Browsing by Author "Levinger, Nancy, committee member"
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Item Embargo Catalyzed chemical synthesis of designer poly(3-hydroxyalkanoate)s: tuning function, microstructure, and architecture of biodegradable polymers(Colorado State University. Libraries, 2022) Westlie, Andrea Hope, author; Chen, Eugene Y.-X., advisor; Miyake, Garret, committee member; Levinger, Nancy, committee member; Herrera-Alonso, Margarita, committee memberThis dissertation describes the development of a chemocatalytic route towards biodegradable poly(hydroxyalkanoate)s (PHAs) based on the ring-opening polymerization of eight-membered cyclic diolide, 8DL, by discrete yttrium complexes. This chemocatalytic platform has transformed the brittle, poly(3-hydroxybutyrate) (P3HB) to high performance, "designer" PHAs through the use of molecular catalysts and the development of a precision polymerization methodology. There continues to be a pressing need for biodegradable polymers in applications where material recovery is unlikely or impossible or where environmental leakage of the plastic waste is highly likely. PHAs are truly biodegradable polyesters that can degrade in ambient conditions such as aerobic soil and marine environments and these polyesters are laden with tunability enabled by their chirality, composition, and architecture. A major challenge in implementing PHAs is to achieve truly tunable thermomechanical properties for any application, coupled with desirable processing conditions at scale. A critical literature review overviews the decades-long history of various chemocatalytic routes towards PHAs with either controlled tacticity or composition. To demonstrate the scope of our chemocatalytic platform, extensive study of homo- and copolymerization of three 8DLR (R = Me, Et, Bu) has been performed. Judicious choice of catalyst to match the steric bulk of the monomer results in high activity and high stereoselectivity ROP of these uncommon PHA homopolymers and allows for highly precise random copolymers of rac-8DLMe with targeted compositions ranging from 5 ~ 40 % incorporation of 8DLR (R = Et, Bu). Moving from aliphatic to aromatic substituents allowed for the synthesis of unnatural and previously unknown PHA with a glass transition (Tg) above room temperature (RT). Aliphatic-aromatic copolymers with designed architecture as random or block copolymers could be synthesized as well. And finally, recently we have designed and synthesized discrete PHA triblock copolymers towards achieving thermoplastic elastomer materials. Overall, this work has used fundamental investigation into a stereoselective, coordination-insertion polymerization mechanism and the resulting structure-property relationships to design higher-performance PHAs that are, in some cases, competitive with commodity polyolefins. This work serves as a platform for further development of PHAs using this chemocatalytic route towards new topologies, compositions, and functions.Item Open Access Developing tools to study the interaction between the lipopeptide surfactin and phospholipid bicelles with infrared spectroscopy(Colorado State University. Libraries, 2012) Blaser, Jennifer M., author; Krummel, Amber, advisor; Levinger, Nancy, committee member; Kipper, Matthew, committee memberSurfactin has been shown to have concentration-dependent effects on lipid membranes with proposed mechanisms of action including ion chelation, ion channel formation, and a detergent-like effect. The concentration ranges for these behaviors have not been established, the structure of surfactin in a membrane has not been determined, and information regarding the dynamics of the surfactin-lipid interaction is limited at best. Therefore, a tunable phospholipid bicelle system was created to study the surfactin-lipid interaction as a function of surfactin concentration using infrared (IR) spectroscopy which can provide both structural and dynamic information. But first, the direct interaction between surfactin and bicelles was confirmed with dynamic light scattering (DLS) measurements that suggest surfactin exhibits detergent-like effects above a 2.0 mM concentration. For surfactin in Tris buffer, the IR spectra displayed a significant concentration-dependent shift in the amide-I band and a distinct change in the amide-I to amide-II band intensity ratio. These data indicate that surfactin experiences a conformational transition over the concentration range studied. The conformational transition may occur due to the formation of surfactin micelles and higher order aggregates upon increasing concentration. Surfactin was also studied in the presence of phospholipid bicelles. At low surfactin concentrations in the presence of bicelles, the amide-I band exhibits nearly identical spectral features to those found for higher concentrations of surfactin in Tris buffer, and the amide-I to amide-II band intensity ratios showed similar trends. The results of these studies indicate that the conformation of surfactin may be similar in micelles, higher order aggregates, and bicelles with the bicelles limiting the conformational distribution of the surfactin molecules. Additional studies are necessary to determine surfactin's structure in these model membranes and obtain dynamic information to better understand the mechanism of the surfactin-lipid interaction.Item Open Access Development and application of conformational methodologies: eliciting enthalpic global minima and reaction pathways(Colorado State University. Libraries, 2014) Allison, Joseph T., author; Rappé, Anthony, advisor; Strauss, Stephen, committee member; Levinger, Nancy, committee member; Shores, Matthew, committee member; Slayden, Richard, committee memberThe information granted by assembling the global minimum and low-enthalpy population of a chemical species or ensemble can be utilized to great effect across all fields of chemistry. With this population, otherwise impossible tasks including (but not limited to) reaction pathway characterization, protein folding, protein-ligand docking, and constructing the entropy to characterize free energy surfaces becomes a reasonable undertaking. For very small systems (single molecule with 1-3 torsions) generating the low-enthalpy population is a trivial task. However as the system grows, the task exponentially increases in difficulty. This dissertation will detail the two sides of this problem, generating the low-energy population of larger and more complex species and then utilizing those populations to garner a greater understanding of their systems. The first discussion describes a new model, Surface Editing Molecular Dynamics (SEMD), which aids in accelerating conformational searching by removing minima from the potential energy surface by adding Gaussian functions. Accompanying this new method are a multitude of new tools that can be utilized to aid in molecular dynamics simulations. The first of these tools, named CHILL, performs a projection of unproductive degrees of freedom from the molecular dynamics velocity to smooth atomic motions without artificially constraining those degrees of freedom. Another tool, Conjugate Velocity Molecular Dynamics (CVMD), rigorously generates a list of productive velocities via the biorthogonalization of local modes with a vector representation of previously explored conformational minima. In addition to these tools, a new description of distance in torsional space was developed to provide a robust means of conformational uniqueness. With each of these tools working in concert, the global minimum and associated low-enthalpy population of conformations have been obtained for various benchmark species. The second section discusses the application of conformational searching and the subsequent electronic structure calculations to characterize the reaction pathway for the ruthenium tris(2,2'-bipyridine) photocatalyzed [2+2] cycloaddition of aromatically substituted bis(enones). The APFD hybrid density functional is used along with a 6-311+g* basis and a PCM solvent model. The reaction is computed to proceed through a rate-limited formation of a cyclopentyl intermediate. Lithium tetrafluoroborate is found to facilitate initial bis(enone) reduction as well as final product distribution. In addition, aromatic substituents are found to impact both initial reduction and final product distribution.Item Open Access Energy transfer interactions with single molecule phenomena in small clusters of quantum dots(Colorado State University. Libraries, 2014) Whitcomb, Kevin James, author; Van Orden, Alan, advisor; Bernstein, Elliot, committee member; Levinger, Nancy, committee member; Chen, Eugene, committee member; Gelfand, Martin, committee memberThis dissertation describes the observed interactions between energy transfer in small clusters of nominally monodisperse semiconductor nanocrystals (quantum dots, QDs) and single molecule phenomena such as fluorescence intermittency (blinking) and antibunching. The relevant literature on energy transfer between QDs has typically invoked the Förster energy transfer mechanism to explain the observations in ensemble measurements. The size dispersion in QDs results in a dispersion in the electronic and optical properties of QDs due to size dependent confinement effects on photogenerated carriers. This size dispersion is thought to be the reason for energy transfer among nominally monodisperse QDs as in the single molecule work in this dissertation. The single molecule measurements in this dissertation were done using confocal microscopy and correlated atomic force microscopy (AFM). The experimental setup is described in detail. Confocal microscopy is used to excite a small region on a surface of sparsely deposited QDs or QD clusters. This allows for observation of individual QDs or individual clusters at a time. The fluorescence from these samples is collected through the microscope objective and spatially filtered using confocal techniques, i.e. spatially filtering the fluorescence with a pinhole. The excitation region can be correlated with a nanoscale topographical image using the light that is backscattered through the microscope objective by an atomic force microscope tip. This provides an additional method for distinguishing individual QDs from QD clusters. Methods for setup, alignment, maintenance of the instruments used will be described with sample preparation and practical measurement considerations. The interaction of energy transfer and QD blinking will be discussed in detail. The major findings are that the mechanism of energy transfer does not affect the individual blinking properties of QDs in a cluster, nor does the close proximity of other quantum dots. The findings will also show evidence that an individual QD governs the fluorescence state of the cluster through energy transfer. The clusters in this work were primarily identified and analyzed using fluorescence properties. The threshold in clusters is not as obvious as in individual QDs so an intensity threshold is set using a model of energy transfer that sets a threshold based on the lifetime. The findings impact future studies of QD clusters and applications that utilize QDs in close proximity to each other. The interaction of energy transfer and photon antibunching will also be discussed in detail. A simple model of energy transfer will be used to model the degree of antibunching in small clusters of QDs. The degree of antibunching observed in QD clusters is more characteristic of an individual emitter than multiple emitters which is a surprising find because it indicates that all QDs interact through energy transfer even in small nominally monodisperse aggregates. This work was done with correlated AFM to be sure that one QD or QD cluster is observed at a time. It is extremely important that only one emitter is in the excitation region because multiple independent emitters confound the analysis of antibunching and the observation of antibunching from multiple emitters heavily impacts single molecule study of QDs. Antibunching is thought to be the single definitive evidence that a single emitter is being probed but this is not so in the case of close proximity QDs even if the QDs are nominally the same size.Item Open Access Exploring model chemical systems through a new lens: combining novel microfluidic technology with infrared analysis techniques(Colorado State University. Libraries, 2016) Barich, Michael, author; Krummel, Amber T., advisor; Levinger, Nancy, committee member; Strauss, Steve, committee member; Kipper, Matt, committee member; Bartels, Randy, committee memberMultiple designer peptides, such as RADA-16, have been used as model systems to investigate the chemical parameters that influence protein folding and self-assembly processes. As such, the cause and effect relationship between folding outcomes and folding environmental factors have been extensively investigated. However, the mechanism of the folding process is largely unexplained due to the lack of an analysis technique that can capture structural changes on the time scale of the folding process. This thesis is the first step towards the ability to monitor the protein folding process with atomic structural resolution in real time. In this work, the sample handling capabilities of microfluidic devices are used to expand the experimental range of both infrared (IR) and two dimensional infrared (2D IR) measurement techniques. This includes the development of novel channel designs, overcoming IR compatibility issues, and setting precedent in monitoring chemical processes within microfluidic devices. Microfluidic channel geometries that perform microsecond mixing were developed to allow access to early reaction kinetics. A novel fabrication technique was developed to afford IR analysis methods to be utilized in microfluidic detection schemes. Lastly, model chemical reactions were studied in both Fourier transform IR microspectroscopy (FTIR microspectroscopy) and 2D IR spectroscopy experiments to highlight the applicability of the technology towards a broad range of chemical and biological systems, including the protein folding and self assembly processes.Item Open Access Exploring nanoaggregate structures of model asphaltenes using two dimensional infrared spectroscopy(Colorado State University. Libraries, 2015) Cyran, Jenée D., author; Krummel, Amber T., advisor; Bernstein, Elliot, committee member; Levinger, Nancy, committee member; Borch, Thomas, committee member; Kreidenweis, Sonia, committee memberAsphaltenes have been an enigma in the scientific community; studies on the molecular masses have differed by orders of magnitude and structures have been debated between island or archipelago structures. Thus, the asphaltene community defines asphaltenes by their solubility. Asphaltenes are n-heptane-insoluble and toluene-soluble. The known nanoaggregation of asphaltenes at different timescales and concentrations causes issues to determine the molecular weight and structure of asphaltene molecules. This thesis is the first step to using two dimensional infrared (2D IR) spectroscopy to study the nanoaggregate structure of model asphaltenes. 2D IR spectroscopy is a vibrational spectroscopy that is advantageous over linear IR absorption due to the ability to spread the spectral information over two axes. The 2D IR spectra give rise to structurally sensitive cross-peaks, affording the ability to probe the structure of the nanoaggregates. The model asphaltenes used in this work are violanthrone-79 and lumogen orange, a perylene derivative. These model asphaltenes consist mostly of polycyclic aromatic hydrocarbons (PAHs), similar to asphaltenes. Violanthrone-79 and lumogen orange also have carbonyl functional groups, which provide vibrational probes. The carbonyl stretching and ring breathing vibrations are used to probe the stacked structure of the nanoaggregates. A quinone series of one, two and three ring systems was used to first study the coupling between the carbonyl stretching and ring breathing vibrational modes. The quinone series provided the foundation for the larger ring systems that emulate asphaltenes. The data from studying the stacked structure of nanoaggregate model asphaltenes can be used to reveal properties of nanoaggregate asphaltenes. This work will allow for continued study of the kinetics of nanoaggregation using 2D IR waiting time experiments for dynamic information. Thus, this work demonstrates the use of 2D IR spectroscopy, which offers femtosecond time resolution, as a viable technique for studying nanoaggregation.Item Open Access High pressure vapor-liquid equilibrium measurements of methane and water mixtures using nuclear magnetic resonance spectroscopy(Colorado State University. Libraries, 2021) Sartini, Michael, author; Windom, Bret C., advisor; Widegren, Jason, committee member; Levinger, Nancy, committee memberGas composition, which can vary from location to location in natural gas pipelines, constrains the allowable operating conditions and compressor package design. Compressor systems are designed such that they provide the optimal balance between efficiency and gas throughput with safety margins to maintain component lifetime. The presence of liquid in the compressor can lead to excessive wear of intake and discharge valves and impact performance. To prevent ingestion of liquid slugs, operating conditions and separation equipment must be selected appropriately using mixture dew point calculations from commercially available mixture property prediction software such as NIST-REFPROP. NIST-REFPROP is highly reliant on mixture Vapor liquid Equilibrium (VLE) data to predict phases. Thus, there is a need for low uncertainty VLE data for gas mixtures at pressures (1 - 10 MPa) and temperatures (<0 – 100 °C) experienced within natural gas infrastructure, especially for mixtures containing H2O, which would lead to more accurate dew point calculations and allow designers to maximize system performance without compromising component wear and tear. For a mixture comprised completely of hydrocarbon species, VLE calculations at high pressures are accurate as the interaction parameters between the constituents are close to unity and there is typically a wealth of low-uncertainty data available. However, when H2O is present in natural gas significant intermolecular interactions cause the mixture VLE to deviate from ideality. In order to accurately model the VLE of these mixtures, the energy associated with these interactions must be known and accounted for in the calculations. As such, high quality experimental VLE data are needed to improve and validate the thermodynamic models. Nuclear magnetic resonance (NMR) spectroscopy allows for high-quality data collection for water containing samples. This thesis provides the groundwork for using NMR spectroscopy to conduct low-uncertainty VLE measurements of water-hydrocarbon mixtures. Two NMR spectrometers were investigated, and methods were developed to accurately characterize the temperature, pressure, vapor phase and liquid phase molar composition of methane-water systems at equilibrium, the five conditions required for VLE measurement. Preliminary results for low pressure (0-2.06MPa) samples of methane and water showed that the liquid phase methane compositional data taken utilizing NMR spectroscopy significantly deviated from the NISTREFPROP model, revealing the lack of low uncertainty VLE data required to determine the needed interaction parameters for methane and water systems. Future work should target the collection of the high-fidelity methane-water VLE data, and NMR spectroscopy has the potential to perform this task.Item Open Access I. Ground-state association between phenothiazine and tris(diimine)ruthenium(II) complexes: its role in highly efficient photoinduced charge separation. II. Ligand modifications of cobalt complexes to increase efficiency of electron-transfer mediators in dye-sensitized solar cells(Colorado State University. Libraries, 2012) Weber, John, author; Elliott, C. Michael, advisor; Rappe, Anthony, committee member; Levinger, Nancy, committee member; Woody, Robert, committee member; Van Orden, Alan, committee memberSupramolecular triad assemblies consisting of a central trisbipyridineruthenium(II) chromophore (C2+), with one or more appended phenothiazine electron donors (D) and a diquat-type electron acceptor (A2+) have been shown to form long-lived photoinduced charge separated states (CSS) with unusually high quantum efficiency. Up to now, there has been no explanation for why such large efficiencies (often close to unity) are achieved from these systems when other, seemingly similar, systems are often much less efficient. In the present study, using a bimolecular system consisting of chromophore-acceptor diad (C2+-A2+) and an N-methylphenothiazine donor we demonstrate that a ground-state association exists between the RuL32+ and the phenothiazine prior to photoexcitation. It is this association process that is responsible for the efficient CSS formation in the bimolecular system and, by inference, also must be an essential factor in the fully intramolecular process occurring with the D-C2+-A2+ triad analogs. Alkyl-substituted bipyridine ligands in cobalt II/III complexes were modified in order to serve as efficient electron-transfer mediators in dye-sensitized solar cells. Attempts at halogen substitution reactions are described. Ultimately isopropyl groups appended to bipyridine ligands were modified by introducing a hydroxyl group at the benzylic position. The electrochemical behavior of the modified ligand is described, as well as its performance as part of a cobalt complex electron-transfer mediator in dye-sensitized solar cells.Item Embargo Investigating the role of chemical additives in the structure and dynamics of electrolyte mixtures via 2D infrared spectroscopy and microscopy(Colorado State University. Libraries, 2022) Tibbetts, Clara Anne, author; Krummel, Amber T., advisor; Wilson, Jesse, committee member; Levinger, Nancy, committee member; Rappe, Anthony, committee memberThe research in this dissertation is focused on the impact that additives have on the chemical structure and dynamics of electrolyte solutions that can be used in electrochemical devices such as batteries or solar devices. Two-dimensional infrared spectroscopy (2D IR) has been used in conjunction with linear Fourier Transform infrared spectroscopy (FTIR), rheology, molecular dynamics, and density functional theory to study organic carbonate and ionic liquid mixtures. In addition, 2D IR microscopy is successfully implemented to study ionic liquid mixtures in different environments including a microdroplet and a copper electrochemical cell. 2D IR and molecular dynamics simulations of organic carbonate mixtures with varied amounts of a common additive, fluoroethylene carbonate (FEC), show that even in small quantities FEC can induce changes in the solvent structure. Experimental results demonstrated that at low concentrations FEC slows spectral diffusion. Cylindrical distribution functions calculated from molecular dynamics simulations in conjunction with experimental results suggest the slowing is due to significant changes in the behavior of one of the solution components, ethylene carbonate. Furthermore, a combination of experimental anisotropy and viscosity, and computational rotational correlation functions shows that local solvent rigidity increases with high amounts of FEC. Moreover, these results show that additional FEC increases macroscopic viscosity which is correlated to global solvent orientational relaxation. In functional batteries FEC is shown to dramatically impact how the solid electrolyte interphase forms, a layer that impacts battery metrics such as lifetime and safety.1–3 Therefore, it is possible that the observed changes in the solvent structure upon addition of FEC has implications in how the solid electrolyte interphase forms. The combination of linear and 2D IR spectroscopy with viscosity measurements is used to study the impact of small amounts of water (between ~1.32 and 21.6% mole fraction water) on the structure and dynamics of room-temperature ionic liquid mixtures. Specifically, the effects of water on a mixture of 1-butyl-3-methylimidazolium tetrafluoroborate (BmimBF4) and 1-butyl-3-methylimidazolium dicyanamide (BmimDCA) room-temperature ionic liquid (RTIL) was investigated by tracking changes in the vibrational features of the dicyanamide anion (DCA). Shifts in the infrared peak frequencies of DCA indicated the formation of water-associated and non-water-associated DCA populations. Time-dependent 2D IR shows differences in the dynamic behavior of the water-associated and non-water-associated populations of DCA at low (below 2.5% χWater), mid (between 2.5% χWater and 9.6% χWater), and high (between 11.6% χWater and 21.6% χWater) water concentrations. The vibrational relaxation occurs more quickly with increasing water content for water-associated populations of DCA, indicating water introduces additional pathways for relaxation, possibly via new bath modes. On the other hand, spectral diffusion of water-associated populations slows significantly with more water, suggesting water induces the formation of distinct and non- or very slowly interchangeable local environments. It is possible that in a functional electrochemical device with a water and RTIL electrolyte the introduction of these diverse local solvent environments might impact device performance. If water could be introduced in a system in a way that increased ion-mobility but does not cause undesirable interfacial interactions near an electrode this could improve device efficiency. Therefore, determining if and how this local heterogeneity presents itself in an operational electrochemical cell is an important next step. Ultrafast 2D IR microscopy is discussed as an emerging imaging platform that is a promising tool for investigating heterogeneous samples across multiple time scales and length scales, including electrochemical devices. However, there are numerous practical considerations in the implementation of 2D IR microscopy. Some of these considerations include mid-IR laser sources, repetition rates, mid-IR pulse shaping, noise reduction, microscope design, and detection limitations. In this work we show the implementation of improvements in spectral resolution and noise reduction and the consequent successful imaging of a BmimDCA:BmimBF4 electrolyte in two different scenarios—a droplet and a copper electrochemical cell. Imaging the BmimDCA:BmimBF4 microdroplet shows how 2D IR imaging can be used to probe dynamics on a spatial scale. Results indicate the solvent dynamics in the microdroplet are spatially homogenous. Imaging experiments of the RTIL electrolyte in a copper cell, demonstrates a practical application of ultrafast 2D IR microscopy to study functional electrochemical devices. 2D IR spectra collected between the copper counter electrode and working electrode showed dramatic changes in peak positions and shapes suggesting the formation of DCA copper complexes. These results suggest 2D IR microscopy will allow chemical exchange dynamics of different species involved in the electrochemical reactions to be monitored as they evolve from the counter electrode to the working electrode. This work establishes 2D IR microscopy as a tool well equipped to connect molecular level condensed phase reaction dynamics to micro- and mesoscale spatial dependence in an electrochemical cell.Item Open Access Investigation of chiral porphyrin aggregates with heterodyne-detected vibrational sum frequency generation spectroscopy(Colorado State University. Libraries, 2018) Lindberg, Kathryn A., author; Krummel, Amber, advisor; Levinger, Nancy, committee member; Sambur, Justin, committee member; Gelfand, Martin, committee memberIn nature, photosynthetic organisms harvest and transport solar energy through the finely-tuned interplay between vibrational, electronic, and excitonic characteristics within photosynthetic reaction centers. These characteristics depend intimately on the precise arrangement of the reaction centers' molecular building blocks. Further knowledge of the relationship between structure and function in these natural systems is key to advancing synthetic solar technologies like dye-sensitized solar cells and artificial photosynthesis. Photosynthetic pigments, such as chlorophyll and bacteriochlorophyll, are of particular interest since their absorptive role is the first step in the solar harvesting process. Porphyrins, a group of macrocyclic organic compounds closely related to these pigments, have gained attention as simpler models for their more complicated natural counterparts. Tetra(4-sulfonatophenyl) porphyrin (TSPP), which closely resembles bacteriochlorophyll, is particularly valuable because it forms molecular aggregates analogous to the highly quantum-efficient light-harvesting "antennae" present in green sulfur bacteria chlorosomes. Imaging and spectroscopic studies indicate that the helical nanotubular TSPP aggregates are chiral and have distinct exciton contributions along different axes. However, the precise arrangement of TSPP monomers within the aggregate walls is still debated, prompting further, more detailed studies. Heterodyne-detected vibrational sum frequency generation (HD-VSFG) spectroscopy is a phase-sensitive, second-order nonlinear technique which probes the vibrational characteristics of noncentrosymmetric molecular environments. HD-VSFG experiments can also probe excitonic and vibronic characteristics via experimental double resonance. By use of polarization conditions, theoretical modeling, and computational fitting, detailed information on the orientation of vibrational, vibronic, and excitonic transition dipoles can be extracted from HD-VSFG spectra. This work presents doubly-resonant HD-VSFG spectra of TSPP thin films drop-cast on gold, which demonstrates the technique's sensitivity to the relationship between complex phase and excitonic versus monomeric characteristics. HD-VSFG is then used to compare spectra of TSPP thin films prepared from racemic and chiral aqueous solutions. This comparison includes a polarization condition sensitive to only chiral environments, further demonstrating HD-VSFG as a valuable tool in the structural investigation of TSPP aggregates.Item Open Access Microfluidics for environmental analysis(Colorado State University. Libraries, 2018) Gerold, Chase T., author; Henry, Charles S., advisor; Krummel, Amber, committee member; Levinger, Nancy, committee member; Finke, Richard, committee member; Dandy, David, committee memberDuring my graduate dissertation work I designed and utilized microfluidic devices to study, model, and assess environmental systems. Investigation of environmental systems is important for areas of industry, agriculture, and human health. While effective and well-established, traditional methods to perform environmental assessment typically involve instrumentation that is expensive and has limited portability. Because of this, analysis of environmental systems can have considerable financial burden and be limited to laboratory settings. To overcome the limitations of traditional methods researchers have turned to microfluidic devices to perform environmental analyses. Microfluidics function as a versatile, inexpensive, and rapidly prototyped analytical tool that can achieve analysis in field setting with limited infrastructure; furthermore, microfluidic devices can also be used to study fundamental chemistry or model complex environmental systems. Given the advantages of microfluidic devices, the research presented herein was accomplished using this alternative to traditional instrumentation. The research projects described in this dissertation involve: 1) the study of fundamental chemistry associated with surfactant surface fouling facilitated by divalent metal cations; 2) the creation of a microfluidic device to study fluid interactions within an oil reservoir; and 3) the fabrication of a paper-based microfluidic to selectively quantify K+ in complex samples. The first research topic discussed involves observation of dynamic evidence that supports the hypothesized cation bridging phenomenon. Experimental results were acquired by pairing traditional microfluidics with the current monitoring method to observe relative changes to a charged surface's zeta potential. Divalent metal cations were found to increase surfactant adsorption, and cations of increasing charge density were found to have a greater effect on surface charge. Analysis of the experimental data further supports theoretical cation bridging models and expands on knowledge relating to the mechanism by which surfactant adsorption occurs. This work was published in the ACS journal Langmuir (2018, 34 (4), pp 1550–1556). The second project discussed herein focuses on the development of the microfluidic Flow On Rock Device (FORD) that was designed to study fluid interactions within complex media. The FORD was designed to be an alternative to existing fluid modeling methods and microfluidic devices that test oil recovery strategies. Fabrication of the FORD was accomplished by incorporating real reservoir rock core samples into the device. The novelty of this device is due to the simplicity and accuracy by which the physical and chemical characteristics are represented. This project has been accepted for publication pending minor revisions in Microfluidics and Nanofluidics. The final project discussed the creation of the first non-electrochemical microfluidic paper-based analytical device (µPAD) capable of quantitatively measuring alkali or alkaline earth metals using K+ as a model analyte. This device was fabricated by combining distance-based analytical quantification in µPADs with optode nanosensors. Experimental results were obtained using the naked eye without the requirement of a power source or external hardware. The resulting distance-based µPAD showed high selectivity and the capacity to quantify K+ in real undiluted human serum samples. This work has been published in the ACS journal Analytical Chemistry (2018, 90 (7), pp 4894–4900). The research projects briefly described above and thoroughly discussed later within this dissertation were made possible by the utilization of microfluidic devices. These projects investigated various aspects of environmental chemistry without the use of traditional instrumentation or methods. The experimental results that were obtained further the fundamental understanding of surfactant adsorption, provide an inexpensive and accurate model to observe fluid interactions within reservoir rock material, and allow for the selective quantification of K+ in a paper-based device without the use of a power source. The funding for each of these projects was supplied by BP plc and Global Good, as is mentioned accordingly within this dissertation.Item Open Access Modeling conformational heterogeneity in biomolecules(Colorado State University. Libraries, 2023) Klem, Heidi, author; Paton, Robert, advisor; McCullagh, Martin, advisor; Levinger, Nancy, committee member; Kennan, Alan, committee member; Geiss, Brian, committee memberRegulation of biocatalytic cascades is essential for biological processes but has yet to be exploited in real-world applications. Allostery is a prime example, where binding of an effector molecule alters function in a remote location of the same biomolecule. V-type allostery is especially fascinating, as the reaction rate can be either increased or decreased in response to effector binding. Determining how conformational changes affect the reaction rate is challenging due to the disparity of timescales between the underlying molecular processes. Experimental methods, such as X-ray crystallography, can help to capture large-scale conformational change. However, the resulting structures are not guaranteed to correspond to the biophysical state relevant to the research questions being addressed. Structural changes that occur during the chemical reaction are particularly elusive to this approach. To understand the connection between conformational change and catalytic consequence, a description of the reaction mechanism and relevant configurations is needed. Quantum mechanical (QM) methods can be used to propose enzyme reaction mechanisms by modeling femtosecond motions of forming and breaking bonds. Large-scale conformational changes take place over much longer timescales that cannot be simulated at the QM level, therefore requiring classical simulation techniques. This dissertation focuses on the challenges posed by conformational change in the field of computational biocatalysis. The first chapter examines the prevalence of conformational change in enzymes, its relationship to catalysis, and the difficulties it presents. The second chapter looks at the influence of active site structural features on reaction rates in the allosteric enzyme IGPS using QM approaches and energy decomposition schemes. The third chapter covers the development of methods that use molecular dynamics (MD) simulations to analyze relevant structural states from simulation data and identify long-range communication pathways in biomolecules. The fourth chapter presents a Python code, enzyASM, that automates the generation of QM-based truncated active site models and discusses ongoing developments that will aid reproducibility and standardization in this field of research. The fifth and final chapter summarizes the implications of this Thesis work in computational biocatalysis and envisions how remaining challenges can be addressed to maximize potential to solve real-world problems.Item Open Access Optically detected ion insertion dynamics in hexagonal tungsten oxide(Colorado State University. Libraries, 2021) Evans, R. Colby, author; Sambur, Justin Barret, advisor; Prieto, Amy, committee member; Levinger, Nancy, committee member; Weinberger, Christopher R., committee memberNanoparticle electrodes are attractive for electrochemical energy storage applications because their nanoscale dimensions decrease ion transport distances and generally increase ion insertion/extraction efficiency. However, nanoparticles vary in size, shape, defect density, and surface composition, which impacts charge storage dynamics and warrants their investigation at the single-nanoparticle level. This dissertation demonstrates a non-destructive, high-throughput electro-optical imaging approach to quantitatively measure electrochemical ion insertion reactions at the single-nanoparticle level. Electro-optical measurements relate the optical density change of a nanoparticle to redox changes of its redox-active elements under working electrochemical conditions. The technique was benchmarked by studying Li-ion insertion in hexagonal tungsten oxide (h-WO3) nanorods. Interestingly, the optically detected response revealed underlying processes that are hidden in conventional electrochemical measurements. This imaging technique may be applied to h-WO3 particles as small as 13 nm in diameter and a wide range of electrochemical materials such as electrochromic smart windows, batteries, solid oxide fuel cells, and sensors. This dissertation will focus on the impact of single particle h-WO3 on smart windows and batteries. Smart windows are devices used to modulate solar radiation into buildings and rely on the same ion insertion reaction as batteries. Electro-optical imaging showed that single nanorods exhibit a particle-dependent waiting time for optical changes (from 100 ms to 10 s) due to Li-ion insertion at optically inactive surface sites. Additionally, longer nanorods have larger optical modulation at equivalent electrochemical conditions than shorter nanorods and exhibit a Li-ion gradient that increases from the nanorod ends to the middle. The particle-dependent ion-insertion kinetics contribute to variable rate for optical density change and magnitudes across large-area smart windows. Single particles modulate optical density (undergo ion insertion reactions) 4 times faster and 20 times more reversibly than thin films made of the same particles. A smart window device architecture is proposed to maximize lifetime based on these findings. More information can be found in CHAPTER 4. Further, the role of crystalline surface facets on the role of ion insertion were investigated. Two samples of h-WO3 were synthesized with different ratios of surface facets exposed to a Li-ion containing electrolyte. The sample with unique {120} facets exhibited reversible optical switching after 500 cycles and negligible variation in interfacial charge transfer resistance. The (120) surface features an open network of square window channels that may enable reversible ion transport and reduced ion trapping, enhancing the optical switching stability. However, the {120}-dominant sample exhibited lower coloration efficiency (CE) than the {100}-dominant sample. The reduced optical density changes in the {120}-dominant sample could be due to a greater fraction of optically inactive trigonal cavity sites on the {001} endcaps. The results indicate surface facet and particle morphology engineering are viable strategies to enhance the CE and long-term stability/lifetime in electrochromic thin films for smart window applications. More information can be found in CHAPTER 5. On average, these h-WO3 particles exhibit a hybrid charge storage mechanism: both diffusion-limited (battery-like, slower) and pseudocapacitive (capacitor-like, faster) mechanisms contribute to the total charge stored. Individual particles exhibit different charge storage mechanisms at the same applied potential. Longer nanorods store more pseudocapacitive charge than shorter nanorods, presumably due to 1) a surface step edge gradient that exposes large hexagonal window Li-ion binding sites along the nanorod length and/or 2) higher structural water content that influences the Li-ion binding energetics and diffusion behavior. Importantly, penetration depth of Li-ion insertion was quantified which showed that Li ions insert as deep as two-unit cells below the surface. The methodology presented herein can be applied to a wide range of solid-state ion-insertion materials and its implications for future discoveries are discussed. More information can be found in CHAPTER 6.Item Open Access Role of homotropic association of luteinizing hormone receptors in hormone mediated signaling(Colorado State University. Libraries, 2012) Crenshaw, Shirley Ann, author; Barisas, B. George, advisor; van Orden, Alan, committee member; Rickey, Dawn, committee member; Levinger, Nancy, committee member; Roess, Deborah, committee memberG protein-coupled receptors (GPCR) are plasma membrane receptors involved in signal transduction and are an important target for drug discovery. Luteinizing hormone receptors (LHR) are GPCRs found on the reproductive organs of both males and females and promote spermatogenesis and ovulation. Understanding how these protein receptors function on the plasma membrane will lead to better understanding of the mammalian reproduction system and other GPCR systems. Studies in the past suggested that these receptors oligomerize after hormone binding, but recent studies performed with LHRs suggest that these receptors maybe constitutively oligomerized in the endoplasmic reticulum and on the plasma membrane. However, these experiments were performed on receptors expressed by transient transfection and using bioluminescence resonance energy transfer (BRET). These methods have potential weaknesses. Transient transfections typically yield a fraction of cells with very high receptor expression and BRET measurements are strongly weighted towards those cells. Hence, this overall approach may have yielded misleading results. Fluorescence energy transfer (FRET) is a similar technique to BRET but has advantages such as allowing imaging examination of single cells. Using FRET, LHR oligomerization was evaluated on cells treated with human chorionic gonadotropin (hCG) or deglycosylated-hCG, hormones which activate and inhibit the receptor function, respectively. FRET measurements demonstrated that, on the surfaces of transiently transfected cells, LHRs exhibit substantial intermolecular FRET which is very slightly increased by hCG treatment and very slightly reduced by exposure to DG-hCG. Closer examination of these data showed that all observed FRET depended linearly on receptor expression and approach zero at low expression levels. This suggests that FRET between LHR on these transiently-transfected cells may arise from inter-molecular proximity induced non-specifically by high receptor surface concentrations. To evaluate the receptor density on cells flow cytometry was used. Flow cytometry revealed that transiently-transfected LHRs are expressed over a broad range of surface densities, including very high expression levels. Using a mathematical model, the FRET efficiencies expected for various receptor surface densities were calculated. These calculations suggest that expression levels observed cytometrically could cause substantial amounts of FRET from molecular crowding and, particularly if the receptors are additionally concentrated in lipid rafts, most of the observed FRET signal could be attributed to non-specific concentration effects.Item Open Access The kinetics of proteins on lipid bilayers(Colorado State University. Libraries, 2017) Nepal, Kanti, author; Krapf, Diego, advisor; Peersen, Olve, committee member; Levinger, Nancy, committee memberSignaling molecules trigger downstream signaling pathways when they arrive at the plasma membrane. They have to be recruited to the plasma membrane by membrane targeting domains. Our experiments throughout focus on understanding kinetics of C2 domain's diffusion on the membrane. In contrast to trans-membrane proteins, interactions between these domains and the plasma membrane is found to be peripheral and transient. These proteins perform two dimensional diffusion on membrane surfaces and faster three dimensional diffusion in the bulk. We label proteins at the single molecule level and do single particle tracking. In addition to two dimensional surface diffusion, it is sometimes observed that they dissociate from the membrane and rebind at a another location of the membrane after a short journey in the bulk solution. The time averaged mean square displacement (MSD) analysis of individual trajectories is linear whereas ensemble average MSD is superdiffusive. The distribution of displacements fit to a Gaussian distribution followed by a long tail which is Cauchy's distribution. This long tail in cauchy's distribution is from the larger displacements caused by jumps of molecule to explore greater area for efficient target search. The second section of this thesis explored the effect of crowding agents on these proteins. Polyethylene glycol (PEG) is used here to simulate crowded cellular environment aiming to understand its effect on membrane targeting C2 domains as well as on the lipid bilayer. In this chapter, we recognized that a crowding agent like PEG plays a significant role in changing the trend on diffusion behavior of C2 domains. When the PEG concentration is increased, there is a decrease in the transition of molecule between the surface and the bulk phase. With the same series of PEG concentration, there is increase in population of immobile C2 domains and desorption time. But no such increasing or decreasing trend is seen on the lipid bilayer alone. Experiments were reproduced and imaged a number of times using total internal reflection (TIRF) and fluorescence recovery after photobleaching (FRAP) techniques. Lastly, a small part of my thesis also dealt with set of experiments done to monitor tethered particle motion of DNA as well as flow extension experiments on DNA and RNA using bright field microscopy. DNA/RNA had beads tethered to one end of the strand and other end to the cover glass. Primary results are presented.Item Open Access The synthesis of the pentacyclic carbon framework of the PF1270 family of natural products(Colorado State University. Libraries, 2014) Sanchez, Michelle A., author; Williams, Robert M., advisor; Kennan, Alan, committee member; Rovis, Tomislav, committee member; Levinger, Nancy, committee member; Crick, Dean, committee memberThe PF1270 family of natural products contains novel indole alkaloids that display interesting biological activity; the synthesis of these natural products and their analogs could lead to the discovery of novel therapeutics. Discussed herein is the synthesis of the complete pentacyclic carbon framework of the PF1270s, accomplished through a key intermolecular Diels-Alder reaction. Other highlights of the synthesis include an acid catalyzed opening lactim ether at a late stage, and a particularly difficult decarboxylation promoted by diphenylphosphoryl azide.Item Embargo Transient phase microscopy using balanced-detection temporal interferometry and a compact piezoelectric microscope design with sparse inpainting(Colorado State University. Libraries, 2024) Coleal, Cameron N., author; Wilson, Jesse, advisor; Bartels, Randy, committee member; Levinger, Nancy, committee member; Adams, Henry, committee memberTransient phase detection, which measures the Re{∆N }, is the complement to transient absorption detection (Im{∆N }). This work extends transient phase detection from spectroscopy to microscopy using a fast-galvanometer point-scanning setup and compares the trade-offs in transient phase versus transient absorption microscopy for the same pump and probe wavelengths. The realization of transient phase microscopy in conjunction with transient absorption microscopy opens a new door to measure the excited-state kinetics with phase-based or absorption-based techniques; depending on the sample and the wavelengths in use, transient phase detection may provide a signal improvement over transient absorption. Up until this point, transient phase microscopy has been a neglected technique in ultrafast pump-probe imaging applications. Additionally, this work evaluates a miniature piezoelectric actuator to replace galvanometers in a compact point-scanning microscope design. Sparsity limitations present in the design are addressed by the construction of a Fourier-projections based inpainting algorithm which could enable faster imaging acquisition in future applications.Item Open Access Ultrafast quantum coherent control apparatus(Colorado State University. Libraries, 2007) Wilson, Jesse, author; Bartels, Randy, advisor; Levinger, Nancy, committee member; Rocca, Jorge J. G., committee memberIn recent years, the availability of ultrafast laser sources has opened up a number of opportunities for exploring molecular dynamics that take place on femtosecond time scales. Coherent control experiments involve creating, manipulating, and measuring these ultrafast phenomena. Such controllable processes include second harmonic generation (SHG), creation of vibrational wavepackets, high-harmonic generation, photodissociation, and more.The foundation to all these experiments is an ultrafast pulse shaper and a high-dimensional search algorithm. Here we present the design and construction of a spectral phase-only pulse shaper, including details on alignment and calibration. We also demonstrate the functionality of the device by producing several pulse profiles that could be potentially useful in coherent control experiments. A covariance matrix analysis evolutionary strategy (CMAES) is also implemented, and demonstrated to optimize SHG in a nonlinear crystal. Finally, recognizing that phase-only shapers cannot produce the full range of temporal shapes available to a given input pulse, we show the design and construction of a pulse shaper which uses only a single linear phase mask to gain control over both spectral phase and amplitude by use of phase gratings.