Submitted by ANA KARLA PEREIRA RODRIGUES (anakarla_@hotmail.com) on 2017-08-01T13:42:01Z No. of bitstreams: 1 arquivototal.pdf: 3885187 bytes, checksum: 43a97495626de95064ede3adad23bcd9 (MD5) / Made available in DSpace on 2017-08-01T13:42:01Z (GMT). No. of bitstreams: 1 arquivototal.pdf: 3885187 bytes, checksum: 43a97495626de95064ede3adad23bcd9 (MD5) Previous issue date: 2016-02-23 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / In this work we performed ωB97XD, CAM-B3LYP, CASSCF, MR-CISD, MRCISD+ Q and NEVPT2 calculations. The basis sets aug-cc-pVDZ and cc-pVTZ were used to assess the stability of certain neutral and protonated N-nitrosamines in the ground and excited states. In addition, we analyzed the effect of methylation on proton transfer. The initial proposal was to characterize the stationary points and the potential energy curves in the ground and excited state, in order to suggest a strategy that results in lower computational demand to be applied in larger systems (cyclic and bicyclic N-nitrosamines). The results indicate that the methodology MR-CISD/cc-pVTZ//MR-CISD/aug-cc-pVDZ may be appropriate to study the N-nitrosamines. The used functionals provided good descriptions to vertical excitation energy, but were not capable to represent the states correctly to dissociation curves. MR-CID+Q/cc-pVTZ results for the system (CH3)2NNO protonated indicate that protonation is more favorable for NDMA_1A, increasing energy in 17.5 kcal mol-1, and that the methylation significantly alter the intramolecular proton transfer barriers. With the aim to find a methodology with lower computational cost, use a reference wave function CASSCF (12, 9) at the level NEVPT2/cc-pVTZ was used study the neutral NDMA and results were consistent with both the theoretical and experimental parameters in the literature. For studies involving larger systems, for example, cyclic and bicyclic N-nitrosamines, NEVPT2 may be used, since it is completely paralyzed, and involves the use of a CASSCF larger than CAS (14, 10), which is a fundamental characteristic to study larger systems. / Neste trabalho foram realizados cálculos ωB97XD, CAM-B3LYP, CASSCF, MRCISD, MR-CISD+Q e NEVPT2. Os conjuntos de base aug-cc-pVDZ e cc-pVTZ foram usados para avaliar a estabilidade de algumas N-nitrosaminas neutras e protonadas nos estados fundamental e excitado. Além disso, foi analisado o efeito da metilação nas transferências de próton. A proposta inicial foi caracterizar os pontos estacionários, as curvas de energia potencial no estado fundamental e excitado, com a finalidade de sugerir uma estratégia que resulte em menor demanda computacional para ser aplicada em sistemas maiores (N-nitrosaminas cíclicas e bicíclicas). Os resultados indicaram que a metodologia MR-CISD/cc-pVTZ//MR-CISD/aug-cc-pVDZ pode ser adequada para estudar as N-nitrosaminas. Os funcionais utilizados forneceram boas descrições para a energia de excitação vertical, mas para as curvas de dissociação não foram capazes de representar os estados corretamente. Os resultados com MR-CISD+Q/cc-pVTZ para o sistema (CH3)2NNO protonado indicam que a protonação é mais favorável para NDMA_1A, aumentando a energia em 17,5 kcal mol-1, e que a metilação altera significativamente as barreiras de transferência de próton intramoleculares. Com a proposta de encontrar uma metodologia com menor custo computacional, utilizou-se uma função de onda de referência CASSCF (12, 9) a nível NEVPT2/cc-pVTZ para estudar a NDMA neutra e os resultados foram compatíveis com os parâmetros experimentais e teóricos existentes na literatura. Para estudos envolvendo sistemas maiores, por exemplo, N-nitrosaminas cíclicas e bicíclicas, NEVPT2 poderá ser usado, uma vez que está totalmente paralelizado e comporta a utilização de um CASSCF maior que CAS (14, 10), característica fundamental para estudar sistemas maiores.

Kyoto University (京都大学) / 0048 / 新制・課程博士 / 博士(工学) / 甲第17595号 / 工博第3754号 / 新制||工||1572(附属図書館) / 30361 / 京都大学大学院工学研究科高分子化学専攻 / (主査)教授 伊藤 紳三郎, 教授 赤木 和夫, 教授 金谷 利治 / 学位規則第4条第1項該当

<div> <div> <div> <p>The Effective Fragment Potential (EFP) is a quantum-mechanical based model potential for accurate calculations of non-covalent interactions between molecules. It can be coupled with ab initio methods in so-called QM/EFP models to explore the electronic properties of extended molecular systems by providing rigorous description of surrounding environments. The current EFP formulation is, however, not well suited for large-scale simulations due to its inherent limitation of representing effective fragments as rigid structures. The process of utilizing EFP method for the molecular systems with flexible degrees of freedom entails multiple sets of parameter calculations requiring intensive computational resources. This work presents development of the EFP method for describing flexible molecular systems, so-called Flexible EFP. To validate the applicability of the Flexible EFP method, extensive benchmark studies on the amino acid interactions, binding energies, and electronic properties of flavin chromophore of the cryptochrome protein have been demonstrated. In addition to methodological developments, excitonic properties of the Fenna-Matthews-Olson (FMO) photosynthetic pigment-protein complex are explored. In biological systems where intermolecular interactions span a broad range from non-polar to polar and ionic forces, EFP is superior to the classical force fields. In the present study, we demonstrate excellent performance of the QM/EFP model for predicting excitonic interactions and spectral characteristics of the FMO wildtype complex. We characterize the key factors for accurate modeling of electronic properties of bacteriochlrophyll a (BChl a) photosynthetic pigments and suggest a robust computational protocol that can be applied for modeling other photosynthetic systems. Developed computational procedures were also successfully utilized to elucidate photostability and triplet dynamics in the FMO complex and spectroscopic effects of single-point mutagenesis in FMO. A combination of polarizable EFP molecular dynamics and QM/EFP vibrational frequency calculations were also applied to understanding and interpreting structures and Raman spectroscopy of tert-butyl alcohol solutions. </p> </div> </div> </div>

A series of picosecond excite-probe experiments was performed on various concentrations of aqueous and ethanolic solutions of rhodamine B in order to determine the existence of dimerization in those solutions. The goals of the research presented in this dissertation were twofold. Initially, various techniques of time-resolved spectroscopy were to be employed to further characterize the ground and excited-state molecular properties of the aqueous RB dimer. The information obtained, and the techniques developed in that study would then be utilized in an effort to secure evidence which would support or refute the claims of rhodamine B dimerization in an ethanolic solution.

Light or photons can excite electrons in a molecule, leading to creation of electronically excited states. Such processes are ubiquitous in nature, such as, vision, photo-protection of DNA/RNA nucleobases, light harvesting, energy and charger transfer etc. This photoexcitation induces nuclear motion on the excited states, leading the excess energy to dissipate either non-radiatively via internal conversion back down to the ground state, isomerization, and dissociation, or radiatively via fluorescence and phosphorescence. In this dissertation, we investigate the non-radiative processes in organic chromophores that ensue in an ultrafast manner, mediated via conical intersections (CoIn). Description of such excited state processes generally require multi-reference treatment because of quasi-degeneracy near CoIns. Hence, most insight about these processes is typically gained by constructing potential energy surface (PES) using multi-reference electronic structure methods along important reaction coordinates. Nonetheless, the aforementioned static treatment fails to provide any dynamical information, such as, excited state lifetime, state populations, branching ratio, quantum yield etc. In this dissertation, we have gone beyond the static treatment by undertaking computationally expensive non-adiabatic excited state molecular dynamics simulations employing trajectory surface hopping (TSH) methodology on PESs created on-the-fly using multi-reference electronic structure methods. This allows us to compare theoretical results to experimental observables, when possible, strengthening the explanations underlying those processes. Our goal is to examine the effect of structure, and of electronic structure methods on the excited state dynamics. We have examined the non-adiabatic excited state dynamics of cis,cis-1,3-cyclooctadiene (cc-COD), a cyclic diene, in an effort to systematically compare and contrast the dynamics of cc-COD to that of other well studied conjugated molecules. Such exploration is very significant, since the majority of the molecules involved in natural photoexcited processes, include an ethylenic double bond or alternating double bonds creating conjugation. Our calculations have revealed ultrafast sub-ps decay for cc-COD, and have illustrated that the internal conversion dynamics is facilitated by CoIns, dominated by twisting of one of the double bonds and pyramidalization of one of the carbons of that double bond, similar to trans-1,3-butadiene and unlike 1,3-cyclohexadiene (CHD). Our high-level electronic structure calculations have also explained the features in the experimental time-resolved photoelectron spectrum of cc-COD. Another molecule of biological importance, uracil, was also investigated using TSH simulations, by systematically increasing dynamical correlation. We have found that the inclusion of dynamical correlation for uracil leads to an almost barrierless PES on S2, leading to a faster decay and no population trap on this state. Uracil also contains a double bond and the simulations have revealed that the ultrafast relaxation is dominated by an ethylenic twist and pyramidalization of a carbon of that bond, increasing importance of such nuclear motion in photoexcited molecular dynamics. A comparison of the molecules studied have illustrated that the rigid molecules, such as uracil, CHD, have a very local CoIn seam space, whereas cc-COD, which is flexible having many low frequency degrees of freedom, has a non-local or extended CoIn seam space. Overall, the work performed in this dissertation, elucidates the significance of structure and conjugation, in the photoinduced coupled electron-nuclear dynamics in organic molecules. / Chemistry

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Neste trabalho de Mestrado, foram feitos estudos do comportamento fotofísico da fisetina em diversos solventes através de medidas de absorção de luz UV-Visível, fluorescência estática e resolvida no tempo e da interação entre fisetina (3,3\',4\',7-tetrahidroxiflavona) e 7-hidroxiflavona com ciclodextrinas ( beta e gama) (CDs) através de experimentos de absorção de luz UV-Visível, sinal induzido de dicroísmo circular, fluorescência estática e resolvida no tempo, anisotropia de estado estacionário e RMN de 1H, focando a dependência destas medidas em função da temperatura e do pH. Os resultados experimentais foram comparados com estudos mecânico-quânticos baseados no modelo semi-empírico SAM1 (AMPAC), e nos funcionais B3LYP e MPW1PW91, da Teoria do Funcional de Densidade, empregando os conjuntos de funções de base 6-311G* e 3-21G**. Os estudos da fisetina em diferentes solventes próticos e apróticos mostraram que a fluorescência da sonda é fortemente dependente do solvente. Resultados experimentais indicam a formação de complexos de inclusão entre as CDs e os flavonóides acima. A fisetina com ?-CD forma complexo de estequiometria 1:1 nos meios neutro/ácido e básico, cujos valores de constante de complexação são 900 +- 100 +_ 240 +_ 90 (L/mol), respectivamente. Os dados teóricos evidenciaram que a inclusão da fisetina na beta-CD ocorre preferencialmente pelo anel fenila. O complexo com a gama-CD apresenta estequiometria de 1:1 em meio ácido/neutro e de 1:2 em meio básico, com constantes de complexação de 94 +- 30 e 130 +- 10 (L/mol), respectivamente. Os estudos com a 7-hidroxiflavona revelaram que somente ocorre a formação de complexos com a beta-CD de estequiometria 1:1 e não há dependência do pH. As constantes de complexação obtidas nos meios ácido/neutro e básico são similares, 1430 +-- 510 e 1220 +- 165 L/mol, respectivamente. / In this work, the photophysics of fisetin (3,3\',4\',7-tetrahydroxyflavone) in several solvents was studied through UV-vis absorption spectra, steady-state and time-resolved fluorescence measurements. The interaction between fisetin and 7-hydroxyflavone and cyclodextrins (b- e g-) (CDs) was also investigated by UV-vis absorption spectra, induced signal of circular dichroism, steady-state and time-resolved fluorescence, steady-state anisotropy, and 1H NMR, with dependence on pH and temperature. Some experimental data were compared with quantum-mechanics studies based on the SAM1 (AMPAC) semi-empirical model, as well as with the B3LYP and MPW1PW91 functional models from the Density Functional Theory using the 6-311G* and 3-21G* basis sets. The study of the photophysics of fisetin in protic and aprotic solvents showed a complex behavior and a strong dependence on the solvent. The occurrence of many equilibria between the possible structures of fisetin, e.g. the normal, a few deprotonated ones, and the tautomer due to the excited state intramolecular proton transfer can be responsible for the complex analyses of these experimental data. The spectroscopic measurements show that, at pH 4.0 and 6.5, the complex fisetin - b-CD is formed in a Fis:b-CD 1:1 stoichiometry and an equilibrium constant (K) of 900 ± 100 L/mol. In basic medium (pH 11.5), K decreases to 240 ± 90 L/mol. Molecular modeling points out that the inclusion complex is formed preferentially via entry of the fisetin phenyl group into b-CD. On the other hand, the fisetin - g-CD has a stoichiometry of 1:1 in acid/neutral solutions and of 1:2 in basic conditions. The K values are 94 ± 30 e 130 ± 10 (L/mol), respectively. The 7-hydroxyflavone can only form inclusion complexes with b-CD. The stoichiometry is 1:1 and there is no dependence on pH. Both equilibrium constants determined either in acid or basic medium is very similar to each other, 1430 ± 510, and 1220 ± 165 L/mol, respectively. For this reason, we suppose that the inclusion of this compound into b-CD is also through the phenyl ring of the flavonoid.