<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>

<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>

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.

<div> <div> <div> <p>Understanding protein-protein interactions (PPIs) in a cell is essential for learning protein functions, pathways, and mechanisms of diseases. This dissertation introduces the computational method to predict PPIs. In the first chapter, the history of identifying protein interactions and some experimental methods are introduced. Because interacting proteins share similar functions, protein function similarity can be used as a feature to predict PPIs. NaviGO server is developed for biologists and bioinformaticians to visualize the gene ontology relationship and quantify their similarity scores. Furthermore, the computational features used to predict PPIs are summarized. This will help researchers from the computational field to understand the rationale of extracting biological features and also benefit the researcher with a biology background to understand the computational work. After understanding various computational features, the computational prediction method to identify large-scale PPIs was developed and applied to Arabidopsis, maize, and soybean in a whole-genomic scale. Novel predicted PPIs were provided and were grouped based on prediction confidence level, which can be used as a testable hypothesis to guide biologists’ experiments. Since affinity chromatography combined with mass spectrometry technique introduces high false PPIs, the computational method was combined with mass spectrometry data to aid the identification of high confident PPIs in large-scale. Lastly, some remaining challenges of the computational PPI prediction methods and future works are discussed. </p> </div> </div> </div>

Competitive metallurgical production is almost impossible without the knowledge of the chemical composition of manufactured and finished melt, or the produced product. With growing customer demands for product quality and product characteristics, increasing technology speed and increasing product purity, there is growing demand for analyzes of chemical composition. These demands are very often against each other, especially the increasing demands on the speed and accuracy of analyzes. Analytical requirements may not only apply to the test technique, but also to the quality of the sample, which is inseparable from it. What is recently seen as the biggest drawback, the new technology is trying to use as its main priority. This is undoubtedly true of atomic emission spectrometry.

The sensitivity, speed, and reproducibility of modern mass spectrometers enable in-depth new functional looks into the cellular proteome. Thousands of proteins can be detected in a single sample. In Co-Fractionation Mass Spectrometry (CF-MS) method, the input sample is fractionated by any biochemical method of choice. The reduced complexity of each fractionated sample leads to better proteome coverage. The separation profiles provide functional information on the proteins. This application has been used to predict organelle localization based on co-purification with marker proteins. More recently, CF-MS is being used to measure the apparent masses and determine the localization of soluble or membrane-associated protein complexes. This Ph.D. dissertation focuses on the extension of the boundary of CF-MS application to learn how protein complex evolution and protein complex composition have been accomplished. In the first part of this dissertation, the data will be presented on the degree to which variation in protein oligomerization across plant species is present, how proteomics in phylogenetic analysis (phyloproteomics/evolutionary proteomics) helps understand the evolutionary changes, and how oligomerization drives neofunctionalization during plant evolution. The latter part will describe that CF-MS coupled with multiple orthogonal chromatographic separations increases the resolving power of the profiling technique, enabling the composition of protein complexes to be predicted in the subaleurone layers of rice endosperm. Lots of novel protein complexes involved in RNA binding protein, translation, and the tissue-species metabolism will be discussed.

<p>Canines can detect different diseases simply by smelling different biological sample types, including  urine,  breath  and  sweat.  This  has  led  researchers  to  try  and  discovery  unique  volatile  organic compound (VOC) biomarkers. The power of VOC biomarkers lies in the fact that one day they may be able to be utilized for noninvasive, rapid and accurate diagnostics at a point of care using  miniaturized  biosensors.  However,  the  identity  of  the  specific  VOC  biomarkers  must  be  demonstrated before designing and fabricating sensing systems. Through  an  extensive  series  of  experiments,  VOCs  in  urine  are  profiled  by  solid  phase  microextraction (SPME) coupled to gas chromatography-mass spectrometry (GC-MS) to identify biomarkers for breast cancer using murine models. The results from these experiments indicated that  unique  classes  of  urinary  VOCs,  primarily  terpene/terpenoids  and  carbonyls,  are  potential  biomarkers  of  breast  cancer.  Through  implementing  chemometric  approaches,  unique  panels  of  VOCs  were  identified  for  breast  cancer  detection,  identifying  tumor  location,  determining  the  efficacy of dopaminergic antitumor treatments, and tracking cancer progression. Other diseases, including COVID-19 and hypoglycemia (low blood sugar) were also probed to identify volatile biomarkers present in breath samples.  VOC biomarker identification is an important step toward developing portable gas sensors, but  another  hurdle  that  exists  is  that  current  sensors  lack  selectivity  toward  specific  VOCs  of  interest.  Furthermore,  testing  sensors  for  sensitivity  and  selectivity  is  an  extensive  process  as  VOCs  must  be  tested  individually  because  the  sensors  do  not  have  modes  of  chromatographic  separation or compound identification. Another set of experiments is presented to demonstrate that SPME  fibers  can  be  coated  with  materials,  used  to  extract  standard  solutions  of  VOCs,  and  analyzed  by  GC-MS  to  determine  the  performance  of  various  gas  sensing  layers.  In  the  first  of  these  experiments,  polyetherimide  (PEI)  was  coated  onto  a  SPME  fiber  and  compared  to  commercial polyacrylate (PAA) fibers. The second experiment tuned the extraction efficiency of polyvinylidene fluoride (PVDF) - carbon black (CB) composites and showed that they had higher sensitivity  for  urinary  VOC  extraction  relative  to  a  polydimethylsiloxane  (PDMS)  SPME  fiber.  These results demonstrate SPME GC-MS can rapidly characterize and tune the VOC adsorption capabilities of gas sensing layers. </p>

O desenvolvimento e validação de métodos analíticos é um procedimento necessário quando um método não normalizado é utilizado por um laboratório de ensaios. A validação de métodos também é um requisito específico da norma ABNT NBR ISO/IEC 17025, que determina os requisitos gerais para a competência dos laboratórios de ensaio e calibração. O objetivo da validação é demonstrar que o método analítico, nas condições em que é executado, produz resultados com a exatidão requerida. O Laboratório de Corrosão, Proteção e Reciclagem de Materiais (LACOR), da UFRGS, tem o ensaio de determinação de metais por fluorescência de raios X, acreditado pelo CGCRE/INMETRO, conforme ABNT NBR ISO/IEC 17025. O ensaio é feito usando o método de espectrometria de fluorescência de raios X por dispersão de energia (EDXRF). Este método, contudo, não é normalizado e, portanto, o mesmo foi validado, neste trabalho de pesquisa, para atender a este requisito. A validação foi feita com base no documento orientativo DOQ-CGCRE-08 e no guia EURACHEM. Os parâmetros de validação, para o ensaio quantitativo por EDXRF, que foram calculados neste trabalho são: seletividade; limite de detecção (LD) e limite de quantificação (LQ); linearidade e faixa de trabalho; veracidade de medição (tendência, erro normalizado, Z-score e comparação com método de referência) e precisão (repetibilidade, precisão intermediária e reprodutibilidade). Além disso, foi desenvolvida uma metodologia de cálculo de incerteza de medição para o ensaio por EDXRF Os resultados obtidos neste estudo demonstram que o método EDXRF, usado na determinação de metais em aços, é um método não normalizado validado e compatível com os resultados obtidos com os métodos de referência: espectrometria de fluorescência de raios X por dispersão de comprimento de onda (WDXRF), fotométricos e espectrometria de absorção atômica (AAS). Inclusive, o WDXRF é um método de referência usado em muitas normas internacionais, que descrevem métodos de análise de aços por fluorescência de raios X, como ASTM E572 ou ASTM E1085. O estudo desenvolvido nesta dissertação permitiu que o LACOR mantivesse sua acreditação no ensaio de determinação de metais por fluorescência de raios X, na avaliação do CGCRE/INMETRO, no presente ano. Outros frutos deste trabalho foram a confecção das curvas de calibração do espectrômetro NITON XL3t GOLDD+ e a revisão do procedimento de ensaio, onde esses novos conhecimentos sobre a técnica EDXRF foram aplicados. Futuramente, este trabalho pode ser usado por outros pesquisadores para desenvolver estudos em outras matrizes metálicas, como cobre, alumínio, titânio ou níquel, e, também, em outras áreas de aplicação como jóias, reciclagem de materiais metálicos ou, até mesmo, para análise elementar de resíduos retidos em membranas de troca iônica. / The development and validation of analytical methods is a required procedure when a non-standard method is used by a testing laboratory. Method validation is also a specific requirement of the ABNT NBR ISO / IEC 17025, which determines the general requirements for the competence of testing and calibration laboratories. The purpose of validation is to demonstrate that the analytical method, under the conditions in which it is performed, produces results with the required accuracy. The Corrosion, Protection and Recycling Materials Laboratory (LACOR), at UFRGS, has the X-ray fluorescence metal analysis, accredited by CGCRE / INMETRO, according to ABNT NBR ISO / IEC 17025. The test is performed using Energy Dispersive X-Ray Fluorescence spectrometry, EDXRF method. This method, however, is not standardized; therefore, it was validated in this research to meet this requirement. The validation was based on the DOQ-CGCRE-08 document and the EURACHEM guide. The method performance calculated in this study for quantitative testing by EDXRF are: selectivity; limit of detection (LOD) and limit of quantification (LOQ); linearity and working range; trueness (bias, normalized error, Z-score and comparison with reference method) and precision (repeatability, intermediate precision and reproducibility). In addition, a measurement uncertainty calculation methodology was developed for the EDXRF testing The results obtained in this study demonstrate that the EDXRF method, used in the determination in the chemical analysis of steels, is a validated non-standard method and compatible with the results obtained with the reference methods: Wavelength Dispersive X-Ray Fluorescence spectrometry (WDXRF), photometric and atomic absorption spectrometry (AAS). In addition, WDXRF is a reference method used in many international standards, which describes analysis of steels by X-ray fluorescence spectrometry such ASTM E572 or ASTM E1085. The study developed in this dissertation allowed LACOR to maintain its accreditation in the test of metal by X-ray fluorescence analysis, in the CGCRE / INMETRO audit, this year. Other fruits of this work were the preparation of calibration curves of NITON XL3t GOLDD + spectrometer and complete revision of testing procedure, where this new knowledge about the EDXRF technique was applied. In the future, this work can be used by other researchers to develop studies in other base metals such as copper, aluminum, titanium or nickel, and also in other areas of application such as jewelry, recycling of metallic materials or even for analysis elemental residues retained in ion exchange membranes.

O desenvolvimento e validação de métodos analíticos é um procedimento necessário quando um método não normalizado é utilizado por um laboratório de ensaios. A validação de métodos também é um requisito específico da norma ABNT NBR ISO/IEC 17025, que determina os requisitos gerais para a competência dos laboratórios de ensaio e calibração. O objetivo da validação é demonstrar que o método analítico, nas condições em que é executado, produz resultados com a exatidão requerida. O Laboratório de Corrosão, Proteção e Reciclagem de Materiais (LACOR), da UFRGS, tem o ensaio de determinação de metais por fluorescência de raios X, acreditado pelo CGCRE/INMETRO, conforme ABNT NBR ISO/IEC 17025. O ensaio é feito usando o método de espectrometria de fluorescência de raios X por dispersão de energia (EDXRF). Este método, contudo, não é normalizado e, portanto, o mesmo foi validado, neste trabalho de pesquisa, para atender a este requisito. A validação foi feita com base no documento orientativo DOQ-CGCRE-08 e no guia EURACHEM. Os parâmetros de validação, para o ensaio quantitativo por EDXRF, que foram calculados neste trabalho são: seletividade; limite de detecção (LD) e limite de quantificação (LQ); linearidade e faixa de trabalho; veracidade de medição (tendência, erro normalizado, Z-score e comparação com método de referência) e precisão (repetibilidade, precisão intermediária e reprodutibilidade). Além disso, foi desenvolvida uma metodologia de cálculo de incerteza de medição para o ensaio por EDXRF Os resultados obtidos neste estudo demonstram que o método EDXRF, usado na determinação de metais em aços, é um método não normalizado validado e compatível com os resultados obtidos com os métodos de referência: espectrometria de fluorescência de raios X por dispersão de comprimento de onda (WDXRF), fotométricos e espectrometria de absorção atômica (AAS). Inclusive, o WDXRF é um método de referência usado em muitas normas internacionais, que descrevem métodos de análise de aços por fluorescência de raios X, como ASTM E572 ou ASTM E1085. O estudo desenvolvido nesta dissertação permitiu que o LACOR mantivesse sua acreditação no ensaio de determinação de metais por fluorescência de raios X, na avaliação do CGCRE/INMETRO, no presente ano. Outros frutos deste trabalho foram a confecção das curvas de calibração do espectrômetro NITON XL3t GOLDD+ e a revisão do procedimento de ensaio, onde esses novos conhecimentos sobre a técnica EDXRF foram aplicados. Futuramente, este trabalho pode ser usado por outros pesquisadores para desenvolver estudos em outras matrizes metálicas, como cobre, alumínio, titânio ou níquel, e, também, em outras áreas de aplicação como jóias, reciclagem de materiais metálicos ou, até mesmo, para análise elementar de resíduos retidos em membranas de troca iônica. / The development and validation of analytical methods is a required procedure when a non-standard method is used by a testing laboratory. Method validation is also a specific requirement of the ABNT NBR ISO / IEC 17025, which determines the general requirements for the competence of testing and calibration laboratories. The purpose of validation is to demonstrate that the analytical method, under the conditions in which it is performed, produces results with the required accuracy. The Corrosion, Protection and Recycling Materials Laboratory (LACOR), at UFRGS, has the X-ray fluorescence metal analysis, accredited by CGCRE / INMETRO, according to ABNT NBR ISO / IEC 17025. The test is performed using Energy Dispersive X-Ray Fluorescence spectrometry, EDXRF method. This method, however, is not standardized; therefore, it was validated in this research to meet this requirement. The validation was based on the DOQ-CGCRE-08 document and the EURACHEM guide. The method performance calculated in this study for quantitative testing by EDXRF are: selectivity; limit of detection (LOD) and limit of quantification (LOQ); linearity and working range; trueness (bias, normalized error, Z-score and comparison with reference method) and precision (repeatability, intermediate precision and reproducibility). In addition, a measurement uncertainty calculation methodology was developed for the EDXRF testing The results obtained in this study demonstrate that the EDXRF method, used in the determination in the chemical analysis of steels, is a validated non-standard method and compatible with the results obtained with the reference methods: Wavelength Dispersive X-Ray Fluorescence spectrometry (WDXRF), photometric and atomic absorption spectrometry (AAS). In addition, WDXRF is a reference method used in many international standards, which describes analysis of steels by X-ray fluorescence spectrometry such ASTM E572 or ASTM E1085. The study developed in this dissertation allowed LACOR to maintain its accreditation in the test of metal by X-ray fluorescence analysis, in the CGCRE / INMETRO audit, this year. Other fruits of this work were the preparation of calibration curves of NITON XL3t GOLDD + spectrometer and complete revision of testing procedure, where this new knowledge about the EDXRF technique was applied. In the future, this work can be used by other researchers to develop studies in other base metals such as copper, aluminum, titanium or nickel, and also in other areas of application such as jewelry, recycling of metallic materials or even for analysis elemental residues retained in ion exchange membranes.