Understanding mechanisms at the molecular level is essential for interpreting and predicting the outcome of processes in all fields of chemistry. Insight into gas-surface reaction dynamics can be gained through molecular beam scattering experiments combined with classical trajectory simulations. In particular, energy exchange and thermal accommodation in the initial collision, the first step in most chemical reactions, can be probed with these experimental and computational tools. There are many questions regarding the dynamic details that occur during the interaction time between gas molecules and organic surfaces. For example, how does interfacial structure and density affect energy transfer? What roles do intramonolayer forces and chemical identity play in the dynamics? We have approached these questions by scattering high-energy, rare gas atoms from functionalized self-assembled monolayers. We used classical trajectory simulations to investigate the atomic-level details of the scattering dynamics. We find that approximately six to ten carbon atoms are involved in impulsive collision events, which is dependent on the packing density of the alkyl chains. Moreover, the higher the packing density of the alkyl chains, the less energy is transferred to the surface on average and the less often the incident atoms come into thermal equilibrium with the surface. In addition to the purely hydrocarbon monolayers, organic surfaces with lateral hydrogen-bonding networks create more rigid collision partners than surfaces with smaller inter-chain forces, such as van der Waals forces. Finally, we find some interesting properties for organic surfaces that possess fluorinated groups. For argon scattering, energy transfer decreases with an increasing amount of surface fluorination, whereas krypton and xenon scattering transfer most energy to monolayers terminated in CF₃ groups, followed by purely hydrocarbon surfaces, and then perfluorinated surfaces. / Ph. D.

This study describes the covalent and the electrostatic attachment of molecules, nano-particles, and proteins to patterned self-assembled monolayers. A scanning probe nanografting technique was employed to produce patterns of various sizes, down to 10 nm. Thus, we are able to demonstrate a degree of surface patterning which is an order of magnitude smaller than that used in the semiconductor industry. One efficient strategy for creating chemically specific nanostructures is to use the extraordinary catalytic properties of enzymes. However, as the dimension of a catalyst patch is reduced down to nanometer scale, it is difficult to detect the very low concentration of product. This study resolves the problem by developing a new strategy: the surface trapping of a product generated by a nanometer-scale patch of surface-bound enzyme. An array of proteins finds use when the array contains a number of different proteins. Toward this end, a new and convenient method for immobilizing enzymes is developed, which will allow the preparation of thin films containing several different catalytically-active enzymes on the nanoscale. The disadvantage of scanning probe nanografting technique is that the AFM tip loses resolution through wear during the patterning procedure. This study examines the possibility of developing a new AFM lithographic method to avoid wear: the use of enzymes covalently attached to a tip as a site-specific catalyst. / Ph. D.

The structure/function relationship between bacteria and biocidal molecules in the vapor or solution phase is well-understood. However, the fundamental structure/function relationship between covalently-bound biocidal surface molecules and bacteria is not. While a number of antibacterial surfaces have been reported, detailed analysis of the molecular scale surface structure has not been performed. The lack of structural knowledge makes it difficult to determine how alterations to the surface affect the viability of the bacteria. Most of the antibacterial surfaces reported to date are composed of polymer systems. Controlling the properties of large surface-bound molecules like polymers is difficult. Self-assembled monolayers, or SAMs, of alkanethiols on gold have been used extensively in the past 20 years as model surfaces for investigation of a large breadth of surface phenomena. SAMs allow for control of the molecular scale surface structure and are amenable to a great number of characterization techniques. The primary objective of the work in this study is to establish the use of SAMs as a tool to investigate the fundamental relationship between surface structure and bacteria viability. The surfaces were characterized before interaction with bacteria by reflection-absorption infrared spectroscopy (RAIRS) and X-ray photoelectron spectroscopy (XPS). Determination of the viability of Escherichia coli on the surfaces was performed via the antibacterial assay. In the assay, a culture of E. coli was sprayed onto the surfaces using a chromatography sprayer. After addition of growth agar and overnight incubation, the number of colony forming units on the surface were counted. Statistical analyses were performed to compare the number of colony forming units on different surfaces. Surfaces were characterized after the assay by RAIRS. The RAIR spectra indicated that no significant change to the well-ordered alkane chain configuration was evident. The structural stability shown by the SAMs will allow for their use in future studies to determine fundamental relationship between surface structure and bacteria viability. / Master of Science

This thesis presents applications of the layer-by-layer (LbL) assembly technique in fabrication of thin films with a primary focus on design and development of electrochromic devices. The optical properties of electrochromic materials change as they alter between redox states. The morphology and properties of LbL-assembled thin films can be modified by varying several processing factors such as dipping duration, ion type, ion concentration, pH, molecular weight, and ionic strength. In the present work, several factors of LbL assembly process were manipulated to tailor electrochromic thin films of desired attributes. An electrochromic device (ECD) with fast optical switching speed was designed and constructed based on poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS). This device exhibited optical switching speeds of 31 and 6 ms for coloration and decoloration respectively, on a 60 mm2 area. Poly(aniline 2-sulfonic acid) (PASA) is a relatively new ionic polymer, and its electrochromic properties have not been previously investigated in much detail. PASA thin film showed several redox states corresponding to color changes from dark blue to gray as it passed different redox states. One particularly interesting and promising design for ECDs is dual electrochrome. Dual electrochrome ECDs based on PANI and polyaniline (PASA) are investigated in this thesis. The PANI/PASA thin film showed superior spectroelectrochemical properties compare to other ECDs reported here or elsewhere. An electrode with single wall carbon nanotubes (SWCNTs) coating was tested as the substrate for an ECD based on poly[2-(3-thienyl) ethoxy-4-butylsulfonate] (PTEBS) to examine performance of the electrochromic polymer on a substrate other than an indium tin oxide (ITO) electrode. Compared to ITO, the SWCNT based device exhibited superior properties. / Master of Science

Interactions of gas-phase molecules with surfaces are important in many ordinary events, such as ozone depletion, corrosion of metals, and heterogeneous catalysis. These processes are controlled by the bonding, diffusion, and reactivity of the impinging gas species. Our research employs molecular beam techniques and well-characterized surfaces to study these processes. The goal of this study is to better understand how the physical and chemical nature of the surface interface influences energy transfer dynamics in gas-surface collisions. An atomic beam is used to probe the energy transfer dynamics in collisions of Argon with model surfaces of functionalized self-assembled monolayers (SAMs) (1-dodecanethiol and 11-mercapto-1-undecanol) on gold. The beam is directed towards the surface at an incident angle of 30 degrees and the scattered Ar atoms are detected at the specular angle of 30 degrees. Time-of-flight scans measure the velocity distributions of atoms leaving the surface, which correlate with the energy transfer dynamics of the impinging gas atoms. Gas-surface energy transfer experiments are accomplished by directing an 80 kJ/mol Ar atomic beam at a clean Au(111) surface and surfaces composed of hydroxyl-terminated or methyl-terminated SAMs on Au(111). The fractional energy transferred to the bare gold surface is 69 %, while it is grater than 77 % for the monolayer-covered surfaces. The extent of thermalization on the surface during the collision is significantly greater for the methyl-terminated surface than for the hydroxyl-terminated surface. Since the two monolayers are similar in structure, packing density, and mass, the differences in scattering dynamics are likely due to a combination of factors that may include differences in the available energy modes between the two terminal groups and the hydrogen-bonding nature of the hydroxyl-terminated SAM. / Master of Science

4-(12-mercaptododecyloxy)phenol (1), 3-(12-mercaptododecyloxy)phenol (2), 4-(12-mercaptododecyl)phenol (3), 4-(12-mercapto-dodecyl)phenol (4), 12-phenyldodecyl-mercaptan (5), 12-phenylundecyoxymercaptan (6), 4-(6-mercapto-hexyl)phenol (7), and 4-(12-mercaptododecyloxy)phenol (8) were synthesized. The thiol products were characterized by NMR, HRMS, and elemental analysis. Self-assembled monolayers (SAMs) on gold substrates were prepared from thiols 1-8, and the resulting monolayer surfaces were analyzed using Reflectance Absorbance Infrared Spectroscopy (RAIRS), contact angle goniometry, ellipsometry, reductive desorption cyclic voltametry, and impedance spectroscopy. Several aromatic C-C vibrational frequencies in the RAIRS spectra, for SAMs of 1-8, reveal a dependence of peak intensity on substitution regiochemistry of the aromatic ring. This result suggests that the orientation of the aromatic ring changes with substitution. Peak intensity, and peak widths of alkyl C-H vibrational features in the RAIRS spectra also reveal a dependence of the environment of the alkyl chain on structure of thiols 1-8. Meta-substitution seems to significantly alter the projection of the terminal -OH group relative to para-substitution. Contact angles were obtained for each SAM surface using water, glycerol, and ethylene glycol. From the contact angle data, Zisman and Fowkes analyses were performed in order to determine surface free energy values and also to determine the dispersive contribution to the surface energy. The energy values obtained from the Zisman plots as well as the dispersive contributions obtained from the Fowkes plots suggest a dependence of surface energy on substitution regiochemistry of the aromatic ring. The results are consistent with the interpretation of the RAIRS spectra as they relate to the effect substitution regiochemistry has on SAM structure and interfacial properties. The results of the reductive desorption measurements performed on each monolayer surface, indicate that changes in substitution regiochemistry do not seem to affect the surface coverage of SAMs 1-8. Desorption potentials however, are affected by the structure of the thiols composing the SAM, which suggests that the lateral stability resulting from interactions of the terminal groups and alkyl chains, is different for each monolayer surface. Specifically SAMs of 12-phenyldodecylmercaptan (5) and SAMs of 4-(12-mercaptododecyloxy)phenol (1) seem to be more stable due to interactions of the terminal aromatic ring in SAMs of (5) and due to an increase in van der Waals interactions in SAMs of (1). Film thicknesses, as determined by ellipsometry, also suggest that meta-substitution of the aromatic ring results in lower thicknesses for SAMs of (4), which is consistent with the interpretation of the structural changes resulting from meta-substitution, suggested by the interpretation of the RAIRS spectrum of SAMs of (4). Thickness measurements also indicate that most of the functionalized SAMs (1-4, 7, 8) react with OTS, which suggests the terminal -OH group is not shielded at the interface and is available for reaction. Following reaction with OTS the RAIRS spectra of the reacted surfaces reveal structural changes to the underlying SAM. Impedance spectroscopic measurements performed on SAMs of 1-8 reveal what seems to be a correlation between the orientation of the aromatic ring and the resistance properties of the SAM. It appears meta-substitution of the ring lowers the monolayers ability to resist electron transfer. These data suggest that meta-substitution of the aromatic ring has a significant impact upon the structure of the resulting monolayer relative to monolayers composed of para-substituted molecules. The data also suggests that there is a correlation between molecular structure and interfacial properties particularly as it relates to surface energy and reactivity. Small atomic changes in the molecules composing the SAM result in measurable differences in macroscopic properties of the interface. It is important to recognize the need for understanding structure-property relationships in self-assembled monolayers particularly if logical design of surfaces is to be achieved and applied towards solving problems associated with corrosion and adhesion of metal surfaces. / Ph. D.

Polarizers and polarization devices are important components in fiber optic communication and sensor systems. There is a growing need for efficient low loss components that are compatible with optical fibers. An all fiber in-line polarizer is a more desirable alternative that could be placed at appropriate intervals along communication links. An in-line fiber polarizer was fabricated and tested. The in-line fiber polarizer operates by coupling optical energy propagating in the fiber to a surface plasmon on a metallic film, which has been deposited onto the surface of the fiber. The device was constructed by polishing a short section of the lateral surface of the cladding to within the evanescent field present around the fiber core. Several thin films including a metal film are applied to the polished section of the fiber. Ionic self-assembled monolayer method was used to coat the polished fiber with thin film. / Master of Science

Adsorption of xyloglucan (XG) onto thin desulfated nanocrystalline cellulose (DNC) films was studied by surface plasmon resonance spectroscopy (SPR), quartz crystal microbalance with dissipation monitoring (QCM-D), and atomic force microscopy (AFM) measurements. These studies were compared to adsorption studies of XG onto thin sulfated nanocrystalline cellulose (SNC) films and regenerated cellulose (RC) films performed by others. Collectively, these studies show the accessible surface area is the key factor for the differences in surface concentrations observed for XG adsorbed onto the three cellulose surfaces. XG penetrated into the porous nanocrystalline cellulose films. In contrast, XG was confined to the surfaces of the smooth, non-porous RC films. Surprisingly surface charge and cellulose morphology played a limited role on XG adsorption. The effect of the non-ionic surfactant Tween 80 on the adsorption of cellulase onto alkane thiol self-assembled monolayers (SAMs) on gold was also studied. Methyl (-CH3), hydroxyl (-OH) and carboxyl (-COOH) terminated SAMs were prepared. Adsorption of cellulase onto untreated and Tween 80-treated SAMs were monitored by SPR, QCM-D and AFM. The results indicated cellulase adsorption onto SAM-CH3 and SAM-COOH were driven by strong hydrophobic and electrostatic interactions, however, hydrogen bonding between cellulase and SAM-OH was weak. Tween 80 effectively hindered the adsorption of cellulase onto hydrophobic SAM-CH3 substrates. In contrast, it had almost no effect on the adsorption of cellulase onto SAM-OH and SAM-COOH substrates because of its reversible adsorption on these substrates. / Master of Science

The compounds 12-phenoxy-dodecane-1-thiol, 4-dodecyloxymercaptophenol and 3-dodecyloxymercaptophenol have been synthesized using a novel synthesis to investigate the effect that the orientation of the functional group has on surface acidity. 3-dodeycloxymercaptophenol and 4-dodecyloxymercaptophenol differ in that the hydroxyl group is substituted on different carbons of the benzene ring. The difference in substitution patterns should present the hydroxyl group in different orientations in the interface between a self-assembled monolayer of the compound and aqueous solutions buffered over a pH range of 3-13. By preparing self-assembled monolayers of these molecules on gold substrates, the ability of the hydroxyl group to donate its proton was shown to depend on the hydroxyl group substitution pattern on the benzene ring through contact angle titration experiments. 3-dodecyloxymercaptophenol clearly showed plateaus at low and high pH with a broad transition between the two plateaus. 4-dodecyloxymercaptophenol showed a clear plateau at low pH but not at high pH, although a transition was observed. Using infrared spectroscopy, it was further shown that the long molecular axis of the benzene ring in 3-dodecyloxymercaptophenol was tilted from the surface normal by 55°. The short molecular axis of the ring was twisted out of the plane of the surface by 28° for self-assembled monolayers of this molecule on gold substrates. In contrast, the tilt angle of 4-dodecyloxymercatophenol was measured to be 46° and was twisted out of the surface plane by 36°. It was also found from cyclic voltammetry experiments in 0.5 M KOH, that the ionized monolayers of 4-dodecyloxymercaptophenol were 2.3 kJ/mol less stable than monolayers of 3-dodecyloxymercaptophenols. This finding suggests that hydrogen bonding and other intermolecular interactions in 4-dodecyloxymercaptophenol are greater than in 3-dodecyloxymercaptophenol. / Ph. D.

The surface of biomaterials can induce contacting blood to coagulate, similar to the response initiated by injured blood vessels to control blood loss. This poses a challenge to the use of biomaterials as the resulting coagulation can impair the performance of hemocompatible devices such as catheters, vascular stents and various extracorporeal tubings [1], what can moreover cause severe host reactions like embolism and infarction. Biomaterial induced coagulation processes limit the therapeutic use of medical products, what motivates the need for a better understanding of the basic mechanisms leading to this bio-incompatibility [2] in order to define modification strategies towards improved biomaterials [3]. Several approaches for the enhancement of hemocompatible surfaces include passive and active strategies for surface modifications. The materials’ chemical-physical properties like surface chemistry, wettability and polarity are parameters of passive modification approaches for improved hemocompatibility and are the focus of the present work. In the present study self assembled monolayers with different surface functionalities (-COOH, -OH, -CH3) were applied as well as two-component-layers with varying fractions of these, as they allow a defined graduation of surface wettability and charge. The ease of control over these parameters given by these model surfaces enables the evaluation of the influence of specific surface-properties on biological responses. To evaluate the effects of different surface chemistry on initial mechanisms of biomaterial induced coagulation, the surfaces were incubated with protein solution, human plasma, blood cell fractions or fresh heparinised human whole blood. Indicative hemocompatibility parameters were subsequently analysed focusing on protein adsorption, coagulation activation, contact activation (intrinsic/ enhancer pathway), impact of tissue factor (extrinsic/ activator pathway) and cellular systems (blood platelets and leukocytes).