Faculty Research Interests and Projects

Professor Anna D. Gudmundsdottir, PI
In the past decade, a series of useful molecular systems known as phototriggers have been used in a wide variety of applications including the release of fragrances from household goods, as an aid in multi-step syntheses, and in drug and gene delivery. We have been developing a new series of phototriggers which are based on Y-hydroxy-Y-phenylcrotonate ester derivatives. Our goal is to determine the rate of release from these esters and to identify the factors that control the rate of release. Thus, we will study the photoreactivity of α-hydroxy-α-phenylcrotonate esters and isolate their photoproducts. We will elucidate the mechanism for release using transient spectroscopy and calculations. The REU student will synthesize the hydroxy-α-phenylcrotonate ester derivatives and do product studies. Thus, the proposed studies will expose the REU student to synthetic and purification methods study. The students will also gain insight into spectroscopy by characterizing the starting material and photoproducts using NMR, IR, mass spectroscopy and X-ray crystallography. Furthermore, the student will also be trained to do transient spectroscopy using our laser flash photolysis apparatus. 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. Thus, the graduate student will also be provided with valuable management and teaching skills for his or her future employment.

Professor Bruce S. Ault, co-PI
An REU student in the Ault group will work on one of two ongoing research projects. The first is an experimental and theoretical study to enhance our overall understanding of the reaction mechanisms of ozone, O3, with carbon-carbon multiple bonds. These reactions are of fundamental interest and have substantial implications for tropospheric chemistry. The second is fundamental study of the mechanism(s) of the reaction of ozone with a range of gas phase organometallic precursors, reactions that are relevant to the chemical vapor deposition (CVD) or atomic layer deposition (ALD) of metal oxide thin films. To achieve these important goals, the student will combine the matrix isolation technique with infrared spectroscopy and theoretical calculations to determine the sequence of reactive intermediates formed and destroyed during the reaction process. Reaction intermediates at different points in the reaction will be formed and trapped in argon matrices at 14 K and examined by FTIR spectroscopy. A student who works on one of these projects will learn cryogenics, high vacuum techniques, infrared spectroscopy and theoretical calculations, as well as critical thinking and the process of scientific research.

Professor Neil Ayres
The use of polymers in society has become ubiquitous from commodity items to high technology and cutting edge therapeutics and diagnostics. However, macromolecular chemists remain unable to synthesize materials possessing the specificity and complexity rivaling naturally occurring biomacromolecules. It is our goal to use N-alkyl urea peptoid/polymer conjugates as a platform to combine polymer synthesis with increased synthetic precision, control of multiple functional and responsive groups, with a simple route to complex architectures. Our projects promote the use of fully synthetic non-natural macromolecules with structure-based functions, or in other words, the ability to combine protein-like self-organizing properties with designed functional activity. This creates a versatile research platform for macromolecular investigations in many areas including therapeutics, new materials, rheology modifiers, and mimics of biomacromolecule structure and functions. We are able to synthesize controlled polymer/N-alkyl urea peptoid conjugates using a combination of peptoid synthesis; Cu catalyzed alkyne/azide cycloadditions; and reversible addition fragmentation chain transfer (RAFT) polymerization chemistry. REU students in my group will contribute to using this chemistry to prepare polymers designed to determine structure/activity relationships for synthetic heparin mimics. This project will result in a rationally designed materials set of precise architecture and functional groups that will provide new, fundamental insights into polymer/blood interactions. Students involved in this project will gain experience in N-alkyl urea peptoid and polymer synthesis and characterization techniques, experimental design, and problem solving techniques.

Professor Mike Baldwin
Students in the Baldwin group will be working on an NSF-funded project entitled “Stimulus-responsive chelates for light-triggered release of metals”. The central goal of this project is to develop new, mixed-donor, -hydroxy acid-containing chelates that will tightly bind Fe(III) or other metals and release them in response to a photochemical stimulus. One objective in obtaining this goal is to determine what structural and electronic factors in the chelate design can be modified to tune the metal binding and photochemical properties of the complexes as needed for different applications. The REU student will contribute to this objective by synthesizing and characterizing members of one of the chelate families we are targeting. The structural motifs that provide the basis for these families include salicylidenes, tripodal amines, bis(imines), azacycles, and natural amino acid-based motifs. Once the chelates and their Fe(III) complexes have been synthesized, the student will conduct photochemical, electrochemical and metal binding experiments to determine trends within their chelate series. Thus, a student working on this project will gain hands-on experience in laboratory techniques that include organic and inorganic synthesis, compound characterization by various physical methods (NMR, IR, mass spectrometry), crystallization methods, photochemical reactions, analytical methods including colorimetric assays, electrochemistry, determination of stability constants, and inert atmosphere methods.

Professor William B. Connick
Participants working with Professor Connick will synthesize and investigate new platinum and palladium complexes that undergo a reversible color change upon exposure to aqueous analytes. In the course of our studies of colorimetric vapor-sensing materials, we have recently discovered that [Pt(tpy)Cl](PF6) undergoes a rapid and distinct color change in the presence of aqueous perchlorate ion, which is an important ground water contaminant near military installations. Upon exposure, the material undergoes anion exchange, resulting in a pronounced color change and dramatic red-shift in luminescence. The response is remarkably selective and no color change occurs upon exposure to common interferents, including halides, nitrate, phosphate, carbonate, or sulfate. The objective of this research is to elucidate the factors that govern the colorimetric and luminescence-based response of salts of d8-electron metal complexes to aqueous anions. The attainment of a detailed understanding of the colorimetric and luminescence-based response of these types of materials, as well as the influence of the surrounding medium and supporting material, is an essential first step toward incorporation in chemical sensing devices. These results will have a significant positive impact, because the identified factors are expected not only to advance understanding of colorimetric materials, but also to fundamentally advance the fields of chemical sensing and materials science. With our membership in the UC Center for Biosensors & Chemical Sensors, we are well prepared to undertake this project because, to the best of our knowledge, we are the only investigators to have discovered these sensing properties, and because we have the wide range of critical expertise (synthesis, structure, spectroscopy) needed to obtain definitive outcomes (see Biographical Sketches). The REU students contributing to this research will gain experience in organic and inorganic synthesis, as well as the application of a wide range of physical methods, including X-ray crystallography, MS, NMR spectroscopy, TGA, DSC, SEM/ESEM, AFM, ITC, FTIR-ATR, and QCM gravimetry.

Professor Ruxandra I. Dima
Dima’s group is engaged in fundamental research related to the modeling of the mechanical behavior of large biopolymer systems. The research is directed at developing new computational approaches for modeling the response of two main cytoskeletal filaments, microtubules and filamentous actin (F-actin), and of their components to the action of applied forces. Elucidating the behavior of the cytoskeleton under tension resulting from cell-cell interactions or from the binding or unbinding of filament associated proteins to the cytoskeleton is fundamental for gaining insight into the role played by forces in the life of the cell. External tension is applied to cells during a variety of processes such as cell-cell adhesion, blood flow, wound closure, axonal growth, and mitosis. As a result, force-induced changes occur in cytoskeletal proteins leading to the deformation of cells and to the transduction of mechanical signals into biochemical signals ultimately inducing biological responses such as alteration of specific genes expression, changes in protein synthesis, and channel activation. A project for an REU student is "Exploration of the role of long-range cooperativity in the mechanical response of large biomolecular assemblies". The goal of this project is to identify and classify the types of long-range interactions between combinations of the most prevalent structural domains that give rise to flexible biomolecular assemblies. A student involved in this project will gain experience with analysis of protein databases, will become familiar with the computational methodology behind realistic modeling of proteins and their cellular environment (water, ions), and will gain extensive knowledge in searching the scientific literature.

Professor Hairong Guan
The research in the Guan group lies at the interface between inorganic chemistry and organic chemistry focusing on homogeneous catalysis with non-precious metals. To rationally design efficient, selective, and inexpensive catalysts, we will investigate the kinetic and thermodynamic driving forces that control the reactivity of nickel and iron complexes. More specifically, we are interested in synthesizing nickel and iron complexes with diphosphinite ligands and studying the elementary reactions with these compounds. The obtained information will guide us to tune the structures of metal complexes for catalytic transformations such as the reduction of carbon dioxide and ketones, the isomerization of olefins, and cross-coupling reactions. Students involved in these projects will learn various synthetic techniques including the handling of air- and moisture-sensitive compounds. They will also be trained to conduct mechanistic studies using NMR spectroscopy, X-ray crystallography, and chemical kinetics. Furthermore, the research projects will teach students the concept of increasing energy efficiency by performing catalytic reactions and the notion of sustainability by using renewable feedstocks and readily available materials.

Professor William R. Heineman
Research projects for REU students are in the general area of chemical sensors and biosensors. New concepts for chemical sensors and biosensors are being developed for environmental and biomedical applications. One project area involves miniature sensors based on microfabricated carbon towers that are functionalized with appropriate chemicals to detect biological agents such as bacteria and viruses and metals ions such as lead in the environment. REU students will gain experience in microfabrication and electrochemistry as applied to sensors. Another project area is sensors based on Spectroelectrochemistry. This new type of sensor combines three levels of selectivity in one device: selective partitioning into a film, electrochemical excitation signal, and optical response signal. The improved selectivity is a breakthrough in sensing methodology. Students on this project gain experience in electrochemistry, absorption and fluorescence spectroscopy, preparation of thin selective coatings, and environmental and biomedical applications. These projects are interdisciplinary in nature and involve collaborations with scientists in physics, biochemistry, engineering, and the medical sciences. REU students will be part of my research group of about 8 graduate students, postdocs, and visiting scholars from other universities.

Professor Patrick A. Limbach
Many types of RNAs are involved in key cellular functions in all living cells. Among all known bio-organic molecules within living cells, RNA molecules are the only ones that store genetic information and act as catalysts. Recently, new experimental strategies, termed experimental RNomics, have been developed to identify non-protein-coding (nc)RNA genes. However, compatible experimental strategies for characterizing ncRNAs at the posttranscriptional level are lacking. Our lab is dedicated to developing new and improved methods for the sequencing and quantification of individual ribonucleic acids (RNAs) present initially within complex mixtures. These methods will yield new strategies for the sensitive, accurate and rapid characterization of RNAs; a database of appropriate signature products for tRNAs from our model systems; and new strategies for the relative and absolute quantification of RNAs. The REU student will gain experience in biochemistry, RNA purification, mass spectrometry and molecular biology during the research period. The REU student will be part of a larger research group characterizing modified RNAs by various bioanalytical techniques. The REU student will gain research experience in the area of structural analysis of biomolecules, with specific training in advanced mass spectrometry and molecular biology techniques. The research experience will expose the student to the interdisciplinary nature of modern structural biology, and will provide the student with experience in biomolecular processes that occur within the protein translation apparatus.

Professor James Mack
The 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 solvent-lees 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 that 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. Tammara Clark, an NSF REU student in my research group from Central State University recently co-authored a paper in Green Chemistry, based on the research she conducted as an REU student. In addition Indre Thiel, a German exchange student who was a part of the iREU program was a co-author along with Tammara on this manuscript. We are currently in the process of submitting another manuscript to Green Chemistry based on their research. We recently submitted the work of Thomas Berkemeier, another iREU student to Chemical Communications. Many of my research papers have undergraduate students as co-authors and I am a firm believer in incorporating undergraduate students fully into my research.

Professor Edward Merino
Reactive oxygen species (ROS) are a double edged-sword. These molecules and the chemistries they make possible are essential for cellular growth and signaling. However, excess reactive oxygen chemistry disrupts cellular function via deleterious modification of DNA, proteins, and other biomolecules. There are four major forms of biologically important ROS: superoxide, singlet oxygen, hydrogen peroxide, and hydroxyl radical. Levels of ROS, formation of oxidative lesions, and antioxidant levels are each critical determinants of cell fate. One of the most important consequences of excess ROS is the formation of a complex set of novel DNA lesions including DNA-protein crosslinks. Despite their importance, the structures of oxidation-induced crosslinks are not well understood limiting their ability to be used as analytes of cell fate. The poor understanding of these critical lesions stems from the inherent complexity of large covalent DNA-protein assemblies and a lack of appropriate model systems. Preliminary small molecule studies suggest that these lesions may be ideal markers of cellular oxidative stress since crosslinks experience ROS-dependent adduct formation. Under the REU program the chemistry and structure of oxidative DNA-protein crosslinks will be probed. Students engaged in research in the Merino Lab will obtain exposure to biochemistry and modern instrumentation. Research in the lab spans the interface of biology and chemistry. Students master many techniques that require substantial skill and technical knowledge including HPLC, MS, organic synthesis, and electrophoresis. By accomplishing experiments towards understanding the biological impact of these oxidative crosslinks student researchers will gain knowledge of a chemical biology lab. This exposure will serve as a critical catalyst to excite students about graduate school.

Professor Laura Sagle
Research in the Sagle group lies at the biological/nanoscience interface and is focused on the development of new plasmonic bionanomaterials for both biosensing and biophysical/spectroscopy studies.  Materials of interest interface biological species, such as proteins and DNA, with noble metal nanoparticles and substrates.  Our research employs a wide range of techniques such as protein expression, inorganic nanoparticle synthesis, and surface nanofabrication to make the samples, atomic force and transmission electron microscopy to characterize the samples, and plasmon absorption and surface enhanced Raman spectroscopy (SERS) to utilize the samples.  One project that an REU student could work on in the Sagle lab utilizes Localized surface plasmon resonance (LSPR) for biosensing.  This technique shows great promise in sensitive, colorimetric, label-free detection of biomarkers for disease diagnostics.  However, biofouling and lack of specificity have prevented measurements in biological fluids such as blood.  We are working to improve biosensing capabilities with protein-nanoparticle arrays both in solution and on a fabricated surface.  In this case, the protein binds a specific biological analyte in solution and changes conformation, which in turn alters the environment of nanoparticles bound to the protein and changes the observed color.  Another project an REU student could work on in the Sagle lab is in the improvement of nanoparticle array-based LSPR and SERS substrates.  This is carried out through the deposition of polymers on a surface followed by the addition of a template, which can be solution-phase nanoparticles and/or magnetic beads.  Surface-bound arrays of gold and silver nanoparticles are then generated in the shape of the template used, creating interesting supramolecular structures, with which the LSPR and SERS properties are investigated.

Professor George Stan
Research in Stan's group is focused on computational modeling of biological nanomachines involved in protein degradation. Intracellular regulatory mechanisms for selective destruction of proteins are critical for the maintenance of vital cellular functions. Clp macromolecular machines, found in all domains of life from prokaryotes to multi-cellular eukaryotes, perform such protein quality control using powerful ATPase components that effect protein unfolding and translocation through narrow pores. Currently, kinetic and thermodynamic requirements of Clp-mediated unfolding and translocation and the coupling of ATP hydrolysis to substrate threading by Clp ATPases are unclear. A specific project for an REU student will concern quantifying the relative contribution of native and non-native interactions to substrate protein unfolding and translocation. Coarse grained models, which include only native interactions, have been shown to describe forced unfolding pathways with similar detail as atomistic representations irrespective of protein fold and to yield results consistent with experimental AFM studies. Based on this versatility of minimalist models, we surmise that, within the framework of forced unfolding, non-native interactions represent only a small perturbation to native interactions. Nevertheless, it is important to quantify the contribution of non-native interactions to the Clp-mediated SP unfolding. The student working on this project will gain knowledge concerning biomolecular simulations of nanomachines and will acquire knowledge in using computational tools for visualization and analysis of biomolecular structure.