2008 Summer Research Program in Chemistry at Pomona College

 

Link to application form

 

The Chemistry Department is pleased to announce its 2007 Summer Undergraduate Research Program which is funded by income from an endowment established by Fred Robbins.  Pomona College students interested in a career in science are encouraged to apply.  Each participant will spend 10 weeks working on a research project and will be paid a stipend of $4000.  A description of research projects available is given below.

 

Those who wish to apply to the program should complete the attached application and return it to the Chemistry Department offices by Monday, February 18th, 2008.  The department will announce the results of the selection process shortly thereafter.  We do not require letters of recommendation.    Although we have sufficient funds to cover the program, the budget is tight and some students selected for the program will be asked to assist in applying for external funding.

 

PROJECTS AVAILABLE

 

Professor Crane: The students in the lab are defining the biology and chemistry that allows life to thrive in the incredibly toxic and hot conditions at deep-sea hydrothermal vents, in boiling sulfur pits (solfatars) on land, and in sites with naturally high levels of arsenic.  We use a wide range of strategies in order to help us understand what types of redox chemistry these microorganisms use to make themselves comfortable in an environment that should be uninhabitable.  Projects include the use of analytical chemistry to characterize small intracellular redox active compounds, studies of the structures and mechanisms of the redox enzymes of thermophiles, and the discovery, isolation and characterization of new microbes able to survive under extreme conditions.

 

Professor Garza: We use computational techniques to simulate diffusion-controlled reactions on surfaces as well as within lattices.  Consider the irreversible reaction A+B→C where A is a diffusing particle and B is a reaction center.  This summer we will look at irreversible reactions of this type in 3-D cubic lattices (such as zeolites) under different boundary conditions.  As demonstrated in our earlier work on hexagonal lattices [1,2], the procedure we have developed, allows us to get analytical expressions of these random walks.   We have just recently submitted another paper in the area [3] where we looked at a diffusing particle on d=2 square planar lattices with a deep trap and such a contribution is getting excellent reviews.

 

 The students participating in this research will use mathematical packages and learn how to write his/her own code, input data, run the programs they write, and analyze their results.  The participants are expected to present their findings in a conference either locally, nationally or internationally.  For more information look at my webpage:

http://www.userwebs.pomona.edu/~ragl4747/home/Garesearch.html

 

[1] R.A. Garza-López, C. H. Lee^*, D. Lin^*, G. López –Mena^*, D. Niu^* and J. J. Kozak,  Chem. Phys. Lett. 356 (2002) 313-7

[2] R.A. Garza-López and J.J. Kozak, Chem. Phys. Lett. 371 (2003) 365.

[3] R.A. Garza-López and J.J. Kozak, Chem. Phys. (2005) submitted.

^*Indicates Pomona College undergraduates.

 

Professor Fred Grieman:   

 

Professor Mal Johal: My research focuses on fabricating “nano-scale” functional materials for optical and biosensing applications by exploiting molecular self-assembly processes that occur in nature. In addition to the “application driven” nature of my research, I am also interested in the subtle interplay between various intermolecular non-covalent interactions that lead to highly ordered macro-structures. There will be opportunities for two students to work on two different projects. The first project will entail the use of ionically driven self-assembly processes to immobilize enzymes and proteins within polyelectrolyte multilayer films. The goal of this project is to construct ultra-thin film assemblies on glass slides for efficient hormone detection. The second project will focus on analysis of binding events, phase transitions, and bilayer formation kinetics using the Quartz Crystal Microbalance (QCM). This project will focus on optimizing the QCM to study the self-assembly processes in lipid membranes under various conditions. The long term goal of the second project is to exploit the molecular-scale architecture of multilayered membrane mimics to fabricate non-linear optical materials.

 

Professor  Steinmetz(Professor Emeritus of Chemistry):

 

PROJECT 1:

Is the Toxicity of Mycotoxins Related to 3D Structure?
Wayne E. Steinmetz
Professor Emeritus of Chemistry

Trichothecene mycotoxins are extremely potent fungal toxins and were used by the Soviet military in southeast Asia. My students and I recently completed a study of the structure and dynamics of verrucarin A and roridin A, two closely related mycotoxins.1 We showed that one can reliably calculate the structure of mycotoxins via molecular mechanics. As the next step in our examination of these toxins, I plan to determine if there is a correlation between their toxicity and three-dimensional structure. Fortunately, there exists a large (N = 29) database of toxicities for mycotoxins.2 The goal of the modeling project is to employ CoMFA, a frequently used tool of three-dimensional QSAR, to determine whether the correlation exists. The student will make heavy use of the modeling program SYBYL.
1) W. E. Steinmetz, P. J. Robustelli, E. Edens, and D. Heineman, J. Nat. Prod., accepted for publication.
2) B. P. Jarvis, G. P. Stahly, and G. Pavanasasivam, J. Med. Chem., 23, 1054-1058 (1980).
 

PROJECT 2:

Three-Dimensional Structure of DX600

 

DX600, a potent and selective inhibitor of Angiotensin Converting Enzyme II, is a peptide with 26 amino-acid residues.  An usual 3D structure is expected because of features in its primary structure such as 6 aromatic residues, 4 prolines, and one disulfide bridge.  The goal of the project is continue the application of NMR spectroscopy and molecular modeling in its determination of its 3D structure in water.  At present, we have obtained a tentative assignment for the proton and carbon-13 NMR spectra.  Modeling calculations have yielded a preliminary structure.  We hope to confirm and validate the assignment and obtain additional experimental constraints on its structure.   Characterization of the dynamics of the peptide is also a goal of the project.