Mixed-quantum classical dynamics simulations have recently become an important tool for investigations of time-dependent properties of electronically excited molecules, including non-adiabatic effects occurring during internal conversion processes. The high computational costs involved in such simulations have often led to simulation of model compounds instead of the full biochemical system. This chapter reviews recent dynamics results obtained for models of three classes of biologically relevant systems: protonated Schiff base chains as models for the chromophore of rhodopsin proteins; nucleobases and heteroaromatic rings as models for UV-excited nucleic acids; and formamide as a model for photoexcited peptide bonds.