Chemistry / Biochemistry
Department Chair:
Michael W. Nee

Administrative Assistant:
Patricia West, A263

Department Email:

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

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

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

Fall 2011 Research

Fall 2011 Research

Ben Altheimer '12 Honors

From: Greensboro, NC  Advisor:  Manish Mehta

Project:  Solid-State NMR Study of Porous Dipeptides

Description: Some peptides crystallize into structures with extended 1-dimensional pores which can accommodate a variety of small guest molecules including organic solvents and gases such as methane and carbon dioxide. These materials may be useful in separation or capture of gases. Designing and utilizing these materials and others like them for these purposes requires a better understanding of the interactions between the pore walls and guest. The interactions between the guest and the pore walls are affected by the size and shape of the pore. The pore can also shift in size and shape to better accommodate the guest by conformation shifts in the pore wall and the interior structural framework of the crystal. We hope to probe this relationship using solid-state nuclear magnetic resonance and density functional theory calculations to better understand how the materials are responding to the guests and how this affects the binding properties of the dipeptides

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

Adam Darer'12 Honors

From: Chestnut Ridge, NY  Advisor:  Matthew Elrod

Project:  Gas Phase Oxidation Kinetics and Mechanisms for Atmospherically Relevant Epoxide Intermediates 

Description: Isoprene, 2-methyl-1,3 butadiene, is the most abundant non-methane hydrocarbon present in the atmosphere. This volatile alkene, produced mainly by trees, undergoes gas phase reactions to form epoxide intermediates. The oxidation of isoprene to epoxide intermediates is related to both tropospheric ozone and secondary organic aerosol (SOA) formation, and thus linked to air pollution and global climate change. We are interested in determining the mechanism and rate constants for the reactions of atmospherically relevant isoprene epoxide intermediates with OH radicals. Specifically, we are investigating the daytime OH radical initiated process using our lab's unique turbulent flow chemical ionization mass spectrometer (TF-CIMS).  These measurements will allow a determination of whether gas phase processes dominate the fate of epoxide intermediates, or whether aerosol phase processes.

Other Interests: Table Tennis, Playing Jazz Saxophone, Dabbling at the piano, Hiking, Canoeing, Beekeeping, and reading.


Liv Dedon '12 Honors

From: Boston, MA  Advisor:  Catherine Oertel

Project:  Synthesis and characterization of tin(II) pyrochlores for photocatalysis

Description: Complex niobium and tantalum pyrochlore oxides are useful as photocatalysts for processes including water-splitting. Pyrochlores have the general formula A2B2O6, and both the A and B cations influence optical and catalytic properties. We have recently prepared tin(II) niobium and tin(II) tantalum pyrochlores using a combination of hydrothermal and ion exchange reactions. The niobium phase has a band gap in the visible range, which is the first requirement for function as a photocatalyst. The goals of this year’s work are to determine the dependence of the band gap on tin(II) content in these compounds, measure photocatalytic performance through an off-campus collaboration, and explore alternative direct syntheses for these pyrochlore phases.

Other Interests: I like to ride horses and cook



Sean Dembrowski '13 Research

From: Altadena, CA   Advisor: Catherine Oertel

Project: Hydrothermal Synthesis of Lead Oxide Carboxylates Description: Lead oxide carboxylates are hybrid inorganic-organic compounds in which Pb2+ ions are coordinated by both oxide anions and carboxylate ligands. Some members of this family occur as corrosion products of lead, while others have the potential to exhibit non-centrosymmetric structures that can give rise to novel optical properties. Very few members of this family of compounds have been characterized structurally. Goals of this year’s work include hydrothermal synthesis and structural characterization of new lead oxide carboxylate phases with ligands including benzoate, tartrate, succinate, and aspartate and application of the partial charge model to understanding factors governing formation of extended inorganic motifs in these compounds.



Derrick Dennis '12

From: Detroit MI  Advisor:  Sean Dectur

Project:  Effects of Hydrophilic and Hydrophobic Residues on Alzheimer's Aβ16-22 Aggregation Mechanism 

Description: Many neurological diseases are started by a misfolding of a certain protein. In the case of Alzheimer’s disease it is the amyloid precursor protein, which gets enzymatically cleaved to form a 40 residue poly-peptide. Aβ(1-40), misfolds and forms plaques in the brain of Alzheimer’s disease patients. In lab we work with a seven residue peptide KLVFFAE, and we substitute different peptides in the nineteenth and twentieth position to see the different effects that each amino acid has on the peptide. This summer I have been substituting different amino acids in the nineteenth and twentieth position of the KLVFFAE peptide and using FTIR to distinguish its secondary shape through various temperature changes, and using UV-vis to see if the peptide aggregates. This is important because it allows us to see the different hydrophobic effects of each substituent and to know if it aggregates.

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

Rae Eaton '13

From: Portland, OR  Advisor:  Robert Thompson

Project:  Understanding the Colorimetric Reactions of the Capsaicinoids

Description: Description: Capsicinoids, N-vanillyl acyl amides, are the "hot" components of chili peppers (genus Capsicum), many spicy foods, some topical pain-relief creams, and most defense sprays. More than twenty naturally-occurring capsaicinoids are known with small, but significant differences in structure. Capsaicin (6-ene-8-methyl) and dihydrocapsacin (8-methyl) are the two most prevalent capsaicinoids, accounting for 80% - 90% of the heat in most hot peppers. Capsaicin (6-ene-8-methyl) is shown at right.  No method exists for simply and reliably determining the amounts of the two major capsaicinoids in fruit extracts in the field. Current research includes developing a colorimetric test that can be used in-field.

Other Interests: Tea, Fiber Arts, Bread, Sherlock Holmes, Human Diseases


Joe Hamilton '12 Honors

From: Apollo, PA  Advisor:  Albert Matlin

Project:  Hydroxylamine Derivatives as Organo-Catalysts 

Description: Having successfully catalyzed a Nazarov Cyclization with a primary amine (hydroxylamine) this past summer, I will be continuing to work with similar organo-catalysts in conjunction with an expanding range of organic reactions previously catalyzed predominantly by strong Lewis acids.

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





Yuhua Lu '12

From: Suzhou, China  Advisor:  Norman Craig

Project:  Synthesis of Pure 1,4-Difluorobutadiene-1-d1 for Use in High-Resolution Infrared Spectroscopy 

Description: New methods are being explored for synthesizing samples of the cis,cis and trans,trans isomers of 1,4-difluorobutadiene-1-d1.  A previous preparation contained 1/3 of the normal species, which interferes with infrared (IR) spectroscopy. New methods depend on exchanging bromoethylene with basic D2O to give its1-d1. isotopic species, a new process that has been confirmed, and finding a way to convert this material into fluoroethylene-1-d1.  Known chemistry that begins with the photochemical reaction of fluoroethylene-1-d1 with 1-bromo-2-fluoroethylene will be used to make the isomers of 1,4-difluorobutadiene-1-d1.  The analysis of rotational structure observed in high-resolution IR spectra will give rotational constants that will contribute to determining an equilibrium (atoms at rest) structure for the two nonpolar isomers of 1,4-difluorobutadiene.  The goal is to determine the influence of fluorine substitution on the CC bond lengths.

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

Melanie Malinas '13

From: Ventura CA/Reno, NV  Advisor:  Manish Mehta

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

Description: p 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

Carl Manhardt '13

From: Everett, WA  Advisor:  Michael Nee

Project:  Synthesis of Organic-Inorganic Hybrid Polymers

Description: We are currently working on synthesizing an organic-inorganic hybrid polymer.  In order to have the organic component of the matrix uniformly dispersed, we are synthesizing 1,4,7-triazonane (TACN), which we will then attach -Si(OR)3 to each of the nitrogens in our TACN.  This compound will then be polymerized using a template that will provide a mesoporous silica with the TACN covalently incorporated within the pore walls.  The TACN groups will serve as chelating agents, which will bind metal cations.




Alison O'Connor '12 Honors

From: Shaker Heights, OH  Advisor:  Robert Thompson

Project:  Trace metal pre-concentration using solid-phase extraction

Description: In determining concentrations of trace metals, samples often require treatment to reduce matrix effects and pre-concentrate the analyte. This can be accomplished by solid-phase extraction (SPE) using complexation or ion exchange chemistry. A commercially available thiourea resin holds promise for pre-concentrating cadmium, copper, and silver. However, an efficient and effective method for releasing these metals from the resin for analysis does not yet exist. To this end, we are testing a variety of known complexing agents as eluents by adding known amounts of metals to the SPE cartridges, applying the chosen eluent, and determining the concentration of metal via atomic absorption spectrometry. Once this procedure is optimized, we will use it to test the levels of cadmium in tobacco, cosmetics, and other materials known to contain trace amounts of cadmium.

Other Interests: Baking vegan goodies, tap dancing, and Joss Whedon shows.

John Paddock '12 Honors

From: Harrison TWP, MI  Advisor: William Fuchsman

Project: Oxidation pathways for NAD(P)H

Description: The Fuchsman research laboratory has been studying the hemoglobin- and myoglobin-catalyzed oxidations in air of NADH and NADPH for some time:  the reactions require O2 and produce H2O2.  Recent studies in our laboratory on protein-free, low pH oxidation of NADH indicate no requirement for O2;  our next steps are to determine whether NAD+ forms (that is, answer the question whether the reaction really is a redox reaction),  to extend the studies to NADPH, and to determine whether the low pH system produces H2O2.  An attractive hypothesis is that at low pH, NADH (a known hydride donor to organic oxidants in enzyme-catalyzed reactions) serves as hydride donor to protons from H3O+, producing H2 rather than H2O2

Other Interests: Taiko Drumming, Reading, languages, Japanese culture, American Indian music, piano, violin, Irish dancing and music.


James Pressley '12

From: North Charleston, SC  Advisor:  Sean Dectur

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

Description: A ß-hairpin is composed of two ß-strands joined by a turn region and a hydrogen bond network between the two strands. Tryptophan Zippers (TrpZips) 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 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.

Laura Rios  '12

From: El Passo, TX  Advisor: Albert Matlin

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 4 π 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"

Jamie Yelland  '13  Research 

From: Sequim, WA    Advisor: William Fuchsman 

Project:  A New Teaching Experiment on Volume Additivity of Liquids.   Description: Jamie is developing a new teaching experiment on when it is safe to assume that volumes of liquids are additive.  We often correctly assume in making solutions and dilutions of solutions that volumes of liquids are additive.  However, lack of volume additivity is sometimes evident when two different miscible liquids are combined (such as water and ethanol) and when concentrated solutions are diluted with their solvents.  The goal of the experiment design is to devise experiments in which lack of volume additivity is not subtle.




Cassie Zentner '13

From: Irwin, PA  Advisor:  Matthew Elrod

Project:  Esterification Equilibria and Kinetics of Methacrolein-Derived Hydroxycarboxylic Acids on Secondary Organic Aerosol 

Description: Isoprene, 2-methyl-1,3 butadiene, is the most abundant non-methane hydrocarbon present in the atmosphere. This volatile alkene, produced mainly by trees, plays a key role in the formation of secondary organic aerosol, which is linked to air pollution and climate change mechanisms. One of isoprene’s gas phase oxidation products, methacrolein, apparently undergoes gas phase conversion to a hydroxycarboxylic acid species, which is then observed to undergo esterification reactions on existing secondary organic aerosol. We will synthesize the gas phase precursor and investigate the esterification equilibrium and  rate constants for the reactions in model solutions that mimic the composition of secondary organic aerosol using nuclear magnetic resonance analytical methods.  These measurements will allow for a more detailed quantitative modeling of isoprene-derived secondary organic aerosol in the atmosphere.

Other Interests: Photography, cello