A doença de Chagas é uma infecção causada pelo protozoário intracelular Trypanosoma cruzi. Atualmente 7 a 8 milhões de pessoas encontram-se infectadas, e há 25 milhões de pessoas em áreas de risco de contaminação. A cada ano ocorrem 56.000 novos casos e, aproximadamente, 12.000 mortes por complicações oriundas da doença. É endêmica em 21 países da América do Sul, e pode ser encontrada, também, na América do Norte e Europa devido a processos migratórios. Somente dois fármacos estão disponíveis para o tratamento da doença de Chagas, o nifurtimox e o benznidazol, que são ativos somente na fase aguda e causam sérios efeitos adversos. Diante deste panorama, é eminente a necessidade de novos antichagásicos. A enzima cruzaína é a principal cisteíno-protease presente no T. cruzi, é importante para a sobrevivência, diferenciação e entrada do parasita no hospedeiro, se apresentando como um excelente alvo biológico na busca de novos quimioterápicos. Derivados de semicarbazona, tais como o nitrofural e o hidroximetilnitrofural demonstraram atividade inibitória da cruzaína, sendo considerados protótipos na busca de antichagásicos. Utilizando estratégias modernas de planejamento de fármacos por meio da integração entre técnicas computacionais, modelagem molecular e docking, e experimentais, síntese e ensaios biológicos, realizou-se neste trabalho o planejamento, síntese e avaliação biológica de bioisósteros do nitrofural como candidatos à antichagásicos. Aplicou-se estudos de modelagem molecular e docking para 10 compostos derivados de aminoguanidina, semi e tiossemicarbazona; observamos nesses estudos que os compostos contendo tiossemicarbazona apresentaram resultados mais favoráveis ao mecanismo de ação proposto, o qual sugere-se um ataque nucleofílico do resíduo de Cys25 presente no sítio catalítico da enzima cruzaína à tiocarbonila presente nesses compostos. Obtiveram-se através da síntese, 6 compostos caracterizados por RMN 1H e 13C. Tais compostos foram submetidos a ensaios de inibição da cruzaína, sendo que os derivados 6, 9 e 10, apresentaram um perfil de inibição favorável em dose de 100 µM, com valores entre 70 e 75% de inibição. Em ensaio de inibição de crescimento celular em formas epimastigotas do T. cruzi o composto 9 apresentou um IC50 de 19,8 µM, sendo o melhor protótipo para desenvolvimento de um novo agente antichagásico. De uma maneira geral os resultados obtidos nos ensaios biológicos corroboram com os dados apresentados na modelagem molecular, uma vez que os compostos contendo a cadeia lateral tiossemicarbazona mostraram melhores resultados em ambos os testes, demonstrando que a integração entre técnicas computacionais e experimentais se apresenta como uma excelente estratégia na busca de novos agentes antichagásicos. / Chagas disease is an infection caused by the intracellular protozoan Trypanosoma cruzi. Currently 7 million to 8 million people are infected, and there are 25 million people in areas at risk of contamination, with 56,000 new cases each year and roughly 12,000 deaths are related to Chagas complications. It is endemic in 21 countries in South America, and can also be found in North America and Europe due to migration processes. Only two drugs are available for treatment of Chagas disease, nifurtimox and benznidazole, which are active only in the acute phase and cause serious adverse effects. Against this background, it is imminent need for new antichagasic. The enzyme cruzain is the major cysteine protease present in the T. cruzi, is important for the survival, differentiation and entry of the parasite in the host, presenting itself as an excellent biological target in the search for new chemotherapeutic agents. Semicarbazone derivatives, such as nitrofurazone and hydroxymethylnitrofurazone showed inhibitory activity cruzain being considered prototypes in search antichagasic. Using modern drug design strategies through the integration of computational techniques, molecular modeling and docking, and experimental synthesis and biological assays. In this work were performed design, synthesis and biological evaluation of the bioisosters nitrofurazone as candidates for antichagasic. Were applied molecular modeling and docking studies for ten derivatives compounds of aminoguanidine, semi and thiosemicarbazone. In these studies thiosemicarbazone derivatives compounds showed more favorable for the mechanism of action proposed, that suggest a nucleophilic attack of the Cys25 residue present in the catalytic site of the enzyme cruzain in the thiocarbonyl group. Six compounds were synthesized and characterized by 1H and 13C NMR. These compounds were tested for inhibition of cruzain, and derivatives 6, 9 and 10 showed favorable enzyme inhibition at single dose of 100 µM, with values between 70 and 75%. In the inhibition assay of cell growth in epimastigotes forms of T. cruzi, the compound 9 showed an IC50 of 19.8 µM, the best prototype for the development of a new antichagasic agent. In general the results obtained by biological assay corroborate the data presented in molecular modeling, since compounds containing side chain thiosemicarbazone showed better results in both tests, showing that the integration of experimental and computational techniques is presented as a excellent strategy in the search for new agents antichagasic

Molecular modeling, using both ab initio and semi-empirical methods has been undertaken for a series of dirhodium complexes in order to improve the understanding of the nature of the chemical bonding in this class of homogeneous catalysts. These complexes, with carboxylamidate and carboxylate ligands, are extremely functional metal catalysts used in the synthesis of pharmaceuticals and agrochemicals. The X-ray crystallography shows anomalies in the bond angles that have potential impact on understanding the catalysis. To resolve these issues, minimum energy structures of several examples (e.g. Rh2(NHCOCH3)4, Rh2(NHCOCH3)4NC, Rh2(CO2CH3)4, Rh2(CO2CH3)4NC, Rh2(CHO2)4, and Rh2(CHO2)4NC) were calculated using Hatree-Fock and Density Functional Theory/B3LYP with the LANL2DZ ECP (Rh), and cc-pVDZ (all other atoms) basis sets.

Alzheimer’s disease is a progressive neurodegenerative disorder generally affecting people above the age of 65 years. Even though the pathophysiological hallmarks of AD were established more than a hundred years ago, there is yet to be a drug that can stop its characteristic neuronal damage. Of the five currently FDA-approved drugs, galantamine has a unique mechanism of action. Apart from being an AChE inhibitor, galantamine can effectively potentiate (positive allosteric modulator) the effect of agonists at nAChRs at concentrations lower than those required for its action as an AChE inhibitor. Perhaps the clinical benefits observed with galantamine are associated mainly with its nAChRs-PAM action and not its AChE inhibitory effect. Inhibiting AChE causes a delay in the degradation of ACh and a prolonged presence of ACh might act at either nAChRs or mAChRs. By indirectly targeting mAChRs as well, AChE inhibitors may lead to potential side effects. Hence there is a need for specific nAChR agents. The aim of this study was to identify the structural features of galantamine that contribute solely towards its a7 nAChR-PAM effect. In doing so, we wish to divorce the structural features that might be important for interacting with AChE. Using the deconstruction approach, we have synthesized structurally abbreviated analogs of galantamine. To study the probable interactions, we docked these molecules in human a7 nAChR homology models. Ultimately, it is of interest to determine which analogs retain the PAM activity of galantamine and to address that, a preliminary screening was performed with a select few analogs using the two-electrode voltage clamp technique

Fasciola cause considerable monetary loss in the agriculture industry, while parasitism of humans is an emerging disease. Fasciola cathepsin L-like proteases are believed to aid parasite invasion and survival through a range of functions including feeding, immune evasion and modulation, tissue migration, egg production and excystment. As such these proteases are considered good targets for chemotherapies and vaccine development. Fasciola cathepsins are evolutionarily divided into clades that reflect function and life stage of expression. Analysis of F. gigantica genomic DNA and mRNA identified novel cathepsin L-like sequences which are incorporated into a phylogenetic analysis of the complete Fasciola cathepsin L-like protease family. Analysis of mRNA transcripts isolated in this study also points to trans-splicing occurring amongst cathepsin transcripts, the first time this has been identified in Fasciola species. S2 subsite specificity is important in determining substrate interactions with cathepsin L-like proteases. Previous work has shown that amino acid substitutions at this site can dramatically influence substrate specificity. A number of substitutions, specifically those that have been observed, or predicted to occur during the evolution of Fasciola cathepsins L-like proteases, were introduced into the S2 subsite of FhCatL5 at aa69 to determine their influence. The introduction of L69C and L69S substitutions resulted in low overall activity indicating their expression provides no functional advantage, thus explaining the absence of such variants amongst fluke. The L69F variant showed an increase in the ability to cleave substrates with P2 proline, indicating F69 variants expressed by fluke are also likely to have this ability, similar to that shown with L69Y and FhCatL2. The introduction of a L69W substitution leads to increased cleavage of substrates with P2 proline, along with a decrease in cleavage of substrates with P2 phenylalanine. FgCatL1G transcripts were isolated from F. gigantica metacercariae. This contrasts with FhCatL5 and FhCatL2 which have been isolated in adult F. hepatica. These cathepsins differ at aa69, possessing tryptophan, leucine and tyrosine respectively. The processing and substrate specificities of each recombinant enzyme was analysed and compared. While FhCatL5 and FhCatL2 process in vitro in a manner similar to that reported for FhCatL1, FgCatL1G requires different processing conditions, including neutral pH. Combined with FgCatL1G possessing increased stability at acidic pH, this reflects the different environment into which FgCatL1G is expressed by immature compared to the adult flukes. The substrate specificity of FgCatL1G also differed from previously reported cathepsins, with a preference for P2 proline and low activity against substrates with P2 phenylalanine. This is the first time recombinant expression and purification of a cathepsin L-like protease specific to the immature life stages of Fasciola has been undertaken and had enzyme specificity analysed. This work has expanded knowledge of the repertoire of cathepsin proteases expressed at various life-stages of the liver fluke. Vaccination and/or drug inhibition studies may in the future be targeted towards cathepsins that are expressed in either the adult or immature stage, or perhaps both in a multi-targeted approach. The knowledge gained in this study may allow such targets to be chosen.

<p>In dye-sensitized solar cells, the functions of light absorption and charge transport are separated. A photosensitive ruthenium-polypyridine dye in the cell absorbs light, injects an electron to a semiconductor and is then regenerated by a redox couple, typically iodide/triiodide. Quantum chemical calculations of the electronic structure of triiodide have been carried out with the restricted active space SCF method, including spin-orbit coupling, and with density functional theory. It was shown that the difference in charge density between the terminal and central atoms results in a splitting of the core levels. The calculations gave a value of the splitting of 0.8 - 1.0 eV for the <em>3d</em> and <em>4d</em> levels. Experimentally, the electronic structure has been investigated with photoelectronspectroscopy. The measured terminal/center splitting is 1.1 eV.The spin-orbit interaction of the <em>4d </em>levels of triiodide has also been calculated. The splitting was determined to be 1.6 eV. The experimental value is 1.7 eV. An assignment of the peaks in the computed spectrum of triiodide was made and the features of the experimental spectrum have beenidentied.The theoretical valence spectrum of triiodide has been computed and assigned. The results can be used in the analysis of photoelectron spectra of the molecule. Information about the electronic structure of the redox couple can help in the understanding of the electron transfer processes and forfurther development of the solar cells.  Furthermore, the solvation structure of the prototype dye, the tris(bipyridine)ruthenium(II) complex, in water and its interaction with iodide and chloride has been studied by means of molecular dynamics simulations. The trajectory analysis showed that the water molecules in the first solvation shell form a chain in between the bipyridine ligands. It was found that the iodide ions are more likely than chloride to enter between the ligands, which can be important for the electron transfer processin the solar cell.</p>

In dye-sensitized solar cells, the functions of light absorption and charge transport are separated. A photosensitive ruthenium-polypyridine dye in the cell absorbs light, injects an electron to a semiconductor and is then regenerated by a redox couple, typically iodide/triiodide. Quantum chemical calculations of the electronic structure of triiodide have been carried out with the restricted active space SCF method, including spin-orbit coupling, and with density functional theory. It was shown that the difference in charge density between the terminal and central atoms results in a splitting of the core levels. The calculations gave a value of the splitting of 0.8 - 1.0 eV for the 3d and 4d levels. Experimentally, the electronic structure has been investigated with photoelectronspectroscopy. The measured terminal/center splitting is 1.1 eV.The spin-orbit interaction of the 4d levels of triiodide has also been calculated. The splitting was determined to be 1.6 eV. The experimental value is 1.7 eV. An assignment of the peaks in the computed spectrum of triiodide was made and the features of the experimental spectrum have beenidentied.The theoretical valence spectrum of triiodide has been computed and assigned. The results can be used in the analysis of photoelectron spectra of the molecule. Information about the electronic structure of the redox couple can help in the understanding of the electron transfer processes and forfurther development of the solar cells.  Furthermore, the solvation structure of the prototype dye, the tris(bipyridine)ruthenium(II) complex, in water and its interaction with iodide and chloride has been studied by means of molecular dynamics simulations. The trajectory analysis showed that the water molecules in the first solvation shell form a chain in between the bipyridine ligands. It was found that the iodide ions are more likely than chloride to enter between the ligands, which can be important for the electron transfer processin the solar cell.

Mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator protein (CFTR) cause cystic fibrosis (CF), the most common life-shortening genetic disease among Caucasians. Although general features of the structure of CFTR have been predicted from homology models, the conformational changes that result in channel opening and closing have yet to be resolved. We created new closed- and open-state homology models of CFTR, and performed targeted molecular dynamics simulations of the conformational transitions in a channel opening event. The simulations predict a conformational wave that starts at the nucleotide binding domains and ends with the formation of an open conduction pathway. Experimentally confirmed changes in side-chain interactions are observed in all major domains of the protein. We also identified unique-to-CFTR substitutions that may have led to channel activity in CFTR. Molecular modeling and simulations are used to compare the effects of these substitutions against a canonical ABC transporter, and suggest that gain of channel function in CFTR may have risen from loss of ATPase function at its NBDs. The models and simulation add to our understanding of the mechanism of ATP-dependent gating in this disease-relevant ion channel.

Thermal properties of pure methane hydrate, under conditions similar to naturally occurring hydrate-bearing sediments being considered for potential production, have been determined both by a new experimental technique and by advanced molecular dynamics simulation (MDS). A novel single-sided, Transient Plane Source (TPS) technique has been developed and used to measure thermal conductivity and thermal diffusivity values of low-porosity methane hydrate formed in the laboratory. The experimental thermal conductivity data are closely matched by results from an equilibrium MDS method using in-plane polarization of the water molecules. MDS was also performed using a non-equilibrium model with a fully polarizable force field for water. The calculated thermal conductivity values from this latter approach were similar to the experimental data. The impact of thermal conductivity on gas production from a hydrate-bearing reservoir was also evaluated using the Tough+/Hydrate reservoir simulator (Revised version of ICGH paper 5646).

Environmental separation processes such as removal of heavy metals from aqueous solutions, electrosorption in groundwater remediation, and capacitive desalination, as well as energy storage in supercapacitors, are based on the electrical double layer (EDL) formation within nanoporous carbon materials. This research is focused on the nano-scale phenomena of EDL formation inside the confined space of nanopores. The electrosorption behavior of nanoporous carbon materials was characterized by measuring the double-layer capacitance using cyclic voltammetry. The presence of micropores results in the occurrence of EDL overlapping, corresponding to a considerable loss of the double-layer capacitance. Hence, pore size distribution plays an important role in determining the double-layer capacitance. EDL formation has significant influence on ion transport and sorption inside nanopores. The data obtained by simple diffusion and electrochemically-aided diffusion experiments demonstrated the size-exclusion effects on pore accessibility by ions. A larger ion-exclusion volume prevents larger ions from penetrating inside the pores. Batch equilibrium electrosorption experiments using nanoporous carbon materials showed that selective electrosorption, imposed by the difference in the size of hydrated ions, occurs in a competitive environment. Molecular modeling based on Monte Carlo methods was developed to simulate the EDL formation in a slit-type nanopore. Simulation results indicated that the competition in asymmetries of ion charge and size not only determines the screening of surface charge but also affects the electrolyte distribution within charged pores. In a mixture of electrolytes, the charge/size competitive effects can dominate pore accessibility. Multivalent counterions with large size have the energetic advantage of screening surface charge. On the other hand, small monovalent counterions present a ¡§size affinity¡¨ to access the pores. Therefore, electrosorption selectivity of counterions with different properties is a result of a counterbalance between minimization of potential energy and size-exclusion effects. Manipulation of electrosorption selectivity to separate ions could in principle be achieved via tuning the EDL formation inside the pores. The findings of the thesis have several significant implications for the development of advanced techniques for selective separation of ions in environmental systems and energy storage.

Advantages such as chemical, mechanical and thermal stability together with high selectivity for the templated analyte render molecularly imprinted polymers MIPs interesting alternatives to routinely applied separation materials or antibodies. Nevertheless, many factors such as the choice of functional monomer, cross-linker, and porogenic solvent, as well as the ratio between template, functional monomer, and cross-linker will affect the resulting imprinting efficiency and polymer particle size and morphology. The research described in this thesis contributes to the development of new synthetic strategies for the generation of imprinted micro- and nanospheres for 17beta-estradiol (E2) focusing on accurate control and optimization of the governing parameters for precipitation polymerization, including the polymerization temperature and the cross-linker, yielding a one-step synthetic approach with superior control on the bead diameter, shape, monodispersity and imprinting efficiency. Thus synthesized imprinting materials for E2 were successfully applied in HPLC separation, solid phase extraction and radioligand binding assays. As the optimization of imprinted materials is based on fundamental understanding of the binding site properties, the investigations is aimed at establishing a more rational basis for further tailoring imprinted materials to the desired analytical application. The relationships between the particle porosity and rebinding properties were detailed, providing useful guidelines for controlling the particle properties for the desired application including, SPE pre-concentration, HPLC separations, and biomimetic binding assays. Furthermore, analytical techniques (1H-NMR and IR, etc.) and molecular modeling were combined in this thesis to facilitate advanced understanding of the fundamental principles governing selective recognition of molecularly imprinted polymers at a molecular level. The molecular interactions involved in the templating process of molecularly imprinted polymers based on the self-assembly approach were simulated in molecular dynamic simulation model by building a modeling system include all the imprinting components with correct ratio, which has never been reported before. Molecular level interactions such as hydrogen bonding, π-π stacking interactions as well as the free energy governing complex formation of E2 with the functional monomers 4-vinylpyridine (4VP) and methacrylic acid (MAA), and the cross-linker divinylbenzene (DVB) were discussed.