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 2009

Summer 2009

Ben Altheimer ’12, Greensboro, NC

Advisor: Michael Nee

Research Project: Synthesis of Adamantane-Based Amine Guests Cucurbit[n]urils (CB[n]) are a family of macrocyclic compounds formed by the condensation of glycoluril units with formaldehyde. They are pumpkin-shaped molecules with carbonyl groups rimming the two openings and they preferentially bind cationic guests. In 2000, larger cucurbiturils were reported, CB[7] and CB[8], and even more recently CB[10] has been isolated. There has been increasing interest in using molecular hosts, like cucurbiturils as molecular containers to alter the chemistry of the guest molecule, where the encapsulated guest molecule behaves differently than the free guest. Cucurbiturils also may be used in drug delivery systems. The larger CB[7], CB[8], and CB[10] have commensurately larger cavities and can bind potentially more useful guests. However, the yield of these larger cucurbiturils is relatively low. Our research is focused on increasing the yield of the larger cucurbiturils. We are attempting to synthesize adamantane-based guest molecules as templates for the preferential formation or stabilization of CB[7], CB[8], CB[10] and perhaps, the so far unisolated, CB[9].

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


 

John Andreoni ’11, Naperville, IL

Advisor: Matthew Elrod

Research Project: Mechanistic Studies of the Atmospheric Oxidation of Aromatics Aromatic compounds make up roughly one quarter of the atmosphere’s organic inventory. It is well known that the oxidation of aromatic compounds leads to the formation of both ground level ozone and visibility-impairing aerosols (smog). However, the specific oxidation mechanisms are not well known. We have undertaken studies of mechanism of the oxidation of several atmospherically abundant aromatic compounds. We are carrying out product identification and kinetics experiments that are performed using the Turbulent Flow Chemical Ionization Mass Spectrometric (TF-CIMS) kinetics technique.

Other Interests: Aside from chemistry I also enjoy: swing dancing, a cappella, reading the New York Times, a cup of red maté tea, anything having to do with the environment, Latin American politics, reading fiction and non-fiction, SSBB, music you can groove to, running, biking, racquet sports, the color green, Italian food, foreign lands, snowboarding and amateur entomology.


 

Zach Berman ’10, Westlake Village, CA

Advisor: Rebecca Whelan

Research Project: Synthesis and Characterization of Peptides from a Cancer Biomarker Protein A long-term goal of the Whelan lab is the development of a nucleic acid ligand (aptamer) that recognizes the ovarian cancer biomarker CA125, for use in screening, diagnosis, and therapy. This project focuses on the synthesis and purification of peptides whose sequence overlaps repeated regions of CA125 and the characterization of these peptides in terms of their structure and affinity for CA125-specific antibodies. Target peptide sequences are assembled using solid-phase peptide synthesis, purified by preparative liquid chromatography, confirmed by mass spectrometry and amino acid analysis, and characterized by a variety of methods including Fourier-transform infrared spectroscopy, surface plasmon resonance spectroscopy, and affinity capillary electrophoresis.

Other Interests: Baseball, Running, Medicine, Economics, Television.


 

Cory Ellen Boberg ’11, Bellevue, WA

Advisor: Jesse Rowsell

Research Project: Synthesis and Processing of Multi-Walled Carbon Nanotubes from a Benchtop Furnace During my internship with local start-up company Nanotech Innovations, I am optimizing the synthesis of multi-walled carbon nanotubes using a benchtop chemical vapor deposition (CVD) furnace. By varying such parameters as the catalyst solution concentration, the temperature of the vaporization chamber and flow dynamics of the gaseous reagent stream, we are working to improve the yield and purity of samples. Products are analyzed using thermogravimetric analysis and scanning electron microscopy to quantify the residual catalyst and amorphous carbon impurities. My individual project explores solvents and methods for preparing nanotube dispersions in order to homogenize samples and cast carbon nanotube paper.

Other Interests: Knitting socks, yarn, Indonesian and Korean food, films, music, Japanese language and culture, travel, coffee, and really terrible puns.


 

Neil Cole-Filipiak ’10, Ypsilanti, MI

Advisor: Michael Nee

Research Project: Separation of Larger Methylated Cucurbiturils Cucurbit[n]urils (CB[n]) are a family of macrocyclic compounds formed by the condensation of glycoluril units with formaldehyde. They are pumpkin-shaped molecules with carbonyl groups rimming the two openings and they preferentially bind cationic guests. Despite interest in cucurbiturils as molecular hosts their utility has been limited by their low solubility in most solvents. Methyl substitution results in cucurbiturils that are much more soluble in water and other solvents. However, methyl substitution results in a large number of isomers that are difficult to separate. We are attempting to synthesize adamantanamine-substituted polymers for use in the separation of different sizes of cucurbiturils.

Other Interests: LEGO, star trek, photography, combinations thereof.     


 

Derrick Dennis ’11, Detroit, MI

Advisor: Sean Decatur

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

 

 

 

 

 

 


 

Clay Easterday ’11, Chardon, OH

Advisor: Jesse Rowsell

Research Project: Optimization of Benchtop Carbon Nanotube Production Using Chemical Vapor Deposition and Development of Product Characterization Techniques. Carbon nanotubes (CNTs) have been the topic of intense scientific research since their existence was confirmed by electron microscopy in the early 1990s. With extremely high tensile strength-to-weight ratios and an array of unique electrical properties, CNTs are widely predicted to be a source of significant technological and scientific advancement. Although numerous methods for producing CNTs are documented, the procedures are often costly, lead to highly impure products and are poorly understood mechanistically. Nanotech Innovations LLC is an Oberlin-based company with the goal of optimizing the production of multi-walled carbon nanotubes (MWNTs) using chemical vapor deposition in a compact, user-friendly furnace. Our current research is focused on improving the reaction conditions and catalyst precursor usage to obtain greater MWNT yields with reduced contamination from carbonaceous and inorganic impurities.

Other Interests: Sleeping, peanut butter, tree climbing, science fiction, irony, world domination, singing in the rain, fancy words and keto-enol tautomerization.


 

Hannah Fuson ’11, Granville, OH

Advisor: Manish Mehta

Research Project: NMR Studies of Alanine- and Glycine-Containing Tripeptides. Small molecules, specifically small peptides, can often rapidly interconvert between multiple conformations in solution at ambient conditions. In thison-going project, we are studying the conformational behavior of all eight alanine- and glycine-containing tripeptides in aqueous solution. Our maininvestigative tool is the 13C and 15N chemical shift. By collecting chemical shift spectra under controlled conditions and with the aid ofquantum chemical ab initio calculations (performed on the Oberlin supercomputer), we can begin to unravel the muti-conformational characteristics of these tripeptides. In a separate part of the project, we will also investigate the 13C and 15N chemical shifts in the crystalline solid-state, where the three-dimensional structure is known from x-ray crystallography. To aid in the chemical shift assignments, we will use recently developed magic angle spinning solid-state NMR experiments.

Other Interests: playing the cello, hiking and climbing, kayaking, traveling, baking, chamber music, and roller coasters.


 

Ethan Glor ’12, Wellington, OH

Advisor: Norman Craig

Reseach Project: Synthesis of Isotopomers of the Isomers of 1,4-Difluorobutadiene for Use in Finding Semi-Experimental Equilibrium Structures by High-Resolution Spectroscopy and Quantum Chemical Calculations New synthetic methods are being developed for preparing 13C-substituted species of the cis,cis and trans,trans of 1,4-difluorobutadiene. Although we have solved the problem of introducing deuterium selectively, we have had to revise our initial strategy for introducing 13C. The new method begins with the cycloaddition of 1,2-difluoroethylene and 1,2-dichloroethylene to form the corresponding halocyclobutane. The synthesis of the 13C2 species of the two haloethylenes is a solved problem in our laboratory. 1,2-Dichloro-3,4-difluorocyclobutane should reduce to 3,4-difluorocyclobutene with zinc. Difluorocyclobutene is known to isomerize thermally into 1,4-difluorobutadiene. Once made, the 13C species will be sent to Pacific Northwest National Laboratory for high-resolution infrared spectra.


 

Kevin Hu ’11, New York, NY

Advisor: Matthew Elrod

Research Project: Kinetics Studies of the Interconversion of Alcohol, Sulfate and Nitrate Species in Atmospheric Aerosols Atmospheric aerosols (particles small enough to remain airborne) have an important effect on air quality and climate through their ability to scatter and absorb radiation and to serve as nuclei for cloud formation. It is important to understand their specific chemical composition in order to predict these properties. While organic nitrate species are known to readily form in the gas phase, they have only been occasionally observed in aerosols. One proposal suggests that organic nitrate species are converted into organic sulfate species in aerosols. In order to address whether such reactions can take place on atmospheric aerosols, we have undertaken NMR-based kinetics studies of reactions of alcohols, sulfates, and nitrates in sulfuric and nitric acid solutions that are representative of atmospheric aerosols.

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


 

Chris Lipski ’10, Ashland, OR

Advisor: Manish Mehta

Research Project: Precision Measurements of Diamagnetic Susceptibilities The NMR chemical shift is sensitive to several molecular factors, such as the local electronic environment, three-dimensional conformation, andsolute-solvent interactions. It is also sensitive to other factors, such as temperature, concentration, and magnetic susceptibility. The latter group of factors need to be controlled and corrected for in any attempt to tease apart molecular details from the chemical shift. In order to aid in the application of magnetic susceptibility corrections, we are designing and building a mass balance-based instrument to determine diamagnetic susceptibilities of common protonated and deuterated NMR solvents. We will use the 14.1 Tesla magnet of the Oberlin 600 MHz NMR spectrometer. When completed, the instrument should yield susceptibilities to four decimal places, along with their temperature dependence.

Other Interests: Cards and board games, tennis/racquetball, addictive television shows, baking (or rather, watching other people bake and maybe helping a little bit), jigsaw puzzles, swimming, sleeping.


 

Emmanuel Magara ’11, Gweru, Zimbabwe

Advisor: Sean Decatur

Other Interests: Chinese, politics, baking, business and roller coasters. Would also like to try sky diving some day.

 

 

 

 

   

 


 

Finn Maloney ’11, Ellicott City, MD

Advisor: Laura Romberg

Research Project: Modeling Polymer Nucleation in Bacterial Proteins When bacterial cells reproduce, a protein called FtsZ assembles into polymers that form a ring at the center of the cell; this ring then constricts as the cell divides in two. In order for the bacteria to divide exactly in half, only one ring must assemble, and it must assemble exactly at the center of the cell. FtsZ assembly occurs in several stages, any of which can be regulated to control ring formation. An unfavorable nucleation step helps to limit the number of rings in a cell. Nucleation acts as a bottleneck to the formation of the longer, more stable polymers necessary for ring formation, but once a polymer ring has been established, additional subunit assembly will readily occur at this ring. The goal of our research is to determine the nature of the unstable polymer nucleus. We have previously developed and analyzed a mathematical model for FtsZ polymerization at equilibrium and are currently developing a kinetic version of the model. The previous analysis shows several possible routes to forming stable polymers; each route involves a different nucleus and exhibits different initial polymerization kinetics. The goal of the current research is to determine which route applies to FtsZ polymerization. To do this, we are using a computer program called Berkeley MadonnaTM to model experimental data for FtsZ polymerization kinetics.

Other Interests: I enjoy watching a lot of old movies, cooking, listening to music, and he occasional game of monopoly. I also have recently become obsessed with Buffy The Vampire Slayer.


 

Asishana Osho ’10, Lagos, Nigeria

Advisor: Laura Romberg

Research Project: Regulation of Bacterial Protein Polymerization When bacterial cells reproduce, a protein called FtsZ assembles into polymers that form a ring at the center of the cell; this ring then constricts as the cell divides in two. In order for the bacteria to divide exactly in half, only one ring must assemble, and it must assemble exactly at the center of the cell. FtsZ assembly occurs in several stages, any of which can be regulated to control ring formation. A protein called EzrA (Extra Z Rings) suppresses inappropriate FtsZ assembly at cell poles. EzrA binds directly to FtsZ to inhibit polymerization, but the specific mechanism by which this occurs is not known. At least three models could explain EzrA's inhibitory activity: 1) EzrA may block end-to-end interactions between FtsZ subunits, preventing formation of individual FtsZ polymers, 2) EzrA may destabilize polymers after they form by accelerating FtsZ's GTP hydrolysis cycle, or 3) EzrA may interact with the sides of FtsZ subunits, allowing formation of single stranded polymers but preventing the formation of larger polymer bundles. The goal of this work is to distinguish among the three models using assays that can measure FtsZ's GTP hydrolysis activity and the formation of single stranded polymers and bundles in the presence and absence of EzrA

Other Interests: Healing arts, French language and literature, sports (especially soccer), video games, traveling, classical music, animals.


 

Tenisha Phipps ’09, Athens, GA

Advisor: Sean Decatur

Other Interests: Chewing gum, running, animals, reading, knitting, spinning yarn, religions of the world, hula hooping.

 

 

 

 

 

 


 

Emma Ross ’10, Independence, VA

Advisor: Rebecca Whelan

Research Project: Characterization of the Volatile Compounds of the Uropygial Secretions of the Grey Catbird This project is a collaboration with Professor Mary Garvin of the Oberlin Biology Department. The uropygial gland of birds produces secretions that are important in maintaining the health and structural integrity of feathers. Volatile compounds have recently been identified in the uropygial secretions of many bird species, and suggesting the possibility of olfactory communication as significant within species (such as in mate selection) and between species (to repel insect pests or larger predators). Because of their role in the cycle of West Nile virus, we are particularly interested in studying the gray catbird and the role that their uropygial secretions play in attracting or repelling the insects that carry West Nile virus. This project involves the use of solid-phase microextraction to sample the volatiles in uropygial secretions of gray catbirds, followed by gas chromatography-mass spectrometry for compound identification. Previous work has identified that linear and branched carboxylic acids are major volatiles in gray catbird secretions, but because captive birds were used, the possibility of seasonal variation resulting from changes in hormone levels or migratory behavior has not been explored. In this study, birds are sampled in the wild at important points in the annual cycle.

Other Interests: Cooking and baking, making homemade pasta, harpsichord, piano, cribbage, reading 19th century novels on the front porch with a cold drink.


 

Jordan Rutter ’12, Silver Spring, MD

Advisor: Rebecca Whelan

Research Project: Characterization of the Volatile Compounds of the Uropygial Secretions of the Grey Catbird This project is a collaboration with Professor Mary Garvin of the Oberlin Biology Department. The uropygial gland of birds produces secretions that are important in maintaining the health and structural integrity of feathers. Volatile compounds have recently been identified in the uropygial secretions of many bird species, and suggesting the possibility of olfactory communication as significant within species (such as in mate selection) and between species (to repel insect pests or larger predators). Because of their role in the cycle of West Nile virus, we are particularly interested in studying the gray catbird and the role that their uropygial secretions play in attracting or repelling the insects that carry West Nile virus. This project involves the use of solid-phase microextraction to sample the volatiles in uropygial secretions of gray catbirds, followed by gas chromatography-mass spectrometry for compound identification. Previous work has identified that linear and branched carboxylic acids are major volatiles in gray catbird secretions, but because captive birds were used, the possibility of seasonal variation resulting from changes in hormone levels or migratory behavior has not been explored. In this study, birds are sampled in the wild at important points in the annual cycle.

Other Interests: Ornithology, learning about the effects of mercury on the environment through birds.


 

Madeline Schultz ’10, Concord, MA

Advisor: Matthew Elrod

Research Project: Kinetics Studies of Acid-Catalyzed Reactions of Epoxides in Atmospheric Aerosols Atmospheric aerosols (particles small enough to remain airborne) have an important effect on air quality and climate through their ability to scatter and absorb radiation and to serve as nuclei for cloud formation. It is now well known that these aerosols have significant organic content, despite the fact that most organic compounds in the atmosphere are expected to be too volatile to readily form condensed phase compounds. The conversion of smaller more volatile organic compounds into larger less volatile compounds via acid-catalyzed reactions has been proposed to explain this seeming contradiction. We have been investigating the conversion of epoxides (intermediates in the atmospheric oxidation of volatile organic compounds) to involatile species. In order to address whether such reactions can take place on atmospheric aerosols, we have undertaken NMR-based kinetics studies of reactions of organic compounds in solutions that are representative of atmospheric aerosols.

Other Interests: reading, writing, dancing, art, music, track and field, being outdoors.


 

Heng Feng (Fall) Tian ’10, Wuhan, Hubei, China

Advisor: Norman Craig

Reseach Project: Synthesis of Isotopomers of the cis and trans Isomers of 1,3,5-Hexatriene for Use in Finding Semi-Experimental Equilibrium Structures by High-Resolution Spectroscopy and Quantum Chemical Calculations Methods have been developed for making carbon and deuterium isotopomers of hexatriene. Hexatriene-1,1-d2 can be synthesized by reducing methyl-2,4-pentanoate to the alcohol with LiAlH4 and oxidizing the alcohol to 2,4-pentadienal, which is subjected to Wittig chemistry with methyl-d3-triphenylphosphonium iodide. Similar chemistry with methyl-13C1-triphenylphosphonium iodide should yield hexatriene-1-13C1. Reduction of the ester with LiAlD4 should lead to hexatriene-2-d1. These reactions produce principally the trans isomer. The cis isomer is available by isomerization with I¬2 catalysis. Methods for making the other isotopomers have yet to be developed. Rotational spectra of isotopomers the nonpolar trans isomer will be obtained by high-resolution infrared spectroscopy, and rotational spectra of isotopomers of the polar cis isomer will be obtained by microwave spectroscopy.

Other interest: reading and sleeping.


 

David Tran ’10, Philadelphia, PA

Advisor: Michael Nee

Research Project: Synthesis of Adamantane-Based Amine Guests Cucurbit[n]urils (CB[n]) are a family of macrocyclic compounds formed by the condensation of glycoluril units with formaldehyde. They are pumpkin-shaped molecules with carbonyl groups rimming the two openings and they preferentially bind cationic guests. In 2000, larger cucurbiturils were reported, CB[7] and CB[8], and even more recently CB[10] has been isolated. There has been increasing interest in using molecular hosts, like cucurbiturils as molecular containers to alter the chemistry of the guest molecule, where the encapsulated guest molecule behaves differently than the free guest. Cucurbiturils also may be used in drug delivery systems. The larger CB[7], CB[8], and CB[10] have commensurately larger cavities and can bind potentially more useful guests. However, the yield of these larger cucurbiturils is relatively low. Our research is focused on increasing the yield of the larger cucurbiturils. We are attempting to synthesize adamantane-based guest molecules as templates for the preferential formation or stabilization of CB[7], CB[8], CB[10] and perhaps, the so far unisolated, CB[9].

Other Interests: reading, cycling, weightlifting, cooking, and gadgets.