Other Chemistry Commons^™

Dynamic, Reconfigurable, And Hierarchical Biosynthetic Composites Via Collagen Self-Assembly Within Highly Crowded Microgel Pastes, Elif Narbay, Abbygail Caine, Sanika Pandit, Gabrielle Montgomery, Marion Harper, E. Daniel Cárdenas-Vásquez, Hatte Hamilton, Megan Hicks, Daniel Mattar, Kyle Choy, Marco Bisoffi, L. Andrew Lyon

Engineering Faculty Articles and Research

The fabrication of a new class of biomimetic biomaterials is reported using nanostructured microgel pastes formed from “overpacked” assemblies of ultrasoft poly(N-isopropyl acrylamide-co-acrylic acid) microgels and their composites with collagen. Despite the solid-like nature of microgel pastes, collagen fibrillogenesis is robust and rapid, with a 3D collagen network forming throughout the paste volume. Structural organization within the composite is interrogated via a suite of microscopy methods, while rheological characterization provides insight into the static and dynamic mechanical properties of the materials. Long-range fibrillogenesis is enabled by local crowding, dynamics, and spatial reconfigurability of pastes at the …

Experimental And Anharmonic Theoretical Spectroscopic Benchmarks Of Nitrogenated And Doubly-Nitrogenated Polycyclic Heterocycles, Selma Bejaoui, Brant E. Billinghurst, Christiaan Boersma, Vincent J. Esposito

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

In this study, we report the first high-resolution gas-phase infrared absorption spectra and anharmonic vibrational simulations for three nitrogenated aromatic molecules, namely indole (C₈H₇N), 1,5-diazabicyclo[4.3.0]non-5-ene (DBN; C₇H₁₂N₂), and 1,8- diazabicyclo[5.4.0]undec-7-ene (DBU; C₉H₁₆N₂) with excellent agreement between measurement and computation. Anharmonic cascade emission spectra (2–8 eV) of the three systems show that nitrogen substitution strongly modifies the emission spectra: indole reproduces the unidentified 3.3 μm emission in Titan’s atmosphere, while DBN and DBU exhibit redshifted aliphatic C–H stretches. In the 5–10 μm region, …

Substituted Piperidines As (Alpha4)3(Beta2)2 Nicotinic Acetylcholine Receptor Positive Allosteric Modulators: In Vitro Pharmacology, Nataly Sanchez, Josue Gaona, Wilder Felix, Nathalia Menegasso, Brisa Cea, Ganesh Thakur, Ayman K. Hamouda

School of Medicine Student Publications and Presentations

Nicotinic acetylcholine receptors (nAChRs) play a crucial role in the pathogenesis of neurodegenerative diseases such as Parkinsonʼs disease (PD). In PD, degeneration of dopaminergic and cholinergic neurons impairs neurotransmitter release, leading to cognitive and motor dysfunction. Current treatments provide only symptomatic relief, highlighting the need for novel therapeutic strategies. The (α4)₃(β2)₂ subtype of nAChRs is expressed on affected neurons, making it a promising druggable target for enhancing neurotransmitter release and providing neuroprotection. To explore the therapeutic potential of positive allosteric modulators (PAMs) of (α4)₃(β2)₂ nAChRs, we evaluated chemical derivatives of CMPI [3-(2-chlorophenyl)-5-(5-methyl-1-(piperidin-4-yl)-1H-pyrazol-4-yl)isoxazole]. We used two-electrode voltage-clamp recordings from Xenopus laevis …

Instability Of The Octahedral Symmetry In Si8o12h8 And Ge8o12h8: A Consequence Of The Pseudo-Jahn–Teller Effect, Jules Tshishimbi Muya, Arnout Ceulemans, Carol A. Parish

Chemistry Faculty Publications

The symmetry breaking in octahedral silsesquioxane and its germanium analogues (Si8O12H8 and Ge8O12H8) has been investigated using the M06-2X/6-31++G(3df, 3pd) method and group theory. Both structures undergo  symmetry breaking, characterized by pseudo-Jahn−Teller stabilization energies of 0.22 kcal/mol for Si-POSS and 9.82 kcal/mol for Ge-POSS. Under the influence of the pseudo-Jahn–Teller effect, the distortion vector involves the vibrational a2g mode with imaginary frequency. The distortion forces in Oh-POSS are predominantly localized on the oxygen atoms and driven by the coupling between the lowest unoccupied molecular orbital (a1g) and the highest occupied molecular orbital (a2g). The symmetry breaking is attributed to a …

Assembly Of Non-Close-Packed Poly(N-Isopropylacrylamide) Microgels On Metal Halide Perovskite Films, Amal Alruwaili, Osama M. Alkhudhari, Ran Wang, Zhenyu Jia, Jennifer M. Saunders, Eugenio Picheo, Daniel T.W. Toolan, L. Andrew Lyon, Brian R. Saunders

Engineering Faculty Articles and Research

Hypothesis

Experiments

Insights Into The Radiation Chemistry Of Flash Radiation Therapy, Alan E. Lopez Hernandez

Dissertations and Theses (Open Access)

Purpose: FLASH radiation therapy (FLASH-RT) is an emerging modality that delivers radiation at ultra-high dose rates (UHDR) and has shown consistent normal tissue sparing while preserving tumor control compared to conventional RT—a phenomenon termed the FLASH effect. Despite promising results, the mechanisms behind the FLASH effect remain unclear. Many hypotheses point to radiolytic interactions, but experimental validation is limited. This work aims to develop a robust experimental platform to evaluate the relationship between radiolytic species production and physical beam parameters relevant to FLASH-RT, alongside dosimetry tools for reliable UHDR beam characterization.

Methods: A beam collector (BC) Faraday cup detector was …

Applying The Learning Cycle To Introduce Research Practices In General Chemistry Lab, Teresa J. Bixby, Matthew Kubacki, Jasmine Casanova

Chemistry Department Faculty Conferences

CUREs are a great way to engage students in research practices but can be onerous for instructors and teaching assistants to administrate and facilitate. There is added challenge in providing research experiences to students at the introductory level when they have developed limited knowledge and skills. Here we describe a more structured approach that applies the learning cycle to a traditional experiment to allow students to explore the technique, “invent” the parameters for systematic analysis, and apply the technique to a researchable question of their own construction.

The Critical Plastocapillary Number For A Newtonian Liquid Filament Embedded Into A Viscoplastic Fluid, Mohammad Tanver Hossain, Wonsik Eom, Arjun Shah, Andrew Lowe, Douglas Fudge, Sameh H. Tawfick, Randy Ewoldt

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The yield stress of a viscoplastic material can stabilize an embedded fluid tunnel against capillarity-induced breakup, enabling remarkable technologies such as embedded 3D printing of intricate, freeform, and small components. However, there is persistent disagreement in the published literature between the observed minimum stable diameter, 𝑑min, and the theoretical plastocapillary length 𝑝𝑐 = 2𝛤∕𝜎𝑦, with interfacial tension 𝛤 and bath yield stress 𝜎𝑦, leading to a prior hypothesis that the apparent surface tension 𝛤 is much smaller to enforce 𝑑min = 𝑝𝑐 . Here we introduce and experimentally test a new hypothesis that the critical diameter is set by the …

Ensemble-Based Binding Free Energy Profiling And Network Analysis Of The Kras Interactions With Darpin Proteins Targeting Distinct Binding Sites: Revealing Molecular Determinants And Universal Architecture Of Regulatory Hotspots And Allosteric Binding, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

KRAS is a pivotal oncoprotein that regulates cell proliferation and survival through interactions with downstream effectors such as RAF1. Despite significant advances in understanding KRAS biology, the structural and dynamic mechanisms of KRAS allostery remain poorly understood. In this study, we employ microsecond molecular dynamics simulations, mutational scanning, and binding free energy calculations together with dynamic network modeling to dissect how engineered DARPin proteins K27, K55, K13, and K19 engage KRAS through diverse molecular mechanisms ranging from effector mimicry to conformational restriction and allosteric modulation. Mutational scanning across all four DARPin systems identifies a core set of evolutionarily constrained residues …

Ph Dependent Structural Characterization Of Ich Ensembles Needed For Catalysis, Kevin C. Prososki

Honors Program: Senior Projects (Public)

No abstract provided.

Complementary Design Of Optical And Photochemical Systems, Joshua Plank

Chemistry Theses and Dissertations

The ability to manipulate chemical systems has been prized through history as the bridge between the macroscopic and microscopic worlds. As an example, the camera obscura has arguably existed since the earliest days of humanity; however, it was the discovery of early silver halide chemistry that lead to the ability to fix these images into the earliest photographs. In modern photolithography employed in electronics manufacturing, the primary resolution limits arise not from the chemistry of the molecules involved, but from the limits of the systems used to project light. Thus, as much as photochemistry advances, optical imaging and projection techniques …

Trade-Off Between Limonene & Geraniol-Based Reprocessable And Non-Reprocessable Epoxy Thermosets: Role Of Aliphatic Diamines In Polymer Networks Design, Priyankkumar Kanubhai Patel

Electronic Theses & Dissertations

The growing demand for sustainable materials, driven by environmental concerns and the rapid depletion of fossil fuels, has garnered significant attention in the fabrication of bio-based epoxy thermosets as renewable alternatives to petroleum-derived thermosetting polymers. The present study focuses on the synthesis and characterization of epoxy prepolymer resins derived from limonene and geraniol via a two-step process, followed by the fabrication of thermally cross-linked flexible epoxy thermoset films using various traditional aliphatic diamine curing agents, namely 1,2-ethylenediamine (EDA), 1,4-butylenediamine (BDA), and 1,6-hexamethylenediamine (HDA). Additionally, the incorporation of cystamine, a disulfide-containing diamine, enabled the formation of a covalent adaptable network through …

Binary Solid/Liquid Equilibrium Of Mixtures Of Thermally Robust Salts And Molecular Compounds For Use As Heat Transfer Fluids, Jared Ridge Mathews

Honors Theses

Fossil fuels, contributors to climate change that may bear catastrophic consequences, power the entire world. The human species is almost entirely dependent on fossil fuels for energy, but other sources of renewable and environmentally friendly energy must be developed. Concentrated solar power (CSP) is a promising source of renewable energy with hampered potential—better heat transfer fluids (HTFs) are needed for it to be economically feasible. Currently, the HTFs in industrial use are predominantly either synthetic oils or nitrate-based molten salts. Synthetic oils are only stable up to 400 °C, and molten salts often have high melting temperatures, making them prone …

Composition And Rich/Lean Loading-Dependent Density Measurements Of A Series Of Aqueous Ionic Amines For Co2 Capture, Claudia Nguyen

Honors Theses

As climate change worsens worldwide, there is a drive to develop more efficient and sustainable methods to mitigate its impact through carbon capture methods like carbon dioxide scrubbing. Carbon scrubbing directly captures carbon dioxide (CO2) emissions from industries or power plants before they are released into the environment. The CO2 captured can be utilized for various applications or can be stored underground. However, this method faces numerous challenges, such as the degradation of the solvent or corrosion of equipment. As a result, research has expanded to find a better medium to overcome these issues. In particular, aqueous ionic amines (AIA) …

Toxicity And Biodegradability Of Novel Boronium Vs Conventional Ammonium-Based Antimicrobial Compounds In Wastewater Treatment Systems, Noor Shalan

Honors Theses

Quaternary ammonium compounds (QACs) are highly effective as disinfectants, herbicides, and pesticides; thus, overuse causes elevated levels of residual toxicity in domestic and industrial wastewater. QACs can be toxic to essential bacteria breaking down pollutants in wastewater treatment plants (WWTPs) and can remain untreated in effluent, harming the environment, and contributing to antibiotic resistance, posing risks to human health. Novel boronium-based antimicrobial compounds have demonstrated efficacy in eliminating bacteria, fungi, and viruses. If the boronium compounds exhibit lower residual toxicity, they could offer a promising alternative to QACs. Because these compounds are still in development, their potential toxicity to the …

Predicting PkA Of Flexible Polybasic Tetra-Aza Macrocycles, Tatum K. Harvey, Kristof Pota, Magy Mekhail, David M. Freire, Donatus A. Agbaglo, Benjamin G. Janesko, Kayla N. Green

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

We present physics-based pK_a predictions for a library of tetra-aza macrocycles. These flexible, polybasic molecules exhibit highly charged states and substantial prototropic tautomerism, presenting a challenge for pK_a prediction. Our computational protocol combines CREST/xTB conformational sampling, density functional theory (DFT) refinement in continuum solvent, and a linear empirical correction (LEC). This approach predicts known tetra-aza macrocycle pK_a to within a root-mean-square deviation 1.2 log units. This approach also provides reasonable predictions for the most stable protomers at different pH. We use this protocol to predict pK_a values for four novel, synthetically achievable, …

In Memoriam - Nora Sabelli: Master Orchestrator Of Grant Programs And Mentor For Advancing The Interdisciplinary Learning Sciences Field, Eric Hamilton, Jeremy Roschelle, Roy Pea, Barbara Means, Louis Gomez, Kim Gomez, Nancy Butler Songer

Education Division Scholarship

On Friday, September 6, 2024, the learning sciences field lost a giant in Dr. Nora Sabelli, 87 years old, a personal mentor to many researchers and an inspiration to so many learning scientists and STEM leaders. Nora’s first professional career was as a computational chemist, and later she became a passionate leader in research for improving STEM education. Nora’s time as a senior program officer at the National Science Foundation’s (NSF) Education and Human Resources (EHR) directorate was legendary; she was a force of nature who reshaped funding priorities for stronger science and a stronger connection of science to education …

Demystifying Misconceptions In Introductory Undergraduate Chemistry Education With 3d Printed Molecular Orbitals, Hiwot Endeshaw, Daniel J. O'Leary

Pomona Senior Theses

Spatial abilities are invaluable skills for the science, technology, engineering, and mathematics (STEM) subjects. However, women, people from low socioeconomic backgrounds, and ethnic minorities are more likely to have less developed spatial abilities, which is one of the many contributing factors for the lack of diversity in STEM subjects like chemistry. Teaching spatial skills to undergraduate chemistry students may address this issue and help increase the diversity of students who go on to continue their education in the subject. 3D printing technology in higher education has exploded in recent years, presenting a unique opportunity to teach “hard to grasp” concepts …

Effects Of Chain Length, Saturation, And Bases On Saponification, Sarah Fenik

Williams Honors College, Honors Research Projects

This project will analyze the effects of chain length and saturation of fatty acids on saponification processes, as well as the effects of the base used in the reaction. Stearic acid, lauric acid, and oleic acid will be used for the fatty acid comparisons, and sodium hydroxide and potassium hydroxide will be used for the base comparisons. Stearic acid is considered a long chain fatty acid, while lauric acid is considered a short chain fatty acid. Oleic acid is a monounsaturated fatty acid. Five soap products are be made: sodium stearate, sodium laurate, sodium oleate, potassium stearate, and potassium oleate. …

Phytochemistry Of Dalea Candida Var. Oligophylla, Ryan E. Galperin

All Master's Theses

The focus of this project was the plant Dalea candida and its phytochemistry. The plant compounds were isolated and purified by an array of chromatographic techniques. The structures of the pure compounds were determined by one-dimensional and two-dimensional ¹H and ¹³C NMR spectroscopy, supported by infrared and ultraviolet spectroscopy, experimental and calculated circular dichroism spectroscopy, and mass spectrometry. Plant parts were worked on separately since they typically differ in content. Purified compounds will be tested for biological activities. Based on our results, eight new or known compound were isolated, specifically four new compounds and four known compounds. Compound …