Although the American Chemical Society’s annual national meeting and expo has been cancelled due to the Coronavirus, research by Albright students was vetted and accepted for presentation to the organization’s thousands of cutting-edge researchers, scholars and scientists.
In addition, several Albright posters were selected for presentation in Sci-Mix — a special session designed to showcase the top 10% of presentations in each division. Albright College researchers achieved this distinction in the Division of Chemical Information, the Division of Inorganic Chemistry, and the Division of Chemical Education. Accepted researchers include:
Sarah Hosler ’20, biology major
Jacquelyn S. Fetrow, Ph.D. ’82, Albright president and professor of chemistry
“Clustering of the phosducin protein family and its functionally relevant groups”
Division of Chemical Information
ABSTRACT: The goal is to functionally classify proteins using their active sites. This method will lead to a detailed understanding of the molecular functional mechanisms. This research can be further used in phosducin research and drug development. The phosducin proteins are mainly found in the retina and bind to G-proteins. Phosducins are also found in other parts of the body, but its other functions are not determined. We classified the phosducin family using auto multi-iterative search sequencing technique (MISST), a set of computer scripts that incorporates Active Site Profiling (ASP), and Deacon Active Site Profiler 3 (DASP3). The program searches protein databases to cluster proteins with similar active site profiles. We have classified phosducins into two functional families. We are also classifying the phosducins on whether they have the binding site. This analysis reveals interesting functional details of this protein family.
Nhu Nguyen ’20, biochemistry major
Amy S. Greene, Ph.D., assistant professor of chemistry and biochemistry
“Thiol conjugation to carboxyl-terminated magnetic beads”
Division of Chemical Education
ABSTRACT: Magnetic Beads are commonly used to separate molecules or proteins using magnetic separation processes. Beads may be coated with different surface functionalities. Thiols provide a convenient functionalization for further chemical modification of beads, and carboxylic-acid terminated beads are readily available in various sizes. Here, we describe a protocol to conjugate thiols onto carboxylic acid-functionalized one micrometer magnetic beads. Cystamine was attached to the beads using via EDC (1-(3-Dimethylaminopropyl)-3-ethylcarbodiimide hydrochloride) and then disulfides were reduced with DTT (dithiothreitol). We performed various experiments to optimize the reaction and storage conditions for thiol functionalization and quantified free thiols with Ellman’s Assay. Reaction yield was optimal in low-pH buffer, and storage with the reducing agent beta-mercaptoethanol maintained free surface thiols.
Mikhayla Reilly ’22, chemistry major
Amy S. Greene, Ph.D., assistant professor of chemistry and biochemistry — along with collaborators Sangjin Ryu and Haipeng Zhang
“Contractile vacuole cycling in Vorticella convallaria at various temperatures”
Division of Chemical Education
ABSTRACT: The contractile vacuole (CV) is an osmoregulatory organelle found in some eukaryotes including the free-living ciliate Vorticella convallaria and human parasites Trypanosoma cruzi and Leishmania. In this research, the CV cycling rates were determined at different temperatures above room temperature. It was found that when cells were heated up, CV rates increased. As predicted from older literature, the results followed an Arrhenius relationship; a graph of natural log of the cycling rate vs the inverse temperature is linear with a slope of 8560 ± 480 K. We hope to perform similar experiments in the presence of potential small molecule inhibitors of the CV to investigate their mechanism and potential for anti-parasitic drug development.
Shaun Hange ’21, chemistry major
Christian S. Hamann, Ph.D., associate professor of chemistry and biochemistry
Nicholas A. Piro, Ph.D., assistant professor of chemistry and biochemistry
“Dihedral angles in dialkylated dimethoxybenzenes and their radical cations: Combined X-ray crystallographic, electrochemical, and computational study”
Division of Chemical Education
ABSTRACT: In the context of an undergraduate organic chemistry lab, we encountered several previously unreported dialkylated dimethoxybenzenes. In order to fully characterize these 1,4-bis(alkyl)-2,5-dimethoxybenzene molecules we turned to X-ray crystallography to unambiguously establish the regiochemistry of the products. However, the solid state structures of these products provided a surprise: the dihedral angle of the two methoxy groups with respect to the aromatic ring was different for each alkyl group, ranging from the expected zero degrees (representing full conjugation of the π system) to almost 40○ out of plane. With the expectation that dihedral angle would affect the redox potential of the electron-rich aromatic system, students in an advanced topics senior seminar class took up these molecules from earlier in their undergraduate career to characterize them by cyclic voltammetry. An unexpectedly congruent trend between solid-state dihedral angle solution phase electrochemical potential led us on the path to fully characterize the radical cations of the system in the solid-state, and to compare our data with computational chemistry results. We have successfully prepared the green radical cations of several members of the dialkyl series via oxidation with silver hexafluorophosphate in dichloromethane and will discuss our results in this presentation.
Julie Schrey ’21, biology/biotechnology major
Christian S. Hamann, Ph.D., associate professor of chemistry and biochemistry
“Bringing order from chaos: FAIR database of sesquiterpenes organized by dihedral angles”
Division of Chemical Information
Accepted for Sci-Mix
ABSTRACT: Farnesyl diphosphate is a biomolecule transformed via a series of carbocation intermediates into the vast number of sesquiterpenes found in nature. Sesquiterpenes are fifteen-carbon secondary metabolites that serve a variety of functions. For example, they aid plants in the protection against predators and in the attraction of pollinators. In addition, they are widely used in the flavors and fragrances industry: some common examples are santalene, which is the characteristic sandalwood scent, and zingiberene, the characteristic flavor of ginger. Scientists estimate there may be 1,000-5,000 sesquiterpene molecules. Each could have 3-5 carbocation intermediates and multiple conformers of these, so in the study of sesquiterpene biosynthesis there could be more than 100,000 isomers or conformers to track! This incredible structural diversity results in a major data organization issue; currently there is no universal way to organize this overwhelming dataset. Further complicating the issue, the majority of datasets regarding sesquiterpene biosynthesis exist within supporting information files or personal research files in a variety of file formats. In the growing movement to make chemical data more FAIR (findable, accessible, interoperable, and reusable), this chaos calls for the formation of a FAIR database of sesquiterpenes. The novel approach described herein uses dihedral angle analysis to uniquely characterize both carbocation pathway intermediates and their resulting natural products. A systematic numbering system, related to but independent of connectivity, has been applied to all data disinterred from the supporting information produced by several research groups. The combination of unique characterization and systematic numbering can facilitate communication amongst different research groups. A more accurate and more useful scientific literature results, as different groups can more easily vet and contextualize new results. Further utility is realized as the database may be mined for new perspectives on the biosynthesis of sesquiterpenes. In summary, the chaos of a vast sesquiterpene database can be brought to order using dihedral angle analysis and a systematic numbering system to develop a searchable database with predictive power, significantly enhancing FAIRness of this dataset.
Kyle Gockley ’22, chemistry major
Kyle Smith ’21, chemistry and physics major
Christian S. Hamann, Ph.D., associate professor of chemistry and biochemistry
“Barriers to rotation in amides, esters, and related functional groups”
Division of Computers in Chemistry
ABSTRACT: The study of barriers to bond rotation typically begins with simple single-bond rotors such as the carbon-carbon sigma bonds found in ethane and butane. Those principles are then used to estimate rotational behavior in more complex molecular structures. Studies of amide bond rotation may begin in undergraduate organic chemistry and an understanding of this phenomenon is required to describe protein (polyamide) structure. Resonance arguments rationalize the double-bond (pi-bond) character of the carbonyl carbon-to-nitrogen bond that is typically drawn as a single bond in Lewis or line-angle structures. Experimental data interpreted through the lens of computational studies have provided an analytical description of the thermodynamic and kinetic parameters governing amide bond rotation in a variety of structural frameworks. This presentation aims to build on these approaches with a computational analysis of barriers to rotation in a homologous series of amides, esters, and related functional groups. Effects of conjugation on bond rotation are described not only for the amide nitrogen or ester oxygen but also for the second group bonded to the carbonyl carbon. Importantly, the effects of acid and base catalysis are contrasted with the barriers for uncatalyzed systems. Control experiments probing nonpolar pi-pi (1,3-diene) conjugation as well as steric bulk are included to estimate the effects of these contributing factors. In summary, a global picture of barriers to rotation that correlates the contributions from individual structural components emerges by directly comparing the behavior of amides, esters, and related functional groups studied under parallel computational conditions.
Jieyu Zhang ’20, biochemistry major
Nicholas A. Piro, Ph.D., assistant professor of chemistry and biochemistry
“Generation and reactivity of a copper nitrene intermediate supported by a bis(guanidinyl)pyridine ligand”
Division of Inorganic Chemistry
ABSTRACT: Guanidine ligands are good donor ligands that have been applied in a variety of contexts. They have been used for their hydrogen bonding abilities, their resistance to oxidation, and their ability to bridge multiple metals. We have studied the reaction of the Cu(I) species [(tbo2Pyr)Cu]OTf (tbo2Pyr = 2,6-bis(tbo)pyridine, where tbo is 1,4,6-triazabicyclooctene) with the nitrene sources PhINTs and Ph*INTs and probed the intermediate spectroscopically and through reactivity studies. One of our goals was to determine the source of hydrogen atom that binds to the nitrene nitrogen following H-atom abstraction. Our results were consistent with the ligand the ligand not being involved in the H-atom abstraction pathway. To further analyze the mechanism of nitrene degradation, we analyzed the kinetics of the reaction via an Eyring analysis between –30 ○C and –70 ○C. This analysis revealed a large and negative entropy of activation, consistent with a bimolecular H-atom abstraction pathway.
Maya Fares ’21, chemistry major
Nicholas A. Piro, Ph.D., assistant professor of chemistry and biochemistry
“Characterizing an oxygenated intermediate in O-atom transfer reactions of a bis(guanidinyl)pyridine copper complex”
Division of Inorganic Chemistry
Accepted for Sci-Mix
ABSTRACT: Guanidine ligands are good donor ligands that have been applied in a variety of contexts. They have been used for their hydrogen bonding abilities, their resistance to oxidation, and their ability to bridge multiple metals. We have studied the nature of an oxygenated copper intermediate obtained from O-atom transfer to the Cu(I) species [(tbo2Pyr)Cu]OTf (tbo2Pyr = 2,6-bis(tbo)pyridine, where tbo is 1,4,6-triazabicyclooctene) and to determine its reactivity patterns with 1- and 2-electron reductants. By tracking the lifetime of the reactive intermediate by UV-visible spectroscopy at –70 ○C and using phosphine and xanthene quenches to accelerate the rate of deoxygenation of the intermediate, it was found that phosphine deoxygenates the copper intermediate at a relatively constant rate despite changes in the amount of added phosphine and that xanthene does not significantly affect the rate of reaction. The manner in which the copper complex can act as a catalyst to insert O-atoms into C–H bonds was also investigated. Our ongoing to better define the structure and reactivity of the oxygenated copper intermediate will be discussed.
Zoe Gehman ’19, chemistry major
Tyler Stauffer ’21, biochemistry major
Nicholas A. Piro, Ph.D., assistant professor of chemistry and biochemistry
“Synthesis of ferrocene-linked binucleating ligands for holding two dissimilar metal ions”
Division of Inorganic Chemistry
Accepted for Sci-Mix
ABSTRACT: Nature is the most successful chemist for activating and interconverting small molecules and a key feature of many enzymes that carry out these transformations is their asymmetric, bimetallic active sites, that is, two metal ions are present, each in a unique coordination environment. This presentation will describe our work towards applying these lessons by developing a ligand that can hold two dissimilar metal ions in unique coordination environments. In particular, we will describe attempted routes to a ferrocene derivative wherein one cyclopentadienyl ring supports a bis(pyridyl)amine ligand and the other cyclopentadeinyl ring supports a phosphine ligand. We also anticipate discussing the coordination chemistry of our ligand with various transition metal ions.
Madelyn Loftus ’20, biochemistry major
Matthew D. Sonntag, Ph.D., assistant professor of chemistry and biochemistry
“Synthesis and characterization of silver nanoparticles for sub-ensemble surface-enhanced Raman spectroscopy”
Division of Physical Chemistry
ABSTRACT: The optical properties of materials vary dramatically based on the number of molecules probed. In the case of an ensemble, the measurement is averaged over the probing volume and interesting dynamics can be overlooked. At the few molecule level, those phenomena become visible and the optical signatures can vary dramatically. This project focused on comparing different methods to synthesize nanoparticles capable of supporting sub-ensemble behavior as probed by surface-enhanced Raman spectroscopy (SERS). Two different methods were used to synthesize silver nanoparticles to control the nanoparticle size and shape, which was characterized using Transmission Electron Microscopy (TEM) and UV-Vis spectroscopy. Each nanoparticle synthetic method was then used in combination with rhodamine dye to determine their ability to support sub-ensemble Raman spectroscopy. The spectra obtained were examined for indications of sub-ensemble behavior.
Matthew D. Sonntag, Ph.D., assistant professor of chemistry and biochemistry
“Utilizing computational chemistry to predict regioselectivity in electrophilic aromatic substitution reactions”
Division of Chemical Education
Accepted for Sci-Mix
ABSTRACT: Electrophilic aromatic substitution (EAS) represents an important class of reactions taught in the undergraduate organic curriculum. The reaction of X-substituted benzene derivatives is generally described as proceeding through a carbocation intermediate and the predominant product is ortho/para or meta depending upon the nature of X. Other molecular properties such as molecular orbitals, Hirshfeld charges, C-13 and H-1 NMR shifts can also predict the directing nature of X. Systems ranging from mono-substituted benzenes to di-substituted benzene derivatives and fused rings are presented. The goal of this laboratory exercise is to demonstrate the power of computational methods to determine the location of the substitution in EAS reactions by moving beyond molecules in which resonance structures can easily predict the product. This approach also provides molecules in which the computed data does not all agree and students must weigh the data to make an argument about where substitution will occur.
Matthew D. Sonntag, Ph.D., assistant professor of chemistry and biochemistry
“Calculating the optical properties of a series of triphenylphosphine chalcogens”
Division of Chemical Education
Accepted for Sci-Mix
ABSTRACT: A laboratory project for the upper-division physical chemistry laboratory is presented in which students compute the optical and NMR spectra of a series of triphenylphosphine chalcogenides. The different chalcogen substituents are oxygen, sulfur, and selenium. This exercise is performed in conjunction with our inorganic chemistry laboratory curriculum where students synthesize the molecules and characterize them spectroscopically. Students carry out Gaussian calculations and compare the calculated spectra to the experimentally obtained data. In addition to comparing the calculated and experimental spectra, students also analyze how the different chalcogens modify the observed behavior. The interdisciplinary nature of the project encourages students to connect computational and synthetic inorganic chemistry.
