Planets form in disks around young stars and the structures and compositions of these protoplanetary disks should shape the planet formation process. Small molecules provide exquisite probes of key disk characteristics that are inaccessible through other means, including kinematics, ionization levels, and the location of snowlines. Some of these molecules are also important in their own right, as tracers of the prebiotic evolution present during planet formation. I will discuss our latest results on how spatially resolved millimeter observations of molecular emission, interpreted in the light astrochemical models and recent laboratory results, are shaping our understanding of protoplanetary disk structures and chemistry.