<p> Mass spectrometry (MS) is one of the most commonly used analytical techniques in bioanalytical analysis, allowing scientists to characterize molecules with very diverse chemical features. The advance in ionization strategies significantly improves the potential in using MS for that purpose, especially electrospray ionization (ESI) can generate ions directly from solution in ambient conditions, showing high flexibility in coupling with other techniques. Moreover, a hallmark of the ESI of large polymeric molecules is also its tendency to generate a distribution of charge states based on their chemical characteristics, allowing us to exploit the multiple charging phenomenon in various applications. </p> <p>This dissertation introduces the relationships between ESI and multiple charging phenomena with different proposed ionization models, and how condensed-phase and gas-phase approaches affect the multiple charging phenomenon. Moreover, multiply charged ions permit gas-phase ion/ion reactions to occur without neutralizing the ions. Therefore, various ion/ion reactions can be utilized for distinct analytical purposes. Objectively, this dissertation focuses on the investigation of the multiple charging phenomenon from ESI-MS, and the applications from taking the multiply charged ions to perform gas-phase ion chemistry in order to a) manipulate the charges of the targeted ions; b) invert the polarity of the targeted ions; c) and characterization of the ions from the gas-phase ion/ion reactions.</p> <p> The first work demonstrates how multiple components (i.e., complicated mixtures) lead to a highly congested spectrum of ions with overlapped m/z values, resulting from the multiple charging phenomenon after the ESI process. Utilizing ionic reactions can de-congest the spectra via manipulating the charges of the ions to separate the overlapped signals. A universal spectral pattern in the ESI mass spectra is observed while analyzing multiply-charged homopolymers. Various parameters, such as the charges of the ions, widths of polymer distributions, monomer mass, and cationizing agent masses, are investigated to show how they can affect the appearance of the unique patterns, which condense the information of the overall distribution of the homopolymers. Combined with gas-phase charge reduction (i.e., proton transfer reaction), we can characterize the size distribution of polydisperse homopolymer samples.</p> <p>Second, a novel type charge inversion ion/ion reaction summarizing the conversion of multiply charged protein ions to their opposite polarity and still holds multiple charges is reported. The reaction occurs via a single ion/ion collision with highly charged reagent ions, which we usually obtain from biological relevant polymers. Hyaluronic acid (HAs) anions and polyethylenimine (PEI) cations are used as the charge inversion reagents to react with protein ions. Remarkably, inversion of high absolute charge (up to 41) from the reaction is demonstrated. All mechanisms for ion/ion charge inversion involve low-energy ions proceeding via the formation of a long-lived complex. Factors that underlie the charge inversion of protein ions to the opposite polarity with high charge states in reaction with those reagent ions are hypothesized to include: (i) the relatively high charge densities of the HA anions and PEI cations that facilitate the extraction/donation of multiple protons from/to the protein leading to multiply charged protein anions/cations, (ii) the relatively high sum of absolute charges of the reactants that leads to high initial energies in the ion/ion complex, and (iii) the relatively high charge of the ion/ion complex following the multiple proton transfers that tends to destabilize the complex.</p> <p>Third, shotgun MS strategies coupled with different gas-phase ion chemistry and tandem MS to analyze glycolipids are demonstrated. Glycolipids contain both carbohydrates and lipids structure components that it is incredibly challenging to analyze with MS. Isomeric cerebrosides (n-HexCer) and glycosphingosines (n-HexSph), which hold isomerisms in diastereomeric sugar head groups (glucose and galactose), anomeric glycosidic linkages (alpha- or beta-), and isomeric amide-bonded monounsaturated fatty acyl chain (double bond location) are successfully differentiated by dissociating gas-phase ion/ion reaction products, the charge-inverted complex cations. Both relative and absolute quantification of the isomers is also achieved, and analytical performances are evaluated in terms of accuracy, precision, and inter-day precision, allowing us to perform mixture analysis. Porcine brains were used to demonstrate the ability to profile and quantify those isomers from biological extracts. Moreover, a parallel workflow is also proposed for gangliosides, which have more complicated structures among their glycan moiety. Metal cation transfer, proton transfer, and charge inversion reactions are utilized to manipulate the ion types to provide better structural information. The proposed workflow allows us to clean up the mass spectra by neutralizing interfering isobaric ions, differentiate isomeric gangliosides, and perform relative quantitation when the standards are available. The workflow also is used to obtain gangliosides profiles from biological matrices. Overall, work in this dissertation takes advantage of the multiple charging phenomenon and couples with gas-phase ion/ion reactions to achieve various analyses among a wide range of biological-related samples.</p>

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>

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This dissertation is a collection of works that investigates issues related to environmental chemistry. The first portion of this research explores the role of water vapor on the kinetics of important atmospheric reactions. Work is presented on the self-reaction of β-hydroxyethyl peroxy radical (β-HEP) and the catalytic increase in reaction rate by water vapor. β-HEP serves as a model system for investigating the possible role of water vapor in perturbing the kinetics and product branching ratio of atmospheric reactions of other alkyl peroxy radicals. The self-reaction rate coefficient of β-HEP was investigated between 276-296 K with 1.0 × 10^15 to 2.5 × 10^17 molecules cm^-3 of water vapor at 200 Torr total pressure by slow-flow laser flash photolysis coupled with UV time-resolved spectroscopy and long-path, wavelength-modulated, diode-laser spectroscopy. The overall disproportionation rate constant is expressed as the product of temperature-dependent and water vapor-dependent terms giving k(T,H2O) = 7.8 × 10^-14 (e^8.2 ^(±2.5) ^kJ/RT)(1 + 1.4 × 10^-34 × e^92 ^(±11) ^kJ/RT[H2O]). The results suggest that formation of a β--HEP-H2O complex is responsible for the observed water vapor enhancement of the self-reaction rate coefficient. Complex formation is supported with computational results identifying three local energy minima for the β--HEP-H2O complex. Both the temperature range and water vapor concentrations used were chosen because of their significance to conditions in the troposphere. As the troposphere continues to get warmer and wetter, more complexes with water will form, which in turn may perturb the kinetics and product branching ratios of atmospheric reactions. Future studies are proposed for the reaction of β-HEP + NO leading to NO2 formation. A laser-induced fluorescence cell was designed, built, and tested in preparation for studies of NO2 formation. Additionally Harriott-cell optics were manufactured and tested to detect HO2 using two-tone frequency-modulated diode-laser spectroscopy. In a related work, the breakdown of the environmental contaminants polychlorinated biphenyls (PCB's) was investigated using a new method. A new method for analyzing anaerobic digestion is also presented. The degradation rate and efficiency of digestion processes are typically measured by introducing a substrate or pollutant into a digester and then monitoring the effluents for the pollutant or substrate, a costly and slow process. A new method for rapid measurement of the rates and efficiencies of anaerobic degradation of pollutants and lignocellulose substrates from various pretreatments is described. The method uses micro-reactors (10-30 mL) containing a mixed culture of anaerobic bacteria obtained from a working anaerobic digester. The rates of degradation and metabolism of pollutants are measured in parallel sets of micro-reactors. Measurements of metabolic rate and pollutant degradation simultaneously is an effective means of rapidly examining pollutant degradation on a micro-scale. Calorimetric measurements alone allow rapid, relative evaluation of various substrate pretreatment methods. Finally calorimetric and electrophoretic methods were used to further knowledge in analytical techniques applied to important problems. In the last section of this dissertation the thermal and photolytic breakdown of promethazine hydrochloride is reported. Promethazine hydrochloride is a mediation that is commonly used as an antihistamine, a sedative, and an antiemetic, and to treat motion sickness. Perivascular extravasation, unintentional intra-arterial injection and intraneuronal or perineuronal infiltration may lead to irreversible tissue damage if the drug is not properly diluted or is administered too quickly. Data on the stability of promethazine hydrochloride diluted in sodium chloride 0.9% are lacking. This study evaluates the thermal and photolytic degradation of promethazine hydrochloride concentrations of 250 µg/mL and 125 µg/mL diluted in sodium chloride 0.9% over a period of 9 days. Degradation rates of promethazine hydrochloride were determined under UV-light, fluorescent light, and no light at various temperatures and concentrations to determine medication stability. The shelf-life (<10% degradation) at 25°C under normal fluorescent lights is 4.9 days, at 25°C protected from light, 6.6 days, and at 7°C in the dark, 8.1 days. These results may increase patient safety by improving current protocols for intravenous promethazine administration

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Oxidation flow reactors (OFRs) using low-pressure Hg lamp emission at 185 and 254 nm produce OH radicals efficiently and are widely used in atmospheric chemistry and other fields. However, knowledge of detailed OFR chemistry is limited, allowing speculation in the literature about whether some non-OH reactants, including several not relevant for tropospheric chemistry, may play an important role in these OFRs. These non-OH reactants are UV radiation, O(¹D), O(³P), and O₃. In this study, we investigate the relative importance of other reactants to OH for the fate of reactant species in OFR under a wide range of conditions via box modeling. The relative importance of non-OH species is less sensitive to UV light intensity than to water vapor mixing ratio (H₂O) and external OH reactivity (OHR_ext), as both non-OH reactants and OH scale roughly proportionally to UV intensity. We show that for field studies in forested regions and also the urban area of Los Angeles, reactants of atmospheric interest are predominantly consumed by OH. We find that O(¹D), O(³P), and O₃ have relative contributions to volatile organic compound (VOC) consumption that are similar or lower than in the troposphere. The impact of O atoms can be neglected under most conditions in both OFR and troposphere. We define “riskier OFR conditions” as those with either low H₂O (< 0.1 %) or high OHR_ext ( ≥  100 s⁻¹ in OFR185 and > 200 s⁻¹ in OFR254). We strongly suggest avoiding such conditions as the importance of non-OH reactants can be substantial for the most sensitive species, although OH may still dominate under some riskier conditions, depending on the species present. Photolysis at non-tropospheric wavelengths (185 and 254 nm) may play a significant (> 20 %) role in the degradation of some aromatics, as well as some oxidation intermediates, under riskier reactor conditions, if the quantum yields are high. Under riskier conditions, some biogenics can have substantial destructions by O₃, similarly to the troposphere. Working under low O₂ (volume mixing ratio of 0.002) with the OFR185 mode allows OH to completely dominate over O₃ reactions even for the biogenic species most reactive with O₃. Non-tropospheric VOC photolysis may have been a problem in some laboratory and source studies, but can be avoided or lessened in future studies by diluting source emissions and working at lower precursor concentrations in laboratory studies and by humidification. Photolysis of secondary organic aerosol (SOA) samples is estimated to be significant (> 20 %) under the upper limit assumption of unity quantum yield at medium (1 × 10¹³ and 1.5 × 10¹⁵ photons cm⁻² s⁻¹ at 185 and 254 nm, respectively) or higher UV flux settings. The need for quantum yield measurements of both VOC and SOA photolysis is highlighted in this study. The results of this study allow improved OFR operation and experimental design and also inform the design of future reactors.

In this licentiate thesis, organic molecules, namely Cobalt Phthalocyanine (CoPc) and Biphenylene, have been studied by means of synchrotron radiation-based spectroscopic methods (Photoemission Spectroscopy (PES) and X-ray Absorption Spectroscopy (XAS) in combination with Density Functional Theory (DFT) calculations. Paper I is a combined experimental and theoretical investigation of electronic structure of CoPc. addressing the atomic character of the Highest Occupied Molecular Orbital (HOMO) and the electronic configuration of the molecular ground state. Both these aspects are still under discussion since different experimental and theoretical studies have given controversial results. Previous works have indicated the CoPc ground state to either be described by the 2A1g or 2Eg, or by a mix of the two electronic configurations. Regrading the debated the atomic character of the HOMO of CoPc, it has been suggested to be either metal 3d-like and localized on the central Co atom or originating in the organic ligand of the molecule. In this thesis the valence photoemission results for CoPc in gas phase and as adsorbed films on Au(111) together with the DFT simulations, consistently indicate that the HOMO is derived only by the organic ligand, with mainly contribution from the carbon atoms with no metal character. Moreover, the good agreement between the experimental and theoretical results, confirms that the ground state of CoPc is correctly described by the 2A1g configuration. In Paper II, PES and XAS have been used to investigate the occupied and empty density of states of biphenylene films of different thicknesses, deposited onto a Cu(111) crystal. The results have been compared to previous gas phase spectra and single molecule Density Functional Theory (DFT) calculations to get insights into the possible modification of the molecular electronic structure in the film induced by the adsorption on a surface. Furthermore, XAS measurements allowed the characterizion of the variation of the molecular arrangement with the film thickness and helped to clarify the substrate-molecule interaction.

Durant la nuit, le radical nitrate (NO3) est le principal oxydant troposphérique des composés organiques. La compréhension de l'implication des composés organiques dans les processus de chimie troposphérique exige donc une connaissance des constantes cinétiques de leurs réactions avec le radical NO3. Toutefois, au regard du nombre considérable de composés organiques émis ou formés dans la troposphère, il est difficilement envisageable d'appréhender la réactivité de chaque composé en nous reposant exclusivement sur des études de laboratoire. Celles-ci se doivent d'être complétées par l'usage de méthodes prédictives. Nous avons donc, au cours de ce travail, développé une relation de type structure-réactivité (SAR) qui permet le calcul des constantes de vitesse des réactions des composés organiques avec le radical nitrate. Cette méthode prédictive empirique permet d'estimer la réactivité d'un composé à partir de sa structure moléculaire et a été élaborée à partir de constantes cinétiques expérimentales publiées dans la littérature. De plus, conjointement au développement de cette SAR, les constantes cinétiques des réactions d'aldéhydes et d'éthers insaturés avec le radical nitrate ont été mesurées au laboratoire. Ces études expérimentales ont ainsi contribué à étoffer la base de données cinétiques sur laquelle repose cette SAR afin de permettre son parachèvement. Cette SAR reproduit, à un facteur deux près, plus de 90% des constantes cinétiques des alcènes et des composés aliphatiques oxygénés saturés et insaturés / The nitrate radical (NO3) is the main oxidant of organic compounds in the night-time troposphere. Thus, comprehension of organic compounds involvement in tropospheric chemical processes requires the knowledge of the rate coefficients for their reactions with the nitrate radical. Nevertheless, considering the wide range of organic compounds emitted or formed in the atmosphere, it is difficult to determine the reactivity of each compound only with laboratory studies. Thereby, these experimental studies have to be completed by predictive methods. In this study, a group-additivity method is therefore used to develop a new Structure-Activity Relationship (SAR) which allows prediction of the rate constants for reactions of organic compounds with the NO3 radical. This empirical method is based on the prediction of a rate constant leaning only on the molecular structure of the organic compound. It relies on experimental rate constants available in the literature. Moreover, the rate constants of unsaturated aldehydes and ethers with the nitrate radical have been measured. Thereby, these experimental studies contribute to expend the kinetic database used for the SAR development and allow its improvement. For saturated and unsaturated oxygenated compounds, more than 90% of the rate constants are reproduced within a factor of two