This dissertation concerns numerical simulations of electronic properties (ESR and UV/Vis absorption) of molecules embedded in non-covalently bound environments (hydrogen-bonded clusters and mimics of protein active centers). The applied simulation methods are based on Frozen-Density Embedding Theory (FDET) and involve additional approximations concerning the choice of the frozen density and more technical factors. The applicability of these approximations was studied in view of the investigated spectroscopic properties. The simulations led to the demonstration that the observed cooperativity in the spectral shifts of 7-cis-hydroxyquinoline in hydrogen-bonded clusters, originate from mutual electronic induction of the molecules in the environment rather than from structural rearrangements in the environment. Concerning methodological developments, the computational protocols were developed for FDET calculations, which were shown to lead to equivalent results to the ones obtained form more costly conventional calculations: a) high-end wave-function based methods in the case of spectral shifts and b) conventional Kohn-Sham calculations in the case of ESR parameters. The developed and tested computational protocols are to be used in the future large-scale calculations.