Biochemistry, Biophysics, and Structural Biology Commons^™

Characterization Of Ru(Ii) Polypyridyl Photosensitizers Bound To Tio2 Supports Through A New Covalent Metal-Ester Bonding Motif, D. M. S. C. Dissanayake, Christopher T. Lebarron, Laura C. Maybach, Joseph J. Kuchta Iii, Seyyedamirhossein Hosseini, Aaron K. Vannucci

Faculty Publications

The development of photoelectrochemical (PEC) devices involves the attachment of molecular photosensitizers onto solid supports. Particularly significant to this work are PECs that rely on ruthenium-based photosensitizers on high band gap metal oxide (MOx) supports. In this study, we have explored a new ester binding motif (MOx-ester) to covalently attach a ruthenium polypyridyl photosensitizer to TiO₂. This new MOx-ester photoanode is compared to the traditional photoanodes that utilize acid/base binding groups to attach the molecular Ru sensitizers to TiO₂. The new MOx-ester binding motif is characterized by cyclic voltammetry UV-Vis, solid state ¹³C NMR, and …

Chasing Disinfection Byproducts Through The Pipes: How 66 Dbps Change Over Time In Chlorinated Vs. Chloraminated Distribution Systems, Erik Niehaves, Patrick T. Justen, Ashley A. Perkins, Alexandria L.B. Forster, Caroline O. Granger, Susan D. Richardson

Faculty Publications

While disinfection byproducts (DBPs) are typically measured at drinking water treatment plants, levels can change dramatically within the distribution system before reaching the consumer. In this study, the spatio-temporal trends of 66 DBPs across 9 different classes were examined in two drinking water distribution systems with similar source waters, but different pretreatments and residual disinfectants. One system uses residual chlorine in the distribution system, and the other uses chloramine, allowing for examination of how DBP concentrations change over time in distribution systems with different residual disinfectants. Four routes were sampled for each system with six time points over three days …

Optimized Photoemission From Organic Molecules In 2d Layered Halide Perovskites, Muhammad S. Muhammad, Dilruba A. Popy, Hamza Shoukat, John M. Lane, Neeraj Rai, Vojtěch Vaněček, Zdeněk Remeš, Romana Kučerková, Vladimir Babin, Chenjia Mi, Yitong Dong, Mark D. Smith, Novruz G. Akhmedov, Daniel T. Glatzhofer, Bayram Saparov

Faculty Publications

In recent years, hybrid organic–inorganic metal halides have been at the forefront of materials research. Typically, the functional (e.g., optoelectronic) properties of hybrid halides are derived from the inorganic structural part, whereas the organic structural units can add extra advantages in terms of stability, rigidity, and processability. Here, we report the design, synthesis, and characterization of two new hybrid materials in which the outstanding photophysical properties originate from the organic structural part. The new compounds, (C₁₅H16N)₂CdCl₄ and((Br)C₁₅H₁₅N)₂CdCl₄, have 2D layered Ruddlesden–Popper-type perovskite structures. These hybrids are blue-white …

Structural Characterization Of Peptide Nanoaggregates At Varying Concentrations And Their Impact On Cellular Responses, Malika Rozmetova

Theses and Dissertations

Peptide nano-assemblies can regulate cellular pathways in a structure-dependent manner. Here, we show that the enzyme-responsive peptide NapFFK(NBD)Yp forms distinct nanoscale assemblies at different concentrations, triggering differential ER stress and extracellular vesicle release in MDA-MB231 cells. These results highlight the importance of supramolecular organization in peptide–cell interactions.

Flux Crystal Growth Of Potassium Lanthanide Double Vanadates With Lanthanide-Dependent Coordination Number Variance, Hunter B. Tisdale, Hans Conrad Zur Loye

Faculty Publications

A series of potassium rare earth double vanadates is presented. Single crystals of double vanadates with stoichiometry K₃Ln(VO₄)₂ (Ln = La, Pr, Nd, and Sm) and crystallizing in the glaserite structure type were synthesized via a molten alkali chloride/fluoride flux reaction. Different structures were observed depending on the constituent rare earth: K₃La(VO₄)₂ crystallizes in an as-of-yet unreported modification of the typical glaserite structure in the space group P2₁/c, likely due to its larger ionic size that results in an increase in the lanthanide coordination number …

Advancing Lipidomics Through Fluoroalcohol-Induced Multiphase Fractionation And Orthogonal Lc×Lc–Ms Detection, Md Al Amin

Chemistry & Biochemistry Dissertations

Comprehensive characterization of the lipidome remains a significant analytical challenge due to the immense structural diversity, wide dynamic range, and complex physicochemical continuum of lipid species. Conventional extraction methods, such as those by Bligh–Dyer and Folch, and one-dimensional liquid chromatography (1D-LC) often fail to resolve this complexity, leading to chromatographic overlap, severe ion suppression, and limited coverage of low-abundance or highly hydrophobic species. This dissertation addresses these bottlenecks by establishing a separation-driven analytical framework that integrates novel fluoroalcohol-induced multiphase systems (FAiTPS) with orthogonal multidimensional liquid chromatography–mass spectrometry (LC×LC–MS).

The core of this research is the development and physicochemical characterization of …

Recirculated Submarine Groundwater Discharge Dominates Nutrient Inputs And Enhances Eutrophication Risk In A Coastal Lagoon, Júlia Rodriguez-Puig, Clara Ruiz-González, Marc Diego-Feliu, Irene Alorda-Montiel, Aaron Alorda-Kleinglass, Daniel Romano-Gude, Andrea G. Bravo, Júlia Dordal-Soriano, Javier Gilabert, Sophia Bergeler, Celine Lavergne, Gemma Casas, Marisol Manzano, Jordi Garcia-Orellana, Valentí Rodellas

OES Faculty Publications

Submarine groundwater discharge (SGD) is a widely recognized pathway for nutrient transport to coastal systems. Prior studies overlook the unique biogeochemical signatures of different SGD pathways, neglecting their differences in biogeochemical transformations and spatiotemporal factors. Here, we present an integrated assessment of nutrient delivery through three SGD pathways (fresh SGD, long‐scale recirculated SGD, and short‐scale porewater exchange), alongside surface water inputs, to evaluate their seasonality and impact on nutrient dynamics in a coastal lagoon. We conducted five field surveys in March, July, and November 2021, July 2024, and March 2025 in the Mar Menor lagoon, an ecosystem facing severe ecological …

Characterization Of Phytoplankton-Excreted Metabolites Mediating Carbon Flux Through The Surface Ocean, Yuting Zhu, Hanna S. Anderson, Eli Salcedo, Samuel E. Miller, Krista Longnecker, Melissa C. Kido Soule, Sheean T. Haley, Gretchen J. Swarr, Rogier Braakman, Sonya T. Dyhrman, Elizabeth B. Kujawinski

Chemistry & Biochemistry Faculty Publications

The marine labile dissolved organic carbon (DOC) pool is a dynamic reservoir of thousands of molecules that cycles approximately one-quarter of Earth’s primary production within days to weeks. After excretion by phytoplankton and other microbes, metabolites are rapidly consumed, resulting in low standing concentrations (picomolar to low nanomolar). Despite the decades-long search for labile DOC sources and molecular identities, marine phytoplankton exometabolomes are not well characterized, largely due to difficulties in measuring small polar molecules in saline water. Here, we profiled the exometabolomes of six axenic phytoplankton species representing key functional groups including a diatom (Thalassiosira pseudonana CCMP1335), a …

Exploring The Limitations Of Substrate Scope In Dimethylallyltryptophan Synthases, Evan T. Miller

Theses and Dissertations--Pharmacy

Natural products (NPs), are the largest source of bioactive compounds in Nature, and are essential to the treatment of human disease. Nearly 50% of drugs approved for use from 1981 to 2019 owe some aspect of their development to NPs, either in terms of their structure, pharmacophore, or mechanism of action. However, NPs are difficult to structurally optimize. Chemoenzymatic methods for NP derivatization have been increasingly seen as practical alternatives to traditional synthetic methods. Prenyltransferases (PTs) are involved in the primary and secondary metabolism of plants, bacteria, and fungi, and they are key enzymes in the biosynthesis of many clinically …

Preliminary Analysis Of Soil Volatile Organic Compounds As Soil Health Indicators, Thorne Taul

Graduate Theses, Dissertations, and Problem Reports (ETD)

Over the past decade, soil health (SH) has gained popularity due to the novelty of sustainable soil use related to human wellbeing. Soil health describes the overall quality of soil and its capacity to function over time. As interest in SH grows, researchers continue to explore new soil health indicators that can improve knowledge on how soil health is assessed and managed. Some indicators directly reflect soil health status, and some indirectly relate to processes and functions occurring within the soil. Volatile organic compounds (VOCs) are naturally occurring compounds that play a role in multiple soil processes. They are associated …

An Investigation Into The Potential Role Of Thioester Bonds In Prebiotic Atp Synthesis, Adam J. Ruf

Williams Honors College, Honors Research Projects

In this project I will attempt to show a potential prebiotic pathway for the synthesis of ATP. This pathway involves the use of thioester bond containing molecules, as derivatives of these bonds have been shown to exhibit enzyme-like catalytic properties. Nuclear magnetic resonance spectroscopy will be utilized to characterize each step of the pathway to ensure it is successful.

Biochemical Investigations Of F420-Dependent Glucose-6-Phosphate Dehydrogenase From Cryptosporangium Arvum, Sarah T. Al-Noubani

2026 Spring Honors Capstones Projects

F₄₂₀-dependent glucose-6-phosphate dehydrogenase (FGD) catalyzes the conversion of glucose-6-phosphate to 6-phosphogluconolactone using the deazaflavin, Cofactor F₄₂₀. FGD from Mycobacterium tuberculosis has been investigated due to its health relevance to prodrug activation. More recently, FGD from Cryptosporangium arvum (Cryar- FGD) has been investigated due to its broader substrate specificity toward multiple sugar phosphates. Kinetic and NMR studies have shown that Cryar-FGD has dual catalytic activity as a dehydrogenase and isomerase. Further investigations are being conducted on Cryar-FGD to characterize key residues involved in catalysis.

To investigate the catalytically active residues of Cryar-FGD, …

A Major Update And Improved Validation Functionality In The Mwtab Python Library And The Metabolomics Workbench File Status Website, P. Travis Thompson, Hunter N. B. Moseley

Markey Cancer Center Faculty Publications

Background: The Metabolomics Workbench (MW) is a public scientific data repository consisting of experimental data and metadata from metabolomics studies collected with mass spectroscopy (MS) and nuclear magnetic resonance (NMR) analyses. Although not as rapidly as in the past, MW has steadily evolved, updating its mwTab and JSON deposition text file formats and its web-based infrastructure. However, the growth of MW has been exponential since its inception in 2013 and continues to be exponential, with the number of datasets hosted on the repository increasing by 50% since April 2024. As part of regular maintenance to keep up with changes to …

Photo And Spatial Control Of Rna Structures And Functions: Exploring Positional Effects And Photo-Responsiveness Of Azobenzene Modified Nucleotides, Jinxi Du

Electronic Theses & Dissertations (2024 - present)

RNA molecules perform many important biological functions by forming complex three-dimensional structures stabilized by base pairing, tertiary interactions, and metal ion coordination. Because RNA function depends strongly on its structure, methods that allow reversible control of RNA conformation and activity are important for understanding RNA behavior and for potential therapeutic applications. However, achieving reversible and site-specific control of RNA structure, especially at the single-nucleotide level, remains challenging. In this dissertation, I developed and applied azobenzene-modified nucleotides as a chemical tool to enable optical and spatial control of RNA structure and function.

The first part of this dissertation focuses on establishing …

Absolute Quantification And Identification Of Rna From Rna-Lipid Nanoparticles Using High Resolution Mass Spectrometry, Jason C. Funderburk, Yasir A. Alshehry, Matthew S. Halquist Phd, Sandro R.P. Da Rocha Phd

Graduate Research Posters

Background

RNA therapeutics are a rising drug category with potential use for a range of conditions encompassing infectious diseases to therapies for cancer, diseases, and genetic disorders. RNA-lipid nanoparticles (RNA-LNPs) are the prominent delivery method for these therapeutics approved products include mRNA vaccines and polyneuropathy treatments. The emergency use authorizations and orphan drug status of current RNA-LNP drugs has allowed approval without finalization of the regulatory analytical procedures for quality monitoring. The objective of the study was to develop an LC-MS assay to simultaneously measure identity and concentration of two therapeutically relevant intact RNA constructs extracted from RNA-LNPs to enhance …

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 …

The Chemistry Of Red Lipstick: The Impact Red Lipstick Has On Society, Lilliana Weldeslassie

Electronic Theses & Dissertations (2024 - present)

Cosmetic chemistry is deeply embedded in everyday life, shaping the products people use from morning to night. Among these, red lipstick stands out as a formulation that blends complex chemistry with a cultural meaning. This thesis examines the scientific foundations of red lipstick through its chemical composition, pigment structure, toxicological history, analytical methods, and evolving sustainability practices. Historically, red lipsticks relied on high-risk ingredients such as lead, mercury, and other toxic metals, reflecting an era before chemical safety and regulatory oversight were incorporated.²¹ Modern formulations have established safer synthetic dyes, natural waxes, plant-based oils, and stabilizers created to optimize …

Overview And Methods Of Molecular Paleontology: A Review, Shelby Touchstone

Williams Honors College, Honors Research Projects

Molecular paleontology—the study of ancient biomolecules preserved in fossils and sediments, including ancient DNA, lipids, and proteins—has motivated researchers since the 1950s, inspiring both scientific inquiry and broader cultural imagination. Think Jurassic Park. This honors thesis presents a comprehensive review of the history, current state, and methods of the field of molecular paleontology. Drawing on peer-reviewed literature and scholarly resources accessed through databases such as EBSCO and Bierce library, this review examines key techniques such as Next Generation Sequencing and amino acid racemization and will go over limitations and controversies in the field. It will also explore potential new …

31p Solution Nmr Investigation Of Abasic Dna, Clarissa R. Krimmel

Graduate Theses/Dissertations

Base excision repair (BER) mechanisms fix single base lesions in DNA, such as T:G mismatches. During the base excision repair mechanism, an abasic site (AP site) is formed as an intermediate. AP sites are unstable and highly mutagenic; they can stop DNA replication. This research investigates how the conformational properties of abasic sites in DNA affect the binding recognition of enzymes involved in DNA repair mechanisms, including BER. Three different abasic sequences are being analyzed for this research project. A second project looks at the effects of a naturally occurring purine derivative, hypoxanthine, on the DNA backbone. These hypoxanthine lesions …

Absolute Quantification And Identification Of Rna From Rna-Lipid Nanoparticles Using High Resolution Mass Spectrometry, Jason C. Funderburk

Theses and Dissertations

RNA therapeutics are a rising drug category with potential use for a range of conditions encompassing infectious diseases to therapies for cancer, diseases, and genetic disorders. RNA-lipid nanoparticles (RNA-LNPs) are the prominent delivery method for these therapeutics approved products include mRNA vaccines and polyneuropathy treatments. The emergency use authorizations and orphan drug status of current RNA-LNP drugs has allowed approval without finalization of the regulatory analytical procedures for quality monitoring. The objective of the study was to develop an LC-MS assay to simultaneously measure identity and concentration of two therapeutically relevant intact RNA constructs extracted from RNA-LNPs to enhance quality …

Computational Methods For Rna 3d Structure Classification And Structural Motif Discovery, Nabila Shahnaz Khan

Graduate Studies Theses and Dissertations 2026

Non-coding RNAs perform diverse and essential cellular functions, and the study of RNA structures is expanding rapidly. The growing volume of RNA 3D structures highlights the need for efficient computational methods to identify recurring structural motifs, which are often conserved and critical to RNA function. However, the complexity and redundancy of RNA structures in existing databases pose significant challenges for motif discovery and structural analysis. To address these challenges, this dissertation presents three complementary computational approaches. First, a non-redundant RNA structural dataset, RNA-NRD, was developed to systematically reduce redundancy in RNA structural data and provide a reliable foundation for downstream …

Understanding The Fidelity And Specificity Of Dna Polymerase I, Bill R. Miller Iii, Andrew V. Yeager, Jake A. Collins, Alexis Blake, Elise Tate, Carol A. Parish, Eugene Y. Wu

Chemistry Faculty Publications

High-fidelity DNA polymerases employ complex mechanisms to catalyze template-dependent DNA synthesis while quickly discarding mismatches. Atomic-level structural details about short-lived states during nucleotide discrimination are necessary to gain insight into the kinetic checkpoints that contribute to fidelity. We performed microsecond molecular dynamics simulations of DNA polymerase I, large fragment, from Bacillus stearothermophilus (Bacillus fragment, or BF) in complex with a template guanine and a mismatched thymidine triphosphate to observe the early events in the process of selection against a mismatch. Although the nucleobases formed a wobble base pair early, the mismatched pair was blocked from fully entering the active site …

Developing A Tool To Measure Resistance To Sustainable Food Choices: A Pilot Study In Ireland And The Netherlands, Kate Flanagan, Bart Sinteur, Patricia J. Bulsing, John M. Kearney

SURE Journal: Science Undergraduate Research Experience Journal

Consumer uptake of a sustainable diet is critical for addressing environmental challenges and promoting public health. Understanding why consumers resist adopting sustainable eating habits can inform targeted interventions and policies. This pilot study examines whether a newly developed scale can effectively detect consumer resistance to a sustainable diet. Currently, there is a lack of research on a tool to measure consumer resistance to a sustainable diet, highlighting the need for a reliable instrument.

The aim of this study is to develop a scale, based on existing literature, to measure consumer resistance to a sustainable diet. Additionally, the study aims to …

Editorial-Sure Journal Volume 7, Issue 2, Geraldine M. Dowling, Eva Campion, Sinead Loughran, Ariane Perez-Gavilan, Josephine Treacy

SURE Journal: Science Undergraduate Research Experience Journal

No abstract provided.

Energetics And Kinetics Of Alkali Ion Exchange In Analcime, Jinyi Liu, An T. Ta, R. Seaton Ullberg, Jean Wilfried Hounfodji, Michael Badawi, Hans Conrad Zur Loye, Simon R. Phillpot

Faculty Publications

We employ density functional theory calculations to investigate the energetics and diffusion mechanisms of alkali metal ions (Na⁺, K⁺, Rb⁺, and Cs⁺) within the analcime framework. While Na⁺preferentially adsorbs at the center of the 8-member ring, DFT calculations show that larger ions, such as Cs⁺, occupy the center of the cage due to steric constraints. The computed exchange energies indicate that exchange of Na⁺by Cs⁺is thermodynamically favorable. Migration energy barriers, determined using the climbing image nudged elastic band method, show that Na⁺is …

Self-Assembling Rna Nanostructures Are Highly Sensitive To Environmental Conditions, Jordan Aposhian, Surya Pratap S. Deopa, Scott Horowitz, Joseph D. Yesselman

Chemistry and Biochemistry: Faculty Scholarship

Recent developments in RNA nanotechnology have led to an increase in the design of specific, higher-order RNA structures, which will ultimately be used in drug delivery and immunomodulation applications. As researchers create RNA nanostructures with the intention of making them a standard tool in molecular biologists' toolkits, further investigation is required into the robustness of RNA designs. Primarily, in what different molecular contexts are the designed and intended nanostructures stable? In this work, we show that RNA nanostructure self-assembly is highly sensitive to environmental conditions by using second-order right-angle light scattering. While a test RNA hexagonal grid nanostructure forms correctly …

Design, Synthesis And Biological Activities Of N-Substituted Phthalimide Derivative, Beaula Mangundah

Honors Theses

Phthalimides are a group of compounds among bicyclic non-aromatic nitrogen heterocycles that have gained recognition for their bioactivity across various fields, notably anti-cancer, anti-microbial, anti-oxidant, and anti-inflammatory. This study discusses the synthesis of a novel phthalimide derivative and provides an analysis of its biological activity. It was conducted through a Boric acid Imide synthesis and yielded a successful derivative using hexylamine. The product was evaluated in vitro for antimicrobial, anticoagulant, and anti-inflammatory properties using Kirby-Bauer disk diffusion, clotting time, hemolysis inhibition, and protein denaturation assays. It showed mild anticoagulant and anti-inflammatory activity.

Geometric And Proximity Based Substrate Targeting By Cullin-Ring Ligases, Jerry Li

UNLV Theses, Dissertations, Professional Papers, and Capstones

Homeostasis, the process of maintaining stable biochemical and biophysical conditions, is a fundamental facet of cellular viability. Biochemical homeostasis is critical to support the biological functions that sustain living organisms. Protein ubiquitylation is one of the primary cellular pathways that regulate protein homeostasis and turnover. Ubiquitylation is initiated through the conjugation of a small globular protein known as ubiquitin, onto a given substrate. There exists a myriad of cellular fates that ubiquitylated proteins may undergo, but the most widely studied pathway is protein degradation, whereby a ubiquitylated protein substrate is shunted to a large macromolecular protease known as the proteasome, …

Book Of Abstracts, Seton Hall University

2025 Augustine Undergraduate Research Symposium

No abstract provided.

Engineered Multifunctional Drug-Loaded Dendrimer Nanoparticles For Glaucoma: Triple Mechanism Via Antioxidant Activity, Iron Chelation, And Enhanced Ocular Transport, Burhan Ates, Ashish Trital, Vimalin Jeyalatha Mani, Lei Xu, Jonathan Kenlee, Nuran Ercal, Hu Yang

Chemistry Faculty Research & Creative Works

In this study, we developed multifunctional nanoparticles based on polyamidoamine (PAMAM) dendrimers functionalized with caffeic acid (CA) and poly (ethylene glycol) maleimide (PEGM) for the topical delivery of hydrophobic antiglaucoma drugs brimonidine (BM) and betaxolol (BX). The PAMAM-CA and PAMAM-CA-PEGM conjugates exhibited antioxidant and iron-chelating activities in a dose-dependent manner. BM- and BX-loaded dendrimer nanoparticles produced using a multi-inlet vortex mixer showed uniform spherical morphology (∼80 nm by TEM) and hydrated sizes of ∼135-144 nm by DLS. Both nano formulations demonstrated high cytocompatibility with human corneal epithelial cells and were nonirritant in the HET-CAM assay, with PEGM further improving cytocompatibility. …