previously. CO 2-1 and HCO+ 3-2 emission are detected and resolved in all disks and show velocity patterns consistent with Keplerian rotation. Where detected, the emission from DCO+ 3-2, N2H+ 3-2, H2…
In this paper, we present preliminary results illustrating the effect of cosmic rays on solid-phase chemistry in models of both TMC-1 and several sources with physical conditions identical to TMC-1 except for hypothetically enhanced ionization rates. Using a recent theory for the addition of cosmic ray-induced reactions to astrochemical models, we calculated the radiochemical yields, called $G$ values, for the primary dust grain ice-mantle constituents. We show that the inclusion of this non-thermal chemistry can lead to the formation of complex organic molecules from simpler ice-mantle consti…
We combine dynamical and non-equilibrium chemical modeling of evolving prestellar molecular cloud cores, and explore the evolution of molecular abundances in the contracting core. We model both magnetic cores, with varying degrees of initial magnetic support, and non-magnetic cores, with varying collapse delay times. We explore, through a parameter study, the competing effects of various model parameters in the evolving molecular abundances, including the elemental C/O ratio, the temperature, and the cosmic-ray ionization rate. We find that different models show their largest quantitative diff…
We developed a chemical network for modeling the chemistry and non-ideal MHD effects from the collapsing dense molecular clouds to protostellar disks. First, we re-formulated the cosmic-ray desorption rate by considering the variations of desorption rate over the grain size distribution. We find that the differential desorption of volatile species is amplified by the grains larger than 0.1 $μ$m, because larger grains are heated to a lower temperature by cosmic-rays and hence more sensitive to the variations in binding energies. As a result, atomic nitrogen N is $\sim$2 orders of magnitude more…
We use a high-temperature chemical network to derive the molecular abundances in axisymmetric accretion disk models around active galactic nuclei (AGNs) within 100 pc using simple radial and vertical density and temperature distributions motivated by more detailed physical models. We explore the effects of X-ray irradiation and cosmic ray ionization on the spatial distribution of the molecular abundances of CO, CN, CS, HCN, HCO+, HC3N, C2H, and c-C3H2 using a variety of plausible disk structures. These simple models have molecular regions with a layer of X-ray dominated regions, a midplane wit…
We present 74 MHz radio continuum observations of the Galactic center region. These measurements show nonthermal radio emission arising from molecular clouds that is unaffected by free-free absorption along the line of sight. We focus on one cloud, G0.13--0.13, representative of the population of molecular clouds that are spatially correlated with steep spectrum (alpha^{74MHz}_{327MHz}=1.3\pm0.3) nonthermal emission from the Galactic center region. This cloud lies adjacent to the nonthermal radio filaments of the Arc near l~0.2^0 and is a strong source of 74 MHz continuum, SiO (2-1) and FeI Ka…
HCN emission from translucent gas and UV-illuminated cloud edges revealed by wide-field IRAM 30m maps of Orion B GMC: Revisiting its role as tracer of the dense gas reservoir for star formation
GEMS is an IRAM 30m 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 TMC 1. Extensive millimeter observations have been carried out with the IRAM 30m telescope (3mm and 2mm) and the 40m Yebes telescope (1.3cm and 7mm) 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 r…
