The optical and electronic properties of atomically thin materials such as single-walled carbon nanotubes and graphene are sensitively influenced by substrates, the degree of aggregation, and the chemical environment. However, it has been experimentally challenging to determine the origin and quantify these effects. Here we use time-dependent density-functional-theory calculations to simulate these properties for well-defined molecular systems. We investigate a series of core-shell structures containing C60 enclosed in progressively larger carbon shells and their perhydrogenated or perfluorinated derivatives. Our calculations reveal strong electronic coupling effects that depend sensitively on the interparticle distance and on the surface chemistry. In many of these systems we predict considerable orbital mixing and charge transfer between the C60 core and the enclosing shell. We predict that chemical functionalization of the shell can modulate the electronic coupling to the point where the core and shell are completely decoupled into two electronically independent chemical systems. Additionally, we predict that the C60 core will oscillate within the confining shell, at a frequency directly related to the strength of the electronic coupling. This low-frequency motion should be experimentally detectable in the IR region.