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

Spring Student Research 2008

Spring Student Research 2008
Margaret Compton
Assiiatou Diallo
Ryan Felix
Amelia Hadler
Robert Hartley
Serena Hsin

 

 

Matthew Leyden
Byran McClain
Emily Minerath
Lee Moore
Isaac Nelson-King
Deacon Nemchick
Alex Nichols



Rachel Randall
Erika Rohrs
Matt Rumizen
Valentin Rusu
Shalini Saha
Karin Sono

 

Edwin Takahashi
Heng Feng (Fall) Tian
Christa Wagner
Sydney Williams
Jaie Woodard

 

 

Margaret Compton ‘09
Le Roy, NY
Advisor: Rebecca Whelan
Research Project: Development of a surface plasmon resonance immunoassay for CA125.

The ovarian cancer biomarker CA125 is a very large (>2 million Dalton), abundantly glycosylated protein that is found at elevated levels in the serum of many women with ovarian cancer. The development of novel detection strategies for CA125 is a central concern in the Whelan lab. Surface Plasmon Resonance Spectroscopy (SPR) provides a means of detecting protein-protein interactions in real time and without the need for labels. One important application of SPR is in the context of assays to detect proteins that are biomarkers of disease. In this project, an antibody molecule that recognizes the ovarian cancer biomarker CA125 will be immobilized onto the sensing surface of an SPR instrument, creating a specific test for CA125.

Other Interests: motorcycles and vintage cars, playing trombone, EMS (Emergency Medical Services), knitting, reading

 

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Assiatou Diallo
New York, NY
Advisor: William Fuchsman
Research Project: On the Interpretation of Saturation Kinetics

Researchers and textbook writers who deal with enzyme-catalyzed reactions tend to over-interpret the mechanistic significance of saturation kinetics. By using the reaction that historically defined saturation kinetics, the catalysis of sucrose hydrolysis by the enzyme invertase, and comparing it with the catalysis of raffinose (another sugar) hydrolysis by invertase, I am trying to show that the presence or absence of saturation kinetics can depend upon the available stock solutions of reactants, even when the reaction mechanism is unchanged.

 

 

 

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Ryan Felix ‘08
Willoughby, OH
Advisor: Albert Matlin
Honors Project: Regiochemical Selectivity in the Intramolecular Photocycloaddition Reactions of Methylene-tethered bis-Enones.

In this study we are investigating the mode of intramolecular [2+2] photocycloaddion reactions of bis-enones to give either bicyclo[n.1.1] or bicyclo[n.2.0] ring systems as a function of the chain length of the intervening methylene chain that tethers the two reacting ends. We are interested in this reaction both in terms of the mechanistic questions posed by this system (and its relationship to other well-known intramolecular [2+2] photocycloadditons) and the synthetic possibilities of producing 5,6-disubstituted bicyclo[2.1.1]hexanes which are of interest in our lab as an advanced synthetic intermediates directed towards the synthesis of bicyclo[2.1.1]hexan-5,6-dione.
Other Interests: Defeating never-do-wells at every step of their evil schemes; taking long walks on the beach while reading to orphans; good books; keeping in shape, because fighting crime just isn’t enough to stay the development of those pesky love-handles; Concerns: developing workaholism.

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Amelia Hadler ’08 Atlanta, GA
Advisor: Catherine Oertel
Honors Project: Synthesis of Inorganic-Organic Network Materials Based on Lead Tungstate

In recent years, there has been increased interest in synthesis of hybrid inorganic-organic network compounds, in which single metal atoms or metal clusters are linked by organic ligands. Some compounds have been prepared using transition metal cations, organic ligands, and complex metallate anions including molybdate (MoO42–) and tungstate (WO42–). In the resulting structures, both the organic ligands and the metallate anions act as bridges between metal centers.
We are applying this strategy to the main-group Pb2+ cation. Because of the stereochemically active 6s2 electron pair on Pb2+, asymmetric coordination of the metal center is often observed. This system could therefore produce low-symmetry materials with the potential for non-linear optic (NLO) or piezoelectric properties. We are using solvothermal synthesis in aqueous and non-aqueous solvents to promote crystal growth. We are using powder X-ray diffraction as a primary means of product characterization, with the goal of using single-crystal X-ray diffraction to determine structures of new network compounds.
Other Interests: Baseball, religion, playing the French horn, books, the Civil War, Pakistan, old movies, and unpretentious music.

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Robert Hartley ‘08
Seattle, WA Advisor: Manish Mehta
Research Project: Computational Studies of Peptide-Solvent Interactions.

As the available computing power continues to increase, computer models of chemical systems are becoming more and more important and informative. I am performing molecular dynamics simulations (which use pre-calculated atom, bond and angle properties to simulate molecular motion) and quantum chemical calculations (which numerically solve the Schrödinger equation) to study the effects of solvation on simple di and tripeptides. We are performing these simulations using desktop machines and Oberlin’s 70-node supercomputer. Our computational studies complement experimental NMR measurements, made locally by other members of the research group, and provide a more detailed view of the structure and dynamics of model proteins in various solvent environments. Our ultimate goal is to apply what we learn about these small peptides to larger ones and to the secondary structure of biologically significant proteins.
Other Interests: Coming of Age Movies from the ‘80s, Novel Computing, EMS, Ice Cream, Diet Pepsi, Wandering Aimlessly,

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Serena Hsin ‘09
Phoenix, AZ
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: Modern/ contemporary dance, dance techniques, Feve brunch, Black River coffee, biking, white peaches, blueberry picking, dresses, healthy-active lifestyle, reading short stories.

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Matthew Aaron Leyden ‘08
Trumbull, CT Advisor: Norman Craig
Research Project: Toward Equilibrium Structures of the cis and trans Isomers of Hexatriene

Recently in cooperation with Dr. Richard Suenram at the University of Virginia, the first microwave (MW) spectra of cis-hexatriene were observed despite the very small (~0.05 D) dipole moment. To obtain much more of this material, which is needed for the MW spectra of the three 13C isotopic variants in natural abundance, various synthetic methods are being explored. We plan to use the rotational constants from the MW investigation to complete the analysis of the rotational structure in several C-type bands observed with high-resolution infrared spectroscopy. The ultimate goal is a semi-experimental equilibrium structure for both the cis and trans isomers of hexatriene. Such structures will test the hypothesis that pi-electron delocalization increases with length of the chain in conjugated polyenes and that this effect is reflected in larger changes in bond lengths than in butadiene.
Other Interests: Music: The Fray, Counting Crows, Goo Goo Dolls, and anything Korean. My iTunes shared music library is called “passwordispyrate.” Academic: ethics, Korean language, math, micro-biology Recreational: socializing, hiking, dancing, dismantling computers… systematically of course

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Bryan McLain ‘08
Downey, CA
Advisor: Robert Thompson
Research Project: Development of a colorimetric assay for capsaicins and noncapsaicins 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:

mcclain2

There exists a need 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) in chili pepper fruit. A simple and quick test would provide chili pepper 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 procedure to determine 6-ene-8-methyl capsaicin (and analogs) and 8-methyl dihydrocapsaicin (and analogs) in chili pepper fruits.
Two candidate color-forming reactions are under study. The products of the reactions between the capsaicinoids and the colorimetric reagents have not been fully characterized in the literature, so our initial goal is to isolate enough of the products to characterize them by liquid chromatography – mass spectrometery and by 13C NMR spectrometry. Then the colorimetric reactions will be tested with extracts of a variety of chili pepper fruits to develop a robust method that can be used in the field. The results of the colorimetric procedure should compare favorably with results from instrumental analysis, specifically LC-MS.
Other Interests: Anatomy and physiology, physics, mathematics, biology, philosophy, guitar (acoustic and classical), music, video games, logic, writing (Tolkien-ish fantasy short stories and novels) and reading (classic literature and sci-fi/fantasy), photography, light sabers and Jedi knights, World of Warcraft, and stealth mode.

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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. In particular, carbonyl-containing organic compounds are known to undergo aldol condensation reactions in acidic media. 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 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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Lee Moore ‘08
Durham, NC
Advisor: Rebecca Whelan
Research Project: Solid-phase peptide synthesis as a route to preparing a cancer biomarker mimetic

CA125 is an important biomarker, widely used in the diagnosis and monitoring of ovarian cancer. Recent structural elucidation of the protein revealed that it contains a large number of tandem repeat units, each 156 amino acids long, and within that repeat domain is a highly conserved 21-mer bounded on each end by cysteine residues. All known antibodies with affinity for CA125 bind to one of two unique sites within this 21-mer, suggesting that this relatively simple peptide could serve as a mimic for the intact protein during the development of CA125 assays. We have used solid-phase peptide synthesis to prepare the 21-mer peptide and are currently optimizing preparative HPLC conditions for its purification. Upon validation that the correct sequence has been prepared and purified, the peptide will be used as the target in an aptamer selection process, to complement the ongoing work in selecting an aptamer that recognizes intact CA125.
Other interests: bike rides and mechanics, emergency medicine, music.

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Isaac Nelson-King ‘08
Woodinville, WA
Advisor: Jason Belitsky
Research Project: Palladium-Catalyzed Methods for the Synthesis of Indole Oligomers Related to the Human Pigment, Eumelanin
Eumelanin is the black to brown pigment in humans and our primary photoprotective agent. It is an unusual nano-structured biomaterial, with many fascinating chemical properties that influence its biology and its role in skin cancer. Long thought to be a high molecular weight polymer, recent advances have shown that eumelanin is instead an assembly of relatively short heterogeneous oligomers of dihydroxyindoles. The ability to study the properties, self-assembly, and resulting nano-structures of well-defined synthetic oligomers will advance our knowledge of natural eumelanin. We are developing a novel approach to the synthesis of dihydroxyindole oligomers, based on palladium-catalyzed chemistry such as the Suzuki reaction, starting with indole-indole Suzuki couplings as a model system. While exploring the Suzuki reaction of indoles, we found an unexpected variation of the reaction itself (homo-dimerization of aromatic boronic acids), which we are pursuing as to its substrate scope and optimized reaction conditions. The refined methodology will be an excellent addition to the basic Suzuki reaction for our long-term goal of oligomer synthesis.
Other interests: linguistics, history, guitar, and cartooning.

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Deacon Nemchick ’09
North Huntingdon, PA
Advisor: Norman Craig
Research Project: Synthesis of Isotopomers of 1,4-Difluorobutadiene for Use in High-Resolution Infrared Spectroscopy and Equilibrium Structures of the cis and trans Isomers

Methods are being applied to synthesize specific deuterium and carbon-13 isotopomers of 1,4-difluorobutadiene. This chemistry depends on preparing isotopomers of fluoroethylene and fluoroiodoethylene, joining these two substances by a photochemical reaction into a difluoroiodobutene, and removing hydrogen iodide with base to make 1,4-difluorobutadiene. High-resolution (0.0013 cm-1) infrared spectra will be recorded of isotopomers of the cis,cis and trans,trans isotopomers by cooperating scientists at the Pacific Northwest National Laboratory. From the rotational constants obtained from analyzing the rotational structure in the high-resolution spectra and from quantum chemical calculations of vibration-rotation constants, an equilibrium structure good to 0.001 Å will be found. The goal is to assess the structural consequences of substituting hydrogen atoms with fluorine atoms in butadiene.
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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Alex Nichols ‘08
Concord, MA
Advisor: Manish Mehta
Honors Project: Hydration studies of a series of alanyl- and glycyl-containing tripeptides using solid-state NMR

By virtue of their size and relatively simple structure, small peptides (short strings of amino acids) often assume a wide range of low-energy conformations in solution. As such, they are exciting and challenging model system for understanding subtle elements of solvation and their effects on backbone torsion angles. Using a combination of liquid NMR, solid-state NMR, X-Ray and neutron diffraction, and quantum mechanical calculations, we seek to understand how the solvation state and associated chemical properties of glycine- and alanine-containing dipeptides and tripeptides change as the molecule transitions from the liquid state to the solid state.
Once branch of our work involves the study of a series of 8 glycine- and alanine-containing tripeptides. Collecting a complete set of chemical shift data requires knowledge of each peptide’s crystal structure as well as high quality crystals. I have therefore divided my efforts this summer between performing liquids experiments to make chemical shift assignments, crystal growth, and performing solids experiments on crystalline samples of known polymorphs.
Other Interests: Guitar, Running, Cycling, Rock Climbing, Russian Kettlebell, Vintage Audio Equipment, Valve Amplifiers, Electronics, Reading, Eating and Drinking Well.

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Rachel Randall ‘08
Fremont, OH
Advisor: William Fuchsman
Honors Project: Assaying Hydrogen Peroxide in the Presence of NADH and NADPH

Previous experimental studies on the oxidase-like catalytic behavior of hemoglobin and related oxygen-carrying proteins have illustrated the problem of trying to use spectrophotometric methods to measure hydrogen peroxide concentrations in the presence of the biological reducing agents NADH and NADPH. I am examining several different spectrophotometric methods for assaying hydrogen peroxide in order to establish whether they are partly or completely inhibited by NADH and NADPH, and if so, whether strategies of prior removal of NADH or three-dimensional calibration curves that take into account concentrations of NADH and NADPH will work to circumvent the inhibition. The information gained will allow more accurate determination of the ratio of NADH (or NADPH) consumed and hydrogen peroxide produced when hemoglobin (or related proteins) catalyzes the reaction of NADH (or NADPH) with oxygen.
Other Interests: Philosophy, aviation, bike rides, and my cat.

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Erika Rohrs ‘09
Kalamazoo, MI
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: electronica, sudoku, pineapple, modern dance, cooking, The Big Swap, medieval siege weapons, reptiles

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Matt Rumizen ‘09
Reading, MA
Advisor: Manish Mehta
Research Project: NMR analysis of Alanine/Glycine “Capped” Dipeptides

Over the past 20 years, nuclear magnetic resonance (NMR) spectroscopy has developed into a powerful technique for determining 3-dimensional protein structures. Our research over the summer involves NMR experimentation on modified dipeptides, which consist of linked pairs of amino acids; as such, they can be considered “smaller versions” of biologically occurring proteins, which may contain thousands of amino acids.
Since a traditional (1-dimensional) NMR spectrum is a series of peaks along a single axis, 2D correlation experiments must be done on each compound to deduce which peak corresponds to which atomic nucleus. After these assignments are made, we can return to the 1D spectra and match each atom with a specific chemical shift: a number that corresponds to the horizontal position of that atom’s peak on the spectrum.
Chemical shift values are extremely sensitive, and are affected by virtually every aspect of a nucleus’s local environment, including bonding geometry, oxidation state, participation in one or more hydrogen bonds, and proximity to neighboring atoms. Using chemical shift data from solution-state and solid-state NMR experimentation, combined with ab initio calculations performed by Jaie Woodard and Rob Hartley on Oberlin’s supercomputer, we can gain insight into the preferred spatial arrangement and solvation states of our dipeptides. Our hope is to place this smaller-scale “close-up” work in the context of general protein structure research.
Other Interests: learning about people, learning out of books, running, planning elaborate road trips, Calvin & Hobbes, outdoor stuff like camping/hiking/sailing, record collecting, biofuels, Elephant 6, Thai cooking, self-actualization, having a porch, and playing/hearing/ seeing music of any kind.

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Valentin Rusu ‘08
Parma, OH
Advisor: Jason Belitsky
Research Project: Aminooxy Serine Peptide Ligation

We are developing a new reaction that will be useful for the synthesis and chemical modification and peptides and proteins. The proposed reaction is member of a class of reactions known as chemoselective ligations that allow specific sites on biomolecules to be modified in aqueous solution without the use of protecting groups. Such reactions are contributing to advances in bio-imaging, proteomics, and drug development. The new reaction, aminooxy peptide ligation, will extend this chemistry to the amino acids serine and threonine, and feature peptide formation and site-specifically labeling in the same pot. Research this semester will focus on reaction development with model systems.
Other Interests: I love learning or practicing foreign languages and traveling to places I haven’t yet been. I also like listening to music, and, when I feel especially creative, playing guitar or writing poems.

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Shalini Saha ‘08
Kolkata, India
Advisor: William Fuchsman
Research Project: Assaying Hydrogen Peroxide in the Presence of NADH and NADPH

Previous experimental studies on the oxidase-like catalytic behavior of hemoglobin and related oxygen-carrying proteins have illustrated the problem of trying to use spectrophotometric methods to measure hydrogen peroxide concentrations in the presence of the biological reducing agents NADH and NADPH. I am examining several different spectrophotometric methods for assaying hydrogen peroxide in order to establish whether they are partly or completely inhibited by NADH and NADPH, and if so, whether strategies of prior removal of NADH or three-dimensional calibration curves that take into account concentrations of NADH and NADPH will work to circumvent the inhibition. The information gained will allow more accurate determination of the ratio of NADH (or NADPH) consumed and hydrogen peroxide produced when hemoglobin (or related proteins) catalyzes the reaction of NADH (or NADPH) with oxygen.
Other Interests: Right now, I am absorbed by my book, An American Tragedy, but in general, I enjoy, jewelry making, animal rights, piano, biology, chemistry, baseball, crime shows, and reading.

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Karin Sono ‘08
Kyoto, Japan Advisor: Jason Belitsky
Research Project: Eumelanin Based Materials as Lead Binding Agents

Eumelanin is the black to brown pigment in humans and our primary photoprotective agent. It is an unusual nano-structured biomaterial, with many fascinating chemical properties that both influence its biology and role in skin cancer, and could also be exploited for non-biological applications, including environmental remediation. Natural and synthetic eumelanins are known to bind a range of metals and organic compounds, and could be applied to the sequestration and potential photodegradation of environmental toxins. Previous research in our lab has demonstrated that polymeric discs coated with melanin derived from human hair, as well as synthetic melanin produced by a variety of routes, can effectively sequester lead and certain organic dyes from aqueous solutions. We are further optimizing and characterizing the lead-binding capability of these materials, particularly those obtained via biomimetic enzymatic polymerization, to develop their potential as lead-binding agents for environmental remediation.
Other Interests: opera, piano, Spanish, religions, 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

Previous experimental studies on the oxidase-like catalytic behavior of hemoglobin and related oxygen-carrying proteins have illustrated the problem of trying to use spectrophotometric methods to measure hydrogen peroxide concentrations in the presence of the biological reducing agents NADH and NADPH. I am examining several different spectrophotometric methods for assaying hydrogen peroxide in order to establish whether they are partly or completely inhibited by NADH and NADPH, and if so, whether strategies of prior removal of NADH or three-dimensional calibration curves that take into account concentrations of NADH and NADPH will work to circumvent the inhibition. The information gained will allow more accurate determination of the ratio of NADH (or NADPH) consumed and hydrogen peroxide produced when hemoglobin (or related proteins) catalyzes the reaction of NADH (or NADPH) with oxygen.
Other Interests: Outdoor activities, track and field and football.

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Heng Feng (Fall) Tian ’10
Wuhan, Hubei, China
Advisor: Catherine Oertel
Research Project: Synthesis and Characterization of Ternary Sulfide Nanoparticles

Synthesis of nanoparticles is currently a very active area of chemical research, largely because of the interesting properties exhibited by these nanometer-scale crystals. The high surface-to-volume ratio of nanoparticles makes them useful in catalysis. Hydrodesulfurization of fuels, particularly diesel, is a process that is frequently catalyzed by molybdenum sulfide activated by nickel and/or cobalt. That is, the active site of the catalyst contains Mo, S, and Co/Ni atoms. The goal of our research is to synthesize nanoparticles of MMoS4 (M = Ni, Cu, Co…) compounds, combining hydrodesulfurization activity with the high surface area offered by nanosize particles.
Both room temperature and solvothermal reaction conditions are being used to prepare these ternary sulfide nanoparticles. In order to control particle size and prevent particle agglomeration, we are using reverse micelle reaction media as well as solvents such as ethylenediamine and ethylene glycol that are capable of capping particle surfaces. Reaction products are characterized using powder X-ray diffraction, scanning electron microscopy, and thermogravimetric analysis.
Other interest: reading and sleeping.

 

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Christa Wagner ‘08
Wayne, PA
Advisor: Catherine Oertel
Honors Project: Synthesis of Hybrid Inorganic-Organic Compounds Using Amino Acid Ligands

In recent years, there has been increased interest in synthesis of hybrid inorganic-organic network compounds, in which single metal atoms or metal clusters are linked by organic ligands. Of particular interest are structures that lack centers of symmetry. These low-symmetry materials have useful applications because they can interact selectively with chiral guest molecules or behave as non-linear optic (NLO) or piezoelectric materials. Use of chiral molecules as linking ligands can promote formation of non-centrosymmetric solids.
We are using room temperature and hydrothermal methods to grow inorganic-organic network compounds with the potential for non-centrosymmetric structures. In particular, we are using the amino acids cysteine, aspartic acid, and glutamic acid – naturally occurring chiral ligands – to coordinate first-row transition metals. We are using powder X-ray diffraction and thermogravimetric analysis as the primary means of product characterization, with the goal of using single-crystal X-ray diffraction to determine structures of new non-centrosymmetric networks.
Other Interests: Baking, running, traveling, knitting, playing instruments, and exploring botanical gardens.

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Sydney Williams (Beckman Research Fellow) ‘09
Chico, CA
Advisor: Rebecca Whelan
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.

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