Scanning Electrochemical Microscopy (SECM) is most commonly used to spatially resolve reaction rates, image surface topography and surface reactivity. In this research, SECM is applied to various chemical systems in order to resolve local reaction chemistry and to produce patterns with dimensions of tens of microns in n-alkanethiol passivated gold substrates. Upon completing construction of the instrumentation, SECM was applied to capillary electrophoresis to accurately and reproducibly place the electrode directly above a very small capillary opening. Feedback SECM was then used to image and pattern surfaces, effectively distinguishing between insulating and conductive domains. Finally, the size of desorbed features patterned on a passivated gold substrate were studied as a function of both applied potential and ionic strength. Electrochemical detection in capillary electrophoresis requires decoupling the voltage applied to the working electrode from the separation voltage applied across the capillary. End-capillary electrochemical detection achieves this by placing the electrode just outside the ground end of the separation capillary. Obtaining adequate signal-to-noise in this arrangement requires using small inner diameter capillaries. Decreasing the inner diameter of the separation capillary, however, increases the difficulty of aligning the microelectrode with the open end of the capillary. Using SECM, the position of the capillary opening is determined while electroactive material is continuously emerging from the end of the capillary. The SECM instrument is then used to place the electrode at the position of maximum current for subsequent separations. Subsequent measurements found that the best signal-to-noise is obtained when the detection electrode is placed directly opposite the capillary opening and just outside of the capillary opening. When the electrode is further above the opening (but still opposite the capillary opening), the signal-to-noise does not dramatically decrease until the electrode is more than 30 μm above the 10 μm inner-diameter capillary. Limits of detection for 2,3-dihydroxybenzoic acid were found to be 8.2 fmol when aligned manually, and 3.8 fmol when the SECM is used to automatically align the microelectrode. SECM was then used to image a series of multi-disk electrode arrays in order to demonstrate the ability of the instrument to discriminate between conductive and insulating domains. Upon demonstrating the capacity of the SECM to image very small domains of conductor on an insulating substrate, n-alkanethiol passivated gold surfaces were patterned using site-selective desorption. A number patterns, potentially useful for enzyme deposition, were subsequently produced in the passivated gold substrate. The feature size of the desorbed domains was monitored as a function of applied potential and the ionic strength of the solution used for desorption. Results showed that applying a more negative potential or increasing the ionic strength of the solution increased the magnitude of the electric field at the surface of the passivated gold substrate and resulted in a more complete, larger desorption. Both ionic strength and applied desorption potential prove to be parameters useful for controlling the size of patterned features in site selective desorption. / Master of Science

Ionic polymer-metal composites (IPMCs) are widely studied for their potential as electromechanical sensors and actuators. Bending of the IMPC depends on internal ion motion under an electric potential, and the addition of an ionic liquid and ionic self-assembled multilayer (ISAM) conductive network composite (CNC) strongly enhances bending and improves lifetime. Ion conducting polyelectrolytes poly(2-acrylamido-2-methyl-1-propanesulfonic acid) (PAMPS) and Nafion® were incorporated into an ISAM CNC film with poly(allylamine hydrochloride) (PAH) and anionic gold nanoparticles actuators to further improve bending. CNC films were optimized for bending through pH adjustments in PAH and adding NaCl to the PAMPS and Nafion® solutions. PAMPS-containing actuators showed larger and faster bending than those containing Nafion® in the CNC. The IPMC actuator was also evaluated for its potential as a humidity sensor based on its relative humidity (RH) dependent steady-state current. The detection range is at least 10-80%RH, with 5%RH increment differentiation and likely better resolution. Effects of CNC presence and thickness were studied, in conjunction with ionic liquid at a range of RH values. A thin CNC (pH 4 PAH) produced the greatest current differentiation between RH values. The current's response speed to a large RH decrease was approximately 4 times faster than that of a fast commercial digital hygrometer. Additionally, the presence of a CNC and ionic liquid improved the current response time. These results indicate that an IPMC based humidity sensor using a CNC and ionic liquid is very promising and merits further study. / Master of Science

Understanding interfacial interactions at the molecular level is important for interpreting and predicting the dynamics and mechanisms of all chemistry processes. A thorough understanding of the interaction dynamics and energy transfer between gas molecules and surfaces is essential for the study of various chemical reactions. The collisions of diatomic molecules on organic surfaces are crucial to the study of atmospheric chemistry. Molecular beam scattering experiments performed in ultra-high vacuum chambers provide insight into the dynamics of gas-surface interactions. Many questions remain to be answered in the study of gas-surface interfacial chemistry. For example, what affects the energy transfer between gas molecules and surfaces? How do intermolecular forces affect the interfacial interaction dynamics? We have approached these questions by scattering diatomic gas molecules from functionalized self-assembled monolayers (SAMs). Our results indicate that the intermolecular forces between gas molecules and surfaces play an important role in the energy transfer processes. Moreover, the stronger the intermolecular forces, the more often the incident molecules come into thermal equilibrium with the surface. Furthermore, most of the previous approaches toward understanding gas-surface interaction dynamics considered the interactions as independent incidents. By scattering O2, N2, CO and NO on both CH3- and OH- terminated SAM, we found a correlation between the gas-surface interactions and a bulk property, solubility. Both being strongly affected by intermolecular forces, the gas-surface energy transfer and solubility of gases in surface-similar solvents (water for OH-SAM, n-hexane for CH3-SAM) have a positive correlation. This correlation facilitates the understanding of interfacial dynamics at the molecular level, and helps predict the outcome of the similar-size gas collisions on surfaces. / Master of Science

Nanoparticles present a myriad of physical, optical, electrical, and chemical properties that provide valuable functionality to thin-film technologies. In order to successfully exploit these aspects of nanoparticles, appropriate dispersion and stability measures must be implemented. In this dissertation, different types of nanoparticles are coated with polymer and metallic layers to enable their effectiveness in both anti-reflection coatings (ARCs) and organic photovoltaics (OPVs). Ionic self-assembled multilayers (ISAMs) fabrication of poly(allylamine hydrochloride) (PAH) and silica nanoparticles (SiO2 NPs) results in highly-transparent, porous ARCs. However, the ionic bonding and low contact area between the film constituents lack sufficient mechanical and chemical stability necessary for commercial application. Chemical stability was established in the film by the encapsulation of SiO2 NPs by a photo-crosslinkable polyelectrolyte, diazo-resin (DAR) to make modified silica nanoparticles (MSNPs). UV-irradiation induced decomposition of the diazonium group and the development of covalent bonds with polyanions. Crosslinked MSNP/poly(styrene sulfonate) (PSS) ISAMs exhibited excellent anti-reflectivity (transmittance >98%, reflectance <0.2% in the visible range) and chemical stability against dissolution in a ternary solvent. Mechanical stability was also achieved by the incorporation of two additional PAH and poly(acrylic acid) (PAA) layers to create PAH/PAA/PAH/SiO2 NP interlayer ISAM ARCs. Thermal crosslinking of PAH and PAA facilitates the formation of covalent amide bonds between the two polyelectrolytes, as confirmed by FTIR. Since PAH and PAA are both weak polyelectrolytes, adjustment of the solution pH causes significant variations in the polymer chain charge densities. At low PAA pH, the decreased chain charge densities caused large SiO2 NP encapsulation thicknesses in the film with great mechanical stability, but poor anti-reflection (≤97% transmittance). At high PAA pH, the high chain charge densities induced thin encapsulation layers, insufficient mechanical stability, but excellent anti-reflection. At trade-off between the two extremes was founded at a PAA pH of 5.2 with excellent anti-reflection (less than 99% transmittance) and sufficient mechanical stability. The normal force required for scratch initiation was increased by a factor of seven for films made from a pH of 5.2 compared to those made from a pH of 6.0. Organic photovoltaics (OPVs) are an attractive area of solar cell research due to their inexpensive nature, ease of large-scale fabrication, flexibility, and low-weight. The introduction of the bulk heterojunction greatly improved charge transport and OPV performance by the blending of the active layer electron donor and acceptor materials, poly(3-hexylthiophene) (P3HT) and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM), into an interpenetrating network with high interfacial area between adjacent nanodomains. However, constrained active layer thicknesses restrict the total optical absorption and device performance. The localized surface plasmon resonance (LSPR) of plasmonic nanoparticles, such as anisotropic silver nanoplates (AgNPs), provides large local field enhancements and in coupling with the active layer, substantial optical absorption improvements can be realized. AgNPs were first integrated into the hole-transport layer (PEDOT:PSS) by ISAM deposition. Here, PEDOT:PSS was used as a negatively-charged ISAM layer. Encapsulation of the AgNPs by PAH (ENPs) provided a positive surface charge and allowed for the creation of ENP/PEDOT:PSS ISAMs. Stability against acidic etching by PEDOT:PSS was imparted to the AgNPs by coating the edges with gold (AuAgNPs). The AuAgNP ISAMs substantially improved the optical absorption, but were ineffective at increasing the device performance. The dispersion effects of functionalized polymer coatings on AgNPs were also deeply investigated. Functionalized AgNPs were dispersed in methanol and spin-coated onto the active layer. When the AgNPs possessed hydrophilic properties, such as unfunctionalized or functionalized by poly(ethylene glycol) methyl ether thiol (PEG-SH), they formed large aggregates due to unfavorable interactions with the hydrophobic P3HT:PCBM layer. However, the hydrophobic functionalization of AgNPs with thiol-terminated polystyrene (PS-SH) (PS-AgNPs) resulted in excellent dispersion, optical absorption enhancements, and device performance improvements. At a PS-AgNP concentration of 0.57 nM, the device efficiency was increased by 32% over the reference devices. / Ph. D. / Investigations are presented on the quality of distribution or dispersion of functional inorganic (composed of silicon dioxide or silver) particles that have dimensions of less than 100 nanometers, called nanoparticles. The nanoparticle surfaces were covered with polymer layers, where polymers are organic materials with repeating molecular structures. The study of these nanoparticle distribution effects were first examined in anti-reflection coatings (ARCs). ARCs induce transparency of windows or glasses through a reduction in the reflection of light. Here, the ARCs were fabricated as self-assembled thin-films (films with thicknesses ranging from 1 to 2000 nanometers). The self-assembly process here was carried out by immersing a charged substrate (microscope slide) into a solution with an oppositely-charged material. The attraction of the material to the substrate leads to thin-film growth. The process can continue by sequentially immersing the thin-film into oppositely-charged solutions for a desired number of thin-film layers. This technique is called ionic self-assembled multilayers (ISAMs). ARCs created by ISAM with charged polymers (polyelectrolytes) and silicon dioxide nanoparticles (SiO2 NPs) can lead to highly-transparent films, but unfortunately, they lack the stability and scratch-resistance necessary for commercial applications. In this dissertation, we address the lack of stability in the ISAM ARCs by adding additional polyelectrolyte layers that can develop strong, covalent bonds, while also examining nanoparticle dispersive properties. First, SiO2 NP surfaces were coated in solution with a polyelectrolyte called diazo-resin, which can form covalent bonds by UV-light exposure of the film. After tuning the concentration for the added diazo-resin, the coated SiO2 NPs were used to make ARCs ISAM films. The ARCs had excellent nanoparticle dispersion, high levels of transparency, and chemical stability. Chemically stability entails that the integrity of the film was unaffected by exposure to polar organic solvents or strong polyelectrolytes. In a second method, two additional v polyelectrolyte layers were added into the original polyelectrolyte/SiO2 NP design. Here, heating of the film to 200 oC temperatures induced strong covalent bonding between the polyelectrolytes. Variation of the solution pH dramatically changed the polyelectrolyte thickness, the nanoparticle dispersion, the scratch-resistance, and the anti-reflection. An optimum trade-off was discovered at a pH of 5.2, where the anti-reflection was excellent (amount of transmitted light over 99%), along with a substantially improved scratch-resistance. A change of pH from 6.0 (highest tested pH) to 5.2 (optimal) caused a difference in the scratch-resistance by a factor of seven. In these findings, we introduce stability enhancing properties from films composed purely of polyelectrolytes into nanoparticle-containing ISAM films. We also show that a simple adjustment of solution parameters, such as the pH value, can cause substantial differences in the film properties. Nanoparticle dispersion properties were next investigated in organic photovoltaics (OPVs) OPVs use semiconducting polymers to convert sunlight into usable electricity. They have many advantages over traditional solar cells, including their simple processing, low-cost, flexibility, and lightweight. However, OPVs are limited by their total optical absorption or the amount of light that can potentially be converted to electricity. The addition of plasmonic nanoparticles into an OPV device is a suitable way to increase optical absorption without changing the other device properties. Plasmonic nanoparticles, which are composed of noble metals (such as silver or gold), act as “light antennas” that concentrate incoming light and radiate it around the particle. In this dissertation, we investigate the dispersion and stability effects of polymer or metallic layers on silver nanoplates (AgNPs). The stability of the AgNPs was found to be greatly enhanced by coating the nanoparticle edges with a thin gold layer (AuAgNPs). AuAgNPs could then be introduced into a conductive, acidic layer of the OPVs (PEDOT:PSS) to increase the overall light absorption, which otherwise would be impossible with uncoated AgNPs. Next, the AgNPs were distributed on top of the photoactive layer or the layer that is responsible for absorbing light. Coating the AgNPs with a polystyrene polymer layer (PS-AgNPs) allowed for excellent dispersion on this layer and contrastingly, dispersion of the uncoated AgNPs was poor. An increased amount PS-AgNPs added on top of the photoactive layer progressively increased the optical absorption of the OPV devices. However, trends were quite different for the power conversion efficiency or the ratio of electricity power to sunlight power in the OPV device. The greatest PCE enhancements (27 – 32%) were found at a relatively low coverage level (using a solution concentration of 0.29 to 0.57 nM) of the PS-AgNPs on the photoactive layer.

A molecular-level understanding of gas-surface energy exchange and reaction mechanisms will aid in the prediction of the environmental fate of pollutants and enable advances toward catalysts for the decomposition of toxic compounds. To this end, molecular beam scattering experiments performed in an ultra-high vacuum environment have provided key insights into the initial collision and outcome of critical interfacial processes on model systems. Results from these surface science experiments show that, upon gas-surface collisions, energy transfer depends, in subtle ways, on both the properties of the gas molecules and surfaces. Specifically, model organic surfaces, comprised of long-chain methyl- and hydroxyl-terminated self-assembled monolayers (SAMs) have been employed to test how an interfacial hydrogen bonding network may affect the ability of a gas-phase compound to thermally accommodate (typically, the first step in a reaction) with the surfaces. Results indeed show that small organic compounds transfer less energy to the interconnected hydroxyl-terminated SAM (OH-SAM) than to the organic surface with methyl groups at the interface. However, the dynamics also appear to depend on the polarizability of the impinging gas-phase molecule. The π electrons in the double bond of ethene (C2H4) and the triple bond in ethyne (C2H2) appear to act as hydrogen bond acceptors when the molecules collide with the OH-SAM. The molecular beam scattering studies have demonstrated that these weak attractive forces facilitate energy transfer. A positive correlation between energy transfer and solubilities for analogous solute-solvent combinations was observed for the CH3-SAM (TD fractions: C2H6 > C2H4 > C2H2), but not for the OH-SAM (TD fractions: C2H6 > C2H2 > C2H4). The extent of energy transfer between ethane, ethene, and ethyne and the CH3-SAM appears to be determined by the degrees of freedom or rigidity of the impinging compound, while gas-surface attractive forces play a more decisive role in controlling the scattering dynamics at the OH-SAM. Beyond fundamental studies of energy transfer, this thesis provides detailed surface-science-based studies of the mechanisms involved in the uptake and decomposition of chemical warfare agent (CWA) simulants on or within metal-organic frameworks (MOFs). The work presented here represents the first such study reported in with traditional surface-science based methods have been applied to the study of MOF chemistry. The mechanism and kinetics of interactions between dimethyl methylphosphonate (DMMP) or dimethyl chlorophosphate (DMCP), key CWA simulants, and Zr6-based metal-organic frameworks (MOFs) have been investigated with in situ infrared spectroscopy (IR), X-ray photoelectron spectroscopy (XPS), powder X-ray diffraction (PXRD), and DFT calculations. DMMP and DMCP were found to adsorb molecularly (physisorption) to the MOFs through the formation of hydrogen bonds between the phosphoryl oxygen and the free hydroxyl groups associated with Zr6 nodes or dangling -COH groups on the surface of crystallites. Unlike UiO-66, the infrared spectra for UiO-67 and MOF-808, recorded during DMMP exposure, suggest that uptake occurs through both physisorption and chemisorption. The XPS spectra of MOF-808 zirconium 3d electrons reveal a charge redistribution following exposure to DMMP. Besides, the analysis of the phosphorus 2p electrons following exposure and thermal annealing to 600 K indicates that two types of stable phosphorus-containing species exist within the MOF. DFT calculations (performed by Professor Troya at Virginia Tech), were used to guide the IR band assignments and to help interpret the XPS features, suggest that uptake is driven by nucleophilic addition of a surface OH group to DMMP with subsequent elimination of a methoxy substituent to form strongly bound methyl methylphosphonic acid (MMPA). With similar IR features of MOF-808 upon DMCP exposure, the reaction pathway of DMCP in Zr6-MOFs may be similar to that for DMMP, but with the final product being methyl chlorophosphonic acid (elimination of the chlorine) or MMPA (elimination of a methoxy group). The rates of product formation upon DMMP exposure of the MOFs suggest that there are two distinct uptake processes. The rate constants for these processes were found to differ by approximately an order of magnitude. However, the rates of molecular uptake were found to be nearly identical to the rates of reaction, which strongly suggests that the reaction rates are diffusion limited. Overall, and perhaps most importantly, this research has demonstrated that the final products inhibit further reactions within the MOFs. The strongly bound products could not be thermally driven from the MOFs prior to the decomposition of the MOFs themselves. Therefore, new materials are needed before the ultimate goal of creating a catalyst for the air-based destruction of traditional chemical nerve agents is realized. / Doctor of Philosophy / A molecular-level understanding of gas-surface energy exchange and reaction mechanisms will aid in the prediction of the environmental fate of pollutants and enable advances toward catalysts for the decomposition of toxic compounds. Our gas-surface scattering experiments performed in an ultra-high vacuum environment have provided key insights into the outcome of critical interfacial processes on model systems. Results show that energy transfer upon gas-surface collisions depends on both the properties of the gas molecules and surfaces. Due to the formation of interfacial hydrogen bonding network in hydroxyl-terminated surface, the small organic compounds transfer less energy to it than to the organic surface with methyl groups at the interface. The dynamics also appear to depend on the properties of the impinging gas-phase molecule. The π electrons in the double bond of ethene and the triple bond in ethyne act as hydrogen bond acceptors when the molecules collide with the hydroxyl-terminated surface. The attractive forces facilitate energy transfer. A positive correlation between energy transfer and solubilities for analogous solute-solvent combinations was observed for the methyl-terminated surface, but not for the hydroxyl-terminated surface. The extent of energy transfer between ethane, ethene, and ethyne and the methyl-terminated surface appears to be determined by the degrees of freedom or rigidity of the gas, while gas-surface attractive forces play a more decisive role in controlling the scattering dynamics at the hydroxyl-terminated surface. Furthermore, this thesis provides detailed surface-science-based studies of the mechanisms involved in the uptake and decomposition of chemical warfare agent (CWA) simulants on or within metal-organic frameworks (MOFs). Dimethyl methylphosphonate (DMMP) and dimethyl chlorophosphate (DMCP), key CWA simulants, physisorbed to the MOFs through the formation of hydrogen bonds between the phosphoryl oxygen and the free hydroxyl groups associated with inorganic nodes or dangling -COH groups on the surface of crystallites. The infrared spectra for UiO-67 and MOF-808 suggest that uptake occurs through both physisorption and chemisorption. The XPS spectra of MOF-808 zirconium 3d electrons reveal a charge redistribution following exposure to DMMP. Besides, the analysis of the phosphorus 2p electrons following exposure and thermal annealing to 600 K indicates that two types of stable phosphorus-containing species exist within the MOF. DFT calculations suggest that uptake is driven by nucleophilic addition of a surface OH group to DMMP with subsequent elimination of a methoxy substituent to form strongly bound methyl methylphosphonic acid (MMPA). With similar IR features of MOF-808 upon DMCP exposure, the reaction pathway of DMCP in MOFs may be similar to that for DMMP, but with the final product being methyl chlorophosphonic acid (elimination of the chlorine) or MMPA (elimination of a methoxy group). The rates of product formation suggest that there are two distinct uptake processes. The rate constants for these processes were found to be nearly identical to the rates of physisorption, which suggests that the reaction rates are diffusion limited. Overall, this research has demonstrated that the final products inhibit further reactions within the MOFs. The strongly bound products could not be thermally driven from the MOFs prior to the decomposition of the MOFs themselves. Therefore, new materials are needed before the ultimate goal of creating a catalyst for the air-based destruction of traditional chemical nerve agents is realized.

Detailed studies are presented of thin films containing a polycation, a nonlinear optically (NLO) active chromophore, and a synthetic hectorite that self-assemble into the noncentrosymmetric structure required for second order nonlinear optical responses. UV/Vis spectroscopy and ellipsometry were used as probes to monitor film growth for upto 25 deposition cycles. Exceptionally homogeneous films were obtained with regular film growth for up to the 25 cycles deposited. ISAM films self-assemble from polyelectrolyte solutions due to coulombic interactions between a charged substrate and the charged polymer in solution. Charges accumulating at the surface restrict further growth due to charge overcompensation at the surface. The entire process occurs relatively quickly as compared to other competing assembly techniques such as Langmuir-Blodgett assembly and covalent self-assembly. Previous studies indicated that second harmonic signal diminishes after the deposition of the first few bilayers. This is potentially due to adjacent layer interpenetration, which becomes prominent moving further away from the hard substrate interface. Laponite RD, a synthetic hectorite was introduced in the films in an effort to minimize interpenetration of adjacent bilayers and hence maintain chromophore orientation in every bilayer of the ISAM film. The film was deposited in quadlayers that have the following sequence: Polycation–Laponite–Polycation–Chromophore. This study is unique in its approach as it investigates the possible implications of film interpenetration on the NLO-activity of ISAM films that can be easily fabricated. It also shows the effects of different interfaces on the NLO-activities of the films. We have investigated the effect of changing the polycation from poly(allylamine hydrochloride) (PAH) and poly(diallyldimethylammonium chloride) (PDDA) and the solution pH to see how these variables affect the growth and NLO properties of ISAM films. At lower pH values (specify relevant range of values), for both polycations, intrachain and interchain repulsion is strong due to little electrostatic screening. This results in polycation deposition in relatively thin, train-like layers. At higher pH levels (specify relevant range of values here) the electrostatic screening is greater due to a higher effective ionic strength. At these conditions, intrachain and interchain repulsion is reduced and so the polymers adsorb to form thicker layers with more loops and tails than for the case at lower pH. This also results in a higher density of the chromophore in the film. Extremely smooth surfaces of Laponite RD in film were obtained as confirmed by AFM imaging on glass. Regular quadlayer growth monitored by UV/Vis spectroscopy and ellipsometry was observed for up to 25 quadlayers. Second harmonic generation (SHG) signal was not conclusively affected by the presence of laponite as the decrease of signal was seen after the first few layers in the laponite containing films. This decrease was however was not as sharp in the films containing laponite as in the films that did not contain laponite. It was also noted that the SHG was not so much affected by the number of layers deposited but more so by the distance of the chromophore layer from the hard glass interface. This study thus brings to light the very important effect of the glass interface on the NLO-activity of these films. / Master of Science

Ionically self-assembled monolayer (ISAM) films are typically an assemblage of oppositely charged polymers built layer by layer through coulombic attraction utilizing an environmentally friendly process to form ordered structures that are uniform, molecularly smooth, and physically robust. ISAM films have been shown to be capable of the noncentrosymmetric order requisite for a second-order nonlinear optical response. However, films fabricated with a nonlinear optical (NLO) polymer result in significant cancellation of the chromophore orientations. This cancellation occurs by two mechanisms: competitive orientation due to the ionic bonding of the polymer chromophore with the subsequent polycation layer, and random orientation of the chromophores within the bulk of each polyanion layer. A reduction in film thickness accompanied by an increase in net polar ordering is one possible avenue to obtain the second-order nonlinear optical susceptibility chi(2) necessary for electro-optic devices. In this thesis, we will discuss the structural characteristics of ISAM films and explore three novel approaches to obtain the desired characteristics for nonlinear optical response. One approach involves the variation of solution parameters of several different cationic polymers separately from the polyanion solution in order to reduce the competitive chromophore orientation at the layer interfaces and to reduce the thickness of the inactive polycation layer. We have found that the complexity of ISAM films does not allow large chi(2) values in polyion-based films, and that the selection of the polymer cation is vital to achieve second harmonic generation (SHG) at all. The second approach involves the incorporation of dianionic molecules into ISAM films in order to eliminate both competitive chromophore orientation and random chromophore orientation inherent with polymer chromophores. We have also studied the effects of complexing dianionic chromophores with beta-cyclodextrin in order to increase solubility and improve chromophore orientation. This approach fails because the outermost monolayer of dianionic chromophore is only tethered to the preceding polycation layer by a single ionic bond for each molecule, so each chromophore can by dissociated during the following immersion into the cation solution. Finally, we have introduced a novel approach of hybrid covalent / ionic self-assembly which overcomes these disadvantages and yields a substantial increase in chi(2) due to the chromophore being locked in place to the preceding polycation layer by a covalent bond. The films fabricated in this manner yield a chi(2) that rival any polymer-polymer films despite the very low first-order molecular hyperpolarizability beta of the incorporated monomer. This suggests that incorporation of high beta molecules may result in significant improvement of chi(2), holding high promise for the hybrid covalent / ionic self-assembly technique. / Master of Science

Ultrahigh vacuum (UHV) surface science experiments were designed to study reaction kinetics and mechanisms of gas-phase NO₃ radicals with well-organized, highly characterized, organic thin films. The surface reactions were monitored in situ with reflection-absorption infrared spectroscopy (RAIRS). The oxidation states of surface-bound molecules were identified with X-ray photoelectron spectroscopy (XPS). Consumption of vinyl groups was observed concurrently with formation of organic nitrates in RAIRS. XPS spectra showed little oxidation of sulfur head groups. The observed rate constant was determined based on the consumption of carbon-carbon double bonds and the formation of organic nitrates. Using this rate constant, the initial reaction probability was determined to be (3 ± 1) X 10⁻³. This reaction probability is approximately two orders of magnitude higher than that for the reactions between the same surface and pure O₃, which is due to the higher electron affinity of NO₃ relative to O₃. These results led to the development of a proposed mechanism that involves electrophilic addition of NO₃ to the double bonds. Reactions between NO₃ and a methyl-terminated SAM were also monitored in situ with RAIRS. In the CH3-SAM studies, hydrogen abstraction was observed during NO3 exposure. The results presented in this thesis should help develop an understanding of the fundamental interfacial reaction dynamics of NO₃ radicals with organic surfaces. / Master of Science

Reactions of strongly oxidizing pollutants with unsaturated hydrocarbon surfaces are important to many areas of scientific interest. For example, reactions of unsaturated hydrocarbons on the surface of tropospheric aerosols could have a great effect on the oxidizing capacity of the troposphere while the reaction products could be involved in the formation of clouds and smog. These reactions are also important in understanding the toxic effect inhalation of these pollutants have on the pulmonary surfactant of the lung, the only amicable air-water interface of the body. The fatty acids of this surfactant are as much as 30% unsaturated, and exposure to oxidizing pollutant is known to alter both the composition and function of the surfactant. Understanding the reaction mechanism will further the knowledge of how this toxicity occurs. While the reactions of strongly oxidizing pollutants, such as ozone and nitrogen dioxide, with alkenes in the gas and solution phases are well known, the interfacial reaction mechanisms of these species is not fully understood. The goal of this study is to determine the reaction mechanism when an unsaturated hydrocarbon monolayer at the gas-surface interface is exposed to gas phase nitrogen dioxide. An olefin-terminated thiol was synthesized and a self-assembled monolayer on Au(111) made and characterized using Reflection-Absorption Infrared Spectroscopy (RAIRS). This unsaturated surface was then exposed to NO2 at a pressure of 1x10-4 mbar in a UHV (Ultrahigh Vacuum) chamber. Time-resolved RAIRS was preformed in situ to monitor the reaction during exposure. X-ray Photoelectron Spectroscopy and RAIRS determined the surface reaction product as an aldehyde. While the mechanism can not be precisely determined, two mechanisms involving either the hydrogen abstraction or radical addition of the NO2 to yield an aldehyde are proposed. / Master of Science

The discovery of large DNA viruses has challenged the traditional perception of viral complexity due to their enormous genome size and physical dimensions. Previously, viruses were considered small, filterable agents until the discovery of large DNA viruses. Among large DNA viruses, the phylum Nucleocytoviricota and its members, which are often called "giant viruses" have large genome sizes (up to 2.5 Mbp) and virion sizes (up to 1.5 um). Due to having large virion and genome sizes, these viruses were often excluded from viral surveys and remained understudied for years. Luckily, the advancement of metagenomic analysis has facilitated the study of large DNA viruses by analyzing them directly from their environment without cultivating them in the lab, which could be challenging for viruses. In the first chapter of the thesis, I investigated 11 metagenome-assembled genomes (MAGs) of giant viruses previously surveyed from Station ALOHA in the Pacific Ocean. St. ALOHA is located near Hawaii and represents oligotrophic gyres which the majority of the ocean is made of them. I focused on 11 MAGs of giant viruses to get insight into their phylogenetic characteristics, genomic repertoire, and global distribution patterns. Despite the fact that metagenomic analysis has facilitated the study of genetic materials of microbes and viruses on a huge scale, it is essential to benchmark the performance of metagenomic tools and understand the associated biases, particularly in viral metagenomics. In the second chapter, I evaluated the performance of metagenomic tools (contigs assembler and binning tool) in recovering viral genomes using annotated dataset. We used a metagenome simulator (CAMISIM) to generate simulated short reads with known composition to assess these processes. Moreover, I emphasized the importance of binning contigs for viral genomes to fully recover the genomes of viruses along with discussing how diversity metrics were differed for contigs, bins populations. / Master of Science / Viruses are generally thought to be small biological agents with small genome (genetic material) sizes and tiny physical structures; for instance, the genome length of a Human Immunodeficiency Virus (HIV) is around 10 kilobase pair (a unit for measuring genetic material in an organism), and the virion size (physical dimension of a virus) can go up to 120 nm. The discovery of large DNA viruses has challenged the idea of considering viruses as small biological entities, as their genome sizes and physical dimensions can be up to 2.5 megabase pairs and 1500 nm, respectively. Famous members of large DNA viruses from the phylum Nucleocytoviricota are often known as "Giant Viruses'' because they have enormous genome sizes and physical dimensions. Due to having large viral particles, these viruses may usually be excluded from viral surveys. For instance, in field studies, samples must be filtered through a fraction (e.g., 0.2 um) to eliminate bacterial and archaeal genomes and cellular debris, which also results in excluding larger viruses. Since these viruses remain understudied for several years because of biases associated with having large viral particles, there is a solid need to discover and investigate more about them. Growing and cultivating viruses in the laboratory may be challenging, as they need specific hosts to be dependent on to produce more viral progeny and some specific laboratory environments. Luckily, with the advancement of biotechnology, scientists could find ways to evade the need for cultivating viruses in the lab and study them with computational tools such as metagenomic analysis and bioinformatic tools. Metagenomics analysis helps to study the genetic materials of microbial or viral populations directly from their habitat without growing them in a laboratory. In short, metagenomic analysis has multiple steps, including collecting and filtering samples, fragmenting DNA within the samples, generating short DNA sequences (short-read sequences) with NGS (Next Generation Sequencing) technology, assembling short-read sequences into large DNA fragments which can be contigs (contiguous DNA fragments) and metagenome-assembled genome (MAGs). With metagenomic analysis, we can recover the genome of multiple organisms, and we name the recovered genome as metagenome-assembled genome (MAGs) as it is generated through metagenomic processes. The metagenomic analysis will allow us to study microbes and viruses in their environment and gain insight into their taxonomic details, genomic content, and how widespread they are. In the first chapter, I studied 11 MAGs of giant viruses previously surveyed from St. ALOHA, Hawaii. St. ALOHA is a good field site for examining microbial processes and diversity and a good representative of oligotrophic waters (low in nutrients). I examined 11 MAGs of giant viruses to investigate their taxonomic characteristics to clarify which order they belong to within their phylum, their genomic content, and their global distribution pattern. Although studies have successfully recovered the genome of large DNA viruses from their habitats and then analyzed them, all these metagenomic processes need to be evaluated so the results will be valid to consider as the genome of our interested organisms. In the second chapter, I developed a workflow for viral metagenomic analysis to assess metagenomic tools' performance in recovering reliable viral genomes, particularly for large DNA viruses. Most of these benchmarking workflows are done for bacterial and archaeal genomes, and in this thesis, I used these metagenomic tools and applied them to recover large DNA viruses genomes. Also, I emphasized the importance of using binning tools to fully recover large DNA viruses genomes, as due to their large genome size, their genomes might remain fragmented into different contigs, which are longer sequences than reads but shorter than MAGs.