Scholarship & Research
Permanent URI for this communityhttps://scholarworks.montana.edu/handle/1/1
Browse
9 results
Search Results
Item The effects of atomic oxygen on silicon-carbon systems in extreme environments(Montana State University - Bozeman, College of Letters & Science, 2021) Chen, David Zuyu; Chairperson, Graduate Committee: Timothy Minton; Chenbiao Xu, Vanessa J. Murray and Timothy K. Minton were co-authors of the article, 'Oxidation of silicon carbide through the passive-to-active transition' submitted to the journal 'The journal of chemical physics' which is contained within this dissertation.; Chenbiao Xu and Timothy K. Minton were co-authors of the article, 'Effect of atomic oxygen on CV-1144-0 and RTV-560 silicones' submitted to the journal 'Acta astronautica' which is contained within this dissertation.; Chenbiao Xu and Timothy K. Minton were co-authors of the article, 'Effect of silicone coating on atomic oxygen reactivity with fiberform and phenolic impregnated carbon ablator' submitted to the journal 'Journal of spacecraft and rockets' which is contained within this dissertation.Vehicles traveling at hypersonic speeds require thermal protection systems (TPSs) that can withstand the extreme temperatures and reactive atomic oxygen species present in these environments. Ultra-high temperature ceramics are candidate TPSs, and many of them contain silicon carbide, allowing them to resist chemical attack by forming a protective oxide-containing layer, called passive oxidation. At very high temperatures, however, the layer will decompose, subjecting the material to ablation from reaction with O-atoms, called active oxidation, through a process called the passive-to-active oxidation transition (PAT). We have conducted molecular beam-surface scattering experiments to investigate the interactions of O-atoms with SiC at high temperatures, which revealed that with a lower fluence of O-atoms above the PAT, the SiC surface undergoes graphitization, while a sufficiently higher fluence of O-atoms promotes active oxidation. Analysis of the oxide layer decomposition revealed a decomposition process that initiated at the oxide-SiC interface. These insights will be useful for the development of more accurate predictive models, but they also aided understanding of the ablation of silicone-coated heat shields for atmospheric entry applications. For these applications, phenolic impregnated carbon ablator (PICA), a material composed of a carbon fiber network (FiberForm) and a resole phenolic resin stable against high heat convection and conduction, is used. Silicone is sprayed onto PICA to reduce dust, but the silicone can also form an oxide layer, which, like on SiC, will resist O-atom attack until it decomposes at very high temperatures, exposing the underlying material to reactive O-atoms. We conducted additional experiments in which a beam of atomic oxygen was directed at silicone-coated and uncoated samples of PICA as well as FiberForm, which revealed high nonreactive O-atom product scattering when the oxide layer was present, while with the decomposition of the oxide, product scattering resembled O-atom scattering from the underlying substrate. Additional studies probed the oxidation layer that is formed on pure silicone during O-atom bombardment, which revealed a three orders of magnitude reduction in erosion yield compared to that of Kapton H, a polyimide. This new data on PICA and FiberForm has been provided to NASA Ames for their development of an ablation model.Item Computational prediction and experimental measurement of time resolved fluorescence properties of tryptophan and 5-fluoro-tryptophan dipeptides(Montana State University - Bozeman, College of Letters & Science, 2016) Fahlstrom, Carl Ashley; Chairperson, Graduate Committee: Patrik R. Callis; Lee Spangler (co-chair)The widely exploited high sensitivity of the amino acid tryptophan (Trp) fluorescence wavelength and quantum yield on local environment in proteins results in multiexponential decay from two mechanisms: quenching rate heterogeneity and/or spectral relaxation. 5-uorotryptophan (5FTrp) reduces quenching rate heterogeneity by suppression of electron transfer quenching. A comparison of fluorescence properties of Trp and 5FTrp provides a means of differentiating between relaxation and heterogeneity. Four observations concerning the fluorescence of Trp dipeptides required further explanation: decay components of approximately 20 ps, a sub 300 fs 10% loss of quantum yield, the quantum yield for Gly-Trp being significantly lower than Trp-Gly, and the fluorescence wavelength of Trp-X being 10 nm shorter than X-Trp at pH 5. With the goal of distinguishing between electron and proton transfer quenching mechanisms, the time resolved fluorescence--with time resolution of 0.5 ns--for dipeptides was measured in the X-Trp and Trp-X configurations(where X=Leu, Gly, Asp, Arg, Met), with 5FTrp substitution, at pH 5 and pH 10, and in water and D 2O solvent--resulting in 84 distinct species. Molecular dynamics simulations were performed on Gly-Trp and Trp-Gly dipeptides with ground and excited state charges employing multiple force fields. The methods developed by Callis and coworkers were used to calculate the instantaneous rates of electron transfer rates, quantum yield, and fluorescence wavelength. Experimentally three types of multiexponential decay were observed: quenching rate heterogeneity with no relaxation, relaxation only, and combinations thereof. The substitution of 5FTrp for Trp reduced quenching rate heterogeneity, resulting in reduction of short lifetime components, allowing for the observation of relaxation components that were most likely masked in the Trp case. Calculated electron transfer rates support lifetimes of approximately 20 ps, but not those less than 300 fs, and predict a lower quantum yield for Trp-Gly than Gly-Trp. Calculated fluorescence wavelengths reproduce the observed shorter fluorescence wavelength of Trp-X zwitterions. Failure to predict quantum yields may be caused by the inability of the molecular dynamics force fields to reproduce the conformational populations. Results support both relaxation and heterogeneity in Trp dipeptides. 5FTrp is a useful tool in distinguishing between heterogeneity and relaxation.Item Simulating electrostatic effects on electronic transitions in proteins(2014-06) Callis, Patrik R.Biopolymer fluorescence in biology and biochemistry is increasingly used for characterising equilibrium, dynamics and imaging. This is typically done by monitoring wavelength and intensity changes without necessarily knowing what causes such changes in detail. Simulations have been at the core of the considerable recent progress in improving the microscopic understanding of wavelength and quenching of fluorescence intensity in biopolymers. This review focuses on one of the most used intrinsic probes for protein behaviour, tryptophan (Trp), which is arguably now one of the best understood probes of internal structure and dynamics for proteins – despite its reputation to the contrary. In this review, we highlight selected classical molecular dynamics in combination with quantum mechanics simulations from our group and others during the past 20 years that support this view. The work includes simulations of time-dependent wavelength shifts in solvents and proteins, fluorescence-quenching rates, dielectric compensation by water, heterogeneity of quenching rates and applications to protein folding.Item Putting Tuberculosis (TB) To Rest: Transformation of the Sleep Aid, Ambien, and “Anagrams” Generated Potent Antituberculosis Agents(2014-12) Moraski, Garrett C.; Miller, Patricia; Bailey, Mai Ann; Ollinger, Juliane; Parish, Tanya; Boshoff, Helena I.; Cho, Sanghyun; Anderson, Jeffery; Mulugeta, Surafel; Franzblau, Scott G.; Miller, Marvin J.Zolpidem (Ambien, 1) is an imidazo[1,2-a]pyridine-3-acetamide and an approved drug for the treatment of insomnia. As medicinal chemists enamored by how structure imparts biological function, we found it to have strikingly similar structure to the antitubercular imidazo[1,2-a]pyridine-3-carboxyamides. Zolpidem was found to have antituberculosis activity (MIC of 10–50 μM) when screened against replicating Mycobacterium tuberculosis (Mtb) H37Rv. Manipulation of the Zolpidem structure, notably, to structural isomers (“anagrams”), attains remarkably improved potency (5, MIC of 0.004 μM) and impressive potency against clinically relevant drug-sensitive, multi- and extensively drug-resistant Mtb strains (MIC < 0.03 μM). Zolpidem anagrams and analogues were synthesized and evaluated for their antitubercular potency, toxicity, and spectrum of activity against nontubercular mycobacteria and Gram-positive and Gram-negative bacteria. These efforts toward the rational design of isomeric anagrams of a well-known sleep aid underscore the possibility that further optimization of the imidazo[1,2-a]pyridine core may well “put TB to rest”.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 use of In(OTf)3 as a Lewis Acid in carbohydrate chemistry, and exploration in silicon tethered reactions(Montana State University - Bozeman, College of Letters & Science, 2008) Bizier, Nicholas Paul; Chairperson, Graduate Committee: Mary J. CloningerThe feasibility of using Indium (III) triflate as a Lewis Acid for a number of different carbohydrate reactions was explored. First, the use of In(OTf)3 as a catalyst in the acylation of a number of carbohydrates was explored. The utility and compatibility of the In(OTf)3 reaction conditions with a number of protecting groups on the sugars were examined by 1H NMR analysis. In the second part of the carbohydrate methodology, the feasibility of using In(OTf)3 to promote glycosylation reactions using a number of glycosyl donors was evaluated. These studies were conducted using 1H NMR, 13CNMR, and Micro-ToF mass spectrometry. In both cases, In(OTf)3 was found to be a viable if highly acidic Lewis acid for these reactions. Silicon tether methodology was explored with the goal of obtaining 1,3 and 1,2-amino alcohols. The parameters for this reaction were explored after precursors and 1,3-amino alcohols were synthesized. These studies were conducted using 1H NMR, 13C NMR, IR spectroscopy, and Micro-ToF mass spectrometry. While some success was achieved, this route is unlikely to be widely adopted due to the multi-step syntheses that are required to obtain viable reaction precursors.Item General chemistry laboratory for engineers : a research-based approach : a research-based approach(Montana State University - Bozeman, College of Letters & Science, 2005) Sorey, Timothy Lowell; Chairperson, Graduate Committee: John R. AmendChanges made in requirements to the Accreditation Board for Engineering and Technology in 2000 have made it possible for several engineering curricula to take one semester of a two part general chemistry series. At Montana State University - Bozeman engineering majors constitute just over 37% of the total 850 students per year in the first term general chemistry population. The single-semester engineering curricula enroll 88% of the engineering students. These students receive an incomplete survey of general chemistry, missing important topics such as equilibrium and kinetics, acids and bases, and electrochemistry that are taught in the second semester. In 2001, discussion was initiated between the Department of Chemistry and Biochemistry and the Dean and Department Heads of the College of Engineering to identify learning objectives and chemistry content important to engineering students. Current learning and teaching theories were used to develop an original laboratory learning approach that supported these objectives. Next, innovative measurement technology was integrated for students' use in gathering experimental data. These materials were tested, evaluated, and refined during MSU freshman labs and in-service technology training for Montana science teachers. The development of this general chemistry lab curriculum for these engineering majors supports both national science education goals and those of the Accreditation Board for Engineering and Technology. This curriculum employs the latest in microcomputer-based technology and guided-inquiry approaches to learning. This innovative approach fosters engineering track students' development of tools and skills necessary for critical thinking and problem solving. Engineering students collaborated as research groups to (a) design and conduct experiments, (b) discuss and evaluate data, (c) prepare and write lab reports, and (d) present an oral report to their peers. This approach creates a research environment for students to connect chemistry in the context of real-world engineering applications. Not only did the treatment group (N=70) outperform their fellow engineering students in lecture exams and quizzes, but over a four and a half fold increase of enrollment into the second semester of general chemistry was observed. This approach shows promise as a transferable template for other interdisciplinary laboratory curriculum in general chemistry and deserves implementation and further research.