Theses and Dissertations at Montana State University (MSU)
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Item Reactive-atom scattering dynamics and liquid-vacuum interfacial structure(Montana State University - Bozeman, College of Letters & Science, 2019) Smoll, Eric James, Jr.; Chairperson, Graduate Committee: Timothy Minton; Maria Tesa-Serrate, Timothy K. Minton and Kenneth G. McKendrick were also authors of the article, 'Review of atomic and molecular collisions at liquid surfaces' in the journal 'Annual review of physical chemistry' which is contained within this dissertation.; Simon M. Purcell, Lucia D'Andrea, John M. Slattery, Duncan W. Bruce, Matthew L. Costen, Kenneth G. McKendrick and Timothy K. Minton were co-authors of the article, 'Probing conformational heterogeneity at the ionic liquid-vacuum interface by reactive atom scattering' in the journal 'The Journal of Physical Chemistry Letters' which is contained within this dissertation.; Timothy K. Minton was an author of the article, 'Scattering-angle randomization in nonthermal gas-liquid collisions' submitted to the journal 'Journal of physical chemistry C' which is contained within this dissertation.; John M. Slattery, Timothy K. Minton were also authors of the article, 'Probing a ruthenium coordination complex at the ionic liquid-vacuum interface with reactive atom scattering, X-ray photoelectron spectroscopy, and time-of-flight secondary ion mass spectrometry' submitted to the journal 'Journal of physical chemistry C' which is contained within this dissertation.Experiments to characterize reactive and nonreactive gas-liquid scattering dynamics were carried out with the use of a crossed molecular beams apparatus configured for beam-surface scattering. In each experiment, the identity of the gas and liquid was strategically selected to reveal fundamental insights on the relationship between scattering observables and liquid-vacuum interfacial structure. This work is crucially important for the experimental advancement of liquid surface science and has the potential to impact our understanding of the chemical role of gas-liquid interfaces in the environment. An extensive literature review suggests that the inherent chemical specificity of reactive scattering is a promising probe of composition at the liquid-vacuum interface. We expand on what has been demonstrated in the literature by exploring F-atom scattering from the liquid-vacuum interface of deuterium labeled variants of the common ionic liquid 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([C 4 mim][Tf 2 N]). The experimental data and new molecular dynamics simulations provide evidence for the extreme surface specificity of reactive scattering and help quantify the relative populations of [C 4mim] + conformations at the liquid-vacuum interface. Also, at a fixed incident angle, the site-specific IS flux angular distributions from [C 4mim] + were discovered to be related by the addition or subtraction of a line-shape proportional to a cos(θf) function. To investigate this phenomenon, a separate study of noble gas scattering from the liquid-vacuum interface of other low vapor pressure liquids was carried out. Our results support the generality of the relative cos(θf) character trend and demonstrate that the relative cos(θf) character between total flux angular distributions from squalane and a perfluoropolyether is independent of gas identity and incident angle suggesting that this metric is an intrinsic property of the liquid pair. The existing evidence suggests that the relative cos(θf) character between flux angular distributions is a result of angle-randomization from multiple collision scattering trajectories induced by atomic-scale corrugation at the liquid-vacuum interface. A study on the liquid-vacuum interface structure of a solution of [RuCl 2(p-cymene)P(C 8H 17) 3] in perdeuterated 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (d 11-[C 2mim][Tf 2N]) is also discussed. The experimental data suggest that [RuCl(p-cymene)P(C 8H 17) 3] + is enriched at the liquid-vacuum interface at the expense of d 11-[C 2mim] + and the hydrocarbon chains of the Ru-complex protrude into the vacuum.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.