Some of our 2020 senior Chemistry and Biochemistry Majors and their research
Hannah Bovee - Advisors: Dr. Nadia Marano and Dr. Lorraine Oldenzenski
Characterization of Amyloid Fibers formed by Resistant Soil Bacteria
Amyloid fibers are proteins formed by repeating protein monomers which stack to create a cross-beta sheet quaternary structure. Though the unregulated production of amyloid fibers is often associated with diseases such as Alzheimer’s and Parkinson’s, amyloid fibers are also produced in a regulated manner by bacteria in biofilms to protect against antibiotics and to attach cells to the surface they live on. Previous St. Lawrence researchers isolated a number of antibiotic resistant soil bacteria from a pig farm in upstate New York. Several of these bacteria produced biofilms which tested positive for amyloid fibers with a Thioflavin T (ThT) assay. An isolation procedure utilizing sonication and differential centrifugation to release and separate fibers from Microbacterium isolate #29 was developed by Jack Mechler ’18. This procedure is being adapted to increase the percent recovery of the isolation and improve purity. Two detergents, Triton-100X and hexadecyltrimethylammonium bromide (CTAB), are being assessed as a means of disrupting the cell membranes to separate them from soluble proteins during the procedure. The fluorescence of the detergents below and above their critical micelle concentrations in the presence of ThT was investigated to determine if adding a detergent treatment step would interfere with the ThT assay (as the commonly used detergent sodium dodecyl sulfate does). Additionally, the original sonication treatment is being compared to an extended sonication treatment to assess if more fibers can be released from the cell membrane. Fibers will be purified further using an SDS-PAGE gel and depolymerized using formic acid. The pure amyloid protein monomers will then be sequenced by a collaborator.
Cory Couture - Advisor: Dr. Jeffrey Chiarenzelli
Characterization of Adirondack Iron Deposits using the Hafnium-Lutetium Isotope System
Iron mining has been an integral part of the history on the Adirondacks. The geochemical properties of the deposits, however, has yet to be completely described. The U/Pb and Hf/Lu isotope composition of zircons from ten iron oxide-apatite ore deposits and their respective host rock was carried out using Laser Ablation-Inductively Coupled Plasma-Mass Spectrometry. The epsilon Hafnium (εHf) of each locality was then calculated to determine genesis relationships. Despite all ore materials being found in the same host rock, the Lyon Mountain Granite, there is a large discrepancy in εHf values. This indicates that the iron enrichment processes did not occur synonymously between each location. Minerology, degree of hydrothermal alteration, and original magmatic composition result in εHf variation between seemingly identical formations. Defining the relationship between these characteristics and εHf values will provide a more comprehensive geochemical understanding for the iron ore deposits in the Adirondacks.
Gabrielle T. Davis - Advisor: Dr. Samuel Tartakoff
Acridines as DNA Intercalators: Synthesis of Proflavine Derivatives
Acridines, such as proflavine, are known DNA intercalators, which makes them extremely useful as chemotherapeutic agents and as probes to understand how DNA-drug interactions occur. Intercalation of these compounds between planar DNA base pairs allows for the unwinding of DNA, causing structural changes to the DNA, which can lead to functional changes, including the inhibition of transcription and replication. These functional changes make DNA intercalators extremely useful in inhibiting replication in cancer cells, leading to their use as potent chemotherapeutic treatments. This project focuses on modifying the structure of proflavine through mostly single-step synthesis, in particular functionalizing the amines, and examining how these changes influence DNA binding. The synthesized compounds will be analyzed for DNA binding and intercalation using various methods. Characterization of prepared compounds will be completed with IR, as well as 1H and 13C NMR. Future experiments will focus on further functionalizing the prepared derivatives and using DNA binding data to synthesize more potent DNA intercalators.
Jack C. Greene - Advisor: Dr. Adam D. Hill
Coordination of Infrared Probe Molecules to All-Inorganic Light Absorbers
Heterobinuclear units (HBNUs) consisting of paired electron deficient and rich metals supported on silica have applications in artificial photosynthesis systems, as their metal- to-metal charge transfer states strongly absorb visible light and produce separated electrons and holes. Materials with zirconium and cobalt are of particular interest as they are also capable of photochemical carbon dioxide reduction. Though the coordination of organic species to HBNUs is important to reactivity, the mode of this coordination has not been previously characterized. Dosing surveys on a variety of mononuclear and heterobinuclear units were conducted with thiocyanate as a probe molecule, and IR spectroscopy was utilized to understand at what concentration the sites become saturated and to which metal the probe coordinates. Additionally, synthesis was performed on glass cover slips, allowing for AFM and EDS imaging. These measurements allow for better understanding of how organic molecules bind to all-inorganic HBNUs.
John Hoefler - Advisor: Dr. Amanda Oldacre
Synthesis of Discrete Supramolecular Self-Assemblies for Sequestration and Catalytic Degradation of Azo Dyes
Organic dyes, used in textile manufacturing, pose a significant environmental threat due to their ubiquity in wastewater, damaging health effects, and the dangerous environmental implications associated with their release. Discrete supramolecular architectures, synthesized using facile coordination-driven self-assembly techniques, can be used for dye sequestration and as catalysts for the degradation of organic pollutants. This work explores the sequestration of methyl orange and congo red as well as the electrochemical properties of discrete Zirconocene-salen tetrahedron architectures used to bind and degrade the dyes. The salen ligand Schiff base probed, N,Nʹ-bis(4-carboxysalicylidene-1,2-diaminoethane) (SED-M) will be metallated with first row transition metals. Methyl orange and congo red are compelling targets for this study of dye degradation due to the electronic properties of azo dyes that depend intimately upon the protonation or deprotonation of the N=N bridging unit that can be observed using electrochemical techniques. The sequestration and degradation of these dyes, using the self-assembly SED-M, will be probed with UV-vis and electrochemical techniques, such as cyclic voltammetry and spectroelectrochemistry.
Amber Jones - Advisor: Dr. Matthew Skeels
The Effect of Cover Crops on Soil Quality
Cover crops are planted in order to benefit crop production by increasing the quality of the soil and protecting the land from runoff and soil erosion. Cover crops are often grown over the winter to diminish nutrient loss and help the growth of crops in the springtime. The goal of this work is to extract and analyze nutrients of interest from multiple cover crops early in the fall, then again later in the fall in order to assess late vs. early planting. The cover crops being looked at include vetch, rye, mixed plating, and hay mulch. The nutrients of interest include sulfate, phosphate, chloride, nitrite, and nitrate. These analytes will be extracted via the Modified Morgan extraction solution and analyzed using Ion Chromatography. An ammonia quantification will be accomplished using a colorimetric salicylate test for ammonia. Metals including potassium, calcium, sodium, manganese, nickel, iron, copper, and zinc will be extracted via the Modified Morgan solution. They will be analyzed via Flame Atomic Absorption Spectroscopy. Total organic matter will be analyzed via loss on ignition. The results from the soil analyses will eventually be used to assess the effects of late vs early planting on the soil quality so farmers can determine the best time to plant their cover crops for effective planting in the spring.
Leah Livernois - Advisor: Dr. Amanda Oldacre
Development of Metal-Organic Frameworks for the Adsorption and Degradation of Azo Dyes
Organic dyes, a significant pollutant of clean water, have harmful effects on the environment and human health. It is crucial to investigate methods of their absorption and degradation into less adverse products or chemical feedstock. The use of Metal- Organic Frameworks (MOFs), a long-standing approach in the adsorption of dyes, is attractive due to their tunable porosity. This works explores MOFs with metallated salen ligands (N,Nʹ-bis(4-carboxysalicylidene-1,2-diaminoethane) and N,Nʹ-bis(4- carboxysalicylidene-1,2-diaminobenzene)). The MOFs in this study will be probed for absorption properties of the dye and catalytic activity. Azo dyes, Congo Red and Methyl Orange, will be used as targets for dye degradation due to the electronic properties of the N=N bridging unit. The sequestration and degradation of azo dyes using the salen- based MOFs, will be probed with UV-vis and electrochemical techniques, such as cyclic voltammetry and spectroelectrochemistry.
Andrew Nicolais - Advisor: Dr. Samantha Glazier
Analyzing Binding Modes of Various Proflavine Derivatives
Proflavine and other acridine dyes have long been known to have the ability to intercalate DNA, however certain derivatives of proflavine may be more effective at this than others. We plan to study a series of derivatives that may provide insight into how structure impacts binding ability of these intercalators. Using calf-thymus DNA and a PCR instrument as a controlled heat source, it is possible to quickly and accurately measure the melting point of DNA bound to proflavine and its derivatives via fluorescence changes. By measuring the melting point of the CT DNA-proflavine complexes a melting curve can be produced and the binding mode can be determined. This allows a way to characterize the binding of each new derivative, including structural features that affect binding mode. If the proflavine derivative intercalates, then the melting point is found to be higher than if it binds to one of the grooves, or does not bind at all. Once the binding mode is known, the strength of binding is calculated from fluorescence-based titrations. Additionally, new derivatives will be analyzed with the Van’t-Hoff method, which determines overall entropy and enthalpy changes. Additionally, the osmotic stress method determines the number of water molecules released or taken-up upon binding. By first determining the melting point, it allows the binding mode to be determined quickly, before more in-depth thermodynamic mechanisms are explored via the Van’t-Hoff plots and water exchange.
Nicole E. Panek - Advisor: Dr. Adam D. Hill
Quantum Chemical Models of Heterobinuclear Units on Silica Surfaces
A future source of renewable energy is artificial photosynthesis (AP), which replicates the natural process of photosynthesis by capturing solar photons and converting carbon dioxide and water into energy-dense fuels. Heterobinuclear units (HBNUs) are possible light absorbers consisting of oxo-bridged heterobimetallic centers bonded to a silica network. These units create a metal-to-metal charge transfer state when excited by absorption of visible light. The efficiency of electron transfer to other device components is limited to the metals’ absorption and thus geometry, but earlier experimental EXAFS results lacked information about the geometry relationship of the silica network to the metal centers. Graph theoretical models captured possible silica structures and how HBNUs bond to silica nanoparticles by calculating the likelihood of finding a structure in actual material using density functional theory to identify the energy of each molecular graph. Predicted experimental IR observations in the presence of probe moieties were also computed. Zirconium-cobalt and titanium-cobalt HBNUs bonded to silica rings and nanoparticles demonstrate trends in preferred bonding orientations.
Heinrich Salzmann - Advisor: Dr. Adam D. Hill
Oxygen-Sensitive Luminescence of Excited States in Heterobinuclear Light Absorbing Units
Light-absorbing units separate charge through photoexcitation and are a crucial part of artificial photosynthesis systems. Photoinduced metal-to-metal charge transfer between two oxo-bridged transition metals on a silica surface yields a displaced electron that can be transferred to a 2,2’-bipyridine chromophore. Luminescence associated with the relaxation of this charge transfer state was monitored by time-correlated single-photon counting (TCSPC). Emission intensity shows a dependency on the gaseous atmosphere in which it occurs, suggesting oxygen quenching. To explore this phenomenon further, a custom-built 3D-printed miniature vacuum cell was used to expose the light absorbing units to different atmospheres. Excitation for TCSPC measurements was carried out using 405 nm and 390 nm pulsed sources with various measurement windows, ranging from 100ns to 50us. The results confirm a unique luminescent excited state from only those systems with the correct arrangement of levels to support electron transfer: the bipyridine-dosed zirconium-cobalt silica nanoparticles. The role of oxygen quenching is explored and further comparison to heteronuclear units containing titanium and hafnium as the early transition metal are made.
Erica Sawyer - Advisor: Dr. Nadia Marano
Isolation and Purification of Amyloid Proteins
Amyloids are a class of aggregated proteins that share a common structural motif, the cross- beta sheet, allowing them to form long fibrils. These fibrils can be pathogenic or can serve many important physiological roles that are not fully understood. Haloferax volcanii, an extremophile species of Archaea, is one microorganism that incorporates functional amyloids into its biofilms; these proteins are proposed to contribute to the structural stability of this matrix. This study aims to improve the efficiency of the isolation and purification of amyloid proteins found in H. volcanii to ultimately allow for further investigation of their structure. Previously, a protocol was established by Lisa Kozodoy ’19 that utilizes differential centrifugation and sonication to isolate amyloid proteins, which are then purified using SDS- PAGE. To improve the effectiveness of this procedure, detergents will be employed during the isolation to disrupt amyloid interactions with the cell membrane, possibly releasing more protein. Additionally, these detergents will prevent the incorporation of Thioflavin T, a fluorescent molecule used to selectively quantify amyloid proteins, into lipid components of the cells that are not removed during the isolation. Triton X-100 and Cetrimonium Bromide, a neutral and cationic detergent, respectively, will be used during the isolation. Then, the yield of pure amyloid proteins will be compared to that obtained without the use of detergents. Purified amyloids will be deaggregated into their monomeric forms using formic acid and resuspended in urea; these proteins can then be sequenced to gain further information regarding their structure.
Joe Settineri - Advisor: Dr. Amanda Oldacre
Synthesis of discrete supramolecular self-assemblies for sequestration and catalytic degradation of azo dyes
Organic dyes, used in textile manufacturing, pose a significant environmental threat due to their ubiquity in wastewater, damaging health effects, and the dangerous environmental implications associated with their release. Discrete supramolecular architectures synthesized using facile coordination-driven self-assembly techniques, can be used for dye sequestration and as catalysts for the degradation of organic pollutants. This work explores the sequestration of alizarin yellow and electrochemical properties of discrete Zirconocene-salen tetrahedron architectures. The salen ligand Schiff base probed, N,Nʹ-bis(4-carboxysalicylidene-1,2-diaminobenzene) (SBD-M), will be metallated with first row transition metals. Alizarin yellow is a compelling target for the study of dye degradation due to the electronic properties of azo dyes, which depend intimately upon the protonation or deprotonation of the N=N bridging unit. The sequestration and degradation of alizarin yellow using the self-assemblies, Zr-SBD-M and Zr-SED-M, will be probed with UV-vis and electrochemical techniques, such as cyclic voltammetry and spectroelectrochemistry.
Kellen M. Wolfe - Advisor: Dr. Samuel Tartakoff
Derivatives of Acridine used for DNA Intercalation
Intercalation is a process by which planar, mostly aromatic compounds can insert themselves between the nucleic acid base pairs of DNA. DNA intercalation can result in inhibition of DNA replication and reduction of the growth of cancer cells. Acridines are one major class of known DNA intercalators. This research project focuses on the formation, preparation and testing of acridine analogues. The information gained from testing these compounds can be used to better understand DNA intercalation. Analysis of compounds will be done using 13C NMR, 1H NMR, IR, and GC/MS. Further study will include functionalization and synthesis of more complex acridine analogues.