Chemistry Commons^™

Reply To Bratchenko And Bratchenko, “Overestimation Of The Classification Model For Raman Spectroscopy Data Of Biological Samples”, Xin Ru Wen, Jia-Wei Tang, Liang Wang

Research outputs 2022 to 2026

No abstract provided.

Chalmers Library Research Award Winner 1 2025, Tasnim Islam Orco

Chalmers Library Research Award

No abstract provided.

Utilizing Drainage Induced Pfas Enrichment In Cascade Generated Foam For Efficient Removal At Wastewater Treatment Plants, Ethan Samuel Coffin

Dissertations

Observed trends in municipal solid waste landfills reveal a distinct disparity between per- and polyfluorinated alkyl substances (PFAS) composition entering in waste, mostly as diPAP and FTOH, and leaching out as FTCA and PFCA. These patterns are elucidated by compiling PFAS compositions in paper, textiles, and carpet, with known precursor transformations that generate FTCA and PFCA in leachate. Landfill leachate is commonly discharged to wastewater treatment plants (WWTP), which are ineffective at degrading PFAS and only serve as key conduits and discharge points for PFAS to the environment. Foam fractionation has been identified as a promising technology for concentrating and …

Expanding The Lexa Bacterial Two-Hybrid System For Human Protein-Protein Interaction Screening: Application To Tumor Suppressor Par-4, Rebecca M. Richardson

Chemistry & Biochemistry Theses & Dissertations

Protein-protein interactions (PPI) are fundamental to cellular function, influencing processes such as signaling, structural organization, and disease progression. Disruptions in PPIs are implicated in cancer and neurodegenerative diseases, highlighting their importance as therapeutic targets. However, traditional methods for studying human PPIs, such as yeast two-hybrid and co-immunoprecipitation mass spectrometry, are costly and technically demanding. This dissertation explores the LexA-based bacterial two-hybrid (LexA-B2H) system as a cost effective and accessible alternative for investigating human PPIs.

This study focuses on the interaction between glucose-regulated protein 78 (GRP78) and cleaved prostate apoptosis response-4 (cl-Par-4), a tumor suppressor protein involved in apoptosis and neurodegenerative …

Mechanochemical Reaction Kinetics—A Theoretical Modeling And Experimental Study, Maria Dolores Masso Ramirez

Mechanical & Aerospace Engineering Theses & Dissertations

Mechanochemical reactions represent a class of chemical processes triggered by mechanical energy, widely recognized for their efficiency, solvent-free nature, and environmental benefits. They are increasingly applied in synthetic chemistry, a branch of science focused on creating new chemical compounds through controlled laboratory reactions. However, the mechanisms underlying mechanical activation remain poorly understood, primarily due to the difficulty in quantifying energy transfer during milling, where solid reactants are ground together using a ball mill. This thesis aims to bridge the gap in understanding the relationship between mechanical parameters and reaction kinetics by developing and validating a theoretical framework based on dimensional …

Kinetic Control And Trapping In The Supramolecular Polymerization Of M-Terphenyl Bis-Urea Macrocycles, Sophya V. Garashchuk, Gamage Isuri P. Wijesekera, Isabella G. Rushton, Vaibhavi A. Samant, Fahidat A. Gbadamosi, Dr. Md Faizul Islam, Sophya V. Garashchuk, Prof. Dr. Linda S. Shimizu

Faculty Publications

Herein, we examine pathway complexity in the supramolecular polymerization of a novel m-terphenyl bis-urea macrocycle. Designed to induce kinetically metastable states, the macrocycle‘s concentration-dependent aggregation was studied via 1H NMR and IR spectroscopy in THF and CHCl₃. Temperature-dependent UV-Vis spectroscopy in water/THF revealed a cooperative nucleation-growth mechanism, indicated by a shift in λmax to longer wavelengths upon cooling. Morphological studies using DLS, AFM, and SEM demonstrated fibrous aggregate formation. Thermal hysteresis observed in assembly-disassembly cycles indicated kinetically trapped species, with cooling governed by kinetic control and heating by thermodynamic processes. Deviations in ΔH values during cooling, compared to van′t …

Click-Based Synthesis Of Hemibastadin Derivatives And Their Applications As Antimicrobial And Biofilm Inhibiting Agents, James B. Daniel Iii

Longwood Senior Thesis Proposal

Antimicrobial agents are one of the most important tools used in the medical industry. With the ever growing numbers of antibiotic resistant bacteria, new strategies have been developed to combat them, one of which being biofilm inhibiting agents. A class of molecules called hemibastadins, first discovered from sea sponges, have been of recent interest in the field. Building from previous work done in this lab on hemibastadins, a hemibastadin derivative containing a triazole in place of the oxime has been identified as a potential antibiofilm agent. This work will target a derivative that will more closely mimic the hemibastadins found …

College Of Natural Sciences Newsletter, Spring 2025, College Of Natural Sciences

College of Natural Sciences Newsletters and Reports

Page 1 Dean's Message from Dr. Sen Subramanian
Page 2 Student Spotlights
Page 3 Kaushik honored, Three-Minute Thesis, & Ice Cores revealed
Page 4 Alumni Spotlight
Page 5 Day of Scholars
Page 6 Cyanide research, Record Research Expenditures, Adhikari awarded Miller Research Award
Page 8 Hanson Receives NSF Grant
Page 9 Snow Lab Research Team
Page 10 Faculty Awards
Page 11 Drone Day
Page 13 Khalaf Awarded Presidential Award

Quantum Effects In Collisional Energy Transfer Simulated Using Mixed Quantum/Classical Theory, Dulat Bostan

Dissertations (1934 -)

Mixed quantum/classical theory (MQCT) was used to study collisional energy transfer between the rotational states of molecules with the focus on reproducing quantum effects related to this process. Namely, rotational energy transfer in the N₂ + O system was studied to replicate quantum interference effects observed as oscillations of scattering cross section as a function of collision energy. Both MQCT code and the full-quantum code MOLSCAT were used for calculations, and results were in excellent agreement with the experiment and the full-quantum infinite-order sudden method from literature. The CO + CO system was used as a case study for …

Computational Investigation Of The Chemical Bond Between An(Iii) Ions And Soft-Donor Ligands, Naomi E. Rehberg

Honors Thesis

The nature of chemical bonding of actinide metal ions with arene and borohydride ligands is investigated through quantum chemical methods to understand how the transuranium elements differ from uranium with respect to their interaction with soft-donor ligands. Specifically, this study examines [An(arene)(BH₄)₃] complexes (An^Me₆; An = Np, Pu, U, arene = C₆Me₆). Density functional theory (DFT) shows that, when the complexes are neutral, electrostatic interactions dominate the interaction between the metal ions and the soft-donor ligands. Molecular orbital analysis, with both the DFT and the complete active space …

Next-Generation Biomedical Implants And Stimuli Responsive Soft Optical Arrays Via Surface Functionalized Elastomeric Materials, John M. Kapitan

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

The demands of emerging technologies, such as soft robotics, stretchable electronics, and next generation biomedical implants, has led to the development of diverse polymeric and hybrid organic/inorganic materials specifically tuned to meet these challenges. These materials typically have low Young’s moduli and are inert with high chemical stability. However, this has led to materials that are static in nature, lacking any meaningful way of responding to changes in their environment and adapting to these changes. This has driven a shift towards the design, manufacturing, and characterization of various stimuli responsive surfaces, relying on precise control of surface chemical coatings and …

Experimental And Computational Investigation Of Ethylene Oxide Hydrate And Its Mixed Hydrates With Propane And Isobutane, Adebayo Paul Adeleye

Master's Theses (2009 -)

Gas hydrates represent an important class of crystalline solids, where water molecules form cage-like frameworks that encapsulate gas molecules. They have garnered significant attention for their unique properties and diverse applications in energy and environmental science. This study investigates the formation and vibrational properties of the ethylene oxide (EO) hydrate (structure I, sI) and EO-seeded hydrates of propane and isobutane (structure II, sII) using matrix isolation Fourier-transform infrared (FTIR) spectroscopy, supported by Density Functional Theory (DFT) calculations at the B3LYP/6-311++G(d,p) level of theory. Under low-temperature and low-pressure conditions, EO hydrate was formed by co-depositing a premix of EO and argon …

Synthetic And Mechanistic Investigations Of Ruthenium Catalyzed Coupling Reactions Via C−C And C−N Bond Activation, Aldiyar Shakenov

Dissertations (1934 -)

Transition-metal catalyzed C-N and C-C bond activation reactions are synthetically valuable reactions for selective and atom-economical synthesis of complex organic molecules. Catalytic reactions that involve activation of unreactive bonds are important for the stereoselective synthesis of molecular scaffolds from readily available substrates derived from bio-mass feedstock. Despite these advances, designing a broadly applicable catalytic method faces challenges of selectivity and harsh reaction conditions. A five coordinate Ru-H complex was found to be an effective catalyst for promoting the multicomponent deaminative coupling reaction of anilines, aldehydes and tertiary amines to selectively afford 2,3-disubstituted quinoline products. The scope of the reaction was …

Discovery And Synthesis Of Novel, Porous Organic Cages Via Dynamic Imine Chemistry In Continuous Flow, Anzhi (Andy) Chen , '25

Senior Theses, Projects, and Awards

In recent years, Porous Organic Cages (POCs) have gained widespread research interest owing to the well-defined porosity and solution dispersity, which have given rise to various applications, such as molecular encapsulation and catalysis. A common synthetic strategy for POCs, Dynamic Covalent Chemistry (DCvC) exploits the reversibility of certain covalent reactions and allows for facile discovery and synthesis of well-defined macromolecules through error-correction mechanisms. Thermodynamic effects of DCvC systems have been widely studied via structure-focused strategies along with empirical methods. More recently, researchers have begun to incorporate kinetic factors in DCvC systems to discover and synthesise new macromolecular structures. However, thermodynamic …

Development Of An Alpha-Diimine Aluminum Catalyst For Atom Transfer Radical Polymerization, Mairo Yamano , '25

Senior Theses, Projects, and Awards

Aluminum is an attractive metal in developing novel homogeneous catalysts due to its natural abundance, low cost, and benign environmental impact. The Graves group has been investigating its chemistry by developing metal complexes with redox non-innocent ligands. Thus, the previously reported (LMes ^2- )AlCl(THF) (L_Mes = N,N′-bis[2,4,6-trimethylphenyl]-2,3-dimethyl-1,4-diazabutadiene) will be investigated as a potential atom transfer radical polymerization (ATRP) catalyst. Using gel permeation chromatography and ¹H-NMR spectroscopy, this study investigates a model ATRP system of methyl methacrylate (MMA) with (L_Mes^2- )AlCl(THF). The dependence of polymerization outcomes on several reaction parameters was tested. In addition, a time-resolved polymerization …

Effects Of High Temperature Compaction On 3d Printed Carbon Fiber Reinforced Polymer Composites, John D. Barber

Mechanical & Aerospace Engineering Theses & Dissertations

The aim of this dissertation was to study the effects of hot temperature compaction (HTC) upon the polymorphism and the mechanical behavior of an additively manufactured (AM), carbon fiber reinforced polyamide (PA6). Different pressure and temperature levels during HTC were tested to determine the overall effect upon the mechanical behavior and the material crystalline composition. Treated, carbon fiber reinforced PA6 samples were analyzed using differential scanning calorimetry, x-ray diffraction, thermogravimetric analysis, scanning electron microscopy, double cantilever beam testing and three-point bending testing. When considered with respect to as-printed samples, an HTC temperature of 190°C combined with 80 psi pressure resulted …

Ancestral Sequence Reconstruction On Antibiotic-Resistance Bacteria, Jeyun Park

SACAD: Scholarly Activities

The spread of antibiotic-resistant bacteria poses a global health threat, and it is predominantly driven by enzymes that neutralize antibiotics or alter their drug targets. This study uses Ancestral Sequence Reconstruction (ASR) to explore the evolutionary history of a key bacterial enzyme that plays a role in antibiotic resistance. Protein sequences were aligned, and a phylogenetic tree constructed utilizing MEGA 11. Ancestral sequences are predicted to identify the conserved regions that are essential for enzyme function. Understanding these conserved locations provides insights into potential drug targets for developing new drugs against resistant strains of bacteria.

Optimizing Transcription Efficiency Through Mutations In The T7 Rna Polymerase, Claire N. Novak

Honors Program: Senior Projects (Public)

The production of RNA is vital for many commercial and research purposes, with one of the more notable reasons being vaccine production. The RNA polymerase, derived from T7 bacteriophage, is commonly used for RNA production due to its ability to produce full-length RNA transcripts. However, researchers have faced limitations in optimizing this polymerase. For example, the polymerase generates heterogeneous RNA products that require additional purification steps during RNA production. Here, we selected three amino acid point substitutions based on a recent publication from Moderna that showed increased RNA purity compared to the wild type T7 RNA polymerase sequence. We created …

Brain-Targeted Reactive Oxygen Species In Hypertension: Unveiling Subcellular Dynamics, Immune Cross-Talk, And Novel Therapeutic Pathways, Renjun Wang, Min Wang, Dongshu Du, Zhiying Shan, Lanrong Bi, Qing-Hui Chen

Michigan Tech Publications

Hypertension (HTN) is a complex disease with significant global health implications, driven by neural and oxidative mechanisms. Reactive oxygen species (ROS), once considered mere metabolic byproducts, are now recognized as one of the key contributors to dysfunction of the autonomic nerve system, which involves the onset and progression of HTN. This review highlights the dynamic roles of ROS in neuronal signaling, subcellular compartmentalization, and brain-immune interactions, focusing on their impacts on synaptic remodeling, neuroinflammation, and epigenetic modifications within key autonomic regions such as the paraventricular nucleus and rostral ventrolateral medulla. We discuss novel ROS sources, including microglia-derived and endoplasmic reticulum …

In-Situ Electrodeposition Of Feco-Mof On Au Ultramicroelectrode For Highly Sensitive Detection Of Epinephrine, Yan Chen, Shang Jian, Si-Yu Wan, Xiao-Tong Cui, Zhong-Gang Liu, Zheng Guo

Journal of Electrochemistry

Metal-organic framework (MOF) nanostructures have emerged as a prominent class of materials in the advancement of electrochemical sensors. The rational design of bimetallic MOF-functionalized microelectrode is of importance for improving the electrochemical performance but still in great challenge. In this work, the bimetallic FeCo-MOF nanostructures were assembled onto a gold disk ultramicroelectrode (Au UME, 5.2 μm in diameter) via an in-situ electrodeposition method, which enhanced the sensitive detection of epinephrine (EP). The in-situ electrodeposited FeCo-MOF exhibited a characteristic nanoflower-like morphology and was uniformly dispersed on the Au UME. The FeCo-MOF/Au UME demonstrated excellent electrochemical performance on the detection of EP …

Study On Dopamine Electrochemical Sensing Based On Au@Mos2, Ning An, Ni Su, Xin-Ran Li, Jian-Yu Liu, Qi-Yan Wang

Journal of Electrochemistry

Dopamine (DA) is a vital neurotransmitter, and accurate detection of its concentration is critical for both clinical diagnostics and neuroscience research. Due to its electrochemical activity, DA is commonly detected using electrochemical methods, which are favored for their simplicity, fast response time, and suitability for in vivo analysis. In this work, a highly sensitive DA electrochemical sensor was developed using an Au@MoS₂ composite, created by modifying molybdenum disulfide (MoS₂) nanosheets with gold nanoparticles through HAuCl₄ reduction, and it was aimed at enhancing DA adsorption and improving detection performance. Scanning Electron Microscopy (SEM), transmission electron microscopy (TEM), …

Recent Advances In Non-Enzymatic Electrochemical Sensors For Theophylline Detection, Gustria Ernis, Yulia M T A Putri, Muhammad Iqbal Syauqi, Prastika Krisma Jiwanti, Yeni Wahyuni Hartati, Takeshi Kondo, Qonita Kurnia Anjani, Jarnuzi Gunlazuardi

Journal of Electrochemistry

Detection of target analytes at low concentrations is significant in various fields, including pharmaceuticals, healthcare, and environmental protection. Theophylline (TP), a natural alkaloid used as a bronchodilator to treat respiratory disorders such as asthma, bronchitis, and emphysema, has a narrow therapeutic window with a safe plasma concentration ranging from 55.5–111.0 μmol·L^–1 in adults. Accurate monitoring of TP levels is essential because too low or too high can cause serious side effects. In this regard, non-enzymatic electrochemical sensors offer a practical solution with rapidity, portability, and high sensitivity. This article aims to provide a comprehensive review of the recent developments …

College Of Natural Sciences 2024 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 New Students in Wecota
Page 6-8 Faculty Excellence
Page 9 SDSU Physics Students Recognized
Page 9 Prairie Doc Watch Party
Page 10-11 Student Excellence
Page 11 Connections Abroad
Page 12-13 CNS’s Research Centers
Page 14 Connections Abroad
Page 14 Dean Wolf-Hall Retired
Page 15 Outreach Program
Page 15 Events and Traditions
Page 16 Student Spotlight
Page 17 Alumni Spotlight
Page 18-19 SDSU Alum at Paris Paralympics
Page 20 Work Anniversaries & Programs

Synergy In Materials: Leveraging Phosphosilicate Waste Forms For Electrochemical Salt Waste, Jonathan S. Evarts, Brian J. Riley, Charmayne E. Lonergan, Michaella S. Harris, Jincheng Bai, Eric W. Bohannan, Iheanyichukwu Ajoku, Saehwa Chong, John S. Mccloy

Materials Science and Engineering Faculty Research & Creative Works

Waste forms containing glassy and crystalline phosphate and silicate phases were produced to immobilize salt waste simulants from pyro processing and characterized by using Raman spectroscopy, Mössbauer spectroscopy, X-ray diffraction, scanning electron microscopy, heat capacity, and chemical durability measurements. In this work, a phosphosilicate waste form is presented to leverage the benefits of both borosilicate glasses and iron phosphate glasses. To improve waste loading, prior to immobilization, salt simulants were successfully dechlorinated using ammonium dihydrogen phosphate, mixed with a borosilicate frit (5–30 wt. %) and Fe2O3, and vitrified. Additions of 2.5–15 wt. % borosilicate glass (NBS3) improved normalized release rates …

A Tutorial For Scanning Electrochemical Cell Microscopy (Seccm) Measurements: Step-By-Step Instructions, Visual Resources, And Guidance For First Experiments, Kamsy Lerae Anderson, Martin Andrew Edwards

Chemistry & Biochemistry Faculty Publications and Presentations

Scanning electrochemical cell microscopy (SECCM) produces nanoscale-resolution electrochemical maps of electrode surfaces using the meniscus at the tip of an electrolyte-filled nanopipette as a mobile electrochemical cell. While the use and range of applications of SECCM have grown rapidly since its introduction, the pathway to performing SECCM measurements can be daunting to those without direct access to expert users. This work fills this expertise gap by providing a step-by-step guide to performing one's first SECCM experiments, including troubleshooting strategies, videos/images, suggested parameters and experimental systems, and representative data (of both successful experiments and common problems). No background in SECCM is …

The Mechanistic Target Of Rapamycin Mediates Clostridium Perfringens-Induced Chicken Necrotic Enteritis Attenuated By Secondary Bile Acid Deoxycholic Acid, Mohit Bansal, Tahrir Alenezi, Ying Fu, Janashrit Shrestha, Ayidh Almansour, Hong Wang, Anamika Gupta, Rohana Liyanage, Xiaolun Sun

Poultry Science Faculty Publications and Presentations

Clostridium perfringens is a prevalent gut bacterial pathogen in humans and animals. This study investigated the role of the mechanistic targets of rapamycin (mTOR) and deoxycholic acid (DCA) on C. perfringens intestinal infection. Chickens were sequentially infected with Eimeria maxima and received the mTOR inhibitor rapamycin and DCA. C. perfringens-induced necrotic enteritis (NE) was evaluated using body weight gain (BWG), histopathology, bile acids, pathogen colonization, cell infiltration and death, and gene expression. The significant difference of p < 0.05 was analyzed by one-way ANOVA and multiple comparisons. Notably, rapamycin strongly reduced the subclinical and clinical NE histopathologies. DCA and DCA combined with rapamycin alleviated clinical NE and BWG loss. Rapamycin, DCA, and DCA + rapamycin attenuated bile acid reduction in NE birds, and they also reduced immune cell infiltration into the intestinal lamina propria as well as immune cell migration in vitro. At molecular levels, DCA and DCA + rapamycin reduced proinflammatory IFN gamma, MMP9, IL23, and IL17 gene expression. Rapamycin, DCA, and DCA + rapamycin reduced NE-induced intestinal cell apoptosis. Together, these results suggest that mTOR signaling mediates C. perfringens-induced ileitis, and combining mTOR inhibition and DCA improves the intervention efficacy against NE ileitis and BWG loss.

Per- And Polyfluoroalkyl Substance (Pfas) Degradation In Water And Soil Using Cold Atmospheric Plasma (Cap): A Review, Victor Somtochukwu Mbanugo, Boluwatife Stephen Ojo, Ta Chun Lin, Yue-Wern Huang, Marek Locmelis, Daoru Han

Biological Sciences Faculty Research & Creative Works

Per- and polyfluoroalkyl substances (PFASs) are persistent organic chemicals found in numerous industrial applications and everyday products. The excessive amounts of PFASs in water and soil, together with their link to severe health issues, have prompted substantial public concerns, making their removal from the environment a necessity. Existing degradation techniques are frequently lacking due to their low efficiency, cost-effectiveness, and potential for secondary contamination. Cold Atmospheric Plasma (CAP) technology has emerged as a promising alternative, utilizing energized reactive species to break down PFASs under ambient conditions. Therefore, this review examines the efficacy and effectiveness of CAP in degrading PFASs by …

Drug Targets Illumination: An Evidence-Based Data Analytics & Informatics Approach To Hypothesis Generation Through Clinical Trials And Genomic Variants, Jeremiah I. Abok

Chemistry and Chemical Biology ETDs

DRUG TARGETS ILLUMINATION: AN EVIDENCE-BASED DATA ANALYTICS & INFORMATICS APPROACH TO HYPOTHESIS GENERATION THROUGH CLINICAL TRIALS AND GENOMIC VARIANTS

Target Illumination Clinical Trial Analytics with Cheminformatics (TICTAC) introduces a scalable data integration pipeline that aggregates multivariate clinical trial evidence to systematically rank disease–target associations. By harmonizing metadata from AACT and employing confidence-scoring techniques, TICTAC facilitates hypothesis-driven target selection for drug discovery, enabling a data-driven approach to therapeutic development. In parallel, a bioinformatics-driven analysis of gnomAD exome mutations in the ZPR1 gene highlights the broader role of genetic variants in disease association. By employing variant effect predictors, protein stability modeling, and …

Frozen-Core Analytical Gradients Within The Adiabatic Connection Random-Phase Approximation From An Extended Lagrangian, Jefferson E. Bates, Henk Eshuis

Department of Chemistry and Biochemistry Faculty Scholarship and Creative Works

The implementation of the frozen-core option in combination with the analytic gradient of the random-phase approximation (RPA) is reported based on a density functional theory reference determinant using resolution-of-the-identity techniques and an extended Lagrangian. The frozen-core option reduces the dimensionality of the matrices required for the RPA analytic gradient, thereby yielding a reduction in computational cost. A frozen core also reduces the size of the numerical frequency grid required for accurate treatment of the correlation contributions using Curtis-Clenshaw quadratures, leading to an additional speedup. Optimized geometries for closed-shell, main-group, and transition metal compounds, as well as open-shell transition metal complexes, …

Thermodynamic Water Activity Explains The Unusual Electrochemical Stability Of Aqueous Deep Eutectic Solvents, Desiree Mae Prado, Aaron Niño Gonzaga, Clemens Burda

Faculty Scholarship

The presence of water in nonaqueous deep eutectic solvent (DES) electrolytes has been debated in recent years, with efforts ranging from its complete removal to willful addition. It was shown that controlled amounts of water can be beneficial, as it not only enhances the physicochemical properties of these electrolytes but also has no significant detrimental effects on their electrochemical stability. Despite these advantages, there is still limited understanding of how water interacts with DES systems at the molecular level. This study examines the water activity in ethylene glycol and glycerol, as well as their binary mixtures with choline chloride to …