Physical Sciences and Mathematics Commons^™

Characterization Of Landfill Leachate For Enhanced Metal Recovery, Hanna Fulford, Amisha Shah, Inez Hua, Nadezhda Zyaykina, Lori Hoagland, Alejandro Rodriguez Sanchez, Umut Bicim

Discovery Undergraduate Interdisciplinary Research Internship

Landfills contain a trove of valuable materials, such as critical, precious, and rare earth metals, that are integral to the United State’s economy and national security. The leachate that filters through landfills picks up these materials, which allows for the possibility of recovery. For this research, samples will be analyzed from landfills throughout the Midwestern United States to provide a baseline on water quality constituents, elements present, and microbial activity. Preliminary data for this study was acquired by analyzing samples of landfill leachate from a landfill in northern Indiana. pH readings indicate that the leachate is slightly basic. It also …

Ambient Ionization - Mass Spectrometry: Advances Toward Intrasurgical Cancer Detection, Alan Keith Jarmusch

Open Access Dissertations

My dissertation research has focused on the development of ambient ionization – mass spectrometry (MS) for clinical measurements, specifically intrasurgical cancer detection. The molecular differences between normal and cancerous tissue were detected via direct tissue analysis in vitro by touch spray ionization (TS) or by analyzing sectioned or smeared tissue using desorption electrospray ionization (DESI). The physical form of the tissue, e.g. in vitro sampling, sectioned, or smeared, was inconsequential in differentiating normal from cancerous tissue; however, the spectra acquired by TS and DESI differed due to differences in ionization processes. We envision that TS-MS and DESI-MS could impact diagnostic …

Preparative Mass Spectrometry Applications In Nanomaterials And Organic Synthesis, Michael Wleklinski

Open Access Dissertations

Preparative mass spectrometry was traditionally a vacuum based experiment where mass selected ion beams were deposited onto surfaces; however, recently ions have been manipulated in the open air to perform accelerated synthesis. The work of this dissertation focuses on the generation of charged ions from microdroplets and their use in organic synthesis and the preparation of atomically precise metal nanoclusters. First the mechanism for charging in the zero volt paper spray will be presented. This works builds a computational model based on the statistical fluctuation of positive and negative charges based on the theory of Dodd. It is found through …

Synthesis And Performance Of Novel Supramolecular Tools For Single-Particle Cryogenic Electron Microscopy And Drug And Gene Delivery, Kyle J. Wright

Open Access Dissertations

High-resolution biomacromolecular structure elucidation is fundamentally important to structure-based drug design and basic research into complex biochemical processes. Cryo-EM is an emerging alternative to XRD and NMR that is complementary in many ways relative to XRD and NMR. Materials approaches to cryo-EM are anticipated to greatly facilitate the cryo-EM process, allowing progress toward a more high-throughput application of cryo-EM to address challenges in structural biology. ^ Various affinity-based approaches inspired by approaches previously introduced for 2D crystallization were developed for facilitation of cryo-EM. A library of affinity lipopolymer constructs were synthesized consisting of lipopolymers of various PEG molecular weights conjugated …

In-Column Polymer Modifications: Advancing Polymer Bonded Phases, Alexis G. Huckabee

Open Access Dissertations

Glycosylation is the most common post-translational modification affecting protein activities, including delivery to cell surface, binding affinity, and mediating different physiological effects. Separations of glycoproteins and their glycoforms are essential for drug discovery and development, identification of potential disease biomarkers and quality control. The efficiency of glycoprotein separations is limited by the bonded phases, requiring advances in chromatographic materials. Such advances would improve resolution, allowing for more species to be isolated from a mixture and studied.

Our group found that submicrometer nonporous silica stationary phases with tethered polymer chains (acrylamide) give excellent hydrophilic liquid chromatography (HILIC), a common method used …

Ultraviolet And Infrared Spectroscopy Of Synthetic Foldamers, Aib Homopeptides, And Solvated 1,2-Diphenylethane In The Gas Phase, Joseph R. Gord

Open Access Dissertations

The work presented here implements a supersonic jet expansion source to funnel the population of model peptides and solvated-bichromophore clusters into their low lying structural minima and to collisionally cool these minima to their respective zero-point vibrational levels. Single-conformation ultraviolet and infrared spectroscopy techniques are then used to probe these systems and investigate their electronic properties and uncover their intrinsic conformational preferences in the gas phase.

Model β/γ-peptides known as synthetic foldamers and aminoisobutyric acid (Aib) homopeptides incorporate structural constraints that are designed/known to impose particular structural motifs. Here the ability of a β/γ-dipeptide to replicate the backbone length of …

The Use Of Stable Isotopes And Particulate Matter In The Investigation Of Local And Regional Atmospheric Chemistry, Tanya Lynn Katzman

Open Access Dissertations

The chemical composition of particulate matter (PM), a known contributor to air pollution, is highly variable, and elemental analysis reveals information about local and regional sources, as well as how air masses and climate influence PM compositions. Seasonal changes in climate, such as temperature, amount of daylight, or meteorological patterns influence source emissions (increased residential heating activities, decreased natural soil emissions) and the relative importance of certain chemical pathways in the atmosphere. Since the magnitude of these seasonal changes are highly dependent on location, each sampling site is unique and the chemical composition of PM provides valuable insight into local …

Advances In Raman Hyperspectral Compressive Detection Instrumentation For Fast Label Free Classification, Quantitation And Imaging, Bharat R. Makani

Open Access Dissertations

Multiple prototypes of hyperspectral compressive detection (CD) Raman spectrometers have previously been constructed in the Ben-Amotz lab and have proven to be useful for fast, label-free chemical identification, quantitation and imaging. The CD spectrometer consists of a volume holographic grating (VHG) that linearly disperses the Raman photons into its component wavelengths and all wavelengths are focused onto a digital micromirror devise (DMD). The DMD is an optical modulator that consists of an array of programmable 10μm mirrors that can reflect photons in either +12° or -12° to the incoming light. The DMD is tilted such that the +12° photons go …

Coupling Qualitative And Quantitative Analyses Of Pharmaceutical Materials Enabled By Second Harmonic Generation Microscopy, Paul D. Schmitt

Open Access Dissertations

The detection and characterization of crystallinity is critical throughout the drug development process. From the initial establishment of an active pharmaceutical ingredient’s (API) crystal structure to stability testing and quality control, the phase of an API affects the solubility, bioavailability, stability, and efficacy of a drug product. Second harmonic generation (SHG) microscopy has recently been developed as a selective and rapid method for imaging crystallinity in drug formulations. While SHG microscopy can enable the high signal-to-noise (SNR) detection of crystallinity, the intrinsic chemical information content within SHG images is relatively low. In cases of trace crystallinity and/ or small crystal …

Polymerizable Lipids For Controlled Functionalization Of Layered Materials, Kortney Kaye Rupp

Open Access Theses

Self-assembled monolayers (SAM’s) offer a straightforward approach to tailoring the interfacial properties of metals, metal oxides and semiconductors. Noncovalent functionalization of single-layer graphene offers the possibility to finely tune surface chemistry for future applications in electronics. Polymerization of photochemically reactive molecules in a lying-down phase has been used to increase the strength of intermolecular interactions between long alkanes and HOPG substrates. Long-chain fatty acid derivatives with internal diyne groups yield a conjugated ene-yne polymer upon UV irradiation. Diyne lipids with phosphocholine (diyne PC) and phosphoethanolamine (diyne PE) groups offer a charged form of the head group that is robust towards …

Direct Drug Screening And Lipid Profiling Using Ambient Mass Spectrometry, Yuan Su

Open Access Dissertations

Mass spectrometry (MS) stands in an outstanding position in analysis of biological specimens owing to its abundant structural information, high accuracy, incomparable sensitivity, high speed, and the large variety of its applications. The ion source, an instrumental part for converting the analyte into ions, has played an important role in analyzing biological specimens by MS. However, the performance of conventional spray-based ionization methods always suffers from chemical interferences derived from complex biological matrices. A series of sample extraction, purification, and separation steps is required before the ionization, so as to ensure excellent performance of MS analysis. In order to simplify …

Purification And Preparation Of Intrinsically Disordered Proteins For Nmr Spectroscopy, Kyle Chamberlain

Open Access Theses

NMR spectroscopy has recently become a promising field for protein characterization and dynamic studies. As the technology and pulse sequences improve for tracking proteins, a greater demand for developing effective purification protocols to produce NMR grade protein samples have arisen. This thesis explores two proteins: histone H4 tail and Mucin 1; Two very different proteins that require different methods of expression and purification to achieve a high enough yield for NMR analysis. H4 is a water soluble protein that weighs ~2.7 kDa, and has no extinction coefficient. Since the protein is too small for many methods of expression and purification, …

Targeted Metabolomics On The Shikimate And Aromatic Amino Acid Biosynthetic Pathways, Robert E. Wheeler

Open Access Theses

The shikimate and aromatic amino acid biosynthesis pathways are some of the most studied biosynthetic pathways in nature due to their fundamental importance. Interest in this field stems from synthesis of the essential amino acids, tryptophan, tyrosine and phenylalanine. The pathways also are important as generating the precursors of thousands of secondary metabolites and lignin. Inhibiting the pathway has led to discovery of herbicides, pesticides as well as tuberculosis drugs. However there is currently a lack of a comprehensive targeted method for detecting and quantifying the majority of the intermediates in these pathways. Often multiple extraction and detection methods are …

Advances In Solid Phase Microextraction For The Analysis Of Volatile Compounds In Explosives, Tire Treatments, And Entomological Specimens, William D. Kranz

Open Access Dissertations

Solid phase microextraction is a powerful and versatile technique, well-suited to the analysis of numerous samples of forensic interest. The exceptional sensitivity of the SPME platform, combined with its adaptability to traditional GC-MS systems and its ability to extract samples with minimal work-up, make it appropriate to applications in forensic laboratories.

In a series of research projects, solid phase microextraction was employed for the analysis of explosives, commercial tire treatments, and entomological specimens. In the first project, the volatile organic compounds emanating from two brands of pseudo-explosive training aids for use in detector dog imprinting were determined by SPME-GC-MS, and …

Mass Spectrometric Characterization Of Peptide Radical Ions And Implication For Radical Chemistry, Lei Tan

Open Access Dissertations

Gas-phase radical ion chemistry has attracted increasing research interest from the mass spectrometry (MS) society because it provides new capabilities in bio-analysis which often complements traditional MS methods developed from even-electron ions. Fundamental studies of biomolecule related radical species are essential to broadening the scope of radical chemistry and pushing the frontiers of its analytical applications. This dissertation mainly discusses the gas-phase chemistry of peptide sulfinyl radicals (-SO·), which has been rarely studied before. In order to establish an effective research approach, a method that can generate site-specific peptide sulfinyl radical ion has been developed. This method is based on …

Studies Of Arctic Halogen Chemistry From The Snowpack To The Gas Phase, Kyle D Custard

Open Access Dissertations

The temporary depletion of both tropospheric ozone and gaseous mercury during the Arctic springtime has been a focus of active research over the past several decades. Both of these phenomena have been linked to chemical reactions with halogen radicals. In particular, bromine atoms have been shown to act as the primary driver for these chemical depletions, although both chlorine and iodine atoms also contribute. Molecular bromine, along with its oxidation products, have been well studied in the Arctic, yet chlorine has not. Chlorine is known to impact the local oxidation capacity via its high reactivity with volatile organic compounds. Despite …

Polarization-Dependent Nonlinear Optical Microscopy Methods For The Analysis Of Crystals And Biological Tissues, Emma L. Kerian

Open Access Dissertations

The ability to solve a high-resolution protein structure is largely dependent on the successful generation and identification of protein crystals prior to X-ray diffraction (XRD). For novel protein targets, high-throughput crystallography often involves generation of multiple targets and thousands of crystallization trials per target to generate diffraction-quality crystals. Second harmonic generation (SHG) imaging has been developed as a fast, non-destructive and sensitive method for the selective identification of protein crystals, even in highly scattering environments. Polarization-dependent SHG microscopy methods were developed to assess the presence of multidomain crystals to provide a handle on crystal quality. In addition, polarization-dependent two-photon excited …

A Bracketing Method For Proton Affinity Measurements Of Dehydro-And Didehydropyridines, Guannan Li

Open Access Theses

Proton affinity (PA) is a fundamental property that is related to the structure and reactivity of a molecule. Currently, very few experimental PA values are available for organic radicals and none for biradicals. Equilibrium methods cannot be used for these measurements. The traditional bracketing method is based on monitoring reactions of different reference bases with known proton affinities with the protonated analyte for the occurrence of exothermic proton transfer to determine the upper and lower limits of proton affinity. However, the energy deposited into the precursor ions upon CAD when forming protonated radicals may cause endothermic proton transfer reactions occur …

Development Of Experimental And Instrumental Systems To Study Biological Systems, Amanda J Hemphill

Open Access Dissertations

Chapters 1-4 of this thesis describes the development of an experimental system to measure diffusion-limited reaction kinetics in a biological environment. About 100 years ago, the relationship between reaction rate and diffusion in homogenous solution, ie water or buffer, was described as a linear relationship by Smoluchowski. Applying this theory naively would suggest that since the diffusion coefficients drop by factors of 4-100 then the rates of reaction would drop by the same amount. However, recent theory and simulations suggest that this does not hold. Even though biological diffusion coefficients drop to 0.1-20% of that in buffer, these recent studies …

Molecular Diagnosis Of Cancer Using Ambient Ionization Mass Spectrometry, Kevin S Kerian

Open Access Dissertations

My dissertation focuses on advancing the development and application of ambient ionization mass spectrometry methodology and technology to the biomedical field. The primary ambient ionization method used in my studies is desorption electrospray ionization mass spectrometry (DESI-MS) imaging, which has been previously used to analyze and differentiate disease state (i.e. tumor and normal) and in some cases tumor subtype of human liver, kidney, bladder, testicular, prostate, and brain cancers. DESI-MS imaging is an ideal method for disease diagnosis, because it can be used to directly correlate disease state with histopathology to develop and validate MS libraries built using the molecular …

Laboratory Studies On The Production Of Alpha-Pinene-Derived Organic Nitrates And Their Atmospheric Fate, Joel David Rindelaub

Open Access Dissertations

Currently, the formation yields of organic nitrates from the oxidation of biogenic volatile organic compounds, such as α-pinene, is highly uncertain, negatively impacting our knowledge on tropospheric ozone production and the fate of atmospheric NO_x. To lower this uncertainty, we quantified the organic nitrate yield from the OH radical oxidation of α-pinene under high NO_x conditions. The α-pinene- derived nitrates created in chamber experiments readily partitioned to the aerosol phase and underwent particle phase hydrolysis, indicating that these processes are likely a sink for atmospheric NO_x. The hydrolysis of organic nitrates was found to be …

Structure-Activity Relationships For The Water-Gas Shift Reaction Over Supported Metal Catalysts, Kaiwalya D. Sabnis

Open Access Dissertations

The Water-Gas Shift (WGS) reaction (CO + H₂O → CO₂ + H₂) is an important chemical process for industrial hydrogen production. The overall goal of this project is to use kinetic experiments and in situ characterization techniques in tandem, in order to derive structure-activity relationships for various catalytic systems. These relationships facilitate the rational catalyst design by identification of catalyst descriptors. In order to establish such relationships, various studies were undertaken, such as (i) effect of transition admetals on the WGS catalysis by molybdenum carbide (ii) effect of residual oxygen content on the performance of …

Aircraft-Based Measurements For The Identification And Quantification Of Sources And Sinks In The Carbon Cycle, Dana R Caulton

Open Access Dissertations

Improved quantification of carbon-cycle sources and sinks is an important requirement for determining mitigation strategies and modeling future climate interactions. Analytically robust measurements require high-precision instrumentation and thoughtful experimental design to produce rigorous and reproducible results despite complex and quickly changing meteorological and environmental conditions. Here, an aircraft platform equipped with a high-precision cavity ring-down spectrometer for CO₂, CH₄ and H₂O quantification was used to acquire data from previously un-sampled sources. The aircraft mass-balance technique was used to quantify CH4 emissions from natural gas well pads in the drilling stage, which were 2-3 orders of …

New Strategies To Reveal Protein Candidates In Protein-Protein Interactome Study, Meng-Chieh Chen

Open Access Theses

Comprehensive protein-protein interaction network analysis can help reveal protein functions in a system-wide manner. A reliable knowledgebase of interaction networks is not only important for selecting the candidates for drug therapies, but also for evaluating the disease risk. In current interaction databases, 322579 interactions comprised of 56460 proteins have been reported (statistical analysis from APID: Agile Protein Interaction DataAnalyzer; http://bioinfow.dep.usal.es/apid/index.htm). The huge datasets are contributed mainly by yeast -two -hybrid (Y2H) screening and affinity-purification followed by mass spectrometry (AP-MS). High false positive rates and failing to cover certain interaction categories are the limitations of these two methods. Here, we developed …

Reverse-Phase Liquid Chromatography Of Small Molecules Using Silica Colloidal Crystals, Natalya Khanina

Open Access Theses

Capillaries packed with a silica colloidal crystal (SCC) of 470 nm nonporous particles have recently been shown to offer significant improvements in the peak width, resolution, and speed of protein analysis due to the reduction of the A and C term broadening contributions of the Van Deemter equation. While protein separations using this technology have shown vast improvements, small molecules remain largely unexplored. As the SCC allows for an approximately diffusion limited system, extremely high plate numbers are expected for small molecule separations. The research presented herein studies the feasibility of pressure-driven small molecule separation using SCCs and commercial instrumentation. …

Metal-Protein Interactions For Proteomics Applications, Keerthi B Jayasundera

Open Access Dissertations

In the quest of deciphering biological mechanisms, the understanding of proteins and their functions is a vital component. However the complexity of the proteome poses an immense challenge for analytical chemists to explore it comprehensively. Currently mass spectrometry is at the forefront of proteome analysis, providing great capabilities to couple with modern separation techniques for wide applications. One major objective of current proteomic technologies is to identify proteins of interest among high background, in particular from complex biological samples. A variety of techniques have been developed over the years to simplify protein samples, which are broadly classified as enrichment, high …

Gas-Phase Ion/Ion Reactions Of Biomolecules: An Examination Of Carboxylate Reactivity And Arginine Based Non-Covalent Complexes, Nathan Zachary Barefoot

Open Access Theses

The advent of Electrospray Ionization with the ability to generate multiply charges ions has contributed significantly to the study of gas-phase ion/ion reactions. With the tools available in mass spectrometry it has been shown that these reactions are effective at transforming one type of gaseous ion into another through a series of reactions. This work examines some of these reactions and their application to field of proteomics specifically focusing on the amino acids of arginine and lysine. NHS reagents have been shown to react to both of these molecules with in the gas-phase under different conditions but have relies on …

Separation Of On-Column Labeled Model Proteins With Packed Capillary Electrophoresis, Yingxu Hao

Open Access Theses

Protein drugs are increasingly developed in the pharmaceutical company. Under the regulation of FDA, high purity of therapeutic proteins needs to be maintained. Before putting those drugs in the market, fast and efficient method is in need to achieve homogeneity. Traditionally, polyacrylamide gel electrophoresis (PAGE), capillary electrophoresis (CE), and size-exclusion chromatography (SEC) are used for the purification process. These methods have the disadvantages of low time and cost efficiency, and this quality assurance process has become the bottleneck of production. In our group, sub-micron silica colloidal particles with polyacrylamide layer on the surface are packed inside capillaries to increase the …

Physical And Chemical Attributes Of A Genetically Modified Fruit Pectin, Carl Patrick Littrell

Open Access Theses

Pectin is an important polymer used in the food industry as a thickening and gelling agent. Though pectin is ubiquitous in plants, chemical and structural differences among pectin molecules prevent most from being viable for industrial use. Enzymes found naturally in fruit cell walls during the ripening process impair many desirable attributes of fruit pectins, rendering them unsuitable for industrial applications. Pectin methylesterase (PME) is one such enzyme whose expression can be altered during ripening through the use of recombinant genetic engineering. Reduction in levels of PME results in increased degree of methylation and molecular size of pectin, greatly increasing …

Investigation Into The Control Of Melittin Secondary Structure And Antimicrobial Activity, Zachary B. Molinets

Open Access Theses

Antimicrobial resistance has been an exponentially growing problem since the discovery of antibiotics. Antibiotics have been misused for many years and this misuse has grown into a real problem for the medical community. While there are countless safeguards to prevent infection by a resistant strain of bacteria, there are still many plagued by it and must be treated with sometimes dangerous antibiotics. Melittin, along with many other peptides, contain potent antimicrobial properties, but are also toxic toward enthrocytes. The control of the secondary structure of peptides provides the key to adjusting their activity.