Bioreactive semiconductor surfaces: preparation and characterization

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(Thesis) Ph.D.
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Bioreactive surfaces are seminal to the fabrication of semiconductor-based biochip devices. Their efficient preparation by the reaction of silicon with organic molecules, and the characterization of the formed monolayer films with spectroscopic and electrochemical techniques were the main objectives of the research described in this thesis. For the formation of a carboxy-terminated monolayer on silicon the conventional protocol consists of two steps: thermally or photochemically initiated reaction of an ester (CH2=CH(CH2)xCOOR) with hydrogen-terminated silicon (111) and subsequent hydrolysis. Vibrational sum frequency generation (SFG) spectroscopic studies have shown that the ester hydrolysis is incomplete and disrupts the molecular orientation of the monolayer structure. Searching for a more direct route to bioreactive silicon surfaces, the kinetics of photochemical reactions of silicon with various organic molecules were investigated. It was found that under UV irradiation, alkenes react much faster than alkanoic acids. Therefore, the reaction of bifunctional molecules can be controlled to preferentially attach the alkene terminus to the silicon surface. Such a one-step reaction eliminates the complications encountered during ester hydrolysis. Studies of DNA monolayers immobilized on silicon revealed that their molecular orientation depends on the DNA-cation affinity: during immobilization of single-stranded DNA, the perturbation of molecular orientation of the monolayer occurred in the order Mg2+ > Ca2+ > K+ ~ Na+, whereas, during hybridization, disruption of the monolayer occurred in the order K+ ~ Na+ > Mg2+ ~ Ca2+. A reliable metal contact on top of organically modified silicon is vital for solid-state electrical measurements. The thermal and sputtering metal deposition protocols have been assessed with SFG spectroscopy and by the electrical characterizations; the deposited gold penetrated and damaged the monolayers in both cases. Therefore, a device using a mercury drop electrode was designed and tested with the hydrogen terminated and the decane monolayer on silicon (111). The J-V curves proved that the mercury contact preserved the monolayer. Furthermore, the capabilities of the device to reveal electrical properties such as effective barrier height and ideality factor in relation to the molecular structures of ω-functionalized monolayers have been demonstrated. These findings are seminal to the future development of DNA-based molecular junctions.
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