Theses and Dissertations at Montana State University (MSU)
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Item Unusual isomerization behavior of organic solutes at the aqueous-silica interface(Montana State University - Bozeman, College of Letters & Science, 2019) Purnell, Grace Elizabeth; Chairperson, Graduate Committee: Robert Walker; Robert A. Walker was a co-author of the article, 'Hindered isomerization at the silica/aqueous interface: surface polarity or restricted solvation?' in the journal 'Langmuir' which is contained within this dissertation.; Robert A. Walker was a co-author of the article, 'Surface solvation and hindered isomerization at the water/silica interface explored with second harmonic generation' in the journal 'The journal of chemical physics' which is contained within this dissertation.; Marshall T. McNally, Patrik R. Callis and Robert A. Walker were co-authors of the article, 'Buried liquid interfaces as a form of chemistry in confinement: the case of 4-dimethylaminobenzonitrile at the silica-aqueous interface' submitted to the journal 'The journal of the American Chemical Society' which is contained within this dissertation.; Marshall T. McNally, and Robert A. Walker were co-authors of the article, 'Isomerization at aqueous-silica interfaces and the role of solute structure' submitted to the journal 'Chemical physics letters' which is contained within this dissertation.Experiments described in this thesis address the question of how strong association between water molecules and the silica surface alter the solvation and isomerization behavior of adsorbed organic molecules from bulk solution limits. The work was motivated by the hypothesis that the ice-like structure induced by strong hydrogen bonding with the surface silanol groups would restrict solute isomerization. This hypothesis was tested using 2 surface-specific spectroscopic techniques: second harmonic generation (SHG) and time-correlated single photon counting in a total internal reflection geometry (TIR-TCSPC). This work examined two different 7-aminocoumarin dyes (Coumarin 151 and Coumarin 152) and dimethylaminobenzonitrile (DMABN). Coumarin 152 and DMABN both isomerize to form a twisted intramolecular charge transfer (TICT) state upon photoexcitation, whereas Coumarin 151 forms a simple (planar) intramolecular charge transfer state. SHG studies characterized the local solvation environment surrounding adsorbed molecules by providing electronic excitation energies that were compared to bulk excitation energies in different representative solvents. TIR-TCSPC measured the time-resolved emission of adsorbed molecules and quantified a solute's tendency to form TICT (or ICT) isomers at the aqueous-silica interface. Together, SHG and TIR-TCSPC provide a cohesive description of the local polarity across an aqueous-silica interface and how restricted solvent dynamics change a solute's photophysical chemistry. TIR-TCSPC studies reported that both C152 and DMABN are unable to isomerize to TICT states at the aqueous-silica interface, acting as if they were solvated in a nonpolar solvent or in a confined geometry. SHG studies confirm that the aqueous-silica interface is, in fact, more polar than the bulk aqueous limit, strongly implying that the observed effects are dynamic in origin rather than polarity driven. In contrast, studies of C151 show that this solute is largely insensitive to anisotropic, restrictive surface effects. Together results from these three molecules lead us to conclude that adsorption to the strongly associating aqueous-silica interface restricts large amplitude isomerization in organic molecules. Adsorption to less strongly associating interfaces does not cause this restriction. In the event that photo-induced isomerization does not require large amplitude motion, interfacial solvation has little effect on adsorbed solute behavior.Item Design and synthesis of novel chromophores for aptamer based imaging(Montana State University - Bozeman, College of Letters & Science, 2015) Robison, Jacob Michael; Chairperson, Graduate Committee: Mary J. CloningerFluorescent proteins are an incredibly versatile tool in biological imaging. Unfortunately, fluorescent proteins cannot be used to track small metabolites in vivo. The purpose of the work described herein was to create novel red-shifted RNA aptamer based probes for use in molecular imaging. All potential dyes were prescreened using molecular modeling and only the dyes that absorbed wavelengths longer than 500 nm were synthesized. The first aminothiophene based imidazolinone dyes (ATI-1 and ATI-2) were synthesized and their electronic properties were evaluated. SELEX was performed on ATI-2 to find several random RNA sequences that were capable of binding the chromophore and activating ATI-2 fluorescence. It is proposed that fluorescence activated cell sorting can be used to separate and isolate the sequences that form the brightest complexes with ATI-2.Item The synthesis and characterization of organic materials for non-linear optic studies(Montana State University - Bozeman, College of Letters & Science, 1996) Duncan, David F.Item Conformational studies of crowded and non-crowded merocyanine dyes(Montana State University - Bozeman, College of Letters & Science, 1989) Monson, John JosephItem Synthesis of zwitterionic cyanine dyes for use in proteomics(Montana State University - Bozeman, College of Letters & Science, 2012) Epstein, Mark Galen; Chairperson, Graduate Committee: Paul GriecoThe CyDye family of fluorescent dyes are the tools currently in use today for applications in two dimensional difference gel electrophoresis (2D-DIGE) techniques. The lysine labeling CyDyes are limited by problems with over labeling resulting in protein precipitation and isoelectric point (pI) drift at high pH's. These limitations have been addressed by a family of highly water soluble and pI balancing zwitterionic BODIPY dyes, which were previously synthesized in the Grieco group. The absorbance maxima of the BODIPY fluorophores were tuned through extension of the pi system to produce a three color, spectrally resolved dye set. However the fluorescence of the green emitting BOPIDY suffered at pH's less than 3.5 and greater than 11, while the red emitting BODIPY was susceptible to Michael addition changing its emission profile. To address the limitations of the BODIPY family of dyes, a new family of zwitterionic 2DDIGE dyes based on the established CyDye fluorophores have been synthesized. A complete three dye zwitterionic minimal labeling set which features a cysteic acid motif, titratable amine functionality and an NHS activated ester group reactive towards lysine residues has been synthesized: Z-Cy2 (QY= 6.8% ± 0.1, epsilon= 155,000), Z-Cy3 (QY= 11.1% ± 0.4, epsilon= 124,500), Z-Cy5 (QY= 43.3% ± 0.6, epsilon= 217,600). In addition, a complete three dye zwitterionic saturation labeling set which incorporates a cysteic acid motif and maleimide functionality reactive towards cysteine residues has also been synthesized: Z-Cy2-Mal (QY= 6.6 % ± 0.1, epsilon= 104,500), Z-Cy3-Mal (QY= 12.4 % ± 0.5, epsilon= 127,700), Z-Cy5-Mal (QY= 40.2 % ± 0.4, epsilon= 217,400).Item The synthesis of fluorescent and phosphorescent dyes for biochemical application(Montana State University - Bozeman, College of Letters & Science, 2010) Sanger, Elizabeth Ann; Chairperson, Graduate Committee: Paul GriecoCurrent dyes for proteomics that are applicable to multiplexing experiments suffer from lack of sensitivity and poor water solubility. A series of tetramethyl rhodamine derivatives were developed to study the effects of substitution patterns on the photophysical properties of the fluorophores. After identifying the superior fluorophore a zwitterionic side chain with properties beneficial for two dimensional applications was coupled to the fluorophore and the photophysical properties were studied. Iridium(III) cationic fluorophores are interesting synthetic targets due to their ultraviolet absorption wavelengths and visible emission properties. A series of Iridium(III) fluorophores, some of which contain a handle for further synthetic extension, has been made to study the ligand effects on the emission properties of the dyes. Finally, some of these dyes have been synthetically modified for proteomic labeling applications.