Abstract
Many astronomical phenomena are conveniently explored through observations of molecular line emission. In this paper, we discuss the chemistry that gives rise to molecular tracers in two scenarios associated with the interaction of stellar jets with molecular clouds. The first situation is the environment of the bow shock near the head of a jet entering a molecular cloud. The second is the case of a clump within a molecular cloud that is affected by the intense radiation field generated in the jet/cloud shock. In both cases, specific molecular tracers of the physical conditions can be identified.
