Chemistry Commons^™

Elucidating The Mechanisms Of Collagenase H From Hathewaya (Clostridium) Histolytica In Collagen Degradation And Developing A Cross-Linked Platform For Efficient Capture And Release Of Adeno-Associated Virus Serotype 2 (Aav2), Adjoa Otubea Bonsu

Graduate Theses and Dissertations

In biological systems, Hathewaya (Clostridium) histolytica secretes collagenases that degrade structural collagen in host tissues and cause tissue necrosis. Despite their detrimental effects, these enzymes have significant therapeutic potential by effectively digesting various collagen subtypes to treat connective tissue disorders. The bacterium produces two homologous collagenases, ColG and ColH, with a catalytic module crucial for hydrolyzing collagen and binding domains, including collagen-binding domains (CBDs) and polycystic kidney disease-like domains (PKDs), for substrate interaction.

Although the crystal structure of the catalytic module of collagenase G (ColG) has been determined, shedding light on its chew-and-digest mechanism, the structure of collagenase H (ColH) …

Atomic Level Characterization For The Transport Cycle Conformational Pathways Of Multidrug Resistance Protein 1 (Mrp1), Samuel Wamwere Mwatha

Graduate Theses and Dissertations

The multidrug resistance-associated protein 1 (MRP1/ABCC1) is an ATP-binding cassette (ABC) transporter that mediates the cellular efflux of endogenous and xenobiotic substrates, including therapeutic drugs. Its overexpression is a major contributor to multidrug resistance in cancer, which tends to result in negative clinical results. Even with considerable progress made in structural biology, the intricate details of how membrane lipid composition affects the conformational changes and functional switches of MRP1 still lack explanation.

This thesis employs long-timescale, all-atom molecular dynamics (MD) simulations to study the influence of various lipids on MRP1 lipid bilayer environments. Both inward-facing and outward-facing conformations of MRP1 …

A Sociocognitive Perspective On The Activation Of Productive Epistemic Resources In College Students' Understanding Of Chemical Equilibrium, Henk Steven Van Den Bogaard

Open Access Theses & Dissertations

Science education, particularly in higher education, has a content coverage problem: it has long been described as "a mile wide, an inch deep" in various consensus documents from the National Academies. In chemistry education, the most common general chemistry curriculum covers topics as chapters based on the popular Sienko and Plane 1960's general chemistry textbook. The limited time available in such fast-paced coverage may limit the instructor's modeling and assessment of key performances in developing a mechanistic understanding of complex chemistry phenomena. In this sociocognitive, qualitative investigation, general chemistry II students' responses to assessment prompts were used to activate cognitive …

Effects Of Ph On Product Yield Of One-Electron Oxidation To Guanine Derivatives, Abdul-Kadir Ibrahim

Electronic Theses and Dissertations

One-electron oxidation plays a major role in oxidative DNA damage in biological cells. Guanine, the most oxidizable DNA base, has been the major focus of studies on oxidative damage to DNA initiated by one-electron oxidation (OEO). The current study aims at understanding the mechanisms of photooxidation of guanine derivatives with OEO in acidic medium. D1A* and D1B*, which are the products of dGuo in acidic medium, were obtained from dGuo upon photolysis at 485 nm of the reaction mixture in the presence of S₂O₈^2- as the oxidant and Ru(II)(bpy)₃²⁺ as a photosensitizer. D1A* and …

A Kinetic Analysis On Hydrolysis And Hydrothermal Conversion Of Cellulose To Dodecane, Joel Nyangoka Onyancha

Electronic Theses and Dissertations

Cellulose, the most abundant biomass on Earth, offers a promising pathway for alternative energy through conversion into alkane hydrocarbons. Traditional methods rely on high temperatures and high-pressure hydrogen, often derived from petroleum. In this study, we investigated the conversion of Microcrystalline Cellulose using hydrogen metal oxides (bronzes) under milder conditions. Following ASTM E3417-24 hydrolysis protocols, we employed hydrogen bronzes with toluene for product extraction. This approach enabled conversion at lower temperatures without pressurized hydrogen. Products were analyzed using Gas Chromatography Mass Spectrometer for identification and Gas Chromatography Flame Ionization Detector for quantification. Our findings revealed the formation of a possible …

Structure Disorder And Magnetic Behavior Of An Olivine-Type Cathode Material, Hamida Hassan, Madalynn Marshall

Symposium of Student Scholars

Our research investigates the structure disorder and magnetic behavior of Li(Mn,Fe)PO₄, an olivine-type material relevant for lithium-ion battery applications. Using single-crystal neutron diffraction at Oak Ridge National Laboratory, we precisely determined Mn and Fe occupancy, revealing a 56% Fe and 44% Mn distribution at the atomic 4c site within the Pnma space group. Additionally, we observed significant lithium site vacancies (78% occupied), influencing the material's electrochemical and magnetic properties. The varying Mn/Fe ratio affected spin reorientation transitions, shifting from antiferromagnetic alignment along the a-axis to the b-axis. Our findings provide crucial insights for optimizing olivine-based cathodes, enhancing energy …

Computational Study Of The Proton Transfer In The H7o3+ Cluster, Anna James, Martina Kaledin

Symposium of Student Scholars

Proton transfer (PT) from one molecule to another is among the most studied phenomena in chemistry. PT requires the bond cleavage and the formation of a new one, AH⁺ + B -> A+ BH⁺. In protonated water clusters, such a process consists of the interconversion of hydrogen bonds. Experimentally, such a process can be observed as a significant increase of a dipole moment. However, other vibrational transitions often occur with small changes in the dipole moment while large changes in polarizability. In this work, we study the PT process in a protonated water cluster, H₇O …

Predicting Healthcare Service Quality Based On A Kalman-Optimized Bi-Lstm-Inspired Deep Learning Model, Mohammed K. Al-Khafaji, Eman S. Al-Shamery

Karbala International Journal of Modern Science

Health is one of the most important aspects of human well-being, and access to high-quality healthcare is essential for a good quality of life. Providing top-level health services at all times is crucial. However, the research in healthcare poses significant challenges due to the diversity and variations of medical practices across different hospitals. This paper aims to tackle the challenge of data missing and scattering during data collection. Then, the quality of services (QoS) offered by healthcare facilities will be analyzed and predicted from the patient's perspective. The model begins preprocessing data by data cleaning, handling missing values, and scattering …

Synthesis Of Surface Bound Ligands Through Click Chemistry For A Tethered Catalyst System Towards The Reduction Of Carbon Dioxide, Emma J. Goehner

Departmental Honors & Graduate Capstone Projects

The electrochemical reduction of carbon dioxide (CO₂) offers a promising strategy for reducing excess atmospheric CO₂ by converting it into valuable chemical products. This process can be catalyzed by transition metal complexes, particularly those with extended aromatic ligands such as terpyridines which coordinate with metals in a tridentate fashion. When tethered to an electrode, the terpyridine-metal catalyst complex allows for stable binding and reusability without the need for chemical separation to recover the catalyst. Self-assembled monolayers (SAMs) of (3-bromopropyl) phosphonic acid were formed on copper surfaces, enabling attachment of terpyridine ligands through a click reaction between a …

Understanding The Through-Space Intermolecular Interactions Of Isothiourea Catalysts In Acylation/Silylation Reactions Of Secondary Alcohols, Ziyuan Gong

Theses and Dissertations

Through space interactions, including cation-π interaction, lone pair-πinteraction, steric hinderance etc. play a central role in organocatalytic reaction. They can control the reactivity or the selectivity of an organic reaction. Previous work in our group has already shown that the chiral isothiourea compounds can catalyze the acylation as well as silylation reaction of secondary alcohol with the possible cation-πinteraction between the catalyst and substrate. However, there is lack of study to understand how the delocalization of the positive charge would affect the reaction rate and whether some unexpected inter- or intramolecular interaction could help stabilize …

Thermodynamic Study Of Ligand Coordination On Lead Halide Perovskite Quantum Dots, Bishal Adhikari

Theses and Dissertations

Inorganic lead halide perovskite (ILHP) has been extensively studied in thin films and bulk crystals as promising materials for their photovoltaic and optoelectronic properties. These are stable enough to be prepared as colloidal quantum dots that can be dispersed, deposited and used to achieve quantum confinement; however, selection of the suitable surface passivating ligand remains challenge for long term stability of the colloidal quantum dots. Several ligand coordination chemistries used to achieve greater stability or specific functions: these can be installed at time of synthesis in some cases they can also be installed to preexisting quantum dots by ligand exchange …

Building A Framework For Analyzing Non-Linear And Multidimensional Kinetics, Mainak Dhar

Theses and Dissertations

Many materials exhibit multiple rates of molecular relaxation due to structural complexities. Standard linear and one-dimensional kinetic cannot extract all the necessary dynamic information about these systems. This dissertation contributes to an overarching scheme to develop new non-linear and multidimensional kinetic experiments to obtain this information. The studies span computation and experiments, picosecond to second timescales, and both single-molecule and pulsed-laser kinetics

Single-molecule kinetics experiments yield time series that contain information about unique structural and dynamic properties of materials. However, these time series are noisy, and data analysis is challenging. Parametric methods are computationally intensive and require strong, unverifiable assumptions …

Expanding Tailored Nanomaterials With Precise Spatial And Morphological Control, Mengxue Zhang

Theses and Dissertations

Multicomponent nanocomposites with precise spatial control are important for diverse fields spanning from energy conversion to optoelectronics and catalysis. Traditional methods using hydrophilic interactions alone are limited to random mixtures when multiple nanoparticle (NP) types are combined. To improve capabilities, a new strategy for polymer micelle design combining orthogonal hydrophilic (H) and fluorophobic (F) interactions to independently control two distinct NP populations was developed.

Initial research aimed at understanding F-interaction adjustments, which further enabled the switchability of FNP distribution states (dispersion vs aggregation) within polymer films through immersion annealing. Next, dual-NP assembly was examined using a diblock poly (H-b-F) where …

Explorations Of Multi-Carboranyl Thiols And Phosphines, Jared Ross Riffle

Theses and Dissertations

In order to ascribe the impact of substituent groups on the bis-ortho-carborane, closo-{C2B10}-closo-{C2B10} multi-cluster system, the first sulfur-containing biscarborane derivatives were synthesized. Biscarborane dithiol, disulfide, bis(methyl)thioether, as well as multiple dithiolate salts were structurally characterized. The exceedingly long C–C bonds and shortened C–S bonds in biscarborane dithiol and its doubly deprotonated dithiolate salts are indicative of significant delocalization of electron density from the sulfur atoms into the cluster. Additionally, a new concept of ligand ambiphilicity is described where, instead of the involvement of only a single center in a ligand, this amphiphilicity relies on the redox behavior of the indirectly …

The Design And Optimization Of Optical Systems For The Detection And Characterization Of Phytoplankton, Caitlyn M. English

Theses and Dissertations

Phytoplankton are among the smallest organisms found in marine and freshwater ecosystems. Despite their small size, phytoplankton play a vital role in sustaining life on Earth as primary producers. Through oxygenic photosynthesis phytoplankton are also responsible for large scale carbon fixation and oxygen production. The distribution of phytoplankton in a given water resource can exhibit a high degree of variability across time and space, and this is in large part due to their varying sensitivities to environmental conditions such as resource availability and grazing by predator organisms. As such, phytoplankton community structure is widely used as an investigative tool for …

Dual Colorimetric And Fluorometric Detection Of Hydrogen Peroxide In Aqueous Samples, Nathan F. Surles, Kaitlin A. Edwards

ATU Scholars Symposium

In this project, a simple, inexpensive colorimetric and fluorometric method for determining hydrogen peroxide in aqueous samples is described. In this method, aryl boronic acid is de-protected to produce a red dye that absorbs and emits in the red/near infrared region of the electromagnetic spectrum. Upon deprotection by the hydrogen peroxide, an intramolecular charge transfer occurs between a strong phenolate donor and a TCF acceptor to produce the strong absorption and bright fluorescence. This allows naked eye detection of hydrogen peroxide within seconds in water under physiological conditions. The detection limit is impressive and falls in the sub-micromolar (µM) range. …

Computational Modeling Of Poly-Peptide Chains, Nathan F. Surles, Kaitlin A. Edwards

ATU Scholars Symposium

Investigations of the structural properties of polypeptides are essential for understanding their conformational behavior, stability, and potential biological interactions. In this study, we employed computational techniques to determine the optimized structures of two model polypeptides: tri-glycine and di-tryptophan.

Synthesis Of Organosilicon Substituted Fₓpczn For The Preparation Of Silica-Based Photo-Catalysts, Reagan E. Daly

Seton Hall University Dissertations and Theses (ETDs)

This study began with the synthesis, purification, and catalytic application of hexadeca fluoro phthalocyanine zinc (F₁₆PcZn) derivatives functionalized with organosilane consuming thiol groups. The F₁₆PcZn was synthesized by reacting tetrafluorophthalonitrile (TFPN) with zinc acetate (Zn(OAc)₂) in 1-chloronaphthalene as a solvent, under a controlled heating process at 185°C for 90 minutes. The resulting blue solid was purified via vacuum filtration and recrystallization techniques to remove residual solvents and by-products, yielding pure F₁₆PcZn. The purity of the product was assessed through UV-Vis spectroscopy, MALDI analysis, and a molar extinction coefficient was determined.

Subsequent nucleophilic substitution of the fluorine atoms on F₁₆PcZn with …

From Clusters To Frameworks: Synthesis, Engineering, And Application Of Sub-2-Nanometer Nanoclusters And Microporous Covalent Organic Frameworks, Melika E Kenari

Chemistry Theses and Dissertations

In this dissertation, we have investigated the complex interplay of atomic composition, structural modifications in covalent organic frameworks (COFs), and atomic-level designs in bimetallic chiral nanoclusters (NCs). By synthesizing COFs and bimetallic NCs, we elucidated how these elements govern their exceptional catalytic, optical, and electronic properties. Our work demonstrates that precise atomic adjustments, tailored pore engineering in COFs, and the strategic use of chiral ligands in NCs enable fine-tuned reactivity and stability. These advancements were applied to enhance photocatalytic performance, optimize iodine adsorption, and facilitate asymmetric A3 coupling reactions, laying a robust foundation for practical applications and future innovations in …

Computational Analysis Of Proton Conductivity Factors In Grotthuss-Style Mechanisms, Brock Dyer

Physics and Astronomy Honors Papers

The mechanism and fundamental molecular properties involved in proton conduction are discussed. Four calculable properties are presented: the proton affinity, binding energy (between protonated and neutral forms), intramolecular tautomerization barrier, and proton hopping barrier. An overview of the computational methods used in this thesis, including an introduction to the many-body Schrödinger equation and Density Functional Theory, as well as a look at Plane-Wave Density Functional Theory and Gaussian-Type Orbital Density Functional Theory are presented. 4,5-dimethyl-[1,2,3]-triazole is used as a model system, with 10 variations being generated with varying amounts and positions of fluorine substitution on the methyl groups. Preliminary calculations …

The Chemistry Of Decomposition: The Mechanisms To Decay The Human Body, Lydia J. Buxa

Senior Honors Theses

Taphonomic analysis separates decomposition into four major stages: fresh, early decomposition, advanced decomposition, and skeletonization. It is easy to demarcate the observable changes to the body, but it is far more difficult to know what underlying biochemical processes are occurring. Fresh decomposition begins with algor mortis, livor mortis, and rigor mortis, which sets the stage for the major workforces of decomposition: autolysis and putrefaction. The external signs of decomposition appear in early decomposition, which can be attributed to the breakdown of proteins, lipids, carbohydrates, and nucleic acids. This also leads to major changes in the moisture levels during advanced decomposition, …

Electrocatalytic Nitric Oxide Reduction To Yield Ammonia Over Fe3C Nanocrystals, Sen Lin, Lang Zhang, Tong Hou, Jun-Yang Ding, Zi-Mo Peng, Yi-Fan Liu, Xi-Jun Liu

Journal of Electrochemistry

Nitric oxide (NO), which generally originates from vehicle exhaust and industrial flue gases, is one of the most serious air pollutants. In this case, the electrochemical NO reduction reaction (NORR) not only removes the atmospheric pollutant NO but also produces valuable NH₃. Hence, through the synthesis and modification of Fe₃C nanocrystal catalysts, the as-obtained optimal sample of Fe₃C/C-900 was adopted as NORR catalyst at ambient conditions. As a result, the Fe₃C/C-900 catalyst showed an NH₃ Faraday efficiency of 76.5% and an NH₃ yield rate of 177.5 μmol·h^–1·cm^{–2 …}

Ordering Degree Regulation Of Pt2Nico Intermetallics For Efficient Oxygen Reduction Reaction, Chen-Hao Zhang, Han-Yu Hua, Jun-Hao Yang, Qian Zhang, Chang Yang, De-Li Wang

Journal of Electrochemistry

Alloying transition metals with Pt is an effective strategy for optimizing Pt-based catalysts toward the oxygen reduction reaction (ORR). Atomic ordered intermetallic compounds (IMC) provide unique electronic and geometrical effects as well as stronger intermetallic interactions due to the ordered arrangement of metal atoms, thus exhibiting superior electrocatalytic activity and durability. However, quantitatively analyzing the ordering degree of IMC and exploring the correlation between the ordering degree and ORR activity remains extremely challenging. Herein, a series of ternary Pt₂NiCo intermetallic catalysts (o-Pt₂NiCo) with different ordering degree were synthesized by annealing temperature modulation. Among them, the o-Pt …

Performance Of Co2/H2O Co-Electrolysis In A Flat-Tube Solid Oxide Electrolysis Cell Stack Under Air-Free Environment, Xiao-Hui Zhong, Fei Wang, An-Qi Wu, Bei-Bei Han, Jian-Xin Wang, Wan-Bing Guan

Journal of Electrochemistry

This work investigates the transient performance and stability of CO₂/H₂O co-electrolysis in an air-free environment using a flat-tube solid oxide electrolysis cell (SOEC) stack. The results show that the transient behavior of the stack with and without blowing gas in the air electrode is almost the same. With a current density of 0.67 A·cm⁻²@750 °C, the stack operated for over 200 h under co-electrolysis conditions with no air blowing, and the voltage drop rate of the stack was approximately 0.203%/100 hours. Microstructure analysis reveals significant loss of Ni particles and formation of an insulating …

Variation Of Membrane Electrode Assembly Catalyst Layer In Unitized Regenerative Fuel Cell, Yollanda Nurcholifah, Dedi Rohendi, Edy Herianto Majlan, Nirwan Syarif, Addy Rachmat, Dwi Hawa Yulianti, Nyimas Febrika S

Journal of Electrochemistry

A unitized regenerative fuel cell (URFC) is a device that may function reversibly as either a fuel cell (FC) or water electrolysis (WE). An important component of this device is the Membrane electrode assembly (MEA). Therefore, this study aimed to compare the performance outcomes of MEA using electrodes with single and three catalyst layers. This study measured Electrochemical Surface Area (ECSA), Electrochemical Impedance Spectroscopy (EIS), X-ray Diffraction analysis (XRD), and X-ray Fluorescence (XRF). Furthermore, the round-trip efficiency (RTE) of the MEA, as well as the performance in FC and WE mode, was measured. In comparison, The ECSA values of Pt-Ru/C …

Identification Of Areas Of Weakness In Forensic Footwear Research, Kathryn Roy

Honors Projects

Forensic footwear examinations have been carried out for almost a century, but the foundational validity of identifying a questioned impression to a particular shoe has been questioned by the National Research Council and the President’s Council of Advisors on Science and Technology. The focus of this paper was to identify the current weaknesses present in forensic footwear impression research. Additionally, a future experiment was proposed to address these concerns and improve the foundational validity of footwear impression comparisons. A total of 15 footwear research studies varying in methodology and content were analyzed and contrasted. From this, a lack of studies …

The Analysis Of Reference Standard Storage Failures Through The Use Of Ibuprofen, Hope Vonder Brink

Honors Projects

Reference standards are commonly used in drug chemistry. They are used to calibrate the instruments and serve as a known point of reference for analysts’ ability to compare unknowns. Drugs can degrade over time or through environmental factors, causing contaminants to be present. In the event of environmental degradation while in storage, such as the exposure to high heat, it would be beneficial to have a database of known breakdown products in common drug reference standards for analysts’ reference. Using ibuprofen as an exemplar drug, this study attempted to identify the thermal breakdown products of ibuprofen and introduce the proposed …

Modeling Cis/Trans Preferences Of Sn("Acac")2cl2 Complexes, Luke L. Rising, Hanna Sunsdahl, Matthew Burrows, Juan Carlos Feregrino Ponce

Research & Creative Achievement Day

Tin(IV) complexes bearing two chloride ligands and two symmetric β-diketonate ligands exhibit octahedral geometries. As such, they can theoretically present in two geometric isomer forms, cis and trans. Modeling of isomeric forms of these Sn(IV) complexes with five different β-diketonate ligands has been conducted to identify overall preference as well as to attempt to ascertain any influence the ligand's own electronic properties has on exhibited isomeric preference. Additionally, modeled IR spectra of cis and trans forms were compared to determine the utility of that characterization method in distinguishing these isomers.

Development Of A Hybrid Synthetic And Computational Teaching Lab Exercise Featuring Budotitane, Kezia J. Lemke

Research & Creative Achievement Day

Budotitane is notable for its reported activity against cancer cells as well as its array of geometric structural possibilities. Preparation of budotitane, bis(1-phenyl-1,2-propanedionato)bis(ethoxy)titanium(IV), and its subsequent characterization by 1H NMR and IR spectroscopies as well as mass spectrometry has been implemented in an upper-level inorganic chemistry course. Computational modeling has also been utilized to predict the most energetically favorable isomer, as well as to generate modeled spectra for comparison to experimentally obtained results.

Progress Towards The Synthesis Of Trans-4-Bromo-2-Heptene, Ava L. Dillon

Research & Creative Achievement Day

trans-4-Bromo-2-heptene (1) is a simple compound that has never been synthesized in pure form and could be a useful starting material for organic synthesis. Therefore, the goal of this research is to synthesize 1 with a multistep synthesis. The synthesis starts with the preparation of hept-2-yn-4-ol (2) via a Grignard synthesis with the triple bond acting as a masking group for the alkene. The alcohol is converted to 4-bromo-2-heptyne (3). Step 3 is the most crucial step of selectively reducing the triple bond to the desired double bond. Finally, because the reduction should produce the cis alkene, the …