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Collaborative Research in the Chemical Sciences |
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Research ProgramsYou will need to select the three research groups you are most interested in working with before completing the online application. |
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Ludwik
Adamowicz: Computational Modeling of Electron Transfer in DMRB Proteins The purpose of this study is to develop and implement computational modeling tools based on molecular quantum mechanics and molecular dynamics to study electron and energy transfer involved in redox reactions of metal centers in proteins of dissimilatory metal reducing bacteria (DMRB), particularly for the bioremediation of toxic metals. The project will involve training students in the use of computational chemistry methods and will be performed in collaboration with Dr. Tjerk Straatsma (Pacific Northwest National Laboratory), where the bioremediation processes are being studied experimentally, including by X-ray analysis. [Website] |
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Neal Armstrong: Self-assembled Ultra-thin Conducting Polymer Films on Inorganic Surfaces The REU student will join our research efforts on the creation and characterization of new self-assembled ultra-thin conducting polymer (CP) films on transparent conducting oxides (e.g. indium-tin oxide, ITO) or metal surfaces (Au), providing new ion-sensitive transducer layers. Tools that are used in this research effort include transmission and ATR UV-visible spectroscopies, reflection/absorption FT-IR, AFM, contact angle measurement, standard voltammetry and potentiometry to characterize the electrochemical activity of these layers, ellipsometry, and surface photoelectron spectroscopies. The project involves collaborations with Profs. Scott Saavedra, Craig Aspinwall and Sergio Mendes (Chemistry). The collaborative nature of this research effort arises from the need to have thorough optical characterization of CP layers. [Website] |
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Craig Aspinwall: Modular Nanosensors Constructed of Polymerizable Phospholipids The REU student will prepare a nanometer-sized, biocompatible chemical sensor for reporting localized oxygen levels within a cell. The sensor will be prepared by encapsulating a an oxygen sensitive ruthenium dye to an aminated dextran in a polymerized phospholipid vesicle. The student will synthesize, purify and characterize the dextran conjugate, prepare and characterize nanometer-sized phospholipid vesicle sensors, use a new class of lipids that is being synthesized by Prof. Saavedra (Chemistry), characterize the temporal and quantitative response of the sensor to oxygen in collaboration with Prof. Hruby (Chemistry), and utilize the sensor to perform cellular measurements of real-time oxygen dynamics using cells provided by Prof. Dominick Deluca (Immunology). [Website] |
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Robert Bates: Structure Elucidation and Synthesis of Natural Bacterial Emulsifying Agents [Website] |
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Michael Brown: Influence of Membrane Phospholipid Content on Conformational Transitions in Rhodopsin The REU student will focus on investigating the meta I-meta II conformational transition of the visual protein rhodopsin, as a function of retinal rod disk membrane phospholipids content. This transition is the triggering event in visual excitation. Flash photolysis methods and plasmon waveguide resonance (PWR) studies will be conducted. This work will afford an ideal opportunity for undergraduate training in biochemistry and analytical and instrumental methods. Students will have the opportunity to learn techniques of density gradient centrifugation, protein characterization by UV-visible spectrophotometry and regeneration and functional assays for the activity of rhodopsin. This research will involve collaboration with Prof. Victor Hruby (Chemistry) and Prof. Gordon Tollin (Biochemistry). [Website] |
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John Enemark: Structural Effects on Intramolecular Electron Transfer in Sulfite Oxidase The molybdenum-containing enzyme sulfite oxidase (SO) is essential for normal neonatal development, and the key feature of the enzyme mechanism is intramolecular electron transfer (IET) between its Mo and heme domains. This reaction can be conveniently followed by laser flash photolysis. In collaboration with Prof. K. V. Rajagopalan (Duke University Medical School) who provide mutant forms of recombinant human SO, our group investigates the IET reactions of SO as a function of pH, medium and solvent viscosity, using laser flash photolysis in collaboration with Prof. Gordon Tollin (Biochemistry). This project provides an undergraduate participant the opportunity to learn to handle small amounts of protein, to make laser flash photolysis measurements, to perform kinetic analysis of the results, to relate these results to probable changes in enzyme structure and to devise new mutants that will allow further understanding of the mechanism of SO and the factors that lead to SO deficiency, an inherited disorder. [Website] |
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Dennis H. Evans: Electrochemical Studies of the Reduction of Dibenzoate Esters of Diols Esters of benzoic acid can be electrochemically reduced to an intermediate anion radical in nonaqueous solvents. This anion radical reacts by cleavage of the O-R bond to give benzoate and R• radicals. Diesters of many diols have been prepared. In preliminary results, different reactivity was found for the diesters compared to monoesters. The diesters underwent a two-electron reduction for form dianions that reacted by double cleavage giving benzil, 3, and –OCH2CH2O–, for the example given. In this project, the mechanism of this double cleavage reaction will be investigated for a variety of diesters. The REU participant will engage in collaborative research with group members, Dr. Norma Macías Ruvalcaba (synthesis) and Mr. Pradyumna Singh (mechanistic aspects). [Website] |
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Dennis Lichtenberger and F. Ann Walker: Photoelectron Spectroscopic Investigation of the Electronic Structure of Heme Models The REU student will join a collaborative effort between Prof. Walker, the Photoelectron Spectroscopy (PES) Facility, and Prof. Lichtenberger to investigate the gas-phase photoelectron spectra of porphyrins, metalloporphyrins and potential axial ligands in order to understand the energies of the highest-occupied molecular orbitals and thus how metalloporphyrins and axial ligands interact with each other. We have redetermined the PES spectrum of the octaethylporphyrin (OEP) free base and have assigned the highest two MOs of OEP and tetraphenylporphyrin by comparison of HeI and HeII PES spectra. The REU student will prepare several divalent first-row transition metal complexes of OEP, for which we find a number of non-Aufbau fillings of metal and porphyrin orbitals, and measure their PES spectra in collaboration with facility manager Dr. Nadine Gruhn. The REU student will also use computation methods in collaboration with Prof. Lichtenberger to match the observed and calculated energies. [Website] |
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Indraneel Ghosh: Controlling Protein Structure and Function Using Small Molecules and Designed Proteins We are developing a general platform for designing and selecting small, highly thermostable peptides/proteins by phage display from billion member library candidates against both biological and small molecule targets. We are also developing a general methodology for designing proteins that fold or undergo a conformational change when activated by small molecule analytes, such as dioxin. REU students have successfully participated in both of the above projects where they learn about peptide/protein synthesis, designing selections for small molecules and multiple biophysical and analytical techniques in collaboration with Profs. Craig Aspinwall (Chemistry), Robert Gillies (Biochemistry) and David Segal (Medicinal Chemistry), who are utilizing designed peptides/proteins as sensor applications. [Website] |
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Richard Glass: Expediting the Biosynthesis of Hydrogenase: Fooling an Enzyme [Website] |
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Victor Hruby: Targeting Melanocortin Receptors with Peptides and Peptide Mimetics Melanotropin peptides and their corresponding melanocortin receptors are involved in many aspects of human health and disease, and our research is to find peptide and peptide mimetic ligands that have high potency and selectivity for one of the five melanocortin receptors involved in these various biological effects. The REU student will: (1) use molecular modeling and biophysical methods (NMR, CD, etc.) to develop insights into conformation-biological activity relationships that can be used to design superior ligands; (2) synthesize of analogs and mimetics of our best leads to obtain insights into structural features critical for agonist and antagonist activity and for receptor selectivity; and (3) study the binding affinities, second messenger activities and other biological properties of new ligands. These projects allow students to participate in state-of-the-art aspects of synthetic organic chemistry, medicinal chemistry, molecular modeling, computational chemistry, 2D NMR spectroscopy, biochemistry, biophysics, molecular pharmacology and molecular biology. We collaborate extensively, and thus students will have a chance to interact with colleagues in biophysics, biochemistry, molecular biology, pharmacology, cancer research, and other areas of biology. [Website] |
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Stephen Kukolich: Microwave Measurements of the Structures of Organometallic Complexes and Hydrogen-Bonded Complexes >complexes and hydrogen-bonded complexes We measure the microwave rotational spectra of complexes in order to determine complete, gas-phase 3-D structures for the complexes. In past years we have had many undergraduates working on various projects in our lab. Some of these projects are: 1) synthesizing the transition -metal complexes for the microwave studies. 2)Making the microwave measurements and analysing data to get structures, 3)Programming PC computer and setting up interfacing to "talk to the machine", and scan and take data, 4)Electronics and microwave projects to improve the spectrometers. [Website] |
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Eugene Mash: Crystal Engineering of Piperazinediones Intermolecular interactions are of fundamental interest and practical importance in chemistry, biology, and materials science. We are presently using a self-assembly paradigm based on orthogonal interactions to study hydrocarbon chain interactions by spectroscopic, crystallographic and thermochemical methods. Piperazinediones that present "H"-shaped topographies have been synthesized, characterized, and shown to exhibit liquid crystal (LC) properties. Piperazinediones that present "T"-shaped topographies will be synthesized by REU student(s) from amino acid derivatives currently on hand and characterized in collaboration with scientists in UA research facilities. [Website] |
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Dominic McGrath: Influence of Polymer Architecture on the Luminescence Efficiency of OLED Chromophores In collaboration with Prof. Neal Armstrong (Chemistry), we are investigating the effect of covalent incorporation of light emitting organic moieties into different macromolecular architectures on device performance. Chromophores used in the manufacture of organic light emitting diodes (OLEDs) have been incorporated into dendrimer based conjugates. Preliminary evidence obtained in the Armstrong group indicates that dendrimer incorporation of these chromophores enhances their luminescence efficiency in thin films over previous device configurations. The REU student will prepare linear polymers of these same chromophores to compare the emission properties with the analogous dendrimer conjugates. The polymers will be characterized by NMR, UV-Vis, fluorescence, MALDI-MS, and GPC(SEC) methods. The REU student will collaborate with the Armstrong group to characterize thin film luminescence efficiencies. [Website] |
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Sergio Mendes: Putting light to investigate the molecular world Based on several photonics technologies, our work focus on the development and applications of novel optical spectroscopic tools for research in molecular films and surface phenomena, and on the development of advanced integrated micro-optic devices for ultra-sensitive detection of chemical and biological materials. [Website] |
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Katrina Miranda: Synthesis of Nitroxyl Donors for Treatment of Heart Failure Recently, we have determined that nitroxyl (HNO) donors induce the ideal cardiovascular effects to allow failing hearts to function with higher efficiency. At present, the only commercially available compound that spontaneously releases HNO under physiological conditions is an inorganic salt (Angeli’s salt; Na2N2O3). Although Angeli’s salt has been adequate to initiate biological study of HNO, its pharmaceutical use will be severely limited due to short half-life and lack of specificity. The REU student will synthesize a new generation of HNO donors containing organic moieties, which can be readily altered for a specific function, and characterize these donors both chemically (spectroscopic features, kinetics and profiles of nitrogen oxide release) and pharmacologically (cellular toxicity). The REU student will be exposed to the interface between chemistry, biochemistry, pharmacology and cardiology. The cardiovascular effects of promising compounds will be examined in a canine model by our collaborator Dr. Nazareno Paolocci (Johns Hopkins Division of Cardiology). [Website] |
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Oliver Monti: Research in the Monti group focuses on the nanoscale physics and chemistry of solar cells based on organic molecules. Solar cells made out of thin films of organic molecules or polymers are extremely versatile and cost effective. This promises to revolutionize solar energy production and technology, with the potential to alleviate dependence on fossil fuels as our principal energy source. These goals are however currently hampered by low efficiency of charge generation and transport in such organic photovoltaic devices. This is attributed in part to nanometer- to micrometer-scale imperfections in the film structures, affecting the energetics for photogenerated electrons and holes. In our group we are implementing a set of unique forms of microscopy to obtain spatially resolved information on the morphology and electronic structure. This allows us to study the fate of the photogenerated charges in these complex environments, providing valuable insight on how organic solar cells may be improved. [Website] |
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Bogdan Olenyuk: Chemical Genetic Approach to Controlling Gene Expression Understanding of a gene function is critical in maintenance of health and in prevention of a disease. The sequencing of the human genome and the recent advances in proteomics provided us with a better understanding of the relationship between the genetic content and disease. As a result, the development of new strategies for controlling of gene expression in diseased cells has become an increasingly important goal. There remain, however, fundamental questions about the mechanism of transcription and the means of predictable regulation of the function of a gene. Many of these questions can not be answered by genetic and biochemical means alone. We are developing a chemical approach to control gene function using designed natural product-like compounds that act as regulators (inhibitors or activators) by altering the functions of key regulatory proteins. Our projects offer the REU student an entry into the exciting world of chemical biology with exposure ranging from target-oriented synthesis of natural products to cell biology and genetics. [Website] |
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Jeanne Pemberton: The Effect of Biosurfactants on the Fate and Transport of Toxic Heavy Metals Soil bacteria produce multiple classes of biosurfactants that can influence toxic heavy metal fate and transport. Recent efforts by our collaborator Prof. Raina Maier (Department of Soil, Water and Environmental Sciences) have demonstrated that rhamnolipids complex heavy metals such as Pb2+ and Cd2+ more strongly than any other naturally-occurring complexing agent such as the humic or fulvic acids. However, the structures and stoichiometries of these metal complexes are completely unknown. Understanding the molecular details of this chemistry is essential for the development of accurate models of the fate and transport of heavy metals in soil environments. Rhamnolipids are harvested from bacterial cultures (Prof. Maier’s group), and rhamnolipid-metal complex structure is being investigated using a combination of molecular spectroscopies (e.g. FTIR, Raman, NMR, ESI-MS) and potentiometry. REU students will become involved in all aspects of these studies. This highly multidisciplinary project provides an effective vehicle for introducing undergraduate students to the realm of largely unexplored problems at the intersection of chemistry, microbiology, and environmental science. [Website] |
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Jeff Pyun: Nanostructured Materials from Polymeric and Nanoparticle Building Blocks We are pursuing a modular synthesis of highly ordered nanostructures by the synthesis and assembly of nanoparticle building blocks. A wide range of organic polymer chemistry will be used to prepare functional polymers for use as surfactants to prepare core-shell magnetic nanoparticles, where the polymer surfactant becomes an encapsulating shell around the colloidal core. By precise tuning of the polymer structure, the functionality and properties of the nanoparticle will be controlled and systematically varied. These nanoparticle precursors will then be assembled into extended one-dimensional nanostructures in the presence of a magnetic field. The overall strategy presents a versatile “bottom-up” approach to the construction of advanced materials for potential applications in microelectronics and biotechnology. The projects offers the REU student an exciting opportunity to be primarily trained in organic polymer chemistry, while also being exposed to interdisciplinary challenges at the interface of physics, engineering and materials science. [Website] |
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Scott Saavedra: Characterization of Transparent Conduction Oxide Coating for IOW Devices The multidisciplinary research activities of our group are organized around several overlapping themes: the chemistry of biointerfaces and techniques appropriate to study them, new molecular assemblies for molecular device technologies (e.g., chemical sensing), and new types of thin film optical devices for use in surface spectroscopy and chemical sensing transduction. Several ongoing projects provide opportunities for undergraduates. One example is development of novel planar integrated optical waveguide (IOW) devices, an area in which we have been involved for more than a decade. The addition of electroactive layers and broad spectral bandwidth to the single-mode, planar IOW platform is a recent focus, and is being pursued in collaboration with Profs. Neal Armstrong and Sergio Mendes (Chemistry). Thus, the student will interact with a diverse group of grad students, postdocs, and staff scientists on a multi-disciplinary, surface and materials characterization effort. [Website] |
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Andrei Sanov: Chemistry from the electronic perspective: Photodetachment imaging of negative ions [Website] |
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Vicente Talanquer: Phase Separation in Fluids and Solids/Evaluation of Web-Based Instructional Materials [Website] |
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Thomas Baldwin and Vicki Wysocki: Probing Protein Conformation with Pulsed Alkylation Mass Spectrometry The REU students will probe the structures of intermediates in protein folding of mutant luciferases using"pulsed alkylation mass spectrometry” (PA/MS). PA/MS is a new strategy to use mass spectrometry to monitor chemical modification of a protein with an alkylating reagent, such as N-ethylmaleimide (NEM), with nucleophilic thiols in the protein. If the protein exists in two states that interchange in a highly cooperative, 2-state process, and if the alkylation time were brief compared with the isomerization time, the “amplitude” of the signal for each thiol will be the difference in the rate constants for the native and fully unfolded protein. In the process, the students will learn both basic protein chemical methods and bioanalytical methods of investigation, with direct contact with two mentors. The experiments are well suited for undergraduate research experiences. [Website] |
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Mary Wirth: Novel Materials for Bioanalytical Separations Our group is investigating crystalline colloidal arrays as new media for fast electrophoresis of proteins and DNA, and supported lipid bilayers as new media for separating integral membrane proteins into functional protein arrays. Students would learn what today's issues are in the analytical chemistry of biomolecules, they would work on the interface of chemistry, biology and materials sciences, and learn some biophysics. Students would also gain an understanding of the interplay between academic research and business applications through our collaborations with industry. [Website] |
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Zhiping Zheng: Synthesis of Organic-Inorganic Hybrid Materials from Polymerizable Clusters Hybrid materials, characterized by spatially identifiable domains of organic and inorganic components organized into a single molecular framework, offer exceptional opportunities not only to combine the desirable properties the two types of components, but also to create, as a result of the inorganic-organic interfacial interactions, unique properties not exhibited by either component. The REU student will explore a novel class of hybrid materials featuring structurally well-defined metal chalcogenide clusters encapsulated by polymer matrices. The REU student will carry out the synthesis, characterization, and polymerization of the clusters, which will provide proficiency in synthesis and manipulation of air-sensitive compounds, crystal growth, X-ray crystallography, analysis of product compositions, and polymer characteri¬zation. The electrochemical studies, including cyclic voltam¬metry and coulometry using a unique thin-layer working elec¬trode, will be conducted with Prof. Armstrong (Chemistry) through our ongoing collaboration. [Website] |
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This material is based upon work supported by the REU Site Program of the National Science Foundation No. CHE-0453466. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the National Science Foundation. |
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Department of Chemistry · The University of Arizona |
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