The Astrochemical Impact of Cosmic Rays in Protoclusters I: Molecular Cloud Chemistry

We present astrochemical photo-dissociation region models in which cosmic ray attenuation has been fully coupled to the chemical evolution of the gas. We model the astrochemical impact of cosmic rays, including those accelerated by protostellar accretion shocks, on molecular clouds hosting protoclusters. Our models with embedded protostars reproduce observed ionization rates. We study the imprint of cosmic ray attenuation on ions for models with different surface cosmic ray spectra and different star formation efficiencies. We find that abundances, particularly ions, are sensitive to the treatment of cosmic rays. We show the column densities of ions are under predicted by the `classic' treatment of cosmic rays by an order of magnitude. We also test two common chemistry approximations used to infer ionization rates. We conclude that the approximation based on the H$_3^+$ abundance under predicts the ionization rate except in regions where the cosmic rays dominate the chemistry. Our models suggest the chemistry in dense gas will be significantly impacted by the increased ionization rates, leading to a reduction in molecules such as NH$_3$ and causing H$_2$-rich gas to become [C II] bright.