Digital Commons Network^™

Functional Consequences Of Lysine Acetylation Of Phosphofructokinase Isozymes, Xinyu Lin, Nour Fatema, Qinglei Gan, Chenguang Fan

Chemistry & Biochemistry Faculty Publications and Presentations

Phosphofructokinase (Pfk) catalyzes the phosphorylation of fructose 6-phosphate and is a key regulatory point in the glycolysis pathway. Multiple lysine residues in both Pfk isozymes, PfkA and PfkB, have been identified to be acetylated in Escherichia coli by proteomic studies, but no studies have been implemented to further characterize these acetylation events. To investigate the role of Pfk acetylation, the genetic code expansion strategy was used to generate homogeneously acetylated Pfk variants at target lysine sites that have been reported to be acetylated in nature. We found that acetylation of K309 of PfkA and K27 of PfkB decreased PfK enzyme …

Investigation Into The Effectiveness Of G-C3n4 For The Degradation Of Indigo Dye In Aqueous Solution Via Electrocatalysis, Rolando R. Barron Jr

Theses and Dissertations

Indigo dye (IUPAC 2-(3-hydroxy-1H-indol-2-yl)indol-3-one) is one of the most used dyes in the textile industry worldwide with more than 40,000 tons produced each year. It can elicit adverse physiological responses in humans including vomiting, diarrhea, and other gastrointestinal conditions, and it is toxic in large amounts. There is also evidence to suggest that indigo is a teratogen and genotoxic in aquatic life. Environmentally, the enormous amount of indigo used in the textile industry has caused rivers and waterways to run blue as well as severely impacting aquatic and plant ecosystems. The chemicals used in its synthesis are also …

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 …

Synthesis And X-Ray Characterization Of Nickel Phosphide Nanostructures For Water Oxidation, David Thompson

Graduate Theses and Dissertations

The pursuit of earth-abundant 3d transition metal catalysts for alkaline water electrolysis remains an active area of research. While NiFe layered double hydroxides (LDH) are currently the most active catalysts for the oxygen evolution reaction (OER), doping Ni-based catalysts with phosphorus to form Ni metal phosphides has emerged as a promising alternative. However, the complex crystalline and amorphous phases of NiP_x have hindered their characterization, and the OER mechanism and origin of activity remain unclear. This dissertation aims to elucidate the synthesis, OER performance, and in situ reconstruction of amorphous NiP_x-based nanomaterials, with a focus on in …

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 …

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 …

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 …

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.

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 …

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 …

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 …

Modeling Sod1 Enzyme Mutations: Biochemistry Ii Lab Class Project, Jenna Bolduan, Elle K. Haumont

Research & Creative Achievement Day

Superoxide Dismutase 1 (SOD1) is an enzyme that catalyzes the detoxification of reactive oxygen species that cause damage to the body. Mutations of this protein can cause diseases, such as Amyotrophic Lateral Sclerosis (ALS). The structures of the SOD1 wild type and two of its deleterious mutations (A4V and L126*) were digitally modeled using the AI program AlphaFold3. Although a literature structure exists for A4V, no experimental structure data has been collected for L126*. The wild type and A4V structures were virtually identical, whereas the wild type and L126* structures had quite different features, with the mutant being smaller and …

An Exploration Of Simple Methods For The Purification And Separation Of Natural Curcuminoids, Eion S. Hinkle

Research & Creative Achievement Day

The separation of curcumin from other naturally occurring curcuminoids, such as demethoxycurcumin and bisdemethoxycurcumin, presents significant challenges due to their similar chemical structures. Conventional methods like column chromatography are energetically and environmentally costly, requiring large amounts of solvents and extended processing times. Alternatively, preparatory scale high-performance liquid chromatography (HPLC) offers high precision but necessitates expensive equipment, making it less accessible for routine laboratory use. This research explores simpler and more sustainable approaches to purify curcumin, aiming to reduce both the environmental impact and the financial burden associated with traditional separation techniques.

Using Fluorimetry And Colorimetry For Quantitative Analysis For Biomaterial-Derived Carbon Dots, Kahun N. Vue

Research & Creative Achievement Day

The pursuit of sustainability in nanomaterial synthesis has led to the exploration of biomaterial-derived carbon dots (CDs) as an eco-friendly alternative to conventional methods. This study investigates the synthesis, characterization, and application of CDs derived from various biomaterials, including shrimp shells, food waste, cellulose, keratin, and saccharides. By employing hydrothermal, microwave, and ultrasound-assisted synthesis techniques, this research aims to develop a green, cost-effective approach to producing CDs while reducing environmental impact.

Previous work used shrimp shells as a starting material for a green CD. This work starts with shrimp shells to ensure reproducibility. In the future, novel materials like food …

Discovery, Purification And Annotation Of A Novel Mycobacteriophage Discovered On The Providence College Campus, Jenna Greene

Chemistry & Biochemistry Student Scholarship

Jenna Greene ’26, Biochemistry major

Faculty mentor: Dr. Kathleen Cornely, Chemistry and Biochemistry

Bacteriophages—viruses that infect bacteria—offer a promising alternative to antibiotics in the face of rising antibiotic resistance. In this project, I isolated a novel phage from a soil sample collected in front of Raymond Dining Hall at Providence College. Using Mycobacterium smegmatis as the host, the sample underwent multiple rounds of purification until a single phage, named GMonster (a nod to my family nickname, “Greene Monster”), was isolated. GMonster was submitted to the PhagesDB database and confirmed through sequencing to belong to the A1 cluster—the first of its …

In Situ Synthesis Of Pbs Shell On Cspbbr3 Qd For Enhanced Stability And Photoluminescence, Noah Pitcher

Undergraduate Honors Theses

Halide perovskite quantum dots (HPQDs) have attracted considerable attention for optoelectronic applications due to their outstanding optical properties, including high photoluminescent quantum yield (PLQY), tunable band gap, high absorption coefficients, etc. However, their practical implementation is limited by poor stability under ambient conditions such as moisture, heat, and light. To overcome these challenges, surface passivation and shelling engineering have emerged as effective strategies to enhance HPQD stability by encapsulating their surface with a protective material. Conventional shelling techniques, however, often face limitations related to lattice mismatch and interfacial incompatibility. In this study, we report the successful synthesis of PbS@CsPbBr3 (shell@core) …

Spherical Spiky Zno/Au Nanostructures For Efficient Photoelectrochemical Watersplitting, Kouroush Sali̇mi̇

Turkish Journal of Chemistry

Spiky zinc oxide (ZnO)/Au nanostructures with spherical shape-defined morphologies were synthesized using polydopamine as a starting template for photoelectrochemical H2 production under visible light-emitting diode (LED) illumination. This low-temperature processing technique not only facilitated the fabrication of ideal plasmon-sensitive heterostructures, but also enhanced the electron mobility of the photoanodes, reaching 5.7 mA/cm² [at 1.0 V vs. the reversible hydrogen electrode (RHE)] under visible LED illumination (30 mW/cm2). This notable value was 28 times greater than that observed under dark conditions, primarily attributed to the close Schottky contact between the Au and ZnO spikes. The highest applied bias photon-to-current efficiency value …

Wo3/Α-Fe2O3/Bi2S3 Ternary Photoanode For Improved Oxygen Evolution Reaction In Photoelectrochemical Water Splitting, Fati̇h Tezcan, Abrar Ahmad, Gülfeza Kardaş

Turkish Journal of Chemistry

This study presents a ternary WO₃/α-Fe₂O₃/Bi₂S₃ photoanode system suitable for photoelectrochemical water-splitting applications. The WO₃/α-Fe₂O₃ heterojunction is obtained using a hydrothermal approach, while Bi₂S₃ is deposited onto WO₃/α-Fe₂O₃ via the successive ionic layer adsorption and reaction (SILAR) method. The cycle count is adjusted to determine the optimal photocatalytic photoanode. X-ray diffraction analysis confirms different morphologies and phases for the photoelectrodes: WO₃ is deposited as plates with monoclinic phases, α-Fe₂O₃ as nanorods with hexagonal phases, …

Synthesis Of Low Ph Stable, Highly Photocatalytic Alginate Hydrogels For Methylene Blue Removal From Wastewater, Emi̇rcan Uysal, Hali̇de Nur Dursun, Emre Can Uysal, Sebahatti̇n Gürmen

Turkish Journal of Chemistry

Chemical compounds in wastewater, including dye molecules, have been identified as significant concerns for environmental integrity and human health. In this study, adsorbent materials were synthesized from biodegradable polymers to remove methylene blue (MB) from wastewater. Calcium alginate hydrogels were produced and coated with chitosan to enhance their pH stability. Furthermore, the calcium alginate gels were doped with silver nanoparticles to improve their photocatalytic properties, promoting MB degradation and enabling gel reuse. The adsorption behavior of the gels was comprehensively examined under dark conditions, considering factors such as time, solid-to-liquid ratio, temperature, and pollutant concentration, all of which significantly impact …

Fabrication Of Au–Pd Bimetallic Dendrites And Their Catalytic Application For4-Nitrophenol Reduction, Jun Liu, Xuanyan Liu, Hongguang Liao

Turkish Journal of Chemistry

Bimetal nanocatalysts hold significant application potential in catalytic reactions due to their compositions, morphologies, and electronic structures. In the present work, a series of AuPd alloy dendrites were successfully prepared using sodium formate, without surfactants or templates. A systematic investigation was then conducted to analyze the composition of the AuPd bimetallic dendrites and the effects of preparation conditions on their structure and catalytic performance. The AuPd alloy dendrites were characterized through various techniques, including scanning electron microscopy, transmission electron microscopy, X-ray energy scattering spectroscopy, X-ray diffraction, and X-ray photoelectron spectroscopy. The results showed that the Au:Pd ratio in the AuPd …

Investigation Of The Interaction Conditions Of As2s5 And Cucl2 Compounds In Water And Ethylene Glycol Medium, Huseyn Imanov, Mahnur Jafarli

Turkish Journal of Chemistry

The article presents the results of interaction conditions of CuCl2 and As2S5 in ethylene glycol and aquatic medium. Besides, results of the obtained samples' physicochemical properties are given by X-ray diffraction (XRD), differential thermogravimetric (DTG), thermogravimetric (TG), elemental and scanning electron microscope (SEM) methods. It was found that when ethylene glycol and water are used as a solvent and CuCl2 and As2S5 as the initial components, Cu3AsS4 is obtained at a temperature of 323-353 K. According to the results of DTA analysis, it was found that the melting point of obtained samples was 964.4 K contrary to the reactions carried …