Dissertations / Theses on the topic 'Aromatic smell'

Photochemistry and photophysics are prominent and important phenomena, being involved in such diverse processes as photosynthesis, vision and solar energy capture. An understand› ing of the mechanisms of energy flow after photoexcitation is integral to the reproduction or control of these processes. Such dynamical considerations are intimately related to spec› troscopy - the study of the interaction of light with matter - and by their nature must be treated using quantum mechanical methods. This work aims to build on the current understanding of, and the methods of monitor› ing , photo-initiated dynamics within individual gas-phase aromatic molecules. Multiphoton ionisation and valence photoelectron spectroscopy are used to excite and probe gas phase molecules that have been cooled by means of a supersonic expansion. A time-resolved ap› proach is employed in order to study the process of vibrational redistribution in electronically excited states; dynamics are initiated by a laser pulse of picosecond duration, and a second ionisation pulse, arriving a variable time delay later, is used to probe the changing state of the molecule. The vibrational state of the molecule is indicated by the energy distribution of the photoelectrons, which is measured using the velocity map imaging (VMI) technique. There is the possibility of resolving peaks corresponding to individual ionic vibrational states due to the relatively narrow bandwidth of the laser pulses. Observations are made of os› cillatory dynamics at a number of different energies in the first electronically excited state of para-difluorobenzene. Analysis reveals previously unobserved vibrational structure and sheds further light on the mechanisms of vibrational redistribution . These observations are compared and contrasted with those from fluorobenzene, toluene and para-fluorotoluene in order to investigate the effect of reducing symmetry and the presence of different functional groups on the observed dynamics. The angular distribution of the photoelectrons is also recorded as part of a VMI measurement. These distributions are determined by interference the between the partial waves that describe the wavefunctions of the outgoing electrons, and can be sensitive to the quantum states and alignment of molecules. The potential for using measurements of photoelectron angular distributions (PADs) to monitor intramolecular dynamics is evaluated.

Loline alkaloids (LA) are secondary metabolites produced by Epichloandamp;euml; (anamorph, Neotyphodium) grass endophytes. They are toxic and deterrent to a broad range of herbivorous insects but not to livestock. This protective bioactivity has spurred considerable research into the LA biosynthetic pathway. LOL, the gene cluster containing nine genes, is required for LA biosynthesis. The regulation of LOL genes during LA production in culture and in symbio is of interest. In this study, coordinate regulation between LOL gene expression and LA production level was investigated in both MM culture and symbiota. Results showed that expression of LOL genes in N. uncinatum MM culture were tightly correlated with each other (p andamp;lt; 0.0005), and all presented a significant temporal quadratic pattern during LA production. Gene expression started before LA were detectable, and increased while LA accumulated. The highest gene expression level was reached before the highest amounts of LA were detected, and gene expression level declined to a very low level after amounts of LA plateaued. Observations suggested that the hierarchical clusters based on the correlation coefficient could help to predict the roles of LOL genes in the LA pathway. In symbiota, coordinate coregulation of LOL gene expression with LA was found in E. festucae-meadow fescue inflorescences and stromata, whereby lower LOL gene expression corresponded with the lower LA level in stromata. In N. uncinatum (or N. siegelii)-meadow fescue vegetative tissues, dramatically higher LA levels were found in younger leaf tissue than in older leaf tissue, yet no evidence was found to relate this difference to LOL gene expression differences. Instead, substrate availability may regulate the LA level. In particular, asparagine was more than 10-fold higher in young leaf tissue than in old tissue, although proline was significantly lower in young tissue. Therefore, different regulatory mechanisms underlie LOL gene expression and LA production in different circumstances. The GUS activity of Pro-lolC2-GUS and Pro-lolA2-GUS in Neotyphodium species was almost undetectable in culture, though the activity could be detected in symbiota. The mRNA of GUS did not exhibit the same pattern as lolC2 or lolA2 in culture during LA production time course. A Pro-lolC2-cre transgene was expressed in complex medium, in which lolC2 mRNA was not detectable. These results suggest that proper regulation of LOL genes in culture or symbiota is dependent on the LOL cluster.

Limited data is currently available for diesel particulate matter (DPM) and polynuclear aromatic hydrocarbon (PAH) exposure in underground coal mines in South Africa. The lack of regulatory exposure limits for DPM and PAH in South Africa makes it difficult for the mining industry to evaluate concerned exposure results effectively. The purpose of this study was to determine load haul dump (LHD) vehicle operator exposure to DPM and PAH in four small to medium sized coal mines. Exposures were measured against international standards which could appropriately be implemented in South Africa. The National Institute for Occupational Safety and Health (NIOSH) method 5040 was used to measure exposure for DPM using submicron elemental carbon as surrogate. NIOSH method 5515 was used to measure exposure towards seventeen PAH compounds. Exposure results for DPM were far below the available exposure limit. The use of two LHD vehicles underground showed results that were 2.6 times higher than when one LHD vehicle was used. Exposure results for PAH showed values below laboratory detection limits. The TC/EC values for the four coal mines indicated that the Mine Safety and Health Administration (MSHA) TC/EC value of 1.3 is not suitable for South African coal mines if the MSHA standards for DPM were to be adopted in South Africa. The findings of this study are consistent with another local study conducted in 2008. To conclude, this study emphasized the urgency to establish regulatory exposure limits for DPM and PAH.<br>Thesis (M.Sc. (Occupational Hygiene))--North-West University, Potchefstroom Campus, 2011.

A new material for use as a proton exchange membrane in fuel cells has been developed: a blend of a perfluorocyclobutane-based block ionomer (S-PFCB) and Poly (vinylidene-co-hexafluoropropylene) (Kynar Flex, KF). This thesis details the work done thus far to characterize the morphology of this material, using small angle x-ray scattering, differential scanning calorimetry, atomic force micrscopy, and some other techniques to a lesser extent. Small angle x-ray scattering (SAXS) of pure S-PFCB showed a strong block copolymer- associated phase separation, on the order of 25 nm. Differential scanning Calorimetry (DSC) confirmed this finding. SAXS also revealed the presence of a peak representing individual ionic aggregates on the order of 3 nm. Finally, it was shown with DSC that no crystallinity develops in the S-PFCB block copolymer, while one of the blocks, known as 6F, crystallizes extensively. SAXS of incremental blend compositions of KF and S-PFCB revealed a steady increase in size of the block copolymer phase separation peak in SAXS, demonstrative of the miscibility of KF and the non-sulfonated 6F block of S-PFCB. Furthermore, this incremental study determined the scattering vector range relevant for comparing amounts of KF crystallinity. DSC of incremental blend compositions revealed two phases of KF crystallinity develops upon cooling a membrane, independent of cooling rate. Atomic force microscopy (AFM), small angle x-ray scattering (SAXS), and differential scanning calorimetry (DSC) corroborate to suggest a nonuniform morphology through the thickness of solution cast membranes. Also, the effect of different casting temperatures and after-casting anneals on morphology was assessed. Future work on this project involves morphological studies at various relative humidities and temperatures, as well as following up on discoveries already made. Finally, transmission electron micrscopy (TEM) should be performed to provide a visual analog, which will greatly help in developing an accurate morphological model.<br>Master of Science

Les Hydrocarbures Aromatiques Polycycliques (HAP) sont des polluants environnementaux majeurs présentant des effets toxiques sur la santé humaine. Parmi les types cellulaires ciblés par les HAP, se trouvent les cellules mononucléaires circulantes du sang (PBMC). La présente étude vise à 1) étudier l'effet du B[a]P, HAP de référence, sur le profil d'expression des microARN (miRNA)in vitro dans les PBMC, ainsi que dans les vésicules extracellulaires (EV) sécrétées par ces cellules, en utilisant une approche de small RNA-seq, 2) Confirmer la présence de miRNA vésiculaires in vivo dans le plasma de rats traités par le B[a]P, 3) analyser, par une approche bioinformatique, les cibles potentielles des miRNA cellulaires et vésiculaires et caractériser, leurs voies de signalisation et fonctions biologiques et 4) comprendre le rôle des EV et de leurs miRNA sur la fonction et le phénotype des cellules endothéliales adjacentes. Nos résultats ont identifié les miARN régulés par le B[a]P dans les PBMCs et l'ontologie a montré que leurs gènes cibles étaient principalement impliqués dans les processus de mort et survie cellulaires. Des études plus approfondies ont révélé l’importance du miR-132, régulé par le B[a]P de manière dose- et temps-dépendants et qui nécessite l’activation du récepteur aryl hydrocarbon (AhR). Nous avons aussi démontré que ce miR-132 était impliqué dans la mort cellulaire induite par le B[a]P, en modifiant la balance des cytochromes P-450 (CYP) de la famille 1, classiquement régulés par l’AhR. Nos résultats rapportent ensuite une augmentation de la libération d'EV à la fois in vitro à partir de PBMC exposées et in vivo dans le plasma de rats exposés au B[a]P et proposent un panel de miRNA vésiculaires régulés par l'exposition aux HAP. Enfin, l'analyse ontologique a révélé différents profils d'expression de miRNA entre les PBMC et leurs EV, en lien avec un adressage sélectif des miRNA à l'intérieur des EV. Cette dernière analyse nous a conduit à nous intéresser au rôle des EV issues des PBMC après exposition aux HAP sur les cellules endothéliales voisines. Nos premiers résultats montrent une internalisation de ces EV associée à une modification de l’expression des gènes endothéliaux impliqués dans l'inflammation, le stress oxydatif et la migration. Au total, ces études proposent les EV et les miRNA comme de nouveaux outils non seulement pour étudier les mécanismes de toxicité des HAP mais aussi pour identifier des marqueurs d’exposition à ces polluants environnementaux<br>Polycyclic Aromatic Hydrocarbons (PAH) are major environmental pollutants with toxic effects on human health. Among the cell types targeted by PAHs are circulating blood mononuclear cells (PBMC). The present study aims to 1) investigate the effect of B[a]P, a reference PAH, on the expression profile of microRNAs (miRNAs) in vitro in PBMCs, as well as in extracellular vesicles (EVs) secreted by these cells, using a small RNA-seq approach, 2) confirm the presence of vesicular miRNAs in vivo in the plasma of B[a]P-treated rats, 3) to analyze, by a bioinformatics approach, the potential targets of cellular and vesicular miRNAs and characterize, their signaling pathways and biological functions and 4) to understand the role of EVs and their miRNAs on the function and phenotype of adjacent endothelial cells. Our results identified B[a]P regulated miRNAs in PBMCs and ontology showed that their target genes were mainly involved in cell death and survival processes. Further studies revealed the importance of miR-132, which is regulated by B[a]P in a dose- and time-dependent manner, and require activation of the aryl hydrocarbon receptor (AhR). We also demonstrated that this miR-132 was involved in B[a]P-induced cell death by altering the balance of family 1 cytochrome P-450 (CYP), classically regulated by AhR. Our results then report an increase in EV release both in vitro from exposed PBMCs and in vivo in plasma from B[a]P-exposed rats and propose a panel of vesicular miRNAs regulated by PAH exposure. Finally, the ontological analysis revealed different miRNA expression profiles between PBMCs and their EVs, related to selective miRNA addressing within EVs. This last analysis led us to investigate the role of EVs from PBMCs after exposure to PAHs on neighboring endothelial cells. Our first results show internalization of these EVs is associated with a modification of the expression of endothelial genes involved in inflammation, oxidative stress, and migration. Altogether, these studies propose EVs and miRNAs as new tools not only to study the mechanisms of PAH toxicity but also to identify markers of exposure to these environmental pollutants

Understanding the behaviour of molecules on a semiconductor surface is necessary if molecular self-assembly is going to be employed, with existing semiconductor technology, to create useful devices. Si(111)-7x7 is an invaluable surface upon which to study molecular adsorption. The surface reconstruction has been well characterized and it possesses seven symmetrically distinct dangling bonds that can serve as reaction sites. Aromatic molecules on Si(111)-7x7 have been investigated with a variety of techniques and have been shown to chemisorb at room temperature. However, it is not trivial to predict how an ensemble of aromatic molecules might distribute themselves amongst the available bonding sites on this surface. The work presented in this thesis begins with a joint STM and ab initio investigation of thiophene on 7x7 that demonstrates kinetics are necessary to describe the chemisorption sites occupied at various coverages. A kinetic Monte Carlo model, taking into account a mobile physisorbed state, is shown to accurately describe this site occupancy at room temperature. This model disregards molecule-molecule interaction because thiophene does not sterically hinder chemisorption to a neighbouring dangling bond. A larger molecule, mesitylene, was then studied on Si(111)-7x7, and shown to form an ordered molecular lattice on the Si(111)-7x7 surface. This is the first demonstration of a porous molecular lattice grown on Si(111)-7x7 at room temperature. Finally, molecular chemisorption on the related 5x5 reconstruction, grown by depositing Ge on 7x7, is studied. It is found that the presence of Ge hinders molecular chemisorption, preventing formation of the mesitylene lattice.<br>Thesis (Ph.D, Physics, Engineering Physics and Astronomy) -- Queen's University, 2009-09-11 10:14:10.118

碩士<br>國立高雄大學<br>應用化學系碩士班<br>102<br>In our laboratory, the interaction between small chiral molecule and enantiomer was used to investigate the chiral self-recognition mechanism. A series of racemate small molecule compound was explored the relation of self-recognition in the solid state. In this work is focused on the various substituents on the aromatic ring that generated the different effects. The crystal structure was analyzed their direction of arrangement in the solid state by X-ray crystallography. N-(3,5-dinitrobenzoyl)leucine diethyl amide is the pioneer compound in our lab. We have been synthesized many derivatives based on N-(3,5-dinitrobenzoyl)leucine diethyl amide. Those derivative compounds also tried to analyze their structure arrangement by X-ray crystallography and explored the influence of π-π interaction from various substituents on the aromatic ring. By the high-performance liquid chromatography analysis, we used the commercially available column to explore the interactions when various substituents through chiral stationary phase. Combine the crystal information and high-performance liquid chromatography analysis, we found some significant factor relate to the substituent effects and π-π interactions. Understanding the key factor of chiral recognition mechanism will help to develop the design of chiral stationary phases, chiral selectors and catalysts.

CXCR4 is a chemokine receptor that has been linked to several disease related pathways including: HIV-1 proliferation, autoimmune disorders, inflammatory disease and cancer metastasis. The interaction of the C-X-C chemokine receptor type 4 (CXCR4) with C-X-C chemokine ligand 12 (CXCL12) plays a key role in triggering these disease related pathways. Various antagonists for these receptors have been synthesized and tested, but many are not useful clinically either because of toxicity or poor pharmacokinetics. Some of the most extensive CXCR4 antagonist libraries stem from a class of compounds, p-xylyl-enediamines, which all feature a benzene ring as the core of the compound. This work focuses on the design and synthesis of a new class of compounds that show potential as CXCR4 antagonists by using heterocyclic aromatic rings (2,6-pyridine, 2,5-furan, 2,5-pyrazine and 3,4-thiophene) as the core of the scaffold. After synthesis, these analogues were probed through a variety of assays and techniques by our collaborators in the Shim lab at Emory University including: preliminary binding assays, Matrigel invasion assays, carrageenan mouse paw edema tests, and in silico analysis. In silico analysis also probed 2,5-thiophene-based analogues previously synthesized. This work has produced the beginnings of a new library of CXCR4 antagonists and has identified fifteen hit compounds that are promising leads for further testing and modification.

The recognition of modified amino acids by reader proteins is governed by the competing interplay of weak, attractive, intermolecular forces and solvation effects. For the recognition of hydrophobic cations like methyl-lysines and methyl-arginines, native reader proteins utilize structural cages always containing multiple aromatic amino acids and sometimes an occasional acidic residue. Through the highly ordered arrangement of multiple aromatic surfaces, reader proteins can invoke the attractive forces of electrostatic, cation-pi, and in the case of arginine, pi-pi interactions. The hydrophobic effect can also significantly affect these binding events in aqueous environments. In this thesis, a number of small molecule, synthetic cages containing significant aromatic surface area have been synthesized. Variation in both total host hydrophobicity and degree of flexibility were explored to determine what effect they have on the overall binding of methylated amino acids in water. Significant flexibility in the first generation of highly aromatic hosts was shown to be detrimental to binding. However, strong binding was observed for guests with significant hydrophobic character despite this flexibility. The cause of the strong affinities in this family of synthetic cages was shown to be due to the hydrophobic effect, rather than any attraction due to cation-pi interactions. Synthetic efforts towards hosts with more rigid structures led to the use of Tröger’s base as a structural building block. Hosts incorporating Tröger’s bases into well-defined aromatic cavities were found to exhibit strong binding to both methyl-lysine and methyl-arginine derivatives in pure water. Differences in guest selectivity were due to the rigid altered host geometry introduced by the Tröger’s base cleft.<br>Graduate

Rainwater contains a large variety of contaminants, namely aromatic compounds, that should be removed if its utilization is intended for domestic purposes. The present work evaluates the degradation of a mixture of three small aromatic compounds (benzoic, 3,5-dihydroxybenzoic and syringic acids), by UV/H2O2, in model solutions and in rainwater. The extent of oxidation was assessed by ultraviolet-visible and molecular fluorescence spectroscopies. It was verified that, during the oxidation of the mixture, new chromophoric compounds are formed, possibly with higher degree of unsaturation and hydroxylation, and these compounds are, then, degraded. It was also demonstrated that, the increase of H2O2 concentration, results in a higher extent of oxidation. On the other hand, it was verified that the pH does not influence the oxidation of the mixture, at least for pH values in rainwater (between 4.0 and 7.0). The optimization of the oxidation of the mixture of contaminants by the UV/H2O2 process was performed through the utilization of the uniform design as experimental design, with the following factors: H2O2 concentration, pH, and reaction time. The response surface model corresponds to a second order polynomial, where the extent of oxidation is a function of the following variables: H2O2 concentration, reaction time, interaction between these two factors and their respective quadratic forms. The optimum region, which corresponds to an extent of oxidation of approximately 100 %, can be observed for a combination of values for the variables, where the optimum chosen corresponds to a lower H2O2 concentration (3.1 mM) and a maximum reaction time (4 h). The application of the optimal conditions to rainwater samples, spiked with a mixture of contaminants, resulted in an extent of oxidation higher than 99.5 %, suggesting that the model is applicable to real samples. The results obtained in this work suggest that the UV/H2O2 process can be used as an alternative for the treatment of rainwater, namely in what concerns the degradation of small aromatic acids.<br>A água da chuva contém uma enorme variedade de contaminantes, nomeadamente compostos aromáticos, que devem ser removidos se se pretender a respetiva utilização para finalidades domésticas. O presente trabalho avalia a degradação de uma mistura de três pequenos compostos aromáticos (ácidos benzóico, 3,5-dihidroxibenzóico e siríngico), através do processo UV/H2O2, em soluções modelo e em água da chuva. A extensão da oxidação foi avaliada por espectroscopias de ultravioleta-visível e fluorescência molecular. Foi verificado que, no decorrer da oxidação da mistura, se formam novos compostos cromofóricos, possivelmente com maior grau de insaturação e hidroxilação, e que posteriormente são degradados. Foi também demonstrado que, o aumento da concentração de H2O2, resulta em taxas de oxidação mais elevadas. Por outro lado, foi verificado que o pH não influencia a oxidação da mistura, pelo menos para valores típicos de pH em águas da chuva (entre 4,0 e 7,0). A otimização da oxidação da mistura de contaminantes pelo processo de UV/H2O2 foi efetuada através da utilização do “uniform design” como planeamento experimental, com os seguintes fatores: concentração de H2O2, pH e tempo de reação. O modelo de superfície de resposta corresponde a um polinómio de segunda ordem, onde a extensão de oxidação é função das seguintes variáveis: concentração de H2O2, tempo de reação, interação entre estes dois fatores e as respetivas formas quadráticas. A região do ótimo, ou seja, uma extensão de oxidação de aproximadamente 100 %, pode ser observada para uma combinação de valores das variáveis, tendo sido escolhido o ótimo correspondente a uma concentração de H2O2 mais baixa (3,1 mM) e ao tempo de reação máximo (4 h). A aplicação das condições ótimas a amostras da água da chuva, às quais foi adicionada a mistura de contaminantes, resultou em extensões de oxidação superiores a 99,5 %, indicando que o modelo é aplicável a amostras reais. Desta forma, os resultados obtidos neste estudo, evidenciam que o processo UV/H2O2 pode ser usado como uma alternativa para tratamento de água da chuva, nomeadamente no que diz respeito à remoção de pequenos ácidos aromáticos.<br>Mestrado em Biotecnologia

Molecular therapies are gaining importance as an effective therapeutic approach for various types of diseases. The most efficient vectors used to introduce the therapeutic genes are of viral origin however, non-viral vectors based on pDNA are gaining popularity due to their superior safety and easy of production. These factors have increased the demand for high quantities of pharmaceutical grade plasmid DNA (pDNA). Therefore, the research for more efficient pDNA purification protocols has also increased. Moreover, the final pDNA product must meet stringent quality criteria established by the regulatory agencies. Liquid chromatography is the method of choice for the purification of pDNA, since it is simple, robust, versatile and high reproducible. The most important features of a chromatographic procedure are the use of suitable stationary phases and ligands. As conventional purification protocols are being replaced by more sophisticated and selective procedures, the focus changes towards designing and selecting ligands of high affinity and specificity. In fact, the chemical composition of the chromatographic supports determines the interactions established with the target molecules, allowing their preferential retention over the undesirable ones. With these facts in mind, the aim of this work was to develop new chromatographic methods for the purification of pharmaceutical grade pDNA, with the purpose of improving the overall procedures to more effective, simple, economic and environmental-friendly ones. The minor groove binder berenil and the intercalator 3,8-diamino-6-phenylphenanthridine (DAPP) where chosen to be used as ligands in pDNA chromatographic purification studies. They were immobilized to an epoxy-activated Sepharose matrix using a relatively mild curing method, without a catalyst and with quite small ligand:Sepharose weight ratios. Berenil binds pDNA preferentially through hydrophobic interactions but other types of interaction contributions cannot be neglected. It was shown to be quite effective at separating and purifying pDNA from clarified and non-clarified cell lysates, using three different approaches, although isoform resolution was not obtained in either case. Using mild amounts of ammonium sulphate in the eluent, berenil-Sepharose support was able to purify distinct pDNA of two different sizes from clarified cell lysates. Moreover, the ability was continual when the clarification process was replaced by a second chromatographic run. In all cases plasmid solutions were in accordance to the specifications of a pharmaceutical product, however the yields were quite different: two consecutive chromatographic runs lead to lower recoveries (33%) and smaller pDNA molecules have higher recoveries using one run through the column (85% vs 45%). A negative chromatography approach was also performed with berenil-Sepharose, showing some advantages in terms of salt usage as well as procedure time. In this case the recovery yield was quite good (87%) and although pDNA solutions had a comparable purity to that obtained with the other approaches, the gDNA reduction was not so effective. DAPP is slightly A-T specific and binds DNA through non-covalent, reversible stacking interactions of the condensed aromatic moiety into two successive base pairs, while the phenyl residue gets inserted into the minor groove. In addition, protonated DAPP molecules bind to DNA much strongly due to the generation of strong electrostatic interactions. Plasmid DNA binding to DAPP-Sepharose varies with pH and is affected by the presence of salt in the eluent. In fact, total retention of clarified lysate components was only possible with a pH below DAPP's free state pKa (5.8) and the presence of salt destabilizes that same retention. So, the elution of bound species was simply performed by adding small amounts of sodium chloride to the buffers. These features were successfully applied for purification of sc pDNA with two distinct sizes that were obtained according to the regulatory agencies specifications. Once more, the recovery yield of the smaller pDNA molecule was higher than the one obtained for the largest one (94% vs 65%). In conclusion, DAPP-Sepharose showed exceptional characteristics to be used as an affinity support for the purification of pharmaceutical grade sc pDNA. In comparison with berenil- Sepharose, it uses much smaller amounts of salt, with less economic and environmental impact, while improving the quality and yield of the obtained plasmid fractions. Moreover, it is able to separate sc pDNA from linear and oc isoforms even in complex lysates. Moreover, combining DAPP-Sepharose chromatography with other optimized production, extraction and clarification procedures, can offer a number of advantages for pharmaceutical pDNA purification. Also, since the most significant disadvantage of this DAPP-Sepharose support is the relatively low capacity for pDNA, which in turn is strongly related to the solid matrix used, other more stable stationary phases with low pressure drops and interconnected macropores, that allow a high mass transfer of solutes, are quite fascinating alternatives.<br>Fundação para a Ciência e a Tecnologia (FCT)