The self-assembly of long-alkyl-chain substituted phenanthroline derivatives on highly oriented pyrolitic graphite (HOPG) and gold(111) is compared. Whereas the adsorption on HOPG is controlled by the affinity of alkyl chains for the substrate, which leads to flat-lying adsorbed molecules, alignments of upright-oriented molecules are formed on gold(111). This situation is explained by the bonding of chelating species with gold(111) surfaces and by the pi-stacking interaction between conjugated moieties. This intermediate situation between strong thiol-like chemical bonding and the weak n-alkane-like physical adsorption opens the route toward laterally organized functional molecular assemblies.