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

Student Research Fall 12

Student Research Fall 12

William Banfield  '15   Concord, MA      Advisor:  Matthew Elrod

Research Project:  Reactions of the Oxidation Products of Pinene-Derived Hydrocarbons on Secondary Organic Aerosol

Description:  Biogenic hydrocarbons (such as isoprene and pinene) play a role in both tropospheric ozone and secondary organic aerosol (SOA) formation, and are thus linked to air pollution and global climate change. We are interested in studying the kinetics of reactions of pinene-derived oxidation intermediates that may take place in SOA environments.  These processes are hypothesized to explain the various organic species that are observed in atmospheric SOA. This work will allow for a more detailed quantitative modeling of biogenic-derived SOA in the atmosphere.

Other Interests:  Improv comedy and Starcraft


Adam Birdsall  '13   Roseville, MN      Advisor:  Matthew Elrod

Honors Project:  Esterification Equilibria and Kinetics of Methacrolein-Derived Species on Secondary Organic Aerosol

Description:  Isoprene, 2-methyl-1,3 butadiene, is the most abundant non-methane hydrocarbon present in the atmosphere. This volatile alkene, produced mainly by trees, plays a key role in the formation of secondary organic aerosol (SOA), which is linked to air pollution and climate change mechanisms. One of isoprene’s gas phase oxidation products, methacrolein, apparently undergoes gas phase conversion to a hydroxycarboxylic acid species, which is then observed to undergo esterification reactions on existing SOA. We will synthesize the gas phase precursor and investigate the esterification equilibrium and rate constants for the reactions in model solutions that mimic the composition of SOA using nuclear magnetic resonance analytical methods.  These measurements will allow for a more detailed quantitative modeling of isoprene-derived SOA in the atmosphere.

Other Interests:  Devouring large quantities of music, drinking tea, enjoying silent film comedies, playing piano and racquetball (not simultaneously) reading, running


Dylan Bleier  '15   Ithaca, NY      Advisor:  Matthew Elrod

Research Project:  Reactions of the Oxidation Products of Pinene-Derived Hydrocarbons on Secondary Organic Aerosol

Description:  Biogenic hydrocarbons (such as isoprene and pinene) play a role in both tropospheric ozone and secondary organic aerosol (SOA) formation, and are thus linked to air pollution and global climate change. We are interested in studying the kinetics of reactions of pinene-derived oxidation intermediates that may take place in SOA environments.  These processes are hypothesized to explain the various organic species that are observed in atmospheric SOA. This work will allow for a more detailed quantitative modeling of biogenic-derived SOA in the atmosphere.

Other Interests:  Acoustic and electric guitar; The Beatles; squash, racquetball, and ultimate frisbee; backpacking and outdoor survival; The Stephanie Miller Show and This American Life; The New York Times and The Huffington Post; politics/current events, solar energy production, environmental issues, chemistry, physics.


William Burke  '15   Alpharetta, GA      Advisor:  Robert Thompson

Research Project:  Forgery or not?  Analysis of Aged Drying Oils in an Oil Painting.

Description:  Our goal is to develop a teaching experiment for analytical chemistry with the focus on an oil painting and whether or not it is genuine based on the drying oil used and its apparent age. The nature and age of the oils in an oil painting can be determined or estimated from analysis of the lipids in the pigment binder. A tiny bit of the paint can be made soluble, treated with reagent to create esters from the fatty acids, and analyzed by gas chromatography - mass spectrometry to reveal the number, type, and relative amounts of fatty acids present. This information can provide a clue as to the original drying oil used, be it linseed oil or walnut oil or other natural oil. The information can also indicate the approximate age of the painting since oxidation products, e.g. dicarboxylic acids from monocarboxylic acids, increase with time.

Other Interests:  At Oberlin,the observatory is an adventure in itself on rainy/snowy evenings. Cartoon/Animation/Anime club after the observatory is the cleanest funnest way to spend a Friday night in my experiences here. Can eat eight Stevenson burgers in one sitting. I enjoy Kendal visits.


Yihui Chen  '13   Singapore, Singapore      Advisor:  Norm Craig

Research Project:  Analysis of the Rotational Structure in High-Resolution Infrared Spectra

Description:  Our primary goal is to obtain accurate equilibrium structures for molecules in which π-electron delocalization plays an important role in modifying the structure. Molecules being studied are trans-hexatriene and the cis,cis and trans,trans isomers of 1,4-difluorobutadiene. Essential to this work is finding rotational constants for a suite of isotopically substituted species, which have been synthesized at Oberlin College. The rotational constants come from the detailed analysis of the rotational structure in high-resolution (0.0015 cm-1), gas-phase infrared spectra, which are recorded at Pacific Northwest National Laboratory. Current work is on the spectra of trans,trans-1,4-difluorobutadiene-1-d1 and trans-hexatriene-3-d1. Pattern-recognition software and other powerful computer programs are essential for finding believable paths of spectral subbands in the exceedingly dense jungle of lines in any band, the first step in the analysis.

Other Interests:  Jesus, education access, the intersection of science and religion, productive unproductivity, (listening to/playing) music, reading eating sleeping.


Sean Dembowski  '13   Pasadena, CA      Advisor:  Rebecca Whelan

Honors Project:  Synthesis of Biologically Functionalized Iron Oxide Nanoparticles

Description:  A promising strategy for cancer treatment is focused hyperthermia, in which tumor cells are transiently exposed to high temperatures, promoting their destruction. One way to achieve localized heating involves magnetic nanoparticles with surfaces covered by affinity molecules. Interaction of the affinity molecules with their target (CA125 in our case) immobilizes the nanoparticle onto a cancer cell. Application of an oscillating magnetic field increases the temperature of the nanoparticle by as much as 40˚C, “melting” the cell membrane. Under mild conditions, this melting reversibly perforates the cell, enabling the introduction of drugs or material for gene therapy. With more vigorous heating, cells can be killed outright. In a pilot study, 100% of prostate cancer cells targeted in this way were dead after 7 min in a magnetic field. Non-cancer cells subjected to identical treatment remained viable. Aptamers are only beginning to be used in applications of this sort, and they have yet to be examined in the treatment of ovarian cancer. Our work will demonstrate the use of aptamer-based targeting of ovarian cancer cells by coated magnetic nanoparticles for focused heating and destruction. This project is supported by the National Cancer Institute.

Other Interests:  Track & Field, Taiko Drumming, Swing and Blues Dancing, Juggling


Joe Duprey  '13   Bainbridge Island, WA      Advisor:  Jesse Rowsell

Research Project:  Method Development in the Synthesis and Characterization of Microporous Copper Carboxylates

Description:  HKUST-1 is a brightly colored microporous material formed from dimeric copper(II) tetracarboxylate clusters. Linking these clusters through trimesate moities leads to the formation of channels within the solid. These channels have the capacity to trap small molecules like alcohols, water and dihydrogen. I am working to develop an efficient way to synthesize HKUST-1 by determining how time, temperature, reaction stoichiometry and crystal seeding affect the crystal growth. To characterize the products, I am employing various forms of crystal structure and compositional analysis, including X-ray diffraction, FT-IR, diffuse reflectance UV-vis, thermogravimetric analysis and solvent exchange. The goal is to find which methods of synthesis and analysis will be most instructive in an inorganic teaching laboratory. 

Other Interests:  Bicycles and Italian Food


Rae Eaton  '13   Portland, OR      Advisor:  Rebecca Whelan

Honors Project:  Selection and Characterization of DNA Aptamers for Ovarian Cancer Biomarker HE4

Description:  DNA aptamers are oligonucleotides that recognize and bind targets of interest. An ongoing focus of the Whelan lab is the selection of aptamers for ovarian cancer biomarkers, with intended applications in novel diagnostic and therapeutic strategies. The aim of this project is to select an aptamer for HE4, a newly discovered ovarian cancer biomarker. HE4 has been found to complement the canonical cancer biomarker (CA125), and on the strength of its potential to detect cases of ovarian cancer missed by the CA125 assay, it was recently approved by the FDA for clinical use. We are using capillary electrophoresis-based systematic evolution of ligands by exponential enrichment (CE-SELEX) to identify DNA oligos with affinity for HE4. This approach has been shown by others to increase the speed and efficiency of the selection process. This work is supported by the National Cancer Institute.

Other Interests:  Tea, Fiber Arts, Bread, Sherlock Holmes, Human Diseases


Henrik Ehrhardt  '13   Oswego, NY      Advisor:  Mike Nee

Research Project:  Synthesis of Mesoporous TACN-Silica Hybrid Materials

Description:   Mesoporous materials are useful because they have pore sizes that can selectively incorporate organic molecules. We are seeking to make new mesoporous materials composed of a chelating organic component, a 1,4,7-triazacyclononane (TACN), and silica gel. The TACN components will act as ligands for manganese(III) ions. It is hoped that these new materials may be useful as an oxidation catalyst, perhaps for the removal of hazardous substances from water.

Other Interests:  Blues dancing

 


Zin Linn Htet  '13   From: Yangon, Myanmar

Advisor:  Sean Decatur

Research Project:  The Self-aggregation of a Polyalanine Octamer Promoted by its C-Terminal Tyrosine

Description: The polypeptide chain AKY(8) with its amino acid sequence (AAAAKAAY) form amyloid-like fibrils at room temperature in acidified aqueous solution. Other Oligoalanines of this size usually exhibit a statistical coil structure in aqueous solution with a predominant sampling of polyproline II conformation. My research is understanding what factors would contribute to the aggregation of AKY8; whether it is the sequence or the composition of amino acid that is important in fibrils formation. We use two different sequence of AKY8; AKY8(R) (AAAAAKAY) and AKY8(L) (AAAKAAAY) to see the effect of sequence on fibril formation.


Michael Jacobs  '15   Dayton, OH      Advisor:  Matthew Elrod

Research Project:  Gas Phase Oxidation Kinetics and Mechanisms for Atmospherically Relevant Epoxide Intermediates

Description:  Isoprene, 2-methyl-1,3 butadiene, is the most abundant non-methane hydrocarbon present in the atmosphere. This volatile alkene, produced mainly by trees, undergoes gas phase reactions to form epoxide intermediates. The oxidation of isoprene to epoxide intermediates is related to both tropospheric ozone and secondary organic aerosol (SOA) formation, and thus linked to air pollution and global climate change. We are interested in determining the mechanism and rate constants for the reactions of atmospherically relevant isoprene epoxide intermediates with OH radicals. Specifically, we are investigating the daytime OH radical initiated process using our lab's unique turbulent flow chemical ionization mass spectrometer (TF-CIMS).  These measurements will allow a determination of whether gas phase processes dominate the fate of epoxide intermediates, or whether aerosol phase processes.

Other Interests:  Watching the Cincinnati Reds play, reading, and watching movies


Andrew Karlin  '14   Poolesville, MD      Advisor:  Manish Mehta

Research Project: 

Description: 

Other Interests:  I am a pitcher for the varsity baseball team

 

 


 

Holden Lai  '15   Hong Kong      Advisor:  Mike Nee

Research Project:  Synthesis of More Water-Soluble Substitiuted Cucurbiturils

Description:  Abstract: Cucurbiturils are macrocyclic barrel-shaped molecules that can act as nanocontainers for guest molecules, especially cationic guests. The low solubility of unsubstituted cucurbiturils limits their utility. Cucurbiturils are relatively unreactive so direct substitution of groups on the cucurbituril is difficult. We are seeking to synthesize more water-soluble cucurbiturils by synthesizing oligomeric precursor molecules that can be closed into substituted cucurbiturils with a substituted glycoluril unit.

Other Interests:  Percussion, Running, Talking, Love Poems


 Hayley Larson  '14   Asheville, NC      Advisor:  Jesse Rowsell

Research Project:  Oxidation/Hydrolysis Reactions of Naphthalenesulfonate Dye Intermediates in Natural Waters

Description:  I am researching the reactivity of the industrially important dye intermediate, H-Acid, which is produced in enormous quantities in China and India. The molecule is considered non-toxic, but it forms many colored byproducts upon reaction with water and air. These byproducts are reported to play central roles in wastewater contamination lawsuits within manufacturing communities in India. Reports describing the chemistry of these byproducts appear to be scarce or non-existent in the scientific literature. I am employing UV-vis and HPLC analytical methods to study the kinetics of these reactions with the goal of determining a robust method for purifying and crystallizing the byproducts. This will lead the way to structure elucidations and evaluations of the toxicities of these species.

Other Interests:  Dancing, art conservation, and cooking


Elaine Liu  '14   Newark, DE      Advisor:  Rebecca Whelan

Research Project:  Characterization of Paint from the Bowers of Satin Bowerbirds

Description:  This project is a collaboration with Professor Gerald Borgia of the University of Maryland Biology Department. As part of the mate selection process, male Satin Bowerbirds build elaborate structures (bowers) out of sticks and decorative objects. Females decide on their mates based in part on the attractiveness of the bowers. A poorly understood aspect of bower construction is the use of “paint” in decorating the bower sticks. The paint appears to be derived from plant material (probably resin from the hoop pine) and females have been observed to taste the paint as part of the assessment process. The goal of this project is to examine sticks collected from bowers in Australia and develop analytical methods to determine the composition of the paint. This is a new project requiring optimization of sample preparation, LC-MS, GC-MS, and UV-vis spectrophotometry methods.

Other Interests:  dancing, cooking and baking, playing soccer, hanging out with friends, and playing bananagrams


Molly MacInnes  '13   Albion, MI      Advisor:  Jesse Rowsell

Honors Project:  New Organosulfonate Complexes from Commodity Chemicals for the Assembly of Microporous Frameworks

Description:  The commodity dye intermediates H-Acid and chromotropic acid (both naphthalene derivatives) have potential chelating groups at the 4 and 5 positions, but their coordination chemistries are virtually unexplored. This project focuses on the bonding of these molecules with boron, aluminum, and selected transition metals; the synthesis of these coordination compounds, their structures and physical characteristics. They have the potential for construction of microporous frameworks through sulfonate groups at the 2,7 positions, which can be utilized to extend the bonding of these molecules to polarizable metal ions.

Other Interests:  riding horses and playing my flute


Melanie Malinas  '13   Ventura CA/Reno, NV      Advisor:  Manish Mehta

Honors Project:  Solid-State NMR Detection of Protein Folding Intermediates

Description:  The “folding funnel” theory of protein folding envisions that polypeptides fold on a energy landscape – a three-dimensional map where the horizontal coordinates of a point represent a particular conformation of the polypeptide, and the vertical coordinate represents the free energy of the polypeptide in that conformation – shaped like a rugged funnel, the fully-folded protein at the bottom of the funnel with the lowest energy. The folding protein can thus take many pathways to the bottom of the funnel, and doesn’t have a structurally well-defined single set of intermediates that it passes through. This theory is widely accepted in the protein folding community, yet no funnel has ever been mapped experimentally in more than one dimension. In this project, we aim to learn more about the folding landscape of a small, fast-folding protein known as Trp cage using solid-state NMR methods. In particular, we want to use a “freeze-quench” method whereby a protein solution is heated to denature the protein and is then very rapidly frozen in isopentane before it can refold. This method might capture a transient intermediate or intermediates in the folding landscape of Trp cage.

Other Interests:  Singing, musical theater, playing with cute animals and children, obsessing about Harry Potter, playing Scrabble, skiing, long walks, reading xkcd, spending time with wonderful people, and doing science, of course.


Venkata Mandala  '15   New Delhi, India      Advisor:  Manish Mehta

Research Project:  Measurements of Diamagnetic Susceptibilities of Common NMR Solvents

Description:  Modern NMR spectrometers allow for very high resolution spectrum imaging. However, their accuracy is often compromised by the unavailability of adequate and precise data of the magnetic susceptibilities of materials, since the chemical shifts of the peaks due to the diamagnetism of the sample cannot be resolved to as high a degree of precision as the spectrum. My work this Winter Term involves completing a precise Gouy balance to measure the magnetic susceptibilities of different materials with a focus on NMR solvents, that was started previously by a student. I first built a crude balance using a 1 Tesla (at my current setting) electromagnet to study the effect of magnetic susceptibilities, and to roughly calculate the susceptibility of Nickel Chloride using that balance. My work also involves completing the final apparatus for the Gouy balance, which is based around the 14 Tesla superconducting NMR magnet. I am testing the current apparatus for errors caused due to air currents, and finding ways to stabilize the mass readings for the experiment. My work also involves operating a new densimeter, the Anton Paar DMA 5000M, and trying different samples to test its accuracy and repeatability. The density readings are essential for the measurement of magnetic susceptibilities, and thus need to be of a high level of precision too.

Other Interests:  Playing soccer, reading and occasionally coding.


Carl Manhardt  '13   Everett, WA      Advisor:  Mike Nee

Research Project:  Synthesis of Mesoporous TACN-Silica Hybrid Materials

Description:  Mesoporous materials are useful because they have pore sizes that can selectively incorporate organic molecules. We are seeking to make new mesoporous materials composed of a chelating organic component, a 1,4,7-triazacyclononane (TACN), and silica gel. The TACN components will act as ligands for manganese(III) ions. It is hoped that these new materials may be useful as an oxidation catalyst, perhaps for the removal of hazardous substances from water.

Other Interests:  Running, reading, Pharmaceutical drug studies


Christina Perez-Tineo  '13         Advisor:  Rebecca Whelan

Research Project:  Selection of DNA Aptamers for the Peptide Epitope of Ovarian Cancer Biomarker CA125

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. This year, we will continue to work on the selection a DNA aptamer that recognizes a peptide that appears many times in 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 work is supported by the National Cancer Institute.

Other Interests:  Likes to read, knit and play La Cross


Thomas Pires  '14   Carlisle, PA      Advisor:  Rebecca Whelan

Research Project:  Synthesis of Biologically Functionalized Gold Nanoparticles

Description:  In addition to its use as a diagnostic marker of ovarian cancer, CA125 has been implicated in metastasis, the spread of cancer beyond the ovary. To better understand this process, we propose to study the distribution of CA125 on the surface of ovarian tumor cells using scanning electron microscopy (SEM). Colloidal gold nanoparticles with surfaces coated by an affinity molecule (an antibody or aptamer) can be used to visualize the location of particular proteins on cell surfaces. Recent work by our collaborators at the University of Wisconsin-Madison suggests that functional tandem repeats of CA125 are found close to each other on the cell surface. We will prepare aptamer-coated gold nanoparticles and incubate them with ovarian cancer cells, then employ SEM to reveal the locations of the tandem repeats on the cell surface. Our recent work at Oberlin has shown that different peptide epitopes from CA125 exhibit varying tendencies to aggregate, in a sequence-dependent fashion, which may be significant in the process of metastasis. We have the ability to use our aptamers to target “aggregation prone” versus “aggregation averse” regions of CA125 and see their distribution on the cancer cell surface. This project is supported by the National Cancer Institute.

Other Interests:  guitar, flute, building guitar amplifiers and effects, politics


Bernadette Schneider  '13   Rocky River, OH      Advisor:  Jesse Rowsell

Research Project:  Synthesis of Isostructural Coordination Frameworks for Characterizing Adsorbed Molecular Hydrogen

Description:  Hydrogen gas fuel cells show great promise as a future incarnation of the combustion engine, however efficient and safe storage of hydrogen is a major obstacle in the pathway of this modern fuel technology.  I am building on past investigations in the Rowsell lab regarding the synthesis and characterization of microporous crystals made from lanthanide metal ions coordinated with an organic carboxylic acid.  The pores created by the rigid crystalline structure hold small molecules such as water and when evacuated may be refilled with hydrogen gas.  I am using infrared spectroscopy, powder x-ray diffraction, and thermogravimetric analysis to characterize the crystals. 

Other Interests:  Dancing!  Particularly ballet and social dancing.  I also like tea parties and co-op cooking/eating.


Shi Shi  '13        Advisor:  Rebecca Whelan

Research Project:  Characterization of Avian Alarm Odors

Description:  This project is a collaboration with Professor Julie Hagelin of Swarthmore College and the University of Alaska-Fairbanks. Little is known about the possible role of alarm odors—chemical messengers emitted by individuals under threat or attack—in bird species, though alarm odors have been characterized in insects and in reptiles. The objective of this work is to examine feces samples from chicks that were subjected to a fear-inducing stimulus and compare these samples to those from birds that were not frightened. We use solid-phase microextraction and gas chromatography-mass spectrometry to determine and quantify the volatile compounds in these samples. (Fun fact: the chemistry of fear was recently featured in the NY Times.)

Other Interests: 


Eleanor Spielman-Sun  '14   Menlo Park      Advisor:  Mike Nee

Research Project:  Synthesis of More Water-Soluble Substitiuted Cucurbiturils

Description:   Cucurbiturils are macrocyclic barrel-shaped molecules that can act as nanocontainers for guest molecules, especially cationic guests. The low solubility of unsubstituted cucurbiturils limits their utility. Cucurbiturils are relatively unreactive so direct substitution of groups on the cucurbituril is difficult. We are seeking to synthesize more water-soluble cucurbiturils by synthesizing oligomeric precursor molecules that can be closed into substituted cucurbiturils with a substituted glycoluril unit.

Other Interests:  Photography, hiking, cooking

 


Tommy Tullius  '15   Boston MA      Advisor:  Peter Chivers

Research Project:  Nickel-coordination Geometry and Intracellular NickelTrafficking

Description:  Bacteria require transition metals for essential metabolic processes. The metals are bound selectively by a modest number of proteins within a cell. These proteins have different cellular functions and thus different metal-binding properties related to function. We are studying the differences in metal-coordination of the nickel-binding proteins of E. coli to understand how nickel ions end up bound to specific proteins as a function of overall nickel availability and intracellular nickel requirement, both of which can vary widely and provide different types of chemical stress to the cell.

Other Interests:  Piano, photography, film, and animation.


 

Tae Kyu (Brian) Uhm  '14   Seoul, Korea      Advisor:  Rebecca Whelan

Research Project:  Selection of DNA Aptamers for the Peptide Epitope of Ovarian Cancer Biomarker CA125

Description:  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. Previous efforts in the Whelan lab used solid-phase peptide synthesis to prepare the 21-mer peptide in pure form and characterize its secondary structure. We are now using the peptide as the target in a capillary-electrophoresis-based aptamer selection process, to complement our ongoing work in selecting an aptamer that recognizes intact CA125. This work is supported by the National Cancer Institute

Other Interests:  Making good coffee, baking brownies, DJ-ing, dancing, and playing piano.


Megan Walkenhorst  '13   St. Louis, MO      Advisor:  Robert Thompson

Research Project:  Forgery or not?  Analysis of Aged Drying Oils in an Oil Painting.

Description:  Our goal is to develop a teaching experiment for analytical chemistry with the focus on an oil painting and whether or not it is genuine based on the drying oil used and its apparent age. The nature and age of the oils in an oil painting can be determined or estimated from analysis of the lipids in the pigment binder. A tiny bit of the paint can be made soluble, treated with reagent to create esters from the fatty acids, and analyzed by gas chromatography - mass spectrometry to reveal the number, type, and relative amounts of fatty acids present. This information can provide a clue as to the original drying oil used, be it linseed oil or walnut oil or other natural oil. The information can also indicate the approximate age of the painting since oxidation products, e.g. dicarboxylic acids from monocarboxylic acids, increase with time.

Other Interests:  Watching movies, cooking, reading, and hanging out with friends.


Jamie Yelland  '13   Omak, WA      Advisor:  Peter Chivers

Honors Project:  Nickel-ligand Complex Recognition by the E. coli NikA protein.

Description:  Bacteria require transition metals for essential metabolic processes. These metals act as cofactors and must be acquired from the environment. E. coli use the five protein NikABCDE complex to import nickel ions, but the specific form of nickel that was transported has been elusive. We have recently discovered that nickel ions are transported into the cell in the form of a Ni-(L-His)2 complex. I am studying the equilibrium binding of Ni-(L-His)2 and related complexes to the purified NikA protein from E. coli and other bacterial species. I have developed a solution-based assay that will be used to compare the binding affinities of various Ni-ligand complexes with each other and with similar complexes formed by other transition metals to understand the properties of the Ni-(L-His)2 that are important for recognition by NikA

Other Interests:  Cycling, backpacking, fencing, Javanese gamelan, bluegrass and old-time banjo, home-brewing, riding motorcycles, exploring and adventuring.


Cassandra Zentner  '13   Irwin, PA      Advisor:  Jesse Rowsell

Honors Project:  Supramolecular Assembly of Microporous Molecular Crystals

Description:  Molecular crystals rarely sustain microporosity upon evacuation of solvents from the structure’s pores due to the weak interactions that determine the packing.  Recently, we observed a molecular crystal of 1,3,5-tris(4-carboxyphenyl)benzene (tcpb) that retained crystallinity even after the evacuation of the solvent.   We will be functionalizing tcpb with cyano groups and then nitro groups on the central ring, crystallizing the product and comparing it to the prototype tcpb crystal structure.   Another direction of the project is to co-crystallize tcpb with other rigid aromatic acids, namely benzene-1,4-dicarboxylic acid (terephthalic acid) and benzene-1,3,5-tricarboxylic acid.   Products will be characterized using powder x-ray diffraction, thermogravimetric analysis, nuclear magnetic resonance, and infrared spectroscopy. 

Other Interests:  Photography, cello