Chemistry / Biochemistry
Contact
Department Chair:
Michael W. Nee

Administrative Assistant:
Patricia West, A263

Department Email:


Phone: (440) 775-8300
Fax: (440) 775-6682

Location:
Science Center A263
119 Woodland St.
Oberlin, OH, 44074

Office Hours: 8:30-noon 1:00-5:00pm

Summer 2011

Summer 2011

Ben Altheimer  '12   Greensboro, NC      Advisor:  Manish Mehta

Research Project:  Cyclo(Gly-Gly):Urea : An incommensurately modulated organic cocrystal

Description:  Translational symmetry is one of the foundations of modern crystallography. However, some crystals lack this basic property, providing challenges to our understanding of how to study and understand these crystals. Incommensurately modulated crystals can be thought of as periodic crystals with a modulation or perturbation applied to the positions of the atoms or some other property. The ratio of the period of the modulation to the unit cell of the average structure is irrational, so the structure never repeats. We are currently studying one such crystal, cyclo(Gly-Gly):Urea. This crystal has multiple molecular components, making it a cocrystal. Through collaborators, we are working on solving the crystal’s structure. We are also studying the cocrystal using solid-state nuclear magnetic resonance (ssNMR) to investigate the effect of the modulation on the lineshapes in the ssNMR spectra. Since each atom is in a unique chemical environment, the modulation should result in broadened and distorted lineshapes.

Other Interests:  Physics, math, climbing, hiking, the great outdoors.

 


Adam Birdsall  '13   Roseville, MN      Advisor:  Rebecca Whelan

Research Project:  Characterization of Alarm Odors in Chicks

Description:  This project is in collaboration with Julie Hagelin of the Swarthmore College Biology Department. Little is known about the possible role of alarm odors—chemical messengers emitted by individuals under threat or attack—in bird species, though alarm odors have been characterized in insects and in reptiles. The objective of this work is to examine feces samples from chicks that were subjected to a fear-inducing stimulus and compare these samples to those from birds that were not frightened. We use solid-phase microextraction and gas chromatography-mass spectrometry to determine and quantify the volatile compounds in these samples.  

Other Interests:  playing piano, drinking tea, reading anything, watching silent film comedies, dj-ing a WOBC radio show, baking bread, running

 


Matthew Crothamel  '11   Philadelphia, PA      Advisor:  Drew Meyer

Research Project:  An EXAFS study of the Pb LIII Edge of Natural and Synthetic Eumelanins and their Application to Water Purification Systems

Description:  Melanins, the familiar biological pigments found in human skin, hair and brain cells, have been found to serve a role in the sequestration and subsequent elimination of toxic metal ions.  Studies have shown that melanin’s ability to bind toxic metals depends not only on the identity and oxidation state of the metal ion, but also on the source of the melanin sample.  Previous studies have found significant difference in the ability of natural vs commercial and synthetic melanins to bind iron ions.  Because not much structural information is available on melanins due to their seemingly disordered structure, our study uses EXAFS, or Extended X-Ray Absorption Fine Structure to locally probe the lead binding sites of various melanin sources.  EXAFS operates by measuring sinusoidal variations in the sample’s X-ray absorption coefficient due to interferences between backscattered electrons and an incoming photon wave. By studying the LIII edge of the melanic lead binding sites, we hope to elucidate such structural information as the identity of various nearest neighbor shells and the identity and distance of lead-bound atoms.  The elucidation of metal binding sites in melanin could provide the basis for in vivo melanic studies and finds applications to the design and refinement of melanin based water purification systems.    

Other Interests:  Riding my bike, playing with cats, screenwriting, and shooting film

 


Liv Dedon  '12   Boston, MA      Advisor:  Catherine Oertel

Research Project:  Hydrothermal Synthesis and Characterization of Basic Lead Carboxylates

Description:  In this project I will attempt to synthesize novel basic lead carboxylates. Some members of this family of compounds occur as corrosion products on lead and lead-tin alloys, yet structures of the compounds are, in general, not well understood.  Basic lead carboxylates previously prepared in our laboratory also show unusual features including reversible dehydration and non-centrosymmetry.  Basic lead carboxylates differ from their commonplace acidic counterparts in both structure and packing; they are also much more difficult to synthesize. We use high pressure methods to increase reactant solubility in water and reach temperatures beyond the boiling point of water. With prolonged cooling and combinatorial methods, some promising crystals of new carboxylates have been synthesized. Initial characterization work is done using powder x-ray diffraction to confirm whether the synthesized product is in fact a novel compound. Once initial characterization work is done, single crystals of the novel compound are sent to Youngstown State University for single crystal diffraction, which gives much better information about the packing of molecules within the crystal's unit cell. I seek to both synthesize and characterize at least one novel basic lead carboxylate and continue work on confirming the previously determined preliminary crystal packing of basic lead benzoate. 

Other Interests:  I like riding horses, cooking, physics, fancy instrumentation, fuzzy animals, and growing plants.

 


Derrick Dennis  '12   Detroit, MI      Advisor:  Sean Decatur

Research Project:  Effects of Hydrophilic and Hydrophobic Residues on Alzheimer's Aβ 16-22 Aggregation Mechanism.

Other Interests: Football, track and field, video games, cards, listening to music, working out, the outdoors, dancing, and watching movies.

 

 

 

 

 

 


Joseph Hamilton  '12   Apollo, PA      Advisor:  Albert Matlin

Research Project:  Iminium Activation as Applied in the Nazarov Cyclization Reaction

Description: The Nazarov cyclization reaction is a useful and important tool in synthetic organic chemistry, particularly in the synthesis of natural organic products. A divinyl ketone is activated using a Lewis or Bronsted acid and then converted to a cyclopentenone via a 4π electrocylic mechanism: Of increasing interest in recent years is the field of organic catalysis, the use of organic molecules as catalysts rather than inorganic compounds. Within this field, iminium activation has seen significant recent development in reactions such as the Diels-Alder cyclization. However this catalytic mechanism has not yet been applied to the Nazarov cyclization, a promising synthetic route requiring less dangerous and greener reagents.  The Matlin group is currently undertaking the synthesis and computational analysis of several divinyl ketone variants in order to optimize iminium activation conditions for these substrates. Major targets in the development of this project are the regio- and stereoselective effects of substituents in the R1 and R2 positions.

Other Interests: I enjoy hiking, biking, watching movies, and cooking.

 


Kevin Hu  '11   New York, NY      Advisor:  Rebecca Whelan

Research Project:  Development of An Immunoassay for Peptide Epitopes of CA125

Description:  The ovarian tumor marker CA125 contains a highly conserved repeat domain that defines the site of recognition for all known classes of CA125 antibodies. Members of the Whelan lab have in recent years succeeded in synthesizing a series of short peptides with the same amino acid sequence as the antibody-binding region of the repeat domain and important variants of the dominant sequence. Compared to native CA125, these synthesized peptides are expected to be more stable, more amenable to structural characterization efforts, and substantially less costly. It is hoped that the antibodies that exhibit affinity for CA125 will also bind the synthetic peptides, and that analytical assays designed to detect the peptides will also be useful in detecting CA125 in the form found in blood. The goal of this project is to develop an enzyme-linked immunosorbent assay (ELISA) that will enable the characterization of affinity between our synthetic peptides and CA125 antibodies.

Other Interests:  Triathlon, Obertones (a cappella), Poetry, Etymology, Entomology, Etymology and Entomology, Medical Ethics, Swing Dance.

 


Nat Kadunce  '11   Beaver, PA      Advisor:  Albert Matlin

Research Project:  Iminium Activation as Applied in the Nazarov Cyclization Reaction

Description: The Nazarov cyclization reaction is a useful and important tool in synthetic organic chemistry, particularly in the synthesis of natural organic products. A divinyl ketone is activated using a Lewis or Bronsted acid and then converted to a cyclopentenone via a 4π electrocylic mechanism: Of increasing interest in recent years is the field of organic catalysis, the use of organic molecules as catalysts rather than inorganic compounds. Within this field, iminium activation has seen significant recent development in reactions such as the Diels-Alder cyclization. However this catalytic mechanism has not yet been applied to the Nazarov cyclization, a promising synthetic route requiring less dangerous and greener reagents.  The Matlin group is currently undertaking the synthesis and computational analysis of several divinyl ketone variants in order to optimize iminium activation conditions for these substrates. Major targets in the development of this project are the regio- and stereoselective effects of substituents in the R1 and R2 positions.

Other Interests: I like to play tennis, cook, hang out with people, read, and drink coffee.

 


Colin Kelly  '13   Redmond, WA      Advisor:  Michael Nee

Research Project:  Thermal Analysis of Cucurbituril-Guest Complexes

Description:  Cucurbiturils are a barrel-shaped molecular container. They can bind a wide variety of cationic and some neutral guest molecules. Cucurbiturils thermally decompose at relatively high temperatures. The goal of this project is to determine how binding inside a cucurbituril affects the thermal decomposition of guest molecules.

Other Interests:  I enjoy playing music, watching south park, and hanging out with friends.

 

 


Yuhua Lu  '12   Suzhou, China      Advisor:  Norman Craig

Research Project:  Synthesis of Deuterium Isotopologues of the cis,cis- and trans,trans-1,4-Difluorobutadiene for Use in the Determination of Semiexperimental Equilibrium Structures

Description: What are the structural effects of substituting fluorine atoms on butadiene?  We seek 2H isotopomers of the cis,cis and trans,trans isomers of 1,4-difluorobutadiene for study with high-resolution infrared spectroscopy.  Rotational constants obtained from the detailed analysis of these spectra combined with vibration-rotation constants computed with quantum chemical calculations will give equilibrium rotational constants.  Fitting these equilibrium rotational constants for a full set of isotopic species will give equilibrium structures with bond lengths determined to 0.001 Å, a high level of accuracy.  The route to the remaining isotopic species involves photochemical reaction of 1-fluoro-2-iodoethylene with fluoroethylene-1-d1 to make an iodofluorobutene, followed by removal of hydrogen iodide with base. 

Other Interests: Playing chess, go. other board games and playing the piano. Performing magic tricks and will be teaching a magic trick exco.

 


Melanie Malinas  '13   Ventura CA/Reno, NV      Advisor:  Manish Mehta

Research Project:  Biosynthesis of Uniformly Labeled 13C, 15N GB1 Protein for ssNMR Spectroscopy

Description: Up until now, research in the Mehta lab has been centered around small peptides: elucidating their structures using solid-state NMR spectroscopy and X-ray crystallography, as well as understanding the nature of their interactions with solvents. This summer, we are foraying into the world of protein biosynthesis in order to produce microcrystalline proteins that we can study using these same physical techniques. We are using E.coli to produce uniformly labeled 13C, 15N β 1 immunoglobulin-binding domain of protein G (known as GB1) by culturing the E.coli cells with ammonium-15N chloride and D-glucose-13C6. Following isolation with fast protein liquid chromatography (FPLC) and purification of the protein by dialysis, we are able to produce GB1 microcrystals by batch crystallization methods. By using solid-state NMR spectroscopy, we can then learn about the microcrystalline structure of the GB1 protein. 

Other Interests: Singing, musical theater, playing with cute animals and children, obsessing about Harry Potter, playing Scrabble, skiing, long walks, reading xkcd, spending time with wonderful people, and doing science, of course.

 


Laura Rios  '12   El Passo, TX      Advisor:  Albert Matlin

Research Project:  Iminium Activation as Applied in the Nazarov Cyclization Reaction

Description: The Nazarov cyclization reaction is a useful and important tool in synthetic organic chemistry, particularly in the synthesis of natural organic products. A divinyl ketone is activated using a Lewis or Bronsted acid and then converted to a cyclopentenone via a 4π electrocylic mechanism: Of increasing interest in recent years is the field of organic catalysis, the use of organic molecules as catalysts rather than inorganic compounds. Within this field, iminium activation has seen significant recent development in reactions such as the Diels-Alder cyclization. However this catalytic mechanism has not yet been applied to the Nazarov cyclization, a promising synthetic route requiring less dangerous and greener reagents.  The Matlin group is currently undertaking the synthesis and computational analysis of several divinyl ketone variants in order to optimize iminium activation conditions for these substrates. Major targets in the development of this project are the regio- and stereoselective effects of substituents in the R1 and R2 positions.

Other Interests: knitting, reading, obscure Rabelais references, squash, electrons, cooking, nanoparticles.

 


Ari Schwartz  '13   Columbus, OH      Advisor:  Rowsell, Nanotech

Research Project:  Summer Research at NTI, 2011

Description:  Nanotech Innovations, LLC is a local company that manufactures bench-top equipment for producing carbon nanotubes. These nanostructured materials have raised a lot of interest for applications in microelectronics and lightweight, high-strength composites. We are investigating the processing of multi-walled carbon nanotubes for thin film deposition by suspending the raw materials in fluids using ultrasonication. In addition, we are prototyping more user-friendly hardware for our chemical vapour deposition furnace.

Other Interests:  playing the piano, singing in choir, watching movies, and playing board games.

 


Herman Van Besien  '11   Chicago, IL.      Advisor:  Norman Craig

Research Project:  Synthesis of Isotopologues of cis- and trans-Hexatrienes for Use in High-Resolution Infrared and Microwave Spectroscopy

Description:  Do the structural effects of pi-electron delocalization increase with chain length in polyenes?  We are making 2H isotopologues of the cis and trans isomers of 1,3,5-hexatriene for study with high-resolution infrared and microwave spectroscopy.  Rotational constants obtained from the detailed analysis of these spectra combined with vibration-rotation constants computed with quantum chemical methods will give equilibrium rotational constants.  Fitting these equilibrium rotational constants for a full set of isotopic species will give equilibrium structures with bond lengths determined to 0.001 Å, a high level of accuracy.  Wittig chemistry, which, for example, involves the reaction of methyl triphenylphosphonium iodide with pentadienal, is the principal way that isotopic species are being made.

Other Interests:  I enjoy playing the piano and guitar, talking to people, and reading. I am also learning Korean at a rate that will make me fluent by age 50.

 


James Pressley  ' 12   North Charleston, SC      Advisor:  Sean Decatur

Research Project:  Monitoring the Effects of Pressure and Temperature on the β-Hairpin TrpZip 

Description:  ß-hairpins are the simplest form of ß-sheets comprised of a turn region connecting two ß-strands with a H-bond network between the two strands. Tryptophan Zippers (TrpZip) are 12-16 residue long ß-hairpins that are the smallest, most stable peptides known. They are stabilized by interactions between cross-stranded tryptophan pairs, interstrand H-bonding, and an extremely secure turn region. Tryptophan pairs produce a hydrophobic cavity that interact with one another, most often, in an edge-to-face geometry based on maximization of electrostatic and dispersion forces. H-bonds between carbonyl and amine groups are frequently observed and extremely strong. The turn region is proposed to be the catalyst for hairpin formation and is characterized, usually, by 2-4 residues that interact to form an energetically favorable dihedral angle capable of a tight beta-turn. Currently, the challenge is determining which of these elements confers the most stability and in what order they occur for hairpin construction. Temperature and pressure experiments, using a beta-hairpin with the amino acid sequence AWAWENGKWAWK-NH2, are utilized to take on this challenge. A lack of pressure experiments in the field has led to the use of a diamond anvil cell (DAC) to monitor how pressure relates to the, proposed, unfolding of the beta-hairpin. The DAC is specifically designed to apply extreme pressure to peptide samples and is used in conjunction with Fourier transform infrared (FTIR) spectroscopy to monitor the peptide’s response. Identifying the unfolding mechanism(s) of ß-sheet structures may help deduce methods that could diminish protein aggregation, which is characteristic of many neurodegenerative diseases such as Alzheimer’s, Parkinson’s and Huntington’s disease.

Other Interests:  I enjoy gymnastics, all forms of dance especially vogueing, fashion, swimming and chowing down on White Fudge Almond Divinity, ice cream.

 


Oluchi Okoro '13 Imo, Nigeria Advisor: Sean Decatur Research Project: H1 Peptide: Probing the possibility of an intermediate process in the formation of β aggregates

Description: Proteins are a class of macromolecules that are vital in the execution of certain activities in the body such as immune protection and cell differentiation. Proper folding of proteins into a specific 3D structure enables the protein to carry out its normal function while misfolding leads to diseases. The prion protein (PrPC) is an example of a protein whose misfolding results in diseases like Creutzfeldt-Jakob disease and fatal familial insomnia. Misfolded proteins accumulate in plaques made of structures called amyloids, which are stable and have high β sheet content. Amyloidogenic regions are basically regions that are susceptible to forming amyloids. Due to the large nature of proteins like prion, we focus our study on the amyloidogenic regions of proteins. For PrPC, H1 peptide is a replication of its most amyloidogenic region. H1 monomers (residue 109-122 of the prion protein, Ac-MKHMAGAAAAGAVV-NH2) are suggested to form equilibrium with β sheet aggregates of the peptide. In this paper, we discuss the possibility of an intermediate process in the equilibrium. While varying concentration and temperature, we use IR spectroscopy to measure useful spectra that give insight into the process of aggregation of H1 peptide. We also apply knowledge of thermodynamics and kinetics in analyzing data. Results show that in varying temperature by increments of 10°C from 25°C-75°C and then back to 25°C, β sheet aggregates increase while random coil decrease. We will vary the concentration along with temperature to determine the effects of concentration on aggregate formation. Based on our results, we hope to question the possibility of an intermediate amorphous aggregate process. Our findings will continue to shed more light on our understanding of plaque formation and most likely, lead us to finding ways to detect and impede plaque formation at an early stage of formation.

Other Interests: Croche, recycling and dance