Chemistry Commons^™

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 …

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 …

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 …

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 …

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 …

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 …

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 …

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.

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 …

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 …

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 …

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 …

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.

Book Of Abstracts, Seton Hall University

2025 Augustine Undergraduate Research Symposium

No abstract provided.

Buffer Vs. Swabs: Efficacy Of Carrier Nucleic Acids In Robotic Extractions, Shawn Cecil

Honors Projects

This study compared the efficiency of two carrier nucleic acid methods, specifically using salmon sperm DNA (spDNA), in robotic solid-phase extractions of cotton swab samples. Robotic extractions reduce processing time and workload but result in substantially lower DNA recovery than manual organic extraction. This research tested 10 µg of spDNA being added to the lysis buffer or pre-treating the swabs with it before DNA was added. Both methods showed a significant increase in recovery compared to extractions with no carrier. In the buffer extractions, recovery ranged from 69.4% to 117.5% and the swabs being pre-treated ranged from 84.2% to 125.8% …

Flux Crystal Growth Of A Series Of Calcium Rare Earth Silicate Chlorides Calnsio4Cl (Ln = Pr, Nd, Sm, Eu, Gd, And Tb): Mixed Anion Materials With A Spodiosite-Type Structure, Maria Goncalves, Mark D. Smith, Hans Conrad Zur Loye

Faculty Publications

A series of calcium rare earth silicate chlorides, CaLnSiO4Cl (Ln = Pr, Nd, Sm, Eu, Gd, and Tb), was obtained as single crystals from flux crystal growth. The structures were determined by single crystal X-ray diffraction and were found to be related to the spodiosite/Wagnerite mineral structure, Ca2PO4F. The obtained compositions are variations of the spodiosite structure that result from two simultaneous elemental substitutions. Replacing one calcium for one rare earth element and the simultaneous replacement of one VO4³⁻ or PO4³⁻ with one SiO4⁴⁻. CaEuSiO4Cl was found to luminesce, and its photoluminescence spectrum is reported.

Water Circulation Beneath A Hovering Suas For Water Quality Monitoring Applications, Erin E. Hackett, Boone Fleenor, Jensine C. Coggin, Duvall Dickerson-Evans, Nikolaos Vitzilaios, Whitney E. Schuler, Paige K. Williams, Michael L. Myrick

Faculty Publications

Water quality has traditionally been measured via in situ sensors and satellites. The latter has limited applicability for smaller inland water bodies, while the former requires significant logistics, labor, and expense for routine sampling, and reactive/spurious sampling is often not feasible as a result (e.g., sampling pre-/post-storm). Consequently, small uncrewed aircraft system-based (sUAS-based) sampling has emerged as a potential solution to bridge these sampling gaps and challenges. But sampling from an sUAS is complicated by the need to pump water from depth, rather than suspending a sensor from the sUAS, due to concern over sampling sUAS-impacted waters. Here, we measure …

Thermodynamic Assessment Of The Li, Na, K, Cs | F, I Reciprocal Salt For Msr Applications, Clara M. Dixon, Mina Aziziha, Amir Mofrad, Jorge Paz Soldan Palma, Ronald E. Booth, Aiswarya Padinhare Manissery, Jack A. Wilson, Hans Conrad Zur Loye, Hunter B. Tisdale, Juliano Schorne-Pinto, Theodore M. Besmann

Faculty Publications

Gibbs energy models necessary to describe the thermochemical behavior of cesium and iodine in molten FLiNaK (46.5LiF-11.5NaF-42KF mol%), a proposed molten salt reactor coolant and fuel solvent, have been developed as they are of concern due to their high radiotoxicity and volatility. The six constituent pseudo-binary systems LiI-CsI, LiI-KI, LiI-NaI, NaI-KI, KI-CsI and NaI-CsI were evaluated using available phase equilibria and mixing enthalpy measurements. The models for the ternary reciprocal salt systems Li,Cs|F,I, Li,K|F,I, Li,Na|F,I, Na,K|F,I, Na,Cs|F,I and K,Cs|F,I were obtained by interpolation of the optimized pseudo-binary systems and parameters fit as necessary based on observed behavior. The additive (common …

Tracing The Journey Of Dissolved Organic Matter: From Leaf Litter Photodegradation To Microbial Processing In Tropical Streams, Samantha Nicole Sullivan

Chemistry & Biochemistry Theses & Dissertations

Dissolved organic matter (DOM) is a major reservoir of organic carbon in aquatic ecosystems and plays a central role in global carbon cycling through its transformation and remineralization to carbon dioxide (CO₂). As DOM moves from terrestrial environments into streams and rivers, its chemical composition is altered by a combination of microbial and photochemical oxidation processes that regulate both its reactivity and its persistence during transport. However, the molecular mechanisms governing these oxidative transitions, particularly in tropical ecosystems characterized by strong hydrologic seasonality and substantial inputs of plant-derived material, remain insufficiently resolved. This dissertation integrates ultrahigh-resolution mass spectrometry, optical characterization, …

Electrochemical Breath Sensors In Medical Diagnostics: Emerging Trends And Future Directions, Natalie E. Strom, Courtney J. Weber, Olja Simoska

Faculty Publications

With the rising prevalence of metabolic diseases, infections, and mental health disorders, there is a growing demand for noninvasive diagnostic tools that enable early detection and continuous health monitoring. In this context, exhaled breath biomarkers provide insight into physiological and pathological processes. Electrochemical breath sensors (EBSs) have emerged as a promising platform for rapid, real-time, and cost-effective disease tracking via the detection of volatile breath biomarkers, such as NH₃, NO, and CO₂. Recent advancements in electrode materials, biological recognition elements, and sensor architectures—spanning nanomaterials, enzymes, aptamers, and molecularly imprinted polymers—have enhanced the analytical performance of EBSs. …

Electrochemical Breath Sensors In Medical Diagnostics: Emerging Trends And Future Directions, Natalie E. Strom, Courtney J. Weber, Olja Simoska

Faculty Publications

With the rising prevalence of metabolic diseases, infections, and mental health disorders, there is a growing demand for noninvasive diagnostic tools that enable early detection and continuous health monitoring. In this context, exhaled breath biomarkers provide insight into physiological and pathological processes. Electrochemical breath sensors (EBSs) have emerged as a promising platform for rapid, real-time, and cost-effective disease tracking via the detection of volatile breath biomarkers, such as NH₃, NO, and CO₂. Recent advancements in electrode materials, biological recognition elements, and sensor architectures—spanning nanomaterials, enzymes, aptamers, and molecularly imprinted polymers—have enhanced the analytical performance of EBSs. …

A New Low-Rate Stable Hydrogel Cathode For Aqueous Zn-Ion Batteries, Roya Rajabi, Shichen Sun, Jamil A. Khan, Morgan Stefik, Kevin Huang

Faculty Publications

Aqueous Zn-ion batteries (ZIBs) are attractive candidates for large-scale energy storage owing to the abundance, low cost, and intrinsic safety of Zn metal. However, their practical application is hindered by poor cycle stability, especially at low current densities, due to cathode dissolution and limited electrochemically active sites (EAS). Herein, a hydrogel-based cathode comprising ammonium vanadate, carbon black, and a Zn-ion-conducting carboxymethyl chitosan–acrylamide hydrogel matrix doped with Zn(ClO4)2 is reported. This design establishes a continuous Zn-ion-conducting network, thereby maximizing EAS density throughout the electrode volume. The ZIB with the hydrogel cathode exhibits outstanding cycling stability, with 77% capacity retention after 2000 …

Pathlength, Altitude And Angle Of Incidence Dependence Of Remote Water Raman Scattering, Whitney E. Schuler, Paige K. Williams, Zechariah B. Kitzhaber, Caitlyn M. English, Tammi L. Richardson, Nikos Vitzilaios, Michael L. Myrick

Faculty Publications

A small remote Raman sensor was used to measure the Raman scattering signal from clear, still water as a function of water depth (12 cm and 396 cm depth), sensor distance above the water surface (20–300 cm), and angle of incidence (0–80°) to the normal of the water surface. Under thick- and thin-sample conditions, the signal depends on either the inverse, or the inverse square, of sensor distance from the water surface, respectively. A model is derived that fits data for different sensor distances, water depths, and angles of incidence. Fits to the measured data are consistent with the known …

Adipose Tissue Estrogen Receptor-Alpha Overexpression Ameliorates High-Fat Diet–Induced Adipose Tissue Inflammation, Marion C. Hope, Christian A. Unger, M. Chase Kettering, Cassidy E. Socia, Ahmed K. Aladhami, Barton C. Rice, Darya S. Niamira, Ben P. Wiznitzer, Diego Altomare Ph.D., William E. Cotham, Reilly T. Enos

Faculty Publications

Context

We created an innovative mouse model that enables inducible overexpression of estrogen receptor-alpha (ERα), specifically in adipose tissue (Adipo-ERα↑). Objective

We aimed to investigate how elevated Adipo-ERα↑ influences the development of high-fat diet (HFD)-induced obesity in both male and female mice. Methods

Male and female Adipo-ERα↑ mice and littermate controls were fed a low-fat diet (LFD) or HFD for 13 weeks. Adipo-ERα↑ was induced at the initiation of dietary treatment. Body morphology and composition, hepatic lipid accumulation, glucose tolerance, fasting insulin concentrations, and adipose tissue mRNA profiling were assessed. Liquid chromatography–mass spectrometry was used to determine circulating and adipose …

Pentanary And Hexanary Alkali Lanthanide Germanates Grown From Lanthanide Rich Flux Growth Reactions, Gregory Morrison, K. Pilar Zamorano, Virginia G. Jones, Ethan N. Adams, Hans Conrad Zur Loye

Faculty Publications

Single crystals of five compounds of a new structure type, the K3Nd52Ge12O100F7 type, were grown from lanthanide rich reactions using a KF/KCl flux: K3Ln52Ge12O100F7 (Ln = Nd, Eu), K3Ln52Ge12O100+δF7-δ (Ln = Pr, Tb), and K3Ca0.872Nd51.128Ge12O99.128F7.872. The five compounds crystallize in the cubic space group I-43d with lattice parameter 22.0350(2) Å for K3Nd52Ge12O100F7. The structure consists of a 3D checkerboard of LnX8, LnX7, LnX6, and GeO4 polyhedra, where X = O/F, and can be conceptually derived from the fluorite structure. K3Eu52Ge12O100F7 exhibits the fluorescence typical of Eu³⁺.

Chemistry And Biochemistry Affiliated Publications: Snapshot Of The Research Publications 2019-2024., Jeremy J. Smith, Lutishoor Salisbury

University Libraries Faculty Publications and Presentations

This report highlights the chemistry and biochemistry faculty publications for the period 2019-2024. It includes tables identifying the types of publications, the characteristics of the authors, inter-departmental and external cooperation, summary of the citations of the publications, and the JCR ranking of the journals in which they published.

Data From: Nek4 Suppresses Cell Proliferation In Bt20 Triple-Negative Breast Cancer Cells By Diminishing Expression Of Cell Cycle Genes, While Its Depletion Mitigates Proliferation In Other Cell Lines, Amanda Ashley

Chemistry & Biochemistry: Datasets

No abstract provided.