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Thesis (Ph. D.) --Memorial University of Newfoundland, 1997. / Restricted until November 1998. Bibliography: leaves 264-281.

Thesis (Ph. D.)--University of Chicago, Department of Chemistry, December 2002. / Includes bibliographical references. Also available on the Internet.

Thesis (Ph. D.)--University of Hong Kong, 2006. / Also available online.

Le développement d'un nouveau médicament est un processus long et coûteux. Entre la détermination d'une cible thérapeutique et la mise sur le marché d'un nouveau médicament, plus de dix ans de recherche sont nécessaires pour un coût supérieur à un milliard d'euros.L'accélération de ce processus et la réduction de son coût restent un enjeu majeur. Pour y parvenir, les simulations numériques, peu coûteuses et rapides, sont massivement utilisées. Malgré cela, elles restent limitées, en partie à cause de la quantité très importante de molécules de solvant à considérer. La théorie de la fonctionnelle de la densité moléculaire permet d'étudier la solvatation de composés de n'importe quelle taille et de n'importe quelle forme. Elle prédit en quelques secondes seulement à la fois l'énergie libre de solvatation et une carte détaillée de la densité d'équilibre autour de ce soluté. Ces grandeurs étant à la base de nombreux autres calculs utilisés par l'industrie pharmaceutique, la MDFT ouvre donc une autre voie d'optimisation de ces process. Cette thèse consiste à effectuer le premier pas vers l'ensemble de ces applications. Pour cela, nous avons adapté la théorie ainsi que le code associé avant de l'appliquer à des systèmes biologiques. / Drug development is time and cost-consuming: It takes in average 10 years and 1 billion euros to move from a therapeutic target to a new drug. To speed up this process and reduce its cost, numerical simulation are massively used. Nevertheless, they remain limited, one reason of which is the huge amount of solvent molecules to consider. The molecular density functional theory is a liquid state theory that allows the study of the solvation thermodynamics of solutes of arbitrary shape. MDFT predicts, in few seconds only, the free energy of solvation and the solvent profils. These parameters are at the heart of many others calculation used by the pharmaceutical industry. This thesis is the first step towards these applications. For that purpose, we adapted the theory as well as the associated code to this new target, then applied them to system of biological interest.

Doctor of Philosophy / Department of Chemistry / Paul E. Smith / Kirkwood Buff (KB) theory is one of the most important theories of solutions. The theory can relate integrals over radial (pair) distribution functions (rdfs) in the grand canonical ensemble to common thermodynamic properties. An inversion of the KB theory has been proposed by Ben-Naim and this has led to the wide spread popularity of KB theory. The idea of the KB inversion procedure is to calculate KB integrals from available thermodynamic properties. The KB theory can be used to validate the force field (ff) parameters used in molecular dynamics simulations. We have tested a series of small molecule ff parameters using KB theory that consists of both atom centered partial atomic charges and extra charge sites. The results indicate that using extra charge sites, derived from QM calculations, does not necessarily provide a more accurate representation of condensed phase properties. A further study aimed at an ongoing project of deriving new biomolecular ff parameters based on KB theory, has developed ff parameters for esters in order to represent the ester conjugation of the phospholipid molecule. The models were further tested against experimental properties. Preferential solvation (PS) is an important concept of solution mixtures that can be described using KB theory. The difference between local composition and bulk composition in solution mixtures leads to the concept of PS. A generalized explanation based on local mole fractions was derived by Ben-Naim using KB theory. However, the original expressions have been modified over years. Here, we propose a new approach based on local volume fractions to explore PS in binary and ternary solution mixtures. Experimental and simulation data were used to examine different approaches to PS. A relationship between the rdf and the triplet distribution function can be obtained using the Kirkwood Superposition Approximation (KSA). A combination of Fluctuation Solution Theory and experimental rdfs are used to examine the KSA at a series of state points for pure water. The accuracy of several other approximate relationships between the pair and triplet correlation functions was also investigated and are in good agreement for regions of the phase diagram where the compressibility is small.

abstract: Molecular dynamics simulations were used to study properties of water at the interface with nanometer-size solutes. We simulated nonpolar attractive Kihara cavities given by a Lennard-Jones potential shifted by a core radius. The dipolar response of the hydration layer to a uniform electric field substantially exceeds that of the bulk. For strongly attractive solutes, the collective dynamics of the hydration layer become slow compared to bulk water, as the solute size is increased. The statistics of electric field fluctuations at the solute center are Gaussian and tend toward the dielectric continuum limit with increasing solute size. A dipolar probe placed at the center of the solute is sensitive neither to the polarity excess nor to the slowed dynamics of the hydration layer. A point dipole was introduced close to the solute-water interface to further study the statistics of electric field fluctuations generated by the water. For small dipole magnitudes, the free energy surface is single-welled, with approximately Gaussian statistics. When the dipole is increased, the free energy surface becomes double-welled, before landing in an excited state, characterized again by a single-welled surface. The intermediate region is fairly broad and is characterized by electrostatic fluctuations significantly in excess of the prediction of linear response. We simulated a solute having the geometry of C180 fullerene, with dipoles introduced on each carbon. For small dipole moments, the solvent response follows the results seen for a single dipole; but for larger dipole magnitudes, the fluctuations of the solute-solvent energy pass through a second maximum. The juxtaposition of the two transitions leads to an approximately cubic scaling of the chemical potential with the dipole strengh. Umbrella sampling techniques were used to generate free energy surfaces of the electric potential fluctuations at the heme iron in Cytochrome B562. The results were unfortunately inconclusive, as the ionic background was not effectively represented in the finite-size system. / Dissertation/Thesis / Ph.D. Chemistry 2012

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.

A modelagem das interações entre macromoléculas e ligantes ainda se depara com diversos desafios na área de desenho de fármacos assistidos por computador. Apesar do crescimento da área, temas como a flexibilidade do receptor, funções de pontuação e solvatação ainda têm sido alvo de intensa investigação na comunidade científica. Com o objetivo de analisar a interação em milhares ou milhões de complexos, é imprescindível uma boa harmonização entre o custo computacional e a acurácia dos métodos computacionais que permitem a classificação de ligantes de acordo com a energia de interação. O LiBELa (Ligand Binding Energy Landscape) é um programa de docagem molecular com abordagem híbrida, ou seja, utiliza informações do ligante e do receptor durante o processo de docagem. Inicialmente, as características estéricas e eletrostáticas de um ligante de referência (cristalográfico, por exemplo) são utilizadas nos cálculos de similaridade e sobreposição, obtendo assim uma conformação inicial pré-otimizada do ligante testado. Em seguida, a energia de interação é minimizada no sítio ativo de receptor a partir de potenciais energéticos. Quatro funções de pontuação baseadas em campo de força foram testadas e otimizadas, compostas por potenciais de van der Waals, de Coulomb, e uma função empírica de solvatação denominada função de Stouten-Verkhivker (SV). A flexibilidade do sistema foi tratada através da geração de confôrmeros que amostram os graus de liberdade dos ligantes descritos como semi-rígidos e através de potenciais atenuados que suavizam a superfície de energia de interação, permitindo interações em distâncias interatômicas antes repulsivas. Como ponto de partida, os métodos implementados no programa LiBELa demonstraram resultados satisfatórios nos testes de cross- e self-docking, mostrando ser uma ferramenta eficiente em encontrar os modos de ligação cristalográficos de forma equivalente ou até melhor às dos programas comparados. Através de testes de enriquecimento nos conjuntos de dados DUD, DUDE e CM-DUD, foram otimizadas de forma sistemática as constantes dielétrica, do termo de solvatação, e dos termos de atenuação. Também foi realizado um paralelo entre as funções de pontuação, incluindo a atenuação e o termo de solvatação. Estes mesmos testes mostraram resultados superiores do LiBELa de 39% e 15% em comparação com um programa baseado puramente no receptor (DOCK 6.6), relativo à média da área sob a curva em escala semi-logarítmica nas bases de dados DUDE e DUD respectivamente. Apesar da função de solvatação SV implementada no LiBELa apresentar boa correlação com dados experimentais (r=0,72) e com o modelo Zou GB de solvatação (r=0,88), não apresentou correlação significativa com os métodos GB e PB implementados no pacote de programas disponível no AmberTools. Comparadas às funções de pontuação do LiBELa, as funções com correção para solvatação apresentaram pior enriquecimento, salvo alguns alvos específicos. Por fim, foram realizados ensaios de docagem molecular utilizando como alvo uma enzima β-galactosidase da família GH42, cuja estrutura fora resolvida em nosso grupo. Os resultados permitiram conclusões acerca de como o modo de ligação interfere na preferência de ligação entre dissacarídeos de ligações glicosídicas distintas, consistentes com dados experimentais de ensaios cinéticos de ligação. / Modeling the interactions between macromolecules and ligands still faces several challenges in the computer-aided drug design area. Despite the growth in the area, subjects such as receptor flexibility, scoring functions and solvation still have been widely explored in the scientific community. In order to analyze the interaction for thousands or millions of complexes, a good harmonization between the computational cost and the accuracy of the calculation methods in molecular docking programs is essential. LiBELa (Ligand Binding Energy Landscape) is a hybrid approach program that uses both ligand and receptor information for ligand docking. Initially, the steric and electrostatic characteristics from a reference binder (crystallographic, for example) are used to similarity and overlay calculations, thus obtaining an initial conformation of the ligand tested. Then, within the receptor´s active site, the interaction energy is minimized using energetic potentials. Four force field-based scoring functions were tested and optimized, composed of van der Waals and Coulomb potentials and an empirical solvation function called Stouten-Verkhivker (SV). Concerning the system flexibility, besides the confomers generation that sample the degrees of freedom for semi-rigid ligands, attenuated potentials smooth the energy surface allowing interactions between previously repulsive interatomic distances. As a starting point, LiBELa performed satisfactorily in the cross- and self-docking tests, showing that is an eficient tool to reproduce crystallographic binding modes equivalently to or even better than reference programs. Through enrichment of DUD, DUDE and CM-DUD datasets, the dielectric constant, solvation and softening terms were systematically optimized. It also allowed a parallel between scoring functions, including attenuation and solvation term. Finally, it revealed the LiBELa showed an enhancement of 39% and 15% as compared to the purely receptor-based program DOCK 6.6, relative to the mean of the area under the curve on a semi-logarithmic scale in the DUDE and DUD databases respectively. Although the SV solvation function implemented in LiBELa showed good correlations with experimental data (r = 0.72) and with the Zou GB / SA solvation method implemented in DOCK6 (r = 0.88), it did not show significant correlation with the GB/SA and PB/SA methods implemented in AmberTools. Comparing all the LiBELa tested scoring functions, those including solvation correction showed worse enrichments, except for some specific targets. Finally, molecular docking experiments using LiBELa were conducted with a β-galactosidase from GH42 family, whose structure was solved in our group. The results allowed conclusions concerning how the binding mode interferes the preference for some disaccharides of distinct glycosidic bonds, consistent with experimental data from kinetic assays.

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.