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 2008

Summer 2008
 
Benjamin Baldwin Christopher Lipski Joseph Thome
Hanna Fuson Emily Minerath Fall (HengFeng) Tian
Edward Huang Deacon Nemchick Sydney Williams
Michaela Hull Craig Packard Jaie Woodard
Hadley Iliff Edwin Takahashi  
     

Ben Baldwin ‘09, Andover, MA
Advisor: Matthew Elrod

Research Project: Kinetics Studies of the Atmospheric Oxidation of Alkenes by Nitrate Radical

The nitrate radical (NO3) is the dominant oxidant in the nighttime atmosphere.   Because both ground level ozone and aerosols are primarily photochemically produced during daytime hours, nighttime oxidation chemistry has less received less study.  We have undertaken studies of the kinetics of the nitrate radical-initiated oxidation of several atmospherically abundant alkene 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:  Music, the news, guitar, rugby sometimes, traveling, the outdoors, the indoors, speaking Spanish poorly, looking at maps.

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Hannah Fuson ’11,  Granville, OH
Advisor: Norman Craig

Research Project: Semi-experimental Structures for the cis and trans isomers of 1,3,5-Hexatriene

We seek semi-experimental structures (atoms at rest) for the cis and trans isomers of 1,3,5-hexatriene to see if an increase in the length of a polyene chain increases pi-electron delocalization, as reflected in bond length adjustments.  Ground state rotational constants will be derived from the analysis of the rotational structure in high-resolution infrared spectra of a series of isotopomers  of the trans isomer.  For the cis isomer, which has a dipole moment, microwave spectroscopy, a direct form of rotational spectroscopy, can be used.  Equilibrium rotational constants will then be calculated with vibration-rotation constants obtained from ab initio quantum chemical calculations, and a structure will be fit to the set of equilibrium rotational constants.  Most of the effort this summer is aimed at developing a synthesis of various 13C and deuterium isotopomers.  The general method involves building the C6 chain from smaller fragments, in which 13C or deuterium has been introduced.
Other Interests: cello and piano playing, chamber music, strawberries, napping, traveling.

 

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Edward (Guozhi) Huang ‘10 
Nanjing, China
Advisor: Michael Nee

Research Project: Template Synthesis of Larger 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. Since the structure of the parent compound, CB[6], was first reported in 1981, extensive studies of the host-guest behavior of CB[6] have been carried out. 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 by the use of tight-binding 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: Although I'm not a good cook, I like to cook Chinese food and eat it up.

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Michaela Hull ‘10, Saint Paul, MN
Advisor: Catherine Oertel

Research Project: Synthesis and Characterization of Basic Lead Carboxylates

Reactions of carboxylic acids with lead play an important role in the atmospheric corrosion of cultural objects.  This is a particular problem for historic lead-tin alloy organ pipes, which can be severely degraded by formic and acetic acids emitted from the wood of organ cases.  Our laboratory has used hydrothermal conditions to crystallize two corrosion products, Pb(CH3COO)2 -2PbO-nH2O and  Pb(HCOO)(OH).  Both had been identified though powder diffraction fingerprints in the Powder Diffraction File, but their structures had never been determined.  Now that single-crystal structures have been obtained, we are further characterizing these compounds with thermogravimetric analysis, Raman spectroscopy, and fluorescence spectroscopy.  We are also using reactions between lead and carboxylic acids to synthesize new members of this family of compounds.
Other Interests: Art, horseback riding, tae kwon do, dance (all kinds), sewing, travel.

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Hadley Iliff ’09 Greensboro, NC
Advisor: Manish Mehta

 

Research Project: Computational Studies of Small Alanine- and Glycine-Containing Peptides

My project this summer concerns using Molecular Dynamics and Quantum Chemical simulations to calculate the chemical shifts of four capped dipeptides – L-Alanyl-L-Alanine, L-Alanyl-Glycine, Glycyl-L-Alanine, and Glycyl-Glycine. These calculated shifts will then be compared to experimental values previously determined by other researchers in the Mehta lab. I am using a desktop computer and Oberlin’s 70-node supercomputer to complete these calculations. The ultimate goal of this research, similarly to the other projects being explored in the Mehta lab, is to examine the more subtle interactions of dipeptides in order to gain more information that can also be applied to larger proteins.
Other interests: knitting and yarn, eating (good) food, playing cards and dominos.

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Chris Lipski '10 Ashland, OR
Advisor: Manish Mehta

 

Research Project: Synthesis and Purification of Isotopically Labeled Tripeptides

Tripeptides are small proteins made of just three amino acids.  These compounds are small enough that they do not adopt one, low-energy structure but instead rapidly switch between several different low-energy structures.  In order to understand which of these structures are preferred, the Mehta lab applies both experimental and computational approaches.  Use of the 600 MHz NMR instrument, and the resulting chemical shift data that comes from analysis of these tripeptides, is key to the experimental side of the Mehta lab work.  For some experiments, the tripeptides need to have isotopic “labels;” that is, they need to have an increased amount of 13C and/or 15N isotopes present in the molecule. These peptides need to be synthesized in lab using starting materials that contain the appropriate labels.  The syntheses are conducted using well-established procedures of solid-phase peptide synthesis and the products are purified using reverse-phase HPLC.  A series of tripeptides will be synthesized this summer using a variety of both amino acids and labeling schemes.
Other Interests: Cards, dominoes, puzzles, swimming, occasionally tennis, addictive tv shows, learning, eating, sleeping.

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Emily Minerath ‘09,  Ann Arbor, MI
Advisor: Matthew Elrod

 

Research Project: Kinetics Studies of Acid-Catalyzed Reactions in Atmospheric Sulfuric Acid 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.    Since sulfuric acid aerosols are ubiquitous in the atmosphere, it has been proposed that these types of reactions are responsible for the build up of organic materials on aerosols.  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 sulfuric acid solutions that are representative of atmospheric sulfuric acid aerosols. Other Interests: Reading, baking, cooking, knitting, ballet and modern dance, aikido, web comics, climbing trees, good food.

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Deacon Nemchick ’09 
North Huntingdon, PA
Advisor: Norman Craig

 

Research Project: Synthesis of Carbon and Deuterium Isotopomers of 1,4-Difluorobutadiene for Use in High-Resolution Infrared Spectroscopy and a Structure Determination.

We seek semi-experimental structures (atoms at rest) for the cis,cis and trans,trans isomers of 1,4-difluorobutadiene to test the effect of fluorine substitution on the length of bonds in the C4 backbone.  Ground state rotational constants will be derived from the analysis of the rotational structure in high-resolution spectra of a series of isotopomers.  Equilibrium rotational constants will then be calculated with vibration-rotation constants obtained from ab initio quantum chemical calculations, and a structure will be fit to the set of equilibrium rotational constants.  Most of the effort this summer is aimed at completing the synthesis of various 13C and deuterium isotopomers by a method that involves the synthesis of isotopically substituted fluoroethylene and coupling this species with 1-fluoro-2-iodoethylene in photochemical process.  The final step involves removal of hydrogen iodide.
Other Interests:  Jack Bauer and Nina Meyers, skiing, ping pong, the Pittsburgh Penguins, digg.com, citrus fruits, bikes, goodies and treats, golfing, Beck, action movies, snow, coffee, Little Debbie Oatmeal Cream Pies, Rubik’s Cubes, and DeCafe sandwiches…that’s it.

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Craig Packard ‘09, Wolcott, NY
Advisor: Michael Nee

 

Research Project: Template Synthesis of Larger 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. Since the structure of the parent compound, CB[6], was first reported in 1981, extensive studies of the host-guest behavior of CB[6] have been carried out. 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 by the use of tight-binding 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:  Dry British humor, monosodium glutamate, thunderstorms, non sequiturs, rather escapist fantasy/science fiction literature, volleyball, and geography.

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Edwin Takahashi ‘09, Mililani, HI
Advisor: William Fuchsman

 

Research Project: Assaying Hydrogen Peroxide in the Presence of NADH and NADPH

We are continuing the examination of methods for counteracting the inhibition of NADH and NADPH on spectrophotometric assays for hydrogen peroxide.  We have found one assay procedure that is relatively insensitive but unaffected by NADH and NADPH, and we are checking whether it is unaffected over the pH range 6-8.  We are extending the use of three-dimensional calibration curves to more than one partially inhibited assay.  We have found an enzymatic method for removing NADH before assaying for hydrogen peroxide, and we are examining a possible enzymatic method for removing NADPH.  We plan to determine the practical applicability of the several methods by using them to follow the time course of a hydrogen peroxide-generating, NADPH-consuming reaction. Other Interests: Outdoor activities, track and field and football.

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Joseph Thome ’10, Middleburg Heights, OH
Advisor: William Fuchsman

 

Research Project: Assaying Hydrogen Peroxide in the Presence of NADH and NADPH

We are continuing the examination of methods for counteracting the inhibition of NADH and NADPH on spectrophotometric assays for hydrogen peroxide.  We have found one assay procedure that is relatively insensitive but unaffected by NADH and NADPH, and we are checking whether it is unaffected over the pH range 6-8.  We are extending the use of three-dimensional calibration curves to more than one partially inhibited assay.  We have found an enzymatic method for removing NADH before assaying for hydrogen peroxide, and we are examining a possible enzymatic method for removing NADPH.  We plan to determine the practical applicability of the several methods by using them to follow the time course of a hydrogen peroxide-generating, NADPH-consuming reaction. Other Interests: playing piano, singing, learning languages, tennis, volleyball, and swing dancing.

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Heng Feng (Fall) Tian ’10,
Wuhan, Hubei, China
Advisor:  Catherine Oertel

 

Research Project: Synthesis of Inorganic-Organic Compounds Based on MoS42– Anions

Hybrid inorganic-organic network materials are made up of metal atoms linked by multitopic organic ligands, which are capable of coordinating more than one metal center.  Using metal clusters or complex metal anions in place of single metal ions is one way of building networks that have useful properties as well as interesting structures.  Tetrathiomolybdate (MoS42-) anions are known for their ability to chelate transition metals and to act as catalysts for hydrodesulfurization and hydrodenitrogenation reactions, both of which are important in production of cleaner-burning fuel sources.  We are using these complex anions as well as organic ligands and single transition metals as building blocks for network compounds.  Resulting compounds could act as porous, high-surface-area catalysts. Other interest: reading and sleeping.

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Sydney Williams (Beckman Research Fellow) ‘09
Chico, CA
Advisors: Rebecca Whelan and Manish Mehta

 

Research Project: Selection of an aptamer that recognizes CA 125

The selective detection of biomolecules in serum is an important tool for basic research and clinical applications. Traditionally, such assays have relied on antibody molecules as the basis of detection. In this project we will explore a relatively new class of affinity molecules—aptamers—and develop analytical assays that exploit their unique advantages. Aptamers are single-stranded nucleic acid molecules with recognition ability comparable to antibodies. The process of aptamer selection begins with a large random pool of oligonucleotides. The oligos are allowed to interact with the target protein of interest, and those that bind well to the target are separated from those that do not. Good binders are amplified by polymerase chain reaction, and the cycle of selection and amplification continues until the pool converges on a small number of excellent binders. This year, we will continue to work on the selection a DNA aptamer that recognizes CA 125, a protein that is widely used as an ovarian cancer biomarker. Capillary electrophoresis is used to separate and collect the population of good binders. This approach has been shown by others to increase the speed and efficiency of the selection process.
Other Interests: drawing, graphic novels, listening to music.

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Jaie Woodard ’11 (Double degree) Jackson, MI
Advisor: Manish Mehta

 

Research Project: Computational Studies of Peptide-Solvent Interactions

Small biological molecules, such as di- and tripeptides, lend themselves well to quantitative computational analysis, as well as experimental investigation. The small tripeptides we are studying are chains of three alanine and/or glycine amino acids. I am using a combination of computational techniques to investigate the secondary structure of these molecules in their solvated state. Molecular dynamics simulations use calculated forces and Newtonian laws of motion to map the trajectories of systems of atoms over periods of nanoseconds or picoseconds.  Ab initio and semiempirical calculations numerically solve the Schrödinger equation, using quantum mechanical principles to calculate various molecular properties. Oberlin’s 70-node supercomputer makes it possible to carry out such highly complex calculations in a reasonable amount of time. Computational results complement experimental data collected by other members of the Mehta lab, using Nuclear Magnetic Resonance (NMR) Spectroscopy. Discoveries we make in studying these small peptides can be applied and expanded to provide insight into important aspects of larger peptides and proteins, including the process of protein folding.
Other Interests: horn playing, music composition, Wagner operas, Mahler symphonies, physics, math, Bach cello suites, history/philosophy of science, competitive walking, Schubert Lieder, Beethoven piano concerti, movies, women’s gymnastics.