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Bio-Orthogonal Chemistry-Based Strategy To Turn-On And Turn-Off Crispr-Cas9 Gene Editing In Solution And In Live Cells, Bhoomika Pandit

Electronic Theses & Dissertations (2024 - present)

The CRISPR–Cas9 system is a widely popular tool for genome engineering. There is a strong interest in developing tools for temporal control of CRISPR-Cas9 activity to address some of the challenges and to broaden the scope of potential applications. In this thesis I describe two biorthogonal based approaches to either Turn-ON and Turn-OFF CRISPR-Cas9 gene editing.

In first project work I describe a bio-orthogonal chemistry-based approach to Turn-ON Cas9 nuclease activity with temporal precision. We report a TCO-acylimidazole reagent that acylates 2′-OH groups of RNA. Poly-acylation (“cloaking”) of RNA was optimized in vitro using a model 18-nt oligonucleotide, as well …

Re-Crosslinkable Hyper-Branched Polymer Gels Based On A Transamidation Reaction, Tao Song, Baojun Bai, Thomas P. Schuman

Patents

The present invention generally relates to the field of conformance control in oil fields, particularly to a re-crosslinkable preformed particle gel system, and composition thereof. The composition of the re-crosslinkable preformed particle gel system contains monomers, crosslinkers, a polymer matrix, and additives. Components in the composition for re-crosslinkable preformed particle gel in the present invention have excellent compatibility with each other, and the obtained gel has excellent long term high-temperature resistance property. Different from prior products, in the recrosslinkable preformed particle gel compositions according to embodiments of the present invention, the components that are used to re-crosslink the particle gels …

Deciphering Ultrafast Photoinduced And Photocatalytic Reaction Dynamics On Oxide Surfaces: Direct Detection Of Radical Intermediates, Fragment Trapping, And Carbon–Carbon, Carbon–Oxygen, And Carbon–Hydrogen Bond Formation Pathways, Aakash Gupta

Graduate Studies Theses and Dissertations 2026

Understanding photoinduced reactions at solid interfaces is essential for advancing heterogeneous photocatalysis, surface photochemistry, and energy conversion technologies. This dissertation investigates the ultrafast dynamics of reactive intermediates, fragment trapping, and radical-mediated bond formation on oxide surfaces using time-of-flight mass spectrometry in conjunction with femtosecond pump-probe spectroscopy. Various experimental findings are validated through collaborations via density functional theory (DFT). By combining temporal, mass, and energy-resolved measurements, this work provides molecular-level insight into the elementary processes governing light-driven surface reactions. The photodissociation dynamics of CH₃I adsorbed on TiO₂(110), TiO₂(100), and amorphous silicon oxide surfaces are examined …

Crispr-Cas9 Unleashed: Gene-Slicing Adventures In The Cancer Battlefield, Shivakuma Sonnaila, Shilpi Agrawal

Chemistry & Biochemistry Faculty Publications and Presentations

Cancer, a global health menace, continues to pose significant challenges in terms of incidence and mortality, necessitating innovative therapeutic strategies. Despite existing treatments, the limitations persist, prompting a quest for novel approaches. The emergence of immunotherapy marked a transformative era in solid tumor treatments, yet its efficacy is constrained by adverse effects. Concurrently, the integration of advanced technologies into cancer treatment explores the vast potential residing at the molecular level through gene analysis and manipulation. This review articulates the role of state-of-the-art genome editing technology, notably clustered regularly interspaced short palindromic repeats (CRISPR-Cas9), in overcoming the constraints of immunotherapy for …

Application Of Organic Geochemistry To The Characterization Of Hydrochar And Biochar: Insights Into Composition And Optimization, Michael A. Kruge, Teresa A. Centeno, Alvaro Amado-Fierro, José Manuel González-Lafuente, Rubén Forján, José Luis Gallego

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

Hydrothermal carbonization has garnered significant attention in recent studies due to potential applications of the hydrochar produced, which overlap with those of torrefied biochar, including soil improvement, carbon sequestration, and energy production. However, unlike the relatively uniform properties of biochar, hydrochar characteristics can vary greatly depending on the feedstock used. Advanced characterization techniques are essential to better understand these materials and enhance their practical applications. Research on hydrochar requires a multi-faceted approach, including molecular-level studies, to optimize production processes and identify specific applications.

In this regard, analytical methods commonly used in organic geochemistry could play a crucial role in deepening …

Synthesis Of The Naga(S1−Xsex)2 Solid Solution From Mechanically Activated Precursors, Louisiane Verger, Julien Trébosc, Santhoshkumar Sundaramoorthy, Amitava Choudhury, Olivier Hernandez, Eric Furet, Sébastien Chenu, David Le Coq, Laurent Calvez, Olivier Lafon

Chemistry Faculty Research & Creative Works

NaGaS₂ and NaGaSe₂ are two recently discovered compounds that crystallize in the same structure type. In this work, NaGa(S_1−xSe_x)₂ (x = 0.5, 0.75 and 1) are prepared using an alternative synthesis route, mechanochemistry followed by heat treatment. Na₂S, Na₂Se, Ga₂S₃ and Ga₂Se₃ are milled in stoichiometric proportions. Differential scanning calorimetry, X-ray diffraction and solid-state nuclear magnetic resonance (²³Na and ⁷¹Ga) show that the compounds after milling are composed of crystalline NaGa(S_1−xSe_x)₂ with an amorphous part. …

Design, Syntheses And Biological Applications Of Fluorescent Probes For Nad(P)H, Hsa And Cellular Microenvironment Sensing, Adenike M. Olowolagba

Dissertations, Master's Theses and Master's Reports

Fluorescent probes have emerged as powerful tools for investigating complex biological processes due to their high sensitivity, selectivity, and capability for real-time, non-invasive imaging. In particular, the detection of key biomolecules such as NAD(P)H, viscosity-related parameters, human serum albumin (HSA), and pH is essential for understanding cellular metabolism, redox homeostasis, and disease progression. In Chapter 2, three coumarin-based fluorescent probes (A–C) were designed, synthesized, and characterized for monitoring NAD(P)H levels in living cells. Probes A and B feature coumarin–cyanine hybrid structures linked via vinyl and thiophene bridges to 3-quinolinium acceptors, respectively, while probe C incorporates a dicyano moiety to replace …

Schiff Bases As Versatile Platforms: From Multinuclear Dysprosium Complexes To Halogen-Mediated Quasiracemic Crystal Engineering, Macy M. Michorczyk

Theses and Dissertations

Understanding the factors that govern molecular assembly is fundamental in both coordination chemistry and crystal engineering. This thesis investigates these processes through two studies that employ single-crystal X-ray diffraction to elucidate the structural principles underlying the formation of multinuclear metal complexes and the crystal packing of quasiracemates.

The first study examines the unexpected formation of multinuclear metal complexes. Structural characterization of a series of dysprosium complexes was used to compare molecular architectures and identify structural relationships that support a proposed pathway of formation. These findings shed insight into the assembly process that may have lead to their formation.

The second …

Exploring New Poly-Anion Based Materials For Lithium – Ion Battery Cathodes, Sutapa Bhattacharya

Doctoral Dissertations

The escalating global demand for sustainable energy storage solutions has driven intensive research into novel electrode materials. Polyanion-based cathode materials have emerged as promising candidates due to their structural stability, safety, and voltage tunability enabled by the inductive effect of polyanionic groups. This research explores the synthesis, crystal structure, and electrochemical performance of new polyanion-based cathode materials featuring vanadium, molybdenum, and iron within phosphate and selenite frameworks.

Novel selenite-based materials, such as LiFe(SeO₃)₂ and Li₀.₂₅V₂O₃(SeO₃)₂, were synthesized and characterized, revealing stable electrochemical cycling associated with Fe2+/Fe3+ and V⁴⁺/V⁵⁺ transitions. Additionally, a systematic investigation was conducted on molybdenum phosphate compounds, including …

Theoretical Study Of Long-Range Molecular Interactions, Adrian Luis Batista-Planas

Doctoral Dissertations

Describing intermolecular forces is fundamental to modeling and predicting the behavior of molecular systems. In particular, long-range molecular interactions—with electrostatic, induction, and dispersion as main components—play a critical role, especially for low-temperature and low-density regimes. Long-range interactions are often described through perturbation theory, representing the electronic charge distribution via multipolar series of the moments and polarizability tensors corresponding to each molecule. However, while the theory is well-established, obtaining the resulting analytical expressions (and their practical implementation) constitutes a highly complex and system-dependent task. To address this challenge, we developed Long-Range-Fit (LRF), an interactive and user-friendly software package designed to automate …

Scope Of Microbial Transglutaminase For Site-Specific And Oriented Immobilization Of Native Antibodies From Various Host Species, Emily Beitello, Kwame Osei, Faith E. Breausche, Jon A. Friesen, Jeremy D. Driskell

Faculty Publications – Chemistry

Modification of antibodies to chemically couple labels or immobilization reagents is essential for developing biosensors. Typically, conjugation occurs through chemical methods that leverage reactive amines and thiols on native antibodies; however, this nonspecific approach can interfere with antibody function. Microbial transglutaminase (mTG) is an enzyme that has been used for site-specific conjugation of chemical modifiers to the F_c region of native antibodies, but thus far mTG-mediated conjugation has been limited to production of antibody-drug conjugates with human IgGs. Here, we assessed the scope and versatility of mTG to target IgGs, with the goal of site-specific conjugation to facilitate oriented …

Diverse C–C Bond Formation Reactions Catalyzed By Oxidized Palladium Nanoparticles Supported On Marine Shell Waste Powder Via Additive-Free Deposition–Precipitation, Jian Hou, Garrett M. Milligan, Zhicheng Cai, Jun-Hyun Kim

Faculty Publications – Chemistry

The formation of carbon-carbon (C–C) bonds is central to modern organic synthesis. Although the use of conventional Pd-ligand complexes as homogeneous catalysts results in highly effective yields, these systems often face some limitations including high cost, difficult recyclability, and thermal stability. Here, we demonstrate the utilization of palladium (Pd)-derived metals supported on finely ground marine shell waste as a reactive and recyclable catalyst for diverse C–C bond-forming reactions. Oyster shell powder (OSP) derived from problematic biowaste, primarily composed of calcium carbonate, provides abundant anchoring sites to immobilize Pd ions via an additive-free deposition–precipitation method, followed by thermally-induced conversion into oxidized …

Flexible Membrane Electrodes For Use In High-Capacity Lithium-Ion Batteries, David A. Denemark

College of Graduate Studies: Theses & Dissertations

Wearable electronic devices require high-capacity flexible batteries to improve user comfort and increase usage time per charge. In this thesis, flexible lithium-ion battery (LIB) electrodes are prepared using a novel and scalable phase inversion method, embedding one-dimensional SnO₂ nanowires and double-walled carbon nanotubes within a porous polyacrylonitrile asymmetric membrane. The optimized electrode delivered an initial specific discharge capacity of 915.93 mAh g⁻¹, approximately 2.5 times greater than conventional graphite anodes, with 61.99% capacity retention after 45 cycles. The incorporation of a carbon mesh substrate further enhanced both electrochemical and mechanical performance, achieving 89.46% capacity retention after 45 cycles and a …

De Novo Protein Binding To Zinc Oxide Through Biomineralization Pathways, Jean-Mark A. Francis

Theses and Dissertations

De novo proteins are structurally distinct from proteins found in nature and thus capable of having their amino acid sequence modified to accomplish tasks such as increasing protein-nanoparticle binding without unfolding or decomposing. Zinc Oxide nanoparticles are functionally distinct from their bulk counterparts and are widely used as semiconductors in a variety of fields such as medicine and agriculture. With demand for these nanoparticles increasing, environmentally sustainable methods of Zinc Oxide nanoparticle synthesis are being investigated as an eco-friendly alternative to currently utilized but environmentally hazardous chemical and physical techniques. This research investigates the binding characteristics between Zinc Oxide nanoparticles …

Computational Design Of Nanoporous Materials For The Adsorption Of Per- And Polyfluoroalkyl Substances, Daniel D. Mottern

Dissertations

Per- and polyfluoroalkyl substances (PFAS) are a large family of chemicals that have seen wide usage due to their fluorinated carbon backbone. The presence of strong C-F bonds in the backbone lends PFAS molecules high thermal and chemical stability, as well as strong hydrophobicity and lipophobicity. This combination of properties has led to heavy use of PFAS as surfactants, non-stick coatings, and aqueous foam forming films and flame retardants. However, these properties bring their own consequences. The high chemical and thermal stability of PFAS renders them persistent, with the C-F bonds resisting naturally occurring forms of degradation. Existing forms of …

Data-Driven Analysis And Atomistic Simulations Of Next-Generation Materials For Energy Conversion And Storage, Yuliang Shi

Dissertations

Metal-organic frameworks (MOFs), with their modular architectures and tunable properties, represent an especially rich domain for accelerated material design and discovery for a range of diverse applications. Within this class of multifunctional materials, two-dimensional (2D) electrically conductive MOFs (EC MOFs) are of particular interest, as their 7r-stacked layered structures combine permanent porosity with electronic conductivity, enabling potential breakthroughs in energy storage, energy conversion, and quantum sensing. But the discovery and design of new EC MOFs based on expensive experimental screening is increasingly impractical due to the infinite chemical space. Furthermore, the practical implementation of EC MOFs for specific tasks depends …

Bio-Papcz: Corn Starch-Based Composite Bioplastic Reinforced With Pineapple Leaf Fiber (Palf), Zinc Oxide (Zno), And Polyvinyl Alcohol (Pva), Marvin C. Caya, Shervin Austin C. Huang, Jovar Khalel J. Maghari, Ruel M. Levida

Sinaya: A Philippine Journal for Senior High School Teachers and Students

Plastic pollution poses a serious global threat, as petroleum-based plastics persist for centuries, and their surging production of over 450 million tons overwhelms ecosystems (Ritchie et al., 2023). Using a quantitative experimental research design, the study examined the effects of varying concentrations of cornstarch-based bioplastic reinforced with pineapple leaf fiber (PALF), polyvinyl alcohol (PVA), and zinc oxide (ZnO) on the bioplastic’s tensile strength and soil degradability. Sample C2 (ZnO 3.0 %w/w; PVA 9.0 %w/w) demonstrated the optimal tensile properties with a tensile strength of 0.76 MPa and an elongation at break of 6.40%, which was attributed to the addition of …

Exploring The Metric Dimension Of The Graph Representing A Four-Ring Polycyclic Aromatic Hydrocarbon: Interstellar 1-Cyanopyrene, Andrei Matthew V. Robino, Sebastian Alex C. Traviña, Karl Benedict P. Narag, Mark Anthony B. Casao, Helix Raven C. Llanes, Azriel C. Alejo, Jonel C. Celamor

Sinaya: A Philippine Journal for Senior High School Teachers and Students

A graph's metric dimension is a parameter that denotes the minimum possible number of vertices in a subset that gives each vertex in the graph a unique representation. Despite extensive research on the metric dimension of polycyclic aromatic hydrocarbons (PAHs), there is currently no focused analysis on the metric basis and metric dimension of 1-cyanopyrene. In chemistry, graphs can be used to depict molecular structures. In this study, graph theory, specifically the concept of metric dimensions, is applied to the molecular structure of 1-cyanopyrene, which was detected in space for the first time in 2024. 1-cyanopyrene is a molecule made …

Two Members Of The Editorial Board Of Journal Electrochemistry, Kai Wu Elected As An Academician Of The Chinese Academy Of Engineering And Yi Cui A Foreign Academician Of The Chinese Academy Of Sciences, Editorial Office Of J.Electrochem.

Journal of Electrochemistry

No abstract provided.

Electrochemical Characterization And Modulation Of Biological Processes, Yue-Qi Li, Wei-Hua Huang, De-Chen Jiang, Bao-Hong Liu, Bin Su, Yang Tian, Jing-Juan Xu, Ping Yu, Feng Zhao, Huang-Xian Ju, Jing-Hong Li

Journal of Electrochemistry

Electrochemical processes lie at the core of biological function, governing energy transduction, metabolic flux, and molecular signaling. Recent advances in electrochemical science now allow these processes to be probed and controlled with unprecedented spatial, temporal, and chemical resolution. In this review, we present an integrated framework that progresses from fundamental mechanisms to analytical technologies and functional modulation. We begin by outlining electron transfer pathways in mitochondrial respiration, microbial extracellular electron transfer, and DNA- and protein-based charge conduction, followed by the principles of photon-electron conversion in photosynthesis and the central role of redox equilibrium in coordinating cellular responses. We then highlight …

A Novel Electrolyte Pyridine Additive For Enhancing Cycle Life Of Lithium-Ion Batteries, Peng-Cheng Wang, Ding-Chang Li, Jun-Tao Li, Guang-Bo Lu, Shi-Wen Wang

Journal of Electrochemistry

Lithium-ion (Li-ion) battery using a graphite (Gr.) anode and a lithium iron phosphate (LiFePO₄, LFP) cathode (Gr.||LFP) has been widespread in energy storage. To match the warranty period of energy storage systems, the lifespan of this kind of Li-ion battery, not only under room temperature but also under relatively high temperature, is critical. Exploration of functional electrolyte additive provides an efficient approach to address this issue. This study reports the usage of pyridine (Py) as a new electrolyte functional additive for Gr.||LFP. In the first cycle, it was found that Py can be reduced before ethylene carbonate and …

Journal Of Electrochemistry Officially Indexed By Leading Oa Databases Oarl And Coaj, Editorial Office Of J.Electrochem.

Journal of Electrochemistry

No abstract provided.

Feature Column Of Journal Of Electrochemistry Nominated For 2025 Top 10 Famous Columns Of Fujian Provincial Newspapers And Periodicals, Editorial Office Of J.Electrochem.

Journal of Electrochemistry

No abstract provided.

Enhancing Analytical Performance Of Tyrosinase-Based Sensors With Nanoparticles For Detection Of Isoproterenol, Aysel Oktay, Sevi̇nç Kurbanoğlu, Gülsüm Gündoğdu, Cem Bülent Üstündağ, Frieder W. Scheller, Aysu Yarman

Turkish Journal of Chemistry

In this work, electrochemical biosensors utilizing tyrosinase (Tyr) for the detection of the nonselective beta-adrenergic agonist isoproterenol (ISO) are presented. Three different configurations for immobilizing Tyr on a graphite electrode (GE) are compared: (1) GE modified with poly(diallyldimethylammonium chloride) (PDADMAC), PDADMAC/Tyr/GE; (2) PDADMAC combined with iridium nanoparticles (IrNPs) in a stepwise preparation, resulting in PDADMAC/IrNPs/Tyr/GE; and (3) a composite of PDADMAC and IrNPs mixed with Tyr at a 1:1 (v:v), forming PDADMAC/(IrNPs-Tyr)/GE. Surface morphology was characterized using scanning electron microscopy (SEM). Cyclic voltammetry (CV) and amperometry were applied to characterize the biosensor’s performance. Within the linear range of 5 μM …

Synthesis, Characterization, And Theoretical Study Of New Cocrystals And Charge-Transfer Compounds, Zari̇fe Si̇bel Şahi̇n, Zeki̇ Kartal

Turkish Journal of Chemistry

This study used single-crystal X-ray diffraction, elemental analysis, infrared (IR) spectroscopy, theoretical nuclear magnetic resonance (NMR), and theoretical ultraviolet spectroscopy to characterize 3 newly synthesized crystalline compounds. Additionally, the nonlinear optical, highest occupied molecular orbital energies, lowest occupied molecular orbital energies, band gap, molecular electrostatic potential, and thermodynamic parameters of the 3 crystalline compounds were examined. The strong correlation between experimental IR spectra and theoretical NMR chemical shifts confirmed the accuracy of computational predictions. The molecular formulas of the 3 newly synthesized crystalline compounds, each containing different ligand molecules, were: C8H14O4·2(C6H4N2), C5H7N2·NCS, and Ni(CN)4·2(C5H7N2)·2(H2O) for compounds 1, 2, and 3, …

New Bis-Piperazine Derivatives: Synthesis, Characterization (Ir, Nmr), Gamma-Ray Absorption, Antimicrobial Activity, Molecular Docking And Dynamics Study, Yasemi̇n Ünver, Arzu Coşkun, Fati̇h Çeli̇k, Hali̇l İbrahi̇m Güler, Kadri̇ye İnan Bektaş

Turkish Journal of Chemistry

A series of novel bis-piperazine derivatives (2a–2f) were synthesized and structurally characterized via Fourier transform-infrared and nuclear magnetic resonance spectroscopic techniques. Their gamma-ray shielding efficiencies were investigated through simulations on the Monte Carlo-based Geant4-GATE platform, and the results were benchmarked against data obtained from the XCOM and Phy-X software. A simulation model incorporating an NaI scintillation detector and a point gamma source was developed. Key shielding parameters, including mass attenuation coefficient, linear attenuation coefficient, half-value layer, and mean free path (MFP), were evaluated at gamma energies of 80, 120, 662, 1173, and 1332 keV. Additionally, the energy absorption buildup factor …

Synthesis Of Biogenic Silver Nanoparticles From Apricot Kernel Extracts For The Colorimetric Determination Of Gold, Ayça Gi̇rgi̇n, Hi̇lal Akbiyik, Buse Tuğba Zaman, Omid Nejati, Ayça Bal Öztürk, Gülten Çeti̇n, Sezgi̇n Bakirdere

Turkish Journal of Chemistry

Gold is abundant in nature, however, precise and reliable analytical methods for its detection are required stemming from its increasing prevalence in environmental, biological, and industrial systems, as well as the growing interest in understanding its function in living organisms and its effects on human health. This study investigates the use of biogenically synthesized silver nanoparticles (AgNPs) for the preconcentration and determination of gold ions prior to determination by UV-Vis spectrophotometry. AgNPs were synthesized by reducing silver nitrate through the use of an apricot kernel extract as both reducer and stabilizer agent. The colloidal yellowish AgNPs interacted with gold ions, …

Structural Categorization And Identification Of Electrostatic Interactions In Two Proposed Human Serum Albumin Dimerization Patterns And Dipyridamole Interaction, Haluk Çeti̇nok, Veyi̇s Karakoç, Erol Erçağ, Yusuf Meli̇h Şekerer, Hasan Demi̇rci̇

Turkish Journal of Chemistry

Human serum albumin (HSA) is a ubiquitous, multifunctional protein responsible for the systemic distribution of both endogenous metabolites and exogenous pharmaceuticals. Its inherent properties, particularly its ability to seep into tissues and its multiple ligand-binding sites, have rendered HSA an attractive vehicle for nanoparticle-based drug delivery systems, particularly for cancer targeting. In this study, we present high-resolution crystallographic data revealing two distinct dimerization patterns of HSA (Protein Data Bank [PDB] ID: 9V61) obtained under high-concentration crystallization conditions, along with results from dipyridamole docking. Both dimer types demonstrate extensive interface areas and a significant number of electrostatic interactions. Comparative analysis with …

Α-Glycosidase Activity Of Novel Coumarin–Triazole–Coumarin Dyads, Ersi̇n Şi̇ri̇n, Esra Sevi̇mli̇, Gökçe Seyhan, Burak Barut, Yunus Kaya, Baybars Köksoy

Turkish Journal of Chemistry

Novel coumarin–triazole–coumarin dyads were synthesized and characterized, and their α-glycosidase inhibitory activities were evaluated spectrophotometrically. Compound 4e exhibited the most pronounced inhibitory effect, with an IC50 value of 38.98 ± 0.77 μM. The IC50 values for 4d and 4a were 93.55 ± 1.70 μM and 95.04 ± 3.55 μM, respectively. The Lineweaver–Burk plot showed that 4e inhibited α-glycosidase in a mixed type. In addition, the Ki value obtained from the Dixon plot was 19.95 ± 0.15 μM for α-glycosidase.

Utilization Of Dual Catalysts For High-Yield Boron Nitride Nanotube Synthesis Via Chemical Vapor Deposition, Şaban Kalay

Turkish Journal of Chemistry

The direct synthesis of boron nitride nanotubes (BNNTs) via chemical vapor deposition (CVD) in high-temperature furnaces remains highly challenging due to difficulties in optimizing key experimental parameters such as synthesis temperature and catalyst composition. These challenges often result in uncontrolled growth behavior, adversely affecting the quality and yield of the BNNTs. In this study, colemanite was effectively utilized as a boron source for the high-yield synthesis of directionally aligned BNNTs. The synthesis was carried out using a CVD method that used a dual-catalyst system comprising Fe2O3 and MgO in conjunction with a silicon carbide template under high-temperature conditions. The resulting …