The planar heterocyclic molecules 1,6,7,12-tetraazaperylene on a Ag(111) metal substrate show different charging characteristics depending on their local environment: next to vacancies in self-assembled islands, molecules can be charged by local electric fields, whereas their charge state is fixed otherwise. This enables the activation of selected molecules inside islands by vacancy creation from scanning-probe-based manipulation. This concept allows for combining the precise mutual atomic-scale alignment of molecules by self-assembly, on one hand, and the implementation of specific functionality into otherwise homogeneous monolayers, on the other. Activated molecules in the direct neighborhood influence each other in their charging characteristics, suggesting their use as molecular quantum cellular automata. Surprisingly, only very few interacting molecules exhibit a rich spectroscopic signature, which offers the prospect of implementing complex functionality in such structures in the future.