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

Student Projects Summer 07

Student Projects Summer 07

Ryan Felix
Nathan Gorham
Robert Hartley
Robin Holmes
Serena Hsin
Michaela Hull
Tera Levin
Matthew Leyden
Katie Mauck
Emily Minerath
Lee Moore
Isaac Nelson-king
Deacon Nemchick
Alex Nichols
Craig Packard
Erika Rohrs
Matt Rumizen
Valenin Rusu
Karin Sono
Melissa Tai
Matt Thayer
Fall Tian
Sydney Williams
Jaie Woodard

 

 

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.

~~~~

 

Isaac Nelson-King ‘08
Woodinville, WA

Advisor: Jason Belitsky
Research Project: Synthetic Eumelanin for Environmental Remediation

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. We are investigating melanin derived from human hair, as well as synthetic melanin obtained through biomimetic enzymatic polymerization, metal-templated oxidation, and step-by-step organic synthesis. The resulting materials are being investigated as binding agents for pollutants such as lead, organic dyes, and PCBs.
Other interests: linguistics, history, guitar, and cartooning.

back to the top

 

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.

~~~~

 

 

Alex Nichols ‘08 Concord, MA
Advisor: Manish Mehta
Research 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.

back to the top

 

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.

~~~~

 

Craig Packard '09 Wolcott, NY
Advisor: Michael Nee
Research Project: Cucurbiturils as Nanocontainer Catalysts for Aza-Cope Rearrangements

Cucurbiturils are pumpkin-shaped macrocyclic molecules with
cavities large enough to bind other molecules inside the cavity. We are
interested in using cucurbiturils as nanocontainers for the catalysis of
reactions. The aza-Cope rearrangement of different vinyl allyl aminium ions has been found to be catalyzed by binding inside a cucurbituril. The shape selectivity of the different sizes of cucurbiturils is being investigated by NMR kinetics studies of this rearrangement reaction.
Interests: Volleyball, musicals/vocal music, armchair philosophy, that feeling in the air just before a thunderstorm, bad puns, alternate histories, chocolate-covered pretzels.

back to the top

 

Katie Mauck ‘09 Worthington, OH
Advisor
: Catherine Oertel
Research Project:
The Role of Sodium Chloride in 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, robbing valuable instruments of their ability to produce sound. Degradation of the pipes, which are made from lead-tin alloys, occurs primarily through attack by acetic acid vapor that is emitted from the wood of organ cases. Surface deposits, such as sodium chloride, that come from an organ’s environment can also influence the corrosion process. While sodium chloride generally increases corrosion of metals, a preliminary set of experiments showed decreased corrosion on samples treated with salt. We are examining in detail the role of sodium chloride on corrosion of lead-tin alloys containing between 1 and 10% Sn.
We are using laboratory exposure experiments in which metal coupons of specific compositions are exposed to low, controlled concentrations of acetic acid vapor. A coating of sodium chloride is applied to sample surfaces using a spraying technique. The extent of corrosion is monitored on treated and untreated samples through gravimetric analysis, and corrosion products are characterized using powder X-ray diffraction and scanning electron microscopy.
Other Interests: art, playing soccer, baking things, making things, art, playing Euchre, Set, and other card games, reading, being amongst greenery, singing.

~~~~

 

Lee Moore ‘08 Durham, NC
Advisor: Rebecca Whelan
Research Project: Synthesis of a peptide mimic of the ovarian cancer biomarker 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. The goal of this project is to synthesize a peptide with the same amino acid sequence as the antibody-binding region of the repeat domain. It is hoped that the antibodies that have affinity for CA125 will also bind the peptide and that analytical assays designed to detect the peptide will also be useful in detecting CA125 in the form found in blood. Compared to the intact protein, the peptide is expected to be more stable, more amenable to crystallization for structural characterization by x-ray diffraction methods, and substantially less costly.
Other interests: bike rides and mechanics, emergency medicine, music.

 back to the top

 

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.

~~~~

 

Deacon Nemchick ’09 North
Huntingdon, PA

Advisor: Norman Craig (supported by a grant from the Dreyfus Foundation)
Research Project: Synthesis of Isotopomers of 1,4-Difluorobutadiene for Use in High-Resolution Infrared

Spectroscopy and Equilibium 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.

back to the top

 

Robin Holmes ‘09 Homewood, IL
Advisor: Norman Craig (supported by a grant from the Dreyfus Foundation)
Research Project: Synthesis of Isotopomers of 1,3,5-Hexatriene for Use in High-Resolution Infrared Spectroscopy and Equilibium Structures of the cis and trans Isomers

Chemistry is being explored for preparing deuterium and carbon-13 isotopomers of 1,3,5-hexatriene. One method involves making methyl ethers of trans,trans-2,4-hexadien-1-ol and 1,5-hexadien-3-ol and subjecting these ethers to hydrogen-deuterium exchange in sodium deuteroxide at 120°C. Another method consists of reducing the ester of 2,4-pentadienoic acid to the aldehyde with dibutyl aluminum hydride and then forming hexatriene with methyl triphenylphosphonium iodide, as the carbon-13 or deuterium isotopomer. The goal is to obtain equilibrium structures of the cis and trans isomers of hexatriene, which should show larger structural consequences of pi-electron delocalization than butadiene, the first member of the polyene series. The spectroscopic and calculational methods described in Deacon Nemchick's project will be applied.
Other Interests: Food, backpacking, horsebackriding, food, sleep, food, Dr. Pepper.

~~~~

 


Nathan Gorham’07 Philadelphia, PA
Advisor: Jason Belitsky
Research Project: Synthetic Eumelanin for Environmental Remediation

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. We are investigating melanin derived from human hair, as well as synthetic melanin obtained through biomimetic enzymatic polymerization, metal-templated oxidation, and step-by-step organic synthesis. The resulting materials are being investigated as binding agents for pollutants such as lead, organic dyes, and PCBs.
Other Interests: weight-lifting, chess, brazilian jiu-jitsu, backpacking and traveling, golf, any one-on-one sport, attempting to learn French.

back to the top

 

Karin Sono ‘08 Kyoto, Japan
Advisor: Jason Belitsky
Research Project: Synthetic Eumelanin for Environmental Remediation

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. We are investigating melanin derived from human hair, as well as synthetic melanin obtained through biomimetic enzymatic polymerization, metal-templated oxidation, and step-by-step organic synthesis. The resulting materials are being investigated as binding agents for pollutants such as lead, organic dyes, and PCBs.
Other Interests: opera, piano, Spanish, religions, and geography.

~~~~

 

Matt Thayer ’08 Livonia, MI
Advisor: Rebecca Whelan
Research Project: Development of an SPR immunoassay for CA125

Surface plasmon resonance (SPR) sensing enables the sensitive detection of protein molecules in real time, and without the need for labels. The goal of this project is the development of an immunoassay for the glycoprotein CA125, the most important biomarker of ovarian cancer. Detection is accomplished on a gold surface that is functionalized in serial fashion, first by deposition of a self-assembled monolayer containing reactive head groups, next by covalent coupling of recombinant Protein G, then by affinity capture of an antibody with affinity for CA125, and finally by binding of CA125 itself. The SPR signal changes with each step in the deposition, enabling the development of a calibration curve when solutions of known CA125 concentration are captured. Preliminary results indicate that our method can reliably detect CA125 at levels three-fold below the clinically relevant threshold with a linear dynamic range of three orders of magnitude.
Other Interests: Microbiology, Middle Eastern Politics & History, Cooking, Hiking, and Electronica.

back to the top

 

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.

~~~~

 

Ryan Felix ‘08 Willoughby, OH
Advisor: Albert Matlin
Research Project: Intramolecular Photocycloaddition Reactions of 4-oxa-1,5-hexadienes

A series of 2-acyl-4-oxa-1,5-hexadienes are being synthesized with the enone system incorporated in a six-membered ring. These compounds are then irradiated with ultraviolet light (? = 350 nm) to give intramolecular [2+2] photocycloadditon products in high yield. Initial results suggest that the 4-oxa substitution does not signficantly change the regiochemistry of the photoreaction from that observed with the deoxy compounds.
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.

back to the top

 

Michaela Hull ‘10 Saint Paul, MN
Advisor: Catherine Oertel
Research Project: Synthesis of Low-Symmetry Inorganic-Organic Network Materials

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. The choices of both metal and ligand can be important in promoting formation of low-symmetry products. Chiral ligands can lead to non-centrosymmetric solids, as can asymmetrically coordinated metals that contain stereochemically active lone pairs.
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 – and Pb2+ as building blocks to promote low symmetry. 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 non-centrosymmetric networks.
Other Interests: Art, horseback riding, tae kwon do, dance (all kinds), sewing, travel…

~~~~

 

Matthew Aaron Leyden ‘08
Trumbull, CT
Advisor: Albert Matlin
Research Project: 5-Hexenyl Radical Cyclizations: A Computational Study
5-Hexenyl radicals cyclize to form either cyclopentyl or cyclohexyl systems.

This reaction has been the subject of numerous mechanistic studies and has found wide application in the synthesis of complex organic molecules. Previous work in the Matlin lab investigated the effect of 4-oxa substition on the regiochemistry and rate of the cyclization. This summer we are carrying out a comprehensive computational study of the cyclization as a function of alkyl substitution at C3 and C5 and oxa substitution for C4. The geometries and energies of several competing transitions states are being calculated inorder to understand the factors affecting the mode (exo vs. endo) of cyclization.
Other Interests: Music: The Fray, Counting Crows, Goo Goo Dolls, and anything Korean. Academic: ethics, Korean language, math, micro-biology Recreational: socializing, hiking, dancing, dismantling computers… systematically of course.

back to the top

 

Melissa Tai, 08 South Kingstown, RI
Advisor: Rebecca Whelan
Research Project: Optimization of tools for aptamer selection

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. A long-term goal of research in the Whelan lab is to explore a relatively new class of affinity molecules—aptamers—and to develop analytical assays that exploit their advantages. Aptamers are single-stranded nucleic acid molecules with recognition ability comparable to antibodies. The process of aptamer selection begins with a large 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 summer, we will optimize the processes by which candidate oligos are amplified and made single-stranded in pursuit of our goal to select a DNA aptamer that recognizes CA 125, a protein that is widely used as an ovarian cancer biomarker.
Other Interests: Viola, Classical Music, cooking, drawing, science fiction and fantasy books, Buffy the Vampire Slayer!!, movies, making jewelry.

~~~~

 

Robert Hartley ‘08 Seattle, WA
Advisor: Manish Mehta
Research Project: 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.

back to the top

 


Sydney Williams ‘09 Chico, CA
Advisor: Rebecca Whelan
Research Project: Selection of an aptamer that recognizes CA125 via capillary electrophoresis

Aptamers are single stranded oligonucleotides—DNA or RNA—that are selected out of a large, random pool on the basis of a particular function. Often aptamers function as high-affinity binders to biological molecules. The process of selecting aptamers relies on repeated cycles of selection and amplification until a small number of oligos with the desired binding property dominate the pool. Selection can occur in one of two formats, on a stationary phase or in free solution. My contribution to this project is the development and optimization of a selection process based on the microscale separations method of capillary electrophoresis that will identify candidate oligos that bind to the ovarian cancer biomarker CA125. It is hoped that such aptamers may form the basis of new detection methods for ovarian cancer.
Other Interests: drawing, graphic novels, listening to music.

~~~~

 

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 summer will focus on the synthesis of O-aminoserine, the unnatural amino acid necessary for the reaction with peptides, and 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.

back to the top

 

Tera Levin ‘07 Champaign, IL Advisors: Rebecca Whelan and Mary Garvin (Biology)
Research Project:
Detection of volatile compounds in the uropygial gland secretions of catbirds

The uropygial gland of birds, also known as the preen gland or oil gland, produces secretions that are important in maintaining the health and structural integrity of feathers. The gland is located at the base of the tail where birds may easily use their bill to squeeze the gland, extract the secretions, and distribute them over the feathers. These secretions are believed to play a number of functions including waterproofing and conditioning the feathers, as well as protection from insect pests, and even predators. Some of the components of the gland secretions, including waxes, lipids, and alcohols, have been described over the past 50 years in several species of birds. However, only in 2004 it was discovered that preen gland secretions contain volatile compounds. Such compounds are particularly interesting because of their potential importance in olfactory communication both within and across species. The goal of this project is the use of solid-phase microextraction headspace sampling followed by gas chromatography-mass spectrometry to detect and identify volatiles in uropygial gland secretions of catbirds.
Other Interests: biology, movies, volleyball, and kittens.

~~~~

 

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.

 

back to the top