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Estudos teóricos e experimentais acerca de danos em biomoléculas induzidos pela captura eletrônica em meio biológico têm sido largamente discutidos ao longo da última década. No presente trabalho, abordou-se o problema da captura eletrônica pelo nucleotídeo monofosfato 3\'-dGMP com técnicas de estrutura eletrônica, explorando estados ligados do ânion. Buscou-se investigar o ânion em fase gasosa e em solução aquosa, além de estimar barreiras de energia pontecial e energia livre associadas à sua dissociação (quebra da ligação ribose-fosfato). Utilizando os modelos de solvatação implícita (PCM) e explícita (simulação computacional com o método de Monte Carlo), concluiu-se que, em meio aquoso, o estado fundamental do ânion 3 -dGMP apresenta caráter de valência sobre a base nitrogenada (orbital com ocupação simples), em oposição ao resultado em fase gasosa, que prevê um estado ligado por dipolo. A barreira de dissociação, relativa ao estiramento da ligação entre os grupos ribose e fosfato, foi estimada em 16-30 kcal/mol, dependendo da técnica de solvatação utilizada. / Theoretical and experimental studies on the damage to biomolecules induced by electron attachment in the biological environment have been widely discussed over the past decade. In the present work, we addressed electron capture by the monophosphate nucleotide 3 -dGMP with electronic structure techniques, exploring bound anion states. We have investigated these anion states in gas phase and in aqueous solution, and estimated the potential and free energy barriers related to the dissociation reaction (breakage of the ribose-phosphate bond). Employing implicit (PCM) and explicit (computer simulation with the Monte Carlo method) solvation models, we have concluded that, in aqueous environment, the ground state of the 3-dGMP specie has valence character with the singly occupied molecular orbital localized on the base. In contrast, the gas phase results point out a dipole-bound ground state. The free energy barrier for the dissociation mechanism, according to the present results, would be around 16-30 kcal/mol in aqueous solution, depending on the salvation model.

Nesta tese apresentamos uma extensão da técnica de espalhamento hiper-Rayleigh (HRS) e sua aplicação para o estudo dos mecanismos que interferem na primeira hiperpolarizabilidade molecular (). Utilizamos um laser Nd:YAG, Q-switched e mode-locked como bombeio para excitar as amostras. Este laser emite pulsos de 100 ps modulados por uma envoltória de Q-switch. A saída é uma seqüência de pulsos com intensidades que acompanham a forma da envoltória. Usamos este trem de pulsos para excitar as amostras na medida de espalhamento hiper-Rayleigh, e um sistema de detecção com resolução temporal suficiente para resolver cada pulso independentemente. Esta modalidade de bombeio permitiu eliminar o controle mecânico da intensidade, o que reduziu o tempo necessário para a medida e melhorou a estabilidade nas condições experimentais. O método com trem de pulsos proporciona meios de identificar contribuições luminescentes e evitar valores superestimados para a primeira hiperpolarizabilidade. Realizamos testes medindo a molécula de paranitroanilina em vários solventes e verificamos muito boa reprodutibilidade dos valores da literatura. Comparamos os resultados medidos com valores calculados a partir do método de Hartree-Fock e corrigimos o engrandecimento por ressonância utilizando um modelo de dois níveis. A comparação entre valores teóricos e experimentais teve uma diferença média de 15%. Um estudo análogo para a molécula de dianilina não reproduziu os valores experimentais e atribuímos a falha à inaplicabilidade do modelo de dois níveis para medidas no regime ressonante. Também estudamos a primeira hiperpolarizabilidade nas porfirinas TDMImP e TPPS4, sob a forma base livre e formando complexos com Zn2+, Fe3+ e Mn3+. Para a TPPS4 estendemos o estudo para observar os efeitos da protonação na base livre e da formação de oxo dímeros na FeTPPS4 e as alterações causadas pela presença de micelas de CTAB. A comparação direta entre os resultados é dificultada em muitos casos pela diferença no engrandecimento por ressonância. Foi possível verificar que a presença de micelas tem o efeito de diminuir o valor de na H2TPPS4 pH 7. As medidas de HRS em ambiente ácido (pH 4) corroboram com a literatura, indicando que a ocorre desprotonação na presença de micelas. Um estudo teórico e experimental dos três isômeros do aminofenol permitiu analisar os efeitos da posição relativa dos grupos radicais e do comprimento da conjugação sobre a primeira hiperpolarizabilidade. Verificamos que a alteração no caráter doador/aceitador para diferentes posições dos grupos radicais tem influência maior no valor de do que o comprimento da conjugação. Utilizamos compostos com o ligante salen, com grupos laterais etano e DR1 e com ligantes H2, Cu2+, Ni2+ e VO2+, para estudar como os diferentes grupos e complexos refletem diferenças no valor de . Foi possível verificar que diferentemente da absorção linear e da seção de choque para dois fótons, o ligante com grupos radicais DR1 causam um aumento na primeira hiperpolarizabilidade que é muito maior do que a soma das contribuições individuais. Os complexos têm primeiras hiperpolarizabilidades maiores do que o ligante com H2 e a comparação entre os dois grupos com diferentes radicais mostra que existe uma correlação entre os aumentos causados por diferentes complexos. / This thesis reports an extension of the Hyper-Rayleigh scattering technique (HRS) and its application to study the mechanisms that contribute to the molecular first hyperpolarizabilities (). We use a Nd:YAG laser, Q-switched and mode-locked, as pumping beam to excite the samples. The laser delivers 100 ps pulses modulated by a Q-switch envelope, and the output is a pulse sequence which intensities follow the shape of the envelope. This pulse train is used to excite the samples in a Hyper-Rayleigh scattering experiment and the signal for each mode-lock pulse is detected independently. This modality of pumping allows the removal of the mechanical intensity control, therefore reducing measurement time and improved experimental stability. The method with pulse train also provides means to identify luminescent contributions and avoid overestimated values for the first hyperpolarizability. We performed test measurements with para-nitroaniline in several solvents and verified very good reproducibility of literature values. We also compared the measured and calculated values, obtained with the Hartree-Fock method and corrected for resonance enhancement with a two level model. The comparison between theoretical and experimental values results in an average difference of 15%. Similar studies for the dianiline molecule failed to reproduce experimental values and we attributed the failure to the inadequacy of the of the two-level model to correct resonance enhancement. We also studied the first hyperpolarizability of the TDMImP and TPPS4 porphyrins, in the free-base form and in complex with Zn2+, Fe3+ and Mn3+. For TPPS4 we extended the study to observe the protonação effects in the free-base and the formation of oxo dimmers in FeTPPS4 complexes. The comparison between results from different compounds is hindered in most cases by different contributions from resonance enhancement. However, it was possible to verify that the presence of micelles has the effect of reducing the value of on H2TPPS4 pH 7. The HRS measurements in acid environment (pH 4) corroborates with the literature, indicating that desprotonation occurs in the presence of CTAB micelles. A theoretical and experimental study of three aminofenol isomers allowed to verify the effects of the relative positions of radical groups and the conjugation length on the first hyperpolarizability. The results show that in this case the change in the donor/acceptor character for different positions of the radical groups is more important than the increase in one unit in the conjugation length. We also studied compounds with the salen ligant, observing the effects of different lateral groups (ethane and DR1) and different complexes (H2, Cu2+, Ni2+ and VO2+) on the value of . It was possible to verify that, differently than the linear absorption the two-photon cross section, the compounds with DR1 shows an increase in the first hyperpolarizability that is much larger than the sum of the individual contributions of DR1 groups. The metal complexes have larger first hyperpolarizabilities than the ligant and the enhancement produced by different complexes follows the same pattern for both radical groups. Even after the strong increase in produced by the DR1 group, the much weaker effect of the complexes is preserved and measurable.

Thesis (Ph. D.)--University of Hong Kong, 2006. / Title proper from title frame. Also available in printed format.

In this dissertation, I present electronic spectroscopy of a few biologically relevant species and their complexes with solvent molecules in the gas phase using a variety of techniques, including resonantly enhanced multiphoton ionization (REMPI), laser induced fluorescence (LIF), and zero kinetic energy (ZEKE) photoelectron spectroscopy. My work on several methylated uracils and thymines and thymine-water complexes alludes to a new interpretation with regard to the origin of the photostability of our genetic code. I believe that it is the water solvent that stabilizes the photophysical and photochemical behavior of these bases under UV irradiation. For systems that demonstrate vibrational resolution in the first electronically excited state (S₁) and the cationic state, I performed vibrational analysis of both states with the aid of ab initio and density functional calculations. These observations are explained in terms of the structural changes from the ground state to S₁ and further to the cation. To bridge results from the gas phase to the solution phase, I also report studies of supersonically cooled water complexes of the three isomers of aminobenzoic acid. Density functional theory calculations are carried out to identify structural minima of water complexes in the ground state. The solvation mechanism is investigated based on vibrational analysis of the S₁ state of the neutral complex and the shift of ionization thresholds with increasing water content. / Graduation date: 2005

This Ph.D. dissertation is focused on the investigation the structure of nitrile anion containing molecules and how the structure and reactivity of those molecules are affected by solvation and counter ion. A systematic approach was employed in this investigation, beginning with an evaluation of the accuracy of three commonly used model chemistries (Hartree-Fock (HF), Second-order Møller-Plesset perturbation theory (MP2), the Becke three-parameter exchange functional coupled with the nonlocal correlation functional of Lee, Yang, and Parr (B3LYP), all paired with the 6-31+G(d) basis set). A series of complexes of various cations with a number of explicit molecules of tetrahydrofuran (THF) and dimethyl ether (DME) were studied with these model chemistries and the results were compared, where possible, with experimental results. From this work, it was determined that the B3LYP models gave the most accurate results for the complexes in question. This work was then extended to acetonitrile anion containing complexes of solvent and cation. Based on the results of that extension, it was determined that cation size and charge density on the cation were critical factors in determining the structure of the acetonitrile anion molecule and in determining if the anion was metalated at the nitrogen or alpha-carbon position, with larger cations favoring carbon metalation and more significant deformation of the alpha-carbon from the expected sp2 hybridization. The final aspect of this dissertation was the determination of reaction coordinate energy profiles for a pair of substitution reactions involving nitrile anion containing cycloaliphatic molecules. The results of this study showed that, due to steric and kinetic factors, the axial products and transitions states associated with these reactions were favored, and that the degree of preference was kinetically controlled. / Bayer School of Natural and Environmental Sciences / Chemistry and Biochemistry / PhD / Dissertation

This thesis investigates the underlying causes of friction and ine ciency within an internal combustion engine, focusing on the ring-liner conjunction in the vicinity of the power-stroke top dead centre reversal. In such lubricated contacts, friction is the result of the interplay between numerous kinetics, with those at micro- and nano-scale interactions being signi cantly di erent than the ones at larger scales. A modi ed Elrod's cavitation algorithm is developed to determine the microscopic tribological characteristics of the piston ring-liner contact. Predicting lubricant tran- sient behaviour is critical when the inlet reversal leads to thin lms and inherent metal-to-metal interaction. The model clearly shows that cavitation at the trailing edge of the ring-liner contact generated pre-reversal, persists after reversal and pro- motes starvation and depletion of the oil lm. Hence, this will lead to boundary friction. A fractal based boundary friction model is developed for lightly loaded asperity con- tacts, separated by diminishing small lms, usually wetted by a layer of molecules adsorbed to the tips of the asperities. In nano-scale conjunctions, a lubricant layering e ect often takes place due to the smoothness of surfaces, which is governed by the surface and lubricant properties. A molecularly thin layer of lubricant molecules can adhere to the asperities, being the last barrier against direct surface contact. As a result, boundary friction (prevailing in such diminishing gaps) is actually determined by a combination of shearing of a thin adsorbed lm, adhesion of approaching as- perities and their plastic deformation. A model for physio-chemical hydrodynamic mechanism is successfully established, describing the formation of thin adsorbed lms between asperities. This model is e ectively integrated with separately devel- oped models that predict the adhesive and plastic contact of asperities.

Kyoto University (京都大学) / 0048 / 新制・課程博士 / 博士(エネルギー科学) / 甲第19092号 / エネ博第316号 / 新制||エネ||64 / 32043 / 京都大学大学院エネルギー科学研究科エネルギー基礎科学専攻 / (主査)教授 木下 正弘, 教授 森井 孝, 教授 片平 正人 / 学位規則第4条第1項該当

The mechanism by which chiral selectivity takes place is complicated by the surface morphology, the possible involvement of the solvent, and the characteristics of the chiral molecules at the surface. My goal is to model and understand the factors which lead to significant discrimination in the case of three closely related chiral stationary phases: N-(1-phenylethyl)-N’-[3-(triethoxysilyl)propyl]-urea (PEPU), [(3,5-dinitrobenzoyl)-amino]-N-[3-(triethoxysilyl)propyl]-2-phenylacetamide (DNB-phenyglycine), and [(3,5-dinitrobenzoyl)amino]-N-[3-(triethoxysilyl)propyl]-4-methylpentanamide (DNB-leucine). Ab initio calculations are used to develop molecular models of these chiral selectors. These models are employed in molecular dynamics (MD) simulations, which provide the theoretical framework for modelling chiral interfaces in different solvent mixtures. The MD simulations of PEPU interfaces show that, in alcohol/water mixtures, the alcohols form domains at the interface with the hydrophobic portions of the molecule tending to orient towards the surface. This disrupts the water hydrogen bonding networks at the interface and leads to the exclusion of water from the surface region relative to the bulk. The MD simulations of DNB-phenylglycine and DNB-leucine selectors in hexane/2-propanol mixtures demonstrate that the interfaces are distinct both in terms of the selector orientations at the surface and in the number of hydrogen bonds formed with 2-propanol. This occurs despite the structural similarity between these two selectors. The interfaces are also prepared experimentally by attaching the chiral selectors onto oxidized Si(111) samples and AFM tips. In particular, for DNB-phenylglycine and DNB-leucine samples, two synthetic routes have been explored. Using AFM, the morphologies of the resulting chiral interfaces are obtained. X-ray photoelectron spectroscopy and refraction-absorption infrared spectroscopy provide information regarding the relative distribution of the compounds on the surface. Using chemical force microscopy (CFM) measurements, chiral self-selectivity is examined in various solvent mixtures. For PEPU interfaces, the extent of hydrogen bonding at the surface is the dominant contributor to the measured forces. In the case of DNB-phenylglycine and DNB-leucine, CFM measurements of the chiral self-selectivity in 2-propanol demonstrate that chiral discrimination is present in both systems, but larger forces are observed for DNB-phenylglycine, consistent with the molecular dynamics study that shows much weaker solvent interactions with this species. / Thesis (Ph.D, Chemistry) -- Queen's University, 2008-08-14 11:26:37.436

With an increasing demand for renewable energy sources, research efforts on different solar cell technologies are increasing rapidly. The dye-sensitized solar cell (DSC) is one such technology, taking advantage of light absorption in dye molecules. The liquid based DSC contains several interesting and important interfaces, crucial for the understanding and development of the solar cell performance. Examples of such interfaces include dye-semiconductor, electrode-electrolyte and solute-solvent interfaces. Ultimately, complete interfaces with all these components included are of particular interest. One major challenge is to understand the key functions of these systems at an atomic level and one way to achieve this is to use an element specific and surface sensitive tool, such as photoelectron spectroscopy (PES). This thesis describes the use and development of PES for studying interfaces in the DSC. The materials part of the thesis focuses on interfaces in DSCs studied with PES and the methodology development parts focus on methods to use PES for investigations of solvated heterogeneous interfaces of interest for photoelectrochemical systems such as the DSC. More specifically, beginning with standard vacuum techniques, dye molecules bound to a semiconductor surface have been studied in terms of energy level alignment, surface coverage and binding configuration. To increase the understanding of solvation phenomena present in the liquid DSC, liquid jet experiments have been performed in close combination with theoretical quantum calculations. As a step towards an in-situ method to measure a complete, functioning (in operando) solar cell, methodology development and measurements performed with higher sample pressures are described using new high pressure X-ray photoelectron spectroscopy techniques (HPXPS).