This thesis presents a combined experimental and computational evaluation of the physical-organic properties of butadiyne-linked porphyrin oligomers. The principal result from the thesis is the synthesis and characterisation of the largest aromatic and antiaromatic systems to date, in the form of an oxidised [6]-porphyrin nanoring, with diameter 2.4 nm. This large electronically coherent system provides insight into the connection between aromatic ring currents and persistent currents in metal and semiconductor mesoscopic rings. Chapter 1 briefly reviews the concepts used in the remainder of the thesis, with a particular focus on aromaticity. In Chapter 2, the barrier to inter-porphyrin torsional rotation in a butadiyne-linked porphyrin dimer is determined computationally and experimentally to be 3 kJ mol^-1. The barrier height is closely related to the resonance delocalisation energy between the porphyrin subunits. In Chapter 3 we show that by oxidising a butadiyne-linked [6]-porphyrin nanoring to its 4+ and 6+ oxidation states, the nanoring becomes antiaromatic and aromatic respectively. In contrast, the neutral oxidation state exhibits only local aromaticity for the six porphyrin units. The 12+ cation can also be generated, and exhibits local antiaromaticity for each porphyrin unit. The characterisation of (anti)aromaticity employs NMR and computational techniques. In Chapter 4, the properties of cation radicals of linear and cyclic porphyrin oligomers are explored. Cations generated by spectroelectrochemistry are measured by optical spectroscopies, and chemically generated radical monocations are examined by cw/pulsed EPR spectroscopies. EPR and optical spectroscopies agree that the dimer monocation radical is fully delocalised, in Robin-Day Class III, whereas the monocations of longer oligomers are localised over 2-3 porphyrin units (Class II). In Chapter 5, photophysical and computational investigations into excited state aromaticity in porphyrin nanorings are presented. The computational results suggest the presence of aromaticity in the triplet excited states, but experiment fails to convincingly demonstrate the effect. Computational results in Chapter 6 show that a butadiyne linked [6]-porphyrin nanoring in which one butadiyne (C≡C-C≡C) is truncated to an alkyne (C≡C) exhibits a reversal of aromaticity and antiaromaticity in its oxidised states, compared to the all-butadiyne linked nanoring, consistent with Hückel's law.

Doctor of Philosophy / Department of Chemistry / Stefan Bossmann / A series of methylene-bridged resorcin[4]arenes featuring electrochemically active and hydrophilic viologene-units chemically attached to their "rim"-regions have been synthesized. Depending on the choices of pendent groups (feet) and the numbers of positive charges on the "rim" (four or eight), moderate to very good solubilities in water were obtained. A fluorescent coumarin tag designed for the purpose of photophysical studies was chemically linked to the feet of some of the synthesized resorcin[4]arenes. These compounds were designed to act as guests in mycobacterial channel proteins (channel blockers). The proven host-guest interaction between resorcin[4]arenes and the mycobacterial porin MspA suggests potential application of my research in TB treatment. Both, hydrophilic nutrients and metabolites have to diffuse through the porin channels of mycobacteria because of the lack of an active transport mechanism. If these channels are successfully blocked, the mycobacteria have either to synthesize new channels, which make their outer membrane more susceptible to conventional antibiotics, or they become dormant. (3,3'-dimethyl)-4,4'-bipyridinium units are very suitable electron relays. They can be reduced stepwise to viologen monoradical cations and then to uncharged viologen diradicals which possess highly negative redox potentials, allowing them to reduce C-Cl bonds. Therefore, the deep cavitand viologen resorcin[4]arenas, are expected to bind and detoxify chlorinated hydrocarbons by reductive dechlorination. In this work, the step wise reduction process of viologen- resorcin[4]arenes and the formation of negative redox potentials of double-reduced viologen resorcin[4]arenes are demonstrated by electrochemistry studies. These results encourage future studies toward an efficient electrocatalytic system for the reductive dehalogenation of organic compounds. Besides highly charged resorcin[4]arene cavitands, the synthesis of a thiol-footed resorcin[4]arene was also attempted. The product was used for gold nanoparticle binding studies. The results of the photochemistry measurements provided a proof-of-concept for using the emission of gold nanoparticles in chemical sensors after covering their surfaces with thiol-footed resorcin[4]arenes. Two heterocylic resorcin[4]arene cavitands were synthesized for DNA-intercalation studies. The results of the photochemical measurements suggested binding between DNA and the heterocyclic resorcin[4]arenes and provided proof-of-principle for potential drug applications of this type of macrocycle.

<div>The first chapter reports a study of aryl nitrene intermediates. Although extensively studied over the past 30 years, phenyl nitrenes have a propensity to undergo rearrangement reactions and form polymeric tars. This is in stark contrast to the phenyl carbenes which are known to undergo several important reactions to produce a library of useful organic compounds. One such reaction is the insertion of phenyl carbenes into a double bond to produce a cyclopropane moiety. If aryl nitrenes can be exploited to conjure a similar reactivity, they would be an excellent synthetic route to produce aziridine rings which are a crucial component of many natural products. This review chapter is a collection of all the efforts that have been made in this regard.</div><div><br></div><div>In the next chapter, the electronic effect of the azide functional group on an aromatic system has been investigated by using Hammett-Taft parameters obtained from the effect of azide-substitution on the gas-phase acidity of phenol. Gas-phase acidities of 3- and 4-azidophenol have been measured by using mass spectrometry and the kinetic method and found to be 340.8 ± 2.2 and 340.3 ± 2.0 kcal/mol respectively. The relative electronic effects of the azide substituent on an aromatic system have been measured by using Hammett-Taft parameters. The σF and σR values are determined to be 0.38 and 0.02 respectively, consistent with predictions based on electronic structure calculations. The values of σF and σR demonstrate that azide acts an inductively withdrawing group but has negligible resonance contribution on the phenol. In contrast, acidity values calculated for substituted benzoic acids gives values of σF = 0.69 and σR = -0.39, indicating that the azide is a strong  donor, comparable to that of a hydroxyl group. The difference is explained as being the result of “chimeric” electronic behavior of the azide, similar to that observed previously for the n-oxide moiety, which can be more or less resonance donating depending on the electronic effects of other groups in the system.</div><div><br></div><div>Phenyl nitrenes undergo bimolecular chemistry under very specific circumstances. For example, having an oxide substituent at the para position of the phenyl ring enables the formation of an indophenol product from a photocatalyzed reaction of the nitrene. Although, this reaction has been reported before, the mechanism involved in this reaction has not been fully understood. A two-electron mechanism involving electrophilic aromatic substitution reaction has been proposed in the literature, however we found evidence that did not support this theory. Instead, we find this reaction analogous to the popular Gibbs’ reaction whose single electron transfer mechanism has been extensively studied. The following chapter encompasses a study of the mechanism of the photolysis reaction to look for evidence of a single electron transfer similar to the Gibbs’ reaction.</div><div><br></div><div>As mentioned earlier, phenyl nitrenes have a proclivity to undergo rearrangement reactions instead of exhibiting bimolecular reactivity that can lead to useful products. One of the strategies to overcome this challenge is to spatially separate the two electrons of an open-shell singlet nitrene so as to minimize electron-electron repulsion. This separation can be achieved by delocalizing the individual electrons over multiple aromatic rings and heteroatoms which can act as radical stabilizers. In this chapter, a short review of literature that sets precedence for developing a unique heteroatom containing aromatic backbone to achieve the necessary stabilization is presented. Our efforts in synthesizing the model azide precursor compound have also been discussed.</div>

<p>High resolution tandem mass spectrometry (MSⁿ) coupled with various separation techniques, such as high-performance liquid chromatography (HPLC) and gas chromatography (GC), is widely used to analyze mixtures of unknown organic compounds. In a mass spectrometric analysis, analytes of interest are at first transferred into the gas phase, ionized (protonated or deprotonated) and introduced into the instrument. Tandem mass spectrometric experiments may then be used to gain insights into structure and reactivity of the analyte ions in the gas phase. The tandem mass spectral data are often compared to those reported in external databases. However, the tandem mass spectra obtained for protonated analytes may be markedly different from those in external databases because protonation site manifested during a mass spectrometric experiment can be affected by the ionization technique, ionization solvents and condition of the ion source. This thesis focuses on investigating the effects of instrumental conditions and analyte concentrations on the protonation sites of 4-aminobenzoic acid. Reactivities of radical species were also investigated. A modified bracketing method was developed and proton affinities of a series of mono- and biradicals of pyridine were measured. In another study, a <i>para</i>-benzyne analog was generated in both solution and the gas phase and its reactivities towards various neutral reagents in the gas phase were compared to those in solution.</p> <p> Chapter 2 discusses the fundamental aspects of the instruments used in this research. In chapter 3, the effects of residual moisture in linear quadrupole ion trap on the protonation sites of 4-aminobenzoic acid are considered. Chapter 4 focuses on the use of gas-phase ion-molecule reactions with trimethoxymethylsilane (TMMS) for the identification of the protonation sites of 4-aminobenzoic acid. Further, the effects of analyte concentration on the protonation sites of 4-aminobenzoic acid are considered. Chapter 5 introduces a modified bracketing method for the experimental determination of proton affinities of a series of pyridine-based mono- and biradicals. In chapter 6, successful generation of <i>para</i>-benzynes in solution is discussed. The reactivity of a <i>para</i>-benzyne analog, 1,4-didehydrophenazine, is compared to its reactivity in the gas phase.</p>

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>

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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>