By tailoring the molecule-substrate interaction, we are able to control the dynamics and the structure of self-assembled monolayers (SAMs), which can dramatically change the physical, chemical, and electronic properties of the underlying substrate. In this dissertation, the interaction of thiophenol and its halogen substituted derivatives with a Cu(111) surface has been studied with a combination of temperature programmed desorption (TPD) and scanning tunneling microscopy (STM) in order to control the structure of SAM's by fine tuning of molecule-substrate interactions. Meanwhile, the diffusion mechanism of well-designed molecular-scale machinery are reported. In addition, the development of several instruments for surface analysis is described. |