A-to-Z Index

Research Topics

In the interest of providing an option of diverse research opportunities, we offer experiences with faculty members in several specialties including organic, inorganic, biochemistry, organometallic syntheses with compound characterization, environmental analytical chemistry, nuclear chemistry, materials science, and physical chemistry.  There has been a separately funded materials science REU site at JMU which is housed in the same building as the chemistry site.  As has been the case in the past, there will be considerable interaction and overlap between these two sites.  General aspects of projects that are representative of the diverse nature of our student research opportunities are described below.  Additional projects may be found in the materials science and Regional NMR websites.

Developing Tools to Assist Interpreters in Communicating Science to the Deaf

The involvement of undergraduate students who are majoring in communication disorders in American sign interpreting (ASL) is complicated not only by having to learn to sign ordinary words and phrases, but also by their general lack of familiarity with scientific terms.  In fact, it has been noted that this is the main obstacle for deaf and hard of hearing people to gain access to the sciences.  Few teachers have been trained for signing in science.  Often deaf students in the school systems are steered away from the sciences by counselors and teachers who naturally favor areas in which they themselves are more comfortable. In the JMU REU program, student interpreters will be assigned to each research group with participants with hearing loss.  The deaf students will be mentored by the chemistry faculty member directing each group.  The student interpreters will be mentored by a professional interpreter who will not only train them and assist them on a day-by-day basis, but also use the opportunity to study the special needs for this system of communication.  The mission will be twofold: to make communication between the chemistry faculty and all students as simple and convenient as possible and to provide a research/learning experience for the interpreters.  The interpreting group effort will also include one high school teacher who can hear but is responsible for educating the deaf, and one deaf teacher who teaches science at VSDB or another school.  There will also be two high school students: one who can hear and one who is deaf.  The importance of recruiting people with hearing disabilities into science at an early age has already been noted. The inclusion of a second high school student of similar age will assist in making the deaf student feel more a part of the group, as well as providing that student with the developmental benefits of involvement in college research.  With the use of videotaping, observation, literature use, daily journals and record keeping and other methods of studying the interaction, it is expected that methods and tools will be developed to assist in training interpreters.  The information thus collected will be disseminated through presentations at conferences such as the “Technology and Persons with Disabilities” conference and the “Interpreters for the Deaf International Convention” and by journal and CD publications.

Dr. Donna S. Amenta and Dr. John W. Gilje, The Preparation and Catalytic Activity of Ruthenium(II) Complexes of Ph2P(CH2)nP(O)Ph2

For several years we have been interested in Ph2P(CH2)nP(O)Ph2 as ligands that contains both a hard Lewis base, the phosphoryl oxygen, which prefers to complex with hard Lewis acids such as early transition metals and lanthanides, and a soft Lewis base, the phosphine phosphorus, that prefers soft acids such as late transition metals.21-25 We have reported that oxygen bonded complexes form with Ln3+ and Al3+.  We are now turning our attention to the late transition metals. With these metals the ligand may coordinate in a monodentate fashion through phosphorus or behave in a chelating, “hemilabile” fashion with a strong M-P bond a weaker M-O(P) interaction. The phosphoryl group then may dissociate, creating an empty coordination site on the metal, while the ligand remains attached to the metal through the M-P bond. Hemilabile ligands have found application in catalysis and materials synthesis.5 Our preliminary data for ruthenium indicate that reactions of the ligands with Cl2Ru(PPh3)3, Ru(NO)Cl3, and  Ru(NO)Cl3(PPh3)2 produce a number of complexes, including Cl2Ru(PPh3)2[Ph2PCH2P(O)Ph2], that contains a chelating ligand, and Ru(NO)Cl3[Ph2P(CH2)nP(O)Ph2]2, n= 1-3, where the ligands are monodentate. Our concentration in this REU project will center on reactions that will either open a coordination site on the metal or produce a cationic derivative, both of which may be important in catalyst development. We will also be particularly interested in removal of NO from the complexes shown above. We have observed, serindipitously, that NO can be removed from Ru(NO)Cl3[Ph2P(CH2)2P(O)Ph2]2 during reactions with AgBF4 to form {RuCl2[Ph2P(CH2)2P(O)Ph2]}+BF4-, a Ru(III) complex with two chelating ligands. We are uncertain of the exact conditions under which this complex forms or of its generality to other members of the series. However, this process is interesting with respect to NO release agents that have potential physiological applications.  The complexes will be characterized by the usual spectroscopic means and by x-ray crystallography, when appropriate. In addition to x-ray structures, the coordination modes of the ligands can be assessed by 31P NMR, where coordinated phosphine and/or phosphoryl phosphorus resonances are significantly downfield from their uncoordinated states. The complexes will be evaluated as hydrogenation catalysts.

Dr. Kevin L. Caran, Synthesis and Supramolecular Aggregation of Novel Amphiphiles

In the Caran lab at JMU, students use the tools of organic synthesis to make and purify novel compounds in an effort to develop self-assembled soft materials (colloids) with well-defined properties. Subsequently a wide variety of tools and analytical methods are used to measure the properties and to understand the modes of self-assembly of the colloidal aggregates formed by these novel compounds. These tools include nuclear magnetic resonance (NMR) spectroscopy, X-ray diffraction (XRD), scanning electron microscopy (SEM), optical microscopy, differential scanning calorimetry (DSC), surface tensiometry, conductivity and attenuated total reflectance infrared (ATR-IR) spectroscopy.  [Project 1] The Caran lab has developed a series of organogelators (compounds that form gels in organic solvents) which self assemble via a combination of hydrogen bonding and pi-pi stacking of complementary arenes [in collaboration with Dr. Michal Sabat and Dr. Lin Pu at the University of Virginia]. Recently, dimeric versions of the original gelators have been shown to form gels in the presence of metal salts. [Project 2] In another project, a number of “bicephalic” (double-headed) surfactants have been prepared, each with two polar head groups and one non-polar tail; these novel compounds self assemble into micelles in an aqueous environment. These bicephalic compounds show unique properties when compared to conventional surfactants with one head and one tail. Furthermore, they also demonstrate a remarkable ability to serve as antimicrobial agents based on recent studies in collaboration with Dr. Kevin Minbiole (JMU Chemistry) and Dr. Kyle Seifert (JMU Biology).

Dr. Thomas C. DeVore, Solid State Decomposition Kinetics

Transition metal oxide nanoparticles have been suggested for use as catalysts in gas and petroleum production, as sensors, in fuel cells, and as photocatalysts for hydrogen generation.  Since catalytic activity and other physical properties depend on the particle morphology, several methods have been used to prepare them.26-40   Many of these procedures use the metal oxalate as the metal source.34-40 The main draw-back of metal oxalates is that they have limited solubility in water, limiting their application in hydrothermal and spray hydrolysis processes.  The amine oxalates are soluble and can be used in these processes.  The research being proposed is to investigate the thermal decomposition pathways for several cobalt, nickel, copper and zinc oxalate amine complexes and to determine the catalytic activity of the metal oxides produced.  This project will consist of three parts.  First, the amine oxalates will be synthesized by dissolving the metal oxalate in amine solution and evaporating the excess solution.  The products will be characterized using attenuated total reflectance – FTIR (ATF-FTIR) and powder x-ray diffraction (XRD).  In the second part of the project,   thermal gravimetric analysis (TGA) and evolved gas analysis – FTIR (EGA-FTIR) will be used to establish the volatile decomposition products and to measure the decomposition kinetics.41,42 ATR-FTIR, XRD, and scanning electron microscopy (SEM) will be used to characterize the solid products.  This should enable the decomposition pathways and the optimum reaction temperatures to prepare the catalyst to be established.   Flow kinetics using the decomposition of 2-propanol will be used to test the reactivity of the catalyst in the third part of the project to establish the nature of the surface sites.43,44  Students working on this project gain hands-on experience with several instruments commonly used for solid state analysis and learn about heterogeneous catalysis.

Dr. Daniel M. Downey, Environmental Analytical Research Projects

Research in this group is currently focusing on three areas of environmental chemistry research.  Inductively coupled plasma/mass spectrometry (ICP/MS) is being studied for the analysis of trace elements in fish otoliths (ear stones). Otoliths are aragonitic calcium carbonates crystals that grow continuously during the life of a fish, develop growth annuli (similar to tree rings) that are used for age determination and uptake trace elements from their surroundings.  We are developing analytical methodology for freshwater species that are collected from streams and lakes where toxic metals (Hg, Pb, Cr, etc.) have been introduced and laser ablation for direct analysis of solid samples.  A second area of research is in the analysis of Endocrine Disrupting Compounds (EDCs) in natural waters. Currently we are studying methods for the determination of estrogens in stream water in relation to the widespread occurrence of intersex male fish found in the Potomac and other rivers in the mid-Atlantic region. This project will be conducted with the new LC-MS being acquired with NSF grant funds.  The third area of research has been application of ion chromatography and other methods for assessment of "acid-rain" impacts.  Field data are collected for these studies for several long term projects (>20 years) and are used to help fisheries managers develop mitigation management strategies.  Students involved in these projects will collect samples in the National Forests or State Game Lands of Virginia, and return them to the laboratory for analysis.  Data thus generated will be used to assess the relative impact of acid deposition on water bodies.  Students will be expected to learn data interpretation as well as the analytical methodology involved.  Both undergraduate and high school students who are deaf or hard of hearing will be included in this research along with hearing college students.

Dr. Daniel Havey, Development of Alternative Atmospheric Greenhouse Gas Sensors

Greenhouse gases, most notably carbon dioxide (CO2), are important species in atmospheric chemistry and climate change. There is growing concern that their continuously increasing concentrations will lead to global surface temperatures producing major climate changes.  A key issue for the next few decades will be to accurately measure the amount of atmospheric CO2 produced at the local, national, and international scale.  This is a difficult technical problem because useful measurements involve measuring small changes on top of a relatively large background (~385 parts per million). The current instruments used for this purpose both may suffer from low sensitivity and/or high costs and typically require calibrations against reference gas standards.  One example research project in the Havey group is development of a portable high-fidelity greenhouse gas sensor for CO2 based on photoacoustic spectroscopy which does not have the aforementioned drawbacks.  Preliminary research done at NIST indicates that this technique has the potential to produce highly accurate data at much lower cost than the instruments currently being used.  We plan to build a laboratory based system and incorporate a detailed model of the acoustic resonator that can be used to adjust its response to atmospheric conditions, develop a protocol using LabVIEW to automatically collect data, and test the system response in the presence of potential interfering compounds such as water vapor.  Once this initial research is finished, we plan to build a portable unit and test it in the field.   This research will be done working closely with undergraduate researchers at James Madison University while maintaining collaboration with the National Institute of Standards and Technology.

Dr. Christine A. Hughey, Mass Spectrometry

Research centers on method development for the characterization, quantification and study of acidic polar compounds in complex environmental and agricultural samples by negative ion electrospray ionization mass spectrometry (ESI MS).   The interdisciplinary nature of this research affords the opportunity to work on a variety of projects from the characterization of phenolics in anti-oxidant rich food extracts to field studies that investigate the use of naphthenic acids as molecular indicators of in-situ bioremediation in crude oil-contaminated soil.  These applied projects have led to studies that investigate the fundamental mechanisms involved in negative ion ESI, which are not well understood such as how mobile phase modifiers commonly used in LC separations effect negative ion ESI ionization efficiency.

Dr. Gina M. MacDonald, Spectroscopic Studies of Nucleotide Binding Proteins

The major focus in our lab has been the study of the Escherichia coli protein RecA and the yeast protein Phosphoglycerate Kinase (PGK).  We are investigating the specific protein structural changes induced by nucleotide binding and/or increased salt concentrations.  To this end we utilize Fourier transform infrared spectroscopy in conjunction with the photolytic release of caged nucleotides to study specific structural changes associated with nucleotide binding.  Infrared and circular dichroism (CD) experiments are used to study protein structural changes induced by nucleotide binding and/or increased salt concentrations.  RecA performs the DNA strand exchange reaction that is utilized in DNA repair and genetic recombination. Nucleotide binding to RecA regulates function by stabilizing alternate protein conformations in a manner similar to other ATP binding, energy-transducing proteins.  Initial infrared studies at JMU resulted in the identification of vibrations associated with the high-affinity (RecA-ATP) and low-affinity DNA (RecA-ADP) forms of RecA in the absence of DNA.  Future difference infrared studies will focus on studying nucleotide binding to RecA in an assortment of different solution and substrate conditions and will be aimed at identifying unique structural changes associated with different nucleotides binding to the protein.  We will also continue to use infrared spectroscopy to monitor nucleotide binding to PGK under a various salt concentrations and pH conditions.  PGK catalyzes a phosphate transfer reaction that is used in glycolysis.  Both PGK and RecA activities are regulated by salt concentration.  All spectroscopic studies are complemented by the appropriate enzyme activity assays.  Circular dichroism studies of RecA and PGK have allowed us to study the aggregation and unfolding of both proteins in a different salt and solution conditions.  RecA experiments have been complemented by fluorescence studies of MANT-ATP binding under the same conditions and dynamic light scattering (DLS) studies performed with collaborators at Los Alamos National Laboratories.   Interestingly, the DLS studies that have shown unique aggregation states for the most thermally stable protein structures that do not unfold even at 105ºC.  Spectroscopic studies on the stability and aggregation of both proteins can be used to gain further insight into protein structure-function relationships.  The study of the salt induced changes in aggregation and unfolding may be relevant for a wide range of studies, including those related to protein aggregation pathways associated with neurological diseases and the development of more stable protein nanostructures.

Dr. Debra L. Mohler, Radical approaches to studying and modulating biomolecular structure and function; and Understanding interfacial electron transfer

Supramolecular assemblies form the foundations for natural and designed systems; and therefore, the elucidation and manipulation of the fundamental principles governing their structures, functions, and reactivities will have widespread impact. Within this framework, our research involves the study of two different supramolecular systems: understanding chromatin structure, and the preparation of photoactive nanomaterials.  The long-term goal of the first area is the elucidation, at the molecular level, of the structural features of nucleosome packing in chromatin and changes therein during cellular processes. The initial objective is to map static chromatin structure via a footprinting approach, which will be accomplished by determining the locations and natures of the modifications of chromatin components by organic radicals. Our approach to studying chromatin structure by footprinting involves examining the reactivity of the photogenerated organic radicals with systems in order from the least complex (purified DNA or histone), to simple protein/DNA assemblies, to nucleosomes, and finally to the most complicated (chromatin).  The second area focuses on elucidating the fundamental factors that govern interfacial electron transfer molecular adsorbates and metal or semiconductor nanoparticles/thin films, which is an essential process in applications including photocatalysis, solar energy conversion, and photography. The emerging field of heterogeneous photocatalysis is of particular interest for its potential to employ “green” methods in functionalizing petroleum-derived materials and in developing new synthetic methods. Because the rate of ET is often a key determinant of efficiency in these systems, the understanding of this process is essential for their design. Most of the current knowledge of these interfacial processes is based on electrochemical studies of slow ET reactions, and little is known about ultrafast ET. Additionally, there has been no systematic study of the effects on ET rate of the identity/properties of the anchoring group or of the electronic coupling between the adsorbate and the semiconductor (through matching of the energy levels of the dye to that of the semiconductor conduction band). Therefore, our research entails the systematic design, synthesis, and photoinduced interfacial ET studies of a series of chlorotricarbonylrhenium bipyridine complexes substituted on the bipyridine ligand with a variety of anchoring groups, tether lengths (to vary distance between the dye and nanoparticle), or substituents (to modulate the energy levels of the ligand -molecular orbitals).

Dr. Barbara A. Reisner, Solid State - Materials Chemistry & Chemistry Education

Hybrid inorganic-organic frameworks are of great interest because of their applications in fields ranging from catalysis to gas separations and storage. My research group is focused on the synthesis and characterization of hybrid frameworks for H2 adsorption. To achieve the storage criteria set forth by the Department of Energy, functional materials that have (1) high surface areas; (2) accessible hydrogen binding sites; (3) reasonable heats of adsorption; and (4) high hydrogen storage capacities at ambient temperature must be designed. Recent work in the field shows that the incorporation of aromatic rings and undercoordinated metal ion sites increases hydrogen-binding strengths.We are investigating poly(azolyl)borate hybrid frameworks as potential hydrogen storage materials. Specifically, we are looking at new frameworks that can be assembled from dihydrobis- and hydrotris- (azolyl)borate ligands (azole = imidazole; triazole). These ligands are readily synthesized by reaction between alkali metal borhydrides and an azole flux and form frameworks related to zeotlitc imidazolate frameworks (ZIFs). All of these materials contain azole rings that have been shown to be strong hydrogen binding sites in the ZIFs. Furthermore, ligands derived from hydrotris(triazolyl)borate contain a pocket that could put a metal ion in an undercoordinated environment. We react these ligands with a number of alkali, alkaline earth, and transition metal compounds to produce new hybrid frameworks. In house structural and thermal characterization is done with PXRD, TGA, FT-IR, NMR, and EGA IR.  Single crystal structure determination is done in collaboration with the University of Nevada Las Vegas and the University of Delaware. Gas adsorption studies are completed in collaboration with the University of Cambridge (UK). We have recently synthesized the porous framework Na[BH(C2H2N3)3]; initial characterization of this material indicates that it may have interesting gas adsorption properties.

Dr. Yanjie Zhang, Biomineralization Templated by Chiral Molecules

Biomineralization is an extremely widespread phenomenon in the biological world. Examples of biominerals include silicates in algae and diatoms, carbonates in invertebrates, and calcium phosphates and carbonates in vertebrates. The functions of biominerals range from magnetic sensing to structural support. However, the understanding about how biomineral growth is mediated by proteins in natural systems is far from complete. In this group, we design appropriate model systems for biomineralization that will help disentangle the complicated interactions at the protein-biomineral interface. Specifically, we will: (I) synthesize a series of amino acid-based model compounds to serve as the template for biomineralization; (II) study the growth of biominerals on the model compounds and characterize the synthesized biominerals. Also, we are using these chiral surfactants as model systems to study chiral interactions at the air-water interface. The goal of these studies is to reveal the specific role of each amino acid involved in the process of biomineralization. Initial studies will focus on the amino acids that are rich in the soluble proteins of bones, teeth, and seashells. This project will provide information about the molecular mechanism for the nucleation and crystallization of biominerals. Ultimately, the initial studies will help design and fabricate better biocompatible materials that can be potentially used as implants into human body or other medical purposes in future efforts.