Individual Research Projects

Porphyrins and their analogues have continued to inspire synthetic chemist over the last century. Their importance for the existence of life on earth inspired scientist around the globe to explore their chemical and physical properties. Others embarked on the preparation of analogues in an attempt to both mimic porphyrins as well as to obtain new, previously unobserved properties. One set of possible analogues started to attract attention only recently. These are the carbaporphyrins, compounds that promise to incorporate classic organometallic chemistry into porphyrin research.

The focus of the carbaporphyrin research is to better understand the nature and reactivity of the internal carbon atom, which has been proposed to act as a nucleophilic carbenoid.These compounds are also targeted because it is expected that they will possess novel chemical and physical properties with applications in divers fields such as catalysis or non-linear optics. Additionally, they will serve to expand our understanding of the theoretical concept of aromaticity.

Specifically, the goal of this research is to further advance the chemistry of inverted or N-confused porphyrins and carbaporphyrins. This will be accomplished by developing novel synthetic strategies as well as by exploring chemical approaches well established in porphyrin research. The ultimate goal is to synthesize a tetracarbaporphyrin, a molecule often considered the “holy grail” of this particular branch of research. Additionally, the metalation chemistry of carbaporphyrins is of great interest. Metalloporphyrins are important parts of numerous biocatalytic processes and this biocatalytic aspect will be explored by preparing metallocarbaporphyrins.

The student participating in this research project will be expected to perform synthetic work, in combination with the characterization of the products of their research. This will result in the student being exposed to both modern synthetic techniques and modern analytical methods, including UV-Vis-, IR-, and NMR-spectroscopy, as well as mass spectrometry.

2. Synthesis of poly(b-hydroxyalkanoates) with terminal unsaturated groups (Faculty Mentor – Carmen Scholz).

This is a project that Dr. Scholz initiated in the summer of 2001. An undergraduate student will synthesize medium chain poly(b-hydroxyalkanoates) using P. oleovorans. The goal of this research is to (i) establish a protocol for the fermentation of P. oleovorans in our laboratory, (ii) produce copolymers with terminal vinyl side groups and (iii) find an optimum carbon-source ratio that guarantees sufficient polymer yield and high vinyl group content. Nonanoic acid will be used as main carbon source and the fermentation broth will be amended with undecylenic acid. The resulting copolymer is expected to carry vinyl-terminated side-groups. Since P. oleovorans has not been previously used in our laboratory the student will first have to establish a protocol for the bacterial growth of this strain. Upon establishing suitable bacterial growth conditions, the student will study bacterial co-feeding using nonanoic acid and undecylenic acid in varying concentrations. The impact of undecylenic acid on the bacterial growth in terms of yield and growth time will be investigated. The resulting copolymers will be analyzed for their molecular structure using ¹H-NMR. This is a seed-project that is expected to expand in the future to include polymer-analogous reactions of these copolymers with thiolated poly(ethylene glycol). Dr. Scholz has shown the feasibility for a radical addition reaction to occur between these two polymers.

3. Isolation and study of proteins from hyperthermophiles (Faculty Mentor – John Shriver).

Research in my laboratory is devoted to structural and thermodynamic studies of proteins from hyperthermophiles. Such proteins are of special interest in structural biology since they are designed to function at the upper temperature limit of life (viz. 80 to 110 ºC). The long-term goal of this work is to utilize the unique attributes of hyperthermophile proteins to increase our understanding of protein energetics and enhance our capabilities in protein engineering and biotechnology.

The determination of the structures of a number of hyperthermophile proteins are now in progress in my lab, and this data will be utilized to propose rational explanations for enhanced stability and function in these proteins at high temperature. Undergraduate research opportunities include the option of growing new thermophilic organisms to isolate new proteins for study, cloning and expression of these proteins, participating in the characterization of the stabilities of these proteins using calorimetric methods, and determining protein structures using multidimensional NMR methods.

Students participating in this work will be expected to contribute in a productive manner at a level sufficient to participate in a national meeting and publish the work in the most well respected journals They will obtain hands on experience in utilizing biophysical methods to understand biomolecular processes. The skills which they obtain will provide a firm foundation in these methods for further work as a graduate student or in the biotechnology industry.

4. Synthesis and characterization of amphiphilic block copolymers (Faculty Mentors – Carmen Scholz - Bernhard Vogler).

This is a project that Dr. Scholz initiated in the summer of 2001. An undergraduate student will synthesize medium chain poly (b-hydroxyalkanoates) using P. oleovorans. The goal of this research is to (i) establish a protocol for the fermentation of P. oleovorans in our laboratory, (ii) produce copolymers with terminal vinyl side groups and (iii) find an optimum carbon-source ratio that guarantees sufficient polymer yield and high vinyl group content. Nonanoic acid will be used as main carbon source and the fermentation broth will be amended with undecylenic acid. The resulting copolymer is expected to carry vinyl-terminated side-groups. Since P. oleovorans has not been previously used in our laboratory the student will first have to establish a protocol for the bacterial growth of this strain. Upon establishing suitable bacterial growth conditions, the student will study bacterial co-feeding using nonanoic acid and undecylenic acid in varying concentrations. The impact of undecylenic acid on the bacterial growth in terms of yield and growth time will be investigated. The resulting copolymers will be analyzed for their molecular structure using ¹H-NMR. This is a seed-project that is expected to expand in the future to include polymer-analogous reactions of these copolymers with thiolated poly(ethylene glycol). Dr. Scholz has shown the feasibility for a radical addition reaction to occur between these two polymers.

5. Novel phytochemical agents for treatment of breast cancer (Faculty Mentor – William S. Setzer).

The purpose of this project is to isolate and identify novel phytochemical agents from tropical rainforest plants that show promising antineoplastic activity against breast tumors. We have identified a number of plant species that show selective in-vitro cytotoxic activity against breast tumor cells:

Students will have the opportunity to participate in field collection and extraction of active plants in Monteverde, Costa Rica. Crude extracts will be subjected to bioactivity-directed chromatographic separation. Students will learn cell culture techniques as well as chromatographic techniques. Biologically active compounds will be isolated and the structures determined using spectroscopic techniques (IR, UV, MS, NMR), so students will be exposed to modern analytical techniques.

6. Cloning, expression and characterization of enzymes from the ubiquitin (Ub) conjugation pathway (Faculty Mentor –Enrico DiGiammarino).

My laboratory will provide molecular biology and protein biochemistry training to a motivated undergraduate. The student will clone, express and characterize an enzyme (or enzymes) from the ubiquitin (Ub) conjugation pathway. The student’s research will provide a foundation for (and may extend to include) studying the solution structure of these proteins by NMR.

The Ub-conjugation cascade is an essential pathway in all eukaryotes and a key aspect of cell growth and differentiation. A wide variety of human diseases, including cancers and developmental disorders, can be traced to errors in this pathway. Many different proteins are targeted for degradation by Ub-conjugation and consequently the machinery for substrate targeting reflects a similar level of diversity.Understanding the intermolecular interactions that lead to the exquisite substrate specificity found in this pathway is the long-term goal of my research. The student will participate in this research by cloning and characterizing an individual component (or components) of the Ub-conjugation pathway.

The student will learn and perform molecular cloning techniques that will include the following: PCR, bacteria culture, use of restriction enzymes and DNA purification and visualization. The student will also learn and perform the following protein biochemistry techniques: expression of recombinant proteins in bacteria, protein purification methods and various spectroscopic protein analysis methodologies. Finally, the student will learn how to interpret results and formulate hypotheses as well as participate in discussions of the theory behind techniques used in the lab and current topics related to our research.

7. Fast-atom reactions at surfaces (Faculty Mentor – Michael George).

A regime of surface chemistry that has only recently begun to be explored is that of neutral atom or molecule chemistry at translational kinetic energies of 1 to 10 eV. Such beams are referred to as hyperthermal since the characteristic temperatures (from ½ mv² = kT) for light gases in the few eV atom^-1 regime are in the range of 10,000 – 100,000 K. The regime covers bond energies over most of covalent and ionic chemistry, yet is below the measured sputtering threshold for physical removal of atoms from their divergence allowing production of masked structures with high fidelity (anisotropic etching or processing) and without charge build-up and associated electrical breakdown problems. Samples of interest in this study will include zinc-cadmium telluride, silicon, germanium and GaAs because of the need to produce stable, very thin oxide layers on these materials for microelectronic and detector applications.

The undergraduate student participating in this research will prepare samples using the UAH Atomic Oxygen Facility. They will prepare surfaces by cutting and polishing the crystals. They will then operate the atomic oxygen chamber recording reaction parameters including time and temperature. After preparation, an analysis of the composition, oxidation state, and surface structure will be carried out. The student will be introduced to reaction kinetics, materials preparation and analysis using X-ray photoelectron spectroscopy and atomic force microscopy. AFM techniques will include the use of electric force and surface potential microscopies. The oxides formed on the substrates may also be characterized by X-ray diffraction.

8. The position of the chemical equilibrium (Faculty Mentor – James K. Baird).

Aluminum oxide, as well as the oxides of many of the metals of the first transition series, dissolve in aqueous acid solution by formation of the hexa-aquo complex. In the mixture isobutyric acid (HA) + water, for example, the dissolution of aluminum oxide involves the reaction:

Al₂O₃ (c) + 6HA(s) + 9H₂O(s) → 2[Al(H₂O)₆]³⁺(s) + 6A^‑(s)

where “c” stands for crystalline and “s” for solution phase. Because there are no inert components in the mixture at chemical equilibrium, the Griffiths-Wheeler rules predict that the absolute value of the temperature derivative, ∂w/∂T, of the solubility, w, should diverge as T approaches the upper critical solution temperature (UCST) of isobutyric acid + water. Consistent with this prediction, we found that the solubility of Al₂O₃, which dissolves exothermically, increases by a factor of two over a temperature range within 2 ºC of critical, while the solubility of MnO₂, which dissolves endothermically, decreases by a factor of ten over the same temperature range. This is the first time that large shifts in the position of chemical equilibrium near a consolute point have been reported. We propose solubility measurements designed to answer the following question: 1) Do solubility critical effects extend to inorganic oxides (and also hydroxides) other than Al₂ O₃ and MnO₂? 2) Can critical isobutyric acid + water be used to achieve enhanced extraction of organic bases while critical triethylamine + water be used to achieve enhanced extraction of organic acids?

The role of the student in this project is to prepare the appropriate solutions of metal salts and subsequently study the dependence of the solubility on temperature.

9. Chemotaxonomy of Neotropical Lauraceae (Faculty Mentor – Bernhard Vogler).

The purpose of this project is to test the hypothesis that members of the Lauraceae (the avocado family) can be classified in terms of their phytochemistry. The results will complement classical taxonomy based on reproductive structures of these plants. The taxonomy of the Lauraceae is poorly defined and suspect, and this research will help to define the different genera and species of the family. Students will have the opportunity to participate in field research at our study site in Monteverde, Costa Rica, and to work in the field with Dr. William Haber (a botanist with the Missouri Botanical Garden). The Lauraceae is well represented in Monteverde, one of the most biologically diverse areas of the world. There are six species of Beilschmiedia, five species of Cinnamomum, four species of Licaria, 12 species of Nectandra, 32 species of Ocotea, eight species of Persea, two Pleurothyrium, and a Rhodostemonodaphne. At least six new species of this family have been discovered in Monteverde by Dr. Haber in the past ten years.

Analysis of Leaf Essential Oils. Leaves of members of the Lauraceae (the avocado family) will be collected from different individuals of species that occur in the Monteverde area. The leaves will be chopped and steam distilled to obtain the essential oils. The essential oils will be brought back to UAH for analysis. Phytochemical profiles for each individual plant will be obtained by gas chromatographic/mass spectral (GC-MS) analysis in order to assess the individual variation within a species and to determine whether or not there are key chemotaxonomic differences between species.

Analysis of Bark Alkaloids. Samples of bark of members of the Lauraceae will be collected and extracted in the field using a mixture of chloroform and ethanol. The crude extracts will be brought to UAH for further separation and analysis.The alkaloids will be separated from other phytochemicals by liquid-liquid extraction with aqueous acid. The acidic fraction will be neutralized with base and re-extracted with dichloromethane to obtain the "free base" alkaloids. The alkaloid mixture will be analyzed by high performance liquid chromatography coupled with mass spectrometry (LC-MS) and nuclear magnetic resonance spectrometry (LC-NMR). The Lauraceae are known to be rich in isoquinoline alkaloids and would therefore be particularly amenable to these analytical techniques.

10. Chemical Analysis of Materials Surfaces (Faculty Mentor – Jeffrey Weimer).

The undergraduate student working with Dr. Weimer will learn about methods used to alter and study the chemistry of surfaces. The goal will be to characterize the chemistry of surfaces that have been prepared using selected treatment methods. A system of particular interest is the bonding chemistry for silane layers absorbed on metal surfaces. The hypotheses are that silanes bond covalently to metal surfaces via hydrolysis reactions with surface metal oxides and that cross-linking reactions in the silane layer stabilize its bonding to the metal surface. The student will learn how to pre-treat a metal surface and prepare a specified layer of silane on the treated surface. The student will also learn how to operate a system for x-ray photoelectron spectroscopy (XPS) and how to interpret results from XPS in order to quantify surface composition and determine chemical bonding.

11. Controlled degradation studies of poly(b-hydroxybutyrate), PHB and block copolymers of PHB and poly(ethylene glycol) (Faculty Mentor – Carmen Scholz).

PHB is a natural biopolyester that is produced by microorganisms. PHB is characterized by very high molecular weights, usually in the order of 500, 000 Da. Therefore, PHB-b-PEG block copolymers are difficult to characterize spectroscopically. The student will study the hydrolytic degradation of PHB and PHB-b-PEG. First, the student will synthesize the respective polymers using A. latus. Protocols established in our laboratory will be used for the fermentation. Secondly, the polymers will then be subjected to hydrolysis with varying time of exposure. The main focus of this project is the development of a procedure for the hydrolysis. Optimum hydrolysis conditions and times need to be established. After recovering the polymer, it will be subjected to GPC and viscometry analysis. In addition, the PHB-b-PEG copolymers will characterized by NMR as well.

12. Pyridine and phenol containing calixarenes for studies in bioorganic chemistry and host-guest chemistry (Faculty Mentor – Andreas Gebauer).

A variety of pyridine and phenol containing calixarenes will be synthesized. These macrocycles are prepared with the appreciation that a wide variety of naturally occurring proteins and enzymes, responsible for such important tasks as electron transfer, dioxygen binding, metal storage, and catalysis, contain subunits with an N₂ S₂ or N₂O₂ binding motive. These compounds will possess a binding pocket that will be either neutral or dianionic when deprotonated, depending on if the ether/thioether or the alcohol/thiol, respectively, are employed.

The primary goal of the investigation of these macrocycles will be to determine their ability to coordinate biologically relevant metals such as copper(II), iron(II), molybdenum(VI) and tungsten(VI).

The student participating in this research project will be expected to perform synthetic work, in combination with the characterization of the products of their research. This will result in the student being exposed to both modern synthetic techniques and modern analytical methods, including UV-Vis-, IR-, and NMR-spectroscopy, as well as mass spectrometry.

13. New pharmaceutical agents from Abaco bush medicine (Faculty Mentor - William S. Setzer).

The purpose of this project is to identify potentially useful medicinal plants from Abaco Island, Bahamas, and to identify promising new drug leads. Participating students will have the opportunity to carry out field research in the Bahamas. The project will involve a survey of local ethnobotanical informants in order to compile a list of plants used in traditional herbal medicine. Plant materials will be collected and extracted at our field site in Marsh Harbour, Abaco. Crude extracts will be brought to UAH and tested for biological activity in our battery of bioassays: antibacterial activity against Bacillus cereus, Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa; antifungal activity against Candida albicans and Aspergillus niger; antineoplastic activity against various human tumor cell lines; as well as Artemia salina lethality. In addition, biochemical tests (ACE inhibition, COX inhibition, xanthine oxidase inhibition, antioxidant activity)will be carried out. The project will identify plant species that may serve as sources for new phytopharmaceuticals for treatment of various human ailments.