Chemistry Commons^™

Increased Backbone Rigidity Of Artificial Transcription Factors, Jasmine Glover, Emma Otey, Joanna K. Kwao, Nicholas Truex

Senior Theses

Programming DNA-binding proteins is an effective strategy for developing therapeutics that regulate gene expression. These proteins can directly bind to DNA to activate or repress transcription of specific genes. Zinc finger proteins are a class of DNA-binding proteins commonly found in eukaryotic organisms. Their DNA-binding function is derived from unique amino acid sequences within each domain that recognizes specific nucleotides, allowing each finger to selectively recognize three DNA base pairs. Adjoining of multiple domains in tandem allows recognition of a specific DNA sequence. Artificial transcription factors can be made of multiple zinc finger domains arranged in tandem and engineered to …

Design And In Silico Modeling Of Heterocyclic-Based Xanthone Derivatives As Potential Anticancer Agents Through Tyrosine Kinase Inhibition, Yehezkiel Steven Kurniawan, Ervan Yudha, Nela Fatmasari, Radite Yogaswara, Harno Dwi Pranowo, Eti Nurwening Sholikhah, Jumina Jumina

Makara Journal of Science

Cancer is one of the deadliest diseases nowadays, and tyrosine kinase receptors play crucial roles in cancer cell survival, differentiation, proliferation, and migration. This study designed and developed a new inhibitor from heterocyclic-based xanthone derivatives to target two tyrosine kinase receptors, epidermal growth factor receptor (EGFR) and platelet-derived growth factor receptor (PDGFR), through in silico screening. Eighteen heterocyclic-based xanthones were evaluated through molecular docking for both receptors. All heterocyclic-based xanthones gave the root mean square deviation (RMSD) value lower than 2.00 Å. Xanthone with isobenzothiazole substituent (iBzThio) was found as the most potent inhibitor with binding energies of -10.60 and …

Interview With Orca Award Winner David Hage, Unl Chemistry; Drug-Protein Interactions, Mark Griep, David Hage

UNL ORCA Interview Series

Prof. David Hage was awarded the ORCA in 2018. He was born in La Crosse, Wisconsin, and earned a bachelor’s in chemistry at the University of Wisconsin in La Crosse. Next, he earned a doctorate from Iowa State University and did postdoctoral work at the Mayo Clinic in Rochester, Minnesota. In 1989, he joined UNL as an assistant professor of chemistry and quickly rose through the ranks. He has won many awards and, for the past 13 years, has been the James Hewet University Professor of Chemistry. Allow me to share some remarkable facts about Dave before we get into …

Role Of Wadsley Defects And Cation Disorder To Enhance Monb12O33 Diffusion, Cj Sturgill, Manish Kumar, Nima Karimitari, Iva Millisavljevic, Coby S. Collins, Aaron Hegler, Hsin-Yun Joy Chao, Santosh Kiran Balijepalli, Scott T. Misture, Christopher Sutton, Morgan Stefik

Faculty Publications

Wadsley-Roth (WR) niobates have emerged as high-rate anode materials that can combine rapid ionic diffusion with good electronic conductivity. WR compounds have been defect-enhanced by limited annealing, however, such materials often contain multiple types of defects. In particular, both Wadsley defects (variable block size) and transition metal disorder have the potential to modify transport rates, however the corresponding effects are not well understood mechanistically. Here, MoNb12O33 (MNO) was calcined at two different temperatures to compare a defect-rich condition (MNO-800) with a proximal order-rich condition (MNO-900) as assessed through XRD, XANES, EXAFS, and STEM characterizations. Galvanostatically cycled lithium half cells of …

Main-Chain Ion-Pair Polybenzimidazole Membranes Enabling Reduced-Temperature Ht-Pemfc Operation (Down To 120°C), Huina Lin, Brian C. Benicewicz

Faculty Publications

Proton exchange membrane (PEM) fuel cells are promising for clean and efficient energy conversion across diverse applications. High-temperature PEM fuel cells (HT-PEMFCs) using phosphoric acid (PA)-doped polybenzimidazole (PBI) can operate up to 200°C, but at lower temperatures, water-induced PA loss often leads to performance degradation and reduced durability. In this work, we present a new class of main-chain ion-pair PBI membranes by integrating the imidazolium-biphosphate ion-pair units directly into the PBI backbone. This design results in membranes with high acid content, stronger acid-polymer interactions and stabilized acid retention. In single-cell tests, the Im⁺-PBI15-3 wt.% exhibits peak power densities …

College Of Natural Sciences 2025 Year-End Publication, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Page 2 Dean's Message 
Page 3 Department Highlights 
Page 4 One Day for State 
Page 5 Ice cores reveal volcanic eruptions in 13th century 
Page 5 How do our cells interpret stress 
Page 6-7 Faculty Excellence
Page 8 New chemical biology consortium will accelerate cancer research
Page 9 SDSU to combat crop disease, biofilms in new NSF-back project 
Page 9 Science as Art Competition 
Page 10-11 Student Excellence  
Page 12 SDSU researcher developing natural alternative to synthetic dyes
Page 12 Browning Retired
Page 13 Quantum technologies through NSF-backed project
Page 13 NASA Funds CNS Development of Model
Page 14 GGS …

Exosome Engineering For Blocking Gut Dysbiosis And Inducing Cell Death Mechanisms In Glioblastoma Multiforme, Ahalya Muraleedharan, Karthik Rangavajhula, Swapan K. Ray

Faculty Publications

Glioblastoma multiforme (GBM) is the most lethal primary brain tumor in adults. Emerging evidence endorses that gut dysbiosis contributes to GBM progression through the gut–brain axis (GBA), promoting inflammation and therapeutic resistance via abnormal short-chain fatty acid production and cytokine dysregulation. Exosomes, naturally occurring nanovesicles (30–150 nm), offer promising therapeutic potential due to their blood–brain barrier permeability, biocompatibility, and versatile cargo capacity. This review examines exosome engineering strategies for dual targeting: inhibiting alterations in gut microbiome and inducing regulated cell death mechanisms such as apoptosis and ferroptosis in GBM. We describe exosome engineering with detailed focus on cargo loading approaches …

Rapid Single-Cell Measurement Of Transient Transmembrane Water Flow Under Osmotic Gradient, Hong Jiang, Jinnawat Jongkhumkrong, Y. J. Chao, Qian Wang, Guiren Wang

Faculty Publications

Aquaporins (AQPs) are critical for transmembrane water transport in response to osmotic gradients, but their gating and regulatory mechanisms remain poorly understood. A central challenge is the lack of methods to measure water flow across AQPs from individual cells with the spatiotemporal resolution and sensitivity equivalent to patch-clamp recordings of ion fluxes—a limitation stemming from the electrically silent nature of water flow. Here, we present a novel optical technique—Flow-Induced Fluorescence Increase Velocimetry (FIFIV) based on Laser-Induced Fluorescence Photobleaching Anemometry (LIFPA)—that enables direct, real-time monitoring of cytoplasmic flow induced by transmembrane water transport under osmotic pressure gradients. Using small molecular fluorescent …

Plants Have A Chemical Defense To Protect Themselves From Herbivory, Isis Cordova

Research on Capitol Hill

All plants produce compounds for survival. My work focuses on how plants remember past attacks and whether that memory leads to stronger/faster responses.

The Structure, Pathogenesis, And Inhibition Of The P53-Mdm2 Pathway, Amanda L. Brown, Xiaoying Lian, Qian Wang

Faculty Publications

The p53 tumor suppressor protein plays a central role in maintaining genomic stability by regulating cell cycle arrest, apoptosis, and DNA repair under cellular stress. Mouse double minute 2 (MDM2), an E3 ubiquitin ligase, negatively regulates p53 via direct binding and proteasomal degradation. Overexpression or amplification of MDM2 can disrupt this pathway and promote tumorigenesis, even in cancers with wild-type p53. This review outlines the structural features of MDM2, particularly its N-terminal hydrophobic pocket and C-terminal RING domain, and their roles in p53 regulation. We further examine the pathological effects of MDM2 dysregulation and SNPs linked to increased cancer risk. …

Ecologic Factors Contributing To West Nile Virus Hyperendemicity In Central South Carolina: An Integrated Vector–Human–Environmental Study, Elba S. Fridriksson, Ahayla Muraleedharan, Kyndall C. Dye-Braumuller, Madeleine M. Meyer, Kia Zellars, Hiuxuan Li, Melissa S. Nolan Ph.D., Mph

Faculty Publications

West Nile virus (WNV) is an endemic arboviral infection in the United States that has undergone phyloge-netic evolution since its introduction 25 years ago. An integrated vector–human–pathogen study was conducted in the summer of 2023 to unearth contemporary Culex quinquefasciatus habitat patterns and human transmission spillover foci in South Carolina, a state with historically little WNV data. A serosurvey revealed WNV seroprevalence 10 times the national average (22% versus 2%, respectively), with unusual epidemiologic risk factors. Female Culex quinquefas-ciatus WNV positivity was low (2.7%), with viral phylogenetics 100% homologous to the WN02 clade. Mosquito vectors clustered in affluent urban neighborhoods …

Boronate Esters For The Binding And Detection Of Low Molecular Weight Volatile Amines, Xiaoning Li, James Boyt, Steven Sloope, Luke T. Lackovic, Mark D. Smith, James J. Lavingne

Faculty Publications

Conjugated thiophene-based diboronate esters, 1–4, were synthesized to investigate how substituents on catechol alter the Lewis acidity and accessibility to boron, and influence binding interactions with low molecular weight Lewis basic amines. Crystallographic analysis indicated that both boron centres bind analyte and that Lewis base coordination induces deplanarization of the conjugated system. Spectroscopic studies demonstrate that amine binding disrupts conjugation, producing distinct and reproducible optical responses that depend on analyte basicity and structure, with association constants in organic solvent ranging from 10³ to 10⁶ M⁻¹. Quantitative binding analyses indicate strong negative cooperativity between the two boron …

Impact Of Iron-Bearing Fillers On The Mechanical Strength And Chemical Stability Of Magnesium Potassium Phosphate Matrices Incorporating Rhenium, Sergey Sayenko, Volodymyr Shkuropatenko, Hans Conrad Zur Loye, Petr Vecernik, Monika Kiselova, Vlastislav Kašpar, Vlastimil Miller, Petr Bezdicka, Jan Šubrt, Petra Ecorchard, Natalija Murafa, Iva Milisavljevic, Scott T. Misture

Faculty Publications

We report on the study of the immobilization process of non-radioactive rhenium (Re), a chemical analogue of technetium-99 (⁹⁹Tc), in compounds based on magnesium potassium phosphate (MKP), as well as the possibility of enhancing their properties with iron-bearing additives/fillers. Powdered Re2O7 was used as the initial Re-containing source. Because of the solubility and high leachability of Tc (VII), which is also volatile at high temperatures, its immobilization for long-term storage and disposal poses a serious challenge to researchers. Taking this into account, low-temperature stabilization technology based on MKP, a cementitious material, is currently considered promising. We prepared experimental …

Monosaccharide Binding To Synthetic Carbohydrate Receptor Microarrays, Milan A. Shlain

Dissertations, Theses, and Capstone Projects

Chapter 1: A glycan detection platform comprised of synthetic carbohydrate receptors (SCRs) immobilized onto polymer brushes was prepared. SCR043, an alkene-containing SCR, was incorporated into grafted-from polymer brushes using hypersurface photolithography, resulting in microarrays of SCR043-functionalized polymer brushes, where brush height (h) and SCR grafting density (Γ) is controlled precisely at each feature in the array. The influence of h and Γ on the binding to five fluorescently labelled monosaccharides – α-glucose (α-Gluc-FL), α-galactose (α-Gal-FL), α-mannose (α-Man-FL), β-glucose (β-Gluc-FL), and β-galactose (β-Gal-FL) – in aqueous buffer …

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 …

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 …

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, …

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 …