Chemistry / Biochemistry
Contact
Department Chair:
Rebecca Whelan

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 2009-2010 Research

Fall 2009-2010 Research

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 include (but are not limited to):  Swing dancing, singing a cappella, tea drinking, hiking, biking, camping, running, swimming, cooking, amateur floristry and reading science fiction and fantasy.

 


Amy Austin ’11
Litchfield, CT
Advisor: Rebecca Whelan           

Research Project: Characterization of the Uropygial Secretions of the Gray Catbird

This project is an ongoing collaboration with Professor Mary Garvin of the Oberlin Biology Department. 

The uropygial gland produces secretions that birds distribute over their feathers during preening. We are interested in studying the uropygial secretions of the gray catbird because of the importance of this widely distributed species in the West Nile virus cycle; volatiles in the secretions may mediate interactions with mosquitoes that carry West Nile virus. We have begun to document how the gray catbird’s uropygial secretion composition changes with age, diet, breeding hormones, and migratory disposition; such variation has been documented in other bird species as well. During Summer 2009, members of the Whelan and Garvin labs collected uropygial secretion samples from nearly 150 wild gray catbirds. The volatile fraction of these samples was analyzed using solid phase microextraction sampling followed by gas chromatography-masss spectrometry (GC-MS). During the 2009-2010 academic year, the non-volatile compounds of the samples will be characterized using  solvent extraction followed by GC-MS. Preliminary data show the extracted samples to be highly complex; the identification of the many unknown compounds will be a central part of this research.

Other Interests: hiking, beading an d jewelry making, reading science-fiction and fantasy.

 


Dain Chatel '11
Scottsdale AZ 
Advisor:  William Fuchsman

Research Project: What Happens To Reducing Sugars When They React With Oxidants?

We are attempting to gain clues to the chemistry involved in oxidation of reducing sugars by monitoring oxidations of reducing sugars by ferricyanide ions (carbanion scavengers) at high pH.  We are examining the effects of changes in sugar structures on the extents of reaction.           
    Other Interests: writing, medicine, exercise, friends and family.

 

 


Matt Chaves ’11
Holliston, MA
Advisor:  Jason Belitsky          

Research Project: Melanin-Based Water Purification

While “melanin” is a well-known biochemical entity among the general public, scientists know surprisingly little about the fundamental biochemistry of melanins.  Nevertheless, what is known about these fascinating nano-structured pigments suggests a range of non-biological applications.  The Belitsky lab is interested in exploring the properties of melanins and synthetic analogs both to understand fundamental melanin biochemistry and to exploit these properties for environmental applications.  For example, eumelanin, the black to brown human pigment, is known to bind a wide range of metals and organic compounds, suggesting applications in water purification.  In particular, the lab has investigated the lead-binding ability of melanin from human hair (an otherwise discarded renewable resource) and synthetic analogs (generated by polymerization chemistry routes) for applications in heavy metal sequestration.  This work has unexpected led to a material that changes color upon binding, which is being developed as a sensor for lead.  This year we aim to further optimize the current class of melanin-based lead-binding materials and extend these studies to other environmental pollutants.    
    Other Interests: Brazilian Jiu Jitsu, swing dancing, cooking.

 


Neil Cole-Filipiak ‘10
Ypsilanti, MI
Advisor: Matthew Elrod

Honors Project:  Synthesis and 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 the synthesis of atmospherically relevant epoxides as well as NMR-based kinetics studies of their reactions in solutions that are representative of atmospheric aerosols. 
    Other Interests: photography, cacography, Lego.

 


Derrick Dennis  ’11
Detroit, MI
Advisors:  Sean Decatur & Alice Smith-Gicklhorm

Research Project: Vibrational Spectroscopy of Amyloids

Protein clumps known as amyloids are often bad actors inside the human body and have proven quite elusive to scientists' investigations.  Amyloids play a role in neurological diseases such as Alzheimer's and Parkinson's and in many other conditions, including diabetes. They are aggregates of extended fibrils composed of misfolded proteins and polypeptides, and they are rich in β-sheets, a flat type of protein secondary structure. Most infamous and most studied among the amyloids is amyloid-β-40 (Aβ40), the one seen in the brains of Alzheimer's patients. Using infrared vibrational spectroscopy techniques, our group can follow the process all the way from monomer states of the protein or polypeptide through soluble aggregates to fibrous aggregates.  We have found that there are two mechanisms of reaggregation and alignment, depending on the peptide concentration.  At low concentrations, strands detach from the aggregate and reattach themselves, sometimes to a different aggregate than the one from which they broke off.  At higher concentrations, strands are less inclined to break off and roam about, so rearrangement tends to be confined within a particular aggregate. At intermediate concentrations, both processes occur.
    Other Interests: Football, track and field, video games, cards, listening to music, working out, the outdoors, dancing, and watching movies. 

 


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.

 


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.

 


Haley Gittleman ’10
East Brunswick, NJ
Advisor:  Jason Belitsky          

Honors Project: Melanin-Based Water Purification

While “melanin” is a well-known biochemical entity among the general public, scientists know surprisingly little about the fundamental biochemistry of melanins.  Nevertheless, what is known about these fascinating nano-structured pigments suggests a range of non-biological applications.  The Belitsky lab is interested in exploring the properties of melanins and synthetic analogs both to understand fundamental melanin biochemistry and to exploit these properties for environmental applications.  For example, eumelanin, the black to brown human pigment, is known to bind a wide range of metals and organic compounds, suggesting applications in water purification.  In particular, the lab has investigated the lead-binding ability of melanin from human hair (an otherwise discarded renewable resource) and synthetic analogs (generated by polymerization chemistry routes) for applications in heavy metal sequestration.  This work has unexpected led to a material that changes color upon binding, which is being developed as a sensor for lead.  This year we aim to further optimize the current class of melanin-based lead-binding materials and extend these studies to other environmental pollutants.    
    Other Interests: tap dance, swing dance, playing harp, skydiving, video games.

 


Alexandra Gould '11 
Haddonfield, NJ
Advisor:  Robert Thompson

Project Title:  Colorimetric Determination of Capsaicinoids Content of Chili Pepper

Two spectroscopic methods for the determination of capsaicinoids, the hot agents of chili pepper, have the potential to serve as field methods. The methods appear to have the requisite specificity and sensitivity to provide a simple color test to assess the "heat" of the chili pepper. However, the products of the reactions are not definitively know, and it would be helpful to know the reaction chemistry in order to optimize the procedures. We will collect and purify the products of the two reactions and then characterize the products. Techniques such as mass spectrometry, infrared spectrophotometry, and NMR spectrometry will be used to identify the products. Synthesis of the compounds and comparison to the identified products will provide additional proof. Once the products are identified the methods will be validated and used to quantitate the capsaicinoids content of a variety of hot peppers.
Other Interests: Tae Kwon Do (third degree black belt), singing, and wire jewelry design,

 


Laura Grossi '12
Strongsville, OH 
Advisor:  William Fuchsman

Research Project: What Happens To Reducing Sugars When They React With Oxidants?

We are attempting to gain clues to the chemistry involved in oxidation of reducing sugars by monitoring reactions of reducing sugars by hydrazides (carbonyl scavengers) after treatment at high pH.  We are examining the effects of changes in sugar structures on the extents of reaction.

 

 

Other Interests: Playing piano and cello, playing soccer, biking, bowling, reading, playing Guitar Hero, and watching football.

 


Kevin Hu ’11,
New York, NY  FALL SEMESTER 2009
Advisor: Matthew Elrod

FALL 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.

SPRING SEMESTER 2010
Advisor: Rebecca Whelan

SPRING Research Project: Development of an immunoassay for peptide epitopes of CA125
 
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.


Michaela Hull 10 
St. Paul, MN 
Advisor:  Robert Thompson

Honors Project: Analysis of Drywall for Mercury

Drywall is made of gypsum, i.e. calcium sulfate. Calcium sulfate used to be mined for use in drywall, but recently the majority of calcium sulfate comes from a waste product at coal-fired power plant. The flue gases at these power plants are scrubbed with calcium hydroxide to remove sulfur-containing gases, and the solid waste is converted to calcium sulfate. A large fraction of the toxic metal, mercury, that originates with the coal is also removed by this process and may end up in the solid waste. We plan to analyze drywall manufactured from 1960 - 2010 and assess its mercury content. The dissolved drywall material will be subjected to cold-vapor atomic absorption spectrophotometry to measure the total mercury concentration. We expect to find an increasing mercury content over time.
Other interests: Weaving, knitting, crocheting, chain mail jewelry, ceramics, baking, strange and obscure facts, drawing, sketching, painting.

 


Jarin Joyner '10 
Atlanta GA 
Advisor:  William Fuchsman

Research Project: What Happens To Reducing Sugars When They React With Oxidants?

We are attempting to gain clues to the chemistry involved in oxidation of reducing sugars by monitoring oxidations of reducing sugars by ferricyanide ions (carbanion scavengers) at high pH.  We are examining the effects of changes in sugar structures on the extents of reaction.          
    Other Interests: violin and sports.

 

 

 


Justin Lenhard ’10 
Rochester, NY
Advisors:  Sean Decatur & Alice Smith-Gicklhorm

Research Project: Vibrational Spectroscopy of Amyloids

Protein clumps known as amyloids are often bad actors inside the human body and have proven quite elusive to scientists' investigations.  Amyloids play a role in neurological diseases such as Alzheimer's and Parkinson's and in many other conditions, including diabetes. They are aggregates of extended fibrils composed of misfolded proteins and polypeptides, and they are rich in β-sheets, a flat type of protein secondary structure. Most infamous and most studied among the amyloids is amyloid-β-40 (Aβ40), the one seen in the brains of Alzheimer's patients. Using infrared vibrational spectroscopy techniques, our group can follow the process all the way from monomer states of the protein or polypeptide through soluble aggregates to fibrous aggregates.  We have found that there are two mechanisms of reaggregation and alignment, depending on the peptide concentration.  At low concentrations, strands detach from the aggregate and reattach themselves, sometimes to a different aggregate than the one from which they broke off.  At higher concentrations, strands are less inclined to break off and roam about, so rearrangement tends to be confined within a particular aggregate. At intermediate concentrations, both processes occur.

 


Chris Lipski  ’10
Ashland, OR
Advisor: Manish Mehta

Honors 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.

 


Zoë McLaughlin '11 
Rochester, NY
Advisor: Norman Craig

Research Project:  Exploration of an Alternative Path for Synthesizing Deuterium and 13C Isotopomers of 1,4-Difluorobutadiene

Through recent work in our laboratory, a lengthy method for synthesizing isotopomers of the isomers of 1,4-difluorobutadiene was developed and applied to making some of the isotopomers. A new method that begins with the possible cycloaddition of 1,2-difluoroethylene and 1,2-dichloroethylene to give halocyclobutanes is being explored. The high-temperature, high-pressure reaction gave unwanted open-chain halobutenes. We are now trying photosensitization of the cycloaddition reaction. A method for converting the halocyclobutane into the difluorobutadiene is known, and isotopomers of the two haloethylenes have been prepared before.
Other Interests: Other interests: Good books, writing stories, Bible trivia, dancing, playing in pit orchestras, the unexplained.

 


Eliza Milner '11 
Oak Ridge, TN 
Advisor:  William Fuchsman

Research Project: What Happens To Reducing Sugars When They React With Oxidants?

We are attempting to gain clues to the chemistry involved in oxidation of reducing sugars by monitoring reactions of reducing sugars by hydrazides (carbonyl scavengers) after treatment at high pH.  We are examining the effects of changes in sugar structures on the extents of reaction.           
    Other Interests: neural modeling, nifty math tricks, co-ops, circus things, punk shows, cooking, pragmatism, and mass transit.

 


Shana Osho ’10    Oberlin Article
Lagos, Nigeria
Advisor: Laura Romberg

Honors Project: Regulation of Bacterial Protein Polymerization

When bacterial cells reproduce, a protein called FtsZ assembles polymerize to 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: Soccer (sports in general), French literature, video games, social justice and music.

 


Clara Shaw '10  Rosevill, MN

Advisor: Rebecca Whelan

Research Project: Characterization of the uropygial secretions of the gray catbird

This project continues a collaboration with Professor Mary Garvin of the Oberlin Biology Department. The uropygial gland produces secretions that birds distribute over their feathers during preening. We are interested in studying the uropygial secretions of the gray catbird because of the importance of this widely distributed species in the West Nile virus cycle; volatiles in the secretions may mediate interactions with mosquitoes that carry West Nile virus. It is unknown how the gray catbird’s uropygial secretion composition changes with age, diet, breeding hormones, and migratory disposition, although such variation has been documented in other bird species.

Other Interests: running, reading, baking muffins, playing with cute animals


Joseph Thome '10
Middleburg Heights OH 
Advisor:  William Fuchsman

Honors Project: Separations of NAD(P), NAD(P)H, and NAD(P)H Dimer.

We are attempting to separate and identify products of NADH and NADPH oxidations by oxygen that are catalyzed by oxidized hemoglobin and myoglobin,   We are collaborating with Rebecca Whelan on the use of HPLC and capillary electrophoresis techniques.

Other Interests: swing dancing, playing the piano, singing opera, and playing tennis.

 


HengFeng (Fall) Tian ’10 
Wuhan, China
Advisor:  Norman Craig         

Honors Project: Syntheses of Isotopomers of the Isomers of 1,3,5-Hexatriene and Analysis of High-Resolution Spectra for Structure Determination

Deuterium and 13C isotopomers of the cis and trans isomers of 1,3,5-hexatriene are being synthesized, and ground state rotational constants are being found from the analysis of C-type bands in the high-resolution infrared the trans isomer and directly from microwave spectra for the cis isomer. From the rotational constants and quantum chemical calculations, semi-experimental equilibrium structures will be found with the goal of assessing the structural consequences of pi-electron delocalization.  To date the 1,1-d2, trans-1-d1, and cis-1-d1 isotopomers have been prepared.  The same synthetic path should yield the 1-13C1 and the 2-d1 species.          
Other interest: reading and sleeping.

 


Sophie Toraby  '11   Cos Cob, CT      Advisor:  Rebecca Whelan

Research Project:  Selection of an aptamer that recognizes a CA 125 epitope

Description:  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.

 

Other Interests:  enjoy knitting, minesweeper and procrastination, singing, dancing, skiing, frisbee, cuddling, sleeping in the sunshine, and long walks on the beach.

 


David Tran  ’10
Philadelphia, PA
Advisors:  Sean Decatur & Alice Smith-Gicklhorm

Honors Project: Vibrational Spectroscopy of Amyloids

Protein clumps known as amyloids are often bad actors inside the human body and have proven quite elusive to scientists' investigations.  Amyloids play a role in neurological diseases such as Alzheimer's and Parkinson's and in many other conditions, including diabetes. They are aggregates of extended fibrils composed of misfolded proteins and polypeptides, and they are rich in β-sheets, a flat type of protein secondary structure. Most infamous and most studied among the amyloids is amyloid-β-40 (Aβ40), the one seen in the brains of Alzheimer's patients. Using infrared vibrational spectroscopy techniques, our group can follow the process all the way from monomer states of the protein or polypeptide through soluble aggregates to fibrous aggregates.  We have found that there are two mechanisms of reaggregation and alignment, depending on the peptide concentration.  At low concentrations, strands detach from the aggregate and reattach themselves, sometimes to a different aggregate than the one from which they broke off.  At higher concentrations, strands are less inclined to break off and roam about, so rearrangement tends to be confined within a particular aggregate. At intermediate concentrations, both processes occur.

 


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.