The University of Pittsburgh's Department of Chemistry will conduct a Research Experiences for Undergraduates (REU) program, in Summer, 2006, the sixth consecutive year of the current program. The projects available each year will vary and will range in scope from traditional to instrument intensive, from one discipline to multi-discipline in flavor, from specific target oriented to more open ended projects. The projects that are currently available are described here, in random order. Not all projects that we expect to be available have been posted yet. (To find out more about a Research Group and what they do, click on the Professor's name; this will open a new browser window with a short synopsis as well as a link to the home page of that Research Group if they have a web site.)
Click here to return to Pitt's REU Home Page
| Professor David Waldeck |
Measuring electron transfer between electrodes and biomolecules |
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Electron transfer at electrode interfaces is
of immense importance to a variety of current and future technologies.
Interfacial electron transfer is central to processes that range from the
ancient (corrosion is an excellent example of an old unsolved problem with
large monetary implications) to the
future (e.g., molecular electronics and bioelectronics). Our group is
investigating the use of organic molecular films (SAMs) to control the
electron transfer between an electrode and a surface bound biomolecule. The
diagram illustrates the underlying architecture used in this approach – a
metal electrode is coated with a monolayer thick organic film that can
selectively bind a biomolecule. This architectural control allows us to
investigate fundamental issues in protein electron transfer kinetics. An
REU student will investigate how the electron transfer rate constant depends
on the protein structure via studies with mutants.
[2/06] [M. Liu, N. Ito, M. Maroncelli, D. H. Waldeck, A. M. Oliver, and M. N. Paddon-Row, ‘Solvent Friction Effect on Intramolecular Electron Transfer’ J. Am. Chem. Soc., 127 (2005) 17867-17876.] |
| Professor David Waldeck |
Measuring electron tunneling between molecules |
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Electron transfer reactions constitute a fundamental
chemical process and are of intrinsic importance in biology, chemistry, and
the emerging field of nanotechnology. Biological processes such as
photosynthesis and respiration rely on electron transfer between molecular
subsystems that interact through a collection of covalent and noncovalent
linkages. Our group is using supermolecules that contain electron donor and
electron acceptor units to investigate how electrons tunnel from one side of
a molecule to another and between two molecules. The diagram illustrates
the architecture of such a molecule in which the electron tunnels from the
donor to the acceptor through a pendant moiety. We are probing how the
electron tunneling probability depends the motion of the pendant group in
the cleft and the rotation of dipolar solvent molecules. An REU student
will investigate how the electron transfer rate constant depends on the
frictional coupling between the tunneling barrier and the solvent.
[2/06]
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Professor Joseph J. Grabowski |
Measuring Volatile Organic Compounds on Breath |
| We are exploring how to use the chemical
understanding that has accumulated, along with the unique instrumental
capabilities of the Flowing Afterglow, to develop applied, analytical
applications for the real-time, quantitative analysis of complex mixtures of
volatile organic compounds. For example, patients being treated with an
experimental anti-cancer drug are being monitored for presence,
concentrations, and time-course of specific drug-related breakdown products,
that appear
in their breath. Our initial work in this area has demonstrated the
limitations of the commonly used hydronium ion for such investigations,
whereas a novel reagent ion investigated last summer looks to
be promising, but still has some limitations. This summer's student will extend the work
initiated last summer and will continue to address the question: "Can
we design specific chemical reactions, which combined with the unique
capabilities of the Flowing Afterglow, can be used to identify and
quantitate a wide range of VOCs (volatile organic compounds), in real time,
in breath, without requiring chromatography and without requiring
calibration curves?" The student working on this project will use our
laboratory based instrument (the SIFT/Flowing Afterglow, Figure) to
investigate the formation of, and then measure the specificity and rapidity
of its ion-molecule reactions in order to completely characterize one or
more reagent ions. The reagent ion will be examined with respect to
its reactivity with a suite of representative compounds. Samples of natural gas, with their added odorants,
and of environmental air samples will be used to evaluate the efficacy of the reagent ions developed. [2/06]
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| Professor Kazunori Koide | Measuring the Reactivity of Cumulene Intermediates to Develop New Organic Reactions |
| Our recent mechanistic
studies (Organic Letters 2006, 8, 199) show that the
treatment of 1 with a tertiary amine generates the cumulene intermediate 2.
This paper also suggests that this intermediate should react with various
electrophiles (E1 and E2) to form the synthetically challenging
tetra-substituted alkenes 3. An REU student will explore this concept by
testing various electrophiles with 1 in the presence of a tertiary amine.
This project provides an opportunity to learn how new organic reactions can
be developed on the basis of mechanistic insight. [2/06]
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| Professor Kazunori Koide | Organic Synthesis and Measurement of Biologically Active Components from Green Tea |
| Our cells are
continuously insulted by reactive oxygen species (ROS). Fortunately, many of
us drink green tea, which contains anti-ROS agents in small quantities.
Based on the chemical structures and reactivities of these natural products,
an REU student will design and synthesize more potent anti-ROS agents and
measure their biological activities in collaboration with biologists. This
project provides an opportunity for the student to learn how chemistry can
be applied to real-world medicinal problems. [2/06]
(-)-epigallocateching-3-gallate: isolated from green tea |
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| Professor Kazunori Koide | Development of Bioactive Molecules that Address Human Diseases: Measurement of the Structure-Activity Relationship of Pigmentation Inhibitors |
| As Africans and
African-Americans migrate to North America and Europe, they are exposed to
far less sunlight, which causes chronic diseases in part due to vitamin D
deficiency. We hypothesize that temporal inhibition of pigments in their
skin could circumvent this global problem. We have recently discovered that
compound A inhibits pigmentation in an animal model, but the structure of A
has not yet been optimized and the structure-activity relationship is poorly
understood. An REU student will synthesize analogs of A, measure the
biological activity in collaboration with a group in our medical school, and
identify the most active pigmentation inhibitor. [2/06]
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| Professor Dennis Curran |
Synthesis and Measurements of New Fluorous Reagents |
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Recently developed
techniques for "fluorous synthesis" unite the reaction and separation
processes in organic reactions (Refs. 1,2). Molecules bearing fluorous
(highly fluorinated) tags can be separated from organic (non-tagged)
molecules by fluorous liquid-liquid or solid-liquid extraction. And
molecules bearing different fluorous tags can be separated from each other
by fluorous chromatography. However, because the field is very young, there
are relatively few fluorous reagents available to pair with the new
separation techniques. Last year, undergraduate coworkers developed new
fluorous carbobenzyloxy (FCbz) groups, protected both natural
and unnatural amino acids with these groups, and used the protected amino
acids in innovative new techniques like quasiracemic synthesis. That work is
now being readied for publication. This year’s project will involve the
synthesis of a new fluorous reagent or protecting group and the study of its
use in representative organic transformations. |
| Professor Billy Day |
Measuring Cellular Proteome Changes in Microtubule Stabilizer-Treated Cancer Cells |
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We are exploring how an important class of anticancer drugs, microtubule stabilizers (the clinically used Taxol and Taxotere, and investigational agents, e.g., (+)-discodermolide, (-)-laulimalide and their derivatives) alters the proteome in cancer cells. Proteomics, a multi-method analytical chemistry platform for measuring changes in protein levels and post-translational modifications, has recently been implemented in our labs. The methods and tools to be used include cell culture, difference 2D gel electrophoresis (a.k.a. DiGE), fluorescence image analysis, solution-phase isoelectric focusing, liquid and sample handling robotics, multidimensional nanoflow HPLC, isotope-coded affinity tagging, electrospray ionization ion trap mass spectrometry (MDLC-ESI-MS), matrix-assisted laser desorption time of flight mass spectrometry (MALDI-TOF-MS) and its tandem form for sequence analysis, MALDI-TOF/TOF-MS/MS (see figure). [2/06] |
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Professor Kenneth D. Jordan |
Measuring the Accuracy of New Polarizable Force Fields for Biomolecule Calculations |
| The participating student will use quantum mechanical methods to characterize the local minima and transition states of small conformationally flexible biomolecules, both in isolation and in the presence of water solvent molecules. These results will be used to test new polarizable force fields for describing these systems. [2/06] | |
| Professor Peter Wipf |
Measuring Relative Rates of Microwave-Accelerated and Conventional Organic Synthesis |
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In recent years, powerful single-mode microwaves have found an increasing number of applications in organometallic chemistry and drug discovery. Many organic solvents are transparent for microwave radiation, and in these cases that dipolar starting materials and intermediates are directly responsible for absorption of microwave energy, and a dielectric heating mechanism is operative. Rate acceleration is particularly effective when the polarity is enhanced from ground to transition state. We have found that transition metals such as alkenylzirconocene and -zinc species are surprisingly stable in the microwave environment under elevated temperature and pressure and thus offer an attractive opportunity for a synthetically advantageous use of this technology. Carbon-carbon bond formations of the type shown below will be studied and new experimental applications of microwave reactors will be developed. [2/06]
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Professor Paul Floreancig |
Development of an Amine-Based Electrophore for Redox Chemistry |
| This project will involve the preparation of b-amino ethers and observing their behavior in single electron oxidation reactions. These reactions, which will proceed through radical cation intermediates, are expected to provide access to either oxygen-stabilized radical or cationic intermediates, depending on the reaction conditions. These studies will provide students with strong training in experimental organic synthesis and with a good education in manipulating chemical reactivity through structural modifications. [2/06] | |
| Professor David Pratt |
Laser-induced Nucleation and Crystal Growth in Solution |
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How do crystals nucleate and grow? Why and how do crystals form such a wide variety of morphologies? These questions have been posed since the seventeenth century, and are still vitally important in the evolution of modern technology. This project will focus on using lasers to induce crystal growth, initially by irradiating supersaturated solutions of urea in water with 1.06 μm pulses from a Q-switched Nd:YAG laser. Recent studies of this system (1) have shown that macroscopic, needle-shaped crystallites of urea form within seconds of irradiation, and that they are oriented in the solution in a way which depends on the polarization of the laser beam. Our experiments will attempt to reproduce this phenomenon, to develop ways of detecting it and analyzing the results, and to apply these techniques to other systems, especially biomolecules. [2/06] (1) B.A. Garetz, et al., Physical Review Letters 77, 3475 (1996) |
| Professor Megan Spence |
LA Novel Membrane Mimetic for Structural Studies of Peripheral Membrane Proteins |
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The structure determination of membrane proteins is one of the most challenging problems facing structural biologists and spectroscopists, in part because of the lack of appropriate lipid membrane mimetics to ensure proper folding of the membrane proteins. A liquid crystalline form of lipid bilayers (bicelles) has been developed and has been used with some success for structural studies, but would benefit from a higher degree of lipid mobility. Higher lipid mobility translates directly into a greater ability to determine the structures of the membrane proteins. This project involves developing a bicelle system composed of highly unsaturated lipid chains, thus opening new opportunities in structural biology. [2/06] |
| Professor Sanford Asher |
Adventures in Photonic Materials |
| The research program involves the synthesis of monodispersed colloidal particles which self-assemble into face-centered cubic arrays and which Bragg diffract light. These particles are polymerized into a hydrogel and the hydrogel is functionalized with molecular recognition agents. When the photonic crystal material encounters the analyte recognized it changes volume which shifts the diffraction. The objective of the work is to develop new sensing materials for important environmental and clinical chemistry analytes. [2/06] | |
| Professor Toby Chapman |
Biodegradable Dendritic Polymers for Biomedical Applications |
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We have previously prepared dendritic polylysine-poly(ethylene glycol)
copolymers for use in such applications as drug delivery, tissue
engineering, and gene therapy. We are not satisfied with their
biodegradability and wish to make the polymers from a suitably derivitized
hybrid (I) of glycolic acid and lysine. We will make the compound and use it
in the preparation of the corresponding dendritic polymer. This new polymer
will have ester linkages that will allow for degradation under physiological
conditions as well as terminal amine groups which will allow for a variety
of chemical modifications.
[2/06]
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| Professor Sunil Saxena |
Measuring the structure of the Glycine Receptor |
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You will use overexpressed Glycine Receptor, a large membrane protein that is involved in electrical signaling between the nerve/nerve synapse. You will incorporate spin labels at specific sites on this protein and use Fourier Transform electron spin resonance spectroscopy (a technique analogous to NMR) to measure the distance between labeled sites. The data will provide constraints, which ultimately will lead to the development of a model for the structure of the the Glycine Receptor, in order to understand how signaling occurs between nerve-cells. [2/06] |
| Professor Chris Schafmeister |
Synthesis of Self Assembling Nanostructures |
| Our laboratory has developed a way of synthesizing nanoscale molecules with designed three-dimensional shapes. We have designed molecules that may self assemble into dimers and may form the building blocks for larger structures formed by the self-assembly of component molecules. You will work with a graduate student to synthesize these molecules and to study the self assembly of these molecules in various solvents using NMR techniques. You will learn to synthesize macromolecules on solid support and to isolate and purify them. You will also learn how to use NMR to study interactions between molecules.. [2/06] | |
| Professor Stephane Petoud |
Lanthanide-Transition Metal Doped Nanomaterials |
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Doped nanocrystals provide emission at well-defined wavelengths depending on
the nature of the dopant. Transition metals present interesting dopant
possibilities because of their different electronic structures.. Moreover,
coupling transition metals with lanthanides in the same nanocrystals creates
an intriguing photophysical system. The transition metal, with its many
donating energy levels, acts as an “electron reservoir” for the lanthanide.
The transition metal pumps electrons into excited energy levels of the
lanthanide, extending the lifetime of the lanthanide (JACS, 2003,
125, 15698-15699). Doped nanocrystals have applications in
electroluminescent materials, which provide efficient luminescence for long
periods of time (LED, self-luminescent flat color displays, etc.). The
efficiency of energy conversion of semiconductor nanoparticles may also be a
solution to actual energy problems (such as novel solar panels). This
project entails the development of these new materials for nanotechnology.
This will include synthesis and characterization of the nanomaterial and of
its photophysical (luminescence) properties.
[2/06]
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| Professor Stephane Petoud |
Lanthanide Doped Nanocrystals for Biological Applications |
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Biological assays involving fluorophores have become more prevalent due to their high sensitivity and moderate cost. There is an increasing demand for luminescent reporters possessing more advanced properties such as strong resistance to photobleaching and whose signal can be discriminated from background fluorescence (biological autofluorescence). The goal of this project is to combine the properties of semi-conductor nanocrystals with those of lanthanide cations. We have recently shown that it is possible to incorporate luminescent lanthanide cations into CdSe semiconductor nanocrystals (J. Am. Chem. Soc., 2005, 127, 16752-16753). In this project, we propose to develop the coating of these doped nanocrystals in order to improve their photophysical properties and to increase their solubility in water to allow their use in biological assays. We propose also to develop lanthanide doped nanocrystals formed with different semi-conductor material in order to fine tune the photophysical properties of the resulting nanocrystals. [2/06] |
| Professor Stephane Petoud |
Cell permeable luminescent dendrimer-lanthanide complexes for detection of hypoxic cancer cells |
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Medical and biological detection require highly sensitive luminescent
reporters for the detection of low concentrations of analytes. In vivo, it
is also necessary to discriminate the signal of the lanthanide reporter from
the background fluorescence (“biological autofluorescence”) to maximize the
sensitivity of the measurements. Lanthanide complexes are ideal candidates
since their emission can be easily discriminated from complex mixtures of
molecules. The very long luminescence lifetimes of these lanthanide
complexes allow for an easy discrimination between signal and fluorescent
background noise through time-resolved measurements. We propose to use
dendrimer ligands as antenna. The end-branches of the dendrimers have been
functionalized with a naphthalamide type groups in order act as an antenna
for the lanthanide cations. The amide groups in the dendrimer core have the
ability to bind several lanthanide cations to maximize the luminescence
intensity.
[2/06]
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| Professor Alexander Star |
Nanoelectronic detection using carbon nanotube field-effect transistors |
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MField-effect transistors (FETs) comprising of single-walled carbon
nanotubes (figure on the left) are emerging as very sensitive transducers
for chemical detection. Their application for detection of carbon dioxide
gas [1] and DNA hybridization [2] have been recently demonstrated. Depending
on molecular sensor molecules – which are schematically depicted in green –
carbon nanotube FETs can detect different molecules with high sensitivity
and selectivity. The objective of this research project is to synthesize
molecular receptors, apply them to sidewalls of carbon nanotubes, and then
test them in device setting for sensor applications.
[2/06]
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REU Web page maintained by Prof. Joseph J. Grabowski. Updated
