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

Student Research

Melanie Malinas '13   From: Reno, NV 

Advisor: Manish Mehta 

Research Project:

Solid-State NMR Detection of Protein Folding Intermediates 

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: Reading, music, performing, playing Scrabble, skiing and watching movies

 


 

Venkata Mandala '15   From: New Delhi, India 

Advisor: Manish Mehta 

Research Project:

Precise measurements of magnetic susceptibilities using a Gouy balance 

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

 


 

Adam Birdsall '13   From: Roseville, MN 

Advisor: Matthew Elrod 

Research Project:

Esterification Equilibria and Kinetics of Methacrolein-Derived Hydroxycarboxylic Acids on Secondary Organic Aerosol 

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   From: Ithaca, NY 

Advisor: Matthew Elrod 

Research Project:

Isomerization and Ether-Forming Reactions of the Oxidation Products of Biogenic Hydrocarbons on Secondary Organic Aerosol 

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 isomerization and ether-forming reactions of isoprene- and 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.

 


 

Michael Jacobs '15   From: Dayton, OH 

Advisor: Matthew Elrod 

Research Project:

Gas Phase Oxidation Kinetics and Mechanisms for Atmospherically Relevant Epoxide Intermediates 

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

 


 

Holden Lai '15   From: Hong Kong 

Advisor: Mike Nee 

Research Project:

Functionalized Cucurbiturils 

Cucurbiturils are barrel-shaped, cyclic polymers of glycourils connected by methylene bridges. They are useful container molecules and can serve as a host for a wide range of cationic guests. Unfortunately, curcurbiturils are essentially insoluble in organic solvents and only slightly soluble in water. We are synthesizing functionalized cucurbiturils to both increase the solubility of the cucurbiturils and to provide a site for chemically modification of the cucurbituril, such as immobilization to solid supports such as silica gel or attachment of polyethylene glycol chains.

Other interests: Percussion, Running, Talking, Love Poems

 


 

Liam Sharninghausen '11   From: Bellingham, WA 

Advisor: Michael Nee 

Research Project:

TACN-Silica Hybrid Materials 

1,4,7-Triazacyclononane (TACN) is a versatile ligand for a range of metal ions. We are seeking to synthesize mesoporous materials with TACN incorporated within the pores. It is hoped that the manganese(III) complex of this incorporated TACN can act as an oxidation catalyst. We are trying two approaches to incorporating the TACN in mesoporous silica materials. One approach is to synthesize TACN with three propyltrialkoxysilane "arms" then combining that with tetraalkoxylsilane in the presence of a polymeric template. The other approach is to prepare mesoporous silica with chloropropyl groups in the pores then bonding the TACN to the propyl groups.

Other interests: Tennis and other racquet sports, Learning Old English and Old Norse, Chemistry, Classical music

 


 

Jamie Yelland  '13     From : Sequim, WA

Advisor:  Peter Chivers

Research Project:

Nickel-ligand complex recognition by the E. coli NikA protein.

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. We are now studying the equilibrium binding of Ni-(L-His)2 and related complexes to the purified NikA protein. The current goal is to develop a solution based assay that can 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.

 

Summer Pizza Lunches  

l-r   Jamie Yelland, Holden Lai, Adam Birdsall, Melanie Malinas, Zin Linn Htet, Cassie Zenter, Dylan Bleier,

Liam Sharninghaousen, Venkata Mandala, Michael Jacobs