The physical evolution of low-mass protostars is relatively well-established, however, there are many open questions on the chemical structure of protostars. The chemical fingerprint generated in the early embedded phase of star formation may be transmitted to the later stages of star, planet and comet formation. The factors that influence the chemical fingerprint are then of interest to study, and determine whether the chemical structure is inherited from the parent cloud or product of the physical processes during star formation. Results of observations and modelling of molecules that trace the cold and warm extended structures of embedded protostars are briefly presented here. Two multiple protostellar systems are studied, IRAS 16293-2422 and VLA 1623-2417, both located in ρ Ophiuchus. We find that the physical structure of the protostars, that is the disk(-like) strucutres, outflow cavity and different luminosities, are important factors in determining the chemical structure of these embedded protostars.