We present an extension of the code ProDiMo that allows for a modeling of processes pertinent to active galactic nuclei and to an ambient chemistry that is time dependent. We present a proof-of-concept and focus on a few astrophysically relevant species, e.g., H+, H2+ and H3+; C+ and N+; C and O; CO and H2O; OH+, H2O+ and H3O+; HCN and HCO+. We find that the freeze-out of water is strongly suppressed and that this affects the bulk of the oxygen and carbon chemistry occurring in AGN. The commonly used AGN tracer HCN/HCO+ is strongly time-dependent, with ratios that vary over orders of magnitude for times longer than 10^4 years. Through ALMA observations this ratio can be used to probe how the narrow-line region evolves under large fluctuations in the SMBH accretion rate. Strong evolutionary trends, on time scales of 10^4-10^8 years, are also found in species such as H3O+, CO, and H2O. These reflect, respectively, time dependent effects in the ionization balance, the transient nature of the production of molecular gas, and the freeze-out/sublimation of water.
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