Browsing by Subject "metal ions"
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Item Computational study of the complexation of metal ion precursors in dendritic polymers(2009-05-15) Tarazona Vasquez, FranciscoMetal ions are important for medical, environmental and catalytic applications. They are used as precursor molecules for the manufacture of metal nanocatalysts, which are promising materials for an array of biomedical, industrial, and technological applications. Understanding the effect of the environment upon a metal ion-dendrimer system constitutes a step closer to the understanding of the liquid phase templated synthesis of metal nanoparticles. In this dissertation we have used computational techniques such as abinitio calculations and molecular dynamics (MD) simulations to investigate the complexation of Cu(II) and Pt(II) metal ions to a polyamidoamine (PAMAM) dendritic polymer from structural, thermodynamic, and kinetic viewpoints. First, we analyze the local configuration of a low generation polyamidoamine dendrimer to understand the role of intramolecular interactions. Then, we examine the local configuration of dendrimer outer pockets in order to determine their capacity to encapsulate water within. Next, the complexation of Cu(II) with a small ?OH terminated dendrimer in presence of solvent and counterions is investigated. This relatively simple system gives insight on how cationic species bind within a dendrimer. The complexation of potassium tetrachloroplatinate, commonly used precursor salt in dendrimer templated synthesis of platinum and bimetallic platinum-containing nanoparticles, with PAMAM dendrimer has been the subject of several experimental reports. So we investigate the complexation of potassium tetrachloroplatinate within a dendrimer outer pocket in order to understand the effect of dendrimer branches, Pt(II) speciation, pH, solvent and counterions upon it. Our study shows that dendrimer branches can improve the thermodynamics but can also preclude the kinetics by raising the energy barriers. Our study provides an explanation of why, where Pt(II) and how Pt(II) binds. We believe that these molecular level details, unaccessible to experimental techniques, can be a helpful contribution toward furthering our understanding of the complexation of Pt(II) and the starting point to study the next step of dendrimer templated synthesis, the reduction of Pt(II) into platinum nanoparticles inside pockets.Item Investigation of an unusual metal-RNA cluster in the P5abc subdomain of the group I intron(Texas A&M University, 2006-04-12) Burns, Shannon NaomiThis dissertation focuses on the spectroscopic and thermodynamic characterization of the unusual metal-RNA cluster found in the P5abc subdomain of the Tetrahymena group I intron. The P5abc subdomain is a part of the P4-P6 domain found in the Tetrahymena thermophila group I intron selfsplicing RNA. From both X-ray crystal structures of the P4-P6 domain, a remarkable cluster of Mg2+ or Mn2+ ions was found in the P5abc subdomain (Cate et al. 1996; Juneau et al. 2001). It is believed that the metal ion core in the P5abc subdomain stabilizes the active conformation of the RNA (Cate et al. 1996). An understanding of the role of these metal ions in facilitating the correct structure of the P5abc subdomain provides insight into how metal ions help overcome the folding barriers of complex RNA structures. Under solution conditions, the properties of this uncommon metal ion core and its influence on the truncated P5abc subdomain structure have been investigated. Both EPR spectroscopy and thermal denaturation experiments have been employed to search for a spectroscopic signature of metal ion core formation and also determine the thermodynamic contribution of the metal ion core on the stability of the folded P5abc structure. A spectroscopic signature of metal ion core formation was assigned for the P5abc subdomain by EPR microwave power saturation studies. Power saturation studies of the P5abc subdomain, P4-P6 domain and corresponding mutants reveal that the addition of 5 equivalents of Mn2+ are required for the wild type P5abc subdomain to form the metal ion core under solution conditions in 0.1 M NaCl. Results from both domain and subdomain microwave power saturation studies suggest that this technique can be applied for detecting clustering of Mn2+ ions in other RNA structures. The thermodynamic consequence of this metal ion core was probed by thermal denaturation techniques including UV-Vis spectroscopy and differential scanning calorimetry (DSC). DSC experiments were utilized to directly determine the thermodynamic contribution of the metal ion core. This value was determined to be an average of ∆∆G of -5.3 kcal/mol and is consistent with ∆∆G values obtained for other RNA tertiary structures.Item Investigation of metal-ion binding in the four-way junction construct of the hairpin ribozyme(Texas A&M University, 2005-08-29) Buckelew, Aurelie LinaThe hairpin ribozyme is a small catalytic RNA that cleaves a phosphodiester bond. In order for cleavage to occur, the hairpin ribozyme must properly fold into its docked conformation, in which the two loops interact to form the active site. Metal ions and the four-way junction play critical roles in the stabilization of the docked conformation. The work presented in this thesis attempts to investigate the metal-ion dependence of the docking of the four-way junction construct of the hairpin ribozyme. In addition, the activity of the hairpin ribozyme in the presence of Mn2+ was observed. Initially, a four-stranded four-way junction construct of the hairpin ribozyme and a loopless mutant were characterized by native gel electrophoresis and thermal denaturation to verify ribozyme formation. A novel interaction between the sulfur of a phosphorothioate-substituted mononucleotide, such as adenosine thiomonophosphate (AMPS) or adenosine thiotrisphoshate (ATPgS), and Cd2+ has been characterized by UV-vis spectroscopy. A feature at 208 nm was identified to be a result of sulfur-to-Cd2+ transfer. The apparent binding affinities, the apparent extinction coefficients, and the binding ratios were determined for each complex.