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Previously, mineral nucleation was described by Classical Nucleation Theory (CNT), a theory based on the thermodynamic properties of bulk materials. However, an alternative model, known as the Prenucleation Cluster Pathway, has been increasingly used to describe nucleation of minerals. This model considers the presence of thermodynamically stable ion clusters known as “prenucleation clusters” (PNCs). In the present research, the nucleation mechanism of calcium fluoride was investigated to identify evidence of PNCs by means of the ion-selective electrode (ISE) method, where a CaCl2 solution was titrated into a NaF solution while investigating the effects of saturation level and the aqueous ratio of [Ca2+] to [F-]. It was concluded that the nucleation of fluorite is better supported by the Prenucleation Cluster Pathway rather than CNT. However further analysis of the accuracy of ion-pair formation constants is necessary in order to confirm.

Exploding bridge wire (EBW) detonators containing pentaerythritol tetranitrate (PETN) were aged alongside free flowing PETN powder in ovens ranging from 50 ˚C to 75 ˚C, for up to 18 months in order to evaluate physical properties such as threshold voltage and Fisher specific particle size as well as chemical changes. In order to evaluate the chemical changes, PETN and aged PETN from the detonators were analyzed using ultrahigh pressure liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UHPLC-QTOF) in order to measure degradation products formed during aging. Following chromatographic analysis, the data was imported into MATLAB utilizing a region of interest (ROI) code that compressed and filtered the data while also maintaining the true mass of ions. Partial least squares (PLS) models were then developed to compare chromatographic data to Fisher specific surface area and threshold voltage of the aged free flowing PETN powder and EBW detonators, respectively. Additionally, feature selection employing a relative standard deviation tile-based variance ranking was used on the chromatographic data to improve PLS models. The PLS models did not present a correlation between the chemistry and the physical properties of the samples even with the feature selection. However, feature selection was able to find significant chemical differences in the data.

We utilized electrospray ionization, collision-induced tandem mass spectrometry, andcomputational chemistry to investigate the gas phase ion structures and dissociationpathways of model deprotonated petroleum acid anions [M-H]-. The combination ofexperimental and theoretical approaches provides a mechanistic understanding of thestructure-specific dissociation chemistry of targeted petroleum acids. We experimentallyand theoretically studied a series of positional isomers and related compounds withvariations in aromaticity, size, alkylation, and heteroatoms. Petroleum acids cause significant corrosion during petroleum refining and havebeen found in weathered petroleum environmental samples as intermediate anaerobicbiodegradation products of naphthalene. The differences in structure, size, alkylation, andaromaticity affect the subsequent reactivity of these naphthenic acid species.Understanding neutral losses and fragments from the structural elucidation of variousisomers is useful in understanding the availability of transformation products ofnaphthalene biodegradation, thus enabling the deduction of the extent of biodegradation.Our experiments revealed that the aryl scaffold in each aromatic acid isunsurprisingly very stable, with little or no fragmentation detected. Decarboxylation (CO2loss) reactions were detected and modeled in all acids. The position of the carboxylatesubstituent on the aromatic or cyclo-aliphatic ring significantly influenced the ease of4decarboxylation. Alkyl-substituted acids are far more labile and thus readily cleaved withrelative ease, depending on the electron density distribution along the alkyl chain length.We observed that smaller and larger aromatic acids can be differentiated based on theirreaction with water. Isomers with cyclo-aliphatic ring systems dissociate through highenergy, unique ring-opening reactions such as methane and formaldehyde neutral loss.Conversely, isomers containing a nitrogen heteroatom exhibited decarboxylation andethene loss with distinct dissociation mechanisms.Generally, petroleum acid isomers containing carboxylate groups on position 2and aromatic ring sides were more experimentally (and theoretically) stable than their 1′substituted isomers with the functional groups on the cyclo-aliphatic ring side. Densityfunctional theory (DFT) calculations supported experimental observations and allowedthe elucidation of our proposed reaction mechanisms for forming all fragments. Finally,ion abundance graphs utilizing differences in relative abundances and unique higher-energy fragments were studied and employed to differentiate unknown mixtures oftetrahydronaphthoic acid isomer concentration ratios.Through collision-induced dissociation tandem mass spectrometry coupled withcomputational chemistry, we have generated an ESI mass spectral library (currently nonexistent) comprising sixteen petroleum acids and their intricate differences in structuralstability. The knowledge of an isomer’s stability and transformation products enableseffective investigations of prevailing biological processes that are active on weatheredpetroleum samples and enables effective predictions of the corrosivity of petroleumcrudes in corrosion studies.

The cardiovascular system is mainly regulated by nitric oxide (NO). A reduction in itssynthesis or bioavailability might underlie the impaired endothelium-dependentvasodilatation, which is observed in the blood vessels of individuals with cardiovasculardisease (CVD). The dysfunction of endothelium, which is a main characteristic of vascularaging, has been associated with low NO production and high production of cytotoxicperoxynitrite (ONOO-). Thus, the ratio of NO to ONOO- is an indicator of endothelialdysfunction. Moreover, vascular NO is produced by an enzyme called (endothelial nitricoxide synthase (eNOS), and its gene exhibits high polymorphism. However, it is unclearwhether polymorphisms or haplotypes in the eNOS gene affect the NO production, ONOO-production, and eNOS coupling, as well as how aging impacts these haplotypes. Theinfluence of the eNOS haplotype (consisting of single nucleotide polymorphisms (SNP) inthe promoter region (T-786C) and (C-665T) and exon 7 (Glu298Asp) and a variablenumber of tandem repeats (VNTR) in intron 4 (4a/4b/4c)) on the production of NO andONOO- and eNOS coupling was investigated. Sanger sequencing and DNA electrophoresiswere used to detect SNPs and VNTRs in the samples, respectively. To evaluate theproduction of NO and ONOO-, nanosensors were used to determine the maximalconcentrations of NO and ONOO- and traditional and low-temperature SDS-PAGE toevaluate the expression of eNOS and the eNOS dimer/monomer ratio, respectively.Interestingly, these results indicated that the eNOS haplotype (H5) combining the “T T/C C44b” of the G894T, T-786C, C-665T, and 27 bp VNTR a/b/c is more susceptible toendothelial dysfunction. Compared with other haplotype samples, it had lower[NO]/[ONOO-] and higher eNOS expression with reduced eNOS dimer/monomer (P

Excess adsorption isotherms of acetonitrile and methanol from water were measured on eight commercial columns. Columns used in this study represent the latest examples in column development and include three different poroshell columns (Kinotex C18, Ascentis C18, and Halo C18) as well as conventional columns with significantly different adsorbent geometries (Allure C18, YMC C18) and various hybrid-silica columns (Gemini C18, Xterra C18, and XBridge C18). Comparison of the excess adsorption isotherms measured on all these columns and expressed in surface-specific form demonstrated significant similarity of the adsorption properties of all columns, which allows the introduction of the Standard Excess Adsorption Isotherm (SEAI) for reverse phase C18 type columns. The methodology of the evaluation of the total amount of adsorbent in the column and the effective surface area of the C18 modified adsorbent is also discussed. These terms are critical for the successful evaluation of surface-specific parameters. One critical but underutilized parameter affecting chromatographic separation is adsorbent surface area (S.A). We introduce a concept of direct determination of the total surface area in chromatographic columns by utilizing non-destructive measurements of eluent component excess adsorption isotherm measurement and the application of the SEAI from acetonitrile-water and methanol-water binary mixtures for direct determination of the S.A. in chromatographic columns. This nondestructive technique was used to determine the surface area for five new C18 commercial columns and one in-house made C18 column. The Brunauer-Emmett-Teller traditional (BET) method was compared to the novel chromatographic nondestructive surface area determination method for adsorbents modified with octadecylsilanes. The chromatographically determined surface area was in agreement with the conventional techniques for all columns used in this study. The difference between the traditional method and our novel chromatographic method is less than 10%. Obtained columns were characterized in terms of adsorbent, geometry ( e.g., pore volume, columns void volume, inter-particle volume), ligands bonding density, and the amount used for the packing material in a chromatographic column were also studied. In addition, we have also shown that our novel non-destructive chromatographic determination of surface area could be used directly in obtaining surface-specific retention factor ks for direct C18 column comparison. The investigation extended to explore the applicability of the Standard Excess Adsorption Isotherm (SEAI) in estimating surface areas for column types beyond C18. Under the influence of the mobile phase, the long-chain ligands adopt a "collapsed configuration." Consequently, the adsorption behavior for stationary phases modified with alkyl chains of varied lengths proves comparable, provided bonding densities of the ligands also remain consistent. Comparable behavior was observed across different chain lengths, indicating the potential of SEAI for surface area determination in columns beyond C18. Stationary phases with varying ligand lengths (C1, C4, C8, and C18) were synthesized in-house and thoroughly characterized. The findings suggest that our innovative, non-destructive approach to surface area determination holds promise for C4, C8, and C18 ligands.

Linear polyenes are a class of compounds containing two or more alternatingcarbon-carbon double and single bonds that have a range of applications fromantioxidants in nature to non-linear optical switches. More recently, other related πconjugated systems (like cinnamaldehyde) with heteroatoms within the π-conjugation arebeing used as chemical additives in fracturing fluids (or “fracking”) in our continuedexploration of crude oil. Though this class of chemicals is considered non-hazardous,they are susceptible to oxidative additions initiated with a free radical oxidant. Because oftheir relative insolubility in water and high solubility in non-polar solvents, theprotonation of conjugated polyenes represents a potential pathway to create novel cyclicconjugated structures in one step or hazardous products in the environment. I willpresent a systematic approach to analyzing the numerous products from the reaction oflinear polyenes with trifluoroacetic acid under Airfree conditions to compare to therelative product distributions. The data generated in this project also provides insight intothe relative stability of carbocation intermediates that are potentially created. Based onthe structure of the products, we will propose mechanisms for the resulting reactionsbased on multivariate spectroscopic data sets. Some of the spectroscopic techniquesinclude 1D and 2D NMR, UV-vis spectroscopy, fluorescence spectroscopy, and MassSpectroscopy. The products that were isolated thus far indicate that inter- andintramolecular cyclization are occurring after the protonation of the polyene occurs.

There is a continuous thrust for cleaner and more sustainable alternatives for energy conversion with the increasing global energy demand. Among them, photovoltaics, specifically thin film solar cells are highly promising and are one of the fastest growing clean energy technologies in the United States. This research presents the synthesis and characterization of a set of novel multinary copper chalcogenide semiconductor nanocrystals (NCs), CuZn2ASxSe4-x consisting primarily of earth-abundant elements for applications in photovoltaic devices. A modified hot-injection method was used to synthesize these semiconductor NCs containing both S and Se chalcogens. The novelty of the new semiconductor NCs lies in the incorporation of multiple cations as well as two different chalcogen anions within the crystal lattice, which is an achievement from the materials synthesis aspect. The composition-controlled optical and photoluminescence properties of the CuZn2ASxSe4-x NCs were investigated via multi-modal material characterization including x-ray diffraction (XRD), ultraviolet-visible (UV-vis) spectroscopy, and photoluminescence spectroscopy (PL). The crystal structure, as determined from the XRD primarily consisted of the metastable wurtzite (P63mc) phase. The NCs exhibited direct band gap in the visible range that could be tuned both by varying the group III cation within the composition as well as the ratio of S/Se, based on the Tauc plot obtained from the UV-vis characterization. This work lays the groundwork for future investigations into the practical applications of copper chalcogenide NCs in solar energy conversion.

Organic sensors emitting in the near-infrared region (600-900 nm) are desirable for biological applications. Through the combination of different functional groups with Excited State Intramolecular Proton Transfer (ESIPT) segments, novel probes have been crafted to attain large Stokes shift, improved sensitivity, selectivity, and the ability to tune emission towards the NIR region. Chapter I summarizes recent progress in this field, by including the photophysical properties inherent in ESIPT dyes, and investigated the impact of structural and environmental factors to their fluorescence. Furthermore, the potential applications of these probes as imaging reagents are exemplified such as labeling intracellular membranes, mitochondria, lysosomes, and detecting biomolecules.In Chapter II, four NIR-emitting ESIPT dyes, each featuring distinct cyanine terminal groups, were scrutinized to assess their fluorescence lifetime characteristics in the polar aprotic solvent. By using time–correlated single–photon counting (TCSPC) method, these ESIPT-based dyes revealed a two-component exponential decay in about 2-4 nanoseconds (ns) which was proved to exclusively from keto tautomer. The model compounds (1.10 and 2.2) as well as low-temperature fluorescence spectroscopy (at -189 ℃) identified intramolecular charge transfer (ICT) as a prominent factor influencing the lifetime values. ESIPT simplified lifetime components.Chapter III includes ESIPT probes with benzoindolium terminal group, which shows large Stokes shift (Δλ≈250 nm) and good quantum yield. The probe also exhibited a minor absorption (~580 nm in DCM) and emission (∼ 610 nm in DCM), attributed to a zwitterionic structure formed through deprotonation of phenolic proton. Fluorescence confocal microscopy investigations highlighted the probe's excellent selectivity for mitochondria, and unusually strong emission in the 595 nm channel rather than the expected 700 nm channel. The study thus illustrated a reaction-based probe for ATP.In chapter IV, two ESIPT-based isomeric cyanines (4,1 and 4.2) with pyridinium terminal segment were synthesized. Because of extended π- conjugation by inclusion of a furan ring, these compounds exhibited significant bathochromic shift in the optical spectra. Probe 4.1 exhibited a larger conjugation and better photostability, in comparison with the 4.2. Both compounds exhibited good selectivity for labeling plasma membrane of prokaryotic cells and hair cells of zebrafishes.

In the past two decades, Marcus and colleagues have led the advancement of capillary-channeled polymer (C-CP) fiber stationary phases for biomacromolecule separations, including proteins and nanovesicles. These stationary phases offer notable advantages, including low cost ($5/column), straightforward column fabrication, and the capacity for on-column surface modification, enabling high chemical selectivity. This study examines a C-CP fiber modification strategy for capturing target proteins and develops a Tween-20-assisted C-CP-based hydrophobic interaction chromatography (HIC) method for the isolation and quantification of exosomes from human urine. The quest for higher-throughput and cost-effective protein isolation techniques remains a key focus in a variety of end uses. The streptavidin-biotin interaction, known for its exceptional specificity and stability, offers a promising avenue for protein purification. In this approach, immobilization of streptavidin (SAV) onto a solid substrate is crucial for the effective capture of biotinylated proteins. This study explores the potential of polypropylene (PP) C-CP fibers as support phases for SAV immobilization via direct adsorption. The PP C-CP fiber columns modified with SAV efficiently capture biotinylated proteins, indicating the promise of this approach for fast and cost-effective target protein capture. Exosomes, membrane-secreted vesicles ranging from 30 to 200 nm, play crucial roles in intercellular communication and hold potential as therapeutic delivery vehicles. Efficient isolation and quantification methods are essential for studying their functions and therapeutic applications. Marcus and coworkers have developed Polyester (PET), capillary-channeled polymer fiber columns, and spin-down tips as high-throughput and cost-effective approaches for exosome isolation. However, selecting the optimal elution solvent remains a challenge, particularly for preserving the structural integrity of the isolated vesicles. This study evaluates Tween-20, a non-ionic detergent, as an elution solvent for exosome recovery from human urine in advancing the versatility of C-CP fiber column-based HIC isolation methods.

One of the major problems facing analytical chemistry challenge is the isomers separation, due to their closely related molecular structures and physicochemical properties. Therefore, in this thesis, we have performed the separation of steroid isomers through the use of ion mobility mass spectrometry, using various chemical approaches. Ion mobility is an effective high-resolution separation techniques that utilizes the mobility of ions in the gas-phase environment. A useful tool for isomeric analysis due to the ability to separate different isomeric classes of steroids according to their varied collision cross-sections, which is achieved by taking advantage of differences in ion mobility. Moreover, the derivatization reactions were employed to introduce distinctive functional structures to the steroid molecules, facilitating enhanced separation through ion mobility spectrometry. In this work, a range of derivatization techniques investigated in order to modify the structure, size and charge of steroid isomers and improve their resolution and detectability. These techniques include the use of “shift reagents” such as 1,1-carbonyldiimidazole, Girard’s Reagent P, dansyl chloride, and 4-(bromomethyl)benzenesulfonyl chloride. To sum up, this thesis provides insight into the continued development and use of advanced techniques for the analysis of steroids, highlighting the role of ion mobility mass spectrometry and the advantage of derivatization reactions in the identification and separation of isomeric forms. The presented methodologies can be a great scientific interest to a large number of fields working with steroids and requiring accurate identification and quantification of isomeric forms, including but not limited to environmental monitoring and pharmaceutical, clinical, and forensic chemistry.

Detection of environmental pollutants, both inorganic and organic, has been an ongoing area of research for nearly three-quarters of a century. In recent years there has been growing research in the discovery of complementary methods for detection of environmental pollutants that are decentralized, rapid, and can be used onsite. A promising approach is the application of biosensors. Two common sensor classes are DNAzymes and Bacteria-Based Sensors (BB sensors). DNAzyme sensors have been discovered for the detection of many different metals. However, DNAzyme sensors have historically had issues with non-specific activity due to the presence of other metal ions with similar valency as their native metal cofactor. Further, they are limited in multiplex detection of environmental pollutants due to the limited number of orthogonal fluorophores. Moreover, there are limited sources in the literature for the design of DNAzyme sensors for the detection of organic pollutants, e.g., per- and polyfluoroalkyl substances (PFAS). In contrast, BB sensors have been developed to detect a broad range of compounds from metals to organic substances. Although many BB sensors have been developed for the detection of organic pollutants, there have been limited reports in the literature of BB sensors designed for the detection of PFAS. This dissertation aims to leverage the nonspecific activity of DNAzyme sensors by using a pattern-based readout to identify metal pollutants. Towards this goal, we investigated the DNAzyme cross-reactivity on five DNAzymes (17E, GR-5m EtNa, Ag10c, and NaA43) with eight different metals, and analyzed the data through several statistical methods. Through this approach, we were able to correctly identify four validation solutions, of which, one validation solution consisted of 100 μM Zn2+, which is a known interferent for 17E. Following this, the dissertation explored a new DNAzyme reporter architecture, DzNanoporeSeq, where sequencing is used as a signal readout instead of fluorescence. DzNanoporeSeq showed high accuracy for determination of validation solutions when compared to the fluorescent substrate architecture. This can especially be observed for the 5 nM Pb2+, where DzNanoporeSeq determined this solution to be 4.95 ± 0.12 nM, while the fluorescent reporter architecture determined this solution to be 14.53 ± 1.22 nM. With the promise of multiplex detection of metals by DzNanoporeSeq, this dissertation sought to explore the possibility of constructing an array for the detection of PFAS but using bacterial biosensors. To achieve this, a commercially available E. coli K12 MG1655 promoter library was mixed for each promoter strain to be present in the same quantity, and then screened using fluorescence activated cell sorting (FACS) for the determination of promoters that would “turn-on” and “turn-off” due to PFAS. However, this research did not elucidate promoters sensitive to PFAS.

Pathogenic microbial contamination of the environment poses a significant threat to human health. Accordingly, microbial surveillance is needed to ensure safe drinking water and air quality. Current analytical methods for microbes are generally either culture-based, gene amplification-based, or sequencing-based. However, these approaches require centralized facilities, well-trained personnel, and specialized instruments that result in high costs and long turnaround times. Surface-enhanced Raman spectroscopy (SERS)-based techniques have been proposed to overcome these limitations. In this dissertation, we discuss work conducted to develop novel SERS-based methods to enable both sensitive microbial quantification and analysis of the interactions of pathogens, their hosts, and the surrounding environment. We first developed a labeled SERS-based lateral flow test for virus quantification. Optimization of the lateral flow design and digital signal analysis enabled high sensitivity towards SARS-CoV-2. To elicit a comprehensive understanding of pathogen infection, label-free living-cell SERS sensors were engineered by incubating host cells with nanoparticles. SERS spectral changes in host cellular components and metabolites during infection were used for viral quantification and offered inherent insights into the temporal and spatial molecular-level mechanisms of infection. These biosensors were validated using bacteriophage Phi6 and then developed for infectious H1N1 influenza. To understand microbial survival in the environment, living-cell SERS methods were applied under various conditions. Results showed cell inactivation and antibiotic treatment induced significant cellular and metabolic responses in the living whole-cell sensors, implying their potential applicability to various environmental conditions. Our research achieves rapid and on-site pathogen quantification and infection mechanism identification.

Rice production in California is a thriving, multi-billion dollar industry, with the Sacramento Valley alone producing over 95% of the nation’s short- and medium-grained rice. The sustainability of this industry is threatened, however, by the rapid evolution of herbicide resistant weeds spurred by long-term monoculture and a lack of herbicides with alternative modes of action. One agent proposed to ameliorate the lack of chemical control options is oxyfluorfen (OXY). OXY is a broad-spectrum, diphenyl ether herbicide that disrupts chlorophyll synthesis through inhibition of the protoporphyrinogen oxidase (protox) enzyme. It has demonstrated effectiveness against rice weeds, including weedy rice (Oryza sativa f. spontanea), a pest for which no herbicide is currently registered, and resistance to its mode of action has not been reported by rice growers. However, OXY is not currently registered for use with rice and its use in- or near-aquatic resources is currently prohibited due to its high toxicity to aquatic organisms. As rice field floodwater is ultimately released into nearby waterways, use of OXY with rice introduces the potential for its transport to the Sacramento River Basin where sensitive aquatic organisms may be harmed. Thus, it is imperative that registered uses be informed by a clear understanding of its transport and dissipation processes and potential for environmental impacts when it’s used as a rice herbicide. To that end, it is the objective of this work to elucidate the environmental fate and aquatic risk of OXY when used as an herbicide in California rice fields.Partitioning processes greatly influence overall fate by determining where a pesticide is found and which processes contribute most to dissipation. Thus, the soil-water partitioning behavior of OXY under simulated California rice conditions was characterized using a batch equilibrium method. Soil-water partitioning was investigated in two soils collected from Sacramento Valley rice fields, at rice field temperatures (15, 25, 35 ℃), and under various rice field salinity conditions. OXY showed high affinity for rice field soil (log[KF] 2.92–3.44) that was largely concentration independent (N 0.87–1.08) and correlated with soil organic carbon (log[Koc] 4.79–5.19) across all soil, temperature, and salinity treatments. Temperature enhanced binding affinity and bound OXY was poorly desorbed (9.3 to 27.0% desorption), exhibiting pronounced sorption hysteresis (HI > 0) in all treatments. These results indicate OXY is likely to concentrate in the sediment where it resists further dissipation, leading to persistence. Volatilization from rice field water is recognized as a significant dissipation route for recalcitrant herbicides. Thus, the air-water partitioning behavior of OXY was investigated through determination of Henry’s law constants (KH) at rice field temperatures. A screening approach for evaluating the feasibility of experimental determination of KH via gas-stripping method was developed and used to demonstrate that KH cannot feasibly be measured for OXY; it must be calculated. Thus, KH was calculated using four air-water partitioning models. Three (3) of the four models (EPI Suite, Kühne, and Two-Point Extrapolation) indicated that OXY is slightly volatile (KH 3.00E-07−1.00E-05 atm·m3·mol-1) at rice field temperatures (15−40 ℃), except at low temperatures (5−10 ℃) where it is nonvolatile (KH < 3.00E-07 atm·m3·mol-1). A single model (AQUAFAC-Sepassi) suggested OXY was substantially volatile (KH > 1.00E-05 atm·m3·mol-1) at all rice field temperatures; however, investigation revealed limitations in the ability of the model to predict key physical properties for OXY, suggesting less robust results. Thus, the preponderance of evidence suggests OXY is nonvolatile to slightly volatile in California rice fields. Partitioning and dissipation processes of OXY, in conjunction with anticipated use patterns in California rice fields, were then simulated using the Pesticides in Flooded Applications Model (PFAM). Estimated environmental concentrations (EECs) were calculated under two (2) California rice field soil conditions and one standard soil condition, with water holding periods of 30 days and 0 days (no holding period). OXY concentrated heavily in sediment (21-day Avg Benthic Sediment EEC: 220,747−411,000 µg/kg-oc) with limited presence in water (21-day Avg Water Column EEC: 2.97−31.4 µg/L). Dissipation was slow and severely limited by microbial metabolism (anaerobic) in the sediment, with an effective half-life of 610.6 days for all treatments. While dissipation in the water column was substantially faster (Cumulative Effective Half-life: 9.4−10.5 days), its limited availability in water rendered OXY less sensitive to water column dissipation pathways. Consequently, water holding period had little effect on rice field and release water concentrations. Overall, these results indicate OXY is likely to accumulate in soil over time, leading to chronic exposure conditions for aquatic life as it slowly releases into water. Risk to aquatic receptors was characterized using calculated EECs and in accordance with ecological risk assessment guidelines. Acute risk was generally low for water column animals (fish and invertebrates) and benthic invertebrates. However, chronic risk to freshwater fish (surrogates for aquatic-phase amphibians) under ultraviolet light conditions, chronic risk to benthic invertebrates, and risks to aquatic plants & algae exceeded risk thresholds under all conditions. California rice field soil conditions were associated with very low acute risk (RQ < 0.1) and less risk overall compared to standard conditions. All risk conclusions were unaffected by holding time, suggesting that water management needs of growers should be considered when stipulating water holding periods for OXY. However, environmental monitoring is suggested to address accumulation and persistence concerns when OXY is applied to California rice field soil.

Glycosylation is a keystone of mammalian cells found primarily on membrane proteinsand lipids, extending into the extracellular space to form the outer-most membrane layer known as the glycocalyx. The physiological functions of glycans are still constantly being discovered in relation to specific glycan structures. These functions include alteration of protein tertiary structure, protection of the peptide backbone, and mediation of interactions. Each of these functionalities, namely the mediation of interactions, has been a recent focus in the field of glycomics. Glycans have been shown to play a significant role in signaling pathways, cancer pathology, neurodegeneration, immune response, and viral, bacterial, and fungal susceptibility pathology. Glycan-mediated interactions are of unique interest in neural physiology and pathology. Previous research has shown aberrant glycosylation of both proteins and lipids to play a significant role in neurological diseases such as multiple sclerosis, Huntington's disease, and Alzheimer's disease. The complexity of elucidating pathology mechanisms stems from the diversity of glycan structures specific to each cell type and how they shape interactions in vivo. Developing analytical methodologies that provide sensitive and reproducible profiles with structural information is critical to elucidate the mechanisms behind glycan interactions. The sheer structural diversity in glycans and their untemplated biosynthesis makes this challenging. The development of robust high-performance liquid chromatography-mass spectrometry workflows capable of generating structural profiles and their application was the primary focus presented in this work.

My research develops tools to enable understanding of how information is encoded in chemical messengers (neurotransmitters; e.g., serotonin, dopamine) in the brain by measuring them in real-time, in awake, behaving mice models. A molecular scale understanding of complex behavior and brain (dys)function would enable better treatments for neuropsychiatric disorders such as anxiety and depression (which affect 50% of families worldwide). A major challenge is the lack of analytical techniques that can detect multiple neurotransmitters simultaneously, across physiologically and behaviorally relevant time scales (ms, min, h). To date, the most suitable technique is voltammetry, which applies a specific voltage waveform to a micron-sized brain-implantable sensor. However, voltammetry is limited by the number of analytes and timescales that can be achieved for in vivo monitoring, impeding an understanding of how our brains encode information across neurotransmitters in a coordinated manner. My graduate work involves developing a new voltammetry technique that combines novel voltammetry waveforms with machine learning. The technique is called rapid pulse voltammetry with partial least squares regression (RPV-PLSR), which utilizes a new type of pulse waveform and data analysis approach. Using RPV-PLSR, we published a proof-of-concept study to monitor serotonin and dopamine at both basal and stimulated levels, simultaneously, and compared these results to conventional approaches. We showed the utility of faradaic and non-faradaic current responses to build robust statistical models. The unique electrochemical signals present in pulse, rather than sweep, waveforms provide valuable chemical information in the background current that other methods do not generate. However, the design of RPV waveforms (and voltammetry waveforms in general) is an arduous and inefficient process. To address this challenge, I developed a machine learning-guided approach for systematic design of novel-yet-optimal voltammetry waveforms using Bayesian optimization. Here, I identified optimal serotonin detection RPV waveforms under various physiologically relevant conditions.Lastly, the custom waveforms and data analysis procedures used for RPV required the development of several open-source software solutions for user-friendly acquisition, analysis, storage, and sharing of voltammetry data at scale, which are reported herein. I outline how future extensions of fast voltammetry and machine learning can address domain generalizability (i.e., the ‘beaker-to-brain’ issue), and how the techniques developed herein will broaden the scope of multi-analyte electroanalytical method development.

High throughput methods are of great interest to multi-billion-dollar industries. High throughput methods can make screening and analysis for assays/experiments efficient and cost-effective. This is especially true for biotechnology or pharmaceutical industries trying to screen for specific analytes of interest produced through genetically modified microorganisms. For this thesis, succinic acid standards in cyanobacteria media were screened using four different instruments. Multiple instruments were used to compare which could be used for high throughput screening for succinic acid. The standards were made in a BG-11, a cyanobacteria growth medium, to simulate as close to an actual sample that could be received. The instruments used for this experiment were HPLC, GCMS, HSGC, and CIMS. Fisher esterification was performed on the succinic acid standards to be analyzed on the GCMS, HSGC, and CIMS. The esterification was conducted not through reflux but by placing the reaction mixture in air-tight crimp vials and placing the vials in a hot water bath. The duty cycles to screen succinic acid per sample through HPLC, GCMS, HSGC, and CIMS were approximately 17min, 5.93min, 5.25min, 3min, respectively.

Multicellular tumor spheroids are a 3D cellular model system that replicate the chemical microenvironments of tumors. This cellular model has played an important role in drug evaluation and clinical chemotherapy. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) has emerged as a powerful analytical technique to visualize molecular distributions. Work presented in this dissertation focuses on the application of MALDI-MSI for both targeted and untargeted analyses in tumor spheroids. In Chapter 2, we optimized a quantitative MSI (qMSI) method to monitor a time-dependent penetration process of a tumor therapeutic. Irinotecan (IR) was selected as a proof of concept drug. By use of a deuterium internal standard, a calibration curve was generated to quantify IR throughout a 72-hour penetration to the spheroids. Moreover, quantification was performed in the inner and outer regions of the spheroids separately. This study is the first time to obtain MALDI-qMSI of a therapeutic within the scale of a single spheroid. In Chapter 3, we optimized the conditions of spheroid fast photochemical oxidation of proteins (FPOP) experiments by performing MSI on spheroids treated with hydrogen peroxide at different concentrations and time lengths. Hydrogen peroxide is too small to be easily detected directly by MALDI but it oxidizes lipids. This lipid oxidation can be used as a surrogate to determine the penetration of hydrogen peroxide. Four lipids were selected as biomarkers according to a discriminative analysis. Putative identifications were perfomed based on database searching and tandom MS was used for more accurate identification. In collaboration with the Jones Lab, proteomic analyses were performed to study protein modifications and residue-level modification after FPOP to interrogate protein interactions within a native tumor microenvironment.Chapter 4 focuses on data analysis for MSI in collabration with the Desaire Lab. Previously, a customized machine learning (ML) method was utilized for classification. These studies demonstrated that metabolic changes in colon spheroids induced by the monoclonal antibody, Cetuximab, are detectable, but modest, at 24 hr, and substantial at 72-hour treatment. Moreover, we designed and applied a user-friendly feature selection workflow based on R for MSI data of spheroids. After developing the code in R, the workflow was tested on spheroids made from four tumor cell lines. Comparisons were performed between each two classes of spheroids with Top 100 features. The results were summarized to find 4 to 26 representative features, respectively, for each cell line. Chapter 5 includes several collaborations using MALDI-MSI to visualize the penetration of various cancer therapeutics in spheroids. Regorafenib, a multikinase inhibitor, treated SILAC spheroids were imaged to ensure penetration for a proteomic study. MSI was performed on cerulenin and TVB-2640, FASN inhibitors, treated spheroids to ensure drug penetration for lipidomic studies. In collaboration with the Hu Lab, we attempted to visualize vincristine in mouse tissues to study the influence of OATP1B2 knockout. Lastly, collaborating with the Xue Lab, MALDI-MSI was utilized to select drug candidates from a series of pyrazole-based drugs functioning dually as Wnt inhibitors and AMPK activators by evaluation of the penetration process of these novel compounds.

Understanding and characterizing the structure of biomolecules is essential for understanding various biological functions. Characterizing proteins with intrinsically disordered regions using high-resolution structural biology methods remains challenging due to their disordered nature and intrinsic heterogeneity. The heterogeneity and complexity of these macromolecular assemblies make nMS spectra difficult to resolve and interpret. To address these challenges, this dissertation aims to integrate novel techniques with native mass spectrometry (nMS) and explore their applications in protein-protein/RNA complexes characterization.Chapter 2 focuses on characterizing complex stability, subunit connectivity, and protein-RNA interaction of a homohexamer protein with six disordered C-terminal domains (CTDs), Hfq. The hexamer with only one CTD and the complex formed by the truncated Hfq and a free CTD were assembled and characterized by nMS coupled with surface-induced dissociation (SID) and ion mobility (IM) to quantify the individual contribution of one CTD to the complex stability. These comparisons show the CTD stabilizes the hexamer through interactions with up to three other subunits. Hfq bound to small RNAs with different lengths and binding sites is characterized by electron capture dissociation (ECD). The results show that the CTD can displace RNA binding to β2 sheet of the core. Chemical cross-linking data of Hfq identifies cross-links between the acidic residues of the CTD and the basic residues on the core.Chapter 3 describes combining charge detection mass spectrometry (CDMS) and SID and applying it in the structural characterization of large and heterogeneous protein complexes. A house-built algorithm was developed and employed to visualize and process SID-CDMS data. For GroEL, SID-CDMS reflects the stacked-ring structure, consistent with previous results on time-of-flight platforms coupled with IM. SID-CDMS provides native topology, subunit connectivity, and proteoform information on the 20S proteasome. For the gene therapy vector, adeno-associated viral (AAV) capsid, SID-CDMS suggests that the 60mer capsid is assembled from 20 VP trimers as the monomer-monomer interface of the trimers has a higher interfacial strength than other interfaces in the capsid.Chapter 4 demonstrates a novel approach using nMS coupled with mass isolation and electron capture charge reduction (ECCR) to resolve extremely heterogeneous glycoproteins, designed SARS-CoV-2 spike trimers (VFLIP). The intact mass measurement from nMS and ECCR showed a more extensive glycan mass distribution than that calculated from the glycoproteomics data, providing insight into glycan occupancy. Mass isolation followed by ECCR shows the difference in global glycan patterns among VFLIP variants, suggesting a dependence of the glycosylation process on sequence/local structure. Mass photometry and CDMS confirm the intact mass measurement using the ECCR-nMS approach.Chapter 5 describes the application of a hybrid device that combines an ECD cell and a split lens SID device coupled with CDMS to characterize macromolecules. Different combinations of techniques (ECCR, SID, and CDMS) were tested using GroEL, establishing different workflows for both intact measurement and structural analysis. The gas-phase dissociation using HCD or SID (w/ ECCR) provides accurate mass measurements of individual ribosomal proteins and enables the determination of PTMs. Combining ECCR with CDMS enhanced the intact mass measurement of AAV and bacteriophage phi29 prohead.

Short-chain fatty acids (SCFAs) are important metabolites produced by gut microbial fermentation of dietary fibers in the human colon. They play an essential role in maintaining gut health by regulating inflammation and providing energy to colonocytes. Alterations in SCFAs levels, arising from dysbiosis, have implications in various diseases, including inflammatory bowel disease (IBD), colorectal cancer, and obesity. Thus, analyzing SCFA levels in fecal samples can provide valuable insights into the gut microbial environment and its association with disease pathogenesis and progression, potentially serving as a diagnostic tool or therapeutic target for various gastrointestinal and metabolic disorders. This dissertation presents a robust and reliable method for quantifying SCFAs in human fecal samples using GC-MS. The study involved the optimization of sample preparation and chromatographic conditions to achieve accurate and reproducible quantification of SCFAs in fecal samples. This method was applied to quantify SCFAs in fecal samples from IBD patients.

This dissertation investigates the electrochemical deposition (ECD) and electrophoretic deposition (EPD) processes involving citrate (cit)-stabilized Au nanoparticles (NPs) and calcium alginate (Ca-Alg-Au NP) hydrogel films. The first part of the dissertation investigates the influence of NP size, surface area (SA) coverage, and ligand stabilizers on the electrochemical growth of Au on Au NPs, aiming to enhance our understanding of the growth process during the nucleation and growth of metal NPs. The growth kinetics depend on Au NP size (4 nm > 15 nm > 50 nm) for a constant SA coverage, as determined by the overpotentials for ECD. The growth rate increases with increasing SA, showing reversible kinetics for all NP sizes above a threshold SA. In addition, alkanethiol self-assembled monolayers (SAM)-coated Au NPs show a decrease in growth kinetics as the SAM chain length increases while showing the same NP size dependence as cit Au NPs. Faster growth kinetics on Au NPs relative to glass/ITO allows for a two-step EPD/ECD amplification for electrochemical detection of fM solution concentrations of Au NPs by anodic stripping voltammetry (ASV). This approach is sensitive, simple, fast, low cost, and has the potential for automation and portability, making it promising for Au detection for mining, electronic waste, and bioassays. The second part of this dissertation explores the EPD of Ca-Alg and hybrid Ca-Alg-Au NP hydrogel films utilizing Au NP-catalyzed electrooxidation of hydroquinone (HQ). This approach induces a localized pH decrease at the electrode surface, facilitating Alg and Au NP deposition followed by Ca2+ gelation. The catalytic action of Au NPs reduces the EPD potential, presenting promising applications in sensors, biological studies, electrocatalysis, and energy-related research. Electrochemical understanding in Ca-Alg-Au NP films involves investigating the behavior of Fe(CN)63-/4- on Pt, Au, and glassy carbon electrodes coated with EPD-deposited Ca-Alg and Ca-Alg-Au NP hydrogel films. Reversible electrochemistry with decreased Fe(CN)63- diffusion follows an initial equilibration time. The amide-functionalized hydrogel impeded electrochemistry, likely due to hindered mass and ion transfer. Incorporating Au NPs initially enhances Fe(CN)63- redox activity but hampers it at higher loads, indicating a significant change in mass and ion transfer, likely altering hydrogel viscoelastic and fluid properties. Finally, EPD of Ca-Alg and Ca-Alg-Au NPs in pipette tips and Pt/Ir scanning tunneling microscopy (STM) tips enables electrochemical measurements (Fe(CN)63-, Au ECD, Au ASV, and Au NP EPD) in microscale hydrogel environments as small as 10 microns. Microscale electrochemistry differs significantly from bulk hydrogels, exhibiting reversible kinetics and the capability to form microscale metal patterns through ECD and EPD.

Graphene-integrated Proton Exchange Membrane (PEM) electrochemical cells have emerged as a novel area of scientific investigation in the realm of hydrogen isotope separation. Chemical Vapor Deposited (CVD) graphene has been especially useful due to its large-scale production capability for scaling-up purposes. The research described in this dissertation explores the role that inadvertent introduction of cations, notably ammonium and copper, during the CVD graphene transfer onto PEM substrates, such as Nafion, might play in affecting hydrogen ion transport and isotope separation in PEM electrochemical cells. An extensive review of existing literature exposed a gap concerning unintentional cation introductions during graphene transfer, and this research posits that observations of apparent isotope separation could be attributable to effects from ammonium or copper cations in the membranes. Central to these studies is the elucidation of the challenges in reproducing optimal H/D selectivities, attributed to methodological inconsistencies. Seeking deeper insights, this study tapped into the capabilities of the Online Electrochemistry Mass Spectrometry (OEMS) system. Rather than relying on comparative studies in separate H and D electrochemical pump cells, the OEMS facilitated time-dependent studies of evolved gases in electrochemical pump cells, allowing for the direct analysis of true isotope separation from gas mixtures. Employing techniques to directly probe H/D separation, this dissertation identifies a minimal impact of graphene on this process. This investigation aligns with other recent works that question established beliefs regarding CVD graphene's pronounced impact on hydrogen isotope separation.

This study delves into the fascinating realm of concentrated ionic systems, such as ionic liquids, superionic materials, organic ionic plastic crystals, and polyelectrolytes, which hold immense potential for energy storage applications. The focus is on understanding the intricate role of ionic correlations in shaping their ionic conductivity behavior. These correlations can either boost or impede conductivity, yet their underlying mechanisms remain elusive. Through extensive investigation of various materials, including ionic liquids with differing anionic masses, pure organic ionic plastic crystals, and doped systems, this research employs advanced techniques like dielectric spectroscopy and innovative momentum conservation models to quantify these correlations. Additionally, the study explores the impact of Li+ doping on the conductivity of organic ionic plastic crystals, providing valuable insights into ways to enhance their conductivity. Ultimately, this research not only contributes to the development of high-conductivity electrolytes for innovative technologies like solid-state batteries but also advances our fundamental understanding of ion transport in concentrated ionic systems.

The field of Raman spectroscopy continues to expand into biological applications due to its usefulness as a non-invasive technique that can be utilized qualitatively and quantitatively. However, the inherent weakness of Raman scattering leads to the need for each collected spectra to undergo a preprocessing step to remove noise, background drift, and cosmic rays. Biological research in particular needs large datasets due to the increased variability in samples. As datasets grow, the need to perform preprocessing on each individual spectra becomes daunting. Often, these steps are done by hand with the help of specialized software programs. Preprocessing can be accelerated by using computer algorithms to automatically correct all spectra at once, but they are constrained by their accuracy while corrections done by hand introduce a new variable into the dataset time-consuming. Many algorithms exist to assist in spectral preprocessing, but these are mainly designed around ‘ideal’ samples with strong Raman signal and limited complexity. Therefore there is a need to design more open-source programs to accurately and efficiently preprocess large Raman datasets in order to advance biological Raman research. This research utilizes a Python-based approach to biological Raman data analysis for a variety of biological studies, including live cell analysis and neurological development.

This dissertation presents work that expands our understanding of the relation between the structural features of soft materials applicable in energy storage systems such as redox flow batteries (RFB) and organic radical batteries (ORB) to their performance. The studies focus on soft materials- nanoparticle organic hybrid materials (NOHMs) and the radical polymer, poly (2,2,6,6-tetramethylpeperidinyloxy-4-yl methacrylate) (PTMA). The results obtained in these studies provide a holistic understanding of the structural features of NOHMs and PTMA in solution that may provide insight to rationally improve the performance of energy storage systems. The first two projects investigate the structure and assembly of nanoparticle organic hybrid materials (NOHMs) in aqueous solution with and without supporting electrolytes using small angle neutron scattering. The first project focuses on the structure and assembly of the polymer canopy and NOHMs with increasing concentrations of NOHMs in aqueous solution with and without supporting electrolyte. The research highlights that a large amount of polymer ungrafts from the nanoparticle surface to free polymer that interact with the grafted polymer canopy. The second project explores the impact of tuning the bonding type (ionic vs. covalent) of the polymer canopy grafted to the nanoparticle in the structure and assembly of NOHMs in aqueous solutions with and without supporting electrolyte. In presence of supporting electrolyte, ionic NOHMs structure observe a collapsed polymer conformation on the nanoparticle surface and covalent NOHMs shows a subtle change in conformation of the polymer canopy. The next part of the research focuses on the assembly of NOHMs near the electrode surface using neutron reflectivity. This research highlights that under applied potential, the ordering of NOHMs dramatically changes, impacting the current density of the NOHMs solution. The final project investigates the conformation and assembly of PTMA in solutions with variations in radical loading in the PTMA backbone and temperature using small angle neutron scattering. The results highlight that the amount of radical loading is the primary factor governing the final conformation of PTMA. Correlating the conformation of PTMA in solutions to the electrochemical performance indicates that PTMA with collapsed chain conformation improves the charge transfer process.

This dissertation combines unconventional techniques and multidimensional mass spectrometry methods aimed at investigating the structure, formation, and bonding associated with various classes of macromolecules. Understanding macromolecule formation and reactivity requires a detailed understanding of their monomers and precursor oligomers. Melanin nanoparticles, poly(electrolytes), protein-polymer complexes, hydrophilic homopolymers, and poly(chlorophosphazenes) were all studied as model compounds for the experiments presented in this dissertation. Bronsted-Lowry acid-base chemistry and electron-transfer reactions within the instrument were also investigated with respect to their underlying role in the observed mass spectra. Although this was not the original intention, the molecules studied also offer insights into either poorly understood or underreported electrochemical and clustering phenomena of electrospray ionization mass spectrometry. Mass spectrometry is a widely used analytical technique for characterizing everything from atmospheric aerosols to complex macromolecules. Chapter II will introduce various mass spectrometry principles. Chapter III contains specific instrumentation, procedures, and materials used in the experiments presented in Chapters IV-VII. Chapter IV discusses a simple, affordable, and green methods for identifying concomitantly the molecular weight distribution and macromolecular composition of polymeric materials using direct injection electrospray ionization and a universal charge deconvolution algorithm. Building off the low-solvent, green method presented in Chapter IV, a solvent-free method for studying the structure, bonding, and polymerization of poly(chlorophosphazenes) macrocycles is presented in Chapter V. Macrocyclic rings were synthesized in an ambient ionization source through thermal activation and characterized via ion mobility and tandem mass spectrometry. Poly(dopamine) polymerization reactions are studied in Chapter VI using unconventional and time-dependent analytical methods. Noncovalent interactions and magic number associations of oligomeric species associated with dopamine and 3,4-dihydroxyphenylalanine (DOPA) were characterized. Finally, Chapter VII discusses the use of an anionic polymer, poly(styrene sulfonate), as a tagging agent for selective noncovalent adducting protein probe (SNAPP) for site specific analyses of surface accessible basic residues. The energetics and salt bridges between conjugate acid pairs in the protein-polymer complexes were studied based on their ability to survive collisional activation while inducing fragmentation along the peptide backbone. This information can be used to understand the role of neighboring residues in protein surface charge, substrate-receptor binding affinities, and higher-order structures.

Surface enhanced Raman spectroscopy (SERS) is a technique that utilizes plasmonic nanostructured metal surfaces to increase the Raman signal. The excitement of the localized surface plasmon resonance (LSPR) of gold nanoparticles leads to enhanced electric fields and increases the Raman signal can also result in the generation of highly energetic or “hot” carriers in the form of electrons or holes. These hot carriers have been further been shown to perform chemical reactions. This dissertation includes the investigation of specific analytes that undergo changes resulting from hot carriers. Chapter 1 introduces Raman and SERS as analytical techniques and explains the fundamentals involved in each technique. The generation of hot carriers through the SERS process is explained as well as how hot carriers have been previously identified to impact SERS signal. An explanation of previous literature and understanding is included to provide support for the studies elaborated on in latter chapters. Chapter 2 introduces evidence of the formation of a tryptophan radical anion species generated that drastically impacts the observed SERS signal. The difference in the SERS and Raman signals are studied through various changes made to the system. This study includes the impact on the SERS identification of tryptophan in proteins through studying a protein that contains a single tryptophan residue and analyzing the SERS signal. The formation of a tryptophan radical anion is accompanied by an electronic resonance that generates surface enhanced resonance Raman scattering, enabling more sensitive detection. Chapter 3 uses computational modelling to explore the vibrational changes observed in the SERS spectrum of tryptophan with gold nanoparticles. DFT calculations are combined with experiments on an analog containing the indole ring moiety. Spectral analysis of the simulated vibrations compared with experimentally observed modes identified specific Raman modes that are impacted by experimental changes and the formation of the radical anion. The indole moiety is identified as the chemical feature that supports the additional electron. The impact of the experimental parameters that impact hot carrier formation and transfer is reported in chapter 4. This chapter focuses on a traditional Raman setup examining a common reporter molecule, 4-mercaptopbenzoic acid (MBA), on gold nanoparticles and references results collected utilizing a wide field imaging setup. Traditional point-focused microspectroscopy provides spectral resolution for the identification of intermediates observed. Further DFT simulations identify additional radical species of MBA formed. However, additional fluctuations observed in the data suggest the formation of other species. Chapter 5 summarizes the main results, makes conclusions, and provides a perspective on the research explained in this dissertation. This research allows for better understanding of how SERS can be further utilized in fields such as plasmonic catalysis, and detection of proteins. Appendices are included to provide the optimized structure coordinates from DFT, how the DFT simulations were run, and brief reports of other results that further support the work shown here. Overall, this dissertation provides new understanding of the molecular impact of hot carriers generated by exciting the LSPR of gold nanoparticles for SERS through experimental work coupled with DFT simulations.

The development of accurate model systems for chemotherapeutic development and testing poses a critical issue in the field of cancer research. Historically, a reliance on conventional two-dimensional cell cultures grown in monolayer have allowed for unsuitable potential therapeutic reagents to make it past initial preclinical testing. This practice, however, leads to significant amounts of time, money, and resources to be wasted on candidates that eventually fail when tested in more complex animal models. As an intermediary model system, three-dimensional cell culture models, such as spheroids and organoids, present a more complex system for preclinical testing while remaining cost effective and easy to grow in large volumes. Spheroid models more accurately depict the tumor microenvironment than two-dimensional monolayer cultures and contain distinct chemical and pathophysiological gradients. These gradients form three distinct cellular subpopulations: the necrotic core, a quiescent layer, and a proliferating layer of cells. By utilizing stable isotope labeling in cell culture (SILAC), these cellular sub-populations can be defined by a particular label state, and their corresponding proteomic changes tracked in response to external therapeutic reagents. The utilization of SILAC within the spheroid model system enables spatial proteomic changes to be tracked in tandem with temporal and metabolic imaging studies, earning the title spatial SILAC. Spatial SILAC allows for combinatory pharmacodynamic and pharmacokinetic studies to take place, making this model system ideal for evaluating the efficacy of potential chemotherapeutics, as demonstrated with the kinase inhibitor regorafenib. However, due to the spectral complexity present with multiplexed labeling, the use of SILAC labels limit this proteomic analysis to data dependent acquisition. This dissertation establishes and evaluates the potential of the spatial SILAC model system, presents alternative labeling techniques for spatial analysis, and compares the merits of data dependent acquisition and data independent acquisition in order to characterize and test the limitations of the three-dimensional spheroid model systems.

The surface of a solution exhibits a number of chemically unique properties compared to the bulkthat are of extreme interest. Several metrics to examine the surface exist, including examining theelectrical nature of the boundary. One method of examining this is the ionizing surface potential method, which allows for measuring the potential across the surface layer of a solution.This work examines experiments using an ionizing surface potential sensor (ISPS) which wasfabricated by Dr. Tehseen Adel with several improvements over older models, such as the use of an Am-241 electrode instead of a Po-210 electrode. The method of data collection, its accuracy, and the trends that can be found among the resulting data will be examined and explained in detail in order toconsolidate the necessary information for the understanding and operation of this instrument. Data was taken of previously examined compounds to use as points of comparison along with some unexamined compounds that can be compared to previously existing trends.

The integration of acyl-CoAs into multiple pathways demonstrates their utility as biomarkers for the study of fatty acid metabolism, particularly in the context of physiological states which affect energy production. Fabry disease is an inherited lysosomal storage disorder that affects multiple organ systems including the heart, for which the underlying mechanisms are poorly understood. A portfolio of LC-MS/MS based targeted and high-resolution untargeted assays were developed to measure key metabolites including acyl-CoAs, acylcarnitines, and tricarboxylic acid cycle intermediates. These methods were used to study a cellular model of Fabry disease using fibroblasts from donors representing 2 different phenotypes (GM00107 & GM00882, Coriell Institute). Stable isotope tracer analysis of 13C2-acetyl-CoA enrichment from fully 13C labeled glucose and palmitate revealed markedly reduced 13C2-acetyl-CoA labeling from both palmitate and glucose in GM00107 Fabry cell line compared to healthy controls, suggesting that there is severe mitochondrial dysfunction preventing normal oxidative metabolism of primary carbon substrates. Untargeted metabolomics revealed a significant decrease of ATP and phosphocreatine in Fabry disease. Therefore, the accumulation of glycosphingolipids in lysosomes may disrupt the cellular homeostasis and energy production of the cell contributing to mitochondrial dysfunction and a shift towards compensatory mechanisms in Fabry disease.

Neuroinflammation, oxidative stress, and glutamatergic excitotoxicity are prevalent in several neurological disorders including stroke, substance abuse, and neurodegenerative diseases. Chemical compounds and biomolecules which can ameliorate those conditions are gaining interest for new treatments. Despite many advances in understanding brain anatomy and physiology, the underlying neuropathological mechanisms behind ischemic stroke are still poorly understood. The purine nucleosides adenosine and guanosine have been shown to exhibit neuroprotective behavior in both in vivo and ex vivo models of ischemia. However, real-time detection of guanosine sub-second signaling dynamics in the brain is not understood. Various techniques have been developed for the detection of guanosine in vivo and in in vitro. We have used fast-scan cyclic voltammetry (FSCV), a novel electrochemical technique for real-time detection of the neurochemical release in sub-second timescales at carbon-fiber microelectrodes (CFME). Previously our lab has observed a significant increase in the concentration of guanosine during ischemia with the help of FSCV, showing a neuroprotective effect in ischemia. Despite prior studies, it is still unknown how guanosine released during ischemia is impacted as the function of ischemic severity. Here, we have developed an ex vivo oxygen-glucose deprivation model to investigate the guanosine signaling changes as a function of ischemic severity. Characterization of three different ischemic conditions was studied: normoxia, mild ischemia, and severe ischemia with the help of an optically dissolved oxygen sensor. triphenyl tetrazolium chloride assay and immunohistochemical staining were used to validate these ischemic conditions. Overall, we have successfully developed and maintained three different ex vivo experimental ischemic condition.

Detection of zinc (Zn(II)) electrochemically has been explored over the last several years specifically for environmental applications; however, electrochemical detection in a biological environment is severely underdeveloped. This is due to the rapid change in concentration that can occur on a millisecond time scale, or faster, which makes using traditional voltammetry difficult for biological processes. Fast-scan cyclic voltammetry (FSCV) has been used in the mechanistic study of neurochemicals, like dopamine, in the brain and lymph node. This dissertation aims to develop electrochemical methods for Zn(II) detection with FSCV and under biological conditions with emphasis on stability, sensitivity, and selectivity.Chapter 2 discusses the detection of Zn(II) with FSCV at carbon-fiber microelectrodes (CFME) and the need for novel waveform development. Chapter 3 investigates the extent to which Zn(II) interacts at graphene-based microfibers and demonstrates co-detection of Zn(II) with purines to improve the possibilities of neurochemical measurements in the brain. Chapter 4 and 5 expand beyond carbon-based materials and explore the use of functionalized gold fibers to improve sensitivity and selectivity of Zn(II) versus interfering analytes. Chapter 4 will investigate the impact of various plasma treatments on the surface characteristics of gold-fiber microelectrodes (AuMe) and correlates those changes in electrochemical detection of Zn(II). In Chapter 5, I develop a novel ionophore-modified AuMe to significantly improve Zn(II) selectivity. A summary of the work shown, and a future outlook will be presented in Chapter 6.This dissertation establishes a complete electrochemical characterization of Zn(II) for FSCV, as well as an in-depth study of how different substrates can affect the detection of Zn(II). Further understanding of Zn(II)’s interaction with different microelectrodes provides mechanistic insight into the Zn-electrode interface leading to improved sensitivity and lower limits of detection. In conclusion, this fundamental advancement of our understanding of Zn(II) detection with FSCV will lead to significantly improved approaches to study the mechanism of the metallotransmitters Zn(II) in the brain.

Today’s society is mainly dependent on fossil energy sources despite being not sustainable, not renewable, and not environmentally friendly, as they generate a lot of carbon dioxide. Hydrogen is a promising substitute for fossil fuels. It is a clean fuel with water as the only oxidation product, thus less production of CO2. Cadmium telluride (CdTe) is a promising semiconductor material that could facilitate the use of solar energy in producing hydrogen gas. CdTe can be a p-type photoelectrode that can perform electron transfer processes with an electrolyte. As a cathode, it reduces hydrogen ions in water to form hydrogen gas. Spray pyrolysis method, which is simple and easy to use, cheap compared to vacuum deposition methods, can produce uniform films over large surfaces within a short time, many small substrates at the same time, and whose concentration of precursor solution remains constant with time, was used in this project. CdTe films for this project were fabricated on stainless steel 304 substrates at different substrate temperatures and spray times. The precursor solution was based on a mixture of CdCl2, TeO2, hydrazine, and EDTA. Characterization of the fabricated films was done using X-ray diffraction, scanning electron microscopy and energy dispersive spectroscopy (SEM-EDS), stylus profilometry, cyclic voltammetry, and linear sweep voltammetry. The fabricated CdTe films had a uniform and highly crystalline surface morphology, that was Te-rich (p-type) and exhibited photoactivity with the evolution of hydrogen gas. The best photoelectrode was fabricated by spraying a mixture of equal volumes of 0.02 M solutions of Cd and Te salts onto a SS 304 substrate held at 330°C for 3 min, which produced a 10 µm-thick film and a photocurrent of 5800 µA/cm2 observed at -0.5 V. When a dispersion of Pt catalyst was reduced onto it, a photocurrent of 7700 µA/cm2 was observed at -0.5 V, which compares well with other fabrication methods.

In Colombia, ethnic communities have traditionally been responsible stewards of natural resources. They recognize the importance of these resources for their livelihood, as well as their ancestral and cultural heritage. El Tiple, a rural Afro-Colombian community, has been affected by the incursion of private corporations that promoted the expansion of sugarcane monocrops in their territory. Since the introduction of the monoculture industry, local freshwater sources have been depleted due to intensive water use for irrigation of the sugarcane crops. Additionally, the intensive usage of agrochemicals has been linked with loss of native flora, damages to family farms, and pollution of surface water. For example, glyphosate, the most used herbicide, is aerially sprayed over the sugarcane fields via light aircrafts and drones. Glyphosate was classified by the International Agency for Research on Cancer (IARC) and the World Health Organization (WHO) as probably carcinogenic to humans, and human exposure to glyphosate can disrupt the endocrine and reproductive systems. While highly accurate laboratory techniques for pesticide measurement exist, continued glyphosate screening in several potentially affected sites is currently unconceivable due to limitations of conventional laboratory techniques, such as the need for complex sample pre-treatments, controlled environmental conditions, high-cost analysis, etc. This project aims to connect pollution science and monitoring technology with the environmental justice struggles in El Tiple. The objectives of this work are (i) to develop a low-cost field-deployable sensor for measuring organophosphorus pesticides, such as glyphosate, in water; (ii) to conduct a water quality assessment and determine human health risks associated with water ingestion in the community of El Tiple, Colombia; and (iii) to identify assets, knowledge, needs, and challenges in El Tiple, Colombia, to inform the design of a training protocol on the use of water quality monitoring tools. For the sensor development, a three-electrode system was fabricated via laser-inscribed graphene. The working electrode was functionalized with copper nanoparticles that have a high affinity toward organophosphate compounds. The sensor showed a limit of detection (LOD) of 3.42 ± 1.69 µM for glyphosate and 17.78 ± 7.68 µM for AMPA. The LOD for glyphosate is lower than the maximum residue limit (MRL) in drinking water (4.14 µM), as established by the United States Environmental Protection Agency (EPA). The water pollution assessment was conducted based on a mixed-methods approach framed within the community-based participatory research (CBPR) approach. Surveys and focus groups were conducted with community participants to determine the exposure frequency of water ingestion. Four water sampling campaigns were conducted in El Tiple to measure water quality parameters such as pH, turbidity, total coliforms, fecal coliforms, pesticides, and several metals. Results from this work indicate that the concentration of total coliforms, glyphosate, and some hazardous metals (mercury, lead, and arsenic) exceeds the regulatory thresholds in several water sources, including deep wells, agricultural irrigation channels, and the Cauca River. Concerning levels of arsenic were found in the filtrates of low-cost household filters recently donated to the community by an energy company. The hazard index associated with water consumption indicates serious risk from exposure to toxic metals/metalloids via ingestion for individuals that rely exclusively on groundwater consumption. Finally, assets, challenges, and needs in El Tiple were identified using community meetings, surveys, and interviews with community members and staff from governmental organizations in Colombia. The community of El Tiple has a strong and organized internal social structure based on five community associations and ten local institutions. The community youth are engaged in leadership and participatory programs involving formal education, workshops, and recreational activities. Government “abandonment” was identified as a major impediment for community welfare. A tailored educational program for environmental monitoring in El Tiple can potentially target the youth population through articulation with well-established community organizations. Information generated from the environmental monitoring program could be used to support local decision-making processes and state policies aimed at protecting vulnerable citizens and the environment.

Multiferroic materials attract significant attention due to their potential utility in a broad range of device applications. The inclusion of heavy metal centers in these materials enhances their magnetoelectric properties, yielding fascinating physical phenomena such as the Dzyaloshinskii–Moriya interaction, nonreciprocal directional dichroism, enhancement of spin-phonon coupling, and spin-orbit-entangled ground states. This dissertation provides a comprehensive survey of magnetoelectric multiferroics containing heavy metal centers and explores spectroscopic techniques under extreme conditions. A microscopic examination of phase transitions, symmetry-breaking, and structure-property relationships enhances the fundamental understanding of coupling mechanisms. In A2Mo3O8 (A = Fe, Zn, Ni, and Mn), we use optical spectroscopy to analyze the electronic properties and compare our findings with first principles electronic structure calculations. We find that Fe2+ ions in the A site create a many-body effect from a valence band due to screening of the local moment – similar to a Zhang-Rice singlet. These findings advance the understanding of unusual hybridization with orbital occupation and the structure-property relationships in various metal-substituted systems. In a chiral, polar magnet, Ni3TeO6, we explore toroidal geometry to complete the set of configurations and develop structure-property relations by combining magneto-optical spectroscopy and first-principles calculations. The formation of Ni toroidal moments is responsible for the largest effects near 1.1 eV - a tendency that is captured by our microscopic model and computational implementation. Furthermore, we demonstrate deterministic control of nonreciprocal directional dichroism in Ni3TeO6 across the entire telecom wavelength range. This discovery will accelerate the development of photonics applications that take advantage of unusual symmetry characteristics. In Co4B2O9 (B = Nb, Ta), we combine variable temperature infrared spectroscopy, lattice dynamics calculations, and several different models of spin-phonon coupling to reveal the mechanism of magnetoelectricity. We reveal a spin-phonon coupling in Co2+ shearing mode near 150 cm−1 with coupling constants of 3.4 and 3.4 cm−1 for Co4Nb2O9 and the Ta analog, respectively. These coupling constants derive from interlayer exchange interactions, which contain competing antiferromagnetic and ferromagnetic contributions. Comparison to other contemporary oxides shows that spin-phonon coupling in this family of materials is among the strongest ever reported, suggesting an origin for magnetoelectric coupling.

The regulation of lipid metabolism is crucial for maintaining the human body, as disruptions in lipid homeostasis have drastic implications. While lipids are known for their roles as energy stores as well as for cellular compartmentalization, certain lipid classes can serve as signaling agents that govern cellular behavior and physiology or as biomarkers whose concentration and spatial organization impacts cell fate. Thus, dysregulation in these processes coincide with a variety of diseases and cancers. However, the ability to track lipids has been a long-standing challenge in the area of chemical biology since lipids are chemically diverse and undergo continuous interconversion within their complex biosynthetic pathways. A popular method to address this challenge is the lipid metabolic labeling platform whereby click-tagged substrates are introduced to cells and metabolized to generate click-tagged lipids. These lipids can be modified through click chemistry to enable selective labeling, detection, and imaging. In Chapter 1, we review scientific endeavors that took advantage of this platform. In Chapters 2 and 3, we describe the development and application of new precursors to add to the chemical toolbox to label a particular phospholipid, phosphatidylserine (PS) by headgroup labeling, and to label several lipid classes by glycerol-tagging. We confirmed the successful infiltration of these precursors into the lipid pathways of S. cerevisiae via mass spectrometry (MS), fluorescence imaging after click reaction with fluorescent dye, and lipid class separation by fluorescence-based thin-layer chromatography (TLC). In Chapter 2, we have synthesized novel azido-serine precursors and confirmed its conversion to PS lipid products. In Chapter 3, the same techniques were applied to assess a panel of azide-tagged monoacylglycerol (MAG) precursors in their ability to label neutral lipids and phospholipids. Chapter 4 describes an extension to the goal of “bulk" glycerophospholipid labeling with the synthesis of an azide-tagged phosphatidic acid precursor. Finally, Chapter 5 describes cysteine and serine analogs equipped with electrophilic and clickable tags as substrate mimics to probe the PS synthase enzyme active site. All in all, this novel set of clickable reporters adds to the rapidly expanding toolbox of lipid probes for chemical biology applications.

This dissertation consists of three research chapters. The first two are environmental studies, which focus on developing modified adsorbents for the removal of perfluorooctanoic acid (PFOA), a persistent and toxic pollutant in surface water. The adsorbents were synthesized using a weak anion exchange resin or activated carbon, respectively, as the base material before modification with a fluoropolymer and then polyethyleneimine through an amine crosslinking reaction. The adsorption of PFOA on the modified adsorbents was evaluated using fixed-bed tests, and their mixed mode hydrophobic and anion exchange adsorption mechanisms were elucidated. Compared with the unmodified base materials, the results showed that the modified adsorbents were effective at removing PFOA from water and could be easily regenerated. The third research chapter focuses on developing new detection techniques for volatile organic compounds. The determination of ethanol using a tin oxide (SnO2) electrochemical sensor combined either with a home-built gas chromatography (GC) or flow injection analysis (FIA) instrument was done. Headspace (HS) sampling technique was applied as the sample preparation method for GC and the detection method for FIA to reduce sample matrix effects. Various experimental conditions including flow rate and injection volume for FIA, and headspace volume for GC, were optimized. The results showed that both HS-FIA-SnO2 and HS-GC-SnO2 are simple and fast techniques for ethanol quantification.

The need for more robust, high-throughput sample preparation methodologies continues to grow as the analytical challenges of the modern world progress. This is apparent from the lowering advisory limits of environmental contaminants to the generation of novel anthropogenic wastes. Solid phase microextraction (SPME) technologies present unique qualities that enable it to tackle these challenges from an alternative approach. To date, there are a variety of matrices, contaminants and analytical tools that are still not well understood or reliably accounted for in the literature. This work advances the field of sample preparation with the development of novel extraction and separation workflows for the quantitative analyses of complex environmental matrices. The first project of this work develops a sample preparation method for crude (4-methylcyclohexylmethanol (MCHM), a chemical blend commonly used in the coal industry for the separation of coal from rock, debris and coal dust by froth flotation. This mixture contains (4-methylcyclohexyl)methanol (68–89%), 4-(methoxymethyl)cyclohexanemethanol (4–22%); methyl 4-methylcyclohexanecarboxylate (5%), dimethyl-1,4-cyclohexanedicarboxylate (1%), and 1,4-cyclohexanedimethanol (1–2%), which all occur in the cis and trans diastereoisomeric forms; along with water (4–10%) and methanol (1%). Significant attention regarding the impact of these compounds on human health arose in 2014, when a spill of crude MCHM into the Elk River resulted in the contamination of drinking water for over 300,000 residents in West Virginia and Kentucky in the United States. In response, a series of studies aimed to investigate the mixture’s capacity for long-term exposure by determining the sorption properties of crude MCHM to pipes and linings. Sorbed MCHM was demonstrated to readily desorb from polyethylene into water at levels above the odor threshold, confirming the risk to residents from contaminated tap water pipelines. In light of this, it is imperative to develop analytical tools that enable the detection of crude MCHM components in environmental water samples for routine water monitoring. In this work, two SPME methods, based on fiber and thin film geometry, were developed and validated and coupled to gas chromatography – mass spectrometry (GC-MS). Their performances were compared with a modified solid-phase extraction (SPE) protocol based on EPA Method 522 for the analysis of volatiles in water. Both SPME methods demonstrated lower limits of quantitation (LOQ) compared to the SPE protocol. Thin film solid phase microextraction (TF-SPME), due its superior sensitivity and faster throughput was selected as the optimal extraction approach for 4-MCHM and other constituents of crude MCHM, with LOQ below the odor threshold for aqueous crude MCHM in distilled water at 19–21 °C (0.55 µg L-1).The second project focuses on the untargeted analysis of unconventional oil and gas waste. Produced water (PW), the primary waste byproduct of these operations, contains a diverse number of anthropogenic additives together with the numerous hydrocarbons extracted from the well. Due to potential environmental hazards, it is critical to characterize the chemical composition of this type of waste before proper disposal or remediation/reuse. In this work, a TF-SPME approach was developed and optimized to characterize produced water. The thin film device consisted of hydrophilic-lipophilic balance particles embedded in polydimethylsiloxane and immobilized on a carbon mesh surface. These devices were chosen to provide broad extraction coverage and high reusability. Various parameters were evaluated to ensure reproducible results while minimizing analyte loss. This optimized protocol, consisting of a 15 min extraction followed by a short (3 s) rinsing step, enabled the reproducible analysis of produced water without any sample pretreatment. Extraction efficiency was suitable for both produced water additives and hydrocarbons. The developed approach was able to tentatively identify a total of 201 compounds from produced water samples, by using one-dimensional GC-MS and data deconvolution.The third project continues work on PW. This waste has been shown to contain petroleum distillates, polycyclic aromatic hydrocarbons (PAHs), and organic fracturing additives, along with dissolved salts, heavy metals, and naturally-occurring radioactive materials (NORMs). Identification of these compounds is critical to develop future reuse and disposal protocols to minimize environmental contamination and potential health risks. In this study, versatile extraction methodologies were investigated for the untargeted analysis of PW. TF-SPME with hydrophilic-lipophilic balance particles (HLB) was utilized for the extraction of organic solubles from eight PW samples from the Permian Basin and Eagle Ford formation in Texas. GC-MS analysis found a total of 266 different organic constituents including 1,4-dioxane, atrazine, pyridine, PAHs, and substituted alkyl chain hydrocarbons. The elemental composition of PW was evaluated using dispersive solid-phase extraction (D-SPE) followed by inductively coupled plasma – mass spectrometry (ICP-MS), utilizing a new coordinating sorbent, poly(pyrrole-1-carboxylic acid). ICP-MS analysis confirmed the presence of 29 elements including major (Mg, Mn, Zn, Se, Ag, Ba) and trace rare earth elements, as well as hazardous metals, such as Cr, Cd, Pb, and U. Utilizing chemometric analysis, both approaches facilitated the discrimination of each PW sample based on their geochemical origin with a prediction accuracy above 90% using partial least squares-discriminant analysis (PLS-DA), paving the way for PW origin tracing in the environment.In the fourth project, an introduction method for direct ambient mass spectrometry was developed and tested for drugs and pesticides in the environment. Direct ambient mass spectrometry (AMS) methodologies significantly increase sample throughput, can be adapted for onsite analysis and are often regarded as semi-quantitative by most developed protocols. One of the limitations of AMS, especially for onsite analysis applications, is the irreproducibility of the measurements related to the occurrence of transient microenvironments (TME) and variable background interferences. In this work, we report an effective strategy to minimize these effects by hyphenating, for the first time, arrow solid phase microextraction (Arrow-SPME) to mass spectrometry via a thermal desorption unit (TDU) and Direct Analysis in Real Time (DART) source. The developed method was optimized for extracting and analyzing pesticides and pharmaceuticals from surface water. It was demonstrated that the hyphenation of the SPME and TDU-DART resulted in reduced background contamination, indicating the suitability of the method for onsite analysis even in variable and non-ideal environments. Model analytes were quantified in the low µg/L range with a total analysis time of less than 5 min, linear dynamic ranges (LDR), and interday reproducibility for most compounds being 2.5 – 500 µg/L and 10 %, respectively. The developed approach provides an excellent analytical tool that can be applied for the onsite high-throughput analysis of water samples as well as air and aerosols. Considering the tunability of our extraction process, time-resolved environmental monitoring can be achieved onsite within minutes.Continuing DART related work, the fifth project develops a strategy for analyzing per- and polyfluoroalkyl substances (PFAS), an emerging toxic class of anthropogenic chemicals that are persistent in the environment, are currently regulated at the low part-per-trillion level worldwide. Quantification and screening of these compounds currently rely mostly on liquid-chromatography hyphenated to mass spectrometry. The growing need for quicker and more robust analysis in routine monitoring has been, in many ways, spearheaded by the advent of direct ambient mass spectrometry (AMS) technologies. Direct analysis in real-time (DART), a plasma-based ambient ionization source that permits rapid automated analysis, has been shown to be effective at ionizing a large range of compound classes, PFAS. This work seeks to evaluate the performance of DART-MS for the screening and quantification of PFAS of different classes, employing a central composite design (CCD) to better understand the interactions of DART parameters on the ionization of PFAS. Furthermore, in-source fragmentation of the model PFAS were evaluated based on the evaluated DART parameters. Preconcentration of PFAS from water samples was achieved by SPME and extracts were analyzed using the optimized DART-MS conditions, which allowed obtaining linear dynamic ranges (LDR) between 10 and 5000 ng/L for the model analytes and LOQs of 10, 25 and 50 ng/L for all analytes. The sixth project focuses on developing novel strategies for the extraction and chromatographic separation of the cyanoneurotoxin β-N-methylamino-L-alanine (BMAA) and its structural isomers. Effective quantitative analysis of BMAA and its isomers without the need for derivatization has always been an analytical challenge due to their poor retention and separation on various liquid chromatography (LC) stationary phases. Previous studies that utilized conventional hydrophilic interaction chromatography (HILIC) demonstrate false negatives compared to reverse-phase workflows with derivatization. This work evaluates the chromatographic behavior of BMAA and its isomers, in their underivatized forms, on selected stationary phases, in particular fluorophenyl-based columns, to attain effective retention and separation. Detection and quantification were achieved with an ion-trap mass spectrometer. Extraction and preconcentration were achieved via SPME by assessing the effectiveness of multiple extraction phases, including HLB and mixed-mode (MM). A MM extraction phase consisting of C8 and benzene sulfonic acid moieties permitted the ideal extraction performance of BMAA and its isomers (2,4-diaminobutyric acid, DABA; N-(2-aminoethyl) glycine, AEG). Chromatographic separation was achieved within 8 min on a fluorophenyl stationary phase, ensuring high throughput without derivatization, and showing exceptional improvement from conventional HILIC methods. Limits of quantification in water for BMAA and AEG were 2.5 µg L-1 and DABA was 5 µg L-1, with linear dynamic ranges from 2.5 µg L-1 - 200 µg L-1 for BMAA and AEG and 5 µg L-1 - 200 µg L-1 for DABA. The final, seventh project continues the work of project six but with more focus on complex matrices. BMAA and its isomers have been demonstrated to bioaccumulate in aquatic fauna such as blue crab, these same toxins have also been detected in the brains of patients with amyotrophic lateral sclerosis (ALS) and dementia. A sample preparation method is developed in this work for the extraction of these toxins in brain and blue crab utilizing SPME hyphenated to LC-MS. Through an initial solvent-extraction approach, SPME device fouling and matrix effects were found to be acceptable. Further expansion of this workflow should enable the robust extraction of cyanoneurotoxins from complex matrices with consecutive reuse of the SPME device.

Human health is adversely affected by exposure to xenobiotics at elevated levels, and the impact of minor exposure is often overlooked. Toxicological behavior of agrochemicals is commonly determined by their ability to bind to plasma protein, as they are significantly more toxic when unbound. Moreover, for pharmaceuticals, plasma protein binding determines their therapeutic effect since only the free form can diffuse to their target sites. In spite of separate investigations regarding pharmaceuticals and pesticides binding to plasma proteins, the binding behaviors of pharmaceuticals in the presence of pesticides have not been comprehensively explored. To determine the effect of xenobiotics binding to plasma protein, a targeted quantitative method coupling solid phase microextraction (SPME) with both liquid chromatography (LC)-mass spectrometry and gas chromatography (GC)-mass spectrometry was developed. The performance of a polydimethylsiloxane/divinylbenzene/ polydimethylsiloxane (PDMS/DVB/PDMS) biocompatible extraction phase was investigated for extraction of xenobiotics from plasma samples via direct immersion solid-phase microextraction (SPME) prior to gas chromatography-mass spectrometry. Under the optimum extraction settings, that included an attentive optimization of the fiber rinsing conditions, the microextraction device was able to endure 100 consecutive extractions from undiluted and diluted plasma with an overall reproducibility up to 28% for all the analytes except chlorpyrifos-methyl. Optimized conditions were used to validate a quantitative method using matrix-matched calibration. Accuracy and precision values for bovine plasma were within 96-132% and 0.05-5.82% respectively. LLOQs for all the analytes were at 1 µg L-1 and LDR ranged within 1-100 µg L-1. The applicability of this method to plasma from different species (human, rat, rabbit) was also investigated. This work represents the first step towards broader use of the biocompatible PDMS/DVB/PDMS extraction phases to analyze multiclass xenobiotics in plasma and other complex biofluids.Chapter 3 describes a quantitative method for the analysis of xenobiotics in plasma based on solid phase microextraction (SPME) coupled with liquid chromatography (LC)-mass spectrometry. Moreover, the developed method was applied to evaluate the matrix effects of plasma from four different species (human, bovine, rat, and rabbit). PAN/C18 SPME fiber, which has previously been demonstrated to have outstanding biocompatibility in plasma, was used for this analysis in order to address the knowledge gap found in the literature, as this fiber has not been evaluated for the analysis of pesticides in biofluids. A group of model analytes containing physically, and chemically different xenobiotics (drugs and pesticides) were selected to determine the matrix effects of plasma in terms of analyte-protein binding and the instrument associate matrix interferences. Absolute matrix effect values, which were calculated by the differences in responses obtained from standards spiked before and after extraction of the matrix, range between the acceptable level of 96-108% for analytes from different plasma sources except for methaqualone and chlorpyrifos-methyl in rat plasma. These results indicate that the developed SPME method can be successfully applied for the analysis of xenobiotics from complex matrices with minimal matrix effects. This study also evaluated the variance of matrix effects due to the differences of interspecies plasma protein binding of analytes by comparing plasma calibration curves from different species with the calibration curve from PBS. Bayesian Hierarchical Model (BHM) was used to correct the variance added to measurements from different plasma types. Correction factors were calculated for each analyte in each plasma type and PBS. The correction factors effectively mitigated measurement bias resulting from different calibration curve types used in human plasma quality control measurements. This work would help to develop cost-effective and efficient calibration strategies for biofluids by utilizing plasma from readily available sources, such as bovine plasma, for method optimization and validation prior to quantitative analysis of plasma available in limited quantities (e.g., rabbit and rat).The developed SPME methods were tested for two different applications. Two different applications were described in chapters 4 and 5. In the fourth project, a high-throughput method was developed for analysis of 79 pesticides, commonly used in agricultural practices, in human plasma, using biocompatible solid phase microextraction (SPME) coupled to liquid chromatography-tandem mass spectrometry. An SPME method was developed using a hydrophilic-lipophilic balanced/polyacrylonitrile (HLB/PAN) extraction phase and demonstrated negligible matrix effects. The performance of the developed SPME method was compared to a QuEChERS- quick, easy, cheap, effective, rugged, and safe method, the most common sample preparation and cleanup approach for pesticide analysis in complex matrices. Comparable accuracy and precision were achieved for both methods, with accuracy values within 70-120% and relative standard deviation

In the first project, we describe the synthesis of an ambient stable high spin organic diradical 4 based on the Blatter moiety. The high-spin (S = 1) organic diradical 4, which consists of two Blatter radical moieties in a conjugated structure, exhibits a nearly exclusive population (88%) on triplet ground state at room temperature as a consequence of a large single-triplet energy gap (ΔEST = 0.5 kcal/mol). The target diradical molecule is synthesized over five steps with structural confirmation by single-crystal X-ray diffraction. The thermogravimetric analysis (TGA) shows the onset of decomposition at ~264 oC, indicating the diradical molecule has good thermal stability. The high spin organic molecules are not only purely organic magnets but also promising building blocks for emerging technologies. The diradical 4 crystal demonstrates good electrical conductivity. Also, the diradical can be evaporated under an ultra-high vacuum to form thin films, which are stable in ambient conditions for at least 18 h. In the second project, we describe the synthesis of a high-spin (S = 3/2) triBlatter triradical analogous to the diradical in the first project. The triradical was characterized by EPR, TGA, and UV-Vis near IR. Attempts to determine the ΔEDQ by EPR variable temperature measurement were performed. In the third project, we design and synthesize an organic radical MRI contrast agent. The structure of contrast agent is composed of a physiologically persistent nitroxide and a mannose sugar moiety. Taking advantage of the metabolic glycan labeling method, after the contrast agent was injected into mice, the nitroxides were expressed on the cell surface through metabolism, consequently changing the relativity of surrounding water molecules. Quantitative analysis of the in vivo NMR experiments and ex vivo EPR study were conducted. Advisor: Andrzej Rajca

Recently, novel and unrecognized endogenous metabolites have been found to impact the risk of CVD not related to established risk factors (residual risk), including metabolites produced by gut microbes. Discovery platforms including metabolomics and metagenomics have identified new biomarkers associated with residual risk, but these platforms’ usefulness is limited by the available methods of data analysis. This thesis aims to develop models of gut microbial metabolism using metagenomic data and new methods to identify unseparated structural isomers in metabolomics data. The gut microbial metabolism of trimethylamine-N-oxide, a metabolite associated with residual CVD risk, is used as a model system to develop predictive models of metabolism based on metagenomic information. An integrated analysis of metabolomics, metagenomics, and several other data types to predict circulating trimethylamine-N-oxide levels shows that while gut microbes play an essential role in trimethylamine-N-oxide synthesis, community composition does not quantitatively predict metabolism well enough to predict clinical risk. Analytical methods are developed to detect and identify structural isomers in metabolomics data. Two structural isomers, the terminal metabolites of niacin metabolism, are detected in human serum and characterized. Multiple clinical studies show these niacin metabolites are associated with residual CVD risk, and animal models show N1-methyl-4-pyridone-3-carboxamide (4PY) enhances vascular inflammation and thrombosis potential. Thus, new microbial and endogenous targets for therapy have been proposed, and new analytical methods have been introduced that may enable further study of residual CVD risk.

Artemisinin (ART) is a sesquiterpene lactone and a popular malaria drug with potential anticancer properties. In this work, LC/TOF MS was used to investigate the reaction of ART with DNA bases and estradiol. ART-deoxyadenosine and ART-deoxycytidine interactions were studied in the presence of Fe (II) ions. ART-deoxyadenosine and ART-deoxycytidine reaction mixtures gave chromatographic signatures that remained unchanged at room temperature but grew after incubation at 37°C. The change in temperature from room temperature to 37°C was the main driver of adduct formation in these reactions. ART was found to react with Fe (II) ions as observed from several new chromatographic peaks. ART-deoxyadenosine as well as ART-deoxycytidine in the presence of Fe (II) ions resulted in the formation of new chromatographic signatures of adducts consisting of DNA bases and ART. It was clear that the addition of Fe (II) to DNA base-ART mixtures gave rise to new reaction products mediated by a different reaction mechanism. Artemisinin-estradiol reactions were studied in the presence of Fe (II) ions. Artemisinin-estradiol reaction mixtures gave chromatographic signatures that remained unchanged at room temperature but grew after incubation at 37oC. Artemisinin-estradiol in the presence of Fe (II) ions resulted in new chromatographic signatures of adducts of estradiol with artemisinin. It was clear that the addition of Fe (II) to estradiol-artemisinin mixtures gave rise to new reaction products mediated by a different mechanism. Studies of ART reactions with DNA and estradiol in vitro are key in elucidating the elusive mechanism of this drug.

This dissertation reports on improvements in nuclear magnetic resonance (NMR) and mass spectrometry (MS) structure determination methods of organic compounds, with particular focus on challenging cyclic peptides. A recent and important innovation in NMR spectroscopy is the combination of theoretical property predictions, such as chemical shifts, using density functional theory (DFT) to aid in challenging NMR structure assignments, such as determination of regio- and stereo-configurations. In the first part of this thesis, a comprehensive benchmark study of DFT chemical shift prediction methods was performed using experimental NMR data collected from 50 well curated compounds, which was referred to as the DELTA50 test set. The best methods for proton and carbon chemical shift predictions were GIAO-WP04/6-311G(2d,p)//B3LYP-D3/6-311G(d,p) and GIAO-ωB97X-D/def2-SVP/B3LYP-D3/6-311G(d,p), respectively. Use of an implicit solvent model (i.e., polarizable continuum model) during both geometry optimization and chemical shift calculation improved the accuracy. The best performing DFT methods were then evaluated for 20 probe structures, which included small to medium-sized organic compounds, including natural products, and these were generally found to be more accurate than reported NMR chemical shift predictions in the literature. The calculated root-mean square deviations (RMSDs) for the probe set were 0.07 to 0.19 for 1H and 0.5 to 2.9 for 13C. Next, several challenging case studies, such as sungucine and (+/-)-anisodamine, for determination of relative stereoconfiguration were examined. Peptides were then studied in detail in the final two chapters. A liquid chromatography ion mobility mass spectrometry MS/MS method was developed to rapidly determine the primary structure of cyclic peptides. This approach was facilitated by a site-selective reaction that cleaves peptides at specific residues (viz., serine, threonine, cysteine, and glutamic acid), allowing for application of an automated de novo sequencing software. In the last chapter, the regio- and stereoconfigurations of reaction products from several newly reported peptide reactions were determined by NMR methods and further confirmed using DFT chemical shift predictions.

The research study included in the thesis aims to create novel Fenofibrate congeners that are simple to synthesize and are effective against hyperlipidemia. The research work carried out during the course of study is related to the development of synthetic methodology and characterization of new metabolites of fenofibrate. The synthesis of the new derivatives was achieved by late-stage derivatization strategy which yielded the desired novel derivatives by simple chemistry as well as shorter route of synthesis as compared to the traditional multi-step organic synthesis. New drug discovery is one of the major applications of the modern organic synthesis and with advancement new synthetic methods, the difficult task for the development of new chemical entities are progressing. Therefore, there is need to take actions for the evolution of new modes, catalysts, and strategies for the fast and economically viable routes for the new drugs and new drug molecules. The present work is related to the discovery of new chemical entities for the control and management of hyperlipidemia a major disorder in the human population. The present effort comprises late-stage modification of the fibrate class of drugs, viz fenofibrate with the objective to develop molecules with improved therapeutic and pharmacokinetic profiles. The work embodied in the thesis is divided into three chapters for the sake of clarity of understanding.

Landfill gas (LFG) can be used as a renewable domestic fuel for electricity generation via solid oxide fuel cells (SOFC) based on yttria-stabilized zirconia (YSZ) if species likely to poison the SOFC's anode and passivate the cell are identified, analyzed, and separated.This work focused on the surface chemistry of methane, the prime constituent of landfill gas.The methodology for this research was to run a Ni/YSZ/LSM button cell at temperatures of 750 – 900 °C with air fed to the lanthanum strontium manganite (LSM) cathode and a reducing gas such as hydrogen fed to the Ni anode before running it on humidified methane gas.After observing current and voltage transients and obtaining galvanic performance curves under methane, the cell was opened up and analyzed for any contamination of the anode using instrumentation such as scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS). These results served as the background for similar experiments using landfill gas (containing ~ 50% CH4) obtained from the Mahoning Landfill as fuel. The cell was again run until a steady state was reached, followed by removal and analysis.Despite the 2- to 2.5-fold water vapor excess, carbon deposition from methane on the anode reduced maximum cell power by 45% in comparison to pure H2. Passivation by LFG gas was even more severe, increasing charge transfer resistance by 654 Ω over simulated LFG at 800 °C and reducing maximum power by 90%.These results point to trace (< 1%) species besides H2S and siloxanes having a greater influence on the performance of the SOFC than the methane content of the LFG.Identifying these contaminants that poison the anode of SOFC cells when run on landfill gas will contribute to developing more efficient and sustainable energy production.

Metal oxide semiconductor materials such as tungsten oxide are promising candidates for use as photoanodes in solar water splitting. Tungsten oxide is an n-type semiconductor that was prepared on stainless steel 304 substrate and subsequently studied for water-splitting applications. This study investigated the effect of the annealing temperature and substrate cleaning reagents on the photoelectrochemical (PEC) properties of tungsten oxide thin films. The main method of synthesis employed was the sol-gel method. Tungsten oxide thin films were deposited from a precursor solution of peroxotungstic acid by doctor blading. The as-deposited amorphous WO3 films were further subjected to heat treatment at various annealing temperatures (200 ℃, 300 ℃, 400 ℃, and 500 ℃) to transform the amorphous material into polycrystalline WO3 nanostructures. Surface morphology, the crystallinity of the film, the thickness of the film, and photoelectrochemical properties were investigated using scanning electron microscopy, (SEM), X-ray diffractometry (XRD), stylus profilometry, cyclic voltammetry (CV), and linear sweep voltammetry (LSV). The optimal WO3 film, at a thickness of 5 µm and annealed at 400 ℃, achieved a photocurrent density of 98.0 µA/cm2 at an applied voltage of 0.53 V vs Ag/AgCl. It is essential to treat the substrate with HNO3 to passivate the surface of the stainless-steel substrate with the Cr2O3 layer.

The changing laws regarding the legal definition of hemp in Ohio have resulted in a need for forensic labs to perform quantitative analysis of cannabinoids, rather than the purely qualitative analysis used in the past. Some methods have been proposed for this, but cannabinoid products come in a wide range of sample matrices which makes it hard to determine how best to extract the regulated substance, delta-9-Tetrahydracannabinil (THC). Four extraction methods were tested for the purposes of comparison: an acetonitrile soak, a QuEChERS method, a method used by the United States Department of Agriculture (USDA), and a method used by the Virginia Department of Forensic Science (VDFS). The methods were performed and changed based on previous research to determine if they could efficiently extract cannabidiol (CBD) from a gummy matrix. CBD is structurally similar to THC, though CBD is unregulated. These four methods were tested on CBDFX mixed berry gummies. The percent recoveries of the methods were statistically different from each other, with QuEChERS performing the best and VDFS the worst. Using percent recovery to determine the best method of the four, QuEChERS was then also tested on R+R Medicinals alpine strawberry and cbdMD tropical mix gummies to determine the consistency of the method’s performance. The QuEChERS method was also found to perform with a significant difference between the cbdMD brand and R+R Medicinals brand gummies. Further research is necessary to develop and optimize a suitable method for the extraction and quantification of CBD and THC from a gummy matrix.

X-Ray Fluorescence (XRF) spectroscopy is a good analytical method for determination of both trace and major elements in different samples, it has the important advantages of allowing direct analysis of soils and sediments and is also non-destructive.The major aim of this study was to develop an XRF method for the determination of total metal concentrations in soils and sediments. Limit of detection and limit of quantitation were used as the figures of merit to evaluate the method. Standard Reference materials: NIST-2586, NIST-2587, NIST-1645 and NIST-1645 were used for calibration. Different calibration methods were explored. background corrected peak height to Background corrected Compton peak height ratio had the highest correlation coefficient (0.99) for Fe, Cu, Mn, Zn, Al, Cr, Ca and Pb.The method was applied to measure 120 sediment samples that were collected from the yellow creek watershed Poland, Ohio. The results of the XRF method were compared with those obtained by ICP-MS. Al, Mn, Zn, Fe and Cu had good agreement. A sequential extraction approach was developed for characterizing the availability of metals in the water from the sediments. Ca and Mn were found to be easily extracted under weakly acidic conditions.

Metals are considered contaminants in the Safe Drinking Water Act. At a certain level, some metals become toxic and result in organ impairment of fish and other aquatic species. Sediment is one of the reservoirs of metals and has direct contact with water. Metals in the sediment should be monitored to prevent pollution of drinking water sources and can be monitored by Inductively Coupled Plasma—Mass Spectrometry (ICP-MS) according to US EPA 200.8 and 6020B.This work was part of a larger study of the Yellow Creek that was performed in collaboration with Prof. Johnston's group (from Biology). Several different water quality parameters were studied, including the different metals and their concentrations in the sediments. As part of the studies, it was important to develop an ICP-MS method and show that it would provide useful measurement results for the metals.Water and sediment samples were collected at three sites along Yellow Creek which have different characteristics in order to evaluate the possible effects of the woods, the traffic and a storm drain on the observed concentrations of metals.An ICP-MS method was fully developed in this study to measure metal concentrations in sediment samples. The method was evaluated in terms of instrument detection limit and interferences and validated based on the recoveries of reference material Buffalo River sediment NIST® RM 8704. The procedure was then applied to measure metal concentrations in the sediment samples collected during a water quality study of the Yellow Creek in Poland, Ohio conducted over three consecutive seasons. Metal concentrations of all samples were generally evaluated based on Freshwater Sediment Screening Benchmarks and Probable effect concentration referenced from US EPA internet database. The trend of metal concentrations over time and in three sampling days were studied. Metal concentrations of the sediments in the Yellow Creek overall appear to be low.Finally, concentrations of metals measured by ICP-MS were compared to those measured by XRF (X-ray Fluorescence Spectrometry). The two methods were compared regarding the level of metals and the trend of changing in concentration over time. XRF is a complimentary method for ICP which can be used to measure some elements that are difficult to be extracted from the sediment, such as Cr and Al. Major elements such as Ca, Fe, Mn, Mg can be measured by XRF which is a direct method, while ICP-MS requires several digestion and dilution steps. Trace elements like Pb, Cd, Co, Ni are better measured by ICP-MS due to their low concentrations in the sediments.

General food and pharmaceutical analysis guidelines have been improved by the United States Pharmacopeia (USP) over the years to help in ensuring the quality, safety, and usefulness of products.Atomic Spectroscopy (AAS, AES and AFS) has been used in sample analysis. These techniques have low detection limits, are precise and can provide reliable information. However, they involve complex sample preparation procedures and expensive reagents required for sample preparations and to maintain the instrument. It is important to develop a method that can be used to directly screen the samples during the production process and do not destroy the matrix. XRF is not destructive, fast process that does not involve a complex sample preparation procedure. The sample screen can be returned to the production conveyer, eliminating waste, and saving time. In our work we developed analytical methods for pharmaceutical and food samples. In the method the samples were analyzed directly with their matrix embedded. The results were cleaned of interferences using background interference corrections as well as fundamentals of Compton scattering techniques. Our analytes were Mn, Fe, Co, Ni, Zn and Cr. The detection limits for these analytes were Mn (1 ppm), Fe (1 ppm), Co (1 ppm), Ni (1 ppm), Zn (4 ppm) and Cr (0.05 ppm).

Ruddlesden Popper (RP) oxides are perovskite-derived functional materials with the general formula An-1Aʹ2BnO3n+1, where A/Aʹ is often a lanthanide or alkaline earth metal, and B is usually a transition metal. These materials contain perovskite-like connectivity, where BO6 units share apexes to form layers that are stacked above each other. The number of layers in each stack is represented by n in the above formula. The spaces between stacks are often occupied by lanthanide or alkaline-earth metals (Aʹ-site metals), which also reside in intra-stack spaces (A-site) between the octahedra. Oxide materials derived from perovskites have been studied for a wide range of applications, such as solar cells, batteries, catalysts, and capacitors. We have studied the electrocatalytic properties of RP materials for water splitting. This is an important application given the need for efficient and economical electrocatalysts for the two half-reactions of water-splitting, namely hydrogen-evolution reaction (HER) and oxygen-evolution reaction (OER). The benchmark catalysts to overcome the sluggish kinetics of OER and HER are Ru, Ir, and Pt-based catalysts. Such catalysts are expensive since they use precious metals, and some of them have stability issues. Owing to their compositional diversity and the thermodynamic stability, multi-element transition metal oxides are promising candidates for electrocatalytic water splitting. The variation of A and B-site metals in RP oxides can lead to changes in physical and chemical properties, such as crystal structure, magnetism, conductivity, and electrochemical catalysis. In this study, several bilayered (n = 2) RP oxides are synthesized followed by systematic study of magnetic, charge transport, pseudocapacitive, and electrocatalytic properties. The effect of structural symmetry on electrocatalytic properties in two isoelectronic materials, Sr2LaMn2O7 and Ca2LaMn2O7, which were synthesized by varying the A-site cation, was investigated. The structural changes identified are associated with systematic variation in the magnetic, electrical charge transport and electrocatalytic properties toward both components of water splitting, namely OER and HER. The effect of the B-site cation on electrocatalytic performance of two RP materials, Sr2LaFeMnO7 and Sr2LaCoMnO7 was also studied. Here, the variation in the B-site cation can result in significant changes in magnetic properties, charge-transport properties, and the activity toward the HER and OER processes. Together with the A/Aʹ and B-site changes of RP oxides, oxygen vacancies in these oxide materials strongly affect the properties including conductivity and electrocatalytic activity. Systematic trends in the series of materials, Sr3Ti2-xMxO7-δ (M = Mn, Fe, Co; x = 0, 1) were observed with the creation of oxygen vacancies which correlate with electrocatalytic and charge-transport properties. The bilayered RP materials have been also explored to understand the oxide intercalation based pseudocapacitance. The change in pseudocapacitive properties as a function of structural symmetry in two materials Ca2LaMn2O7 and Sr2LaMn2O7 was studied in the alkaline medium. Overall, in the bilayered RP oxides, the electrical, electrochemical and electrocatalytic characteristics can be modified by changing the elemental composition, symmetry, and oxygen vacancies.