2009 Undergraduate Research
Opportunities
Welcome to the Undergraduate Research Program at Trinity University’s Department of Chemistry! The
Chemistry faculty take great pride in being one of the top undergraduate chemistry programs in the
country. This informational packet serves as a brief introduction to the undergraduate research
opportunities available in our department. The general information is directed towards current Trinity
undergraduates, high school students looking at potential colleges, and local high school students
interested in research opportunities. We believe that it will also be valuable to anyone interested in
learning more about our program. All of the Chemistry faculty will be glad to discuss the program and
individual research topics, so if you have any questions, please do not hesitate to contact any of the
faculty through our website:
http://www.trinity.edu/departments/chemistry/index.html
Program Scope
The chemistry department is comprised of 8 full time faculty members representing all of the
major disciplines (Analytical, Biochemistry, Inorganic, Organic and Physical Chemistry). All of the
faculty members run active research programs that allow undergraduate students to work on cutting edge
projects using state of the art research equipment. Many faculty members collaborate with researchers at
major research institutions and national laboratories. These collaborations allow us to offer substantial
advanced research opportunities to our most motivated students.
Each faculty member has individual laboratory space in which their research groups operate.
Departmental instructional facilities (see list of major equipment on our website) are also utilized by
faculty research groups, particularly in the summer. The size and composition of each research group
varies within the department, but a typical group might consist of a postdoctoral research fellow,
anywhere from 3 to 12 undergraduate researchers, and one or two high school students. Increasingly,
research projects are at the interface of traditional research disciplines and there are a number of
collaborations between chemistry research groups and other research groups on campus.
The strength of our program is evidenced by the external funding that the faculty have
successfully attracted. In 2008 chemistry faculty managed more than $2 Million in active externally
funded grants from the National Science Foundation, Welch Foundation, Camille and Henry Dreyfus
Foundation, Research Corporation and Petroleum Research Fund. These funds help to support summer
stipends for undergraduate and high school students, major research equipment, research supplies,
instructional equipment, and salaries for postdoctoral research associates. The Department also currently
participates in inter-departmental initiatives, which have provided an additional $2 Million in equipment
and student stipends over the last 3 years.
Summer Research Program
The Chemistry Department offers no courses during the summer term; consequently, the
department is focused entirely on research during the summer. All instructional laboratories, facilities,
and equipment are all available for summer research students. In 2008, faculty and departmental grants
allowed us to support 40 undergraduate students for a 10-week summer program. This makes our
program one of the largest chemistry summer undergraduate research programs in the country. All
summer research students receive a substantial stipend (ca. $3500). Trinity University also covers the
basic dormitory costs for students supported on external grants and provides 1-hour course credit free of
charge to students who fully participate in the program.
One of the hallmarks of our program is that it is extremely accessible to students early in their
academic careers. Our 2008 summer researchers consisted of 13 juniors, 12 sophomores, and 12 first
years. The application process generally starts at the end of January with an informal meeting between
interested students and faculty. Applications are typically due in mid February and the program will run
from May 24 to August 1.
Research During the Semester
Research opportunities are also available for course credit or on a volunteer basis during the
semester. Faculty generally expect about 6 hours of work in and out of the lab per week for one hour of
credit. Students are asked to talk with at least 3 faculty members to discuss research opportunities before
being admitted into a research group.
Research Descriptions
The following pages give short research descriptions of the current Chemistry faculty, organized
by sub-discipline. If you have questions about the opportunities in specific research groups, please do not
hesitate to contact any of our faculty. All of us would enjoy the opportunity to give you more information
about our programs and our department. For questions about the summer research program, please
contact our Summer Research Program Coordinator, Dr. Laura Hunsicker-Wang: (210) 999-7895;
laura.hunsickerwang@trinity.edu.
Dr. Michelle M. Bushey
Analytical Chemistry
Separations & Bioanalytical Chemistry
Our activities are geared around separation processes, especially
those targeting problems of biochemical/biological interest.
One of our projects involves identifying the location of
phosphorylation sites in proteins. Phosphorylation is a common and
important posttranslational modification of specific amino acids in a
protein sequence. This is a collaborative project with Dr. Jon King of
the Trinity Biology department. Dr. King is interested in a particular protein because the phosphorylation
sites determine how this protein maintains cell tight junctions. Our lab is interested in developing
methods, beyond those typically used now, to rapidly identify the phosphorylation locations in this large
protein. Liquid chromatography, immobilized metal affinity chromatography, capillary electrophoresis
(CE), and mass spectrometry will all potentially be used to identify specific sites of phosphorylation in
our protein of interest. Students working on this project will likely gain experience in these three methods
and may also work periodically with Dr. King to prepare the protein for use in our lab.
A second interdisciplinary project involves determining the changes that take place in plant flavonoids
upon exposure to UV light. This is a collaborative project with Dr. Jim Shinkle of the Trinity Biology
department. Dr. Shinkle is interested in determining the chemical changes that take place regarding plant
flavoniods, which ones are produced, in what quantities, and what subsequent modifications take place as
plants respond to UV damage. Our role in this project is similar to the phosphorylation project, to develop
the methods to identify these changes in the plant extracts. Liquid chromatography, CE, capillary
electrochromatography, and mass spectrometry are all expected to play a role in defining these samples.
Another project in the lab involves making porous polymer monoliths for use in capillary
electrochromatography (CEC). CEC is a blending of CE and liquid chromatography. A capillary is filled
with a monomer solution and the polymerization process started. The polymer is formed in the capillary.
These polymeric stationary phases are then used to separate the components of a variety of samples.
Analytes are moved through the column under the influence of an electric field. The speed at which
individual analytes move through the column is a result of analyte interactions with the polymeric
stationary phase and analyte behavior in electric fields. We are interested in correlating the physical
characteristics of these columns with their separation performance for a variety of analytes and
preparation conditions. In this way it would be possible to design a polymeric separation system for a
particular situation. These columns will also be used to in the phosphorylation and flavonoid projects as
well as other novel applications. The performance of these monolith columns when used in an
electrophoretic mode will be examined and compared to when they are used in a liquid chromatographic
mode. Thus, the individual sources of band broadening can be attributed to particular phenomena.
Interfacing these columns with mass spectrometry, again used in either electrophoretic or
chromatographic modes, will also be explored.
Several of the links listed on my (http://www.trinity.edu/mbushey/links.htm) links page have excellent
descriptions of CE and CEC, some of these include animated cartoons.
Dr. Jessica J. Hollenbeck
Biochemistry
Chemical Biology & Molecular Recognition
Multivalent interactions are important in a variety of biological processes. Many proteincarbohydrate interactions, including those involved in viral entry and cell surface adhesion, utilize
multivalent binding to achieve high affinity and specificity. Our research involves the design and
synthesis of novel glycopolymers using a naturally-occurring repeat protein scaffold (the ankyrin repeat)
to study multivalent interactions in biological systems.
The ankyrin repeat (AR) is one of the most common protein sequence motifs. AR proteins are
composed of tandem repeats of ca. 33 amino acid residues that form a  -turn followed by two antiparallel
-helices (see below). These repeats stack together to form an elongated structure ideally suited for the
presentation of multiple functional groups and/or recognition elements in a multivalent fashion.
Importantly, compared to synthetic polymers, the molecular composition (i.e., length/valency) of the
scaffold will be precisely defined by the gene sequence encoding the protein.
We will use our designed ankyrin repeat proteins as tools to address fundamental questions in
bacterial chemotaxis, the process by which bacteria sense and respond to stimuli in their environment.
Chemotaxis is mediated by a series of cell surface receptors that transform extracellular sensory
information into a behavioral response. Synthetic polymers displaying simple monosaccharide residues
promote chemotactic responses in both E. coli and B. subtilis. Using a series of AR glycopolymers, we
will investigate how the physical properties (i.e., length/valency, rigidity, curvature) of the polymer
scaffold can affect taxis in these same bacteria.
Students in my laboratory will use a variety of techniques ranging from synthetic organic chemistry
to microbiology. In addition, they will be exposed to advanced topics in modern biochemistry including
multivalent recognition, signal transduction, protein design, and molecular evolution. This type of
interdisciplinary training should be attractive to students interested in both chemistry and biology and
should be excellent preparation for careers in a variety of fields.
(a) Consensus amino acid sequence from N- to C-terminus of the ankyrin repeat motif (x = any amino
acid). The related secondary structural elements are indicated above the sequence. (b) Structure of a
single ankyrin repeat. (c) Schematic representation of an ankyrin repeat protein displaying four
monosaccharide residues.
Dr. Laura Hunsicker-Wang
Biochemistry
Biochemistry & Bioinorganic Chemistry
Research in the Hunsicker-Wang laboratory
will focus on studying enzymes that utilize or
bind metal ions, called metalloproteins. There
are two major areas of interest: iron-sulfur
cluster enzymes and copper chaperones.
Fet3
ceruloplasm
Ccc2
CCS
Cu Zn Cu Zn
CopZ
Copper
Atx
Cu-Zn SOD
Metal ions inside of a cell can play one of two
Cu
roles. They can be found at the active site of an
Sco1
Cu
Cox17
enzyme, and play critical roles in the life of a
Cu
cell. However, if the metal ions are left free,
Cox11
Cytochrome c
they can do damage to critical parts of the cell.
Oxidase
For this reason, a system of proteins called
Overview of the copper chaperone families.
chaperones have evolved, which bind and
deliver metal ions to their respective
metalloprotein. One family of these chaperones is the coppers chaperones, which shuttle copper ions to
Cu/Zn SOD, Fet3, and cytochrome oxidase. The research in the Hunsicker-Wang lab will work toward
identifying, purifying, and characterizing copper chaperones from the thermophilic eubacterium, Thermus
thermophilus. We will also explore how copper chaperones select for only copper.
+
A
B
Iron-sulfur proteins make up ~30% of all metalloproteins. These proteins utilize iron and sulfur atoms
that are organized into clusters. These proteins are often involved in electron transfer reactions.
Specifically, the Rieske protein contains a 2Fe-2S cluster, which is ligated to the protein via 2 cysteine
and 2 histidine residues. The reduction potential of this protein depends on the organism and the type of
system that it was derived from. Previous studies have shown that the number of hydrogen bonds to the
cluster, the solvent accessibility, and the type of charge residues near the
cluster all affect the reduction potential. Research on this protein will
involve making site-specific mutations, purifying, crystallizing and
solving the structure of the mutant enzymes. The reduction potentials of
these mutants will also be evaluated. Thus, the protein will be purified,
the effect on reduction potential evaluated, and the structural
consequences of the mutation determined. Future studies will work
toward evolving a new function of a larger enzyme complex, called a
dioxygenase, which has a Rieske domain. The new function would be to
Crystal structure of the Rieske
break down environmental pollutants, and would be accomplished by
protein from T. thermophilus
making randomized mutations to both the Rieske domain and the
substrate-binding domain.
Dr. Bert Chandler
Inorganic & Materials Chemistry
Nanotechnology & Environmental Heterogeneous Catalysis
Our research combines the fields
Thiol Monolayer
of
nanotechnology
and
Protected Clusters
environmental
heterogeneous
catalysis. We are motivated by
the desire to rationally design new M n+
A
materials in order to solve a MBn+
variety
of
environmental
Homogeneous
NaBH4
problems, particularly chemistry
Catalysts
CO+O2 CO2
associated with alternate fuel
Heterogeneous
sources (biomass & hydrogen)
Catalysts
and cleaner selective oxidation
chemistry. Supported metal nanoparticles are important catalysts for these reactions and our approach is
to begin developing a fundamental understanding of these catalysts, their properties, and reaction
mechanisms.
In order to study these catalytic reactions, we are developing new methods for preparing and studying
well defined bimetallic nanoparticles based on Pt and Au. We use a special class of polymers called
dendrimers to prepare new bimetallic nanoparticles. Polyamidoamine (PAMAM) dendrimers are
hyperbranched polymers with chemical functionalities that allow them to bind a controlled number of
metal ions. Their architecture consists of a porous periphery and open interior, which create an ideal
environment for trapping guest species. The wide potential applications of these macromolecules include
drug delivery vehicles, enzyme mimics, and nanoscale assembly.
We use PAMAM dendrimers as nanoreactors to prepare dendrimer encapsulated metal nanoparticles
(DENs) with controllable sizes (20-100 atoms) and compositions (see above). The DENs are deposited
onto an oxide and activated to yield supported metal nanoparticles catalysts. We are interested in all of
the steps pictured above and projects can be tailored to student interests, background, and ability.
Representative projects include studying metal-dendrimer coordination chemistry, dendrimer properties,
solution nanoparticle chemistry and interactions with probe molecules, supported nanoparticle properties,
catalysis, and catalytic mechanisms.
We are also investigating ways to use proteins to template oxides in order to design new surfaces and
catalytic sites (see below). The basic idea is to use proteins such as Lysozyme or polypeptides to template
small regions of oxide surrounded by an organic over-layer. These directed sites will be used to
controllably assemble catalytic sites, such as nanoparticles or the molecules like the one pictured below.
Current interests include organic synthesis of acid-base bifunctional molecules for enzyme-inspired
catalysts, biorenewables conversion for alternative energy sources, and catalyst design.
proteins
SiO2
The research in our group is inherently interdisciplinary,
involving chemistry, biochemistry, and engineering. Most
students have individual projects and opportunities to work in
several of our larger areas of interest. We collaborate with
several research groups at Trinity and at
major research universities. Students
who work in the group for longer
periods of time have opportunities to
travel to some of these schools to use
specialized equipment, carry out unique
catalysis experiments, and work with
other leading groups in our field.
O
SiO2
OH
Surface functionalization
Organic Layer
SiO2
Protein removal
Organic Layer
SiO2
O
NH
NH2
(R O)3 Si
Si(OR )3
Dr. Steven M. Bachrach
Organic Chemistry
Computational Chemistry
My research interests involve the application of
computational techniques to problems in organic
chemistry. While this research involves extensive use of
computers and visualization, interested students need not
be experts in programming. Projects can be designed for
the computer novice to the expert; what is needed is a
strong motivation to learn and explore.
Our use of computational chemistry is to solve the
Schrödinger equation using ab initio techniques, the most
rigorous and complete computational method. We use a
number of packages to solve the physics, providing us with
optimized geometries, electron distributions, molecular
orbitals, and reaction energetics. We are currently
exploring two major areas of chemistry: reactions of
anions, particularly nucleophilic substitution, and the
underlying nature of host-guest interactions. For the first
category, we have had a long interest in the mechanism of
nucleophilic substitution at heteroatoms, especially at sulfur and selenium. Instead of following the S N2
mechanism, like for nucleophilic substitution at carbon, nucleophilic substitution at sulfur and selenium
occurs via an addition-elimination route. We are looking now at the effect of solvation on these reactions,
which are important in a variety of biochemical process like protein folding. In the area of host-guest
chemistry, we have interests in a two areas. First, we are collaborating with Dr. Urbach on modeling the
complexation of peptides to Q8. This involves some novel computational techniques: these complexes are
relatively large and require computational methods that can scale appropriately with increasing size.
Furthermore, the role of solvent may be critical in understanding the nature of the host-guest interaction,
and we are currently working on approaches to incorporating solvent. The other host-guest chemistry we
are working in involves reactions that are accelerated inside some host species. This work follows on the
experiments of Dr. Rebek at Scripps, who has devised clever hosts to enhance the rates of the Menshutkin
reaction and certain rearrangements. We are interested in discerning what is responsible for the catalytic
behavior of these hosts.
I have a long-standing interest in the mechanism of pericyclic reactions involving heteroatoms and will
continue to explore new applications. Recently, we have examined the effect of solvent upon the DielsAlder reaction of carbonyl compounds. Another project has involved symmetry properties of the DielsAlder transition state, and we would like to expand this technique to other related pericyclic reactions.
The molecule pictured above comes from a study of extended p-bonds in multiple dimensions. This is
also a project that can be extended by a new student.
Dr. Nancy Mills
Organic Chemistry
Synthetic Organic Chemistry; Aromaticity & Antiaromaticity
One of the most important concepts in organic chemistry is that of aromaticity. Benzene, the
quintessential aromatic molecule, has a unique set of “behaviors” that indicate that something special is
going on in the molecule and that special character of benzene is called aromaticity. Unfortunately, it is
difficult to determine which of the ways that benzene behaves, its structure, or stability, or magnetic
properties, is the best way to measure and evaluate aromaticity, this key concept in organic chemistry.
The flip side of aromaticity is antiaromaticity and people have tended not to study
antiaromaticity because they assumed that the necessary species would be very difficult to
make and study. Through a stroke of luck, we have identified compounds like 1 that appear to
be antiaromatic, in terms of their magnetic properties, but are still stable enough to
characterize. That means that we can begin to compare the behavior of our “antiaromatic”
species to that of benzene to begin to sort out which properties are truly characteristic of
aromaticity. This is pretty cool because we are looking at one of the big questions in organic
chemistry and doing so with the efforts of undergraduate researchers!
R
1
While our initial work was with antiaromatic dications, we
have recently discovered that we can make antiaromatic
dianions,
like
2-4.
The
theory
of
aromaticity/antiaromaticity considers only the number of
R
R
electrons in a ring, not whether the ring is anionic or
R
2
4
cationic. Recently we have found that anions behave
differently from cations with the same number of
3
electrons, in terms of their aromaticity/antiaromaticity.
This is a phenomenon that no one ever thought of exploring. We are doing two kinds of projects. Part of
the group is looking at species like 1 above which we have characterized by magnetic properties and are
characterizing them by other properties, such as stability or by examining their structure. Other students
are expanding the investigation to new species that theory says should have increased antiaromaticity, to
see if theory is correct and if so, to see if there are new, unexpected behaviors in these previously
unknown compounds, like the difference we see between anions and cations.
Students working in my group spend a lot of time making the molecules that are converted to 1-4. The
vast majority of the molecules we need are ones that have never been made before. Since everyone in the
group gets a molecule of his or her own, you also get the opportunity to be the first person in the world to
see a particular compound, which is pretty neat. Much of the efforts of the group involve organic
synthesis, purification via chromatography, and characterization by NMR and IR spectroscopy. Since we
also predict behavior of these compounds before we make them or rationalize their behavior by
calculations, students with a particular interest in computer science and chemistry can become involved in
computational chemistry.
Dr. Adam R. Urbach
Organic Chemistry
Bio-Organic Chemistry and Molecular Recognition
Bioorganic chemistry uses techniques in organic chemistry, like
synthesis and NMR spectroscopy, to study proteins, nucleic acids, and other
biological molecules. The major goals are to understand the structure and
reactivity of biomolecules, and to create new compounds that can selectively
bind to (or “recognize”) them, giving us a way to increase or inhibit their
reactivity. Drugs do this—they recognize a specific protein, bind tightly to it,
and inhibit its activity. The ultimate challenge of bioorganic chemistry is to
be able to design a drug that can selectively bind to any protein we want.
Another important goal is to make compounds that act as “sensors” by
binding to and revealing the presence and quantity of a specific biomolecule,
either by changing color or by producing light or electricity. Sensors are key
components of medical diagnostics technology, such as a device that can
measure the amount of a hormone in a patient’s blood.
A synthetic compound
bound to a specific sequence
of DNA.
Students in the Urbach laboratory design, synthesize, and study
compounds that can recognize and bind tightly to specific peptides. Peptides
(small proteins) are short, linear chains of amino acids, and since there are 20 common amino acids, even
small peptides can have a wide variety of structures and properties. We have recently discovered that the
big donut-shaped molecule we call Q8 (see figure below) can bind tightly and specifically to certain
peptides, and what’s exceptionally cool is that this happens in water! This might seem like a given since
all biological chemistry happens in water, but the fact is that the vast majority of synthetic compounds
don’t even dissolve in water, and it is particularly rare to find one that can dissolve in water and bind
tightly to specific peptides. What’s more, when certain peptides bind to Q8, the sample turns orange, and
so we can use this system to sense the presence of a peptide and tell us (by the intensity of color) how
much peptide is present. Current projects in the group use this technology to sense important proteins
such as insulin, and to demonstrate new concepts in molecular recognition. There are many aspects to
this work, and individual projects are geared to the student’s interest.
Students in the group learn a variety of techniques, even in their first year (see caption below).
These can include: 1) organic and solid-phase synthesis to make peptides and other small molecules; 2)
NMR, mass spectrometry, and X-ray crystallography to characterize molecular structure; 3)
microcalorimetry, stopped-flow spectroscopy, and capillary electrophoresis to measure the
thermodynamics and kinetics of binding; and 4) UV-visible, fluorescence, and circular dicrhoism
spectroscopy to study electronic properties. This combination of methods and approaches offers students
a breadth of technique and depth of study that is excellent training for many career paths.
This image, generated from X-ray diffraction
data, shows a high-resolution snapshot of the synthetic
compound Q8 (stick structure) wrapped around two
copies of a short peptide. The image is rendered in
stereoscopic mode, so if you cross your eyes and focus
on the middle of your vision, you may see the
structure in three dimensions. A student in the Urbach
group discovered this very unique complex and
characterized its structure and binding properties in
her first year of college.
Dr. Chris Pursell
Physical Chemistry
Atmospheric Surface Chemistry; Fuel Film Evaporation; Adsorption Studies
1.
Atmospheric Surface Chemistry - Our research group has been
examining chemical reactions in ice and on ice surfaces. The
motivation is to help develop a better understanding of the
heterogeneous reactions that occur in the atmosphere and lead to the
seasonal loss of ozone over the poles. In the laboratory we simulate
the surface of these atmospheric ice particles, known as Polar
Stratospheric Clouds or PSCs, using thin films of pure water ice and
mixtures of water with nitric acid. The interaction of reactive species
with the ice surface is monitored using infrared transmission
spectroscopy. The overall goal is to provide detailed experimental
information that will help us better understand the chemical reactivity of the ice surface and ice-like
surfaces. Results from these studies will lead to a better understanding of the heterogeneous chemistry
that occurs on atmospheric ice particles. Very recently we have extended our studies of ice and have
begun to study the physical and chemical properties of the molecular cousins of ice, namely solid
ammonia and solid hydrogen sulfide. These studies involve using infrared spectroscopy, very low
temperatures (10-180 K), and a vacuum environment. We have already discovered some very fascinating
spectroscopic differences between these “cousins” and ice. We hope to now study chemical reactions of
these solids in order to compare and contrast their chemical and physical behavior.
2.
Fuel Film Evaporation - This is a joint project with Dr. Kelly-Zion in the Engineering Science
department. Thin films of fuel can be deposited in the interior of an automobile engine, especially under
cold, initial operation. These fuel films lead to reduced performance and increased pollution. We are
studying the evaporation process of model films that represent these automobile fuel films. The general
goal of this research is to elucidate the complex coupling between thermal and mass transport processes
during the evaporation of multi-component films. As a film evaporates, its overall composition can
change due to the preferential evaporation of the more volatile components. Both temperature and
composition gradients are induced in the film and the physical properties may vary in both time and
space. These studies include (1) using infrared spectroscopy to watch the individual components
evaporate, (2) using light interference from a laser to measure the film thickness during evaporation, and
(3) using laser light interaction with the film’s surface and capturing the image with a digital camera.
3.
Adsorption Studies - Recently we have been collaborating with Dr. Chandler (also in Chemistry),
examining the adsorption of gas phase CO to gold supported nanoparticle catalysts. Using a special
pressure/vacuum/temperature apparatus, along with infrared transmission spectroscopy, we are able to
quantify the amount of CO adsorbed, the binding constant, and the heat of adsorption. This allows a
thorough characterization of the various gold catalysts.