Some of our 2021 Senior Chemistry and Biochemistry Majors and their Research

Quinlan Ashmore - Advisor: Dr. Adam Hill
Characterization of Heterobinuclear Light Absorber Units for Application Within Artificial Photosynthesis Devices
Artificial photosynthesis would capture sunlight as chemical fuels, but systems that could catalyze this process require light-absorbing units with the ability to separate charge following photoexcitation: a metal-to-metal charge transfer state (MMCT). Previous experiments on synthesized bimetallic, oxo-bridged units attached to the surfaces of 12 nm silica nanoparticles showed that photoexcitation releases an electron that is transferred to a 2,2’- bipyridine (bipy) molecule coordinated to the system. The bipyridine’s long-lived excited state allowed for measurements of the MMCT to be taken, but understanding the structure of the [binuclear unit]+[bipy] center is necessary to put those measurements in context. This set of characterizations uses spectroscopy of transparent pressed pellets to do that. The binuclear unit characterization began with a bipyridine dosing survey. Samples were created with varying concentrations of bipy on Zr-SiO₂np and ZrOCo-SiO₂np substrates and analyzed using FTIR infrared spectroscopy to better understand how bipy coordinates to the system. Characterization continued with the fabrication of a custom, 3D-printed vacuum cell which could be easily attached to an Ocean Optics UV-vis spectrometer. This cell allowed for UV-visible spectroscopy data to be taken on binuclear unit samples under an inert argon atmosphere. The two spectroscopy data sets are the final pieces of a complete characterization of these binuclear light absorber units. This characterization gives a better understanding of the system’s properties and ability to function in the renewable energy role for which it was intended.

Philip Battiste - Advisor: Dr. Matthew Skeels
Development of Low-Cost Indoor Air Quality Monitoring Devices
Past methods of indoor pollution detection have proven effective, but have also been found to be expensive, time consuming, and sometimes inefficient.  As a result, many environmental chemists and engineers have worked to create a better method of monitoring indoor air quality.  These efforts have led to the development of lightweight, low-cost indoor sensors meant to overcome the weaknesses of previously utilized processes.  In our work, we have been experimenting with such devices to test their efficacy in the presence of many different pollutants and see if functionality is maintained at high levels of humidity.  Using our prototype metal-oxide sensors and a sealed testing chamber, we’ve performed several controlled of chemical contaminants.  These injections allow us to inspect the strengths and weaknesses of the devices under our experimental conditions.  Ideally, these sensors may be utilized in homes, businesses, and industrial environments as a cheap, yet still effective method of monitoring indoor air quality. 

Ben Carnahan - Advisor: Dr. Samuel Tartakoff
Synthesis of Proflavine Derivatives
Proflavine has shown promise as a potential anti-cancer drug in the form of a DNA intercalator. This research aims to utilize proflavine as a starting point and functionalize water soluble derivatives to help develop an extensive library of potential DNA intercalators that can then be further tested. Specifically, this experiment is utilizing polyphosphoric acid as an umpolung agent for nitromethane to create a hydroxy-formimidamide, that will then undergo ring closing with carbonyl diimidazole. This species will then be able to undergo further functionalization. Products will be confirmed via ¹H NMR spectroscopy.

Emmanuella Dwomo Agyei - Advisor: Dr. Nadia Marano
The Depolymerization of Isolated Amyloid Protein from Haloferax volcanii
The extracellular matrix of archaea is mainly made up of polysaccharides, extracellular DNA, and amyloid proteins. Amyloid proteins are formed from soluble proteins which aggregate into insoluble fibers. The amyloid fibers serve as protein scaffold, aids in adhesion to surfaces, and make the organism resistant to environmental stresses. Microorganisms assemble functional amyloids under controlled pathways. The assembly of amyloid fibers is thermodynamically favorable since the amyloid proteins can seed or cause their own oligomerization. This favorability makes it challenging to produce stable amyloid monomers when proteins that promote their polymerization are present. A previous study by Heather Raimer ‘17 reported the repolymerization of amyloid monomers when resuspended in water. This research aims to find a method of depolymerizing the amyloid fibers of Haloferax volcanii into stable monomers and also study the ability of the monomers to repolymerize back into its polymeric state. Ultimately, this will allow us to be able to study the structure and composition using sequencing and atomic force microscopy respectively. The amyloid fibers from Haloferax volcanii will be isolated and purified using sonication, differential centrifugation, and tube gel electrophoresis. The amyloid fibers will be depolymerized with formic acid and resuspended in water or urea which maintains proteins in an unfolded state. SDS-PAGE and ThT assay will be used to confirm the depolymerization. The effect of other variables such as the solution the monomers are resuspended in and concentration of the monomers could be studied to determine their impact on the repolymerization of the amyloid monomers.

Hannah Kenney – Advisor Dr. Samuel Tartakoff
Exploration of Novel Proflavine Derivatives as Chemotherapy DNA Intercalators
The search for new chemotherapy agents is of great importance in chemistry research. As cancer cells proliferate rapidly, synthesizing novel DNA intercalators is key for such studies. Intercalators bind between planar DNA base pairs, preventing polymerases from transcribing and replicating DNA. Proflavine, an acridine derivative, has previously been explored as a chemotherapy and antibacterial agent, and it is a promising starting point for exploration of new intercalators. This research aims to synthesize proflavine derivatives by further the functionalizing proflavine amine groups, while maintaining solubility in aqueous systems. Diester functionalization with dimethyl acetylenedicarboxylate (DMAD) is explored with hopes of developing a molecule for further testing with DNA. The compounds synthesized are purified with flash column chromatography and characterized with ¹H NMR. Future experiments involve functionalization of proflavine with maleic anhydride and determination of DNA binding modes associated with these intercalators.

Allison Krauss – Advisor: Mr. Stacy Vassar
Bringing Technology Into the Organic Chemistry Lab: QR codes and Step-by-Step Instructional Videos
Due to the current challenges of the world, learning through videos is a crucial part of class preparation. Educational videos offer students the opportunity to learn in a safe environment. They are unique in their ability to allow students to see something first hand, but are accessible from anywhere. The goal of this project is to create a series of organic chemistry lab tutorials. These videos will allow students to view the content from home and come into lab with a better understanding of what they are meant to be doing. Research on chemistry pedagogy and video production, allowed for the compilation of a list of steps aimed to streamline the production of organic chemistry lab instructional videos.  A series of videos covering the topics of melting point, recrystallization, and drying agents were produced. Videos were previewed by current organic chemistry students to ensure quality. The feedback was positive and showed improved understanding and visualization, thus making this process a success. This project will continue further with the production of videos on different procedures, uploading of videos onto YouTube, and implementation of QR codes which will enable students to scan a barcode and be directly connected with the video of interest.

Leo R. Romanetz - Advisors: Dr. Samantha Glazier and Dr. Catherine Jahncke
Kinetic Characterization of Intercalating Chemotherapy Drugs Using Temperature-Jump Techniques
There are certain planar molecules that can insert themselves between the base pairs of DNA and disrupt the helical structure. The effect of these intercalators can be to prevent DNA replication upon cell division and thereby thwart cancerous cell growth. The acridine derivative, proflavine is a well-known intercalator that is implemented in some forms of cancer treatment but falls short in its widespread application due to reported toxic and carcinogenic effects. Elucidating the binding pathway of proflavine from a kinetics perspective could offer insight that might contribute to effective modification of the drug for future utility that sidesteps the harmful effects.  In particular, deciphering the binding step of the drug as to either the major or minor groove of DNA would offer useful implications for the correlation between structure and binding mechanism for the drug. In order to probe the extremely fast DNA-intercalation process, time-resolved fluorescence spectroscopy was paired with the perturbation-relaxation technique known as temperature-jump using a home-built instrument. The kinetic pathway of the drug-binding was investigated using this technique and competitive binding methods.  Blocking the minor groove was accomplished with the well-known selective groove-blocker, Hoechst 33258. Blocking the major groove is more challenging because very few molecules are known that bind to DNA in this way. Fortunately, one such major groove binder, Methyl green binds tightly and does not overlap spectroscopically with proflavine. A combination of rate constants from kinetics data with previously acquired thermodynamics binding constants for proflavine could provide a clearer picture of the intercalative mechanism of the drug.  Specifically, this would be the first known report of experimental evidence for major groove involvement and could signal directions for the modification of proflavine.

Rachel Siegel – Advisor Dr. Samantha Glazier
Detection of TNT via Quenching of Fluorescent Polymers: A Mechanistic Study
TNT is a dangerous explosive that represents a hazard to both human and environmental safety. The use of trained dogs is currently the most common method of detecting TNT, due to its high sensitivity, however, it is often less reliable and more expensive than chemical sensing methods. Therefore, there is a need for further research into new sensors that can detect trace amounts of TNT without being too expensive so that widespread usage is feasible Therefore, the quenching of fluorescent polymers has been proposed as an alternative method for the sensing of TNT. The polymer will be created from a simple molecule, 4-hydroxystyrene, that has undergone cross metathesis and polymerization. This polymer has been selected due to its electron rich structure and its high level of conjugation. Once synthesized, titrations of TNT with the polymer will be studied using steady-state fluorescence spectroscopy and time-correlated-single-photon-counting fluorescence lifetime measurements. The Stern-Volmer equation will be used to determine the quenching strength of the polymer. The mechanism of quenching will be analyzed using Förster energy transfer and Dexter electron exchange models.

Haley Snodgrass – Advisor Dr. Emily Dixon
A study of the function of the yeast gene SEF1
In my project, I am using bioinformatics, growth assays, and RNA sequencing to learn about the function of SEF1, a transcription factor of unknown function in the baker’s yeast Saccharomyces cerevisiae. This transcription factor is hypothesized to exist inside of the nucleus of eukaryotic organisms, but the function has not been confirmed. Its name stands for suppressor of essential function, but the essential function is still unknown. I used bioinformatics to discover the basics of SEF1. While there was little known, I was able to gather clues about its function. A growth assay was used to determine growth differences in wild type Saccharomyces cerevisiae and a mutant containing the sef1 deletion strain in three different treatments: a 30°C control, 37°C-25°C cold shock treatment, and a 1M sorbitol treatment. This growth experiment was used to show a difference in growth between the wild type and the mutant strain missing SEF1 in the various conditions. The DNA of the large and small colonies of the mutant strand were isolated and sent for sequencing to determine which colony is the mutant. After the mutant is known and a significant treatment is established, the RNA will be sequenced from the mutant strain and studied in comparison to transcription factors with a similar makeup.  

Beinan Yang – Advisor: Dr. Samuel Tartakoff
Design and Synthesis of Proflavine-Derived DNA Intercalators
Intercalation is the process by which ligands insert between two base pairs thus causing the local unwinding of double stranded DNA. This process is commonly used to analyze DNA molecules and it is the basis of chemotherapeutic treatment that using DNA intercalators. As one of the intensively studied DNA intercalators, proflavine can cause the base-pair deletions or insertions, thus inhibiting the DNA replication. This project focuses on synthesizing the condensation product of proflavine and Itaconic acid. The compound obtained will be purified by hot filtration and recrystallization. IR, H¹ and C¹³ NMR will be used to characterize the product. The kinetics and DNA intercalation of synthesized compound will be analyzed using models developed by Dr. Glazier Research group. Future experiments will focus on further functionalizing the derivative molecule and studying the kinetics data for better understanding of the mechanism of DNA intercalation.