Protoplanetary disks are extended structures with a particular temperature and density structure. The gas and dust are coupled through various processes, such as drag and turbulence. The gas in the disk is also subject to various physical processes, such as heating and cooling, while the dust is subject to settling and growth.
The physics and chemistry of protoplanetary disks are complex and interrelated, with various processes occurring simultaneously. As one moves away from the host star in the disk mid-plane, the temperature falls and so does the density. On the other hand, the density falls on moving vertically upwards, but the temperature increases. This is because, with increasing density, the disk mid-plane is very optically thick, which prevents the stellar (or any other interstellar) flux to enter, leading to a lowering of temperatures in the mid-plane. This makes the mid-plane, the place where planet formation will happen, almost invisible to our telescopes, because high densities that do not allow any photons to escape the system and reach us and low temperatures, which reduce the net emission from the region altogether.
This extended and intricate physical structure of the disk, in terms of density and temperature, affects the chemistry of the system. The chemical composition of protoplanetary disks is also complex, with various molecular species present, ranging from simple diatomic molecules to complex organic molecules. Chemical reactions are very sensitive to the local temperatures, due to the dependence of reaction rates on temperatures, and also on the local density, due to the presence of reactions that deal with gas-grain interactions. Hence, one can see an intricate distribution of various chemicals too, which closely follow the distributions of the physical parameters. Along with the concentration, the chemicals also vary in the phases they are present in, in different parts of the disks. Closer to the mid-plane, one can see the presence of large amounts of ices (owing to lower temperatures) while more gas phase molecules can be found towards the surface of the disk. These physical and chemical features of the protoplanetary disks are what leads to the formation of the huge variety of planets that we have observed till now.