We investigate the electronic structure of molecular model systems in order to improve our understanding of the nature of the contrast, which is observed in the scanning tunneling microscopy (STM) imaging of organic adsorbates on graphite. The model systems consist of a benzene molecule, representing the substrate surface, interacting with various molecules representing alkyl chains, oxygen- and sulfur-containing groups, fluorinated species, and aromatic rings. We perform quantum-chemical calculations to determine the geometric structure, stability, and electronic structure of these molecular complexes and analyze the theoretical results in relation with experimental STM data obtained on monolayers physisorbed on graphite. It appears that the STM contrast can be correlated to the energy difference between the electronic levels of the substrate and those of the adsorbate. Finally, we observe that the introduction of a uniform electric field in the quantum-chemical modeling can enhance the electronic interaction between the partners in the complex.