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

Fall 08 - Spring 09

Fall 08 - Spring 09

Ben Baldwin, Andover, MA
Advisor: Michael Nee

Honors Project: Template Synthesis of Methyl-Substituted 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. 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 relatively low solubility of cucurbiturils in water and other solvents limits the utility of these molecules. Methyl substitution along the equator of cucurbiturils significantly increases the solubility of these compounds. However, so far only CB[5]s and CB[6]s have been synthesized and isolated with methyl substitution. We investigating the use of template molecules to synthesize methyl substituted CB[7]s and possibly CB[8]s.
Other Interests:  Music, the news, guitar, rugby sometimes, traveling, the outdoors, the indoors, speaking Spanish poorly, looking at maps.



Neil Cole-Filipiak, AYpsilanti, MI 
Advisor: Michael Nee

Research Project: Template Synthesis of Methyl-Substituted 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. 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 relatively low solubility of cucurbiturils in water and other solvents limits the utility of these molecules. Methyl substitution along the equator of cucurbiturils significantly increases the solubility of these compounds. However, so far only CB[5]s and CB[6]s have been synthesized and isolated with methyl substitution. We investigating the use of template molecules to synthesize methyl substituted CB[7]s and possibly CB[8]s.   Other Interests: photography, Star Trek, cooking, Legos, useless trivia.



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 lengthening 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 small dipole moment, microwave spectroscopy, a direct form of rotational spectroscopy, can be used and has been for the unsubstituted cis isomer.  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 current effort 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.



Kaitlyn Gam ’10, San Francisco. CA
Advisor: William Fuchsman

Research Project: The Stoichiometry of Hemoglobin- and Myoglobin-Catalyzed NAD(P)H Oxidase Reactions

Using our newly developed methods for measuring hydrogen peroxide concentrations in the presence of excess NADH and NADPH, we are examining the pH dependence of the stoichiometry of hydrogen peroxide-producing reactions of oxygen with NADH and NADPH.  We also are testing the hypothesis that deviations from the idealized 1:1 stoichiometry of NAD(P)H consumed to hydrogen peroxide produced might involve catalyzed reactions of hydrogen peroxide with NAD(P)H that produce water.  Interests: cooking,  open water swimming, and peer health education.



Robin Gent ’09, Cheshire, CT
Advisor:  Robert Thompson

Research Project: Development of a Colorimetric Assay for Capsaicinoids in Chili Peppers
Capsaicinoids, 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. 6-ene-8-methyl capsaicin:

 

There exists a need in the chili growers’ community for a simple test for the capsaicins (double-bond in the acyl chain of the capsaicinoid molecule) and non-capsaicins (all single bonds in the acyl chain).  A simple and quick test would provide growers important feedback as they attempt to breed both hotter and milder chilis.  The goal of this project is to design and develop a colorimetric method to determine capsaicin (and analogs) and dihydrocapsaicin (and analogs) in chili pepper fruits.

The extraction and separation should only require stirring and filtering, and the quantitation should only involve a color comparison.  We will begin by examining two promising color-forming reactions with the goal of understanding the reaction chemistry and identifying the colored products.  Other Interests: natural science (ie, chemistry, geology, biology, oceanography and the like), hiking, cannoeing, writing and literature.

 



Robin Holmes ’09  Ellicott City, MD
Advisor: Albert Matlin

Honors Project: Intramolecular Photocycloaddition Reactions of bis-Enones

Recently the Matlin lab has been investigating the photocyclization of bis-enone tethered by alkyl bridges of varying length to give bicyclic di-ketones.  These studies have shown that the nature of the addition (head-to-head vs. head-to-tail) and the yield varies as a function of the length of the tether.   When the tether is  -CH2-CH2- the cyclization produces a bicyclo[2.1.1] system but the reaction is not clean and produces several other unidentified products.  This year Robin will study the effect of rigidifying the tether using a cyclohexane group to lock the enones in a more favorable geometry for cyclization.  Other Interests: interests: running, sailing, growing plants, and wheat chex.



Serena Hsin ‘09 Phoenix, AZ
Advisor: Matthew Elrod

Honors 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: Modern/ contemporary dance, dance techniques, Feve brunch, Black River coffee, biking, white peaches, blueberry picking, dresses, healthy-active lifestyle, reading short stories.



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. 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.



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 recently used hydrothermal conditions to crystallize two corrosion products, Pb(CH3COO)2•2PbO•nH2O and  Pb(HCOO)(OH).  We are now using reactions between lead and carboxylic acids to synthesize new members of this family of compounds.  Products are characterized using powder and single-crystal X-ray diffraction as well as thermogravimetric analysis and Raman spectroscopy.  Other Interests: Art, horseback riding, tae kwon do, dance (all kinds), sewing, travel.



Hadley Iliff ’09 Greensboro, NC
Advisor:  Catherine Oertel

Honors 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 interests: knitting and yarn, eating (good) food, playing cards and dominos.



Ben Jakubowski ’11 St. Cloud, MN
Advisor: Albert Matlin

Research Project: Photochemical and Thermal Enanantioselective Nazarov Cyclizations
    
The classical Nazarov cyclization involves treating a cross-conjugated dienone with strong acid to produce substituted cyclopentenones.  In some systems the reaction can be carried out by irradiating the dienone with ultraviolet light.  In this study Ben will be trying to develop an enantioselective variant of this reaction using chiral amines (to create chiral iminium salts).
Other interests: Beyond my academic endeavors, I am interested in nature writing, folk music, and Northern Minnesota's environmental history. In my free time, I like playing guitar, backpacking, contra dancing, and reading.



Emmanuel Magara ’11 Gweru, Zimbabwe
Advisor: William Fuchsman

Research Project: A New Look at an Old Reaction:  The Dinitrosalicylate Assay for Reducing Sugars

The conventional wisdom that when reducing sugars react with oxidants, carboxaldehyde groups on the sugars oxidize to carboxylate groups, is inconsistent with preliminary comparisons of calibration curves for different reducing sugars, which show chain-length dependency and also differences between reducing sugars that are monosaccharides and those that are disaccharides.  We  are comparing the reactions of different reducing sugars with dinitrosalicylate and attempting to get some clues about the nature of the reaction. Other interests: Chinese language and culture, philately (stamp collecting), cooking and baking.



Katie Mauck ’09 Worthington, OH
Advisor:  Catherine Oertel

Research Project: Corrosion of Lead-Tin Alloys:  Applications to Conservation of Organ Pipes

Around the world, pipes in historic organs are suffering from damaging corrosion that eventually causes formation of cracks and holes in the metal, robbing valuable instruments of their ability to produce sound.  Organ pipes are most commonly made from lead-tin alloys, ranging in composition from pure lead to pure tin.  We are studying corrosion of these alloys with the goal of learning how deterioration of organ pipes can be prevented or slowed.  Specifically, we are studying how alloy composition affects the susceptibility of pipe metal to attack by acetic acid, which is emitted in appreciable quantities by the wood of organ cases.  In addition, we are examining the role of surface deposites, such as sodium chloride, that come from an organ’s environment.    
We are using laboratory exposure experiments in which metal coupons of specific compositions are exposed to low, controlled concentrations of acetic acid vapor.  The extent of corrosion is monitored through gravimetric analysis, and corrosion products are characterized using powder X-ray diffraction and scanning electron microscopy. Finally, in collaboration with the Center for Surface Analysis of Materials at Case Western Reserve University, we will use focused ion beam milling to carry out detailed analyses of corrosion sites.  Interests: art, food, French, singing, completing crossword puzzles.



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

Honors 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: Knitting, baking, reading, playing cards and dominoes, ballet and modern dance, homemade granola, watching thunderstorms, being outdoors.



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

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

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.  Ground state rotational constants have been secured for the two unsubstituted isomers.  A sequence of steps, dependent on assembling two haloethylenes, to synthesize the isotopomers has been fully developed with non-isotopic materials and is now being applied to making the needed deuterium and carbon isotopomers.
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.



Saki Nishi  ’09 Kobe, Japan
Advisor:  Robert Thompson

Research Project: The Argentation Solid Phase Extraction of the Capsaicins

Capsaicinoids, 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. 6-ene-8-methyl capsaicin:


One of the means of separating the capsaicinoids is by argentation chromatography, in which silver ion interacts strongly with those compounds containing a double bond in the acyl chain (the capsaicins).  Argentation chromatography is usually carried out by incorporating silver ion in the stationary phase and eluting with nonpolar solvents. Solid phase extraction (SPE) can be viewed as low pressure and low performance chromatography and is widely used to clean up samples prior to instrumental analysis. We employ argentation SPE to fractionate the capsaicinoids from chili pepper fruit (Talanta 2006, 70, 315-322). Several commercial SPE stationary phases can be used for this purpose. The goal of this project is to compare these SPE products for use in isolating the capsaicins, to measure the amount of silver that leaches from the cartridges, and to determine the efficiency of separation. Measurement techniques will include UV spectrophotometry, atomic absorption spectrophotometry,  and liquid chromatography-mass spectrometry. Other interests: Biking, baking, shopping, languages and dogs.



Bret Nolan ’09 Medina, OH
Advisor: William Fuchsman

Research Project: A New Look at an Old Reaction:  The Dinitrosalicylate Assay for Reducing Sugars

The conventional wisdom that when reducing sugars react with oxidants, carboxaldehyde groups on the sugars oxidize to carboxylate groups, is inconsistent with preliminary comparisons of calibration curves for different reducing sugars, which show chain-length dependency and also differences between reducing sugars that are monosaccharides and those that are disaccharides.  We  are comparing the reactions of different reducing sugars with dinitrosalicylate and attempting to get some clues about the nature of the reaction.
Other Interests: Running, Reading good books, knitting, travel, chai tea.



Craig Packard ‘09   Wolcott, NY
Advisor: Michael Nee

Honors 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. 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.



Robin Rohwer ’09  Ellicott City, MD
Advisor:  Robert Thompson

Honors Project: The Prevalence of Bisphenol A in the Diet of Oberlin Students Bisphenol A (BPA) is a precursor chemical for many commercial products, including food and beverage can liners and  reusable water bottles made from poly-carbonate plastic (recycling #7).  The compound has received much recent negative  press recently because it has been found to leach from containers and is a suspected agent in cancer and reproductive abnormalities. Some manufacturers are already phasing out products with BPA.
An early goal of this project is to adapt a literature method for bisphenol A to our particular setting with our instrumentation. The method involves extractions followed by liquid chromatography – mass spectrometry.
Once the method is in place we will examine cans and bottles in the Oberlin environment for leached bisphenol A and explore other sources of this chemical in the Oberlin student diet. We may compare cans with BPA-containing liners and those without and compare bottles made from polycarbonate and those made from other plastics.  Other interests: running, sailing, baking bread, eating fruit.



Edwin Takahashi ‘09 Mililani, HI
Advisor: William Fuchsman

Honors Project: The Stoichiometry of Hemoglobin- and Myoglobin-Catalyzed NAD(P)H Oxidase Reactions

Using our newly developed methods for measuring hydrogen peroxide concentrations in the presence of excess NADH and NADPH, we are examining the pH dependence of the stoichiometry of hydrogen peroxide-producing reactions of oxygen with NADH and NADPH.  We also are testing the hypothesis that deviations from the idealized 1:1 stoichiometry of NAD(P)H consumed to hydrogen peroxide produced might involve catalyzed reactions of hydrogen peroxide with NAD(P)H that produce water.  Other Interests: Outdoor activities, track and field and football.



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

Research Project: The Stoichiometry of Hemoglobin- and Myoglobin-Catalyzed NAD(P)H Oxidase Reactions

Using our newly developed methods for measuring hydrogen peroxide concentrations in the presence of excess NADH and NADPH, we are examining the pH dependence of the stoichiometry of hydrogen peroxide-producing reactions of oxygen with NADH and NADPH.  We also are testing the hypothesis that deviations from the idealized 1:1 stoichiometry of NAD(P)H consumed to hydrogen peroxide produced might involve catalyzed reactions of hydrogen peroxide with NAD(P)H that produce water.  Other Interests: playing piano, singing, learning languages, tennis, volleyball, and swing dancing.





Sydney Williams (Beckman Research Fellow) ‘09 Chico, CA
Advisor: William Fuchsman

Honors Project: A New Look at an Old Reaction:  The Dinitrosalicylate Assay for Reducing Sugars

The conventional wisdom that when reducing sugars react with oxidants, carboxaldehyde groups on the sugars oxidize to carboxylate groups, is inconsistent with preliminary comparisons of calibration curves for different reducing sugars, which show chain-length dependency and also differences between reducing sugars that are monosaccharides and those that are disaccharides.  We  are comparing the reactions of different reducing sugars with dinitrosalicylate and attempting to get some clues about the nature of the reaction. Other Interests: drawing, graphic novels, listening to music.



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.