Low energy (tens of eV) ion-surface collisions carried out in a tandem mass spectrometer are investigated as a tool to characterize self-assembled monolayer (SAM) films. The target films are prepared by spontaneous chemisorption of thiol-based (HS-R) compounds onto Au (111) substrates. Most of the films used as targets contain alkane or fluoro-alkane backbones, some with unique groups in the terminal position (e.g., -CD₃, -OH, -OC(O)CF₃). Pyrazine is the most frequently used probe ion, however in certain cases other small organic molecules are also used. Common interactions between the impinging ion and the target film that vary as a function of film characteristics include, but are not limited to, reactive scattering, neutralization and T → V conversion. Pyrazine ion readily reacts when colliding with hydrocarbon films at 20-eV, forming product ions that incorporate a hydrogen atom or a methyl group. Several examples of the utility of these processes to characterize film properties are presented. For hydrocarbon films, ion-surface reactions of pyrazine ion resulting in addition of a hydrogen atom or a methyl group are shown to vary with the quality, chemical composition and orientation of the target film. Experiments with isotopically labeled films show that the ion beam interacts predominantly with the end groups of the film, however interactions with underlying groups increase as the film or substrate quality decreases. The orientation difference of odd and even chain length n-alkanethiols produces a measurably different degree of hydrogen addition with the higher free energy odd chain length orientation being more reactive. The composition of mixed component films (H, D or H, F) is tracked by measuring the abundance of unique reaction products, energy transfer (translational to vibrational conversion) and charge exchange properties. When mixed films containing deuterium labeled and unlabeled n-alkanethiols are subjected to collisions of 20-eV pyrazine ion, the D-addition ion abundance increases linearly with the surface concentration of D-containing alkane chains. When mixed films containing different ratios of H and F components are the target, several processes track with the changing population of surface species. As the target films become more fluorocarbon in nature H-addition decreases, total ion current reaching the detector increases, and dissociation increases. Several properties of electron transfer from the film to the ion are examined. When the probe ion and collision energy remain consant, charge exchange is shown to be primarily governed by the work function of the film and the thickness of the adsorbed layer. Fluorocarbon films, which have a higher work function than hydrocarbon films, consistently show less charge exchange. When comparing hydrocarbon films of varying chain lengths (ranging from 15 to 18 carbons), a increase of ∼1% in total ion current measured at the detector is observed for each additional methylene in the chain.

Organic thin films (alkanethiolates chemisorbed on gold) were employed in low-energy (eV) ion-surface collisions to validate the technique as a surface analysis tool and to further investigate processes associated with ion-surface interactions. Low-energy ion surface collisions of small polyatomic and atomic ions with self-assembled monolayers (SAMs) ascertain the chemical composition, structure, and quality of SAMs utilizing four processes: energy transfer (fragmentation of projectile ions: surface-induced dissociation (SID)), electron transfer (neutralization of the projectile ions), atom/group transfer (reaction between the projectile ion and atom/groups from SAMs), and chemical sputtering. Low-energy ion-surface collisions were used to investigate newly synthesized fluorinated compounds where the degree of fluorination of the thiolate tail group increases. Data indicate that substitution of CH₃ with CF₃ as the terminal group has a substantial influence on energy transfer, electron transfer, and atom/group transfer. Slight penetration into a depth of SAM films is illustrated by the formation of certain ion-surface reaction products (a result not observed for previously characterized Langmuir-Blodgett (L-B) films). A novel neutralization mechanism for reaction between methyl cation and hydrocarbon and fluorocarbon SAMs was established. Ion neutralization (besides direct electron transfer) results from a hydride ion transfer, methyl anion transfer, or fluoride transfer between hydrocarbon and fluorocarbon SAMs and incoming methyl cations. Experimental ion-surface and ion-molecule data support the ion neutralization mechanism originally proposed by ab initio and thermochemical calculations. Ion-surface processes were also used to characterize three mixed SAM systems (system 1: hydroxyl/hydrocarbon mixed SAMs and systems 2 and 3: fluorocarbon/hydrocarbon mixed SAMs). The mixed SAMs were prepared from binary thiol solutions and uniform solutions of asymmetrical disulfides. These ion-surface data can be useful for qualitative (identification of the sample's chemical composition) and quantitative analysis (calculation of the surface concentration of a chemical species for a mixed SAM). An in-line Sector-Time-of-Flight (TOF) tandem mass spectrometer with low-energy ion-surface collisions was characterized. Research involved testing the versatility of the instrument in terms of effective ion activation (peptide fragmentation) and surface analysis of organic thin films. This prototype will aid further implementation of SID into commercial TOF instruments for efficient ion activation and surface analysis capabilities.

This dissertation has focused on (i) the characterization and optimization of the near-surface region of indium-tin oxide (ITO) thin films, and (ii) the characterization of the microstructure and electrical properties of thin films of several new self-organizing liquid crystalline phthalocyanines (Pcs). Commercial ITO surfaces were explored through a combination of high resolution X-ray photoelectron spectroscopy and electrochemical techniques. It was determined that sputter-deposited ITO films undergo hydrolysis immediately upon exposure to atmosphere, creating InOOH and In(OH)₃ species, which appear to inhibit charge transfer reactions. The surface coverage of these InOOH and In(OH)₃-like species can be controlled by various solution and vacuum pretreatments, including etching with EDTA solutions, and RF-plasmas. Characterization of new discotic mesophase Pc materials has focused on modifications of the original Pc in this series, CuPc(OCH₂CH₂OBz)₈, including a polymerizable version, CuPc(OCH₂CH₂OCH₂CH=CH-Ph)₈, and the sulfur analogs of these molecules, CuPc(SCH₂CH₂OBz)₈ and CuPc(SCH₂CH₂OCH₂CH=CH-Ph)₈. The self-organizing properties of these new Pcs are altered by the changes in side chain composition, but still show the same "column-forming" tendencies as the parent Pc, with long range order. The polymerizable Pc materials can be photolithographically patterned with features as small as 2 microns. Electrical anisotropies in these films were measured with a conductive tip AFM and with OFETs, and anisotropies in current (j(∥)/j(⊥)) were ca. 10 on the micron scale, and up to 1000 on the submicron scale. OFET measurements showed low hole mobilities, which are attributed to poor contact between the Pc column and the Au electrodes. Chemical modification of these electrodes shows that considerable improvements in OFET performance result from this modification strategy. Understanding and controlling the microscopic structure of these Pc films is important for optimizing their electrical properties. A considerable effort was focused on developing a quantitative protocol to combine transmission and reflectance vibrational spectroscopic data to determine the three Euler angles that determine the orientation of these Pcs in an LB-deposited film on a planar substrate. Changes in orientation upon annealing and polymerization were observed, but in general these molecules display tilt angles away from the surface normal of <20° and twists about the surface normal of ca. 25°.

Raman spectroscopy is used to determine rotational and conformational order of a series of high-density octadecylsilane stationary phases as a function of numerous chromatographic parameters. The effect of these conditions on the conformational order of the alkylsilanes offers information about molecular interactions at the chromatographic interface, which can be used to gain insight to the mechanisms of solute retention in reversed-phase liquid chromatography. The use of Raman spectroscopy to investigate fundamental interactions of chromatographic systems is also extended to studying ion exchange systems. In addition to the characterization of existing phases, alkylsilane-based stationary phases are fabricated using a novel solution modifier approach. This simple approach allows for the synthesis of materials that vary in surface coverage using the same reaction chemistry. Phases have alkylsilane structure, architecture, and give chromatographic performance comparable to existing phases of similar coverage.

The relative efficiencies of low energy (< 100 eV) collisional activation techniques were determined for peptide sequencing by tandem mass spectrometry (MS/MS). Tryptic peptides were fragmented using either collision induced dissociation (CID) or surface induced dissociation (SID) to generate spectral databases. Statistical analysis of the resulting fragment ions and success rates for automated peptide sequencing by publicly available algorithms provided a measure of the value of sequencing information content of CID and SID MS/MS spectra. Typical success rates were determined for automated sequencing by SEQUEST¹⁻³, MS-Tag⁴, Mascot's⁵ MS/MS Ion Search and Sequence Query using low energy CID spectra. The ability of an algorithm to match peptide sequences to raw MS/MS data directly depended on various factors including the mass spectrometer from which the spectra were acquired, the precursor ion charge state, and the mass accuracy and resolution available in the spectra. Statistical analysis demonstrated the presence of similar fragment ions in SID and CID spectra. A lack of long contiguous ion series in SID spectra prevented automated sequencing using conventional approaches. Thus, "patchwork peptide sequencing"⁶, an unconventional method to derive specific sequence criteria for unknown peptides from SID spectra, was performed. Submitting this information to Mascot's Sequence Query allowed database searching strategies to achieve automated peptide sequencing with SID spectra. Some aspects of gas phase ion chemistry were explored for the unexpected formation of fragment ions from cleavage C-terminal to proline residues. Semi-empirical calculations suggest the most stable structure for valineprolyl-b₂ ion is a diketopiperazine, although the MS/MS/MS fragmentation pattern for VP-b₂ is indicative of an oxazalone structure. Support for a diketopiperazine structure is provided by similar fragmentation patterns for VP-b₂ and a synthetic diketopiperazine VP, and prevention of the formation of VP-b₂ by acetylation of the free N-terminus. Substitution of N-methyl alanine for proline produces a b₂ ion that fragments by loss of a portion of the valine residue, consistent with an oxazalone structure. However, theoretical calculations suggest the N-methyl alanine-containing b₂ ion is a diketopiperazine. The differences in fragmentation patterns indicate that the gas phase ion structures for the proline- and N-methyl alanine-containing b₂ ions are different, although stability calculations suggest otherwise.

Lipid films are often described as potential surface coatings for the 'biofunctionalization' of solid interfaces because of the ability to support tethered and integrated receptor protein activity and their ability to suppress the non-specific adsorption of soluble proteins. One significant shortcoming of lipid assemblies is the inherent lack of stability required for many technological applications because the non-covalent forces between the constituent lipids are relatively weak. In this work, polymerized, supported lipid bilayers ((poly)PSLBs) composed of diene functionalized lipids have been prepared and characterized. Several parameters relating (poly)PSLB structure and stability to observations made in studies of polymerized bilayer vesicles will be described, including a comparison of UV photopolymerization and redox-initiated radical polymerization, the number and location of the polymerizable moieties in the lipid monomer, and a comparison to PSLBs produced with diacetylene lipids. Redox-initiated polymerization of films composed of bis-substituted diene lipids with at least one polymerizable moiety located near the acyl terminus produces dried PSLBs that are highly uniform and stable. All other conditions yielded PSLBs that contained a high density of defects after drying, including those formed from diacetylene lipids. The nonspecific adsorption of bovine serum albumin (BSA) is used to further characterize the polymer films to fluid PC bilayers, which have been established as protein adsorption "inert" surfaces. The results show that the protein resistance of a cross-linked (poly)PSLB composed of bis-sorbyl phosphatidylcholine (bis-SorbPC) is equivalent to that of a fluid PSLB composed of 1-palmitoyl-2-oleoylphosphatidylcholine (POPC), even after the former has been dried and rehydrated. Furthermore, the (poly)PSLB films can be formed in patterns or patterned with immobilized proteins by microprinting techniques which may facilitate their use in microarray detection schemes.

A novel approach to sol-gel thin film fabrication has been developed which leads to the production of ultrathin ∼2 nm to 100 nm thick silica and conductively-doped silica films on metal and semiconductor substrates. The research described herein focuses on the development, characterization and potential application of these thin films in current technology. These ultrathin films were fabricated by a sol-gel procedure, which utilized highly diluted silica precursor compounds. The [H₂O]:[Si] ratio ranged from 50 to 1000, far above the typical values (4-10) used in sol-gel film preparation. This dilution leads to highly densified silica when spin-cast onto an appropriately compatible surface. The surface examined included Si(111)/SiO₂; ITO; and 3-(mercaptopropyl)trimethoxysilane (3MPT) modified Au and Ag. These surfaces must act as wetting control agents for the sol-gel precursor, while simultaneously providing adhesion to the nm sized sol-gel aggregates. The 3MPT-Ag monolayer was examined in detail by Tl, Pb and Cd underpotential deposition electrochemistry, to understand the interfacial structure of the molecule. These results show that the 3MPT monolayer is very stable to outside influences (i.e. Tl and Pb reversibly deposit monolayers at the metal surface). The UPD of metal ions is highly size dependent with Tl depositing with fewer kinetic limitations than Pb and Cd not depositing at all. Raman spectral characterization shows that 3MPT undergoes some reversible rearrangement during the UPD process. The electronic properties of the pure silica films were examined in great detail. The results suggested that in solution, a solvated gel layer at the film-solution interface gives rise to an anomalously low capacitance <100 pF/cm², which has no comparison in the current literature. In the dry state, these silica films have a dielectric constant of ε = 3.5, which is close to that of thermally-grown silica on silicon (3.9). These films were doped with 1,1'-bistriethoxysilylferrocene, an electrochemically-active sol-gel material. The results suggest that under the proper precursor solution conditions, thin ( <10 nm), uniform films can be fabricated. By simply adjusting the ratio of the ferrocene moiety in solution, the film composition can be adjusted. XPS verifies that the atom ratio in solution is near to the observed atom ratio in the films, with some indication of surface segregation of the ferrocene moiety. Electrochemical analysis of these films suggests that electron hopping between the ferrocene centers drives the electrochemical response only when there are pinhole defects, to support counterion conduction to the surface. (Abstract shortened by UMI.)

Many important and interesting processes, which are essential components of electrochemical technologies, occur at the electrode/electrolyte interface. Using spectroscopic and electrochemical methods, this research elucidates the interfacial structure in nonaqueous solvents existing at metal electrodes. The behavior of trace interfacial H₂O and Li⁺ and Br⁻ ions at Ag electrodes in the normal alcoholic solvents methanol, ethanol, propanol, butanol and pentanol is examined using surface-enhanced Raman scattering (SERS) and differential capacitance measurements. SERS spectra in the ν(O-H) region exhibit four bands from interfacial H₂O molecules which are a sensitive function of the nature of the solvent, the residual H₂O concentration, and the electrode potential. The results of this study indicate that in the interface, H₂O molecules cluster around Li⁺ and Br⁻ ions and are not homogeneously dispersed. Br⁻ specific adsorption and interfacial solvent behavior in the series of alcohol solvents are interpreted quantitatively through differential capacitance and SERS experiments. Br⁻ surface coverage is calculated using the "Hurwitz-Parsons" analysis of differential capacitance-potential data in these media. These results indicate that almost a monolayer of Br⁻ adsorb on Ag electrodes, but much less Br⁻ ions adsorbs on Au electrodes at positive potentials. The potential of zero charge (pzc) is also quantitatively estimated from these measurements. The technique of "emersion" of an electrochemical interface from electrolyte has opened the door to new possibilities for fundamental electrochemical studies. The relationship between in-situ and emersed electrochemical systems is probed through the study of the interfacial structure of dimethyl sulfoxide (DMSO) on Ag electrodes. The results of this study indicate that pronounced restructuring of the DMSO in the interface is found in the vicinity of the pzc. The solvent orientation is generally retained upon emersion, but a negative emersion-induced potential shift in the interface is observed due to the reorientation of DMSO molecules at gas/solution boundary phase. These data represent the first spectroscopic evidence for the existence of this emersion-induced potential shift.

Graphite furnace atomic absorption spectrometry has excellent detection limits and accepts a wide variety of samples with little or no sample preparation. The method does, however, suffer from matrix interferences and a lack of highly capable multielement instrumentation. Continuum sources have been employed to GFAAS for multielement determinations, but the one dimensional array detectors used in these instruments can only observe a limited spectral range, limiting the multielement capabilities of these instruments. A continuum source, multielement graphite furnace atomic absorption spectrometer was developed here which employed a prototype echelle polychromator with charge injection device(CID) detection. The detection system employed a new device, the CID&sim;38, and camera control unit, the SCM5000E, with previously unavailable abilities. The camera system was developed and evaluated to determine its spectroscopic characteristics, and reprogrammed to provide rapid, continuous monitoring of many absorption signals simultaneously. A data acquisition and analysis scheme was developed for the prototype system, and the instrument demonstrated detection limits comparable to single-element line source GFAAS. The low ultraviolet throughput of the prototype echelle limited the spectral range that could be observed. Light scattering inside the spectrometer caused the sensitivity to decrease as the number of elements observed increased. A second echelle spectrometer system with higher wavelength resolution and increased throughput in the far ultraviolet was incorporated in to the instrument. The new system increased the spectral range which could be monitored, allowing more elements farther in the ultraviolet to be determined. The detection limits for the new system are comparable to single-element GFAAS, but degrade farther in the ultraviolet due largely to decreasing source output.

Solid phase extraction (SPE) is an extension of conventional liquid chromatographic methods. In the case of SPE the desired separation is digital in nature. Under one solvent condition total retention occurs while under a second solvent condition total elution occurs. The role of SPE as a sample preparation tool is becoming more dominant in the field of analytical chemistry. The need for high throughput, decreased solvent usage, and automation makes SPE the method of choice over other extraction methods. Ionic interactions at modified silica sorbents are studied with respect to the impact on the isolation and purification of analytes. The interactions are characterized by quantitating absolute recoveries for a variety of analytes under different conditions, and qualitative analysis of analytical interferences. Extractions of ionizable compounds were found to be dependent on a myriad of factors. These factors include sample pH, buffer composition, solution concentration, and elution solvent composition. Selectivities for ionizable analytes can be increased by utilizing ionic interactions, particularly in a mixed-mode operation. The extraction of basic compound compounds is generally robust, while methods for the acidic analytes are more highly dependent on the type of counter-ion. Ion selectivities observed were different than those recorded for polymer-based ion-exchange sorbents. The organization of water in the near surface region of the silica-based sorbents is the reason for the disparity between the two types of materials. The utility of a polymeric polystyrene divinylbenzene sorbent for the analysis of analytes from biological matrices is demonstrated. It was shown that these sorbents can withstand harsh chemical environments that would preclude using a silica-based material. Analysis times were shortened and extraction efficiencies were comparable to the silica materials. The extractions were not as selective as those performed on mixed-mode sorbents however.