Dissertations / Theses on the topic 'Free Electron Model Calculations'

This thesis contains two parts. The first part concerns the research work on free molecules using synchrotron-radiation-related techniques. Auger electron spectra of two free open-shell molecules, O₂ and NO, were studied experimentally and theoretically. Photoionization experimental technique with tunable synchrotron radiation source was used to induce core-level electron ionization and obtain the KVV normal Auger electron spectra. A quantitative assignment of O₂ normal Auger spectrum was obtained by applying ab initio CI calculations and LVI Auger line shape simulations including the bond length dependence of Auger transition rates. The photon energy dependence of normal Auger electron spectra was focused on with photon energies in the vicinities of core-ionization threshold energies. Consequently, the MAPCI (Molecular Auger Post Collision Interaction) theory was developed. Taking the near-threshold O₂ normal Auger spectrum as an example, the two extreme cases of MAPCI effect, “atomic-like PCI” and “molecular PCI”, were discovered and discussed. The effect of shape resonance on near-threshold molecular normal Auger spectrum was discussed taking NO near threshold normal Auger spectra as example.

The second part deals with research work on the chemisorption of small epoxy organic molecules, ethylene oxide, methyl oxirane, on Si (100) surfaces. Synchrotron radiation related techniques, UPS, XPS and NEXAFS, were applied. Based on the valence photoemission spectra, C 1s and Si 2p XPS spectra, the epoxy ring opening reactions of these molecules in chemisorption process were proved. Further tentative search for the surface-adsorbate CDAD effect was performed, and no evident circular dichroism was confirmed.

Värmelära upplevs ofta som ett abstrakt område i gymnasiefysiken och elever tenderar att tolka känseln som en termometer. Värmelära kan därmed bli en tuff utmaning för många elever. Genom att introducera värmekameror i undervisningen ges elever möjligheten att se annars osynliga värmefenomen. Eftersom värmekameran inte ännu blivit etablerad i undervisningen finns det ett intresse att studera elevernas interaktion med värmekameran. Syftet med studien är att undersöka hur interaktionen ser ut och hur värmekameran kan hjälpa elever i begreppsbildandet av värmerelaterade fenomen. Denna studie har gjorts på ca 140 elever som går sitt första år på det naturvetenskapliga programmet på en gymnasieskola i Mellansverige. Eleverna fick utföra en laboration designad enligt prediction-observation-explanation-metoden. Laborationen innehöll tre stationer där de centrala begreppen var värmeledning, stöt och friktion. Eleverna använde en värmekamera som hjälpmedel för att förklara de olika fenomenen. Elevernas interaktioner vid laborationen dokumenterades med video- och ljudupptagning i syfte att ge grund för en kvalitativ analys. Analysen av materialet kom att handla om tre delar: hur eleverna resonerar kring värmeledning, respektive friktion och stöt, och hur värmekameran kan stimulera det kreativa tänkandet hos eleverna. Det visade sig att många elevgrupper kom långt i det makroskopiska och en bra bit i det mikroskopiska resonemanget kring värmeledning genom att tillämpa en modell av fria elektroner i metall de hade lärt sig från kemin. De flesta grupperna hade svårt att resonera kring energiomvandlingar vid stöt både på en makroskopisk och mikroskopisk nivå. Det kreativa undersökandet resulterade i en röra. Värmekameran lockar elevernas nyfikenhet, ger ”disciplinary affordance” och stimulerar dem till ”instant inquiry”. När eleverna gick utanför instruktionerna och bedrev egna undersökningar resulterade det i en röra då de prioriterade bort sina nykonstruerade hypoteser.
Thermodynamics is often perceived as an abstract field in secondary school physics. Thermodynamics can thus be a tough challenge for many students. By including thermal imaging cameras in teaching, students are given the opportunity to see otherwise invisible thermal phenomena. Since the infrared camera has not yet been established in teaching, there is an interest in studying the interaction between students and the thermal imaging camera. The purpose of this study is to investigate the interaction between student and the infrared camera and to see how the infrared camera can help students in the conceptual formation of heat-related phenomena. The study included about 140 students attending their first year on the science program at an upper secondary school in central Sweden. The students had to perform laboratory experiments designed according to the prediction-observation-explanation method. The laboratory experiments consisted of three stations where the key concepts were heat conduction, collision and friction. Students took help of an infrared camera to explain the various phenomena. The students' interactions at the lab were documented with video and audio recording in order to set the basis of a qualitative analysis. The analysis of the material consisted of three parts: how students reason concerning heat conduction, their reasoning concerning dissipative processes as friction and collision, and how the infrared camera can stimulate the students' creative thinking. Many student groups were successful in the macroscopic and quite successful in the microscopic reasoning regarding heat conduction by applying a model of free electrons in the metal which they had learned in chemistry class. Other studies have shown that students find it hard explaining heat conduction and that they tend to interpret the physical touch as a thermometer. The group that examined friction and collision found it difficult explaining the transformation from kinetic energy into thermal energy in collision at both the macroscopic and microscopic level. The creative investigation resulted in a mess. The infrared camera attracts students' curiosity, gives ”disciplinary affordance” and stimulates them to ”instant inquiry”. When the students went beyond their instructions and conducted own investigations it resulted in a mess when they prioritized away the recently created hypotheses.

The cyclic peroxides: diphenoyl peroxide (1), spiro-adamantyl-1,2-dioxetanone (2) and 4-(3-tert-butyldimethylsilyloxyphenyl)-4-methoxyspiro[1.2-dioxetane-3.2\'-adamantane] (3) synthesized, purified and characterized, also their kinetic and chemiluminescence (CL) properties were determined. The influence of solvent polarity on the chemiexcitation parameters of the catalyzed decomposition of 1 and 2, as well as the induced decomposition of 3 were examined in several binary solvent mixtures with different polarity and polarizability parameters, but similar viscosities. For solvents with low polarity, singlet quantum yields for the intermolecular catalyzed decomposition of diphenoyl peroxide (1,) and 1,2-dioxetanone (2) increase in function of medium polarity, showing maximum values in mediums of intermediate polarity, and decreasing in highly polar mixtures. For the induced decomposition of 3, the quantum yield showed to increase with increasing solvent polarity, including high polar solvent systems. In the binary solvent systems studied, the polarizability parameter showed to be contrary to the polarity values, therefore, it might appear that an increase of polarizability leads to a decrease in the singlet quantum yields for catalyzed decomposition of diphenoyl peroxide (1) and the induced decomposition of 3, however an increase in the singlet quantum yields for 1,2-dioxetanone 2. The three CL systems were also studied in binary solvent mixtures with different viscosities but similar polarity and polarizability parameters and singlet quantum yields showed an increase with increasing medium viscosity. Data were analyzed by using the collisional and the free volume models. The highly efficient intramolecular system induced 1,2-dioxetane 3 decomposition showed to be much more sensible to viscosity effects than the inefficient intermolecular systems. This surprising fact indicates that, even showing a significant solvent-cage effect, the induced 1,2-dioxetane should occur by an intramolecular electron back transfer. Moreover, chemiluminescence parameters of these systems were studied in several pure solvents. The obtained singlet quantum yields were correlated with viscosity, polarizability and polarity parameters by using multiple linear regression analysis.
Os peróxidos cíclicos: peróxido de difenoila (1), spiro-adamantil-1,2-dioxetanona (2) e 4-(3-terc-butildimetilsililoxifenil)-4-metoxispiro[1,2-dioxetano-3.2\'-adamantano] (3) foram sintetizados, purificados e caracterizados e as suas propriedades cinéticas e de quimiluminescência (CL) determinadas. A influência da polaridade do solvente sobre os parâmetros de quimi-excitação da decomposição catalisada de 1 e 2, e a decomposição induzida de 3 foi examinada em diversas misturas binárias de solventes com parâmetros de polaridade e polarizabilidade diferente, mas viscosidades semelhantes. Para solventes com baixa polaridade, os rendimentos quânticos singlete para a decomposição catalisada intermolecular do peróxido de difenoila (1) e 1,2-dioxetanona (2) aumentam em função da polaridade do meio, mostrando valores máximos em meios com polaridade intermediária, e diminuim para misturas altamente polares. Para a decomposição induzida de 3, o rendimento quântico mostrou aumentar com o aumento da polaridade do solvente, inclusive para sistemas com alta polaridade. Nos sistemas binários de solventes estudados, os parâmetros de polarizabilidade mostraram-se contrários aos valores de polaridade, portanto, parece que um aumento da polarizability leva a uma diminuição nos rendimentos quânticos singlete para a decomposição catalisada do peróxido de difenoila (1) e a decomposição induzida de 3, no entanto, um aumento nos rendimentos quânticos singlete para a 1,2-dioxetanona 2. Os três sistemas de CL também foram estudados em misturas binárias de solventes com diferentes viscosidades, mas com parâmetros de polaridade e polarizabilidade semelhantes e os rendimentos quânticos singlete mostraram aumentar com o aumento da viscosidade do meio. Os dados foram analisados usando tanto o modelos colisional quando o modelo de volume livre. Surpreendentemente, o sistema altamente eficiente decomposição induzida intramolecular do 1,2-dioxetano 3 mostrou-se muito mais sensível aos efeitos da viscosidade do que os sistemas intermoleculares ineficientes, o que indica claramente que a decomposição induzida do 1,2-dioxetano deve ocorrer por um processo de retro-transferência de elétron intramolecular. Além disso, os parâmetros de quimiluminescência destes sistemas foram estudados em vários solventes puros. Os rendimentos quânticos singlete obtidos foram correlacionados com parâmetros de viscosidade, polarizabilidade e polaridade usando análise de regressão linear múltipla.

The phenomenon of energy loss that occurs when an ion interacts with matter, also called stopping power, has been investigated for more than a century, and has provided findings of interest. However, reliable procedures for obtaining accurate experimental measurements and a fully theoretical comprehension of the process are tasks still in high demand by the scientific community. Moreover, stopping power data are prerequisites in several applications in modern science, such as engineering, ion implantation and modification of materials, damage to electronics devices (e.g. space radiation), medical physics (e.g. proton therapy), among others. In this thesis we i) develop a rigorous experimental protocol to measure stopping power with high precision, and ii) investigate the collapse of the free electron gas (FEG) model in energy loss of light ions (protons) at a low energy range in transition and rare-earth metals. In the first part, we present an approach to obtain, with high accuracy, the stopping cross sections in the pure materials Al and Mo for protons in the energy range of [0.9 - 3.6] MeV by means of the transmission method. The traceability of the sources of uncertainties are fully evaluated and the final accuracy of the results is 0.63% (0.32% rand. and 0.54% syst.) for Al, and 1.5 % (0.44 % rand. and 1.4% syst.) for Mo, with both results primarily limited by the quality and homogeneity of the stopping foils. For Al, this high accuracy represents an improvement compared to the results obtained in previous studies and serves as a benchmark for our procedure. The most important sources of uncertainties were random - the uncertainty in the peak positions and in the Gaussian fits; and systematic - the non-uniformity thickness of the foils (a special procedure was developed to correct this). Even though the final uncertainty for Mo is higher than for Al, our results improve on the amount of data currently available for the energy range considered. Both data sets are compared with the most commonly employed theoretical models and Monte Carlo codes in the literature. In the second part, electronic stopping cross sections of nontrivial solids, that is, transition and rare earth metals (Ta and Gd) for slow protons are experimentally investigated, and the data were compared with the results for Pt and Au, to understand how energy losses in these metals are correlated with electronic band structures, and to understand the failure of the FEG model predictions. The higher stopping powers found for Ta and Gd cannot be explained by means of the FEG model; however, these effects are successfully correlated with the high density of states (DOS) of both the occupied and unoccupied electronic levels in these metals. For the case of Gd, the experimental data are extended in the energy range until the Bragg\'s peak is reached. The two parts of this thesis were published in Physical Review A 93 022704 (2016), and in Physical Review Letters 18 103401 (2017), respectively.
O fenômeno de perda de energia quando um íon interage com a matéria, também conhecido como poder de freamento, vem sendo investigado por mais de um século, gerando grandes descobertas. Entretanto, conseguir obter medidas experimentais com alta precisão, ou elaborar um completo entendimento teórico dos processos de perda de energia são tarefas extremamente difíceis e ainda muito requeridas pela comunidade científica. Além disso, dados de perda de energia são pré-requisitos em várias aplicações e ramos da ciência moderna, tais como: engenharia, implantação e modificação de materiais, danos em dispositivos eletrônicos (radiação espacial), física médica (próton terapia), etc. Esta tese tem dois focos: i) desenvolver um rigoroso protocolo experimental para medir stopping power com alta precisão e ii) investigar a quebra de validade do modelo de Gás de Elétrons Livres (FEG) para a perda de energia de prótons lentos em metais de transição e terra raras. Na primeira parte apresentamos uma abordagem experimental para obter com alta precisão o poder de freamento em materiais puros (Al e Mo) para prótons no intervalo de energia de [0,9 - 3,6] MeV pelo método de transmissão. A rastreabilidade das fontes de incerteza foi determinada e as incertezas finais encontradas foram: 0,63 % (0,32 % aleat. e 0,54 % sist.) para Al e 1,5 % (0,44 % aleat. e 1,4 % sist.) para Mo, ambas devido a qualidade e homogeneidade das folhas freadoras. Para Al, esta acurácia representa um avanço comparado com publicações anteriores e, assim, serviu como uma referência de nosso procedimento. As mais importantes fontes de incerteza foram: aleatória incerteza das posições dos picos e dos ajustes Gaussianos e sistemática não-uniformidade das folhas-alvo (um procedimento foi desenvolvido para corrigir isso). Embora a incerteza final do Mo é um pouco maior do que do Al, nossos resultados ajudaram a complementar a baixa quantidade de dados disponíveis para o intervalo de energia considerado. Ambos conjuntos de dados foram comparados com os mais comuns modelos teóricos e códigos de Monte Carlo na literatura. Para a segunda parte, poder de freamento em metais não tão comuns tais como transição (Ta) e terras-raras (Gd) para prótons com baixas velocidades foram experimentalmente investigados, e os dados comparados com resultados de Pt e Au, a fim de entender como o stopping power destes metais está correlacionado com as estruturas de bandas eletrônicas, e assim tentar explicar a falha do modelo de FEG. Os altos valores das perdas de energias encontradas para Ta e Gd não puderam ser explicadas pelo modelo de FEG, e portanto foram correlacionados com a densidade de estados (DOS) em ambos os níveis ocupados e não ocupados destes metais. Para o caso do Gd, os dados experimentais foram estendidos em um intervalo de energia até alcançarem o pico de Bragg. A primeira parte desta tese foi publicada na Physical Review A 93 022704 (2016), e a segunda parte na Physical Review Letters 18 103401 (2017).

Etude parrpe et par des mesures de la conductivite dc et de la reponse dielectrique ac hyperfrequence. Mise en evidence de la nature radicalaire de type pi du systeme, a l'etat cristallin comme en solution; effet du solvant et de la temperature; observation de sauts de l'electron non apparie d'un macrocycle a l'autre a une frequence voisine de 1 mhz. Mise en evidence de la possibilite de formation de deux systemes cristallins (empilement de chaines ou de plans paralleles) et de leur caractere 1d ou 2d au moyen du modele de richards. La susceptibilite du systeme mesomorphe indique un desordre magnetique comparable a celui de la phase liquide; la conductivite est celle des systemes desordonnes. Les cristaux solvates sont des semiconducteurs moleculaires intrinseques

博士
國立臺灣大學
物理研究所
92
We have developed a novel model in order to study the transport electron in various structures with realistic boundary conditions. The effective mean free path is the main physical quantity used to specify the electron transport in the system; therefore, this model is called the effective mean-free-path model. This model is based on the assumption that the difference between the effective mean free path and the original mean free path is completely attributed to all e¤ective diffusive scatterings in system. Moreover, the general solution for the electron distribution in an applied electric field is related to the effective mean free path, and the undetermined coeffcient in the general solution for the electron distribution is associated with all effective diffusive scatterings. Furthermore, we provide a diagrammatical method to determine all effective diffusive scatterings associated with the effective mean free path and with the solution for the electron distribution. This diagrammatical method has clear physical interpretations and can be used to determine the electron transport in the analytical convergent form. All solutions for the electron distributions obtained from the effective mean-free-path model can be proven to be equivalent to those derived by use of solving the complicated coupled equations from the linear response Boltzmann transport equation in the relaxation time approximation with the given boundary conditions.

Dissertação de mestrado, Inovação Quimica e Regulamentação, Faculdade de Ciências e Tecnologia, Universidade do Algarve, 2015
Sulfa-drug derivatives, such as Benzenesulfonamide (BSA), para-Toluenesulfonamide (p-TSA), ortho-Toluenesulfonamide (o-TSA), and Sulfanilamide (SAM), are widely used in the chemical industry. However, these polar organic compounds constitute emerging environmental concerns. Unfortunately, there is lack of eco-toxicological data for these substances but some insight can be obtained by analyzing the molecular structure and conformational properties of the compounds which can aid with the understanding of their biological mechanisms. Rotational spectroscopy coupled with high level theoretical calculations can supply these data. In this dissertation, the structural information and conformational properties of the sulfa-drug derivatives were obtained by a combined study of rotational spectroscopy in free jet expansions and quantum chemical calculations (B3LYP and MP2 at 6-311++G** level of theory). The effect of the added substituents (ortho/para-CH3 and para-NH2), in terms of structural parameters, were investigated as well since BSA is the molecular backbone of o-TSA, p-TSA, and SAM. Results showed that the four sulfa-drug derivatives favour the eclipsed conformation of the –NH2 and –SO2 groups but rationalization behind this preference varies among the compounds. Conversely, addition of –CH3 and –NH2 in the para position has no significant effects on the structural parameters of BSA but addition of ortho-CH3 brought some dramatic changes in the bond angles.
European Commission: scholarship funded within the Erasmus+ KA1 Programme, ref. 2013-0241 – Erasmus Mundus Joint Master Degree in Chemical Innovation and Regulation

碩士
國立臺灣大學
物理學研究所
87
Current spin polarization and tunneling magnetoresistance (MR) of single and double magnetic tunneling junctions have been calculated within the free electron model by solving rigorously the 3D Schrodinger equation for different bias voltages and barrier widths. For single barrier junction, it is found that in general, the MR would decrease with voltage and become negative at some large voltages, a trend in agreement with both earlier and recent experiments. Also, it is revealed that for certain barrier widths, the MR would oscillate with bias voltage which is a prediction to be confirmed by experiments. We also describe a principle for designing double barrier magnetic tunneling structure that could produce spin current with controllable spin direction or have optimal spin valve effect. The principle is based on the finding that by tuning the energy position of spin dependent resonant tunneling level of a double barrier junction, fully spin-polarized current and optimal MR effect could be readily achieved.

Infrared multiple photon dissociation (IRMPD) spectroscopy has been coupled with electronic structure calculations in order to elucidate the structures of several small biological molecules including: uracil, 5-fluorouracil, 5-fluorocytosine, ferulic acid, and a number of their related analogs. IRMPD is a powerful technique, that when combined with electronic structure calculations can provide convincing evidence for the structural characterization of ions in the gas phase. Isomers of uracil and 5-fluorouracil (5-FU) have been characterized by calculations performed at the MP2(full)/aug-cc-pVTZ level of theory; however, infrared multiple photon dissociation spectroscopy experiments proved to be unsuccessful for these species. Geometry optimization and frequency calculations have isolated the dominant isomer(s) for neutral and deprotonated uracil and 5-fluorouracil, along with several cluster interactions involving water, methanol, ammonia, and methylamine. For both uracil and 5-FU, a single relevant neutral isomer was determined, with each isomer existing in the diketo, as opposed to the enol form. Following the deprotonation of this neutral isomer, both uracil and 5-FU were permitted to form anionic cluster ions with water, methanol, ammonia, or methylamine, and based on the relative Gibbs free energies (298 K) of the calculated isomers, relevant cluster interactions were determined. For each cluster, several sites of intramolecular interaction were found to exist; however, interaction at the site of deprotonation was the most favourable in every instance. Ionic hydrogen bond interactions have been found in several clusters formed by 5-fluorocytosine (5-FC). The chloride and trimethylammonium cluster ions, in addition to the cationic and anionic dimers have been characterized by infrared multiple photon dissociation (IRMPD) spectroscopy and electronic structure calculations performed at the B2PLYP/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. IRMPD spectra in combination with calculated spectra and relative energetics have indicated, quite conclusively, that a single isomer for each 5-FC cluster that is likely being observed experimentally except in the case of the anionic dimer, in which a combination of isomers is probable. For the 5-FC-trimethylammonium cluster specifically, the calculated spectrum of the lowest energy isomer matches the experimental spectrum remarkably well. Interestingly, the cationic dimer of 5-FC was found to have a single energetically relevant isomer (Cationic-IV) in which a unique tridentate ionic hydrogen bond interaction is formed. The three sites of intramolecular ionic hydrogen bonds in this isomer interact very efficiently, leading to a significantly large calculated enthalpy of binding of 180 kJ/mol. The magnitude of the calculated binding energy for this species, in combination with the strong correlation between the simulated and IRMPD spectra, indicates that the tridentate-bound dimer is observed predominantly in experiment. Comparison of the calculated relative Gibbs free energies (298 K) for this species with several of the other isomers considered also supports the likelihood of the dominant protonated dimer existing as Cationic-IV. Protonated ferulic acid has been characterized using infrared multiple photon dissociation spectroscopy and electronic structure calculations at the B3LYP/6-311+G(d,p) level of theory. Neutral ferulic acid has been determined to undergo protonation on the carbonyl oxygen of the acid group, forming an ion of m/z 195. Due to its extensively conjugated structure, protonated ferulic acid (m/z 195) is observed to yield three stable fragment ions in IRMPD experiments. It is proposed that two parallel fragmentation pathways of protonated ferulic acid are being observed. First, proton transfer occurs from the carbonyl oxygen to the hydroxyl oxygen within the acid group, resulting in the loss of water and subsequently carbon monoxide, forming ions of m/z 177 and 149, respectively. The second proposed fragmentation pathway undergoes proton transfer from the phenolic group to the methoxy group resulting in loss of methanol and rearrangement to a five-membered ring of m/z 163. IRMPD spectra have been obtained for the ions m/z 195 and m/z 177, and anharmonic calculations have been performed on these species at the B3LYP/6-311+G(d,p) level of theory. The calculated anharmonic spectra for these ions match the experimental spectrum exceptionally well and strongly support the proposed fragmentation mechanisms.

Mass-selected infrared multiple photon spectroscopy (IRMPD), Fourier transform ion cyclotron resonance (FT-ICR) kinetic experiments, RRKM and electronic structure calculations have been performed in order to propose a complex mechanism involving the formation of the proton-bound dimer of water (H5O2+) from 1,1,3,3-tetrafluorodimethyl ether. It has been found that the reaction is facilitated by a series of sequential exothermic bimolecular ion-molecule reactions. Evidence for the dominant mechanistic pathway involving the reaction of CF2H-O=CHF+, an ion of m/z 99, with water is presented. The primary channel occurs via nucleophilic attack of water on the ion of m/z 99 (CF2H-O=CHF+), to lose formyl fluoride and yield protonated difluoromethanol (m/z 69). Association of a second water molecule with protonated difluoromethanol generates a reactive intermediate which decomposes via a 1,4-elimination to release hydrogen fluoride and yield the proton-bound dimer of water and formyl fluoride (m/z 67). The 1,4-elimination of hydrogen fluoride is found to be strongly supported by the results of both RRKM theory and electronic structure calculations. Lastly, the elimination of formyl fluoride occurs by the association of a third water molecule to produce H5O2+ (m/z 37). The most probable isomeric forms of the ions with m/z 99 and 69 were found using IRMPD spectroscopy and electronic structure theory calculations. Thermochemical information for reactant, transition and product species was obtained using MP2/aug-cc-pVQZ//MP2(full)/6-31G(d) level of theory. Ionic hydrogen bond (IHB) interactions, resulting from the association of ammonia and two of the protonated methylxanthine derivatives, caffeine and theophylline, have been characterized using mass-selected IRMPD and electronic structure calculations at the MP2/aug-cc-pVTZ//B3LYP/6-311+G(d,p) level of theory. It was found that the formation of a proton-bound dimer (PBD) of caffeine and ammonia was elusive under the experimental conditions. The low binding energy of the caffeine and ammonia PBD is responsible for the perceived difficulty in obtaining an IRMPD spectrum. The IRMPD spectrum of the PBD of theophylline and ammonia was obtained and revealed bidentate IHB formation within the complex, which greatly increased the binding energy relative to the most stable isomer of the PBD of caffeine and ammonia. The IRMPD spectra of the protonated forms of caffeine and theophylline have also obtained. The spectrum of protonated caffeine showed the dominant existence of a single isomer, whereas the spectrum of protonated theophylline showed a mixture of isomers. The mixture of isomers of protonated theophylline resulted as a consequence of proton-transport catalysis (PTC) occurring within the PBD of theophylline and ammonia. All calculated harmonic spectra have been produced at the B3LYP/6-311+G(d,p) level of theory with fundamental frequencies scaled by 0.9679; calculated anharmonic spectra have also been provided at the same level of theory and were found to greatly improve the match with the IRMPD spectra obtained in all cases. Ionic hydrogen bond (IHB) interactions, resulting from the association of caffeine and theophylline with their protonated counterparts, forming proton-bound homodimers, have been characterized using mass-selected IRMPD and electronic structure calculations at the MP2/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) level of theory. It is found that the IRMPD spectra of the proton-bound homodimers of caffeine and theophylline are complicated resulting from the existence of several pairs of enantiomers separated by a narrow range of relative Gibbs free energies (298 K) of 15.6 and 18.2 kJ mol-1, respectively. The IRMPD spectrum of the proton-bound homodimer of theophylline is dominated by a unique isomer facilitated by formation of a bidentate IHB. Formation of this interaction lowers the relative Gibbs free energy of the ion to 9.75 kJ mol-1 below that of the most favourable pair of enantiomers. The IRMPD spectrum of the PBD of caffeine is complicated by the existence of at least two pairs of enantiomers with the strong likelihood of the spectral contributions of a third pair existing. The most favourable enantiomeric pair involves the formation of a O-H+⋯O IHB. However, verification of a pair of enantiomeric PBDs containing a N-H+⋯O IHB is also observed in the IRMPD spectrum of the PBD of caffeine due to the presence of three free carbonyl stretching modes located at 1731, 1751 and 1785 cm-1. The mass-selected IRMPD spectra of the sodium cation-bound dimers (SCBD) of caffeine and theophylline also have been obtained. Both the mass-selected IRMPD spectra and electronic structure calculations predict the most likely structure of the SCBDs of caffeine and theophylline to form by an efficient O⋯Na+⋯O interaction between C=O functional groups possessed by each monomer. The frequencies of the C=O-Na+ stretch are found to be nearly identical in the IRMPD spectra for both of the SCBDs of caffeine and theophylline at 1644 and 1646 cm-1, respectively. However, the degenerate free C=O symmetric and asymmetric stretches for the SCBDs of caffeine and theophylline found at 1732 and 1758 cm^(-1), respectively, demonstrating a red-shift for caffeine possibly linked to a steric interaction absent in theophylline. Free rotation about the O⋯Na+⋯O bond is found to greatly decrease the complexity of the IRMPD spectra of the SCBDs of caffeine and theophylline and demonstrates excellent agreement between the IRMPD and calculated spectra. Electronic structure calculations have been done at the MP2(full)/aug-cc-pCVTZ/6-311+G(2d,2p)//B3LYP/6-311+G(d,p) level of theory using the aug-cc-pCVTZ basis set for Na+ and all Na+-interacting heterotatoms, and the 6-311+G(2d,2p) basis set for all non-interacting atoms within the SCBDs, in order to provide accurate electronic energies. Currently, installation and implementation of a pulsed electrospray high pressure ion source mated to an existing high pressure mass spectrometer (HPMS) is underway. The new ion source will greatly increase the range of possibilities for the study of ion-molecule reactions in the McMahon laboratory. One of the unique features of the new design is the incorporation of a gas-tight electrospray interface, allowing for more possibilities than only the study of cluster-ion equilibria involving hydration (H2On⋯S+), where S+ is an ion produced by electrospray. Other small prototypical biological molecules such as amines and thiols can be used without concern for the toxicity of these species. Another unique design feature allows electrosprayed ions to associate with neutral solvent species in an electric field free reaction chamber (RC). This ensures that values of equilibrium constants determined are truly representative of ions in states of thermochemical equilibrium. The existing HPMS in the McMahon laboratory is limited to the study of small volatile organic molecules. The new ion source will permit the exploration of systems involving non-volatile species, doubly charged ions and many biologically relevant molecules such as amino acids, peptides, nucleobases and carbohydrates.

This dissertation covers a series of related topics in the mathematical modelling of mass spectrometry data. The dissertation opens with a presentation of an optimal algorithm for the generation of the fine isotopic structure. We further show the applications of that algorithm to the problem of deconvoluting mixed isotopic signals, in two different ways. We also approach the problem of estimating the deep parameters of mass detectors, estimating the parameters of a function that relates the instrument-generated intensities to the numbers of ions. These solutions are applied to the problem of understanding Electron Driven reactions, whose principal aim is to induce ion fragmentation and, in that way, enhance the instrument’s identification capabilities. Finally, we show how to apply the mathematical theory of reaction kinetics to estimate the reaction rates of the electron transfer reactions.
Niniejsza rozprawa doktorska dotyczy szeregu tematyk z zakresu matematycznego modelowanie widm masowych. W pracy przedstawiam algorytm służący obliczeniom związanym z rozkładami izotopowymi cząsteczek. Algorytm ów wykorzystuję w problemie dekonwolucji mieszanek sygnałów ze znanych źródeł molekularnych, na dwa różne sposoby. Przedstawiam również sposób na wyznaczenie zależności pomiędzy zarejestrowanym sygnałem a liczbą jonów dla różnych detektorów jonów. Powyższe rozwiązania zostają również wykorzystane w celu dokładniejszego zrozumienia za- sad działania fragmentacji jonów za pomocą transferu elektronu, która znacząco poszerza możliwości identyfikacji substancji. Pokazuję również sposób na wyestymowanie parametrów tych reakcji, wykorzystując w tym celu matematyczny model kinetyki reakcji.

Cryo-electron microscopy (cryo-EM) has been established as the leading imaging technique for structural studies from small proteins to whole cells at a molecular level. The great advances in cryo-EM have led to the ability to provide unique insights into a wide variety of biological processes in a close to native, hydrated state at near-atomic resolutions. The developments of computational approaches have significantly contributed to the exciting achievements of cryo-EM. This dissertation emphasizes new approaches to address image processing problems in cryo-EM, including tilt series alignment evaluation, simultaneous determination of sample thickness, tilt, and electron mean free path based on Beer-Lambert law, Model-Based Iterative Reconstruction (MBIR) on tomographic data, minimization of objective lens astigmatism in instrument alignment and defocus and magnification dependent astigmatism of TEM images. The final goal of these methodological developments is to improve the 3D reconstruction of cryo-EM and visualize more detailed characterization.