<p>The first part of this study details the formation and characterization of octadecanethiol (ODT) self-assembled monolayers (SAMs) on GaAs (100) substrates from solution and vapor phases. The liquid-phase-deposited monolayers were prepared by immersing the substrate in an ethanolic solution, while vapor-deposited monolayers were prepared by the vapor phase transport of ODT in an ultrahigh vacuum (UHV) environment. The structural and optical properties of the resulting SAMs were examined with contact angle (CA) analysis, photoluminescence (PL) spectroscopy, atomic force microscopy (AFM), high-resolution x-ray photoelectron spectroscopy (HRXPS), and spectroscopic ellipsometry. Although well-ordered films were formed by both preparation routes, PL, AFM, CA analysis, HRXPS, and ellipsometry measurements revealed that the overall quality, structure, and durability of the mono layers depend on the deposition technique. Collectively, the results suggested that more robust monolayers exhibiting greater surface coverage and therefore, increased passivation and stability characteristics are assembled from vapor phase. </P> <P> The second part of this work describes the development of a hybrid GaAsaptamer biosensor for the label-free detection of analytes. The implemented sensmg strategy relies on the use of functional alkanethiol SAMs as biorecognition elements as well as the sensitivity of the GaAs PL emission to the local environment at its surface. Specifically, GaAs substrates were modified with thiol-derivatized aptamers and exposed to the target biomolecules. The resulting modification in the PL intensity is attributed to a specific aptamer-target biorecognition interaction and the accompanying ligand-induced structural change in the aptamer conformation. Modeling the performance data by means of Poisson-Boltzmann statistics in combination with the dead layer model indicates a good correlation between the structural conformation of the aptamers and the GaAs PL yield. The results demonstrate the potential of the prospective luminescence-based GaAs-SAM biosensor in real-time sensing assays requiring a simple and effective means of direct analytical detection. </p> / Thesis / Doctor of Philosophy (PhD)

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Self-assembled monolayers (SAMs) were investigated with regard to their application as templates to control processes down to the nanometre length scale. With applications of SAM for electrochemical nanotechnology in mind, the range of aspects studied comprises patterning on different length scales, behaviour of SAMs under the conditions of electrochemical metal deposition, and the influence of the head and tail groups on formation and structure of SAMs. On a micrometre scale, laser scanning lithography (LSL) was used to pattern SAM covered Au surfaces. With this technique, localized regions of a SAM are desorbed by scanning the focal spot of a laser beam. Thermal desorption occurs as a result of the high substrate temperature produced by the laser pulses. Patterns with line width as small as 0.9 µm were produced by LSL. It is demonstrated that SAM can not only be patterned by laser radiation but can also be rendered more passive as revealed by electrochemical metal deposition. Such blocking effect is explained by annealing of defects upon irradiation at the appropriate laser energy. This effect can block deposition of bulk copper particles, but does not prevent the underpotential deposition. Based on this passivation effect, large passivation areas can be created, which can be used as substrate for further nano/micro fabrication. The combination of SAM patterning and electrochemical metal deposition was also demonstrated to be an effective way to prepare superhydrophobic surfaces, exhibiting a contact angle of 165° (water droplet). Aiming for the generation of smaller structures, scanning tunneling microscopy (STM) is used as a tool to pattern SAMs. Several phenomena observed in STM based manipulation of SAMs are addressed. The first one is sweeping effect. Deposited metal particles on top of SAM and SAMs are swept by STM tip by choosing appropriate I/V parameters. The closer the tip (higher current, lower bias), the more effective it is. Molecularly resolved images confirm that after sweeping, the scanned area is still covered by SAM molecules. This is explained by diffusion. The sweeping process can be repeated, thus, resulting in a layer by layer etching. The second effect is field-induced desorption. Applying a positive voltage (2.5-5V), a SAM is damaged beneath the area of the tip. The damage depends not only on the bias applied, but also on the current setpoint right before applying the bias. The third effect is nanografting. Nanografting was observed that a SAM having a stronger assembling ability can replace the weaker one (matrix layer) in hexadecane solution by STM scanning under normal I/V parameters combination that are usually used for imaging. It is found that longer chain can replace the shorter chain thiol, alkanethiol can replace biphenyl thiol. This method can be applied to pattern SAM. Defects (punched holes) were created purposely on the SAMs covered Au surface and in situ STM was used to investigate the process of Under-Potential Deposition (UPD) and bulk metal deposition. Bulk metal deposition on punched holes depends on the size. Small scale patterning by punching is sufficient for applications based on UPD but not for bulk metal deposition. Several SAMs assembled on Au(111) surface (1-mercaptoundecanoic acid (MUA), Dodecyl Thiocyanate (C12SCN) and bis(pyrazol-1-yl)pyridine-substituted thiol (bpp-SH) and thiocyanate (bpp-SCN)) were investigated with the aim to expand the type of SAMs that can be used as template for further application, such as metal coordination. High quality thiolate monolayers formed by cleavage of the S-CN bond can be obtained on Au(111). Thus, organothiocyanates appear to be a promising alternative to thiols. Well-ordered MUA monolayers are formed in a few hours at the temperature range of 323-363 K by Physical Vapour Deposition (PVD). Self-assembled monolayers of bpp-SH and bpp-SCN on Au(111)/mica were studied with STM. Preparation conditions such as temperature, solvent, and contamination affect the formation of SAMs on Au(111) much more than other common thiols such as alkanethiols and biphenythiols.

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The formation of a functional surfaces combines the properties of a substrate and monolayer to produce a new hybrid that can combine aspects of each. Monolayers can be made on many surfaces, and well defined functionalized monolayers were assembled on for silicon(111) and polydicyclopentadiene (PDCPD). Acid terminated monolayers were assembled on silicon(111) and their functionalization chemistry explored. It was shown that using trifluoroacetic anhydride to generate an intermediate reactive anhydride, the surface could be functionalized with amines. It was further shown that using soft lithography these functionalized surfaces could be patterned. Mixed monolayers of methyl and olefin terminated surfaces on silicon(111) were used to develop a new soft lithographic technique with polydimethylsiloxane (PDMS). PDMS can be controllably etched using fluoride species. The surface is first activated by the attachment of the Grubbs' 1st generation catalyst. A PDMS microfluidic device is then placed on the surface. By using a cross metathesis reaction, the exposed channel can be pacified. The next step, a fluoride etchant is used to remove PDMS, exposing an unreacted surface. Polymer brushes were then grown by ring opening metathesis polymerization (ROMP) in this region. Functionalization of the emerging polymer PDCPD was conducted through two different routes. ROMP formed PDCPD has double bonds that can be functionalized. In the first process, the double bonds were reacted with bromine. This is a rapid reaction and proceeds to a significant depth in the material. Bromines can then be displaced with amines in a substitution reaction. This was demonstrated with a fluorinated amine that when examined by XPS were shown to be present only at the surface, further more we were able to pattern this surface too. Secondly, a process using epoxides was developed. The epoxidation reaction could not be quantified, but formation in the second step of an amine functionalized surfaces was observed by XPS. Further reaction of surface hydroxyls was also observed. This was also used to grow polyethylimine from the surface to sufficient thickness that it became observable by infrared spectroscopy.

The field of organic-based opto-electronic devices such as organic light- emitting diodes (OLEDs) or field-effect transistors (OFETs) has grown in interest over the past two decades. Optimizing the performance of these applications requires a better understanding of the processes taking place inside the devices and especially at their interfaces. We focused in this Ph.D. work on the electronic structure of metal/organic interfaces where the charge injection mechanism occurs. The latter process can be modulated and fine tuned by the control of the work function of the metallic electrodes. Chemisorption of self-assembled monolayers (SAMs), i.e., a two-dimensional layer of polar molecules deposited onto metal surfaces proves to be an efficient way to tune the work function of electrodes in OLED and OFET devices. However, the role played by the dipole moment of the adsorbed molecules as well as the description of the electronic effects taking place at the metal/SAM interfaces are not yet well understood. Our Ph.D. work aims at rationalizing at a theoretical level (via quantum- chemical calculations) the electronic processes occurring at metal/organic interfaces. For this goal, we focused our investigations on a well-characterized system : a methanethiolated SAM on gold-(111) surface. The adsorption energy and the influence of the anchoring site on the work function shift were evaluated beforehand in order to validate our methodology. The decomposition of the interfacial dipole moment into its interfacial and molecular components was assessed in a second stage for this system following two different procedures which differ by the treatment of the molecular backbone. The incorporation of a third component, generally not treated in an explicit way, was taken into consideration to unify the description of the interface dipole. The influence of the packing density was also described. In a next step, we have extended this study by changing the SAM chemical structure and by investigating the influence of a modification of the anchoring atom, a fluorination of the methyl group and a change in the nature of the metal surface (Ag, Cu, Pt). In order to probe the influence of intermolecular interactions, we have finally considered longer alkanethiol chains having various terminal chemical functions and analyzed the influence of the structural geometry on the change in the electrostatic potential.

Calamitic (rod-shaped) and discotic (disc-shaped) thermotropic liquid crystalline (LC) compounds were spread at the air-water interface, and their ability to form monolayers was studied. The calamitic LCs investigated were found to form monolayers which behave analogously to conventional amphiphiles such as fatty acids. The spreading of the discotic LCs produced monolayers as well, but with a behaviour different from classical amphiphiles. The areas occupied per molecule are too small to allow the contact of all hydrophilic groups with the water surface and the packing of all hydrophobic chains. Various molecular arrangements of the discotics at the water surface to fit the spreading data are discussed.

Understanding electron-transfer (ET) processes in proteins is of fundamental importance. In a series of photophysical studies of well-behaved peptide model systems, it has become evident that the ET through peptide spacers is greatly influenced by the separation between the acceptor (A) and the donor (D), the nature of the peptide backbone, the amino acid sequence, and the resulting flexibility of the peptide conjugates. In particular, it was suggested in the literature that the presence of H-bonding will increase the rate of ET, and there is experimental evidence, mostly in proteins, to suggest that H-bonding indeed increases the rate of ET.<p>My aim was to develop a potential-assisted deposition method for ferrocene peptide disulfides onto gold surfaces and investigate the electrochemical properties of these films. We made use of two classes of Fc-peptides: acylic ferrocenoyl (Fc)-peptide disulfides and cyclo-1,1-Fc-peptide disulfides, allowing the preparation of tightly packed films of cyclic and acylic Fc-peptides on gold surfaces within 30 minutes. This is a significant benefit compared to the conventional soaking method of self-assembly requiring several days for the assembly of well-packed films. Such films exhibited considerably improved stability. This electrodeposition method should find wide-spread applications for the formation of tightly-packed films from disulfides. Our studies allowed a direct comparison of the electron transfer kinetics of cyclic and acyclic Fc-peptide disulfide systems. Our results showed faster ET kinetics for films prepared from cyclic Fc-peptide conjugates compared to the acyclic systems, presumably as a result of the enhanced rigidity of the Fc-peptide conjugates on the surface and/or an increase of the number of conductive peptide wires to the surface. Following the idea of peptide dynamics as a major contributor to the observed electron transfer rate in peptides and peptide conjugates, variable temperature electrochemical studies of Fc-peptide films were performed. An estimation of the reorganization energy associated with ferrocene/ferrocenium (Fc/Fc+) redox process allowed us to probe the role of peptide dynamics. Three counter-ions were tested, exhibiting different strengths of association with the Fc+ group (BF4- < ClO4- < PF6-) and the reorganization energies were evaluated in each case. The highest reorganization energy was obtained for the weakly interacting anion BF4-. Weakly interacting anions also showed significant broadness in the redox peaks and emergence of the second oxidation peak which is attributed to phase separation of the ferrocene group. Ferrocene agglomeration was not observed for any of the cyclic Fc-peptide conjugates but occurred for some of the acyclic systems. In particular, for acyclic Val and Leu containing Fc-peptide conjugates agglomeration were observed and was presumably caused by lateral interactions between the hydrophobic side-groups of the peptides. Further experiments involving the interaction of Fc-peptide films with alkali metal ions gave additional evidence that electron transfer is influenced significantly by peptide dynamics.