research opport page

This page contains brief descriptions of projects that the chemistry and biochemistry faculty are currently undertaking and that may have undergraduate research assistantships open. Undergraduate research can be done by students at all levels, as special studies, honors or summer research. Employment, in the form of prep-room positions, are also sometimes available. Students are encouraged to contact faculty whose research is of interest to them.

Directing Chemical Reactions with DNA-Small Molecule Conjugates: Increasingly, chemical reactions are called upon to transform molecules in non-traditional, complex contexts, such as in biological or environmental samples. To direct chemical reactions to a particular target in mixtures, we will combine the selective and high-affinity binding of DNA aptamers to their targets with the versatility and efficiency of low molecular weight catalysts by covalently linking the two to create catalytically active DNA-small molecule catalyst conjugates (DCats). We will synthesize and evaluate DCats for their ability to selectively transform a target molecule. Please see the Gorin web page.
Catalytic Methylation of Oyxgen Nucleophiles: Methylations of carboxylic acids, phenols, and aliphatic alcohols are ubiquitous transformations in organic synthesis, and have been used in a tremendous array of applications. We aim to develop safer alternatives to the highly toxic and unstable methylating agents currently in use. We will identify stable, commercially available sources of "methyl," and then design and test catalysts that facilitate methyl transfer to oxygen nucleophiles. Please see the Gorin web page.
Laser photoacoustic spectroscopy: Near-infrared and visible wavelengths excite vibrational overtones, typically in O-H, C-H, or N-H stretches, in small gas-phase molecules. Since the absorption processes are weak, however, monitoring overtone excitation requires a sensitive method such as laser photoacoustic spectroscopy. Describing the motions in highly vibrationally excited molecules and understanding their spectra requires quantum mechanical calculations. Current molecules of interest include heterocycles such as ethylene oxide, ethylene sulfide, and azetidine. For a photo of the laser photoacoustic setup, please see the lab webpage. -- S. Hsieh Lab
Photochemistry of hydroperoxides: Exciting hydroperoxides with visible or UV light can induce reactions including the formation of the atmospherically important OH radical. Investigating this reaction involves synthesizing hydroperoxides, characterizing their absorption using laser photoacoustic spectroscopy, and detecting OH radicals using laser-induced fluorescence. Please see the lab webpage for previous work on this ongoing project.-- S. Hsieh Lab
Cuprous oxide semiconductor surfaces: The goal of this project is to determine the surface termination and surface interactions of several semiconductor materials such as cuprous oxide with different morphologies. We will also investigate how these interactions play a role in photoelectrochemical properties and stability. The semiconductors will be synthesized using electrodeposition and surface termination will be studied using atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS). The semiconductor materials will also be characterized using scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDX), and X-ray diffraction (XRD).--Read Lab
Synthesis and Gas-Phase DNMR Study of N-trifluoroacetyl Cyclic Compounds: The goal of this project is to study the effect cyclic N substitution has on the internal-rotational energy barrier of trifluoroacetamides. N-trifluoroacetyl pyrrolidine, piperidine and morpholine will be synthesized and their energy barriers to internal rotation compared. Solution and gas-phase data will be used in order to elucidate the effect solvents play in this process.--Suarez Lab
Sodium flux by ²³Na NMR spectroscopy: This project is a collaboration with Dr. Adam Hall (Biological Sciences). The purpose of this project is to develop a protocol to use Nuclear Magnetic Resonance (NMR) spectroscopy to study the flow of sodium ions through ion channels in phospholipid membranes. A possibility to apply this protocol to biochemical systems is in the works with Dr. David Bickar (Chemistry).--Suarez Lab
Chemical modification of nanoscale topography: Surface topography on the nanoscale (features ~100 nm or less in size) can affect the attachment and proliferation of microorganisms on those surfaces. We have developed a simple, reproducible way to generate these kinds of nanoscale features on silicon, and we are currently exploring ways to vary the surface chemistry on these surfaces while maintaining the underlying topography. By exploring the differential reactivity of the sides and tops of these features, we will explore the potential for varying chemistry in a controlled way, thus allowing us to have spatial control of both topography and chemistry at the same time. This work involves some simple organic synthetic techniques coupled to traditional semiconductor wet surface chemistry. The resulting surfaces are characterized with a combination of infrared spectroscopy, atomic force microscopy and contact angle goniometry. For details see Professor Queeney.
Adsorption of biomolecules to rough surfaces: Our lab has done a significant amount of work on the protein-mediated adsorption of polysaccharides to flat surfaces. We are now extending that study to the nanoscale toporgaphies described above, since biomolecule adsorption plays an important role in the interactions of microorganisms with these surfaces. We use the optical technique of ellipsometry to measure film thickness on our surfaces, and applying that technique to rough surfaces requires us to use a different model to convert the ellipsometric data to thickness. By comparing this approach to infrared spectroscopy of some thin films on our surfaces, we can potentially provide the first direct experimental evidence for theories that compare the effects of roughness on these two optical techniques. For details see Professor Queeney.
The combined effects of surface chemistry and surface topography on biofilm nucleation: This project is a collaboration with Prof. Rob Dorit in Biological Sciences. We prepare surfaces in our lab with varied surface chemistry and topography, then allow biofilms of Pseudomonas aeruginosa to nucleate on these surfaces. Both the amount and the spatial organization of the adhering bacteria are quantified using fluorescence and confocal microscopy, allowing us to test the hypothesis that both surface chemistry and surface topography are important for biofilm formation. For details see Professor Queeney.
Calculational Studies of Molecular Structure and Bonding: The area of interest in these studies is the factors that govern the stability of compounds and the associated structure of those molecules. We ask why each is as it is. Currently of interest is the structure of metal carbonyl compounds, the association of metal ions with benzene and benzene derivatives, and the oxidation of molecular phosphorous. For details talk to Mr. Linck.

Synthesis and Biological Activity of Farnesyl Derivatives: (Student co-workers - 2001-2003 Josephine Nakhla ’03 and summer 2003 Jen Breidenich '05) Our initial goal is to develop a new method for the quick and efficient synthesis of farnesyl derivatives. Farnesyl pyrophosphate is natural product that is directly involved in cholesterol biosynthesis and cellular signal transduction. It has also been implicated in pathways responsible for cancer. We hope to prepare numerous farnesyl analogs, including several natural products, and then test them for biological activity.(Students should have completed Organic II (CHM 223) and Synthesis (CHM 226) before starting them)-- Shea Lab
Synthesis of Novel Cyclic Compounds by the Combination of Two Cobalt-Mediated Reactions: (Student co-workers - since the summer of 2002 Miriam Quintal '04 and since the fall of 2003 STRIDE scholar Kristi Closser '07. Funded through a grant from the Research Corporation.) The goal of this project is to combine the Nicolas and Pauson-Khand reactions (both mediated by Co₂(CO)₈) to enable the quick and efficient construction of polycyclic products. An extension of this method should also allow us to investigate several key points regarding the scope of the Pauson-Khand reaction. (Students should have completed Organic II (CHM 223) and Synthesis (CHM 226) before starting them)-- Shea Lab
Reactivity of Dienes Containing a Cobalt-Alkyne Complex in the Diels-Alder Reaction: (Student co-worker - since the fall of 2003 Jen Breidenich '05.) The goal of this project is to explore the reactivity of a compound recently discovered in our lab by Miriam Quintal '04. Miriam prepared a diene conjugated to a cobalt-complexed alkyne, and we were excited to learn that this molecule is unknown in the chemical literature. We currently plan to study the behavior of this compound in a variety of Diels-Alder reactions. (Students should have completed Organic II (CHM 223) and Synthesis (CHM 226) before starting them)-- Shea Lab
Development of a New Radical Reaction: (Student co-worker since the summer of 2002 Christina Longo '04.) In collaboration with Prof. Melanie Wills at Holy Family University, we hope to develop a new carbon-carbon bond forming radical reaction. Christina plans to demonstrate the feasibility of the initial idea, and we hope that a new student will expand the scope of the reaction by applying it to the synthesis of several natural products. (Students should have completed Organic II (CHM 223) and Synthesis (CHM 226) before starting them)-- Shea Lab

Chromium-Induced DNA Damage: Chromium(VI) is a well-established carcinogen that causes different types of DNA damage. One area of investigation in the lab is to examine the effect of chromium-induced lesions on the thermodynamic stability of DNA using differential scanning calorimetry. We are also interested in using NMR spectroscopic techniques, in collaboration with Prof. Cristina Suarez, to gain structural information for some of these unusual lesions. In collaboration with Prof. Megan Nunez at Mt. Holyoke College, we are studying the effect of these DNA lesions on nucleosome particles. We hope that by more fully characterizing some of these DNA lesions, we will better understand the processes that occur in cells and how chromium causes cancer. -- Jamieson Lab

Summer Jobs: Funded internships on campus. SSEP is a residential program for high school women designed to enrich and support their achievements in the sciences and engineering. SSEP interns serve as a research/teaching assistants to faculty in astronomy, biology, biochemistry, chemistry, computer science, engineering, english (writting) and women's health, as well as residential counselors for the high school students. For more information contact Becci Thomas and check out the SSEP web page: www.smith.edu/summerprograms/ssep.