Abstract: The gas and dust of protoplanetary disks are a window into the history of the Solar System and extrasolar planetary systems, but there are still many aspects of the chemistry in these planet forming regions that are not well understood. This talk will be divided into two questions that, when combined, will provide a clearer picture of the gasses available to forming planets. These questions are: 1) How does the central star (and X-ray flaring events in particular) impact the cold gas? 2) How does the hot gas close to the star evolve over time? To answer these questions, I will present a combination of results and future projects using chemical-disk models and observations from ALMA, SMA, and JWST observing facilities.