Les travaux présentés dans cette thèse démontrent l'utilité des simulations de dynamique moléculaire pour l'étude de processus complexes de reconnaissance moléculaire en solution, de complexation et de l'extraction liquide-liquide, avec un regard particulier porté sur les événements microscopiques qui se produisent à l'interface entre deux liquides non miscibles. Des études préliminaires concernent la représentation adéquate des cations trivalents terres rares La3+, Eu3+ et Yb3+ dans les simulations de dynamique moléculaire classiques, en explorant des aspects structuraux et énergétiques d'un système modèle caractérisé expérimentalement, impliquant des ligands de type pyridine dicarboxamide. La complexation de ces cations par un calixarène développé récemment a été étudiée montrant des caractéristiques inattendues, notamment la position du cation dans le complexe. Une étude expérimentale indépendante publiée par la suite a confirmé ces résultats. Un autre volet de ce travail concerne des systèmes d'extraction liquide- liquide industriels impliquant le tri-n-butyl phosphate (TBP) comme co- solvant, extractant, surfactant et agent de synergie. Nous examinons 1) des effets de concentration avec des simulations de jusqu'à 60 TBP à l'interface eau/chloroforme, 2) l'acidité de la phase aqueuse en considérant des modèles neutre et ionique de HNO3 et 3) des aspects de synergie dans des systèmes d'extraction mixtes TBP/calixarène. Ces simulations apportent les premières vues microscopiques de tels phénomènes. Enfin, nous avons simulé les aspects énergétiques du transfert d'un soluté à travers l'interface eau/chloroforme. Le potentiel de force moyenne d'un tel processus a été calculé et par des méthodes standards et par des approches nouvelles.

Huntington’s disease (HD) is a neurodegenerative disorder caused by the inheritance of one mutant copy of the huntingtin gene. Mutant huntingtin protein (mHtt) contains an expanded polyglutamine repeat region near the N-terminus. Cleavage of mHtt releases an N-terminal fragment (N-mHtt) which translocates, and accumulates in the nucleus. Nuclear accumulation of N-mHtt has been directly associated with cellular toxicity. Decreased transcription is among the earliest detected changes that occur in the brains of HD patients and is consistently observed in all animal and cellular models of HD. Transcriptional dysregulation may trigger many of the perturbations that occur later in disease progression and an understanding of the effects of mHtt may lead to strategies to slow the progression of the disease. Current models of N-mHtt-mediated transcriptional dysregulation suggest that abnormal interactions between N-mHtt and transcription factors impair the ability of these transcription factors to associate at N-mHtt-affected promoters and properly regulate gene expression. We tested various aspects of these models using two N-mHtt-affected promoters in in vitro transcription assays and in two cell models of HD using techniques including overexpression of known N-mHtt-interacting transcription factors, chromatin immunoprecipitation, promoter deletion and mutation analyses and in vitro promoter binding assays. Based on our results and those in the literature, we proposed a new model of N-mHtt-mediated transcriptional dysregulation centered on the presence of N-mHtt at affected promoters. We concluded that simultaneous interaction of N-mHtt with multiple binding partners within the transcriptional machinery would explain the gene-specificity of N-mHtt-mediated transcriptional dysregulation, as well as the observation that some genes are affected early in disease progression while others are affected later. Our model explains why alleviating N-mHtt-mediated transcriptional dysregulation through overexpression of N-mHtt-interacting proteins has proven to be difficult and suggests that the most realistic strategy for restoring gene expression across the spectrum of N-mHtt affected genes is by reducing the amount of soluble nuclear N-mHtt.

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Stepwise covalent synthesis of large molecules is often time consuming and laborious and thus generally ends in a low yield of the target product. It is also difficult to achieve a large desired product where the controlling force is a non-directional weak interaction. Instead, by utilizing stronger metal-ligand directional coordination bonding approach, one can easily prepare the desired large molecules using appropriate molecular units. Further attractive feature of this approach is the incorporation of functional groups into final structures to make the assemblies functional. It is found that symmetrical polypyridyl and rigid linkers have been used widely in the construction of finite supramolecules of Pd (II) and Pt(II). Flexible linkers are rarely used since they are less predictable in self-assembly and have a tendency to form undesired polymer. However, flexible linkers may generate pseudo rigid assemblies that can distort their shapes to obtain a more thermodynamically stable conformation for host-guest interactions. Similarly, use of non-symmetric or ambidentate linkers is not explored much. These linkers may generate a mixture of several linkage isomeric products and thus difficult to monitor the reaction. Moreover, isolation of these products in pure form is also a challenging task. On the other hand, recent research revealed that porous polyacetylene organic compounds are suitable sensors for the detection of electron deficient nitroaromatics, which are the chemical signatures of many commercial explosives. Possibility of discrete supramolecules as sensors for these explosives is very less studied. The main thrusts of the present investigation are to incorporate flexible and nonsymmetrical linkers in the construction of finite discrete assemblies of Pd/Pt; and to design appropriate π-electron rich supramolecules as sensors for the detection of electron deficient nitroaromatics. Chapter 1 of this thesis gives a brief introduction to the supramolecular chemistry. It also gives a brief introduction to the design principle of metal-ligand coordination driven selfassembly approach towards the generation of large architectures. Chapter 2 reports the synthesis of a series of two-dimensional supramolecular architectures via coordination driven self-assembly of Pt/Pd containing ditopic acceptors and non-symmetrical donor ligands. The use of non-symmetrical donor ligands in coordination driven self-assembly is a challenging task because they may generate a mixture of isomers due to different connectivity of the non-symmetric (ambidentate) linkers. But in all the cases exclusive formation of a single linkage isomer was established. Na-nicotinate was treated with [cis-(dppf)Pd(OTf)2] to yield [(dppf)3Pd3(L3)](CF3SO3)3(H2O)2(MeOH)7(Et2O) as the single linkage isomeric triangle. An analogous treatment using Na-isonicotinate instead of Na-nicotinate yielded a mixture of single isomeric square and triangle with the later one as the major product in solution. Further extension of this study using cis-(tmen)Pd(NO3)2 instead of [cis-(dppf)Pd(OTf)2] also showed the formation of a mixture of square and triangle [tmen = N,N,N’,N’- tetramethylethane-1,2-diamine]. Surprisingly, in both the cases square was the product which was crystallized exclusively in solid state though triangle was the major component in solution. The square-triangle equilibria in both the cases were studied by diffusion ordered NMR spectroscopy (DOSY) and variable temperature multinuclear NMR. Moreover, this chapter reports the incorporation of amide functionality into a Pt(II) nanoscopic molecular rectangle via self-assembly of an organometallic “clip” and a non-symmetric amide ligand. Chapter 3 presents synthesis of several metallamacrocycles via coordination driven selfassembly using Pd/Pt-P bonding interaction as driving force instead of much widely used Pd/Pt-N bonding interaction. It is also established that Pd/Pt-P bonding interaction is indeed better than the widely used Pd/Pt-N interaction. Several macrocycles were also synthesized by the combination of several Pd containing 90° angular subunits and a bisimidazole ditopic flexible donor. In this case also the bonding interaction between the imidazole and Pd(II) was found to be stronger than the interaction between pyridyl donor and Pd(II). Chapter 4 describes synthesis of several new Pt2 and Pt3 shape selective organometallic linkers incorporating ethynyl functionality. The Pt2 molecular clip was assembled with several linear dipyridyl linkers to prepare a series of molecular rectangles. In one case N, N’-bis(4-pyridylidene)ethylenediamine was used as donor to create a N4 pocket in the macrocycle. This rectangle was fluorescent in nature and showed efficient fluorescence quenching in solution upon binding of hard transition metal ions (Fe3+, Cu2+ and Ni2+) into the N4 pocket. The non-responsive nature of the fluorescence quenching upon addition of soft metal ions (Zn2+ and Cd2+) containing d10 configuration makes it an interesting example of sensor for transition metal ions. The Pt3 linkers were used in combination with organic clip-type linkers to prepare a series of molecular prisms by [2 + 3] self-assembly (Scheme 1). Incorporation of ethynyl functionality helped to make the resulting supramolecules π-electron rich and luminescent in nature. Possibility of these supramolecules as sensors for the detection of electron deficient nitroaromatics (TNT and picric acid), which are the chemical signatures of explosives has been explored. A complementary approach was also used to prepare trigonal prism using organic tritopic donor and the Pt2 molecular clip. Chapter 5 presents the design and self-assembly of two new flexible supramolecular nanoballs. These assemblies incorporate two flexible tritopic amide/ester based building blocks and were prepared in excellent yields (96-97%) via coordination driven selfassembly. The first one was resulted from the reaction of four equivalents of a new tritopic ester ligand N, N', N''-tris(4-pyridylmethyl) trimesic ester with three equivalents of C4 symmetric Pd(NO3)2. The second analogous structure was obtained by the selfassembly of the flexible N, N', N''-tris(3-pyridylmethyl)trimesic amide and Pd(NO3)2. The assemblies were characterized with multinuclear NMR spectroscopy, electrospray ionization mass spectroscopy, elemental analysis and TGA. The ester based ball showed the inclusion of NEt4 + in solution. This chapter also describes the exclusive formation of a Pt(II) trigonalbipyramidal (TBP) cage upon the treatment of a Pt(II) 90° acceptor with a new tripodal flexible ligand containing ester functionality. The formation of Pt(II) TBP cage in this case is due to the flexibility of the donor arms of the ligand due to the presence of flexible ester functional group. In continuation of this work, a rigid tripodal ligand 1,1,1-tris(4-pyridyl)COOR with an ester cap [where R = Ph-CH(C2H5)] was assembled with cis-(PEt3)2Pt(OTf)2 to yield a somewhat unusual double-square cage by [4 + 6] self-assembly.

A contínua mudança na qualidade da carga de alimentação das unidades de destilação atmosférica introduz incertezas na operação do processo de refino. A caracterização precisa do petróleo bruto, cuja composição varia devido à sua natureza intrínseca e às condições de transporte e armazenamento nas refinarias, poderia auxiliar na redução destas incertezas. O processo clássico de caracterização, baseado nas curvas de destilação TBP (True Boiling Point, Ponto de Ebulição Verdadeiro), ainda não permite detectar essas mudanças de modo mais dinâmico, o que reduz a precisão da simulação do processo e, portanto, uma menor confiabilidade nas condições de operação determinadas a partir dela. No Brasil, petróleo pesado é produzido de forma predominante, que é misturado freqüentemente com petróleo leve importado antes do refino. Como conseqüência, nas refinarias brasileiras as características do petróleo mudam em média, a cada três dias, sendo esta taxa de variação incompatível com a determinação das curvas de destilação TBP. A análise SimDis (Simulated Distillation, Destilação Simulada) é atualmente a técnica de laboratório alternativa para aproximar as curvas de destilação. Porém, ainda apresenta algumas características que a tornam tão limitantes quanto a análise TBP. A espectroscopia NIR (Near InfraRed, Infravermelho Próximo), tem se consagrado como uma técnica analítica rápida e viável em inúmeras aplicações industriais na determinação de diversos parâmetros qualitativos. Neste trabalho, metodologias inovadoras de caracterização são desenvolvidas visando reproduzir com maior dinamismo o processo de refino. A reprodução das curvas de destilação das cargas ao processo de destilação atmosférica da Refinaria de Capuava (RECAP ? Petrobras S.A.) através do seu espectro NIR tem sido o ponto de partida no desenvolvimento do trabalho. Métodos de calibração multivariada e redes neurais foram utilizados na construção de algoritmos computacionais que permitem a previsão dos perfis de destilação do petróleo processado, os quais foram utilizados na simulação do processo para avaliar o impacto da aplicação desta metodologia. A boa qualidade da reprodução das propriedades físico-químicas do petróleo através do NIR foi comprovada, uma vez que os modelos construídos foram condicionados às características da matéria analisada. Quanto à reprodução do cenário real do processo através da simulação, os resultados obtidos são promissores, mostrando que a caracterização da carga é útil para reproduzir mudanças no processamento. Porém, alguns aspectos precisam ainda ser aprofundados visando o melhor desempenho das metodologias. Contudo, os resultados desta pesquisa reforçam a relevância do papel da espectroscopia NIR, juntamente com técnicas clássicas de laboratório utilizadas, numa nova concepção de caracterização, que tem na rapidez e confiabilidade os seus principais aliados e pode ser aplicada na simulação de um processo visando uma melhor qualidade de operação. / The continuous variation in the quality of the feed petroleum to atmospheric distillation unities brings uncertainty to the operation of the refining process. The characterization of the crude oil, whose composition varies due to its intrinsic nature and the transport conditions and storage in refineries, could be useful in reducing the uncertainty. The classic process of characterization, based on TBP distillation curves (True Boiling Point), still does not permit to detect these changes in a more dynamic manner, which reduces the precision of the process simulation and, consequently, less confidence in the operation conditions determined from it. In Brazil, heavy petroleum is produced predominantly, which is typically blended with light imported petroleum before refining. As a consequence, in Brazilian refineries the characteristics of the petroleum change, on the average, about every three days. This rate of the petroleum change is incompatible with the determination of TBP curves. Nowadays, SimDis analysis (Simulated Distillation) is an alternative laboratory technique able to approximate the distillation curves. However, it still presents some limiting characteristics like those of TBP analysis. In the last decades, the NIR spectroscopy (Near InfraRed) has showed to be a both fast and feasible analytical technique for innumerous industrial applications in the determination of various qualitative parameters. In the present work, an innovative characterization methodology is developed aiming to reproduce more dynamically the refining process. The reproduction of distillation curves of the feed to the atmospheric distillation process of the Refinery of Capuava (RECAP ? Petrobras S.A.) from its NIR spectral determination has been the initial point for the development. Multivariate calibration methods and neural networks have been used in the construction of computational algorithms that allow the prediction of distillation profiles of the petroleum processed. These profiles were applied in process simulation in order to evaluate the impact of the application of this methodology. The good quality of the physicochemical properties of petroleum reproduction using NIR was confirmed, it is due to the fact that constructed models were conditioned to the characteristics of the samples analyzed. With respect to the reproduction of the real process behavior through simulation, the results obtained are promising, which show that the feed characterization is useful in order to reproduce process variations. However, some aspects need to be analyzed deeply in order to improve the performance of the methodologies. Finally, the results of this research strengthen the role of NIR spectroscopy together with classic laboratory techniques used in a new characterization concept, whose major advantages are the rapidity and the trustworthiness of its predictions, that can be applied in order to improve the quality of the simulation of a process.

Nous avons étudié par simulations de dynamique moléculaire la solvatation de molécules hydrophobes chargées dans des liquides purs et à des interfaces liquide / liquide. <br />La première partie concerne l'hypothèse TATB qui suppose que les deux ions AsΦ4+ (TA+) et BΦ4- (TB-) ont la même énergie de solvatation dans tout solvant. Nous avons montré que les deux ions étaient solvatés différemment dans des liquides purs (eau, chloroforme, acétonitrile) ainsi qu'à une interface chloroforme / eau. Des calculs de différences d'énergie libre de transfert ont confirmé cette tendance, de même que des simulations sur des ions "hypothétiques" S+ et S-, analogues sphériques de AsΦ4+ et BΦ4- qui répondent exactement aux critères de l'hypothèse. De nombreux tests méthodologiques ont été effectués et ont permis de montrer l'importance (i) d'une description correcte des interactions à "longue distance", (ii) de la répartition précise des charges atomiques et (iii) du modèle de solvant utilisé notamment pour l'eau, sur la différence de solvatation de "gros" ions hydrophobes selon leur charge. <br />La seconde partie décrit les premières simulations avec le CO2 supercritique dans le cadre de l'extraction liquide / liquide de cations métalliques. Nous avons étudié le comportement d'ions (Cs+, UO22+, Eu3+), de molécules extractantes (tri-n-butylphosphate, calixarène), de complexes de ces cations avec ces molécules extractantes et d'acide nitrique à une interface préformée CO2 / eau et lors de simulations de séparation de phase, en partant de solutions binaires homogènes CO2 / eau. Ces études démontrent l'importance des phénomènes interfaciaux, des conditions de simulations, ainsi que de la concentration en acide et en extractant, dans les processus d'extraction vers le CO2 supercritique.

Le dioxyde de carbone supercritique (SF-CO2) a été choisi afin d'étudier l'extraction en milieu supercritique d'ions métalliques tels que le césium et l'uranium. Un intérêt particulier a été porté au rôle de l'eau lors de ces extractions ainsi qu'à son interaction avec des agents chélateurs (AC). En première partie, les éthers couronne ont été choisis comme AC du césium et leur interaction avec l'eau a été étudiée dans le SF-CO2 en utilisant la spectroscopie InfraRouge à Transformée de Fourier (IR-TF). La configuration sandwich entre deux éthers couronne et une molécule d'eau a été observée dans le SF-CO2. Pour les configurations simple et pontée, l'équilibre a été défini et l'enthalpie de formation de la liaison hydrogène a été calculée. Ces résultats ont ensuite été comparés à ceux obtenus dans des mélanges de CHCl3 et de CCl4 en utilisant la spectroscopie à Résonance Magnétique Nucléaire (RMN). Pour conclure cette première partie, le rôle de l'eau a été étudié lors de l'extraction du picrate de césium par le DCH18C6 et les constantes d'équilibre ont été calculées. Dans une deuxième partie, l'extraction de l'uranium a été étudiée dans le SF-CO2. Des complexes de Phosphate de TriButyle (TBP), d'eau et d'acide nitrique ont été utilisés comme AC et oxydants. L'IR-TF a été utilisée pour étudier l'interaction entre le TBP et l'eau dans le SF-CO2. Ces résultats ont été comparés à ceux trouvés dans le CHCl3 en utilisant la RMN. Cette même spectroscopie a été utilisée pour comprendre les interactions entre l'acide nitrique, le TBP et l'eau, seuls puis dissous dans du CHCl3. La formation de microgouttelettes d'acide et d'eau dues à l'effet anti-solvant a été observée et quantifiée. Pour conclure ce travail de thèse j'ai réussi à optimiser l'extraction et la récupération d'uranium enrichi provenant de cendres d'incinération de déchets de fabrication de combustible nucléaire. Un complexe de TBP, d'eau et d'acide nitrique dissous dans du SF-CO2 a été utilisé à cette fin.

A contínua mudança na qualidade da carga de alimentação das unidades de destilação atmosférica introduz incertezas na operação do processo de refino. A caracterização precisa do petróleo bruto, cuja composição varia devido à sua natureza intrínseca e às condições de transporte e armazenamento nas refinarias, poderia auxiliar na redução destas incertezas. O processo clássico de caracterização, baseado nas curvas de destilação TBP (True Boiling Point, Ponto de Ebulição Verdadeiro), ainda não permite detectar essas mudanças de modo mais dinâmico, o que reduz a precisão da simulação do processo e, portanto, uma menor confiabilidade nas condições de operação determinadas a partir dela. No Brasil, petróleo pesado é produzido de forma predominante, que é misturado freqüentemente com petróleo leve importado antes do refino. Como conseqüência, nas refinarias brasileiras as características do petróleo mudam em média, a cada três dias, sendo esta taxa de variação incompatível com a determinação das curvas de destilação TBP. A análise SimDis (Simulated Distillation, Destilação Simulada) é atualmente a técnica de laboratório alternativa para aproximar as curvas de destilação. Porém, ainda apresenta algumas características que a tornam tão limitantes quanto a análise TBP. A espectroscopia NIR (Near InfraRed, Infravermelho Próximo), tem se consagrado como uma técnica analítica rápida e viável em inúmeras aplicações industriais na determinação de diversos parâmetros qualitativos. Neste trabalho, metodologias inovadoras de caracterização são desenvolvidas visando reproduzir com maior dinamismo o processo de refino. A reprodução das curvas de destilação das cargas ao processo de destilação atmosférica da Refinaria de Capuava (RECAP ? Petrobras S.A.) através do seu espectro NIR tem sido o ponto de partida no desenvolvimento do trabalho. Métodos de calibração multivariada e redes neurais foram utilizados na construção de algoritmos computacionais que permitem a previsão dos perfis de destilação do petróleo processado, os quais foram utilizados na simulação do processo para avaliar o impacto da aplicação desta metodologia. A boa qualidade da reprodução das propriedades físico-químicas do petróleo através do NIR foi comprovada, uma vez que os modelos construídos foram condicionados às características da matéria analisada. Quanto à reprodução do cenário real do processo através da simulação, os resultados obtidos são promissores, mostrando que a caracterização da carga é útil para reproduzir mudanças no processamento. Porém, alguns aspectos precisam ainda ser aprofundados visando o melhor desempenho das metodologias. Contudo, os resultados desta pesquisa reforçam a relevância do papel da espectroscopia NIR, juntamente com técnicas clássicas de laboratório utilizadas, numa nova concepção de caracterização, que tem na rapidez e confiabilidade os seus principais aliados e pode ser aplicada na simulação de um processo visando uma melhor qualidade de operação. / The continuous variation in the quality of the feed petroleum to atmospheric distillation unities brings uncertainty to the operation of the refining process. The characterization of the crude oil, whose composition varies due to its intrinsic nature and the transport conditions and storage in refineries, could be useful in reducing the uncertainty. The classic process of characterization, based on TBP distillation curves (True Boiling Point), still does not permit to detect these changes in a more dynamic manner, which reduces the precision of the process simulation and, consequently, less confidence in the operation conditions determined from it. In Brazil, heavy petroleum is produced predominantly, which is typically blended with light imported petroleum before refining. As a consequence, in Brazilian refineries the characteristics of the petroleum change, on the average, about every three days. This rate of the petroleum change is incompatible with the determination of TBP curves. Nowadays, SimDis analysis (Simulated Distillation) is an alternative laboratory technique able to approximate the distillation curves. However, it still presents some limiting characteristics like those of TBP analysis. In the last decades, the NIR spectroscopy (Near InfraRed) has showed to be a both fast and feasible analytical technique for innumerous industrial applications in the determination of various qualitative parameters. In the present work, an innovative characterization methodology is developed aiming to reproduce more dynamically the refining process. The reproduction of distillation curves of the feed to the atmospheric distillation process of the Refinery of Capuava (RECAP ? Petrobras S.A.) from its NIR spectral determination has been the initial point for the development. Multivariate calibration methods and neural networks have been used in the construction of computational algorithms that allow the prediction of distillation profiles of the petroleum processed. These profiles were applied in process simulation in order to evaluate the impact of the application of this methodology. The good quality of the physicochemical properties of petroleum reproduction using NIR was confirmed, it is due to the fact that constructed models were conditioned to the characteristics of the samples analyzed. With respect to the reproduction of the real process behavior through simulation, the results obtained are promising, which show that the feed characterization is useful in order to reproduce process variations. However, some aspects need to be analyzed deeply in order to improve the performance of the methodologies. Finally, the results of this research strengthen the role of NIR spectroscopy together with classic laboratory techniques used in a new characterization concept, whose major advantages are the rapidity and the trustworthiness of its predictions, that can be applied in order to improve the quality of the simulation of a process.

CHDS State/Local / Approved for public release, distribution is unlimited / The planning methodologies used today by most U.S. fire departments are excellent for traditional missions, but wholly inadequate for the threats posed by terrorism. Planning in the fire service and the rest of the first responder community historically has relied on a one-dimensional approach that uses a scenario-based planning (SBP) methodology. This thesis argues that the fire service and others in the first responder community will be able to contribute to homeland security missions much more effectively, and efficiently, by switching to specially adapted versions of capabilities-based planning. This thesis proposes a new integrated planning methodology that combines the planning strengths of scenariobased planning, threat-based planning, and capabilities-based planning. The new method identifies capabilities that could be used to manage and mitigate the consequences of the different types of contingencies within the various response spectrums. It allows an organization to perform analysis and efficiency studies to evaluate the different spectrums of contingencies against existing capabilities and create a menu of capabilities necessary for the first responder to respond to all its missions, including immediate threats and terrorism, in the most efficient and cost-effective manner. / Battalion Chief, Fire Department City of New York