Spatially resolved continuum observations of planet-forming disks show prominent ring and gap structures in their dust distribution. However, the picture from gas observations is much less clear and constraints on the radial gas density structure (i.e. gas gaps) remain rare and uncertain. We want to investigate the importance of thermo-chemical processes for the interpretation of high-spatial-resolution gas observations of planet-forming disks and their impact on derived gas properties. We apply the radiation thermo-chemical disk code ProDiMo (PROtoplanetary DIsk MOdel) to model self-consistently the dust and gas disk of HD 163296, using the DSHARP gas and dust observations. With this model we investigate the impact of dust gaps and gas gaps, considering chemistry and heating/cooling processes, on the observables and the derived gas properties. We find distinct peaks in the radial line intensity profiles of the CO line data of HD 163296 at the location of the dust gaps. Our model indicates that those peaks are not only a consequence of a gas temperature increase within the gaps but are mainly caused by the absorption of line emission from the back side of the disk by the dust rings. For two of the three prominent dust gaps in HD 163296, we find that thermo-chemical effects are negligible for deriving density gradients via measurements of the rotation velocity. However, for the gap with the highest dust depletion, the temperature gradient can be dominant and needs to be considered to derive accurate gas density profiles. Self-consistent gas and dust thermo-chemical modelling in combination with high-quality observations of multiple molecules are necessary to accurately derive gas gap depths and shapes. This is crucial to determine the origin of gaps and rings in planet-forming disks and to improve the mass estimates of forming planets if they are the cause of the gap.
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