Poly(dimethylsiloxane) (PDMS) and similar polymers have proved to be of widespread interest for use in microfluidic and similar microanalytical devices. Surface modification of PDMS is required to extend the range of applications for devices made of this polymer, however. Here we report on the grafting of perfluorooctyltriethoxysilane via hydrolysis onto an oxidized PDMS substrate in order to form a fluorinated microchannel. Such a fluorinated device could be used for separating fluorous tagged proteins or peptides, similar to that which has been recently demonstrated in a capillary electrophoresis system, or in an open tubular capillary column. The modified polymer is characterized using chemical force titrations, contact angle measurements and X-ray photoelectron spectroscopy (XPS). We also report on a novel means of performing electroosmotic measurements on this material to determine the surface zeta potential. As might be expected, contact angle and chemical force titration measurements indicate the fluorinated surface to be highly hydrophobic. XPS indicates that fluorocarbon groups segregate to the surface of the polymer over a period of days following the initial surface modification, presumably driven by a lower surface free energy. One of the most interesting results is the zeta potential measurements, which show that significant surface charge can be maintained across a wide range of pH on this modified polymer, sufficient to promote electroosmotic flow in a microfluidic chip. Matrix-assisted time of flight mass spectrometry (MALDI-TOF MS) measurements show that a fluorous-tagged peptide will selectively adsorb on the fluorinated PDMS in aqueous solution, demonstrating that the fluorinated polymer could be used in devices designed forenrichment or enhanced detection of fluorous-labeled proteins and peptides. However, the non-specific adsorption of other proteins may interfere with the test results. The adsorption of four different proteins (cytochrome-C, carbonic anhydrase, insulin and ubiquitin) onto the unmodified, oxidized and fluorinated PDMS surfaces respectively was studied here with MALDI-TOF MS measurements. The results showed us that when rinsed in water/methanol solutions of high methanol concentration, cytochrome-C strongly adheres to the fluorinated surface. Carbonic anhydrase shows the opposite trend. Retention of ubiquitin on the surface shows relatively little sensitivity to either the nature of the substrate or the solution composition. Finally, the results using insulin demonstrated that this protein adheres relatively strongly to the oxidized PDMS surface as compared to the fluorinated or unmodified PDMS and showed a relative independence on the composition of the washing solution. The influence of the hydrophilicity of the protein, the surface and solvents, stability and size of proteins are discussed in the context of these observations. / Thesis (Master, Chemistry) -- Queen's University, 2008-05-12 16:49:23.672