The present thesis deals with two main topics. First, I study in detail the interaction of a delocalized molecular matter-wave with a standing-wave laser grating. Due to absorption of photons in an optical grating, molecules can get excited and numerous internal photophysical processes are induced. For the theoretical description of the molecule-light interaction I take three relevant internal molecular processes into account: intersystem crossing, fluorescence and internal conversion. Furthermore, the fact that molecules can change their optical properties because of the photoexcitation is shown to have a measurable effect on matter-wave interferometry. The second topic of this thesis is about collisions between a polar molecule and non-polar environmental gas atoms, and their effects on the coherence of the center-of-mass state. Because the scattering potential depends on the molecular orientation the molecular rotational state must also be considered. Assuming a slow rotation of the molecule compared to the scattering time and that the molecular mass fairly exceeds the mass of a gas atom, I present a master equation of collisional decoherence, which depends on the molecular orientation. Its predictions for matter-wave interferometry are discussed both in the near and far field.