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.
