Faculty Research Interests and Projects

Professor Bruce S. Ault, PI

The Ault group uses cryogenic techniques to carry out mechanistic studies of the reactions of O₃ and NO₃ with substrates containing carbon-carbon multiple bonds, reactions that are very important to the chemistry of the troposphere.  While these reactions have been studied extensively and many of the details of the reaction mechanisms have been worked out, the key intermediates have not been isolated and characterized.  First and foremost among these is the Criegee intermediate, arising from the rearrangement and fragmentation of the primarily ozonide formed in the reaction of O₃ with olefins.  We are developing strategies for the isolation, stabilization and characterization of this intermediate and related species.  Students carry out these studies with the combination of matrix isolation, infrared and visible/UV spectroscopy and theoretical calculations.

Professor Anna D. Gudmundsdottir, co-PI

We study the reactivity of triplet vinyl nitrene intermediates in solution and in the solid-state. Our goal is to identify the factors that control the reactivity of the triplet vinyl nitrene intermediate so that we can render them stable, and use them as building blocks for assembling high-spin organic molecules. We will study the reactivity of triplet vinyl nitrene intermediates which are formed from photolyzing isoxazole derivatives. We are specifically interested in determining whether substitution on the isoxazole ring affects the lifetime of the triplet vinyl nitrenes. The REU student will synthesize and purify isoxazole derivatives and study them using laser flash photolysis. The students will also gain insight into spectroscopy by characterizing the isoxazole derivatives with NMR, IR, mass spectrometry and X-ray crystallography. Furthermore, the students will learn to use the laser flash apparatus to measure the lifetimes of the triplet vinyl intermediates. Each of the REU students will be assigned to a specific project but they will be working in close collaboration with a specific graduate student, who will teach them how to think critically about their research.

Professor William B. Connick

Participants will synthesize and characterize the redox chemistry of new platinum and palladium two-electron reagents.  The research will expose students to organic and inorganic synthetic methods, as well as electrochemical and spectroscopic (e.g., NMR, UV-visible, emission) methods.  These activities will contribute to the objective of Professor Connick’s research program, namely elucidation of the factors that govern the outer-sphere electron-transfer reactions of d⁸/d⁶ two-electron reagents.  The central hypothesis is that cooperative two-electron transfer reactions are favored for complexes with ligand architectures capable of interconverting between square planar 4-coordinate and 6-coordinate geometries with minimal reorganization.  The proposed research is significant because it is expected to provide the knowledge needed for rationally coupling cooperative two-electron transfer reactions to substrate bond-making and breaking steps.  The broader societal impacts of the proposed research include enabling new technologies, improving energy efficiency and helping to shrink the human environmental footprint.

Professor Ruxandra I. Dima

The Dima group is developing and applying database-mining approaches and other bioinformatics methods to the determination of binding motifs at interfaces between various biological molecules to be used in targeted drug-design. The information obtained through this bioinformatics effort is coupled with computational modeling of biological macromolecules dynamics in order to gain insight into mechanisms of macromolecular assembly with specific applications to amyloid diseases (such as Alzheimer's and Mad Cow Disease) and mechanosensitivity of the cell. A special focus is on "Bioinformatics studies of sequence variability among mechanosensitive proteins". This topic is particularly well suited for undergraduate research as it introduces students to a variety of concepts and techniques in computational biology. The modular nature of this project allows students to solve well defined problems within the 10 weeks of the REU program.

Professor William R. Heineman

Professor Suri S. Iyer

There is a great need to develop synthetic biomarkers that exhibit antibody-like selectivity and sensitivity and are robust, inexpensive, amenable to scale-up and require no refrigeration for use in diagnostics and therapeutics. Oligosaccharides are inexpensive, can be tailored, are amenable to scale-up and can be stored at standard operating temperatures without facile decomposition. Furthermore, they are unique recognition molecules that modulate a number of biochemical processes such as cell proliferation, migration and differentiation. While Nature performs these tasks with apparent ease, synthetic glycoconjugates suffer from selectivity and sensitivity for practical sensing applications.  Specifically, we are interested in developing ligands for Shiga toxin serotypes and Influenza variants. This study is expected to advance scientific knowledge in the area of saccharide-pathogen interactions and provide a model that researchers could potentially use to modulate glycoconjugate-based recognition events for other disease states.  In this project, the REU student will develop suitable ligands that would be assayed against various serotypes. The nature of this interdisciplinary project will foster interactions with other members of my group, faculty members of the sensor group and collaborators at the medical school. The student will learn organic synthesis, bioconjugation chemistry and biological assays that will provide a framework for the development of a successful interdisciplinary career in the Sciences.  

Professor Patrick A. Limbach

The ribosome is an amazing biomolecular machine responsible for synthesizing proteins within cells rapidly and mistake-free. Our group is interested in understanding the specific intermolecular interactions among the various ribonucleic acids (RNA) and proteins present in the ribosome. One particular interest in our lab is determining how antibiotics interact with ribosomes over time leading to antibiotic-resistant strains of pathogens. We use modern biochemical and bioanalytical techniques to figure out how the ribosome works as well as it does. In this research project, a student would be exposed to a number of state-of-the-art techniques including cell culturing, protein and RNA isolation, separations, and mass spectrometry. The student will be working with other research group members on culturing various bacterial cells in the presence and absence of particular antibiotics. Ribosomes will be isolated and characterized by the methods described above in order to map out changes in RNA-protein interactions that occur when antibiotics are present.

Professor James Mack

A research focus of the Mack group is in the development and understanding of solvent-free organic reactions.  In our research laboratory we employ the novel solvent-free technique of high-speed ball milling (HSBM).  Under this process we use a high-velocity ball bearing to pulverize particles to the point that a reaction occurs.  In addition to conducting solventless reactions, we also design our reactions such that they are environmentally friendly.  Our purification procedure generally involves only a water wash, thus minimizing harmful solvent use both in the reaction as well as at the purification stage. In order to create a new generation of environmentally conscious chemists who think of the environmental ramifications alongside the potential solutions to scientific problems, aspects of green chemistry must be taught to them early in their careers.  NSF-REU students in my laboratory will work on various reactions using the HSBM technique as well as learn of other areas of green chemistry.  There are expected to be many opportunities for the results of a NSF-REU student to be published in scientific journals and presented at scientific meetings.  My last two research papers have undergraduate students as co-authors and I am a firm believer in incorporating undergraduate students fully into my research projects. 

 

Professor David B. Smithrud

Developing intracellular transport agents requires a multidisciplinary team.  An REU student will join the researcher at UC and the Genome Research Institute (GRI) to help develop the transporters and to investigate their biological properties.  To ensure that the student obtains a meaningful exposure to this wide range of experiments, a known transporter will be modified, and its ability to associate with and transport a variety of guests will be determined using well-established methods.  The student will first perform a series of Monte Carlo and Molecular Dynamic simulations to model the transporter-guest complexes.  The modified transporter will then be synthesized, which should require only two or three synthetic steps.  Product authenticity will be determined through a combination of NMR and mass spectrometric analyses.  Analysis of fluorescence quenching assays will provide association constants for the transporter-guest complexes.  Additional information about complex structure will be found using 2D-NMR analysis (COSY, TOCSY, NOESY, and ROESY experiments). The REU student will also perform the cellular transport studies.  The student will expose plated cells to the agents and use fluorescence microscopy to find fluorescent cells and capture their image on film.  These experiments will be performed in the Drew Research Group at the GRI. Besides hands-on research experiences, the REU student will attend our weekly group meetings where we present cutting-edge research ideas and he or she will have informal discussions with researchers at the GRI who are experts in a wide range of disciplines and have diverse research interests. 

Professor Apryll M. Stalcup

Currently, the fastest growing areas of high performance liquid chromatographic separations are in the areas of biomolecule separations and liquid chromatography-mass spectrometry.  Biomolecule separations are challenging because they present a variety of interaction modalities ranging from hydrophobic to polar to electrostatic.  Our work addresses the urgent need for improved technologies for novel and more universal separation strategies for biopolymers (e.g., polypeptides, proteins, oligonucleotides).  We have integrated the emerging field of ionic liquids into novel separation strategies for biomolecular separations with the goal of providing multimodal retention for the separation of a wide variety of biomolecular analytes.  Novel ionic liquids and ionic liquid-like stationary phase surrogates are synthesized, purified and characterized using a variety of spectroscopic techniques.  The project provides excellent educational opportunities for undergraduate students.  The integration of synthesis, materials characterization and separations in this project engenders the multi-faceted skill set and critical thinking expertise that is required both in graduate school and in the modern workplace.

Professor Pearl Tsang

The research in the Tsang lab is aimed at elucidating the interactions between human lysyl aminoacyl tRNA synthetase and lysyl tRNA using biophysical techniques.  The canonical function of this enzyme (‘hKRS’) is aminoacylation of human lysyl tRNA with the amino acid lysine.  The tRNA binding properties of  hKRS are not fully understood, due to the poorly characterized function of its N-terminal domain, a domain which is present primarily present in mammalian forms of this enzyme only.  These studies are aimed at understanding the full function and structure of hKRS since these are integral to our understanding of important biological processes ranging from mammalian protein biosynthesis to HIV-1 virus assembly.  The methods employed range from molecular biology, protein expression, gel shift assays, as well as various types of spectroscopy such as CD, fluorescence and solution NMR.