Projects

Projects are listed below by faculty name and broad research area. These descriptions are meant to give you a general idea of the research interests that you may pursue with Chem-SEEDS. However, as you may expect rapid evolving projects may change or they may become unavailable. The description of interests in your application will serve us to suggest the best match with a faculty researcher or project. Our researchers will be happy to respond to specific questions you may have about other current projects.

Click on a researcher's name to the see their research website.


Enantioselective Reduction of Imines: A Strategy for the Construction of the Dragmacidin Core and Potential Structural Analogues



Jon Antilla, Ph.D., Associate Professor, Organic Chemistry

The goal of this project is to continue our studies into an area of catalytic chemistry in which our laboratory has a demonstrated track record  the design and implementation of new organocatalysts based on chiral phosphoric acids. First, the undergraduate REU students will be involved in the preparation of new chiral phosphoric acid catalysts by known procedures in our laboratory. This first step allows the REU students to develop synthetic skills and to build up catalyst for their methodological studies to follow. In the second phase of the work, the REU students will partner with graduate students on specific method projects. We will first begin with is asymmetric hydroboration. The students will learn important problem-solving skills as they optimize conditions for the reaction and expand substrate scope so eventual application to synthesis of biologically relevant targets can be achieved. (Ingle, et al., 2011; Larson, et al., 2011)



Synthesis of Bioactive Molecules and Multivalent Delivery Vehicles



Kirpal Bisht, Ph.D., Associate Professor, Organic Chemistry

Our laboratories are involved in design and synthesis of small molecule therapeutics that possesses promising biological activity. We are also developing multivalent scaffolds for enhancing the activity of the small molecules therapeutics. Construction and investigation of functional biodegradable polymeric materials for drug delivery is also an active area of research in my laboratories. Undergraduate students will be involved in synthesis, isolation and characterization of small molecules (bioactive molecules and monomers for polymerization), polymers (ring opening and emulsion polymerization) and multivalent scaffolds. The research projects offer students training in various aspects dealing with organic and polymer synthesis. It fosters expertise in critical thinking, problem solving, and effective communication skills. (JBC, (2013) 288: 26834-26846. American J. Pathol. (2012) 181(3), 858-65. Bioorg. Med. Chem. Lett., (2012), 22, 1402-1407. Tet. Lett. (2010), 51, 1407-1410. Chem. Comm., (2009), 1822-1824. Chem. Comm., (2007) 4901 - 4903. Tetrahedron, 63, 1116-1126 (2007).



High Molar Mass Self healing Polymer Nanotube Composites



Julie Harmon, Ph.D., Professor, Physical Chemistry/Polymers

This project focuses on the development of high molar mass, self-healing polycarbonate-containing polyurethane (PCU) nanotube composites. Healing in these materials is autonomous, intrinsic as well as reversible. This research offers the challenge to delve into the mechanisms behind the healing process and to greatly enhance the understanding of these remarkable materials. Unlike most autonomous, intrinsic healing systems that use lower molar mass matrices held together by non-covalent interactions, USF research demonstrated that a special class of high molar mass (covalently bonded) thermoplastic polyurethanes (PU) exhibit self-healing properties. Further, self-healing properties are enhanced by creating composites of the polycarbonate-containing polyurethane and single-wall (SW) or multi-wall (MW) carbon nanotubes (CNTs). The undergraduate taking part in this research will be responsible for synthesizing polymers, processing PU/nanotube composites and for testing physical properties of the composites. Bernard Knudsen (graduate student) will mentor the undergraduate researcher. (McCann, et at., 2010; Hilker, et al., 2011)



Development and Application of Optical Spectroscopy and Electrochemistry in Characterizing Important Processes



Xiao (Sheryl) Li, PhD, Assistant Professor, Analytical Chemistry

Core-shell structured nanoparticles for the detection of neurotransmitters. Our objective is to develop a highly sensitive method for the detection of neurotransmitter such as dopamine in vitro using surface-enhanced Raman spectroscopy (SERS) by employing Au nanoparticles with particular core-shell structure: Ag core-Au shell or Silicon core-Au shell. Au and Ag nanoparticles with different size and shapes have already been synthesized and well characterized in the lab and were demonstrated to have relatively high SERS activity. In this project, undergraduate students will learn to synthesize Au nanoparticles with core-shell structures. More importantly, the students need to control the shape, size and structure of those nanoparticles through varying both the synthetic methods and the experimental conditions including temperature, pH, molar ratio, concentration, and aggregating agents. Also, the students will learn to characterize the nanoparticles using different techniques like UV-Vis absorption spectroscopy, and further examine the SERS activities of those nanoparticles. Graduate student mentors: Seong-min Hong and Sungyub Han. (Oldenburg, et al., 1999; Pedersen, et al., 2007; Yang, et al., 2008)



Photophysical Studies of Metal-Organic Materials



Randy Larsen, Ph.D., Professor, BioPhysical Chemistry

The primary research areas of the Larsen group are molecular biophysics and photochemistry/photophysics. Specifically our interests are in the area of time resolved optical spectroscopies and photothermal methods to probe the mechanisms of protein function both in solution and in the confined space of porous materials. In the area of metal organic materials (MOMs) our interests are focused on 1) encapsulating small biological molecules within extended porous MOMs with the goal of both understanding the role of confined space in protein function as well as to develop novel BioMOM hybrid materials, 2) examining the interactions between biological molecules and discrete soluble MOMs in order to enhance biological activity and 3) to utilize small fluorescence molecules to probe the molecular environment within porous MOMs as well as to probe the photophysical properties of the MOMs themselves. REU projects in our lab will not only involve the photophysical characterization of MOMs but also utilizing spectroscopic probes for deciphering the complex mechanisms through which MOMs form in solution.



Sol-Gel Germania-based Phases for On-line Sample Preconcentration in Ultra-trace Analysis by Capillary Microextraction Coupled to High-Performance Liquid Chromatography.



Abdul Malik, Ph.D., Associate Professor, Analytical Chemistry

Silica (SiO2)-based stationary phases and extraction media are predominantly used in chromatographic separations. One serious shortcoming of silica-based materials is their poor pH stability. Titania- and zirconia-based materials have been used as an alternative to overcome this limitation. However, it is quite difficult to derivatize zirconia- and titania surfaces with organic ligands to provide a chromatographically useful ligand density. The location of germanium in the periodic table indicates that GeO2 and SiO2 would possess similar properties and surface chemistry. Recently, Dr. Maliks group demonstrated exceptional pH stability of germania-based organic-inorganic hybrid phases Undergraduate researchers will be involved in two different projects: Development of Sol-gel germania-based coatings and Development of Sol-gel germania-based Monolithic Beds. The practical aspect of these two projects will involve the creation of sol-gel germania-based coatings and monolithic beds within fused silica capillaries using various sol-gel precursors and organic ligands, and evaluation of their performance in capillary microextraction and chromatographic separation. (Segro, S., Triplett, J., & Malik, A., 2010)



Investigation of the Mechanism of Oxidation/Hydroxylation and DNA Cleavage Reactions Mediated by Cu(II) and Fe(III) Complexes of Linear Copolymers and Peptides.



Li-June Ming, Ph.D., Professor, Inorganic Chemistry/Biochemistry

Vicky Lykourinou, Ph.D., Instructor, Inorganic Chemistry/Biochemistry

Our research is focused in the design, synthesis, physical/spectroscopic and catalytic characterization of metal-complexes constructed using peptides (metallopeptides) and linear co-polymers (metallopolymers). The REU participants will prepare and purify various metallopolymers thus using organic synthesis techniques. They will also learn the proper handling, preparation and quantification of peptide or antibiotic standard solutions using standard biochemical techniques. Various physical methods will be used for characterization of the metal binding to the selected ligands as well as the resulting catalytic intermediates exposing students to a broad array of techniques and spectroscopic methods such as: use of Schlenk line to prepare oxygen free solutions, UV-Vis spectroscopy for metal binding characterization and investigation of reaction rates, Nuclear Magnetic Resonance (NMR), Electron Paramagnetic Resonance (EPR) and Fluorescence for detailed characterization of the metal binding environment. The investigation of the catalytic mechanism of action of all the complexes described above will expose students to principles of enzymology through discussion and understanding of enzyme kinetics for investigation of reaction mechanism as well as collection of kinetic measurements, catalytic action of metalloproteins and related three-dimensional structures of biomolecules. The REU participants will also be trained in the preparation of plasmid DNA using molecular biology techniques and further characterization of catalytic DNA cleavage using gel electrophoresis. (Epperson, et al., 2001; Lykourinou, et al., 2009)



Computer simulation of protein-induced DNA bending



Arjan van der Vaart, Ph.D., Assistant Professor, Bio-Physical/ Computational Chemistry

Research in the van der Vaart laboratory focuses on the application and development of computer simulation techniques to problems in biochemistry. Several projects in our group focus on the highly unusual conformational dynamics of sequence-specific DNA-binding (SSDB) proteins such as transcription factors. The binding of these proteins to their target DNA sequences often involves the (partial) folding or unfolding of the protein and the bending and kinking of the DNA. While the thermodynamic aspects of the binding are well-understood, detailed information on it microscopic origin are still missing. We use molecular dynamics simulations to help address these questions and we have developed an efficient algorithm to study the flexibility of DNA in the presence and absence of proteins. The REU participant will apply these methods to the binding of the Ets-1 transcription factor, which partially unfolds upon binding and bends the DNA by 27°. The research will address how the protein stabilizes the DNA and why a specific angle of 27° is observed in the complex. The REU student will be trained in the theory and application of molecular simulation, the use of the UNIX operating system and advanced simulation and visualization software (CHARMM and VMD), and the biochemistry of SSDB proteins. Graduate student mentor: Aleksandra Karolak. (Jen-Jacobson, Engler, L. E., Jacobson, L. A., 2000; Brooks, et al., 2009; Maragakis, P., van der Aart, A., Karplus, M., 2009)



Brian Space, Ph.D., Professor, Computational Chemistry

The undergraduate research involves porting both iterative many body polarization equations and closely related van der Waals methods (obtaining van der Waals attractions via the same equations supplemented with a Drude polarizable parameter for each atom type) to GPUs. While Thole/Applequist many body polarization methods are extremely effective and highly transferable, the computational cost has been prohibitive to use these methods in complex molecular dynamics simulations. Preliminary work in my group has demonstrated that performing these calculations on GPU's has the potential to completely eliminate the bottleneck and thus this project provides the possibility of materially changing the way molecular dynamics simulations of soft matter and biological systems are performed—improving accuracy and giving physical insight into dispersion interactions. The resulting code will be integrated into our highly parallel (Grand Canonical, Canonical, Microcanonical, hybrid) Monte Carlo sorption code. The student will then conduct Grand Canonical simulations of gas mixtures in metal organic materials using the new methods. (Belof, Stern, & Space, 2009; Chen, et al., 2009)



Development of a Web-based Portal for Molecular Simulations



H. Lee Woodcock, Ph.D., Assistant Professor, Computational Chemistry

Computer simulation of molecular systems is a complex process, requiring the successful practitioner to possess knowledge of fundamental physical science, sophisticated techniques, and skills with one or more software packages. In particular, CHARMM, one of the most widely-used and feature-rich simulation programs, can be extremely intimidating for new users. To overcome this, interfaces such as CHARMMing (CHARMM interface and graphics) have been developed. The projects for the REU participants will revolve around the continued development of CHARMMing and will require some computer programming education; however, experience with molecular simulations is not needed and will be obtained during the course of this work.



Synthesis and Applications of Porphyrin-Based Metal-Organic Materials



Peter Zhang, Ph.D., Professor, Organic Chemistry

Porphyrins and metalloporphyrins are a class of chemically and biologically important compounds that have found a broad spectrum of applications in different fields. Due to their attractive physical, chemical, and biological properties, they provide a unique platform for developing advanced materials. It has been well documented that the properties of porphyrins can be fine-tuned or dramatically altered through the use of peripheral substituents having varied electronic and steric properties. Based on several powerful methodologies recently developed in the Zhang group, functionalized porphyrins that contain additional metal coordination sites will be designed and synthesized. They will be employed as building blocks for the construction of porphyrin-based metal organic frameworks (MOFs). This new type of metal-porphyrin frameworks (MPFs), which possess the combined advantages of porphyrins and metal-organic materials (MOMs), will be employed for important applications such as catalysis, hydrogen storage, and solar energy conversion. Depending on their interests, REU participants in our group will work on three interrelated research projects for the synthesis and applications of porphyrin-based metal-organic materials: 1) Organic Synthesis—synthesis of various porphyrin ligands using modern organic synthetic methodologies; 2) Inorganic Synthesis—preparation and structural study of MPFs containing different metal ions; and 3) Applications—examination of the properties of resulting MPFs and exploration of their various applications with advanced instrumentation and analysis. (Burda, et al., 2011; Uygun, et al., 2011)