Protoplanetary disks are challenging objects for astrochemical models due to strong density and temperature gradients and due to the UV photons 2D propagation. In this paper, we have studied the importance of several model parameters on the predicted column densities of observed species. We considered: 1) 2-phase (gas and homogeneous grains) or 3-phase (gas, surface, and bulk of grains) models, 2) several initial compositions, 3) grain growth and dust settling, and 4) several cosmic-ray ionization rates. Our main result is that dust settling is the most crucial parameter. Including this effect renders the computed column densities sensitive to all the other model parameters, except cosmic-ray ionization rate. In fact, we found almost no effect of this parameter for radii larger than 10 au (the minimum radius studied here) except for N2H+. We also compared all our models with all the column densities observed in the protoplanetary disk around DM Tau and were not able to reproduce all the observations despite the studied parameters. N2H+ seems to be the most sensitive species. Its observation in protoplanetary disks at large radius could indicate enough N2 in the gas-phase (inhibited by the 3-phase model, but boosted by the settling) and a low electron abundance (favored by low C and S elemental abundances).
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