In the last several decades, polycyclic aromatic hydrocarbons (PAHs) have been the subject of extensive investigation due to their presumed abundance in the interstellar medium (ISM). My thesis concentrated on investigating the dissociation of ionized PAH molecules in the gas phase under similar conditions of the ISM. The twelve PAHs studied were naphthalene (NAP), anthracene (ANT), phenanthrene (PHN), cyclopenta[d,e,f] phenanthrene (CYC), pyrene (PYR), fluoranthene (FLN), perylene (PER) and coronene (COR). In addition, two dihydro PAHs were studied to examine potential intermediates in H2 catalysis, 1,2-dihydronaphthalene (DHN) and 9,10-dihydrophenanthrene (DHP), and two stabilized fragments of PAHs, acenaphthylene (ACE), fluorene-H (FLU). These ions were studied using atmospheric pressure chemical ionization (APCI) to generate the ions and the fragmentation was produced by collision-induced dissociation (CID). The CID experiments were done at different lab frame collision energies to produce breakdown curves for all fragments in each molecule. These curves were fitted by using Rice – Ramsperger-Kassel- Marcus (RRKM) theory to derive the activation energy (E0) at 0K and the entropy of activation (∆‡ S) for each reaction. The primary dissociation channel observed was H loss and this fragmentation channel was a common fragment to all PAHs molecules studied. Also, there were other fragments (CH3, C2H2, C4H2) observed in all of these molecules studied except perylene and coronene. The final step in this project was to compare these results with results derived from imaging photoelectron photoion coincidence spectroscopy (iPEPICO) reported by West and co-workers in order to determine the suitability of the APCI-CID technique for deriving reliable kinetic parameters for this class of ions.

In the technologically driven information age, the consumption of power is as vital to daily life as food and shelter. The generation of that power comes from a variety of sources of which coal is the predominant provider of electrical energy. Coal combustion is a well-known technology and the United States possesses the most abundant coal deposits on Earth, however, the drawback accompanying this process is the significant emissions which are released during combustion. Over the years, much effort has gone into reducing the emissions of majority constituent elements CO2, CO, NOx, SOx, etc. but it is only in the last decade or so that much attention has been given to the trace metals present within coal. Most of the work into examining these trace metals has been upon Hg and how it speciates within the flue gas in order to determine the most effective means of removal. In this study, the trace metals arsenic (As) and selenium (Se) will be investigated in a similar manner to evaluate the speciation of these elements. While previous experimental work has been performed in this area, it has been limited to thermodynamic studies which determine the speciation after equilibrium has been reached, this ignores the fact the residence times within the flue are often only several minutes during which time rapid quenching is taking place. This study takes a different approach by examining the speciation using computational chemistry which affords the advantage of being able to perform a kinetic study which is more useful in creating a flue gas model. Using ab initio the properties of various As and Se species can be evaluated compared to existing experimental data for validation. After which, a number of reactions may be selected and the structure of the transition state for each identified. Once the properties of the transition structure are known, the appropriate kinetic model, be it Transition State Theory, RRKM Theory, etc. can be applied and the rate constant determined. It is by the determination of these rate constants that the kinetic model of the flue gas can be improved and a more accurate depiction of the speciation of these race metals created.

As a first project, collision-induced dissociation experiments were carried out using electrospray ionisation mass spectrometry on gas phase complexes involving different poly(methylmetacrylate) oligomers with three amino acids: glycine, leucine, and phenylalanine. After acquiring breakdown diagrams, RRKM modeling was used to fit the experimental data in order to obtain the 0 K activation energy and the entropy of activation. These thermodynamic data were then used to understand the competing dissociation channels observed (except for gas phase complexes involving glycine that had only one dissociation channel). Molecular dynamics simulated annealing calculations were carried on the gas phase complexes to understand further the energetic and entropic effects involved as well as the 3D conformation of these complexes. Valuable insight information was found on the 3D conformations, on a qualitative level. Using rotational constants and vibrational harmonic frequencies, it was possible to evaluate the entropy variation between the experimentally observed competing channels. Reasonable agreement was found between the experimental and theoretical variations of entropies. Finally, the proton affinity of poly(methylmetacrylate) oligomers is being discussed. Even though no absolute values for the proton affinity were found, the experimental and computational results help to understand the variation that accompanies the oligomers length. The second project presents the development an efficient and reproducible screening method for identifying low molecular weight compounds that bind to amyloid beta peptides (Abeta) peptides using electrospray ionization mass spectrometry (ESI-MS). Low molecular weight (LMW) compounds capable of interacting with soluble Abeta may be able to modulate/inhibit the Abeta aggregation process and serve as potential disease-modifying agents for Alzheimer’s disease. The present approach was used to rank the binding affinity of a library of compounds to Abeta1-40 peptide. The results obtained show that low molecular weight compounds bind similarly to Abeta1-42, Abeta1-40, as well as Abeta1-28 peptides and they underline the critical role of Abeta peptide charge motif in binding at physiological pH. Finally, some elements of structure-activity relationship (SAR) involved in the binding affinity of homotaurine to soluble Abeta peptides are discussed. As a third project, the gas phase binding of small molecules to the Abeta1-40 peptide generated by electrospray ionization has been explored with collision-induced dissociation mass spectrometry and kinetic rate theory. This project presents a simple procedure used to theoretically model the experimental breakdown diagrams for the Abeta1-40 peptide complexed with a series of aminosulfonate small molecules, namely homotaurine, 3-cyclohexylamino-2-hydroxy-1-propanesulfonic acid (CAPSO), 3-(1,3,4,9-tetrahydro-2H-beta-carbolin-2-yl) propane-1-sulfonic acid, 3-(1,3,4,9-tetrahydro-2H-beta-carbolin-2-yl)butane-1-sulfonic acid, and 3-(cyclohexylamino) propane-1-sulfonic acid. An alternative method employing an extrapolation procedure for the microcanonical rate constant, k(E), is also discussed.

As a first project, collision-induced dissociation experiments were carried out using electrospray ionisation mass spectrometry on gas phase complexes involving different poly(methylmetacrylate) oligomers with three amino acids: glycine, leucine, and phenylalanine. After acquiring breakdown diagrams, RRKM modeling was used to fit the experimental data in order to obtain the 0 K activation energy and the entropy of activation. These thermodynamic data were then used to understand the competing dissociation channels observed (except for gas phase complexes involving glycine that had only one dissociation channel). Molecular dynamics simulated annealing calculations were carried on the gas phase complexes to understand further the energetic and entropic effects involved as well as the 3D conformation of these complexes. Valuable insight information was found on the 3D conformations, on a qualitative level. Using rotational constants and vibrational harmonic frequencies, it was possible to evaluate the entropy variation between the experimentally observed competing channels. Reasonable agreement was found between the experimental and theoretical variations of entropies. Finally, the proton affinity of poly(methylmetacrylate) oligomers is being discussed. Even though no absolute values for the proton affinity were found, the experimental and computational results help to understand the variation that accompanies the oligomers length. The second project presents the development an efficient and reproducible screening method for identifying low molecular weight compounds that bind to amyloid beta peptides (Abeta) peptides using electrospray ionization mass spectrometry (ESI-MS). Low molecular weight (LMW) compounds capable of interacting with soluble Abeta may be able to modulate/inhibit the Abeta aggregation process and serve as potential disease-modifying agents for Alzheimer’s disease. The present approach was used to rank the binding affinity of a library of compounds to Abeta1-40 peptide. The results obtained show that low molecular weight compounds bind similarly to Abeta1-42, Abeta1-40, as well as Abeta1-28 peptides and they underline the critical role of Abeta peptide charge motif in binding at physiological pH. Finally, some elements of structure-activity relationship (SAR) involved in the binding affinity of homotaurine to soluble Abeta peptides are discussed. As a third project, the gas phase binding of small molecules to the Abeta1-40 peptide generated by electrospray ionization has been explored with collision-induced dissociation mass spectrometry and kinetic rate theory. This project presents a simple procedure used to theoretically model the experimental breakdown diagrams for the Abeta1-40 peptide complexed with a series of aminosulfonate small molecules, namely homotaurine, 3-cyclohexylamino-2-hydroxy-1-propanesulfonic acid (CAPSO), 3-(1,3,4,9-tetrahydro-2H-beta-carbolin-2-yl) propane-1-sulfonic acid, 3-(1,3,4,9-tetrahydro-2H-beta-carbolin-2-yl)butane-1-sulfonic acid, and 3-(cyclohexylamino) propane-1-sulfonic acid. An alternative method employing an extrapolation procedure for the microcanonical rate constant, k(E), is also discussed.

Submitted by Fabio Sobreira Campos da Costa (fabio.sobreira@ufpe.br) on 2016-05-20T12:56:17Z No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Tese_Ayyaz-Mahmood.pdf: 9023674 bytes, checksum: beecc131e286e19ce6d03dec91f319d8 (MD5) / Made available in DSpace on 2016-05-20T12:56:17Z (GMT). No. of bitstreams: 2 license_rdf: 1232 bytes, checksum: 66e71c371cc565284e70f40736c94386 (MD5) Tese_Ayyaz-Mahmood.pdf: 9023674 bytes, checksum: beecc131e286e19ce6d03dec91f319d8 (MD5) Previous issue date: 2015-11-27 / Realizamos estudos do mecanismo, da seletividade e regiosseletividade da metilação de nitronatos [R1R2CNO2]− com CH3I, em que R1 = R2 = H (1), R1 = CH3 e R2 = H (2), R1 = R2 = CH3 (3); e R1 + R2 = c-(CH2)2 (4), usando método quântico ab initio MP2/CBS método e as teorias ADO e RRKM e simulações numéricas. As estruturas de todos os pontos estacionário no perfil da reação, incluindo os estados de transição, foram obtidas com sucesso e forneceram as energias de ativação (Δ‡) e de reacção (Δr) para todos os caminhos reacionais. Estas reações iniciam com a formação de complexo de reagente do tipo íon-molécula (RC@C ou RC@O) que se converte no respectivo complexo de produto (PC@C e PC@O), através do estado de transição (TS@C e TS@O) correspondente. As constantes de velocidade para a conversão do RC ao PC foram calculadas com a teoria RRKM. Ao contrário da proposta da literatura para o mecanismo de reação, a C-metilação é a via termodinâmica e cinética preferencial, com as seguintes seletividades: PC@C:PC@O = 89:11 (1), 97:03 (2-E), 97:03 (2-Z), 100:0 (3) e 100:0 (4). Isto é corroborado pela concordância qualitativa e quantitativa entre a ordem da reatividade calculada e experimental: 4 >> 3 > 2 > 1. A regiosseletividade para a C-alquilação é explicada pela maior exotermicidade desse canal de reação em comparação com a O-alquilação. O aumento da reatividade com o aumento do impedimento estérico ao redor do carbono central é explicado pelas diferenças de carácter sp3 deste átomo e pela diminuição da frequência vibracional associada à piramidalização ao redor deste átomo de carbono. Uma avaliação de funcionais híbridos- e duplo-híbrido DFT e do método MP2 para estas reações foi realizada a fim de verificar a confiabilidade e precisão destes métodos e sua utilização em modelagens similares. Os métodos mais precisos e robustos, que apresentam menor demanda computacional, foram M06- 2X and MP2 com as funções de base aug-cc-pVTZ-PP. A fim de revelar os efeitos solvente e do agente alquilante, a metilação do nitronato [MeCHNO2]− (2) com Me3O+ (oxônio) foi estudada em fase gás e em solução com o método B2PLYP/6-311+G(d,p). Os resultados mostraram regiosseletividade para a O-metilação em fase gás e principalmente em solução (diclorometano), o que concorda com os dados experimentais. Além disso, eles mostram que a regiosseletividade é fortemente dependente do agente alquilante (MeI vs. Me3O+). Este mesmo método foi utilizado para as reações [XC6H4CHNO2]− + MeCl (X = H, p-MeO, p-NO2) em fase gás e em solução (DMF). Os resultados em solução mostram uma pequena seletividade favorável à O-metilação, contudo, considerando que o agente metilante usado experimentalmente era o metil-p-bromobenzenossulfonato (MeOBS), o qual é muito mais reativo que o MeCl, é esperado que a utilização do MeOBS nas modelagens moleculares deva aumentar esta regiosseletividade para a O-metilação. / We performed a mechanistic, selectivity and regioselectivity study of methylation of nitronates [R1R2CNO2]− by CH3I in the gas-phase, where R1 = R2 = H (1), R1 = CH3 and R2 = H (2), R1 = R2 = CH3 (3); and R1 + R2 = c-(CH2)2 (4), using ab initio MP2/CBS method, ADO and RRKM theories and kinetics simulations. The structures of all stationary points, including transition states, were successfully obtained to provide energies of activation (Δ‡) and of reaction (Δr) for all reaction pathways. These reactions proceed with the formation of ion-neutral reactant complex (RC@C or RC@O) that is converted into the respective product complex (PC@C and PC@O) through the corresponding transition state (TS@C and TS@O). The rate constants for the conversion of RCs into PCs were calculated with the RRKM theory. Contrary to a previous proposal for the reaction mechanism, the C-methylation is the thermodynamics and kinetics preferred pathway with the following PC@C:PC@O selectivites 89:11 (1), 97:03 (2-E), 97:03 (2- Z), 100:0 (3), and 100:0 (4). This is corroborated by the agreement between the calculated and experimental reactivity trend 4 >> 3 > 2 > 1. The regioselectivity towards the C-alkylation is explained by the much larger exothermicity of this reaction channel compared to the Oalkylation. The increase of reactivity upon the increase of crowdedness of the central carbon atom is explained by differences of sp3 character at this atom and the decrease of the vibrational frequency associated with pyramidalization around this carbon atom. An assessment of hybrid- DFT functionals and MP2 method for these reactions was performed in order to ascertain the reliability of these methods for similar molecular modeling. The most accurate and robust methods, with the least computational demand, were M06-2X and MP2 with aug-cc-pVTZ-PP basis sets. In order to reveal the solvent and alkylating agent effects, the methylation reaction [MeCHNO2]− (2) + Me3O+ (oxonium) was studied in the gas-phase and in solution with B2PLYP/6-311+G(d,p) calculations. The results show regioselectivity towards O-methylation in the gas-phase and more significantly in solution (dichloromethane), which is in agreement with the experimental observation. In addition, it shows that the regioselectivity is highly dependent upon the reactivity of the alkylating agent (MeI vs. Me3O+). This same method was employed for the [XC6H4CHNO2]− + MeCl (X = H, p-MeO, p-NO2) reactions in the gas-phase and in solution (DMF). The results in solution show a slight regioselectivity towards O-methylation; however, considering that the methylating reagent used in the experiments was methyl pbromobenzenesulfonate (MeOBS), which is much more reactive than MeCl, it should thus be expected an increase of the calculated selectivity.

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