Understanding the behaviour of molecules on a semiconductor surface is necessary if molecular self-assembly is going to be employed, with existing semiconductor technology, to create useful devices. Si(111)-7x7 is an invaluable surface upon which to study molecular adsorption. The surface reconstruction has been well characterized and it possesses seven symmetrically distinct dangling bonds that can serve as reaction sites. Aromatic molecules on Si(111)-7x7 have been investigated with a variety of techniques and have been shown to chemisorb at room temperature. However, it is not trivial to predict how an ensemble of aromatic molecules might distribute themselves amongst the available bonding sites on this surface. The work presented in this thesis begins with a joint STM and ab initio investigation of thiophene on 7x7 that demonstrates kinetics are necessary to describe the chemisorption sites occupied at various coverages. A kinetic Monte Carlo model, taking into account a mobile physisorbed state, is shown to accurately describe this site occupancy at room temperature. This model disregards molecule-molecule interaction because thiophene does not sterically hinder chemisorption to a neighbouring dangling bond. A larger molecule, mesitylene, was then studied on Si(111)-7x7, and shown to form an ordered molecular lattice on the Si(111)-7x7 surface. This is the first demonstration of a porous molecular lattice grown on Si(111)-7x7 at room temperature. Finally, molecular chemisorption on the related 5x5 reconstruction, grown by depositing Ge on 7x7, is studied. It is found that the presence of Ge hinders molecular chemisorption, preventing formation of the mesitylene lattice. / Thesis (Ph.D, Physics, Engineering Physics and Astronomy) -- Queen's University, 2009-09-11 10:14:10.118