We aimed to study the molecular composition of the interstellar medium (ISM) surrounding an Active Galactic Nucleus (AGN), by making an inventory of molecular species and their abundances, as well as to establish a chemical differentiation between starburst galaxies and AGN. We used the IRAM-30 m telescope to observe the central 1.5-2 kpc region of NGC1068, covering the frequencies between 86.2 GHz and 115.6 GHz. Using Boltzmann diagrams, we calculated the column densities of the detected molecules. We used a chemical model to reproduce the abundances found in the AGN, to determine the origin of each detected species, and to test the influence of UV fields, cosmic rays, and shocks on the ISM. We identified 24 different molecular species and isotopologues, among which HC3N, SO, N2H+, CH3CN, NS, 13CN, and HN13C are detected for the first time in NGC1068. We obtained the upper limits to the isotopic ratios 12C/13C=49, 16O/18O=177 and 32S/34S=5. Our chemical models suggest that the chemistry in the nucleus of NGC1068 is strongly influenced by cosmic rays, although high values of both cosmic rays and far ultraviolet (FUV) radiation fields also explain well the observations. The gas in the nucleus of NGC1068 has a different chemical composition as compared to starburst galaxies. The distinct physical processes dominating galaxy nuclei (e.g. C-shocks, UV fields, X-rays, cosmic rays) leave clear imprints in the chemistry of the gas, which allow to characterise the nucleus activity by its molecular abundances.
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