Thesis (Ph.D.)--McMaster University (Canada), 1992. / Source: Dissertation Abstracts International, Volume: 54-08, Section: B, page: 4153. Adviser: Adam P. Hitchcock.

Thesis (M.S.)--University of North Texas, Dec., 2008. / Title from title page display. Includes bibliographical references.

xvi, 218 p. : ill. (some col.) / Our theoretical studies involve the control of electronic energy transfer in molecular dimers through the preparation of specific vibrational coherences prior to electronic excitation. Our control strategy is based upon the fact that, following impulsive electronic excitation, nuclear motion acts to change the instantaneous energy difference between site-excited electronic states and thereby influences short-time electronic excitation transfer (EET). By inducing coherent intramolecular vibration in one of the chromophores prior to short-pulse electronic excitation, we exert external control over electronic dynamics. As a means to monitor this coherent control over EET, we propose using multidimensional wave-packet interferometry (md-WPI). Two pairs of polarized phase-related femtosecond pulses following the control pulse would generate superpositions of coherent nuclear wave packets in optically accessible electronic states. Interference contributions to the time- and frequency-integrated fluorescence signal due to overlaps among the superposed wave packets provide amplitude-level information on the nuclear and electronic dynamics. We test both the control strategy and its spectroscopic investigation by calculating pump-probe difference signals for various combinations of pulse polarizations. That signal is the limiting case of the control-influenced md-WPI signal in which the two pulses in the pump pulse-pair coincide, as do the two pulses in the probe pulse-pair. We present calculated pump-probe difference signals for a variety of systems including a simplified model of the covalent dimer dithia-anthracenophane (DTA) in which we treat only the weakly Franck-Condon active ν 12 anthracene vibration at 385 cm -1 . We further present calculated nl-WPI difference signals for an oriented DTA complex, which reveal amplitude-level dynamical information about the interaction of nuclear motion and electronic energy transfer. We also present pump-probe difference signals from a model system in which a CF 3 group, whose torsional angle is strongly Franck-Condon active, has been added to the anthracene monomers which make up DTA. We make use of electronic structure calculations to find the torsional potential of the monomer, from which we calculate the spectroscopic signals of the dimer. We show that a significant measure of control over short-time EET is achievable in this system. This dissertation includes previously published coauthored material. / Commitee in charge: Dr. Michael E. Kellman, Chair; Dr. Jeffrey A. Cina, Advisor; Dr. David R. Herrick; Dr. Andrew H. Marcus; Dr. Daniel A. Steck

This dissertation focuses on the development of analytical methods based on Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and their applications for separation and structural characterization of oligosaccharides. Porous graphitized carbon liquid chromatography (PGC-LC), gated-trapped ion mobility spectrometry (Gated-TIMS), and electronic excitation dissociation tandem mass spectrometry (EED MS/MS) are three essential techniques employed here. First, the EED method was optimized to generate more informative glycan tandem mass spectra for accurate structural analysis. Glycans were reduced and permethylated or labeled with a reducing-end fixed charge to increase sensitivity, avoid gas-phase structural rearrangement, and facilitate spectral interpretation. EED of glycans produced nearly complete series of Z-, Y- and 1,5X-ions, that appear in the spectra as triplets with characteristic spacing, thus facilitating accurate determination of the glycan topology. Additional radical-driven dissociation pathways were identified, from which different types of linkage-diagnostic ions (cross-ring, secondary, or internal fragments) were generated. The results demonstrated that linkage analysis can be accomplished by utilizing one or a combination of several linkage-diagnostic fragments. EED MS/MS was then implemented, in conjunction with PGC-LC or Gated-TIMS, for on-line separation and characterization of complex mixtures of glycans. These two methods were successfully applied for high-throughput and detailed structural analysis of N-glycans released from human serum, O-glycans released from bovine submaxillary mucin and free oligosaccharides. The performance of these methods was tested and improved through analysis of different types of glycans from a variety of biological sources. Finally, in collaboration with bioinformaticians, a spectral interpretation algorithm, GlycoDeNovo, has been developed for automated and de novo glycan topology reconstruction from their tandem mass spectra. A large number of EED tandem spectra of glycan standards generated in house were used as the training dataset to establish appropriate IonClassifiers for candidate ranking. GlycoDeNovo is capable of identifying correct topologies from MS/MS spectra of glycans in different derivatized forms. Several aspects of this collaborative project were covered in this thesis, including glycan derivatization, data acquisition and manual spectral interpretation to guide the development and evaluate the performance of the automated approach. In this thesis research, integrated approaches utilizing PGC-LC–EED-MS/MS and Gated-TIMS–EED-MS/MS, and the appropriate bioinformatics software, have been established for structural analysis of glycan mixtures. They hold great potential for comprehensive, automated, and de novo glycome characterization.

Orientador: Marco Aurelio Pinheiro Lima / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Fisica Gleb Wataghin / Made available in DSpace on 2018-08-07T11:03:34Z (GMT). No. of bitstreams: 1 Arretche_Felipe_D.pdf: 1126375 bytes, checksum: 09c67543e39406702bd45e2373d9c616 (MD5) Previous issue date: 2006 / Resumo: Nesta tese investigamos a modelagem teórica de colisões pósitron-molécula no regime de baixas energias utilizando o método Schwinger multicanal. Nosso objetivo inicial foi sofisticar o procedimento de cálculo do parâmetro de aniquilação¸ Zeff . Esta quantidade é diretamente proporcional a taxa de aniquilação de pósitrons com elétrons da nuvem molecular. Infelizmente o método subestima Zeff com relação aos dados experimentais. Uma investigação mais detalhada sugere que esta deficiência está ligada a uma descrição pobre do cúspide elétron-pósitron na função de onda de espalhamento. Para tanto, inserimos um potencial complexo tipo delta de Dirac na Hamiltoniana de espalhamento com o objetivo de melhorar o cálculo de aniquilação direta e possivelmente adaptá-lo para descrever o canal de formação do positrônio real. Aplicação a sistemas modelo como átomo de He e molécula de H2 mostraram que esta técnica alternativa produz resultados similares ao cálculo perturbativo usual. Neste sentido a discrepância entre o parâmetro de aniquilação teórico obtido via método Schwinger multicanal e os dados experimentais continua em aberto. Recentemente o grupo da Universidade de San Diego, na Califórnia, desenvolveu um aparato experimental para medir seções de choque de excitação eletrônica de átomos e moléculas por impacto de pósitrons. O método Schwinger multicanal é o único que tem atacado sistematicamente este problema para moléculas na literatura. Neste trabalho, damos continuidade a este programa de pesquisa calculando seções de choque de excitação eletrônica para as moléculas de H2 e CO com variados níveis de aproximação. Nossos resultados indicam que as seções de choque integrais são insensíveis ao nível de acoplamento multicanal utilizado na modelagem da colisão e que efeitos de polarização podem ser particularmente importantes para energias imediatamente acima dos limiares de excitação eletrônica. Finalmente, e este sem dúvida é o maior resultado desta tese, aprendemos a tratar as bases variacionais usadas no cálculo de espalhamento. A evidência de que tal nível de maturidade foi atingido é a convergência das seções de choque com relação aos métodos de cálculo dos elementos de matriz da função de Green, anteriormente obtida somente por ajuste (popularmente conhecido como "chute") do conjunto de primitivas Gaussianas utilizado no cálculo de espalhamento / Abstract: In this thesis we investigate the theoretical modelling of positron-molecule collisions in low energy regime using the Schwinger multichannel method. Our initial objective was to sophisticate the procedure of calculation of the annihilation parameter Zeff. This quantity is directly proportional to the annihilation rate of positrons with molecular cloud electrons. Unhapilly the method underestimates Zeff compared to the experimental data. A more detailed investigation suggests that this deficiency is connected with a poor description of the electronpositron cusp of the scattering wave function. To this end, we inserted a complex potential of Dirac delta type in the scattering Hamiltonian with the major objective of improving the direct annihilation calculation and possibly to adaptate it to describe the real positronium formation channel. Aplication to model systems like He atom and H2 molecule showed that this alternative technique produce similar results compared to the usual perturbative calculation. In this sense, the discrepancy between the theoretical annihilation parameter generated by Schwinger multichannel method and the experimental data remains as an open problem. Recently the research group of San Diego University, in California, developed an experimental apparatus to measure electronic excitation cross sections for atoms and molecules by positron impact. The Schwinger multichannel method is the only that has sistematicaly attacked the problem for molecules in the literature. In this work, we continue this research program calculating electronic excitation cross sections for H2 and CO molecules with varied degrees of approximation. Our results indicate that integral cross sections are insensible to the level of multichannel coupling used in the collision model and that polarization effects can be particularly relevant for energies immediately above electronic excitation thresholds. Finally, and this doubtless is the greater result of this thesis, we learnt to treat the variational basis used in the scattering calculation. The evidence that such level of maturity was reached is the convergence of the cross sections by the methods of computation of the Green¿s function matrix elements, obtained before only by "guessing" of the set of primitive Gaussians employed in the scattering calculation / Doutorado / Física Atômica e Molecular / Doutor em Ciências

Elektroninio sužadinimo evoliucija šviesai jautriose molekulėse yra reiškinys, kuriuo remiantis įmanoma nagrinėti daugelį natūralių ir dirbtinių procesų: augalų ir bakterijų fotosintezę, regos mechanizmą, optomechaninių bei optoelektroninių prietaisų (pavyzdžiui, organinių šviestukų) veikimą. Teoriškai šis reiškinys modeliuojamas sprendžiant laikinę Šriodingerio lygtį. Deja, toks sprendimas realiems, praktiškai panaudojamiems junginiams šiandien yra per sudėtingas uždavinys, todėl jį tenka keisti supaprastinant nagrinėjamų junginių modelius arba sprendimo metodiką. Šioje disertacijoje aprašomų tyrimų tikslas buvo elektroninės struktūros skaičiavimų metodais (t. y. sprendžiant paprastesnę nuostoviąją Šriodingerio lygtį) ištirti elektroninio sužadinimo sukeltus procesus fotoaktyviose molekulėse ir sudaryti sužadinimo relaksaciją apibūdinančius potencinės energijos paviršių modelius. Parodoma, jog ta pačia metodika atliekamų tyrimų rezultatai paaiškina įvairiuose junginiuose vykstančius reiškinius: bakteriorodopsino baltymo funkcinės grupės vykdomą protono pernašą poliniame tirpiklyje, indolo-benzoksazino junginio optomechaninį ciklą, našią fosforescenciją organiniame silicio polimere bei šviestukams naudojamo metaloorganinio komplekso su prijungtomis krūvininkų pernašos grupėmis ypatybes. / Evolution of the electronic excitation is a general process that can be used to explain many natural and artificial phenomena, such as photosynthesis in plants and bacteria, biological mechanism of vision, and operating principles of optomechanical and optoelectronic devices. This process is theoretically modeled by solving the time-dependent Schroedinger equation. However, such treatment is too computationally expensive to be used for practical molecular systems. Therefore, either models of the structure of the systems or the solving procedure itself must be simplified to get the desired results. The main goal of the research presented in this dissertation was to study processes caused by the electronic excitation in photoactive molecules using computational methods of electronic structure (i. e. solving the simpler time-independent Schroedinger equation) and to construct the potential energy surface models describing the energy relaxation in the investigated molecules. It is shown that the results of different investigations performed using the same procedure provide explanations of different phenomena in various compounds, such as: proton transfer in polar solvent, performed by a functional group of the bacteriorhodopsin protein; optomechanical cycle of the indolo-benzoxazine compound; efficient phosphorescence of the silicon-based organic polymer; and optical properties of organometallic emitter compound with additional charge-carrier groups.

Evolution of the electronic excitation is a general process that can be used to explain many natural and artificial phenomena, such as photosynthesis in plants and bacteria, biological mechanism of vision, and operating principles of optomechanical and optoelectronic devices. This process is theoretically modeled by solving the time-dependent Schroedinger equation. However, such treatment is too computationally expensive to be used for practical molecular systems. Therefore, either models of the structure of the systems or the solving procedure itself must be simplified to get the desired results. The main goal of the research presented in this dissertation was to study processes caused by the electronic excitation in photoactive molecules using computational methods of electronic structure (i. e. solving the simpler time-independent Schroedinger equation) and to construct the potential energy surface models describing the energy relaxation in the investigated molecules. It is shown that the results of different investigations performed using the same procedure provide explanations of different phenomena in various compounds, such as: proton transfer in polar solvent, performed by a functional group of the bacteriorhodopsin protein; optomechanical cycle of the indolo-benzoxazine compound; efficient phosphorescence of the silicon-based organic polymer; and optical properties of organometallic emitter compound with additional charge-carrier groups. / Elektroninio sužadinimo evoliucija šviesai jautriose molekulėse yra reiškinys, kuriuo remiantis įmanoma nagrinėti daugelį natūralių ir dirbtinių procesų: augalų ir bakterijų fotosintezę, regos mechanizmą, optomechaninių bei optoelektroninių prietaisų (pavyzdžiui, organinių šviestukų) veikimą. Teoriškai šis reiškinys modeliuojamas sprendžiant laikinę Šriodingerio lygtį. Deja, toks sprendimas realiems, praktiškai panaudojamiems junginiams šiandien yra per sudėtingas uždavinys, todėl jį tenka keisti supaprastinant nagrinėjamų junginių modelius arba sprendimo metodiką. Šioje disertacijoje aprašomų tyrimų tikslas buvo elektroninės struktūros skaičiavimų metodais (t. y. sprendžiant paprastesnę nuostoviąją Šriodingerio lygtį) ištirti elektroninio sužadinimo sukeltus procesus fotoaktyviose molekulėse ir sudaryti sužadinimo relaksaciją apibūdinančius potencinės energijos paviršių modelius. Parodoma, jog ta pačia metodika atliekamų tyrimų rezultatai paaiškina įvairiuose junginiuose vykstančius reiškinius: bakteriorodopsino baltymo funkcinės grupės vykdomą protono pernašą poliniame tirpiklyje, indolo-benzoksazino junginio optomechaninį ciklą, našią fosforescenciją organiniame silicio polimere bei šviestukams naudojamo metaloorganinio komplekso su prijungtomis krūvininkų pernašos grupėmis ypatybes.

We present recent theoretical and methodological explorations on the dynamics of sodium clusters in the framework of Time-Dependent Density Functional Theory (TDDFT), coupled non-adiabatically to Molecular-Dynamics (MD). In particular, a hierarchical approach, in the spirit of Quantum-Mechanical/Molecular-Mechanical methods, has been developed for the description of metal clusters in interaction with a dynamically polarizable substrate, as rare gases or MgO. Numerous examples of application of this approach (Na clusters in or on Ar substrate, Na clusters deposited on MgO; optical response, dynamical deposition, laser irradiation, ...) are reviewed. We also briefly discuss complementing research activities. Formal developments on the Self-Interaction Correction issue in DFT and TDDFT are discussed in a word. We have furthermore extended our TDDFT-MD theory to the case of organic (C, N, O, H made) systems and a few examples of investigated dynamical processes are presented. Recent calculations of photoelectron angular distributions of free metal clusters are reported as well. We finally sketch with some perspectives for the years to come.

Le but de cette thèse est la compréhension de pourquoi certains complexes de ruthénium sont soit pasluminescents soit avec un temps de vie très courte de l’état excité. Des calculs de type théorie de lafonctionnelle de la densité (DFT) ou DFT dépendante du temps (TD-DFT) étaient effectués pour cinqcomplexes existants et aussi pour un complexe hypothétique. Selon la théorie de champs de ligand (LFT),la plus proche sont les énergies des états de type transfert de charge métal-ligand (MLCT) à un état de typemétal centré (MC), alors le plus facile est-ce à peupler l’état MC ainsi menant à une dèsexcitation nonradiative de l’état MLCT. Les calculs DFT/TD-DFT s’avéraient suffisants pour reproduire les géométrieset spectres d’absorption expérimentales. Ceci, ensemble avec la technique de densité d’états partielle,permettaient une validation de l’idée fondamentale issue du modèle LFT en confrontant les résultats denos calculs avec les temps de vie mesurés. / Density-functional theory (DFT) and time-dependent DFT (TD-DFT) were carried out for 5 rutheniumcomplexes and one hypothetical one. The goal was to understand the lack of luminescence or very shortexcited state lifetimes at room temperature in some of them. According to ligand-field theory (LFT), thecloser the energies of the metal-to-ligand charge transfer (MLCT ) and the metal-centred (MC) states,the easier it is to populate the MC state, leading to radiationless disactivation of the luminescent MLCT.DFT/TD-DFT calculations proved adequate in reproducing experimental geometries and absorption spectra.Verification of LFT explanation was done by use of partial density of states whose results agreedreasonably well with the usual hypothesis.

Optical current sensors (OCSs) are initially developed to measure relatively large current over a wide range of frequency band. They are also used as protective devices in the event a fault occurs due to a short circuit, in the power generation and distribution industries. The basic principal used in OCS is the Faraday effect. When a light guiding faraday medium is placed in a magnetic field which is produced by the current flowing in the conductor around the magnetic core, the plane of polarization of the linearly polarized light is rotated. The angle of rotation is proportional to the magnetic field strength, proportionality constant and the interaction length. The proportionality constant is the Verdet constant V (λ, T), which is dependent on both temperature and wavelength of the light. Opto electrical methods are used to measure the angle of rotation of the polarization plane. By measuring the angle the current flowing in the current carrying conductor can be calculated. But the accuracy of the OCS is lost of the angle of rotation of the polarization plane is dependent on the Verdet constant, apart from the magnetic field strength. As temperature increases the Verdet constant decreases, so the angle of rotation decreases. To compensate the effect of temperature on the OCS, a new method has been proposed. The current and temperature are measured with the help of a duel frequency method. To detect the line current in the conductor or coil, a small signal from the line current is fed to the reference of the lock in. To detect the temperature, the coil is excited with an electrical signal of a frequency different from the line frequency, and a small sample of this frequency signal is applied to the reference of the lock in. The temperature and current readings obtained are look up at the database value to give the actual output. Controlled environment is maintained to record the values in the database that maps the current and temperature magnitude values at the DSP lock in amplifier, to the actual temperature and current. By this method we can achieve better compensation to the temperature changes, with a large dynamic range and better sensitivity and accuracy.