Chemistry & Biochemistry Theses and Dissertations
Permanent URI for this collectionhttp://hdl.handle.net/1903/2752
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Item LOCAL MOLECULAR FIELD THEORY FOR NON-EQUILIBRIUM SYSTEMS(2019) Baker III, Edward Bigelow; Weeks, John D; Chemical Physics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Local Molecular Field (LMF) theory is a framework for modeling the long range forces of a statistical system using a mimic system with a modified Hamiltonian that includes a self consistent molecular potential. This theory was formulated in the equilibrium context, being an extension of the Weeks Chandler Andersen (WCA) theory to inhomogeneous systems. This thesis extends the framework further into the nonequilibrium regime. It is first shown that the equilibrium derivation can be generalized readily by using a nonequilibrium ensemble average and its relevant equations of motion. Specifically, the equations of interest are fluid dynamics equations which can be generated as moments of the BBGKY hierarchy. Although this approach works well, for the application to simulations it is desirable to approximate the LMF potential dynamically during a single simulation, instead of a nonequilibrium ensemble. This goal was pursued with a variety of techniques, the most promising of which is a nonequilibrium force balance approach to dynamically approximate the relevant ensemble averages. This method views a quantity such as the particle density as a field, and uses the statistical equations of motion to propagate the field, with the forces in the equations computed from simulation. These results should help LMF theory become more useful in practice, in addition to furthering the theoretical understanding of near equilibrium molecular fluids.Item DEVELOPMENT OF A MICROSCALE ELECTROCHEMICAL PLATFORM FOR THE ANALYSIS OF THERMAL PROFILES OF IMMOBILIZED DNA SECONDARY STRUCTURES(2019) Robinson, Sarah; Lee, Sang Bok; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Understanding the thermal stability of DNA secondary structures is important to the pharmaceutical industry, as drug molecules that strongly bind will increase the stability of the structure, leading to higher measured melting temperatures. Development of an electronic platform that can measure the thermal profiles of small-volume samples with automation and methodology that is scalable for high-throughput screening (HTS) would represent an important asset for the drug discovery process. This thesis endeavored to produce and demonstrate the feasibility of such a technology. A microelectronic device has been fabricated in the configuration of a planar electrochemical platform with an embedded platinum thin film that can function as both a platinum resistance thermometer (PRT) and as a resistive microheater. The device assembly as well as automation of the temperature control and electrochemical methods have been instituted to increase measurement repeatability with the microscale device. The operational program was developed with a variety of features, including a PID controller, and has been demonstrated for a two-device array; functioning is scalable to larger device arrays with the addition of suitable electronics. A proof-of-concept methodology has been shown for monitoring the stabilization effects of ligand binding to duplex DNA. Results are presented for both refrigeration with resistive heating, and thermoelectric cooling and heating. The technology has also been adapted to examine other DNA secondary structures, such as G-quadruplexes, and the stabilization of these structures. The resulting analysis of such immobilized intramolecular secondary structures has demonstrated that the systems are more complicated and further fundamental studies are needed. With the future incorporation of microfluidics and larger-device arrays, a range of effects can be tested based on the demonstrated technology to understand binding events of relevance to drug discovery and the complexities of the surface chemistry effects on the analysis of thermal profiles.Item CHARACTERIZATION OF NON-CODING RNAS VIA NMR SPECTROSCOPY: ANALYSIS OF STRUCTURE, THERMAL STABILITY, AND DYNAMICS(2019) Nam, Hyeyeon; Dayie, Theodore K; Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Non-coding RNAs are involved in various cellular processes and characterization of these RNAs may provide better insights into their functional roles. NMR spectroscopy is a powerful biophysical tool that can provide residue-specific information. Herein we examine an RNA triple helix at the 3' end of the lncRNA MALAT1, which may be a potential therapeutic target for cancer treatment. We investigate the local stability of the MALAT1 triple helix by analyzing the individual base-pair stability via NMR spectroscopy. In addition, we screened small molecules to identify the compounds that can selectively target the MALAT1 triple helix. In the second part, we studied the effect of dipolar couplings on the relaxation measurements of various non-coding RNAs using both computational and experimental measurements. The results suggest an increasing contribution of the dipolar coupling effect with the increasing size of the RNA.Item PROTEIN FOLD SWITCHING: INVESTIGATING THE MECHANISM OF αβ-PLAIT TO 3α FOLD INTERCONVERSION(2019) Solomon, Tsega Lily; Orban, John; Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Naturally occurring metamorphic proteins have the ability to interconvert from one folded state to another through either a limited set of mutations or by way of a change in the local environment. However, the design of these types of proteins has remained challenging. This dissertation shows that it is possible to switch reversibly between two different but common folds employing only temperature changes. The study demonstrates that a latent 3α state can be unmasked from an αβ-plait topology with a single V90T amino acid substitution in a designed system, populating both forms simultaneously. The equilibrium between these two states exhibits temperature dependence, such that the 3α state is predominant (>90%) at 5°C, while the αβ-plait fold is the major species (>90%) at 30°C. The structure and dynamics of these two temperature-dependent topologies, as well as their energetics and kinetics of interconversion, are characterized utilizing NMR spectroscopy. Additional analysis show that the temperature-dependent characteristics of the 3α<->αβ-plait fold switch can be modulated by mutations. Stability studies through H-D exchange approach provide insight on the energetic basis for temperature induced 3α<->αβ-plait fold conversion. Further investigations demonstrated that interconversion between the 3α and αβ-plait states can be triggered by additional environmental factors including pressure, ligand binding, and redox state. This dissertation adds to the growing body of literature on protein fold metamorphism providing the first description of switching between two distinct monomeric protein folds using only temperature or pressure. Additionally, the studies of ligand- and redox-induced 3α<->αβ-plait fold switching emphasize the ability to mimic by design some of the mechanisms of fold interconversion that are found in naturally occurring metamorphic proteins. Given the high occurrence of the 3α and αβ-plait folds in the universe of known protein structures, the results suggest that such fold switching events may have occurred in the evolutionary expansion of function for natural versions of these topologies.Item POLYMER ASSISTED ASSEMBLY OF INORGANIC MATERIALS FOR NEXT GENERATION BATTERIES(2019) Carter, Marcus; Rodriguez, Efrain; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Nanoscale materials have desirable electronic features (e.g. high surface areas, reduced mass and transport paths) that can be harnessed for a variety of technological applications. In most storage devices, there is a particular interest in nanostructured electrodes and solid-state electrolytes. A key challenge is the reproducible fabrication of these nanostructured materials. Polymers are nanoscale materials that could be used for nanoscale fabrication with improved reproducibility. In this thesis I explored two nanostructured systems using novel polymer assisted assembly methods. I fabricate a nano-structured MoS2 electrode and a nano-structured Li7La3Zr2O12 solid-state electrolyte with a garnet-type structure. A clear redox mechanism for MoS2 is currently being sought. Using our electrode, we propose a mechanism to understand the total or partial decomposition of the electrode and the formation of long soluble polysulfides. We complete a fundamental study to determine the peaks on a cyclic voltammetry curve of nanostructured MoS2. We resolve these peaks by building a novel but simple system of restacked MoS2 with a conformal polyaniline (PANI) coating. We propose that the novel coating functions by absorbing, capturing, and promoting charge transfer (oxidization and reduction) of sulfur atoms remaining at the surface. Our data suggests that PANI acts as redox mediator. Redox mediators can be molecules or solid surfaces that aid in the charge transfer to redox species, traditionally oxide species. Our findings suggest that sulfur behavior dominates the redox chemistry at 0.7 V even earlier than the proposed deep discharge. We propose that longer chain polysulfides are formed through surface mediated interactions with persistent lattice planes of MoS2. Solid-state electrolytes like cubic garnet type Li7La3Zr2O12 offer safety advantages over flammable liquid electrolytes, which is especially significant to the advancement of high energy density battery devices. Garnet however is unstable in air, suffers from low preparation efficiency and degradation into a two competitive phases, tetragonal type garnet and lithium carbonate phases, which have low conductivity. For two polymers systems, poly(styrene)-block-poly(acrylic acid), PS(0.3)-b-PAA(0.7) and PS(0.8)-b-PAA(0.2), we synthesize cubic Li7La3Zr2O12 garnet. We systematically investigate the effect of growth parameters, temperature and excess lithium content, to find the optimized synthesis conditions of 750 °C for ~5 h with 60 wt.% and 65 wt.% excess lithium salt, for the polymer systems.Item ISOTHERMAL DNA DETECTION UTILIZING BICYCLIC AMPLIFICATION OF PADLOCK PROBES(2019) Zimmermann, Alessandra C.; Kahn, Jason D; White, Ian M; Biochemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)As healthcare worldwide changes to more patient-centric models, medical diagnostics need to adapt to being used in settings outside of the central lab. Current strategies to bring diagnostics to the patient’s bedside involve miniaturizing complicated amplification techniques, such as polymerase chain reaction, or building convoluted microfluidic assays that are difficult to operate. Ideally, a patient-centric diagnostic would require little instrumentation or training to operate, for which isothermal amplification techniques are ideal. Recent developments in catalytic DNA have enabled novel ways of iterating on amplification strategies to detect medically-relevant target sequences in systems that require little manipulation to operate. In this thesis we improve upon the body of research on DNAzymes, catalytic DNAs that can self-cleave in the presence of a cofactor, used in concert with amplification techniques. We create a one-pot, bicyclic amplification assay capable of detecting single-stranded oligonucleotides, with straightforward extensions to double-stranded targets, multiplexing, and integration into advanced detection platforms. The target is detected through its hybridization to a circle template, using the sequence specificity of DNA to splint the ligation of this ‘Template I,’ with minimal detection of off-target sequences. The circular Template I is copied through rolling circle amplification (RCA), with the amplicon containing a DNAzyme that will self-cleave in the presence of copper ions. This generates a second primer in situ that can be used to prime a second, pre-ligated, Template II to elevate the RCA amplification scheme from a linear method to a polynomial one. This Circle II template can then be used in a variety of detection modalities. The second amplicon can be used to cleave a hybridized FRET probe through the same copper ion cleavage mechanism as the primer generation, resulting in real-time fluorescence tracking. Alternatively, the RCA of the second circle can produce G-quadruplexes, which can be visualized with ABTS as a colorimetric endpoint that can be seen by eye, reducing the need for peripheral electronics. Finally, this thesis demonstrates the performance of the bicyclic RCA system in a phase-change system providing sequential mixing of components separated by wax layers, allowing the assay to proceed without any user interaction other than heating.Item OXYGEN STORAGE PROPERTIES OF TERNARY METAL OXIDE SYSTEMS FOR CHEMICAL LOOPING REACTIONS(2019) Jayathilake, Rishvi Sewwandi; Rodriguez, Efrain E; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)We have studied the reversible uptake and release of oxygen in the layered metal oxide system AB2O4 to understand their suitability as oxygen storage materials. We examined their structures at their most reduced, oxidized, and intermediate phases of AFe2O4 for A= Lu, Yb, Y, and In, and studied their structures with high-resolution synchrotron X-ray diraction. Under simulated chemical looping conditions, we monitored their structures and reactivity towards H2 and O2 utilizing in-situ X-ray diraction, neutron diraction, and thermogravimetric analysis measurements. The nature of the trivalent A cation aects the oxidation kinetics, thermal cycling stability, and oxygen storage capacity (OSC). With the exception of the A = In analogue, these layered oxides underwent various phase transitions above 200 °C that included the creation of a superstructure as oxygen incorporates until a high temperature phase is established above 400 °C. To understand trends in the oxygen incorporation kinetics, we employed bond valence sum analysis of the Fe-O bonding across the series. The more underbonded the Fe cation, the more facile the oxygen insertion. During the cycling experiments all samples exhibited reversible oxygen insertion at 600 °C for this series, and displayed OSC values between 0.2-0.27 O2 mol/mol. The Y analogue displayed the fastest kinetics for oxidation, which may make it the most suitable for oxygen sensing applications. The structure of the oxidized phase was solved from with simulated annealing and Fourier dierence maps. Structural parameters were reported with combine neutron and X-ray Rietveld renement. PDF and XAS were used to conrm the nal structural model. As the nal steps experiments were carried out to explore the chemical looping reactivity of AB2O4 layered oxides, with A= Lu, Yb, Y and B=Mn, Fe. We reported the reactivity with methane of AB2O4 layered oxides for the rst time. The RT pristine structure was regenerated at 600 °C under methane. Mn substituted compounds exhibited faster kinetics and also higher oxygen storage capacities. We conclude that the layered, ternary metal oxide system, AB2O4, is a suitable candidate as an oxygen storage material for the potential application in chemical looping reactions.Item STRUCTURE AND PROPERTIES OF ALLOYED CHALCOGENIDES WITH THE ThCr2Si2 TYPE STRUCTURE(2019) Virtue, Austin; Rodriguez, Efrain E; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The ThCr2Si2-type structure has proven itself to be an incredibly robust structure type. Its ability to incorporate elements from the majority of the periodic table has earned it the moniker of \The perovskite of intermetallics". This layered structural motif has the nominal formula of AM2X2, where typically, A is an electropositive atom, M is a transition metal, and X is a main group element. They are ordered as a layered structure of layers of two-dimensional MX-n4 edge sharing tetrahedra separated by layers of An+ cations. The wide variety of different compounds that have been characterized with this structure has resulted in almost as wide a variety of properties, including superconductivity. This dissertation demonstrates the affects that having a mixed metal site has on the properties of these compounds. Powder and single crystal samples are prepared for a series of compounds so that these effects can be compared for different X atom chalcogenides. We demonstrate that increasing the bond distances through changing the X atom from sulfur to selenium has a pronounced effect on the magnetic and electrical properties. Possible magnetic structures for KCuMnS2 are proposed for the first time. Different methods at tuning the structure to obtain new compounds are discussed.Item UNDERSTANDING THE SURFACE CHEMISTRY OF GAS PHASE ORGANOPHOSPHORUS CHEMICAL WARFARE AGENTS WITH SORBENT MATERIALS(2019) Holdren, Scott; Zachariah, Michael R.; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)Chemical warfare agents (CWAs) pose a serious threat to civilians and warfighters due to their high toxicity and usage in recent attacks. Although existing filtration media (ASZM-TEDA) used in gas mask devices absorbs and decomposes a wide spectrum of CWAs, the filtration performance of this material can be compromised in the battlefield due to poorly understood mechanisms. The high toxicity of CWAs remains a barrier for most research institutions to study these compounds experimentally which hinders the search for improved filtration materials. To overcome this issue, studies are performed using relatively benign simulant compounds that have similar adsorption and decomposition properties as toxic CWAs. In this work, a report of experimental findings will be presented regarding how dimethyl methylphosphonate (DMMP), an organophosphorus CWA simulant, will adsorb and decompose on components that makeup ASZM-TEDA. The work presented in this dissertation deconstructs the components that makeup ASZM-TEDA in order to identify the role of specific metal oxides and the carbon support. This approach was facilitated using different analytical techniques including TGA, FTIR spectroscopy, and DFT modeling to gain a molecular understanding of how DMMP interacts with porous carbon (Chapter 3) and metal oxide nanoparticles/surfaces (Chapters 4 and 5). Lastly, a new method is described (Chapter 6) that overcomes many of the difficulties encountered in conventional measurements that monitor gas phase DMMP adsorption/desorption processes on sorbent materials. This method can be used to obtain reliable quantitative measurements and parameters (e.g. adsorption capacities, ∆Hads, and kads) of low vapor pressure adsorbate/sorbent systems making it particularly useful for CWAs/CWA simulants and new filtration materials (e.g. DMMP and porous carbon).Item CHROMOPHORIC DISSOLVED ORGANIC MATTER (CDOM) IN THE OPEN OCEAN: OPTICAL AND CHEMICAL PROPERTIES AND THEIR RELATION TO CDOM STRUCTURE AND SOURCES.(2019) Cartisano, Carmen Marie; Blough, Neil V; Chemistry; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)The carbon contained as dissolved organic matter (DOM) in the Earth’s oceans is an important factor in the global carbon cycle, but studying and tracking DOM in the aquatic environment can be challenging. However, the light-absorbing and emitting subcomponents of DOM, called chromophoric dissolved organic matter (CDOM) and fluorescent dissolved organic matter (FDOM) can be directly probed using absorption and fluorescence spectroscopy, respectively. Detailed studies on CDOM from the open oceans are limited with many of the existing studies having very limited data sets (only select wavelengths or indices). To address this, the optical properties of CDOM from a variety of geographic locations (North Pacific Ocean: NPO, Equatorial Atlantic Ocean: EAO, Middle Atlantic Bight: MAB, Delaware River and Delaware Bay) were compared, and chemical tests performed (sodium borohydride (NaBH4) reductions and pH titrations). The responses to the chemical tests along with similarities and differences in the optical properties were examined to compare the structures present in terrestrial, coastal and open ocean samples. A long-pathlength capillary waveguide spectrometer was used to characterize open ocean CDOM samples, with the need for a calibration and validated protocol addressed prior to use. The optical properties of the NPO samples did not vary significantly at depths from ~300-4500 meters with only the surface samples showing significant differences. Solid phase extraction of the natural waters did remove unique absorbing and emitting bands in the UV region that could be marine in origin, while enriching the “humic-like” fraction. The open ocean samples showed similarities to the coastal and riverine samples including: 1) monotonically decreasing and unstructured absorbance with increasing wavelength; 2) loss of absorption upon NaBH4 reduction at all wavelength, with the largest percent loss in the visible; 3) enhanced absorption with increasing pH with spectral changes that occurred over the same pH ranges as the pKas of carboxylic acids and phenols; 4) attenuation of absorption enhancement with increasing pH following reduction at most wavelengths. These similarities not only suggest that there are structural similarities throughout all samples, but also indicate that there may be a terrestrial source of CDOM in the open ocean.