<div>Mass spectrometry (MS) is a powerful and versatile analytical tool that is extensively used for the identification and analysis of complex mixtures. The ability to couple MS to atmospheric pressure ionization techniques and high-performance liquid chromatography (HPLC) or gas chromatography (GC) provides a high degree of experimental flexibility. MS is based on the analysis of gas-phase ions. Gas-phase ions are manipulated within the mass spectrometer and separated for detection based on their mass-to-charge (m/z) ratio.</div><div>One of the most commonly used techniques for complex mixture analysis is tandem mass spectrometry (MSⁿ). MSⁿ involves the isolation of the desired ion and allowing it to undergo reactions, such as collision-activated dissociation (CAD) or ion-molecule reactions. Based on the generated product ions, structural information can be obtained for unknown analytes in complex mixtures. In addition, MSⁿ methods based on diagnostic gas-phase ion-molecule reactions have been demonstrated to provide a general and predictable tool to identify specific functional groups in unknown ionized analytes and to classify unknown analytes into different compound classes depending on their functionalities.</div><div>The research described in this dissertation mainly focuses on the development of tandem mass spectrometric methods based on gas-phase ion-molecule reactions and/or CAD for the identification of the <i>N</i>-nitroso functionality, which is present in some potentially mutagenic drug impurities. Furthermore, the dissertation discusses combining machine learning and MSⁿexperiments based on diagnostic ion-molecule reactions of 2-methoxypropene to predict reaction outcomes in a semiautomated fashion for protonated analytes containing specific functional groups. Lastly, chemical characterization and gas-phase reactivity of the boron-centered radical dianion [B₁₂I₁₁]^2-• toward some organic molecules are discussed.</div>

Positively charged aromatic carbon-centered σ-type mono-and biradicals have been studied previously in the gas phase. However, very little is known about the properties of related polyradicals. In this dissertation, the reactions of series of quinolinium-and acridinium-based bi-, tri-, and tetraradicals were studied with cyclohexane and allyl iodide in the gas phase by using tandem mass spectrometry. I atom abstraction and allyl group abstraction were observed as dominant reactions for all the studied radicals upon reactions with allyl iodide. Sequential H atom abstractions were observed as the major reactions for the studied bi-and tetraradicals upon reactions with cyclohexane. Surprisingly, triradicals appeared to undergo addition followed by elimination of a H atom as one of the major reactions upon interactions with cyclohexane. Vertical electron affinity and spin-spin coupling between radical sites were found to control the radical reactivities.<div><br></div><div>The radical site(s) which react first with cyclohexane were experimentally determined. For the studied biradicals, the first reacting radical sites were found to be the ones that are predicted to be more reactive based on the reactivities of related monoradicals. For the studied triradicals, the first reacting radical sites are the ones that are least strongly coupled to the other radical sites. For tetraradicals, the first two sites reacting with cyclohexane are more weakly coupled than the other two radical sites.<br></div><div><br></div><div>The mechanisms for the reactions of the triradicals with cyclohexane were proposed based on tandem mass spectrometry experiments and supported by quantum chemical calculations. Briefly, the least strongly coupled radical site of a triradical reacts with cyclohexane first by abstracting a H atom. The more reactive radical site insome of the produced biradicals will then abstract a H atom from the cyclohexyl radical within the product collision complex to generate a monoradical and cyclohexene. Some of these monoradicals undergo addition to cyclohexene within this product complex,followed by elimination of a H atom. When allowed to react with allyl iodide, all of the monoradicals and most of the biradicals demonstrated predominant I atom abstraction. The quinolinium-based meta-and para-benzynes exhibited allyl group abstraction as the major reaction. The triradicals with a meta-benzyne moiety in the pyridinium ring demonstrated dominant allyl group abstraction, which is likely to occur at the pyridinium moiety. The reaction efficienciesof these triradicals toward allyl iodide are correlated with their calculated vertical electron affinities. The other triradicals showed I atom abstraction as the major reaction. These triradicals react with allyl iodide through different mechanisms compared to those mainly abstract an allyl group. Therefore, their reactivities are not directly related to their calculated vertical electron affinities.<br></div><div><br></div><div>In the tetraradicals, spin-spin coupling between all the radical sites affects their reactivities. The coupling of the radicals in a benzyne moiety is weakened by the couplings of radical sites between two benzyne moieties. This interaction results in higher reaction efficiencies for the tetraradicals than the related benzynes. Particularly, the 2,4,7,8-tetradehydroquinolinium cation was found to have much higher reactivity than the related meta-benzyne, the 2,4-didehydroquinolinium cation. This was rationalized based on the low distortion energy of the meta-benzyne moiety in the tetraradical.<br></div><div><br></div><div>Spin-spin coupling between the radical sites in bi-, tri-, and tetraradicals significantly affect their reactivity. To better understand the relation between the effects of spin-spin coupling and the spatial distance between two radical sites, a series of acridinium-based mono-and biradicals were studied in the gas phase. The acridinium-based monoradicals are less reactive than the related quinolinium-based monoradicals, which is possibly because of the steric hindrance of the additional benzene ring. Unlike quinolinium-based biradicals, which are less reactive than the related monoradicals, acridinium-based biradicals showed higher reactivities than the monoradicals with similar vertical electron affinities. In order to better illustrate the coupling strength in the studied biradicals, the natural logarithm of their total reaction efficiencies toward cyclohexane was plotted as a function of their calculated vertical electron affinities. The plots indicate that the coupling of quinolinium-based biradicals hinders the radical reactivity, while for acridinium-based biradicals, the coupling is negligibly weak and the biradicals react as two individual monoradicals.<br></div>

<p> Illicit drug abuse is a widespread issue in the United States and worldwide. Many methods  seek to ease the analytical workload required to collect, analyze, and identify these drugs. Paper  spray-mass spectrometry (PS-MS) is one response to this analytical workload as it offers a rapid,  affordable, and simple means for drug identification by mass spectrometry. This work centers on  the use of pressure-sensitive adhesive (PSA) lined paper as a PS-MS substrate for drug recovery  and detection. The use of PSA paper as a sampling and analysis substrate has been previously  established but is expanded herein with new capabilities and applications. Chapter 2 introduces  the combination of color tests followed by PS-MS for presumptive and confirmatory drug  identification. Three color tests (cobalt thiocyanate, Simon, or Marquis) were performed on the  PSA paper with subsequent drug confirmation occurring by PS-MS. Chapter 3 examines the use  of PSA paper and PS-MS for the recovery and detection of fentanyl, fentanyl precursors, and  analogs from shipping-related surfaces and in the presence of high amounts of cutting agents. The  use of a cartridge that accommodates a full-sized PSA paper ticket was also explored for drug  detection. Chapter 4 assesses PS-MS with PSA paper on portable MS instrumentation. Analyte  recovery and carryover as well as instrument robustness were evaluated. The color test and PS-MS protocol examined in Chapter 2 was also successfully applied to a portable MS instrument.  Application of PS-MS to the portable system highlights the potential fieldability of the technique. </p>

<p> Mass spectrometry (MS) has become one of the most powerful and versatile tools for chemical analysis due to its ultra-high sensitivity, high throughput, ease of automation, and the large amount of information obtained. Nowadays, MS is extensively used in many tasks, such as identification and quantitation of drug metabolites, analysis of the products of biomass pyrolysis, and study of reactive intermediates, to name a few. However, these mass spectrometric analyses are not without challenges. For example, the requirement for quantifying trace amounts of substances in a complex mixture constantly pushes the detection limit of mass spectrometers, and the increased sample complexity demands higher and higher mass resolution. Therefore, MS is constantly evolving to address more difficult analytical challenges. A variety of MS techniques have been developed over the years, including soft ionization methods that facilitate mass spectrometric analysis of macromolecules, such as proteins and antibodies that enables the development of new therapeutic agents, benchtop high-resolution mass spectrometers, such as the orbitraps that can be used to analyze some of the most complex mixtures, and portable mass spectrometers which can be used in the home and garden and even in cancer surgery. Besides its applications in chemical analysis, MS can serve as a unique tool for the fundamental study of gas-phase ion/molecule reactions, these gas-phase reactions can be used to better understand the reactivities of many reactive intermediates and to obtain structural information for unknown analytes.</p><p></p><p> This thesis is aimed at addressing challenges involved in mass spectrometric analyses of isomeric drug metabolites (Chapter 4), quantitation of drug metabolites by using tandem mass spectrometry coupled with liquid chromatography (LC-MS/MS) (Chapter 5), delineating cellulose depolymerization mechanisms upon fast pyrolysis by using pyrolysis-tandem mass spectrometry (py-MS/MS) (Chapter 6), and studying the reactivities of vinyl cation intermediates (Chapter 7). An overview of the dissertation research is given in Chapter 1, the instrumentation and principles of linear quadrupole ion trap (LQIT) mass spectrometer are discussed in Chapter 2, and the organic synthesis performed for several studies is detailed in Chapter 3.</p>

<div>Mass spectrometry (MS) is a powerful and versatile analytical tool, especially for identification and analysis of complex mixtures. Coupling to high-performance liquid chromatography (HPLC) or gas chromatography (GC) provides additional dimension for mixture analysis. MS manipulates ionized analytes and separates them based on their mass-to-charge (<i>m/z</i>) ratios. MS is capable of providing molecular weight (MW) information by generating pseudo-molecular ions of the analytes. Detailed elemental compositions can be also obtained if high resolution MS is used. MS can also provide extensive structural information of the analyte ions. One of the most commonly used technique is tandem mass spectrometry (MSⁿ). Ions of interest are isolated and subject to sequential reactions (reactions with other molecules or dissociation reactions) to generate product ions that can provide structural information. MS is also a powerful tool for generating and studying highly reactive reaction intermediates, such as organic polyradicals.</div><div><br></div><div>The research described in this dissertation mainly focuses on the generation and gas-phase reactivity studies of different organic biradicals. Their reactions with various organic reagents are studied, and the reactivity-controlling factors are discussed. For example, the reactivity of several substituted pyridine-based biradical cations with 2,6-topology are discussed (all with singlet ground states), and their special reactivity from their excited triplet states are illustrated. Besides, several quinoline-based biradicals and cyano-substituted pyridine-based <i>para</i>-benzyne cations are also discussed. Some of the radicals (or ions) described in this dissertation are generated for the first time, i.e. the quinoline-based oxenium cations. Their structural characterization and gas-phase reactivity toward some organic molecules are discussed in the dissertation. Further, an electrophilic anion, <i>closo</i>-[B₁₂X₁₁]^- (X = Cl, Br) and its application in the activation of C-H and C-C bonds in hydrocarbon molecules are described in the dissertation.</div>

<div> <div> <p>Continuous flow chemistry for organic synthesis is an emerging technique in academia and industry because of its exceptional heat and mass transfer ability and, in turn, higher productivity in smaller reactor volumes. Preparative electrospray (ES) is a technique that exploits reactions in charged microdroplets that seeks to accelerate chemical synthesis. In Chapter 2, the flow synthesis of atropine, a drug which is included in the WHO list of essential of medicines and currently in shortage according to the U.S Food and Drug Administration (FDA)is reported.The two steps of atropine synthesis were initially optimized separately and then continuously synthesized using two microfluidic chips under individually optimized condition.The telescoped continuous-flow microfluidics experiment gave a 55% conversion with an average of 34% yield in 8 min residence time. In Chapter 3, a robotic HTE technique to execute reactions in 96-well arrays was coupled with fast MS analysis. Palladium-catalyzed Suzuki-Miyaura (S-M) cross-coupling reactions were screened in this system and a heat map was generated to identify the best reaction condition for downstream scale up in continuous flow. <br></p><p><br></p><p>In Chapter 4, an inexpensive and rapid synthesis of an old anticancer drug, lomustine,was synthesized. Using only four inexpensive commercially available starting materials and a total residence time of 9 min, lomustine was prepared via a linear sequence of two chemical reactions performed separately in two telescoped flow reactors. Sequential offline extraction and filtration resulted in 63% overall yield of pure lomustine at a production rate of 110 mg/h. The primary advantage of this approach lies in the rapid manufacture of lomustine with two telescoped steps to avoid isolation and purification of a labile intermediate, thereby decreasing the production cost significantly. A high throughput reaction screening approach based on desorption electrospray ionization mass spectrometry (DESI-MS) is described in Chapter 4 and 5 for finding the heat-map from a set of reaction conditions. DESI-MS is used to quickly explore a large number of reaction conditions and guide the efficient translation of optimized conditions to continuous flow synthesis that potentially accelerate the process of reaction optimization and discovery. Chapter 5 described HTE ofSNAr reactions using DESI-MS and bulk techniques with 1536 unique reaction conditions explored using both in DESI-MS and bulk reactors. The hotspots from the HTE screening effort were validated using a microfluidic system that confirmed the conditions as true positives or true.<br></p> </div> </div>

The function of many biological processes depends on the structure and composition of the biomolecules involved. Both spectroscopy and mass spectrometry provide complimentary information regarding the three-dimensional conformation and the composition, respectively, as well as many other things. Here, double resonance conformer specific spectroscopy coupled with the latest ab inito computational methods is used to make structural assignments at the atomic resolution as well obtain information regarding propensities of intramolecular interactions. Additionally, rapid cooling in conjunction with IR excitation to modulate and measure the relative populations of conformers present in the expansion. Two different designer peptide systems are studied, including an achiral acylated 𝛼-aminoisobutryic acid dipeptide (Ac-AIB2-R) with various C-terminal protecting groups (R=NHBn, NHBnF, 𝛼-methylbenzylamine) and an acylated 𝛾4-phenylalanine (Ac-𝛾4Phe-NHMe) with the a methyl amine C-terminal protecting group. Mass spectrometry is used to determine the kinetics of gas-phase covalent tagging reactions used to enhance the sequence coverage. The covalent modification reactions utilize click chemistry between NHS or HOBt substituted sulfobenzoic acid tags with nucleophiles present on the residues of the amino acids composing the backbone. Effective temperatures are approximated using the Tolmachev model, which relates the statistical average internal energy of the molecule to a temperature.

The work described herein is related to gas-phase ion-molecule reactions studied by using mass spectrometry. Chapter 2 describes density functional theory, a method used in chapters 4 and 5 to propose reaction mechanisms for reactions previously observed by others by using mass spectrometry. Chapter 3 describes a study that demonstrates that the fragmentation of saturated hydrocarbons occurs due to proton-transfer reactions that occur between these species and protonated molecules generated from molecules present in air such as nitrogen and water. Saturated hydrocarbons are studied in a wide variety of fields, and better methods to analyze complex mixtures of these compounds would facilitate their analysis. Chapter 4 discusses mechanisms of reactions for previously studied ion-molecule reactions of pyridynes studied by others by using mass spectrometry. Reactions of pyridynes are important to study arynes have been previously used in organic synthesis, and pyridine moieties are particularly common in biological compounds. Chapter 5 discusses density functional theory calculations used to determine why some organic polyradical undergo hydride abstractions from cyclohexane while others do not. The study discusses reactions taking place between both singlet and triplets states of the 2,5-didehydropyridinium cation and cyclohexane as a model, which are compared to reactions of the 2-pyridyl cation and 2-dehydropyridinium cation with cyclohexane. These studies may help improve our understanding of the reactivity-controlling factors of organic polyradicals, which may help improve toxic drug candidates like cytostatic enediynes.

<p>Mass spectrometry (MS) is a versatile analytical tool that is especially useful for identification of unknown compounds in mixtures when coupled with chromatography. In MS experiments, the analytes are ionized, separated based on their mass-to-charge (<i>m/z</i>) ratios, and detected. The molecular weight of the analyte can often be derived from the mass spectrum if stable molecular ions (M^•+) or stable protonated/deprotonated analyte molecules ([M+H]⁺ or [M-H]^–) are generated. Further, MS can also be used to obtain structural information for the ionized analytes via their fragmentation reactions. Tandem mass spectrometry (MSⁿ) experiments are powerful for the characterization of unknown compounds in mixtures without the need for coupling them with chromatography. In MSⁿ experiments, the analytes are ionized, the ions of interest are isolated and subjected to reactions, such as collision-activated dissociation (CAD) or ion-molecule reactions with neutral reagent molecules. The fragmentation pattern or the diagnostic ion-molecule reaction product ions can be utilized to elucidate the structures of the analytes. The fragment ions or diagnostic product ions can further be subjected to CAD to obtain more structural information. Besides analytical purposes, MSⁿ also provides a powerful tool for exploring the reactivities of reaction intermediates that are elusive, such as phenylcarbyne anions and phenylcarbene anions.</p> <p>The research described in this dissertation mainly focuses on the development of MSⁿ methods based on diagnostic gas-phase ion-molecule reactions followed by CAD for (1) the characterization of differently substituted ureas and (2) the differentiation of sulfonate esters from their isomeric analogs, such as sulfite esters and sulfones. HPLC was coupled with the MSⁿ methods discussed above to demonstrate its usefulness in the identification of compounds in mixtures. Additionally, a gas-phase reactivity study on phenylcarbyne anions is discussed in this dissertation. The phenylcarbyne anions were generated by CAD of two nitrogen molecules from negatively charged phenyl tetrazole precursors. Their reactivities towards various reagents were explored and rationalized with the help of quantum chemical calculations.</p>

<p>Mass spectrometry, the science and technology of ions, owes much of its current popularity to the development of electrospray ionization. The development of electrospray ionization, along with its low flow-rate analog nanoelectrospray ionization, has increased the chemical space that can be investigated using mass spectrometers by orders of magnitude. While the interfacial chemistry of charged microdroplets that are generated by nanoelectrospray has been studied in detail, the physics of their motion, particularly in the presence of an applied field at ambient pressures, remains relatively unexplored. In this dissertation, an increase in ion currents detected by a commercial triple quadrupole mass spectrometer is used to demonstrate that: (i) the orthogonal injection of counterions into an electrode assembly can compensate for space charge effects and enhance the sampling of charged microdroplets from a nanoelectrospray focused electrostatically under ambient conditions into the mass spectrometer; and (ii) the ease of ion evaporation from charged microdroplets may be elucidated for small molecules based on their relative transmission through an electrode assembly for the simultaneous ambient electrostatic focusing of two nanoelectrosprays. In each case, the development is characterized by using ion trajectory calculations in conjunction with experiments, using homebuilt devices designed and fabricated in-house as rapid prototypes via 3D printing. In the open air, charged microdroplets have low kinetic energies with a narrow energy spread. Despite these limitations, this dissertation demonstrates, through the electrostatic manipulation of charged microdroplets produced via nanoelectrospray ionization, that a better understanding of the physics of moving charges in the open air can be used to increase the sensitivity of atmospheric pressure ionization.</p>