Theses and Dissertations at Montana State University (MSU)
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Item Exploring exchange and transport dynamics in complex systems through nuclear magnetic resonance(Montana State University - Bozeman, College of Letters & Science, 2021) Nelson, Madison Lee; Chairperson, Graduate Committee: Joseph D. Seymour and Sarah L. Codd (co-chair); This is a manuscript style paper that includes co-authored chapters.Nuclear magnetic resonance (NMR) is uniquely qualified for non-invasive studies of systems providing insights into macro-, meso-, and microscale structures. NMR relaxation and diffusion methods are applied to characterize transport and magnetization exchange dynamics in various complex systems. These techniques are highly sensitive to molecular mobility restrictions which correlate to the ability to monitor thermodynamic phase transitions and changes in molecular environment. NMR diffusion and relaxation measurements are applied to characterize the effect of xylose on transport within zeolite beads. The ability for NMR to explore the transport phenomenon on multiple length and time scales is exploited to characterize how the introduction of xylose effects the transport structure of the bead. Eigenvector simulations of magnetization evolution within a coupled pore system during multidimensional NMR measurements, T1-T2 relaxation correlation experiments, allowed for insights into complex diffusion and exchange occurring within multiple systems. Additionally, multidimensional relaxation NMR measurements, in the form of varying echo-time spin-spin relaxation dispersion T2(tau) and spin-spin relaxation exchange T2-T2 experiments, are demonstrated to successfully characterize thermodynamic structural rearrangements of two natural straight-chained hydrocarbons and a natural wax. Temperature dependent magnetization exchange was found in both the longitudinal and transverse magnetization. The results indicate the ability of NMR relaxometry to detect magnetization exchange without mass or molecular exchange, also known as spin diffusion, including in the transverse magnetization. Spatial domain extent can be inferred from the exchange timescale and an estimate of the spin diffusion coefficient. NMR relaxometry methods were extended to glycerol behenate, a common pharmaceutical component. Glycerol behenate was decomposed into its three base components to explore how polymorphic structure and exchange depend on temperature within each pure lipid through T2(tau) and T2-T2 NMR relaxation experiments. These methods allowed for in-situ monitoring of thermodynamic dependent exchange across domains in addition to decoupling of transverse and longitudinal exchange. The results allow for calculation of exchange length scales across the micro- and mesoscales within the lipids. Ultimately, multidimensional NMR relaxometry is successfully demonstrated to be an effective technique for characterizing and monitoring structural changes in lipids across various phase transition temperatures and time and length scales.Item Implementing student created atomic scale depictions across multiple units to improve understanding of molecular interactions in high school chemistry(Montana State University - Bozeman, College of Letters & Science, 2019) Jones, Christopher S.; Chairperson, Graduate Committee: Greg FrancisOne of the most difficult aspects of studying chemistry is that one must imagine the atoms and molecules interacting to understand many of the concepts. A plan was developed to repeatedly draw out representations of the processes studied at the molecular scale in a high school chemistry curriculum. The goal was to provide increased understanding that would be reflected in exam scores. Analysis of exam results for the treatment year were compared to previous years' results of the same exams. Students were also surveyed about the perceived instructional benefit and enjoyment of the activities. Exam scores for the treatment year were not significantly higher or lower than in previous years. One aspect that was remarkable was the discrepancy between the students' belief in the efficacy of the intervention despite their lack of affect for it. The students generally believed the curriculum was more effective than it was. They also tended to express less satisfaction with the drawing treatment as the year progressed. Interviews were conducted with students who voluntarily expressed both positive and negative experiences, as well as others who were selected randomly.Item Fluorescence quenching in 2-aminopurine-labeled model DNA systems(Montana State University - Bozeman, College of Letters & Science, 2019) Remington, Jacob Michael; Chairperson, Graduate Committee: Patrik R. Callis; Abbey M. Philip, Mahesh Hariharan and Bern Kohler were co-authors of the article, 'On the origin of multiexponential fluorescence decays from 2-aminopurine labeled dinucleotides' in the journal 'The journal of chemical physics' which is contained within this thesis.; Martin McCullagh and Bern Kohler were co-authors of the article, 'Molecular dynamics simulations of 2-aminopurine-labeled dinucleoside monophosphates reveal multiscale stacking kinetics' in the journal 'Journal of physical chemistry B' which is contained within this thesis.For the last 50 years changes to the fluorescence properties of 2-aminopurine have been used to probe the structure and dynamics of DNA. 2-Aminopurine's utility has arisen from the quenching of its emission when pi-stacked with neighboring nucleobases. In the time-domain, the emission decay profile of 2-aminopurine requires multiple exponential decay components to model. Despite its extensive usage, the microscopic origin of the decay heterogeneity is not clear. In this thesis, steady-state absorption, fluorescence, and time-resolved fluorescence results are compared to multiple microsecond molecular dynamics simulations of 2-aminopurine-labeled adenine containing single-stranded DNA oligomers of varying length and position of the 2-aminopurine probe. First, previous reports of ultrafast electron transfer in pi-stacked adenine oligomers are used to build a new model for quenching of 2-aminopurine that is pi-stacked with adenine. For dinucleotides, a static distribution of unstacked structures combined with a distance dependent electron transfer mechanism is posited to explain the disperse emission decay timescales. Investigating the dinucleotides with molecular dynamics simulations analyzed with Markov state models quantify the structural heterogeneity of the dinucleotides. At least seven structures are sampled that could alter the quenching of 2-aminopurines's fluorescence. The Markov state models also demonstrate the timescales for transitions between these structures range from 1.6 to 25 ns, suggesting 2-aminopurine, with its monomer-like lifetime of 10 ns, is sensitive to the conformational dynamics of the dinucleotides as well. This dual fluorescence quenching and molecular dynamics simulation approach is extended to 2-aminopurine labeled trinucleotides and 15 base oligomers to interrogate the position dependent structural heterogeneity and conformational dynamics in these systems. Both shifts in the experimental absorption spectra, and molecular dynamics simulations agree that the interior base is more likely to be stacked than the exterior bases. Time-resolved emission experiments reveal emission from 2-aminopurine is quenched faster on the 5' end relative to the 3' end, in agreement with the faster stacking kinetics observed for bases on the 5' end relative to the 3' end obtained from molecular dynamics simulation. These results suggest that the time-resolved emission from 2-aminopurine may serve as an experimental observable for calibration of the dynamical properties predicted by molecular dynamics simulation.Item Spectroscopic studies of noncovalent interactions at interfaces and their effects on interfacial structure, organization, and association(Montana State University - Bozeman, College of Letters & Science, 2015) Gobrogge, Eric Andrew; Chairperson, Graduate Committee: Robert Walker; B. Lauren Woods was an author and Robert A. Walker was a co-author of the article, 'Liquid organization at polar solid/liquid interfaces' in the journal 'Faraday discussions' which is contained within this thesis.; Jessica H. Ennist was an author and Kristian H. Schlick, Robert A. Walker and Mary J. Cloninger were co-authors of the article, 'Cyclodextrin-functionalized chromatographic materials tailored for reversible adsorption' in the journal 'ACS applied materials & interfaces' which is contained within this thesis.; Robert A. Walker was a co-author of the article, 'Partitioning of binary solvents at solid/liquid and solid/vapor interfaces' in the journal 'Journal of physical chemistry letters' which is contained within this thesis.Studies described in this dissertation used linear and nonlinear optical methods to examine the effects of noncovalent forces on molecular structure, organization and reactivity at solid/liquid, solid/vapor and liquid/vapor interfaces. These studies address three general questions: 1) Solvent structure at solid/liquid interfaces; 2) Solute adsorption to chemically tailored solid and liquid interfaces; and 3) Partitioning of binary solvents at solid/liquid and solid/vapor interfaces. 1) Solvent structure at solid/liquid interfaces. Vibrational sum frequency spectroscopy (VSFS) was used to study the interfacial organization of different alkanes and alcohols at the silica/liquid interface. Results showed that solvent organization depended sensitively on both interactions with the interface and on the solvent's molecular structure. Silica/methanol and silica/ethanol interfaces were also compared in order to determine why ethanol gives a VSFG spectrum but methanol does not. 2) Solute adsorption to chemically tailored interfaces. VSFS and fluorescence spectroscopy were used to characterize and analyze the effectiveness of silica substrates functionalized specifically to promote adsorption of organic analytes in aqueous solutions through catch and release chemistry. VSFS has also been used to study cooperative adsorption at aqueous/vapor interfaces to explore how insoluble surfactants can increase near-surface concentrations of soluble species. 3) Binary solvent partitioning at solid/liquid and solid/vapor interfaces. VSFS was used to study molecular organization at silica/binary solvent interfaces where the binary solvent consisted of acetonitrile and methanol in varying mole fractions. The vibrational spectra indicated that while methanol adsorbed ideally at the silica/vapor interface, acetonitrile accumulated in excess relative to the vapor phase composition. At the silica/liquid interface, methanol appeared to remain strongly associated with the surface until an acetonitrile mole fraction of 0.85 was reached. At higher mole fractions, interfacial acetonitrile adopts an antiparallel bilayer organization. This binary mixture was also compared to various other binary mixtures at the silica/vapor and silica/liquid interfaces.Item Normal mode visualization(Montana State University - Bozeman, College of Engineering, 1992) Reddy, Madhusudhan Y.Item Ethereal oxygen effects on structure and reactivity(Montana State University - Bozeman, College of Letters & Science, 1988) Johnson, David KentItem Models for disorder in thiourea host/guest adducts(Montana State University - Bozeman, College of Letters & Science, 1987) Fait, James FrancisItem Molecular structure at sites of HIV-1 gp120-CD4 interaction(Montana State University - Bozeman, College of Letters & Science, 1997) Moffett, Daphne BryceItem Determination of the relative steric sizes of alkyl groups using a calculational approach(Montana State University - Bozeman, College of Letters & Science, 1986) Bowler, Ann Marie