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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.

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

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.

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

Protein adsorption on solid surfaces is a common yet complicated phenomenon that is not fully understood. Self-assembled monolayers have been utilized in many studies, as well-defined model systems for studying protein-surface interactions in the atomic level. Various strategies, including the use of single component SAMs[1, 2], combinations of long and short alkanethiolates with methyl- and hydroxyl- terminal groups[3, 4], and using mixtures of alkanethiolates with similar chain length and varying terminal functional group [5] have been used to effectively control the surface wettability and determine the effect of surface composition and wettability on protein adsorption. In this dissertation we report key new findings on the effect of surface density of functional groups on protein adsorption phenomenon. In The first phase of this research, we developed a novel approach for preparation of low-density self-assembled monolayers(LD-SAMs) on gold surfaces, based on radical-initiated thiol-yne click chemistry. This approach provides exceptional adsorbate stability and conformational freedom of interfacial functional groups, and is readily adapted for low-density monolayers of varied functionality. The resulting monolayers have two distinct phases: a highly crystalline head phase adjacent to the gold substrate, and a reduced density tail phase, which is in contact with the environment. First, we investigated the feasibility of the proposed chemistry in solution-phase. In this approach, we synthesized “Y” shaped carboxylate-terminated thiol adsorbates via radical-initiated thiol-yne reaction. The LD-SAMs were then prepared through immersion of gold substrates into the solution of synthesized adsorbate molecules in hexane. The chemical structuring and electrochemical properties of resultant LD-SAMs were analyzed and compared with those of analogous traditional well-packed monolayers, using techniques such as Fourier transform infrared spectroscopy, ellipsometry, electrochemical impedance spectroscopy, reductive desorption, and contact angle goniometry. Characterization results indicated that resulting LD-SAMs have a lower average crystallinity, and higher electrochemical stability compared to well-packed monolayers. In addition, using a three-electrode system, we were able to show a reversible change in LD-SAM surface wettability, in response to an applied voltage. This remodeling capacity confirms the low density of the surface region of LD-SAM coatings. The second area of work was focused on using the developed chemistry in solid-phase. The solid-phase approach minimized the required synthesis steps in solution-phase method, and used the photo-initiated thiol-yne click-reaction for grafting of acid-terminated alkynes to thiol-terminated monolayers on a gold substrate to create similar LD-SAMs as what were prepared through solution-phase process. We characterized the resulting monolayers and compared them to analogous well-packed SAMs and the also low-density monolayers prepared through the solution phase approach. The results confirmed the proposed two-phase structure, with a well-packed phase head phase and a loosely-packed tail phase. In addition, the electrochemical studies, indicated that the resultant monolayers were less stable than the monolayers prepared via solution-phase, but they are yet significantly more stable than typical well-packed monolayers. The less stability of these monolayers were attributed to the partial desorption of adsorbates from the gold substrate due to UV irradiation during the grafting process. Building on the established chemistry, we studied the effect of lateral packing density of functional groups in a monolayer on the adsorption of Bovine serum albumin protein. we used surface plasmon resonance spectroscopy (SPR) and spectroscopic ellipsometry, to evaluate BSA adsorption on carboxylate‑, hydroxyl-, or alkyl- terminated LD-SAMs. It was found that for the LD-SAMs, the magnitude of protein adsorption is consistently higher than that of a pure component, well-packed SAM for all functionalities studied. In addition, it was seen that the magnitude of BSA adsorption the LD-SAMs, was consistently higher than that of a pure component, well-packed SAM for all functionalities studied. The difference of protein adsorption on LD-SAMs and SAMs can not be associated to difference in lateral packing density, unless we eliminate the impact of other contributing factors in protein adsorption such as surface energy. In order to better understand the impact of packing density on protein-surface interactions, we prepared the mixed SAMs of (carboxylate/alkyl) and (hydroxyl/alkyl) with matching surface energy as the carboxylate and hydroxyl terminated LD-SAMs. It was found that the energy-matched mixed SAMs of carboxylate and hydroxyl functionality adsorbed more protein than the LD-SAMs. However, an opposite trend was seen for the alkyl surfaces, where surface energies are comparable for LD-SAMs and pure component SAMs, indicating that BSA proteins have higher affinity for methyl- terminated LD-SAMs than well-packed SAMs.

Continuous scaling down of the dimensions of electronic devices has made present day computers more powerful. In the front end of line, the minimum lateral dimensions in a transistor have shrunk from 45 nm in 2007 to 22 nm currently, and the gate oxide film thickness is two to three monolayers. This reduction in dimensions makes surface preparation an increasingly important part of the device fabrication process. The atoms or molecules that terminate surfaces function as passivation layers, diffusion barriers, and nucleation layers. In the back end of line, metal layers are deposited to connect transistors. We demonstrate a reproducible process that deposits a monolayer of aminopropyltrimethoxysilane molecules less than one nanometer thick on a silicon dioxide surface. The monolayer contains a high density of amine groups that can be used to deposit Pd and Ni and subsequently Co and Cu to serve as the nucleation layer in an electroless metal deposition process. Because of the shrinking device dimensions, there is a need to find new transistor channel materials that have high electron mobilities along with narrow band gaps to reduce power consumption. Compound III--V channel materials are candidates to enable increased performance and reduced power consumption at the current scaled geometries. But many challenges remain for such high mobility materials to be realized in high volume manufacturing. For instance, low defect density (1E7 /cm²) III--V and Ge on Si is the most fundamental issue to overcome before high mobility materials become practical. Unlike Si, dry etching of III-V semiconductor surfaces is believed to be difficult and uncontrollable. Therefore, new wet etching chemistries are needed. Si has been known to passivate by etching in hydrofluoric acid, but similar treatments on III--Vs are known to temporarily hydrogen passivate the surfaces. However, any subsequent exposure to the ambient reoxidizes the surface, resulting in a chemically unstable and high defect density interface. This work compares old and new wet etching chemistries and investigates new methods of passivating the III--V semiconductors.

Doctor of Philosophy / Department of Chemistry / Daniel A. Higgins / This dissertation describes the application of single molecule spectroscopy and tracking to investigations of the nanoscale properties of thin-film chemical gradients and the transport dynamics of molecules dispersed within and upon these gradients. Chemical gradients are surface bound materials that incorporate gradually changing chemical and/or physical properties. A continuous and gradual change in the properties of gradients are expected and often required for their intended applications, which range from directed growth of cell colonies to combinatorial materials science. In reality, such conditions are almost never met due to spontaneous demixing and dewetting processes that can lead to properties variations on microscopic length scales. A better understanding on the properties of chemical gradients on microscopic length scales will aid in the production of better engineered materials. Single molecule spectroscopy (SMS) allows for gradient properties to be probed on nanometer-to-micrometer length scales. In this dissertation, quantitative measurements of gradient polarity (i.e., dielectric properties) are made along a sol-gel derived thin film that incorporates a macroscopic polarity gradient. These measurements report on the microscopic heterogeneity of the gradient film, and point to the occurrence of phase separation of the polar and nonpolar components along the gradient. Single molecule tracking (SMT) provides an important means to examine the dynamics of molecular mass transport in thin films and on surfaces. In this dissertation, SMT is employed to study mass transport in thin water films condensed over monolayer wettability gradients under ambient environments. The results show that the rate and the mechanism of molecular transport depend on the surface wettability, and on the ambient relative humidity. Finally, wettability gradients have been broadly used to drive the transport of liquid droplets. In this dissertation, these applications are extended to achieve spontaneous stretching of DNA by the propulsion of liquid droplets along the gradient. Single molecule fluorescence imaging of DNA stretched along these gradients demonstrates that hydrophobic surfaces play an important role in DNA stretching. The study also shows the surface tension force acting at the gradient-droplet contact line (interface) to be responsible for DNA elongation and alignment. Overall, single molecule methods have been shown to be highly useful for better understanding the properties of chemical gradients as described in this dissertation.

Cette thèse s’inscrit dans le domaine de la spintronique moléculaire. Elle s’intéresse plus précisément aux nouvelles opportunités de façonnage de la polarisation de spin qui découlent de l'hybridation métal ferromagnétique/molécule à l'interface : le nouveau concept de « spinterface ».Dans une première partie nous présentons l’étude de nanojonctions tunnel magnétiques à base de monocouches auto-assemblées (SAMs). Ce système est un des plus prometteur dans l’optique de moduler les propriétés des dispositifs de spintronique par ingénierie chimique, tel un LEGO moléculaire. Nous y présentons la fonctionnalisation de la manganite demi-métallique (La,Sr)MnO3 (LSMO) avec des SAMs d’acides alkylphosphoniques et la fabrication de nanojonctions LSMO/SAMs/Co avec une surface de quelque 10 nm2. Une magnétorésistance de 30% à 50% est observée dans la majorité des dispositifs avec une magnétorésistance tunnel (TMR) jusqu'à 250 % à basse température. Un point remarquable est aussi le comportement très robuste du signal avec la tension: environ 20% de TMR est encore observée au-dessus d’une tension de 1 V. L'influence de la longueur de la chaîne moléculaire a été aussi étudiée et représente un premier pas vers la modulation des dispositifs au niveau moléculaire. Dans une deuxième partie nous présentons l’étude des dispositifs organiques à base de métaux ferromagnétiques à haute TC (température de Curie) et semi-conducteurs organiques. Nous avons réalisé des vannes de spin de Co/Alq3/Co avec des sections de 50 ou 100 µm et fabriquées in-situ par « shadow mask ». Des mesures à température ambiante ont permis d’observer -4% de magnétorésistance (MR) dans une vanne de spin Co/Alq3/Co et +8% MR dans une vanne de spin de Co/MgO/Alq3/Co. Le rôle des deux interfaces sur les propriétés de polarisation de spin des dispositifs est aussi étudié et détaillé. Une forte hybridation métal/molécule dépendant du spin à l'interface inferieure de Co/Alq3, présentant un effet de spinterface (inversion de la polarisation en spin), est observée. Ces études montrent que les effets de spinterface, comme l’inversion de la polarisation de spin, peuvent persister dans un dispositif jusqu’à température ambiante. / This thesis targets the field of molecular spintronics and more particularly the new spin polarization tailoring opportunities, unachievable with inorganic materials, which arise from the ferromagnetic metal/molecule hybridization at the interface.: the new concept of Spinterface.In a first part we investigate Self-Assembled Monolayers (SAMs) based magnetic tunnel nanojunctions. This system appears to be a highly promising candidate to engineer the properties of spintronics devices at the molecular level since SAMs are the equivalent of a molecular LEGO building unit. We present the functionalization of the half-metallic manganite (La,Sr)MnO3 (LSMO) with alkyl phosphonic acids SAMs and the fabrication of LSMO/SAMs/Co magnetic tunnel nanojunctions with an area of few 10 nm2. MR of 30% to 50% is observed in most of the devices, while we report even up to 250% tunnel magnetoresistance (TMR) at low temperature. The most striking point is the robustness of the signal with bias voltage with still 20% TMR observed in the volt range. The influence of the molecular chain length is also investigated and represents a first step towards achieving molecular tailoring.In a second part we develop organic spintronics devices relying on high Curie temperature metallic ferromagnetic electrodes and standard organic semiconductor such as Co/Alq3/Co organic spin valves (OSVs). Junctions have a large area (section of 50 or 100 µm) and are fabricated in-situ by shadow mask. Magnetoresistance (MR) effects at room temperature are investigated with -4% MR observed in Co/Alq3/Co OSVs and +8% MR in Co/MgO/Alq3/Co OSVs. The role of the two interfaces on the spin polarization properties of the devices is also investigated. A stronger spin-dependent hybridization is found to occur at the bottom Co/Alq3 interface inverting the spin polarization on the first molecular layer. The observation of spin polarization inversion at room temperature demonstrates that spinterface effects can strive up to room temperature.