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  • About
  • The Global ETD Search service is a free service for researchers to find electronic theses and dissertations. This service is provided by the Networked Digital Library of Theses and Dissertations.
    Our metadata is collected from universities around the world. If you manage a university/consortium/country archive and want to be added, details can be found on the NDLTD website.
1

A Computational Tool for Biomolecular Structure Analysis Based On Chemical and Enzymatic Modification of Native Proteins

Sweeney, Deacon John 21 September 2011 (has links)
No description available.
2

THE EVALUATION OF LARCH ARABINOGALACTAN AS A NEW CARRIER IN THE FORMULATION OF SOLID DISPERSIONS OF POORLY WATER- SOLUBLE DRUGS

Thakare, Kalpana January 2013 (has links)
Advanced drug discovery techniques have produced more lipophilic compounds. Formation of an amorphous solid dispersion of such poorly water-soluble drugs improves their solubility and dissolution. This results in greater in vivo bioavailability. Thus, it is one of the recent trends in the development of oral dosage forms. In solid dispersions, the carrier is crucial for ensuring the functionality and stability of these systems. Larch arabinogalactan FiberAid grade (AGF) is generally recognized as safe (GRAS) designated, amorphous polymer. The objective of this dissertation project was to perform a comprehensive evaluation of AGF as a carrier for amorphous solid dispersions. First, a detailed characterization of the AGF polymer was performed. A special focus on its use as a solid dispersion carrier was emphasized. The glass transition temperature and the degradation temperature of the AGF polymer were ~82 oC and ~185 oC, respectively. The AGF polymer had good hygroscopicity. Ibuprofen-AGF solid dispersions were evaluated for dissolution enhancement. Ibuprofen-Hydroxypropyl methylcellulose grade K3 (HPMCK3) solid dispersions were investigated simultaneously as a control polymer dispersion. The ibuprofen-AGF solid dispersions were amorphous at nearly 20% ibuprofen load. The dissolution of the ibuprofen from AGF solid dispersions was significantly greater than that of the neat ibuprofen. The formation of the amorphous state of ibuprofen and solution-state ibuprofen-AGF interactions were the mechanisms of the ibuprofen dissolution enhancement. At a 10% ibuprofen load, the dissolution of the AGF solid dispersion was found greater than that of the dissolution of the HPMCK3 solid dispersion. Secondly, the itraconazole-AGF solid dispersions and the ketoprofen-AGF solid dispersions were characterized and compared them with the ibuprofen-AGF solid dispersions. The comparisons were established for the miscibility and dissolution enhancement. The order of increase in dissolution was ketoprofen-AGF solid dispersions > itraconazole-AGF solid dispersions> ibuprofen-AGF solid dispersions. The same order was observed for the solid-state miscibility of these drug-AGF solid dispersions. Additionally, the solid dispersions of 9 drugs with the AGF polymer were investigated to elucidate the detailed mechanism of drug crystallization inhibition by the AGF polymer. The inherent tendency of the AGF polymer to inhibit the drug crystallization, drug-AGF solid-state hydrogen bonding and the anti-plasticizing effect of AGF were the mechanisms underlying the crystallization inhibition by the AGF polymer. Last, a storage stability of ibuprofen-AGF amorphous solid dispersions after storage under accelerated conditions (for 3 months) and ambient conditions (for 6 months) was investigated. The amorphous ibuprofen from AGF solid dispersions was physically and chemically stable under stability conditions. In summary, the AGF polymer was evaluated as a novel carrier for formation of an amorphous solid dispersions. The studies established that the AGF polymer was comparable to HPMCK3 polymer. The AGF polymer could be more advantageous than the HPMC polymer for the preparation of solid dispersion when faster dissolution is desired at lower drug load. / Pharmaceutical Sciences
3

A structural and functional study of the second periplasmic loop P2 of MalF in the maltose transporter of Escherichia coli

Jacso, Tomas 25 November 2010 (has links)
ABC (ATP-binding-cassette)-Transporter katalysieren den ATP-abhängigen Transport diverser niedermolekularer Substanzen durch die biologische Zellmembran. Ihr Vorkommen erstreckt sich auf alle drei Domänen des Lebens. Der Maltose Transporter von E.coli gehört zu dieser Superfamilie der ABC-Transporter. Die Kristallstrukturen des Transporters MalFGK2 wurden kürzlich gelöst für dessen inaktiven Zustand als auch für dessen katalytischen Zwischenzustand. Um den Transportmechanismus besser verstehen zu können, müssen die Kristallstrukturen des Transporters und seiner Komponenten unter physiologischen Bedingungen genau geprüft werden, um den daraus katalytischen Mechanismus zu bewerten. Im rahmen der Dissertation konnte mittels Lösungs-NMR kann gezeigt werden, dass die periplasmatische Schleife P2 von MalF eine unabhängige Faltung aufweist und eine wohl definierte Tertiärstruktur einnimmt, die vergleichbar ist mit der im Kristall vorliegenden Konformation. MalF-P2 interagiert unabhängig von der Transmembranregion von MalF und MalG mit dem Maltose-Bindeprotein in An- und Abwesenheit des Substrats mit einem KD im mikromolaren Bereich. NMR Untersuchungen zu den an der Interaktion beteiligten Aminosäuren stehen in Einklang mit den Kristallstrukturdaten. Die Analyse residualer dipolarer Kopplungen (RDC) zeigt, dass die Konformation der zwei individuellen Domänen von MalF-P2 in Abwesenheit von MalE erhalten bleibt und der im Kristall ähnelt. Die Zugabe von MalE induziert eine Änderung der relativen Orientierung der zwei Domänen von MalF-P2 um so dem räumlichen Anspruch des Liganden gerecht zu werden. Besonders betroffen hiervon ist die Domäne 2 von MalF-P2, deren Konformation abweicht von der in der Kristallstruktur. Die Struktur der Domäne 1 dagegen bleibt konserviert, während sich lediglich ihre relative Orientierung zu Domäne 2 ändert. MD Simulationen des MalF-P2-MalE-Komplexes deuten auf eine stark dynamische Interaktion von MalF-P2 mit der MalE Bindungsregion hin. NMR CPMG Kinetikstudien weisen auf die Bildung eines ungewöhnlichen Knicks in alhpa-Helix alpha2 während der Assoziation hin. Diese konformelle Änderung der alpha-Helix findet auf einer Zeitskala von Millisekunden statt, was im Einklang mit der Austauschrate der Komplexbildung ist. / ABC (ATP-binding-cassette)-transporters catalyze the ATP-dependent transport of diverse solutes across the cellular membrane. They are present in all three kingdoms of life. The E.coli maltose transporter belongs to the ATP binding cassette (ABC) transporter superfamily. Recently, the crystal structures of the full transporter MalFGK2 in its resting and a catalytic intermediate state was solved. At the present state of research, it is of particular interest to scrutinize the X-ray structures of the transporter and its components under physiological conditions as well as to evaluate their implications for the catalytic mechanism. In the context of the PhD thesis, it could be shown using solution-state NMR that the periplasmic loop P2 of MalF folds independently in solution and adopts a well-defined tertiary structure, which is similar to the one found in the crystal structure. MalF-P2 interacts with the maltose binding protein, independent of the transmembrane region of MalF and MalG, with a KD in the µM range, in the presence and absence of substrate. NMR studies showed good agreement of the residues interacting in solution to those identified in the X-ray structure. Analysis of residual dipolar coupling (RDC) experiments shows that the conformation of the two individual domains of MalF-P2 is preserved in the absence of MalE, and resembles the conformation in the X-ray structure. Upon titration of MalE to MalF-P2, the two domains of MalF-P2 change their relative orientation in order to accommodate the ligand. In particular, a conformational change of domain 2 of MalF-P2 is induced, which is distinct to the conformation found in the X-ray structure. Domain 1 retains its structure but changes its relative orientation to domain 2. MD simulations of the MalF-P2 – MalE complex show a highly dynamic interaction of MalF-P2 to the MalE interface. From NMR CPMG kinetic studies, a peculiar kink of alpha-helix alpha2 can be seen introduced upon association. The transition time of this conformational change of the alpha-helix is on the ms timescale, which is matching the exchange rate of the complex formation.
4

Modulation of Nanostructures in the Solid and Solution States and under an Electron Beam

Sanyal, Udishnu January 2013 (has links) (PDF)
Among various nanomaterials, metal nanoparticles are the widely studied ones because of their pronounced distinct properties arising in the nanometer size regime, which can be tailored easily by tuning predominantly their size and shape. During the past few decades, scientists are engaged in developing new synthetic methodologies for the synthesis of metal nanoparticles which can be divided into two broad categories: i) top-down approach, utilizing physical methods and ii) bottom-up approach, employing chemical methods. As the chemical methods offer better control over particle size, numerous chemical methods have been developed to obtain metal nanoparticles with narrow size distribution. However, these two approaches have their own merits and demerits; they are not complementary to each other and also not sustainable for real time applications. Recent focus on the synthesis of metal nanoparticles is towards the development of green and sustainable synthetic methodologies. A solid state route is an exciting prospect in this direction because it eliminates usage of organic solvents thus, makes the overall process green and at the same time leads to the realization of large quantity of the materials, which is required for many applications. However, the major obstacle associated with the development of a solid state synthetic route is the lack of fundamental understanding regarding the formation mechanism of the nanoparticles in the solid state. Additionally, due to the heterogeneity present in the solid mixture, it is very difficult to ensure the proximity between the capping agent and nuclei which plays the most decisive role in the growth process. Recently, employment of amine–borane compounds as reducing agents emerged as a better prospect towards the development of sustainable synthetic routes for metal nanoparticles because they offer a variety of advantages over the traditional borohydrides. Being soluble in organic medium, amine– borane allows the reaction to be carried out in a single phase and due to its mild reducing ability a much better control over the nucleation and growth processes is realized. However, the most exciting feature of these compounds is that their reducing ability is not only limited to the solution state, they can also bring out the reduction of metal ions in the solid state. With the availability of a variety of amine–boranes of varying reducing ability, it opens up a possibility to modulate the nanostructure in both solid and solution states by a judicious choice of reducing agent. Although our current understanding regarding the growth behavior of nanoparticles has advanced remarkably, however, most often it is some classical model which is invoked to understand these processes. With the recent developments in in situ transmission electron microscopy techniques, it is now possible to unravel more complex growth trajectories of nanoparticles. These studies not only expand the scope of the present knowledge but also opens up possibilities for many future developments. Objectives • To develop an atom economy solid state synthetic methodology for the synthesis of metal nanoparticles employing amine–boranes as reducing agents. • To gain a mechanistic insight into the formation mechanisms of nanoparticles in the solid state by using amine–boranes with differing reducing ability. • Synthesis of bimetallic nanoparticles as well as supported metal nanoparticles in the solid state using ammonia borane as the reducing agent. • To develop a new in situ seeding growth methodology for the synthesis of core@shell nanoparticles composed of noble metals by employing a very weak reducing agent, trimethylamine borane and their transformation to their thermodynamically stable alloy counterparts. • Synthesis of highly monodisperse ultra-small colloidal calcium nanoparticles with different capping agents such as hexadecylamine, octadecylamine, poly(vinylpyrrolidone) and a combination of hexadecylamine/poly(vinylpyrrolidone) using the solvated metal atom dispersion (SMAD) method. To study the coalescence behavior of a pair of calcium nanoparticles under an electron beam by employing in situ TEM technique. Significant results An atom economy solid state synthetic route has been developed for the synthesis of metal nanoparticles from simple metal salts using amine–boranes as reducing agents. Amine–borane plays a dual role here: acts as a reducing agent thus brings out the reduction of metal ions and decomposes simultaneously to generate B-N based compounds which acts as a capping agent to stabilize the particles in the nanosize regime. This essentially minimizes the number of reagents used and hence simplifying and eliminating the purification procedures and thus, brings out an atom economy to the overall process. Additionally, as the reactions were carried out in the solid state, it eliminates use of organic solvents which have many adverse effects on the environment, thus makes the synthetic route, green. The particle size and the size distribution were tuned by employing amine–boranes with differing reducing abilities. Three different amine–boranes have been employed: ammonia borane (AB), dimethylamine borane (DMAB), and trimethylamine borane (TMAB) whose reducing ability varies as AB > DMAB >> TMAB. It was found that in case of AB, it is the polyborazylene or BNHx polymer whereas, in case of DMAB and TMAB, the complexing amines act as the stabilizing agents. Several controlled studies also showed that the rate of addition of metal salt to AB is the crucial step and has a profound effect on the particle size as well as the size distribution. It was also found that an optimum ratio of amine–borane to metal salt is important to realize the smallest possible size with narrowest size distribution. Whereas, use of AB and TMAB resulted in the smallest sized particles with best size distribution, usage of DMAB provided larger particles that are also polydisperse in nature. Based on several experiments along with available data, the formation mechanism of metal nanoparticles in the solid state has been proposed. Highly monodisperse Cu, Ag, Au, Pd, and Ir nanoparticles were realized using the solid state route described herein. The solid state route was extended to the synthesis of bimetallic nanoparticles as well as supported metal nanoparticles. Employment of metal nitrate as the metal precursor and ammonia borane as the reducing agent resulted in highly exothermic reaction. The heat evolved in this reaction was exploited successfully towards mixing of the constituent elements thus allowing the alloy formation to occur at much lower temperature (60 oC) compared to the traditional solid state metallurgical methods (temperature used in these cases are > 1000 oC). Synthesis of highly monodisperse 2-3 nm Cu/Au and 5-8 nm Cu/Ag nanoparticles were demonstrated herein. Alumina and silica supported Pt and Pd nanoparticles have also been prepared. Use of ammonia borane as the reducing agent in the solid state brought out the reduction of metal ions to metal nanoparticles and the simultaneous generation of BNHx polymer which encapsulates the metal (Pt and Pd) nanoparticles supported on support materials. Treatment of these materials with methanol resulted in the solvolysis of BNHx polymer and its complete removal to finally provide metal nanoparticles on the support materials. An in situ seeding growth methodology for the synthesis of bimetallic nanoparticles with core@shell architecture composed of noble metals has been developed using trimethylamine borane (TMAB) as the reducing agent. The key idea of this synthetic procedure is that, TMAB being a weak reducing agent is able to differentiate the smallest possible window of reduction potential and hence reduces the metal ions sequentially. A dramatic solvent effect was noted in the preparation of Ag nanoparticles: Ag nanoparticles were obtained at room temperature when dry THF was used as the solvent whereas, reflux condition was required to realize the same using wet THF as the solvent. However, no such behavior was noted in the preparation of Au and Pd nanoparticles wherein Au and Pd nanoparticles were obtained at room temperature and reflux conditions, respectively. This difference in reduction behavior was successfully exploited to synthesize Au@Ag, Ag@Au, and Ag@Pd nanoparticles. All these core@shell nanoparticles were further transformed to their alloy counterparts under very mild conditions reported to date. Highly monodisperse, ultrasmall, colloidal Ca nanoparticles with a size regime of 2-4 nm were synthesized using solvated metal atom dispersion (SMAD) method and digestive ripening technique. Hexadecylamine (HDA) was used as the stabilizing agent in this case. Employment of capping agent with a longer chain length, octadecylamine afforded even smaller sized particles. However, when poly(vinylpyrrolidone) (PVP), a branched chain polymer was used as the capping agent, agglomerated particles were realized together with small particles of 3-6 nm. Use of a combination of PVP and HDA resulted in spherical particles of 2-3 nm size with narrow size distribution. Growth of Ca nanoparticles via colaesence mechanism was observed under an electron beam. Employing in situ transmission electron microscopy technique, real time coalescence between a pair of Ca nanoparticles were detected and details of coalescence steps were analyzed.
5

Soil Organic Matter Composition Impacts its Degradability and Association with Soil Minerals

Clemente, Joyce S. 11 December 2012 (has links)
Soil organic matter (OM) is a complex mixture of compounds, mainly derived from plants and microbes at various states of decay. It is part of the global carbon cycle and is important for maintaining soil quality. OM protection is mainly attributed to its association with minerals. However, clay minerals preferentially sorb specific OM structures, and clay sorption sites become saturated as OM concentrations increase. Therefore, it is important to examine how OM structures influence their association with soil minerals, and to characterize other protection mechanisms. Several techniques, which provide complementary information, were combined to investigate OM composition: Biomarker (lignin phenol, cutin-OH acid, and lipid) analysis, using gas chromatography/mass spectrometry; solid-state 13C nuclear magnetic resonance (NMR) spectroscopy; and an emerging method, solution-state 1H NMR spectroscopy. OM composition of sand-, silt-, clay-size, and light fractions of Canadian soils were compared. It was found that microbial-derived and aliphatic structures accumulated in clay-size fractions, and lignin phenols in silt-size fractions may be protected from further oxidation. Therefore, OM protection through association with minerals may be structure-specific. OM in soils amended with maize leaves, stems, and roots from a biodegradation study were also examined. Over time, lignin phenol composition, and oxidation; and aliphatic structure contribution changed less in soils amended with leaves compared to soils amended with stems and roots. Compared to soils amended with leaves and stems, amendment with roots may have promoted the more efficient formation of microbial-derived OM. Therefore, plant chemistry influenced soil OM turnover. Synthetic OM-clay complexes and soil mineral fractions were used to investigate lignin protection from chemical oxidation. Coating with dodecanoic acid protected lignin from chemical oxidation, and overlying vegetation determined the relative resistance of lignin phenols in clay-size fractions from chemical oxidation. Therefore, additional protection from chemical oxidation may be attributed to OM composition and interactions between OM structures sorbed to clay minerals. Overall, these studies suggest that while association with minerals is important, OM turnover is also influenced by vegetation, and protection through association with clay minerals was modified by OM structure composition. As well, OM-OM interaction is a potential mechanism that protects soil OM from degradation.
6

Soil Organic Matter Composition Impacts its Degradability and Association with Soil Minerals

Clemente, Joyce S. 11 December 2012 (has links)
Soil organic matter (OM) is a complex mixture of compounds, mainly derived from plants and microbes at various states of decay. It is part of the global carbon cycle and is important for maintaining soil quality. OM protection is mainly attributed to its association with minerals. However, clay minerals preferentially sorb specific OM structures, and clay sorption sites become saturated as OM concentrations increase. Therefore, it is important to examine how OM structures influence their association with soil minerals, and to characterize other protection mechanisms. Several techniques, which provide complementary information, were combined to investigate OM composition: Biomarker (lignin phenol, cutin-OH acid, and lipid) analysis, using gas chromatography/mass spectrometry; solid-state 13C nuclear magnetic resonance (NMR) spectroscopy; and an emerging method, solution-state 1H NMR spectroscopy. OM composition of sand-, silt-, clay-size, and light fractions of Canadian soils were compared. It was found that microbial-derived and aliphatic structures accumulated in clay-size fractions, and lignin phenols in silt-size fractions may be protected from further oxidation. Therefore, OM protection through association with minerals may be structure-specific. OM in soils amended with maize leaves, stems, and roots from a biodegradation study were also examined. Over time, lignin phenol composition, and oxidation; and aliphatic structure contribution changed less in soils amended with leaves compared to soils amended with stems and roots. Compared to soils amended with leaves and stems, amendment with roots may have promoted the more efficient formation of microbial-derived OM. Therefore, plant chemistry influenced soil OM turnover. Synthetic OM-clay complexes and soil mineral fractions were used to investigate lignin protection from chemical oxidation. Coating with dodecanoic acid protected lignin from chemical oxidation, and overlying vegetation determined the relative resistance of lignin phenols in clay-size fractions from chemical oxidation. Therefore, additional protection from chemical oxidation may be attributed to OM composition and interactions between OM structures sorbed to clay minerals. Overall, these studies suggest that while association with minerals is important, OM turnover is also influenced by vegetation, and protection through association with clay minerals was modified by OM structure composition. As well, OM-OM interaction is a potential mechanism that protects soil OM from degradation.

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