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Protonated hydrogen cyanide, HCNH$^{+}$, plays a fundamental role in astrochemistry because it is an intermediary in gas-phase ion-neutral reactions within cold molecular clouds. However, the impact of the environment on the chemistry of HCNH$^{+}$ remains poorly understood. With the IRAM-30 m and APEX-12 m observations, we report the first robust distribution of HCNH$^{+}$ in the Serpens filament and in Serpens South. Our data suggest that HCNH$^{+}$ is abundant in cold and quiescent regions, but is deficit in active star-forming regions. The observed HCNH$^{+}$ fractional abundances relative to H$_{2}$ range from $3.1\times 10^{-11}$ in protostellar cores to $5.9\times 10^{-10}$ in prestellar cores, and the HCNH$^{+}$ abundance generally decreases with increasing H$_{2}$ column density, which suggests that HCNH$^{+}$ coevolves with cloud cores. Our observations and modeling results suggest that the abundance of HCNH$^{+}$ in cold molecular clouds is strongly dependent on the H$_{2}$ number density. The decrease in the abundance of HCNH$^{+}$ is caused by the fact that its main precursors (e.g., HCN and HNC) undergo freeze-out as the number density of H$_{2}$ increases. However, current chemical models cannot explain other observed trends, such as the fact that the abundance of HCNH$^{+}$ shows an anti-correlation with that of HCN and HNC, but a positive correlation with that of N$_{2}$H$^{+}$ in the southern part of the Serpens South northern clump. This indicates that additional chemical pathways have to be invoked for the formation of HCNH$^{+}$ via molecules like N$_{2}$ in regions in which HCN and HNC freeze out. Both the fact that HCNH$^{+}$ is most abundant in molecular cores prior to gravitational collapse and the fact that low-$J$ HCNH$^{+}$ transitions have very low H$_{2}$ critical densities make this molecular ion an excellent probe of pristine molecular gas., Comment: 25 pages, 26 figures, accepted for publication in A&A

In the centre of pre-stellar cores, deuterium fractionation is enhanced due to the low temperatures and high densities. Therefore, the chemistry of deuterated molecules can be used to study the earliest stages of star formation. We analyse the deuterium fractionation of simple molecules, comparing the level of deuteration in the envelopes of the pre-stellar core L1544 in Taurus and the protostellar core HH211 in Perseus. We used single-dish observations of CCH, HCN, HNC, HCO$^+$, and their $^{13}$C-, $^{18}$O- and D-bearing isotopologues, detected with the Onsala 20m telescope. We derived the column densities and the deuterium fractions of the molecules. Additionally, we used radiative transfer simulations and results from chemical modelling to reproduce the observed molecular lines. We used new collisional rate coefficients for HNC, HN$^{13}$C, DNC, and DCN that consider the hyperfine structure of these molecules. We find high levels of deuteration for CCH (10%) in both sources, consistent with other carbon chains, and moderate levels for HCN (5-7%) and HNC (8%). The deuterium fraction of HCO$^+$ is enhanced towards HH211, most likely caused by isotope-selective photodissociation of C$^{18}$O. Similar levels of deuteration show that the process is likely equally efficient towards both cores, suggesting that the protostellar envelope still retains the chemical composition of the original pre-stellar core. The fact that the two cores are embedded in different molecular clouds also suggests that environmental conditions do not have a significant effect on the deuteration within dense cores. Radiative transfer modelling shows that it is necessary to include the outer layers of the cores to consider the effects of extended structures. Besides HCO$^+$ observations, HCN observations towards L1544 also require the presence of an outer diffuse layer where the molecules are relatively abundant., Comment: 27 pages, 17 figures, accepted for publication in A&A

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