Switchable surfaces, also called smart surfaces or controllable surfaces, respond to changes in their local environment resulting in altered surface properties. There are various environmental perturbations that can cause changes to the surface properties but the focus of this thesis is on the affect of electrostatic potential. Significant evidence is provided from previous reports on electrochemical and infrared spectroscopic experiments suggesting that self-assembled monolayers (SAMs) of 4-mercaptobenzoic acid (4-MBA) undergo protonation-deprotonation by the application of an electric field. However, there are plenty of aspects of this electric field driven protonation-deprotonation mechanisms using carboxylic acid terminated SAMs that are not well understood. Most importantly, there is a lack of model independent measurements to validate this process. As such, experimental techniques utilizing infrared spectroscopy were employed to correlate electrochemical measurements and models.<p> This body of work demonstrates the importance of the intermolecular hydrogen bonding network on the measured voltammetric peak associated with the protonation-deprotonation of these SAMs. The voltammetric peak height diminishes with increasing exposure to an electrolyte solution. This behaviour is attributed to the replacement of the carboxylic acid protons with electrolyte cations and ultimately the disruption of the hydrogen bonded network.<p> We attempted to further our ex-situ infrared measurements by using an in-situ spectroelectrochemical technique. We had some initial successes, presented within, but more work is needed to complete this picture and is beyond the scope of this thesis. To summarize, the protonated state of SAMs of 4-MBA can be driven by the application of an electric field providing a potential platform to build a controllable smart surface.

The speed of microelectronic devices is controlled by the size of the transistor gate. In order to create faster devices, the size of this transistor gate must shrink. Microlithography is the method used to define patterns in semiconductor devices, and it is optimized periodically to create smaller features. It is a subtractive process that relies on the selective removal of sections of a photosensitive polymeric film called photoresist. This photoresist is exposed to patterned ultraviolet radiation that changes the local solubility of the film and allows for the creation of relief patterns in the resist using a developing solvent. Decreasing the wavelength of the light used to expose the patterns is the primary method for decreasing the minimum feature size that can be printed by this process. There are a number of challenges associated with decreasing the exposure wavelength for conventional lithographic processes. First of all, the polymeric films must be transparent at the exposure wavelength in order to allow light to propagate through the entire thickness of the film. Secondly, there is a limit in the thickness of the photoresist films that can be used. This thickness limits the etch resistance of the film. In fact, the issues concerning etch resistance and transparency are generally in opposition. This makes designing photoresist platforms for future lithographic applications very difficult. Therefore, to overcome these limitations, we are developing an unconventional approach to microlithography. In our approach, entitled Surface Monolayer Initiated Polymerization, polymer structures are formed on a surface by polymerizing a monomer in a patterned fashion using a self-assembled monolayer that can be locally activated to initiate the reaction. This process has been demonstrated by creating patterned polystyrene films on native silicon dioxide surfaces. In these initial studies, it took more than one day to create features. This is unacceptable for a lithographic application. The kinetics of all the processes involved in making these patterned layers is described. Along with these rate constants, means of optimizing these rates are also presented. Additionally, the patterns grown in these initial studies exhibited poor uniformity. Methods of optimizing the patterns formed are also presented.

Biologically-inspired materials have emerged as promising substrates for enhanced repair in various therapeutic and regenerative medicine applications, including nervous and vascular tissues, bone, and cartilage. These strategies focus on the development of materials that integrate well-characterized domains from biomacromolecules to mimic individual functions of the extracellular matrix (ECM), including cell adhesive motifs, growth factor binding sites, and protease sensitivity. A vital property of the ECM is the fibrillar architecture arising from supramolecular assembly. For example, the fibrillar structure of fibronectin (FN) matrices modulates cell cycle progression, migration, gene expression, cell differentiation, and the assembly of other matrix proteins. Current biomaterials do not actively promote deposition and assembly of ECM. In this research, we describe the rational design and investigation of non-fouling biomimetic surfaces in which an oligopeptide sequence (FN13) from the self-assembly domain of FN is tethered to non-fouling substrates. This surface modification directs cell-mediated co-assembly of robust fibrillar FN and type I collagen (COL) matrices reminiscent of ECM, and increases in cell proliferation rates. Furthermore, the effect of this peptide is surface-directed, as addition of the soluble peptide has no effect on matrix assembly. We have also identified a critical surface density of the immobilized peptide to elicit the full activity. These results contribute to the development and design of biomimetic surface modifications that direct cell function for biomedical and biotechnology applications.

High-resolution lattice periodicity images of a variety of well-defined surfaces, including graphite, mica, and Au(111), validated the good stability of our atomic force microscope (AFM) system. Combining self-assembled monolayer (SAM) and AFM technology, we demonstrated the capabilities of pattern fabrication as well as modification of surface functionality. AFM-based nanolithography operating conditions, such as scan rate, deflection setpoint, and number of scan were studied to obtain the optimized quality of the fabricated patterns. Thiolated-DNA probe molecules could be patterned at a nanometer scale on a gold substrate. However, we found that the surface coverage began to drop notably with the probe length (number of DNA bases). Therefore, the displaced DNA molecules during nanoshaving were reversibly adsorbed, and patterning became unreliable. We were unsuccessful in detecting the subsequent hybridization reactions at these nanopatterns from AFM measurements. To realize the DNA hybridization, further studies on the incubation temperature, probe length and even DNA sequences are required to demonstrate that this AFM-based gene diagnostic method is truly operational.

Electronic structure calculations of organic molecules are an important set of tools to gain understanding of molecular structures. This thesis presents two separate contributions to applying quantum chemistry to organic molecules. In the first section, the computational cost of a post-Hartree-Fock method is improved for large molecules by using graphical processing units. In this work, the resolution-of-the-identity second-order Møller-Plesset perturbation theory (RI-MP2) algorithm was adapted to send the large matrix multiplication steps to be run on a graphics co-processor. As a result, the calculations were performed up to 15x faster than a standard implementation for large molecules such as taxol. In the second section of the thesis, density functional theory is used to predict the molecular dipole moments of molecules that form self-assembled monolayers (SAMs) on metal surfaces. The dipole moment of the molecule that is aligned perpendicular to the surface in a SAM changes the work function of the surface. The calculated dipole moments correlate with the current density measured for the junctions by experimental collaborators. This result holds for a series of alkane chains with even and odd numbers of carbons and for molecules that have an amide group substituted for an ethylene unit. / Chemistry and Chemical Biology

Computer processor chips of the last generation are based on silicon, modified to achieve maximum charge mobility to enable fast switching speeds at low power. III-V semiconductors have charge mobilities that are much higher than that of silicon making them suitable candidates for boosting the performance of new electronic devices. However, III-V semiconductors oxidize rapidly in air after oxide etching and the poor quality of the resulting oxide limits device performance. Our goal is to design a liquid-phase process flow to etch the oxide and passivate the surface of III-V semiconductors and to understand the mechanism of layer formation.Self-assembled monolayers of 1-eicosanethiol (ET) dissolved in ethanol, IPA, chloroform, and toluene were deposited on clean InSb(100) surfaces. The InSb passivated surfaces were characterized after 0 to 60 min of exposure to air. Ellipsometry measurements showed a starting overlayer thickness (due to ET, oxides, or both) of about 20 Å in chloroform and from 32 to 35 Å in alcohols and toluene. Surface composition analysis of InSb with X-ray photoelectron spectroscopy after passivation with 0.1 mM ET in ethanol confirmed the presence of ET and showed that oxygen in the Auger region is below detection limits up to 3 min after the passivation. Our results show that a thiol layer on top of a non-oxidized or low-oxide semiconductor surface slows oxygen diffusion in comparison to a surface with no thiol present, making this a promising passivation method of III-V semiconductors.

Self-assembled monolayers (SAMs) of organosulfur precursors on gold have been extensively used since they offer a wide range of technological applications such as corrosion inhibition, lubrication, adhesion promotion/inhibition, nanofabrication, chemical and biosensors, catalysis, and molecular electronics. Furthermore, the electronic and optical properties of aromatic SAMs make them a potential candidate for molecular electronics. However, these practical applications are limited by the short-range ordering, low packing density, irreproducibility, and inferior quality of SAMs, which are more critical for aromatic SAMs. Therefore, the discovery of alternative precursors is essential. This thesis reports for the first time, the use of organic sulfenyl chlorides as precursors for the modification of gold surfaces. These precursors may help to overcome some practical limitations of the traditional organosulfur precursors. The modification is done in a non-aqueous medium. Characterization of the modified surfaces is performed by X-ray photoelectron spectroscopy (XPS), cyclic voltammetry (CV), polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS), and scanning tunnelling microscopy (STM). Through the use of 4-nitrophenyl sulfenyl chloride, evidence for the formation of well-ordered aromatic SAMs formation on gold is provided. XPS data shows that the modification involves the scission of the S-Cl bond. PM-IRRAS studies further indicate that the adsorbed molecules are nearly vertically oriented on the surface. Both short and long-range well-ordered aromatic SAMs (a 4 x √3 rectangular and √3 x √3 hexagonal unit cells) are obtained from the STM images using two different modification conditions. This molecular density is usually only observed for aliphatic SAMs using the traditional precursors. Along with the main hexagonal lattice, the reversible distinct superstructures including hexagons, partial hexagons, parallelograms, and zigzags resulting from specific arrangements of adsorbed molecules provide submolecular details. This is the first direct experimental example, where the STM has shown its effectiveness to provide physical structure information of standing-up aromatic SAMs at room temperature. This work also provides some insight into a heavily debated issue regarding the origin of the various features and contrasts obtained in STM images of SAMs. The use of 2-nitrophenyl sulfenyl chloride and 2,4-dinitrophenyl sulfenyl chloride for the formation of aromatic SAMs on Au provides some insight regarding the modification extent and the effect of a nitro substituent (at ortho position ) on the quality of nitrophenyl thiolate SAMs on gold. XPS, PM-IRRAS, electrochemistry and STM provide evidence for the formation of less ordered, low density and less stable SAMs that may decompose to sulfur at longer modification times. The efficient deposition of sulfur on gold is observed using a series of substituted methane sulfenyl chlorides (triphenylmethane sulfenyl chloride, trichloromethane sulfenyl chloride and chlorocarbonyl sulfenyl chloride). The XPS, STM and electrochemical data show the formation of high density sulfur phases. These include rhombus, rectangular, and zig-zag sulfur structures. A mechanism is suggested involving the cleavage of the S-Cl bond and the ejection of the molecular backbone. This study also suggests that substituted methane sulfenyl chlorides do not form long-range ordered SAMs.

Thesis(M.S.)--Auburn University, 2005. / Abstract. Vita. Includes bibliographic references.

The components necessary to propagate a synthetic ionic signal are described, and experiments leading to the required experimental system are the focus of this work. Two thiol-derivatized fluorescent probe molecules were synthesized that balanced both electrochemical and fluorescent properties necessary for trace analysis. Self-assembled monolayers (SAMs) of 11-(1-1’-biphenyl-4-yloxy)-1-undecanethiol were formed on Au/glass slides by open-circuit incubation and potential-assisted adsorption methods. A potentiostat was built capable of producing current responses on the microsecond time-scale. Monolayer integrity was established by two methods: cyclic voltammetry and chronoamperometry. Monolayers formed under potential-assisted adsorption conditions showed attenuation of the peak current due to Fe(CN)6 3−/4− redox probe in cyclic voltammetry, indicating a tightly packed monolayer. Chronoamperometric studies also confirmed the monolayer integrity by fitting the current response of a potential-step to an equivalent circuit. The chronoamperometric study was dependent on solvent and electrolyte. In water, the difference between bare Au and monolayer protected Au was large, whereas in DMF, the difference was negligible. Likewise, the use of tetra-butyl ammonium hexafluorophosphate as the electrolyte showed little difference between bare Au and monolayer protected Au. The electrochemical reduction of the SAMs was done in various solvents and electrolytes and the products were analysed by HPLC with fluorescent detection. Along the series of solvents from water to MeCN to DMF the current efficiencies for release increased but still were very low. In water and MeCN, the thiol was the sole detectable product, while in DMF, the sole detected product was the disulfide. Reproducibility of release was poor in MeCN and water, probably due to the low solubility of the thiol. Single-channel analysis of two acyclic bola-amphiphiles (diester and diamide) was done to establish their feasibility as components of a synthetic signal propagation system. Channels from the diester derivative have a Na+ conductance of 10.2 pS and a Cs+ conductance of 39.3 pS. Channels from the diester have a Cs+/Na+ permeability ratio of 4.7, Cs+/Cl- permeability ratio of 7.5 and a Na+/Cl- permeability ratio of 3.1. Channels of the diester bola-amphiphile have two lifetimes; 117 ms and 842 ms at -100 mV, 1 M CsCl electrolyte and DiPhyPC lipid at 25 °C. Similarly, Channels from the diamide derivative have a Na+ conductance of 10.3 pS and a Cs+ conductance of 38.9 pS. Chaimels of the diamide have a Cs+/Na+ permeability ratio of 5.2, Cs+/Cl- permeability ratio of 7.2 and a Na+/Cl- permeability ratio of 2.1. The diamide bola-amphiphile channels have a lifetime of 277 ms at +100 mV, 1 M CsCl electrolyte and DiPhyPC lipid at 25 °C. Both channels show a regular non-uniform step-conductance pattern. The sublevel openings, when graphically represented with lifetime data, show the trend that the lower conductance states of one-level openings are also the shorter-lived channels. A traceless linker to release alcohols from a gold surface was developed. Thiobutyric acid was found to undergo intramolecular thiolactone formation after electrochemical reduction from an Au-electrode to liberate the alcohol. A thiobutyric ester at the C-terminus of gramicidin was synthesized. This compound released gramicidin by chemical reduction with DTT as seen by HPLC analysis and MALDI TOF MS. The electrochemical release of the Au-immobilized thiobutyric ester of gramicidin adjacent to a lipid bilayer, as monitored by bilayer clamp technique, produced an increase in channel activity that is consistent with incorporation of gramicidin. / Graduate

Advances in microfabrication and surface chemistry techniques have provided a new paradigm for the creation of in vitro systems for studying problems in biology and medicine in ways that were previously not practical. The ability to create devices with micro- to nano-scale dimensions provides the opportunity to non-invasively interrogate and monitor biological cells and tissue in large arrays and in a high-throughput manner. These systems hold the potential to, in time, revolutionize the way problems in biology and medicine are studied in the form of point-of-care devices, lab-on-chip devices, and biological microelectromechanical systems (BioMEMS). With new in vitro models, it will be possible to reduce the overall cost of medical and biological research by performing high-throughput experiments while maintaining control over a wide variety of experimental variables. A critical aspect of developing these sorts of systems, however, is controlling the device/tissue interface. The surface chemistry of cell-biomaterial and protein-biomaterial interactions is critical for long-term efficacy and function of such devices. The work presented here is focused on the application of surface and analytical chemistry techniques for better understanding the interface of biological elements with silica substrates and the development a novel Bio-MEMS device for studying muscle and neuromuscular biology. A novel surface patterning technique based on the use of a polyethylene glycol (PEG) silane self-assembled monolayer (SAM) as a cytophobic surface and the amine-terminated silane diethyeletriamine (DETA) as a cytophilic surface was developed for patterning a variety of cell types (e.g. skeletal muscle, and neural cells) over long periods of time (over 40 days) with high fidelity to the patterns. This method was then used to pattern embryonic rat skeletal muscle and motor neurons onto microfabricated silicon cantilevers creating a novel biological microelectromechanical system (BioMEMS) for studying muscle and the neuromuscular junction. This device was then used to study the effect of exogenously applied substances such as growth factors and toxins. Furthermore, a whispering-gallery mode (WGM) biosensor was developed for measuring the adsorption of various proteins onto glass microspheres coated with selected silane SAMS commonly used in BioMEMS system. With this biosensor it was possible to measure the kinetics of protein adsorption onto alkylsilane SAMS, in a real-time and label-free manner.