(Abridged) Organic molecules are important constituents of protoplanetary disks. Their ro-vibrational lines observed in the near- and mid-infrared are commonly detected toward T Tauri disks. These lines are the only way to probe the chemistry in the
inner few au where terrestrial planets form. To understand this chemistry, accurate molecular abundances have to be determined. This is complicated by excitation effects. Most analyses so far have made the assumption of local thermal equilibrium (LTE). Starting from estimates for the collisional rate coefficients of HCN, non-LTE slab models of the HCN emission were calculated to study the importance of different excitation mechanisms. Using a new radiative transfer model, the HCN emission from a full two-dimensional disk was then modeled to study the effect of the non-LTE excitation, together with the line formation. We ran models tailored to the T Tauri disk AS 205 (N) where HCN lines in both the 3 {mu}m and 14 {mu}m bands have been observed by VLT-CRIRES and the Spitzer Space Telescope. Reproducing the observed 3 {mu}m / 14 {mu}m flux ratios requires very high densities and kinetic temperatures ($n > 10^{14}$ cm$^{-3}$ and $T > 750$ K), if only collisional excitation is accounted for. Radiative pumping can, however, excite the lines easily out to considerable radii $sim$ 10 au. Consequently, abundances derived from LTE and non-LTE models do not differ by more than a factor of about 3. Models with both a strongly enhanced abundance within $sim$ 1 au (jump abundance) and constant abundance can reproduce the current observations, but future observations with the MIRI instrument on JWST and METIS on the E-ELT can easily distinguish between the scenarios and test chemical models. Depending on the scenario, ALMA can detect rotational lines within vibrationally excited levels.
(Abridged) Transition disks are recognized by the absence of emission of small dust grains inside a radius of up to several 10s of AUs. Due to the lack of angular resolution and sensitivity, the gas content of such dust holes has not yet been determi
ned, but is of importance to constrain the mechanism leading to the dust holes. Transition disks are thought to currently undergo the process of dispersal, setting an end to the giant planet formation process. We present new high-resolution observations with the Atacama Large Millimeter/ submillimeter Array (ALMA) of gas lines towards the transition disk Oph IRS 48 previously shown to host a large dust trap. ALMA has detected the $J=6-5$ line of $^{12}$CO and C$^{17}$O around 690 GHz (434 $mu$m) at a resolution of $sim$0.25$$ corresponding to $sim$30 AU (FWHM). The observed gas lines are used to set constraints on the gas surface density profile. New models of the physical-chemical structure of gas and dust in Oph IRS 48 are developed to reproduce the CO line emission together with the spectral energy distribution (SED) and the VLT-VISIR 18.7 $mu$m dust continuum images. Integrated intensity cuts and the total spectrum from models having different trial gas surface density profiles are compared to observations. Using the derived surface density profiles, predictions for other CO isotopologues are made, which can be tested by future ALMA observations of the object. The derived gas surface density profile points to the clearing of the cavity by one or more massive planet/companion rather than just photoevaporation or grain-growth.
Observations of the high-mass star forming region AFGL 2591 reveal a large abundance of CO+, a molecule known to be enhanced by far UV (FUV) and X-ray irradiation. In chemical models assuming a spherically symmetric envelope, the volume of gas irradi
ated by protostellar FUV radiation is very small due to the high extinction by dust. The abundance of CO+ is thus underpredicted by orders of magnitude. In a more realistic model, FUV photons can escape through an outflow region and irradiate gas at the border to the envelope. Thus, we introduce the first 2D axi-symmetric chemical model of the envelope of a high-mass star forming region to explain the CO+ observations as a prototypical FUV tracer. The model assumes an axi-symmetric power-law density structure with a cavity due to the outflow. The local FUV flux is calculated by a Monte Carlo radiative transfer code taking scattering on dust into account. A grid of precalculated chemical abundances, introduced in the first part of this series of papers, is used to quickly interpolate chemical abundances. This approach allows to calculate the temperature structure of the FUV heated outflow walls self-consistently with the chemistry. Synthetic maps of the line flux are calculated using a raytracer code. Single-dish and interferometric observations are simulated and the model results are compared to published and new JCMT and SMA observations. The two-dimensional model of AFGL 2591 is able to reproduce the JCMT single-dish observations and also explains the non-detection by the SMA. We conclude that the observed CO+ line flux and its narrow width can be interpreted by emission from the warm and dense outflow walls irradiated by protostellar FUV radiation.
