Many efforts have been made to model the mass distribution and dynamical evolution of the circumnuclear gas in active galactic nuclei (AGNs). However, chemical evolution is not included in detail in three-dimensional (3-D) hydrodynamic simulations. T
he X-ray radiation from the AGN can drive the gas chemistry and affect the thermodynamics, as well as the excitation of the interstellar medium (ISM). Therefore, we estimate the effects (on chemical abundances and excitation) of X-ray irradiation by the AGN, for atomic and molecular gas in a 3-D hydrodynamic model of an AGN torus. We obtain the abundances of various species from an X-ray chemical model. A 3-D radiative transfer code estimates the level populations, which result in line intensity maps. Predictions for the CO J=1-0 to J=9-8 lines indicate that mid-J CO lines are excellent probes of density and dynamics in the central (<60 pc) region of the AGN, in contrast to the low-J CO lines. Analysis of the X_CO/alpha conversion factors shows that only the higher-J CO lines can be used for gas mass determination in AGN tori. The [C II] 158 um emission traces mostly the hot (T_k>1000m K) central (<60 pc) region of the AGN torus. The [C II] 158 um line will be useful for ALMA observations of high redshift (z>1) AGNs. The spatial scales (>0.25 pc) probed with our simulations match the size of the structures that ALMA will resolve in nearby (<45 Mpc at 0.01) galaxies.
