Structural characterization of self-assembled monolayers within molecular junctions: Effects of metallization and of substrate lateral confinement

The structure of the molecules within metal-organic-metal junctions (MOMs) fabricated via evaporation of a metal on a self-assembled monolayer (SAM), as well as the nature of the interface between the molecule and the metallic leads, can determine the electronic properties measured using these junctions. The effects that vapor deposition of a copper overlayer has on the conformation, degree of order and defect density of SAMs of both test molecules (alkanethiols) and of a prospective molecular wire (an oligo(phenylene-ethynylene), OPE) were investigated. A combination of electrochemistry, FTIR, XPS and Ion Scattering Spectroscopy was used. Results indicate that molecular conformation, orientation and monolayer order, change upon metal evaporation. Therefore, probing the conductivity of SAMs within MOMS is not necessarily equivalent to probing their conductivity prior to the formation of the second metallic contact. The nature of the SAM/Cu interface was also investigated, determining that copper tends to diffuse throughout the thickness of the monolayer over time, and that chemical interactions can take place between copper atoms and the terminal groups of molecular wires.; We also report on the fabrication of gold nanowell electrode ensembles that were used to determine the density of defects found in SAMs assembled on substrates whose lateral dimensions are confined to the few hundred nanometer range. SAMs of dodecanethiol (DT) and OPE were characterized via metal decoration on polished gold macro- and nanoelectrodes (200 nm diameter). It was found that whereas OPE SAMs display a comparable number of defects on both macro- and nanoelectrodes, DT SAMs are more defective on nanoelectrodes.; The second part of this thesis describes results obtained for two additional research projects. First, an investigation toward the development of an enzymatic assay for detection of native DNA nucleotides is reported. Second, the design of an aerosol deposition system for calcium carbonate particles a few hundred of nanometers in size.; The last part concerns the development of experiments for the Physical Chemistry Laboratory: first, the use of infrared spectroscopy of CO2 to illustrate Pauli's principle, and, second, the use of vibrational spectroscopy to estimate the dissociation energy of the C-H bond in chloroform.