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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
141

Estudos estruturais de agonistas de acetilcolina pela espectroscopia de RMN e calculos teoricos / Structural studies of acetylcholine agonists by NMR spectroscopy and theoretical calculations

da Silva, Julio Cesar Araujo, 1974- 13 February 2008 (has links)
Orientador: Roberto Rittner / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Quimica / Made available in DSpace on 2018-08-11T06:54:29Z (GMT). No. of bitstreams: 1 daSilva_JulioCesarAraujo_M.pdf: 2287772 bytes, checksum: ee8613d61a9f9feb9fa6894b5197e36f (MD5) Previous issue date: 2008 / Resumo: Neste trabalho é apresentado o estudo conformacional dos agonistas muscarinicos da acetilcolina (ACh+): carbacol, metacolina e pilocarpina. O estudo baseou-se na análise das constantes de acoplamento 3JHH e nos dados obtidos pelos cálculos teóricos ab initio. O comportamento conformacional destes compostos é descrito principalmente por apenas dois dos seus ângulos diedros. Os resultados dos cálculos teóricos realizados com o nível teórico B3LYP/6- 311+G(d,p), bem como os dados experimentais, apontaram a conformação gauche como a predominante para todos os compostos estudados para o diedro responsável pela atividade farmacológica dos agonistas independente do solvente utilizado. Atribui-se a estabilização da forma gauche a interação eletrostática entre o atomo de nitrogênio positivamente carregado e o átomo de oxigênio da porção éster (OCH2). Os cálculos teóricos mostraram que os conformeros mais estáveis possuem uma distância N+/O menor. Em adição, estudos de NBO mostraram a importância das interações hiperconjugativas sC5H5 s* C6N7 e sC5H5s* O4C5 na maior estabilização dos conformeros gauche. Os conformeros mais estáveis para cada composto sao: aceticolina, TG-; carbacol, AG+; metacolina, TG+; pilocarpina, TG+C / Abstract: This work describes the conformational analysis of muscarine agonists of acetylcholine (ACh+): carbachol, metacholine and pilocarpine. It was performed from the analysis of 3JHH coupling constants and from ab initio theoretical calculations. Their conformational behavior is discussed taking into account the most important dihedral angles. Both the results from theoretical calculations at B3LYP/6-311+G(d,p) as the experimental data indicated that the gauche conformer is predominant, considering the dihedral angle wich is responsible by their pharmacological activity regardless the solvente employed. The stabilization of the gauche conformer was ascribed to the eletrostatic interaction between the positively charged nitrogen atom and the (OCH2) oxygen atom of the ester fragment. This was confirmed by the N+/O smaller distance for the most stable conformers. In addition, NBO data showed the relevant role of sC5H5 s* C6N7 e sC5H5s* O4C5 hyperconjugative interactions of the gauche conformers. The most stable conformers for the above compounds are: : acetycholine, TG-; carbachol, AG+; methacholine, TG+; pilocarpine, TG+C / Mestrado / Quimica Organica / Mestre em Química
142

Estudo teorico do Piroxicam e sua foto-reação, no vacuo e em presença de solventes / Theoretical study of piroxicam and its photo-reaction in vacuum and in presence of solvents

Souza, Kely Ferreira de 22 February 2008 (has links)
Orientador: Rogerio Custodio / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Quimica / Made available in DSpace on 2018-08-11T20:32:26Z (GMT). No. of bitstreams: 1 Souza_KelyFerreirade_M.pdf: 2708513 bytes, checksum: 018efeaf228676a57ca3b884dc55ca80 (MD5) Previous issue date: 2008 / Resumo: Piroxicam é um fármaco com atividade analgésica, antiinflamatória e antipirética de uso muito difundido. Apresenta algumas reações adversas, dentre as quais a possibilidade de foto-sensibilidade cutânea após exposição do paciente à radiação solar. Por este motivo, o fármaco tem sido alvo de inúmeros estudos, mas até os dias atuais não se conhece o mecanismo envolvido na foto-sensibilidade. Com o objetivo de buscar maiores informações sobre o fármaco, o presente trabalho partiu de estudos preliminares tanto da forma ceto quanto da enólica, através do método AM1. Os resultados, em conjunto com dados experimentais, apontaram para o Piroxicam enol como principal tautômero envolvido nos mecanismos de foto-toxicidade. Construiu-se então uma superfície de potencial para o Piroxicam enol, agora com o método DFT/B3LYP/CEP-31G(d,p). Estudaram-se as barreiras de interconversão entre os confôrmeros mais estáveis através do método QST2. Calculou-se o espectro eletrônico destas espécies empregando o método TD-DFT/B3LYP/CEP-31G(d,p) utilizando-se o modelo PCM para inclusão do efeito de solvente. De posse do confôrmero de maior interesse, partiu-se para o estudo de uma proposta de mecanismo obtida da literatura para a reação entre o Piroxicam enol e a molécula de oxigênio no primeiro estado excitado singlete. Partindo-se da otimização em DFT/B3LYP/CEP-31G(d,p) das geometrias das espécies envolvidas no mecanismo, realizou-se a busca por estados de transição entre as mesmas através dos métodos QST2 e QST3. Estruturas de transição entre os caminhos testados foram obtidas, mostrando a possibilidade do mecanismo ocorrer. Os resultados do trabalho apontam, ainda, para um dos confôrmeros como o mais provável de se envolver em foto-reações / Abstract: Piroxicam is a widely used drug with analgesic, antiinflamatory and antipiretic properties. Undesirable side effects are observed in some patients, among which the photosensitivity skin after exposure to solar radiation. For that reason the drug has been widely studied, but until the present days the mechanism involved in the photosensitivity is still unknown. Looking for more information about the drug, preliminary studies were carried out on two tautomers of Piroxicam ¿ ceto and enol structures, using the AM1 method. The calculated and experimental data suggest that Piroxicam Enol is the main tautomer involved in the phototoxicity mechanisms. A new potential surface, now using the DFT/B3LYP/CEP- 31G(d,p) method, was calculated. The interconversion barriers were studied using the QST2 method. The electronic spectrum was calculated with the TD-DFT/B3LYP/CEP- 31G(d,p) method and the solvent effect was investigated applying the PCM model. The predominant conformer was studied in combination with the singlet excited oxygen molecule and a mechanism proposed in the literature was investigated. From the optimized geometries of the species involved in this mechanism, the transition states between them were studied using the QST2 and QST3 methods indicating a feasible reaction path. The results also show one of the conformers as the most important agent responsible by the photochemical sensitivity / Mestrado / Físico-Química / Mestre em Química
143

Dinâmica molecular de celulases : estudos de reconhecimento de substrato e propriedades conformacionais / Molecular dynamics of cellulases : study of substrate recognition and conformational properties

Stankovic, Ivana, 1986- 25 August 2018 (has links)
Orientador: Munir Salomão Skaf / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-25T12:12:30Z (GMT). No. of bitstreams: 1 Stankovic_Ivana_D.pdf: 27307159 bytes, checksum: 42c2cb1272b20efd40baf8597dd8f156 (MD5) Previous issue date: 2014 / Resumo: A degradação enzimática da celulose proveniente de biomassa para a produção de bioetanol é realizada por um conjunto de proteínas denominadas celulases, as quais são produzidas por vários fungos e bactérias. O mecanismo molecular das interações físicas entre as celulases e a celulose é pouco conhecido. Para investigar estas interações, bem como as propriedades conformacionais e dinâmicas, nesta Tese usamos simulações por dinâmica molecular (MD). Abordamos duas celulases: a Endoglucanase 3 de Trichoderma harzianum (ThEG3) e a Endoglucanase de Xanthomas campestris pv. campestris (XccEG). O estudo dos mecanismos de reconhecimento de substrato por ThEG3 que falta o módulo de ligação à celulose (CBM), revela que a ausência de um CBM nesta estrutura é compensada pela presença de resíduos similares aos resíduos típicos de um CBM. O segundo estudo, sobre seletividade da XccEG, explica por que esta enzima catalisa a hidrólise somente de oligossacarídeos de cadeia igual ou maior que quatro unidades. Nossas simulações indicam que os quatro subsítios característicos da fenda de ligação ao substrato da XccEG precisam ser simultaneamente estabilizados pelas interações com substrato para promover uma ligação efetiva substrato-enzima. No terceiro estudo, investigamos as propriedades mecânicas do linker entre o domínio catalítico (CCD) e o CBM desta mesma enzima, composto por blocos de Thr e Pro, utilizando a técnica de replica exchange MD. Nossos resultados sugerem as bases moleculares da maior rigidez deste linker em comparação ao linker de celobiohidrolases II de Trichoderma reesei. Por fim, adaptamos o método de MDFF (flexible fitting MD) para gerar modelos de estrutura terciária a partir de dados de SAXS e o aplicamos para criar um modelo da estrutura intacta CCD-linker-CBM de XccEG / Abstract: The enzymatic degradation of the cellulose for the production of bioethanol is performed by a group of proteins called cellulases which are produced by various fungi and bacteria. The molecular mechanism of the physical interactions between the cellulases and a cellulose is little-known. In this work we use molecular dynamics simulations (MD) to investigate these interactions as well as conformational and dynamic properties. We have studied two cellulases: the endoglucanase 3 from Trichoderma harzianum (ThEG3) and the endoglucanase from Xanthomas campestris pv. campestris (XccEG). The study of the mechanisms of substrate recognition by ThEG3 which lacks the cellulose binding module (CBM) shows that the absence of a CBM in this structure is compensated by the presence of residues similar to typical CBM residues. The second study, on the selectivity of XccEG, explains why this enzyme catalyses only the hydrolysis of four or more units long oligosaccharides. Our simulations indicate that the four characteristic subsites of the substrate binding cleft of XccEG need to be simultaneously stabilized by the interactions with the substrate to provide an effective enzyme-substrate binding. In the third study, we investigated the mechanical properties of the linker between the catalytic domain (CCD) and CBM of the same enzyme, composed of Thr-Pro blocks, using the replica exchange molecular dynamics (REMD). Our results suggest the molecular basis of greater rigidity of this linker in comparison to the linker of cellobiohydrolase 2 from Trichoderma reesei. Finally, we have adapted the method of Molecular Dynamics Flexible Fitting (MDFF) to generate tertiary structure models from SAXS data and applied it to create a model of the intact structure CCD-linker-CBM of the XccEG / Doutorado / Físico-Química / Doutora em Ciências
144

Interações estereoeletrônicas na preferência conformacional de 3-halo-2-hidroxi-tetraidropirano (HALO = F, Cl, Br e I) por cálculos teóricos e espectroscopia de RMN / Stereoelectronic interactions on the conformational preferences of 3-halo-2-hydroxytetrahydropyrans (halo = F, Cl, Br and I) through theoretical calculations and NMR spectroscopy

Barbosa, Thaís Mendonça, 1988- 25 August 2018 (has links)
Orientador: Roberto Rittner Neto / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-25T19:37:30Z (GMT). No. of bitstreams: 1 Barbosa_ThaisMendonca_M.pdf: 9099514 bytes, checksum: b19c5546ad282ce6721161bf8ee4df26 (MD5) Previous issue date: 2014 / Resumo: Este trabalho cujo título é: INTERAÇÕES ESTEREOELETRÔNICAS E SEUS EFEITOS NA PREFERÊNCIA CONFORMACIONAL DE 3-HALO-2-HIDROXI-TETRAIDROPIRANO (HALO = F, Cl, Br, e I) tem como objetivo avaliar o efeito das interações estereoeletrônicas na estabilidade conformacional das haloidrinas derivadas do pirano. Os estudos foram realizados através da espectroscopia de Ressonância Magnética Nuclear, apoiadas por cálculos teóricos da estrutura eletrônica. Realizou-se a síntese dos compostos propostos e, após a sua purificação, foram obtidos os espectros de RMN de 1H, 13C, HSQC, COSY, NOESY e TOCSY para caracterização dos compostos. Os cálculos teóricos foram efetuados com a teoria do funcional de densidade (DFT), empregando o funcional híbrido M062X, e teoria ab initio com o método MP2, utilizando as funções de base do tipo aug-cc-pVTZ, disponível no pacote Gaussian09, para a determinação das energias e geometrias dos confômeros mais estáveis na fase isolada. Realizou-se ainda um estudo da estrutura eletrônica dos confôrmeros mais estáveis, através da análise da função de onda pela aproximação NBO; QTAIM and NCI, para verificar quais interações estereoeletrônicas são responsáveis pela estabilidade conformacional. A análise conjunta de todos esses dados permitiu verificar quais são os fatores responsáveis pelo equilíbrio conformacional dos compostos em estudo / Abstract: This work titled: STEREOELECTRONIC INTERACTIONS AND THEIR EFFECTS IN THE CONFORMATIONAL PREFERENCES OF 3-HALO-2-HYDROXY-TETRAHYDROPYRAN (HALO = F, Cl, Br and I) aims to evaluate the effect of stereoelectronic interactions on the conformational stability of halohydrins derived from pyran (3-halo-2-hydroxy-tetrahydropyran halo = F, Cl, Br and I). The study was performed through NMR spectroscopy, supported by electronic structure calculations. The compounds were synthesized, purified and identified by their 1H, 13C, selective TOCSY NMR spectra as well as by their HSQC, COSY and NOESY contour map. The theoretical calculations were performed through Density Functional Theory (DFT) applying B3LYP hybrid functional and also ab inito theory was used applying MP2 method, for both theory aug-cc-pVTZ basis set were used to obtain the geometry and energy for the most stable conformers for the isolated molecule. NBO (natural bond orbitals), QTAIM (Quantum Theory of Atoms in Molecules) and NCI (Non-Covalent Interactions) analysis were applied to allow us to find out which stereoelectronic interactions are responsible by conformational stability. The combined analyses of all these data have shown which are the factors responsible for the conformational preferences of the compounds under study / Mestrado / Quimica Organica / Mestra em Química
145

Estudos conformacionais pela espectroscopia no infravermelho e calculos teoricos de alguns compostos heterociclicos 2-substituidos / Infrared and theoretical investigation of conformational isomerism in some 2-substituted heterocyclic compounds

Mesquita, Alexandre Pinto 24 February 2005 (has links)
Orientador: Roberto Rittner / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Quimica / Made available in DSpace on 2018-08-04T14:36:06Z (GMT). No. of bitstreams: 1 Mesquita_AlexandrePinto_M.pdf: 3953195 bytes, checksum: 418e539bcacd86a111fd5ab90fb668d9 (MD5) Previous issue date: 2005 / Mestrado / Quimica Organica / Mestre em Química
146

Analise conformacional por ressonância magnética nuclear e cálculos teóricos em anéis de cinco membros : 2-Halociclopentanonas / Nuclear magnetic resonance and theoretical investigation on the conformational analysis of five-membered ring systems : 2-Halocyclopentanones

Martins, Carina Rabelo 28 February 2005 (has links)
Orientador: Roberto Rittner Neto / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Quimica / Made available in DSpace on 2018-08-04T16:43:04Z (GMT). No. of bitstreams: 1 Martins_CarinaRabelo_M.pdf: 2440804 bytes, checksum: 5902fcc19589dcc81792e0806f7ae9f6 (MD5) Previous issue date: 2005 / Resumo: Este trabalho apresenta estudos sobre o isomerismo conformacional das 2-halociclopentanonas (halo= cloro e bromo) utilizando a constante de acoplamento JHH, cálculos teóricos e a teoria de solvatação. Foi realizada a otimização das geometrias e das energias dos confôrmeros mais estáveis na forma C2 (meia cadeira) dos diferentes compostos, utilizando o programa Gaussian 98, sendo que a conformação mais estável obtida no vácuo foi a pseudo-axial para todos os compostos estudados. Os dados experimentais de JHH dos derivados clorado e bromado, juntamente com o resultado da otimização das geometrias e das energias nos níveis B3LYP e MP2 foram tratados computacionalmente pelos programas Models e BESTFIT, o que permitiu a análise do equilíbrio conformacional destes compostos em diferentes solventes. Os dados obtidos apontam para uma estabilização do confôrmero pseudo-equatorial (de maior momento de dipolo) de acordo com o aumento da polaridade do solvente, conforme o esperado. Estes resultados foram comparados aos resultados obtidos pela análise dos espectros de infravermelho, cujos resultados também mostram a estabilização do confôrmero pseudo-equatorial com o aumento da polaridade do meio. / Abstract: The present work reports an NMR metthod using the variation of the JHH coupling constants with the solvents, togethr with theoretical calculations and solvation theory for the conformational analysis of 2-halocyclopentanones (halo = chlorine and bromine). The results trom Ab initio calculations, performed with GAUSSIAN 98 program using DFT/B3LYP and MP2, showed that the theories for the chlorine and bromine-derivatives. The pseudo-axial half-chair (C2) form is stable, in vapour phase, for both compounds. The H NMR spectra were obtained in solvents of various polarities. The essential parameters for the solvation energy calculations were obtained through MODELS program using the optimized geometries trom Gaussian. The best values of intrinsic coupling constants tor each conformer and the experimental energy difference, in the vapour, phase were obtained through BESTFIT program, using the experimental coupling constants and data from theoretical calculations. These gave that the pseudo-equatorial conformer is stabilized with the increase in the solvent polarity. The results were complemented with data from infrared spectroscopy, which are in complete agreement with theoretical data. / Mestrado / Quimica Organica / Mestre em Química
147

Etude structurale par RMN de la protéine TolAIII impliquée dans le mécanisme d'infection de Vibrio cholerae par le bactériophage CTXphi / NMR Structural study of TolAIII protein involved in the infection of Vibrio cholerae by CTXphi bacteriophage

Navarro, Romain 02 December 2016 (has links)
Vibrio cholerae acquiert les gènes de la toxine cholérique suite à l’infection par le phage CTXphi et devient par la suite une bactérie pathogène. L'infection se déroule en deux étapes : une interaction entre le pilus TCP et le domaine pIIIN2ctx, puis la formation du complexe TolAIIIV.c/pIIIN1ctx. Cette seconde étape est l’étape limitante de l’infection. L’objectif général de ma thèse a été d’étudier les forces motrices associées à cette étape.1) J’ai étudié les mécanismes moléculaires associés à la spécificité phage/bactérie en ciblant les interactions électrostatiques et le feuillet intermoléculaire par RMN et double hybride bactérien.2) J’ai résolu la structure de TolAIIIV.c libre par RMN. La comparaison des structures de cette protéine à l’état libre et liée ont permis de mettre en évidence un changement conformationnel et de proposer un mécanisme moléculaire d’ajustement induit. De plus, l’étude de la flexibilité de la protéine par RMN à haute pression (HP) a montré l’importance de la cavité interne de la protéine TolAIII pour favoriser l’ajustement induit lors de la formation du complexe TolAIIIV.c/pIIIN1CTX.3) J’ai vérifié si l’ajustement induit observé précédemment était lié à la présence de cette cavité d’une manière générale chez les protéines TolAIII. Une étude de dispersion de relaxation et de RMN à HP de la protéine TolAIIIE.c a permis de vérifier l’importance de cette cavité pour le mécanisme d’ajustement induit essentiel à cette famille de protéine. De plus, nous avons corrélée la flexibilité particulière de la protéine TolAIIIE.c à la présence d’une boucle qui lui confère une certaines flexibilité nécessaires pour interagir avec plusieurs partenaires. / Vibrio cholerae becomes a pathogen after CTXphi phage infection. The phagic infection is a wo step mechanism: first TCP pilus binds to pIIIN2ctx, then TolAIIIV.c binds to pIIIN1ctx. The second step is essential for the acquisition of genes of cholera toxins leading to cholera disease. The main goal of my thesis is to study the driving forces associated to the phage infection.First, I studied the molecular mechanism associated to phage/bacteria specificity targeting electrostatic bonds and hydrophobic interactions within the intermolecular sheet. These experiments use NMR and bacterial two hybrids methods. Our results show that electrostatic bonds are essential for the complex formation.Second, I solved the solution structure of TolAIIIV.c using NMR. The comparison of the structures of free and bound states of TolAIIIV.c, shows an associate conformational change and lead us to propose a model for the molecular mechanism of the induced fit. Then the study of the TolAIII flexibility, using high pressure NMR shows the importance of TolAIII cavity to promote the induced fit during TolAIIIV.c/pIIIN1ctx complex formation.Finally, we wanted to show if the induced fit is correlated to the presence of cavity in TolAIII family. A study using NMR relaxation dispersion and high-pressure NMR experiments on TolAIIIE.c shows the importance of this cavity for the induced fit. The presence of a loop at the top of the N-terminal helix in TolAIIIE.c leads to the protein to have several conformations necessary to interact with many partners.
148

Análise conformacional de alguns ésteres metílicos de aminoácidos e seus N-acetil-derivados / Conformational analysis of some methyl esters of amino acids and their N-acetyl-derivatives

Duarte, Claudimar Junker, 1984- 03 May 2015 (has links)
Orientador: Roberto Rittner Neto / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Química / Made available in DSpace on 2018-08-27T10:22:25Z (GMT). No. of bitstreams: 1 Duarte_ClaudimarJunker_D.pdf: 13121295 bytes, checksum: 3401d9f1581d3385c70c6c859f152c76 (MD5) Previous issue date: 2015 / Resumo: Neste trabalho, o equilíbrio conformacional de alguns ésteres metílicos de aminoácidos não acetilados (L-Serina, L-Treonina e L-Triptofano) e N-acetilados (Glicina, L-Alanina, L-Serina, L-Treonina e L-Triptofano) foi avaliado através de cálculos teóricos e técnicas experimentais de espectroscopia no Infravermelho e de RMN. A metodologia aplicada baseou-se em RMN de 1H (através do comportamento da constante de acoplamento spin-spin 3JHH) e deconvolução analítica do espectro de infravermelho na região de estiramento da carbonila. Os resultados obtidos foram utilizados para determinar a variação populacional de cada derivado de aminoácido em vários solventes. Além disso, cálculos teóricos em fase isolada e também considerando o efeito do solvente foram realizados para determinar os valores de 3JHH e a frequência de estiramento C=O. Os resultados calculados estão em boa concordância com os valores experimentais e proporcionam informações sobre o comportamento conformacional induzido por cada solvente. Adicionalmente, a análise dos Orbitais Naturais de Ligação e a Teoria Quântica dos Átomos em Moléculas foram empregadas para investigar a importância de efeitos clássicos e não clássicos sobre o equilíbrio conformacional dos sistemas supracitados. Diferente de várias propostas da literatura, foi demonstrado que efeitos estéricos e de hiperconjugação são interações importantes para o equilíbrio conformacional para o equilíbrio conformacional dos diversos derivados de aminoácidos avaliados, enquanto que ligações de hidrogênio apresentam contribuição secundária / Abstract: In this work, the conformational equilibrium of some methyl esters of amino acids non-acetylated (L-Serine, L-Threonine and L-Tryptophan) e N-acetylated (Glycine, L-Alanine, L-Serine, L-Threonine and L-Tryptophan) was evaluated by theoretical calculations and Infrared and 1H NMR spectroscopies. The applied methodology was based on the 1H NMR data (through the behavior of the 3JHH spin spin coupling constant) and analytical deconvolution of infrared spectra on the C=O stretching region. The obtained results were used to determine the populational variation of each amino acid derivative in several solvents. In addition, theoretical calculations in isolated phase and taking into account the solvent effect were carried out in order to obtain the values of 3JHH and C=O stretching vibration. The calculated results are in good agreement with the experimental data and provide insights into the conformational behavior induced by each solvent. Additionally, Natural Bond Orbital analysis and the Quantum Theory Atoms In Molecules were employed to investigate the importance of classic and non-classic effects over the conformational isomerism of aforementioned systems. In disagreement of several publications in the literature, it was found that steric effect and hyperconjugation are interactions important to conformational preferences of all amino acid derivatives evaluated whereas H-bonding plays a secondary role / Doutorado / Quimica Organica / Doutor em Ciências
149

Structure and function of the disordered regions within translesion synthesis DNA polymerases

Powers, Kyle Thomas 01 December 2018 (has links)
Normal DNA replication is blocked by DNA damage in the template strand. Translesion synthesis is a major pathway for overcoming these replication blocks. In this process, multiple non-classical DNA polymerases form a complex at the stalled replication fork called the mutasome. This complex is structurally organized by the replication accessory factor PCNA and the non-classical DNA polymerase Rev1. One of the non-classical DNA polymerases within the mutasome then catalyzes replication through the damage. Each non-classical DNA polymerase has one or more cognate lesions, which the enzyme bypasses with high accuracy and efficiency. Thus, the accuracy and efficiency of translesion synthesis depends on which non-classical DNA polymerase within the mutasome is chosen to bypass the damage. In this thesis, I discuss how the most appropriate polymerase is chosen. In so doing, I examine the components of the mutasome; the structural motifs that mediate the protein interactions in the mutasome; the methods used to study translesion synthesis; the definition of a cognate lesion; the intrinsically disordered regions that tether the polymerases to PCNA and to one another; the multiple architectures that the mutasome can adopt, such as PCNA tool belts and Rev1 bridges; and the kinetic selection model in which the most appropriate polymerase is chosen via a competition among the multiple polymerases within the mutasome. Taken together, this thesis provides and inclusive review of the current state of what is known about translesion synthesis with conclusions at its end suggesting what major questions remain and ideas of how to answer them.
150

Synthesis of Peropyrene and Tetracene Derivatives for Photochemical Applications

Rodríguez López, Marco Tulio 05 1900 (has links)
A novel route for the synthesis of the polycyclic aromatic hydrocarbon peropyrene (Pp) is reported along with the efforts to synthesize derivatives of Pp, 2,2′- and 5,5′-linked tetracene dimers as candidates for study as singlet fission materials in photovoltaic devices. Peropyrene was synthesized by the McMurry coupling conditions from phenalenone and low-valent titanium species. The crystal structure of Pp is formed by π-stacked molecular pairs in a herringbone arrangement. The direct functionalization of Pp was studied, and several indirect methods for the functionalization of Pp via phenalenone derivatives are reported. Nucleophilicly dependent, regioselective Michael addition pathways for phenalenone are described. Phenalenone forms a nucleophilic complex with bispinacolatodiboron and yields chiral 3,3′-linked phenalenone dimers and a bicyclo[3.2.1]octane derivative product of an unusual 3,4 addition. An active complex product of phenalenone and (dimethylphenylsilyl)boronic acid pinacolic ester forms Pp directly. The synthesis of 2,2′- and 5,5′-linked tetracene dimers led to the study of the reduction of 1-arylprop-2-yn-1-ol derivatives via TFA-catalyzed hydride transfer from triethylsilane. Substrates with terminal and TMS-protected alkynes showed silane exchange upon reduction. A TMS-protected, terminal alkyne became triethylsilyl-protected by about 50% whereas only triethylsilyl-protected, terminal alkyne was observed from the reduction of an unprotected, terminal alkyne. A new conformational polymorph of 1,4-bis(triisopropylsilyl)buta-1,3-diyne is reported. Five other rotamers are studied by density functional theory as possible candidates of conformational polymorphism by the analysis of torsional strain energies. The relative stabilities and interconversion equilibria of the seven conformational isomers are studied.

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