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 dir="ltr">Conducting polymers have garnered enormous attention due to their unique properties, including tunable chemical structure, high flexibility, solution processability, and biocompatibility. They hold promising applications in flexible electronics, renewable energies, sensing, and healthcare. Despite notable progress in conducting polymers over the past few decades, most of them still suffer from complicated synthesis routes, limited processability, low electrical conductivity, and poor ambient stability compared to their inorganic counterparts. Additionally, the susceptibility of conducting polymers to high temperatures makes them not applicable in real-life electronics. To address the challenges of developing high-performance and stable conducting polymers, we present two key approaches: dopant innovation for polymer-dopant interaction engineering and the discovery of new conjugated polymer hosts. From the perspective of dopant design, we first utilize cross-linkable chlorosilanes (C-Si) to design thermally and chemically stable conductive polymer composites. C-Si can form robust siloxane networks and simultaneously<i> </i>dope the host conjugated polymers. Besides, we have introduced a new class of dopants, namely aromatic ionic dopants (AIDs). The use of AIDs allows for the separation of doping and charge compensation, two processes involved in molecular doping, and therefore leads to highly efficient doping and thermally stable doped systems. We then provide insights into the design of novel conjugated polymer hosts. Remarkably, we have developed the first thermodynamically stable n-type conducting polymer, n-doped Poly (3,7-dihydrobenzo[1,2-b:4,5-b′]difuran-2,6-dione) (n-PBDF). n-PBDF is synthesized from a simple and scalable route, involving oxidative polymerization and reductive doping in one pot in the air. The n-PBDF ink is solution processable with excellent ink stability and the n-PBDF thin film is highly conductive, transparent, patternable, and robust. In addition, precise control over the doping levels of n-PBDF has been achieved through chemical doping and dedoping. By tuning the n-PBDF thin films between highly doped and dedoped states, the system shows controllable conductivity, optical properties, and energetics, thereby offering potential applications in a variety of organic electronics. Overall, this research advances the fundamental understanding of molecular doping and offers insights for the development of high-conductivity, stable conducting polymers with tunable properties for next-generation electronics.</p>

No description available.

No description available.

<p><a></a><a></a><a></a><a></a><a></a><a></a><a></a><a></a><a></a><a></a><a>ABSTRACT</a></p> <p>Phenols are ubiquitous in our surroundings including biological molecules such as L-Dopa metabolites, food components, such as whiskey and liquid smoke, etc. This dissertation describes a new method for detecting phenols, by reaction with Gibbs reagent to form indophenols, followed by mass spectrometric detection. Unlike the standard Gibbs reaction which uses a colorimetric approach, the use of mass spectrometry allows for simultaneous detection of differently substituted phenols. The procedure is demonstrated to work for a large variety of phenols without <i>para</i>‐substitution. With <i>para</i>‐substituted phenols, Gibbs products are still often observed, but the specific product depends on the substituent. For <i>para</i> groups with high electronegativity, such as methoxy or halogens, the reaction proceeds by displacement of the substituent. For groups with lower electronegativity, such as amino or alkyl groups, Gibbs products are observed that retain the substituent, indicating that the reaction occurs at the <i>ortho</i> or <i>meta</i> position. In mixtures of phenols, the relative intensities of the Gibbs products are proportional to the relative concentrations, and concentrations as low as 1 μmol/L can be detected. The method is applied to the qualitative analysis of commercial liquid smoke, and it is found that hickory and mesquite flavors have significantly different phenolic composition.</p> <p>In the course of this study, we used this technique to quantify major phenol derivatives in commercial products such as liquid smoke (catechol, guaiacol and syringol) and whiskey (<i>o</i>-cresol, guaiacol and syringol) as the phenol derivatives are a significant part of the aroma of foodstuffs and alcoholic beverages. For instance, phenolic compounds are partly responsible for the taste, aroma and the smokiness in Liquid Smokes and Scotch whiskies. </p> <p>In the analysis of Liquid Smokes, we have carried out an analysis of phenols in commercial liquid smoke by using the reaction with Gibbs reagent followed by analysis using electrospray ionization mass spectrometry (ESI-MS). This analysis technique allows us to avoid any separation and/or solvent extraction steps before MS analysis. With this analysis, we are able to determine and compare the phenolic compositions of hickory, mesquite, pecan and apple wood flavors of liquid smoke. </p> <p>In the analysis of phenols in whiskey, we describe the detection of the Gibbs products from the phenols in four different commercial Scotch whiskies by using simple ESI-MS. In addition, by addition of an internal standard, 5,6,7,8-tetrahydro-1-napthol (THN), concentrations of the major phenols in the whiskies are readily obtained. With this analysis we are able to determine and compare the composition of phenols in them and their contribution in the taste, smokey, and aroma to the whiskies.</p> <p>Another important class of phenols are found in biological samples, such as L-Dopa and its metabolites, which are neurotransmitters and play important roles in living systems. In this work, we describe the detection of Gibbs products formed from these neurotransmitters after reaction with Gibbs reagent and analysis by using simple ESI‐MS. This technique would be an alternative method for the detection and simultaneous quantification of these neurotransmitters. </p> <p>Finally, in the course of this work, we found that the positive Gibbs tests are obtained for a wide range of <i>para</i>-substituted phenols, and that, in most cases, substitution occurs by displacement of the <i>para</i>-substituent. In addition, there is generally an additional unique second-phenol-addition product, which conveniently can be used from an analytical perspective to distinguish <i>para</i>-substituted phenols from the unsubstituted versions. In addition to using the methodology for phenol analysis, we are examining the mechanism of indophenol formation, particularly with the <i>para</i>-substituted phenols. </p> <p>The importance of peptides to the scientific world is enormous and, therefore, their structures, properties, and reactivity are exceptionally well-characterized by mass spectrometry and electrospray ionization. In the dipeptide work, we have used mass spectrometry to examine the dissociation of dipeptides of phenylalanine (Phe), containing sulfonated tag as a charge carrier (Phe*), proline (Pro) to investigate their gas phase dissociation. The presence of sulfonated tag (SO₃^-) on the Phe amino acid serves as the charge carrier such that the dipeptide backbone has a canonical structure and is not protonated. Phe-Pro dipeptide and their derivatives were synthesized and analyzed by LCQ-Deca mass spectroscopy to get the fragmentation mechanism. To confirm that fragmentation path, we also synthesized dikitopeparazines and oxazolines from all combinations of the dipeptides. All these analyses were confirmed by isotopic labeling experiments and determination and optimization of structures were carried out using theoretical calculation. We have found that the fragmentation of Phe*Pro and ProPhe* dipeptides form sequence specific b₂ ions. In addition, not only is the ‘mobile proton’ involved in the dissociation process, but also is the ‘backbone hydrogen’ is involved in forming b₂ ions. </p> <p> </p>

<p>  </p> <p>Organic synthesis is the application of one or more reactions to the preparation of a particular target molecule, and can pertain to a single-step transformation or to a number of sequential chemical steps depicted by a scheme overall. The selection of a reaction or series of reactions while considering chemo-, regio-, and stereoselectivities in addition to protecting group strategies & redox manipulations highlights the complexity in designing & executing a synthetic plan while making a judgement about what is the most effective and efficient plan to synthesize any given chemical compound among numerous available options. To this end, chemical synthesis is the unifying theme of this thesis & was utilized and strategically applied to construct increasingly complex and diverse molecular architectures. </p> <p>Being the precise science that organic chemistry is, this discipline extends into many areas such as technology, biology & medicine, and even into the fine arts since it fosters unparalleled creativity and imagination in its practice. Research foci in chemical synthesis can encompass both the discovery and development of powerful reactions and the invention of strategies for the construction of defined target molecules, natural or man-made, more or less complex. Studies in the former area, synthetic methodology, fuel and enable studies in the latter area, target molecule and total synthesis campaigns, where the latter area offers a testing ground for the former. Consequently, the bulk of this research work is in organic methodology and will be covered in greater depth during chapters 2 and 3 where strategies, optimizations, & analyses are elaborated upon in light of searching & navigating the vast body of chemical literature in an effort to broaden and strengthen one's laboratory expertise as a synthetic chemist. Lastly, chapter 4 focuses not on traditional synthesis but on organic structure analysis relying on various techniques such as nuclear magnetic resonance (NMR), infrared (IR), ultraviolet-visible (UV-Vis) spectroscopy in combination with mass spectrometry (MS) and/or X-ray crystallography to hypothesize and confirm established structures, specifically phenolic oligomers. An ability to use spectroscopic data to evaluate organic structures by combining practical experience with fundamental knowledge will serve as a hallmark skill in one’s ability to problem-solve as an organic chemist.</p>

<p dir="ltr">Tandem mass spectrometry (MSⁿ) has become the most widely used analytical technique for the chemical characterization of unknown organic compounds in complex mixtures. It has led to the development of a large number of mass spectrometers with different mass analyzers as well as a wide array of ionization methods. This technique can be coupled with a diverse range of chromatography methods, such as gas chromatography (GC) and high-performance liquid chromatography (HPLC). Some of the primary strengths of MS include its great sensitivity, its versatility to seamlessly integrate with various chromatography techniques and its flexibility in the sense of access to different mass analyzers and different ionization methods. During MS experiments, analytes are evaporated and ionized and the resulting ions are separated based on their mass-to-charge (<i>m/z</i>) ratios and then detected. On the other hand, MSⁿ experiments involve isolating a specific ion of interest from all other ions and subjecting them to reactions such as collision-activated dissociation (CAD) or ion-molecule reactions. These reactions generate product ions that can be used to obtain structural information for the analyte. In addition, MSⁿ experiments can be used to generate and study the chemical properties of reaction intermediates, such as oxenium cations. </p><p dir="ltr">The mass spectrometer and the ionization source used to perform the research discussed in this thesis are described in Chapter 2. After this, the development of experiments involving ion-molecule reactions accompanied by collision-activated dissociation in a linear quadrupole ion trap is discussed, with the goals of differentiating the aziridine functionality from structurally related functional groups, such as the amino group and identifying aromatic aldehyde functionalities in protonated oxygen-containing monofunctional analytes. The integration of machine learning with mass spectral data has become an increasingly prevalent and valuable way to interpret data faster and more accurately without human bias than conventional manual approaches. Chapter 5 discusses combining machine learning-guided automated HPLC analysis coupled with MSⁿ experiments based on diagnostic ion-molecule reactions for the structural elucidation of unknown compounds. Finally, experimental and computational studies on the gas-phase reactivity of quinoline-based ground-state singlet oxenium cations are discussed.</p>

Die vorliegende Arbeit hat die Synthese und Charakterisierung von chromophoren Arylboronsäureestern mit besonderem Augenmerk auf einer breiten strukturellen Variation zum Inhalt. An dieser Verbindungsklasse wird die Wechselwirkung mit Lewis-Basen tiefgehend untersucht. Die Koordination von Lewis-Basen am Bor-Atom führt zu einer Beeinflussung der elektronischen Eigenschaften des borbasierten Substituenten, wobei der Charakter eines direkt am Bor-Atom gebundenen pi-Elektronensystems von pull zu push-pull geschaltet werden kann. In der vorliegenden Arbeit wird beschrieben, wie geometrische und elektronische Strukturmerkmale von boronsäureesterfunktionalisierten Chromophoren durch die Lewis-Säure-Base-Wechselwirkung am Bor-Atom beeinflusst werden. Die Veränderung von molekularen Eigenschaften wird mit Hilfe der UV/vis-Absorptions- und Fluoreszenzspektroskopie, 1H- und 11B-NMR-Spektroskopie sowie mit röntgendiffraktometrischen Methoden untersucht. Die experimentellen Daten werden durch quantenchemische Berechnungen auf DFT-Niveau unterstützt.

Die vorliegende Arbeit hat die Synthese und Charakterisierung von chromophoren Arylboronsäureestern mit besonderem Augenmerk auf einer breiten strukturellen Variation zum Inhalt. An dieser Verbindungsklasse wird die Wechselwirkung mit Lewis-Basen tiefgehend untersucht. Die Koordination von Lewis-Basen am Bor-Atom führt zu einer Beeinflussung der elektronischen Eigenschaften des borbasierten Substituenten, wobei der Charakter eines direkt am Bor-Atom gebundenen pi-Elektronensystems von pull zu push-pull geschaltet werden kann. In der vorliegenden Arbeit wird beschrieben, wie geometrische und elektronische Strukturmerkmale von boronsäureesterfunktionalisierten Chromophoren durch die Lewis-Säure-Base-Wechselwirkung am Bor-Atom beeinflusst werden. Die Veränderung von molekularen Eigenschaften wird mit Hilfe der UV/vis-Absorptions- und Fluoreszenzspektroskopie, 1H- und 11B-NMR-Spektroskopie sowie mit röntgendiffraktometrischen Methoden untersucht. Die experimentellen Daten werden durch quantenchemische Berechnungen auf DFT-Niveau unterstützt.