One of the key challenges in chemistry is the ability to selectively break and form specific bonds in a complex organic molecule that possesses a range of different functional groups. The resulting knowledge provides a basis for the advancement of the molecular nanotechnology, where the key functionalities of the molecules are essentially determined by the functional groups attached. Here we used the scanning tunneling microscope (STM) to induce a sequence of targeted bond dissociation and formation steps in single thiol-based π-conjugated molecules adsorbed on a NiAl(110) surface (1).