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The incorporation of photopolymerizable diacetylene structures within spontaneously organized monolayers has facilitated the fabrication of robust interfacial assemblies with covalent molecular scaffolding. Through selective ultraviolet-induced polymerization, the resulting polydiacetylene monolayers permit precise structural control in the lateral domain through phototemplating. Results presented in this article demonstrate that these unique monolayer polymers also allow control of the vertical domain within the monolayer through variation of the conjugated polymer backbone position along the length of the alkyl chains. Small variations in the vertical position of the diacetylene groups of less than a nanometer are found to have a profound impact on both polymerization efficiency and the resulting conjugation length of the polymer interface. Furthermore, the relative position of this polymer backbone within the alkyl chains can be utilized to manipulate the overall properties of the assembly such as the long- and short-range order. In this article, spectroscopic and electrochemical techniques are utilized to demonstrate the range of interfacial environments obtainable with these unique polymer monolayers. These advances are currently being utilized to create robust assemblies with three-dimensional control of the physical and chemical properties on a micro- to nanometer scale. © 1999 American Vacuum Society.