The impact of attenuation on cosmic-ray chemistry: I. Abundances and chemical calibrators in molecular clouds

The chemistry of shielded molecular gas is primarily driven by energetic, charged particles dubbed cosmic rays (CRs), in particular those with energies under 1 GeV. CRs ionize molecular hydrogen and helium, the latter of which contributes greatly to the destruction of molecules. CR ionization initiates a wide range of gas-phase chemistry, including pathways important for the so-called "carbon cycle", C$^+$/C/CO. Therefore, the CR ionization rate, $ζ$, is fundamental in theoretical and observational astrochemistry. Although observational methods show a wide range of ionization rates -- varying with the environment, especially decreasing into dense clouds -- astrochemical models often assume a constant rate. To address this limitation, we employ a post-processed gas-phase chemical model of a simulated dense molecular cloud that incorporates CR energy losses within the cloud. This approach allows us to investigate changes in abundance profiles of important chemical tracers and gas temperature. Furthermore, we analyze analytical calibrators for estimating $ζ$ in dense molecular gas that are robust when tested against a full chemical network. Additionally, we provide improved estimations of the electron fraction in dense gas for better consistency with observational data and theoretical calibrations for UV-shielded regions.