Self-Assembled Monolayers (SAM) on Au(111) are able to control the functionality of a gold surface. We use scanning tunnelling microscopy (STM) in air and contact angle measurements to compare the morphology and the chemistry of three alkylthiol SAMs differing by their tail groups: 1,9-nonanedithiol (NDT) and 1,4-butanedithiol (BDT) and 11-mercaptoundecanol (MUOH). STM reveals very different morphologies: hexagonal lattice for MUOH and parallel rows for NDT and BDT. In the case of NDT, we find that the thiol tail groups may form disulfide bridges for long immersion times. The availability of –SH group for chemical reactions is checked by attaching gold nanoparticles (AuNPs). When the thiol tail group is available, AuNPs readily attach as shown with atomic force microscopy (AFM). When disulfide bridges are formed the gold surface is not able to bind nanoparticles.