N-Nitrosodimethylamine (NDMA), which is a carcinogenic and toxic N-nitrosamine, can be found in water resources associated with a multitude of processes in various industrial facilities or merely as a by-product of water or wastewater treatment. Therefore, the removal of NDMA from drinking water represents an important human safety and public health concern. The present paper presents a density functional theory study of NDMA adsorption in all-silica MFI, Na-ZSM-5 and H-ZSM-5 zeolites. The stability of NDMA inside the zeolite pores was investigated by calculating the amount of energy released during adsorption. Various configurations of adsorbed NDMA to the zeolites were investigated, predominantly at the intersection of straight and sinusoidal channels. The strength of the adsorption energies followed the order H-ZSM5 > Na-ZSM-5 > all-silica MFI. NDMA has a dipole moment and the strongest binding of NDMA occurred through the interactions of the negatively charged O atom of the molecule to positive atoms of the zeolite. Similar calculations were performed for water adsorption in these three zeolites. The adsorption energy of water to these three structures followed the order Na-ZSM5 > H-ZSM-5 > all-silica MFI. We also incorporated van der Waals corrections in the simulations, which had the effect of stabilizing NDMA within the zeolite channels, but did not significantly change the relative stability of the different adsorption geometries. It was concluded that H-ZSM-5 is the best choice to remove NDMA because it is strong enough to adsorb NDMA and it is not too strong in adsorption of water molecules.

Iridoides são metabólitos secundários provenientes de angiospermas eudicotiledôneas, presentes principalmente em espécies das ordens Gentianales e Lamiales. Os iridoides dividem-se em carbocíclicos e seco-iridoides, ocorrendo comumente na forma glicosilada. Estes compostos são marcadores taxonômicos em algumas famílias vegetais e apresentam diversas atividades biológicas tais como cardiovascular, neuroprotetora e anti-Leishmania. Diante da importância dos iridoides, este trabalho teve como finalidade a prospecção química destes metabólitos em espécies nativas do Rio Grande Grande dos Sul, bem como a semissíntese de análogos e a investigação da atividade anti-Leishmania através de ensaios in vitro e modelagem molecular. Os compostos isolados foram identificados através de métodos espectroscópicos e os resultados comparados aos descritos na literatura. A partir de Escallonia bifida e Escallonia megapotamica (Escalloniaceae) foram isolados asperulosídeo, desacetilasperulosídeo, geniposídeo, ácido geniposídico e dafilosídeo, sendo que o asperulosídeo foi convertido em asperulosídeo tetraacetilado por meio de semissíntese. De Angelonia integerrima (Scrophulariaceae) foram obtidos galiridosídeo e antirrídeo. Nos experimentos in vitro para atividade anti-Leishmania, asperulosídeo, galiridosídeo, geniposídeo, ipolamida e teveridosídeo, nas concentrações 5-100 μM, não demonstraram inibição frente às formas promastigotas de Leishmania amazonensis. O estudo de modelagem molecular destes iridoides e daqueles descritos na literatura com atividade anti-Leishmania propôs um modelo farmacofórico que demonstrou que as diferenças estruturais não são responsáveis pela inatividade das moléculas isoladas neste trabalho. A perspectiva é realizar ensaios enzimáticos de tripanotiona redutase, bem com docking molecular e estudos de dinâmica molecular para investigar as interações entre grupamentos farmacofóricos das moléculas isoladas e o sítio de ligação de tripanotiona redutase. / Iridoids are secondary metabolites of eudicotyledonous angiosperms, present mainly in species of the orders Gentianales and Lamiales. The iridoids are divided into carbocyclic and seco-iridoids, occurring commonly in the glycosylated form. These compounds are taxonomic markers in same families of plants and have shown cardiovascular, neuroprotective and anti-Leishmania activities. In view of the importance of iridoids, this work aimed to the chemical prospection of these metabolites of native species of Rio Grande do Sul, as well as semi-synthesis of analogues and to investigate the anti-Leishmania activity through in vitro assays and molecular modeling. The isolated compounds were identified by spectroscopic methods and the results compared to those described in literature. From Escallonia bifida and Escallonia megapotamica (Escalloniaceae) asperuloside, deacetylasperuloside, geniposide, geniposidic acid and daphyloside were isolated, being asperuloside developed in asperuloside tetraacetylated by means of semi- synthesis. From Angelonia integerrima (Scrophulariaceae) galiridoside and antirride were obtained. In the in vitro experiments for anti-Leishmania activity, asperuloside, galiridoside, geniposideo, ipolamiide and theveridoside in concentrations 5-100 μM, did not demonstrate inhibition in promastigote form of Leishmania amazonensis. The molecular modeling study of these iridoids and those described in the literature with anti-Leishmania activity proposed a pharmacophoric model that demonstrated that the structures are not responsible by the inactivity of the molecules isolated in this work. The prospect is to carry out enzymatic assays of trypanothione redutase as well as molecular docking and molecular dynamics studies to investigate the interactions between pharmacophoric grouping of the isolated molecules and the trypanothione reductase binding site.

A self-healing material has the inherent ability to partially reverse damage such as crack formation that might have occurred during its service. Significant evidence exists in the literature to indicate that asphalt binder is a self-healing material. It is also well known that healing has a substantial affect on the performance of asphalt mixtures and consequently on the serviceable life of asphalt pavements. For example, shift factors from laboratory experimental data to field observed data show that laboratory data underpredict field observations. There is a need to understand the mechanisms that are responsible for healing in asphalt binders as well as to develop test methods that can be used to determine properties related to these mechanisms. This thesis presents details and findings from a two-part study that addresses each one of these two aspects. In the first part of this study, a test method based on the use of a Dynamic Shear Rheometer (DSR) was developed to determine the parameters of characteristic healing function of asphalt binders. In the second part of this study, Molecular Modeling (MM) techniques were used to determine the interrelationship between molecular structure, surface free energy, self diffusivity, and other healing properties of asphalt binders.The healing characteristic equation parameter (Ro) which represents the instantaneous healing nature of the asphalt binders is analogous to surface energy in terms of effect on healing in asphalt binders. Ro values for three asphalt binders AAM, AAD and ABD are calculated and compared with the surface energy values available from the literature. It was observed that the Ro values are proportional to surface energy values. Surface energy values for five asphalt binders AAM, AAD, AAB, AAG and AAF are calculated using MM method based on SHRP representative molecules. These values were observed to be proportional to the surface energy values from literature. Bulk and surface diffusion coefficients of asphalt molecules are calculated using MM method. Parametric analysis was done to determine the effect of chemical structure of asphalt on its diffusion properties. It was observed that the higher percentage of saturates in the chemical structure results into higher diffusion coefficients.

Bitter taste signaling in humans is mediated by a group of 25 bitter receptors (T2Rs) that belong to the G-protein coupled receptor (GPCR) family. Previously, several bitter peptides were isolated and characterized from bitter tasting food protein derived extracts, such as pea protein and soya bean extracts. However, their molecular targets in humans were poorly characterized. In this study, we tested the ability of the bitter tasting tri- and di-peptides to activate the human bitter receptor, T2R1. Using a heterologous expression system, T2R1 gene was transiently expressed in C6-glioma cells and changes in intracellular calcium were measured following addition of the peptides. We found that the bitter tasting tri-peptides are more potent in activating T2R1 than the di-peptides tested. Furthermore, to elucidate the potential ligand binding pocket of T2R1 we used homology molecular modeling. The ligand binding pocket in T2R1 is present on the extracellular surface of the receptor, and is formed by the transmembrane helices 1, 2, 3 and 7 and with extracellular loops 1 and 2.

Bitter taste signaling in humans is mediated by a group of 25 bitter receptors (T2Rs) that belong to the G-protein coupled receptor (GPCR) family. Previously, several bitter peptides were isolated and characterized from bitter tasting food protein derived extracts, such as pea protein and soya bean extracts. However, their molecular targets in humans were poorly characterized. In this study, we tested the ability of the bitter tasting tri- and di-peptides to activate the human bitter receptor, T2R1. Using a heterologous expression system, T2R1 gene was transiently expressed in C6-glioma cells and changes in intracellular calcium were measured following addition of the peptides. We found that the bitter tasting tri-peptides are more potent in activating T2R1 than the di-peptides tested. Furthermore, to elucidate the potential ligand binding pocket of T2R1 we used homology molecular modeling. The ligand binding pocket in T2R1 is present on the extracellular surface of the receptor, and is formed by the transmembrane helices 1, 2, 3 and 7 and with extracellular loops 1 and 2.

Iridoides são metabólitos secundários provenientes de angiospermas eudicotiledôneas, presentes principalmente em espécies das ordens Gentianales e Lamiales. Os iridoides dividem-se em carbocíclicos e seco-iridoides, ocorrendo comumente na forma glicosilada. Estes compostos são marcadores taxonômicos em algumas famílias vegetais e apresentam diversas atividades biológicas tais como cardiovascular, neuroprotetora e anti-Leishmania. Diante da importância dos iridoides, este trabalho teve como finalidade a prospecção química destes metabólitos em espécies nativas do Rio Grande Grande dos Sul, bem como a semissíntese de análogos e a investigação da atividade anti-Leishmania através de ensaios in vitro e modelagem molecular. Os compostos isolados foram identificados através de métodos espectroscópicos e os resultados comparados aos descritos na literatura. A partir de Escallonia bifida e Escallonia megapotamica (Escalloniaceae) foram isolados asperulosídeo, desacetilasperulosídeo, geniposídeo, ácido geniposídico e dafilosídeo, sendo que o asperulosídeo foi convertido em asperulosídeo tetraacetilado por meio de semissíntese. De Angelonia integerrima (Scrophulariaceae) foram obtidos galiridosídeo e antirrídeo. Nos experimentos in vitro para atividade anti-Leishmania, asperulosídeo, galiridosídeo, geniposídeo, ipolamida e teveridosídeo, nas concentrações 5-100 μM, não demonstraram inibição frente às formas promastigotas de Leishmania amazonensis. O estudo de modelagem molecular destes iridoides e daqueles descritos na literatura com atividade anti-Leishmania propôs um modelo farmacofórico que demonstrou que as diferenças estruturais não são responsáveis pela inatividade das moléculas isoladas neste trabalho. A perspectiva é realizar ensaios enzimáticos de tripanotiona redutase, bem com docking molecular e estudos de dinâmica molecular para investigar as interações entre grupamentos farmacofóricos das moléculas isoladas e o sítio de ligação de tripanotiona redutase. / Iridoids are secondary metabolites of eudicotyledonous angiosperms, present mainly in species of the orders Gentianales and Lamiales. The iridoids are divided into carbocyclic and seco-iridoids, occurring commonly in the glycosylated form. These compounds are taxonomic markers in same families of plants and have shown cardiovascular, neuroprotective and anti-Leishmania activities. In view of the importance of iridoids, this work aimed to the chemical prospection of these metabolites of native species of Rio Grande do Sul, as well as semi-synthesis of analogues and to investigate the anti-Leishmania activity through in vitro assays and molecular modeling. The isolated compounds were identified by spectroscopic methods and the results compared to those described in literature. From Escallonia bifida and Escallonia megapotamica (Escalloniaceae) asperuloside, deacetylasperuloside, geniposide, geniposidic acid and daphyloside were isolated, being asperuloside developed in asperuloside tetraacetylated by means of semi- synthesis. From Angelonia integerrima (Scrophulariaceae) galiridoside and antirride were obtained. In the in vitro experiments for anti-Leishmania activity, asperuloside, galiridoside, geniposideo, ipolamiide and theveridoside in concentrations 5-100 μM, did not demonstrate inhibition in promastigote form of Leishmania amazonensis. The molecular modeling study of these iridoids and those described in the literature with anti-Leishmania activity proposed a pharmacophoric model that demonstrated that the structures are not responsible by the inactivity of the molecules isolated in this work. The prospect is to carry out enzymatic assays of trypanothione redutase as well as molecular docking and molecular dynamics studies to investigate the interactions between pharmacophoric grouping of the isolated molecules and the trypanothione reductase binding site.

Iridoides são metabólitos secundários provenientes de angiospermas eudicotiledôneas, presentes principalmente em espécies das ordens Gentianales e Lamiales. Os iridoides dividem-se em carbocíclicos e seco-iridoides, ocorrendo comumente na forma glicosilada. Estes compostos são marcadores taxonômicos em algumas famílias vegetais e apresentam diversas atividades biológicas tais como cardiovascular, neuroprotetora e anti-Leishmania. Diante da importância dos iridoides, este trabalho teve como finalidade a prospecção química destes metabólitos em espécies nativas do Rio Grande Grande dos Sul, bem como a semissíntese de análogos e a investigação da atividade anti-Leishmania através de ensaios in vitro e modelagem molecular. Os compostos isolados foram identificados através de métodos espectroscópicos e os resultados comparados aos descritos na literatura. A partir de Escallonia bifida e Escallonia megapotamica (Escalloniaceae) foram isolados asperulosídeo, desacetilasperulosídeo, geniposídeo, ácido geniposídico e dafilosídeo, sendo que o asperulosídeo foi convertido em asperulosídeo tetraacetilado por meio de semissíntese. De Angelonia integerrima (Scrophulariaceae) foram obtidos galiridosídeo e antirrídeo. Nos experimentos in vitro para atividade anti-Leishmania, asperulosídeo, galiridosídeo, geniposídeo, ipolamida e teveridosídeo, nas concentrações 5-100 μM, não demonstraram inibição frente às formas promastigotas de Leishmania amazonensis. O estudo de modelagem molecular destes iridoides e daqueles descritos na literatura com atividade anti-Leishmania propôs um modelo farmacofórico que demonstrou que as diferenças estruturais não são responsáveis pela inatividade das moléculas isoladas neste trabalho. A perspectiva é realizar ensaios enzimáticos de tripanotiona redutase, bem com docking molecular e estudos de dinâmica molecular para investigar as interações entre grupamentos farmacofóricos das moléculas isoladas e o sítio de ligação de tripanotiona redutase. / Iridoids are secondary metabolites of eudicotyledonous angiosperms, present mainly in species of the orders Gentianales and Lamiales. The iridoids are divided into carbocyclic and seco-iridoids, occurring commonly in the glycosylated form. These compounds are taxonomic markers in same families of plants and have shown cardiovascular, neuroprotective and anti-Leishmania activities. In view of the importance of iridoids, this work aimed to the chemical prospection of these metabolites of native species of Rio Grande do Sul, as well as semi-synthesis of analogues and to investigate the anti-Leishmania activity through in vitro assays and molecular modeling. The isolated compounds were identified by spectroscopic methods and the results compared to those described in literature. From Escallonia bifida and Escallonia megapotamica (Escalloniaceae) asperuloside, deacetylasperuloside, geniposide, geniposidic acid and daphyloside were isolated, being asperuloside developed in asperuloside tetraacetylated by means of semi- synthesis. From Angelonia integerrima (Scrophulariaceae) galiridoside and antirride were obtained. In the in vitro experiments for anti-Leishmania activity, asperuloside, galiridoside, geniposideo, ipolamiide and theveridoside in concentrations 5-100 μM, did not demonstrate inhibition in promastigote form of Leishmania amazonensis. The molecular modeling study of these iridoids and those described in the literature with anti-Leishmania activity proposed a pharmacophoric model that demonstrated that the structures are not responsible by the inactivity of the molecules isolated in this work. The prospect is to carry out enzymatic assays of trypanothione redutase as well as molecular docking and molecular dynamics studies to investigate the interactions between pharmacophoric grouping of the isolated molecules and the trypanothione reductase binding site.

Tryptases are trypsin‐like serine proteinases found in the granules of mast cells. Although they show 40% sequence identity with trypsin and contain only 20 or 21 additional residues, tryptases display several unusual features. Unlike trypsin, the tryptases only make limited cleavages in a few proteins and are not inhibited by natural trypsin inhibitors, they form tetramers, bind heparin, and their activity on synthetic substrates is progressively inhibited as the concentration of salt increases above 0.2 M. Unique sequence features of seven tryptases were identified by comparison to other serine proteinases. The three‐dimensional structures of the tryptases were then predicted by molecular modeling based on the crystal structure of bovine trypsin. The models show two large insertions to lie on either side of the active‐site cleft, suggesting an explanation for the limited activity of tryptases on protein substrates and the lack of inhibition by natural inhibitors. A group of conserved Trp residues and a unique proline‐rich region make two surface hydrophobic patches that may account for the formation of tetramers and/or inhibition with increasing salt. Although they contain no consensus heparin‐binding sequence, the tryptases have 10–13 more His residues than trypsin, and these are positioned on the surface of the model. In addition, clustering of Arg and Lys residues may also contribute to heparin binding. Putative Asn‐linked glycosylation sites are found on the opposite side of the model from the active site. The model provides structural explanations for some to the unusual characteristics of the tryptases and a rational basis for future experiments, such as site‐directed mutagenesis.

DNA microarrays are a potentially disruptive technology in the medical field, but their use in such settings is limited by poor reliability. Microarrays work on the principle of hybridization and can only be as reliable as this process is robust, yet little is known at the molecular level about how the surface affects the hybridization process. This work uses advanced molecular simulation techniques and an experimentally-parameterized coarse-grain model to determine the mechanism by which hybridization occurs on surfaces and to identify key factors that influence the accuracy of DNA microarrays. Comparing behavior in the bulk and on the surface showed, contrary to previous assumptions, that hybridization on surfaces is more energetically favorable than in the bulk. The results also show that hybridization proceeds through a mechanism where the untethered (target) strand often flips orientation. For evenly-lengthed strands, the surface stabilizes hybridization (compared to the bulk system) by reducing the barriers involved in the flipping event. Additional factors were also investigated, including the effects of stretching or compressing the probe strand as a model system to test the hypothesis that improving surface hybridization will improve microarray performance. The results in this regard indicate that selectivity can be increased by reducing overall sensitivity by a small degree. Another factor that was investigated was the effect of unevenly-lengthed strands. It was found that, when unevenly-lengthed strands were hybridized on a surface, the surface may destabilize hybridization compared to the bulk, but the degree of destabilization is dependent on the location of the matching sequence. Taken as a whole, the results offer an unprecedented view into the hybridization process on surfaces and provide some insights as to the poor reproducibility exhibited by microarrays. Namely, the prediction methods that are currently used to design microarrays based on duplex stability in the bulk do a poor job of estimating the stability of those duplexes in a microarray environment.

Cross-linked polymers are of great importance to industrial practice and theoretical studies. The unique network structures of these materials have endowed them with many superior properties. In this thesis, we study cross-linked polymers from both of experimental and theoretical sides, with an emphasis on the formation process and properties of the prepared networks. Two specific problems are investigated: development of polymer coatings over solid particles with in situ curing, and molecular dynamics (MD) study of network formation kinetics and structure-property relationship. In the study of polymer coating, a hot-melt coating process for solid particles is developed. Phenolic resin is used to coat the substrates and subsequently cured in situ. Among various processing parameters, temperature is found to play an especially important role in the coating performance. Higher temperature leads to stronger coating layers with better barrier properties, whereas lower temperature is preferable for better surface morphology. These two trends can be partially reconciled with ramping temperature profiles; however, the improvement is eventually limited by the rate of heat transfer. In MD study, the effects of precursor topology on the formation, structure and mechanical properties of polymer networks are studied. Cross-linked polymer networks are synthesized from three sets of precursors with varying chain length. Little difference is observed between these networks in typical properties including radial distribution function, overall statistics of network connectivity, and glass transition behaviors. The elastic modulus of the network is found to correlate strongly with the number of elastic strands in the network, except at the highly-cross-linked limit where substantial discrepancy is observed between networks from different precursors. Although these final networks contain a similar level of structural defects, the choice of precursor has a significant effect on the spatial distribution of the defects, which explains the precursor dependence of their mechanical property observed in the tensile test. / Thesis / Master of Applied Science (MASc)