Department
of
Chemistry and Biochemistry
Faculty
Research
Projects
Fall 2016
Research Projects: Belitsky Lab
Mr. Belitsky
Melanin and Catechol Chemistry:
Fundamental Understanding to Environmental Applications
Our lab is inspired by melanins, biological pigments that are well known to the general
public but surprisingly under-studied in the scientific community. Melanins are one of several
biomaterials that contain catechol subunits; such natural materials and their synthetic analogs
have a combination of fascinating properties that are exploited biologically, and are of growing
interest to the materials science community. In our lab, we have focused on gaining a
fundamental understanding of these materials and their molecular recognition properties, and
utilizing these properties for environmental applications such as heavy metal binding and
sensing. Projects range from synthetic organic chemistry and spectroscopic characterization, to
colorimetric sensor development and water purification trials.
Many Oberlin Chemistry & Biochemistry majors will participate in related projects
through the NSF-funded “Bioorganic Chemistry of Eumelanin” course-based research
experience in Chem 254.
Possible Projects – Fall 2016
•
Synthesis of eumelanin model compounds (organic chemistry required)
•
Development of metal ion-binding coatings as colorimetric sensors
•
Investigation of catechol and melanin polymerizations
•
Studies toward synthetic melanin/carbon nanotube-based water purification
agents, in collaboration with Nanotech Innovations, a local company in Oberlin that
produces carbon nanotubes.
Research Project: Matthew Elrod
Mechanisms of Organic Chemical Transformations in the Atmosphere
Tropospheric ozone (the most toxic gaseous component of air pollution) is produced as a result
of the gas phase photochemical oxidation of hydrocarbons in the presence of high levels of
nitrogen oxides. For some hydrocarbons, the oxidation process also results in the formation of
aerosol particles (solid or liquid phase particles small enough to remain airborne). These
particles can also be toxic, but are best known for their light scattering influence (visibility loss)
during air pollution events. The particles themselves can serve as mini chemical reactors which
allow for new types of solution phase chemical processes to occur, as well. Therefore, in under
to understand the full range of organic chemical transformations possible in the atmosphere,
both gas phase and solution phase reaction mechanisms must be investigated.
Isoprene-Derived Nitrate Particle Phase Processing Project. It is well known that isoprene (a
biogenically-derived C5H8 compound) forms organic nitrates in its gas phase atmospheric
oxidation processes. We have previously investigated particle phase processes (isomerization
and nucleophilic substitution reactions) for nitrates that possess the original isoprene carbon
backbone, and have shown that they are capable of rationalizing the types of species found in
ambient atmospheric particles. We are now interested in investigating the particle phase
mechanism and kinetics of reaction of nitrates that are derived from fragmentation oxidation
products of isoprene (such as the four carbon species methyl vinyl ketone and methacrolein).
Students will learn the techniques of product identification and kinetics measurement techniques
via 1H, 13C, and correlation NMR methods, as well as solution kinetics analysis methods.
Students will also synthesize atmospherically relevant compounds for use in the work described
above. This project will likely have an opening for an Honors student starting in Fall 2016
and for Research students starting in Winter Term 2017.
The project has chemical mechanism development as the primary organizing framework and is
appropriate for students who have completed the introductory chemistry sequence. Additional
experience in organic chemistry will be useful, but is not required.
Research Projects: Manish Mehta
Not offered Fall 2016
Next offered: Winter Term 2017
Solid-state NMR, Diffraction, and Computational Studies of Co-Crystals
Co-crystals are stoichiometric, non-covalent molecular complexes with 2 or more different
molecules in the crystalline unit cell. Co-crystals have gained special attention in the
pharmaceutical sector, as the ability to co-crystallize an active pharmaceutical ingredient with a
co-former molecule provides a novel way to alter bulk properties, such as solubility and
bioavailability. Co-crystals may be formed by solvent evaporation or they may be formed
exclusively in the solid state by grinding (via a process called mechanochemistry). A
mechanistic understanding of co-crystal formation in the solid state remains elusive, though, it is
agreed, there must be some mode of mass transfer at the molecular level.
In my lab, we use a combination of solid-state NMR, X-ray diffraction, and high-level
computational methods to investigate the formation and structure of a variety of co-crystals. In
this context, solid-state NMR has the potential advantage of detecting non-diffracting phases,
which are hypothesized mechanistic intermediates in solid-state reactions. We use magic angle
spinning 13C and 15N solid-state in situ NMR to investigate the formation of co-crystals in real
time by tracking the resonances (chemical shifts) of the reactants and products.
The solid-state NMR experiments are performed on the department’s 600 MHz NMR
spectrometer, the powder diffraction experiments on Oberlin’s state-of-the-art powder
diffractometer, the single-crystal diffraction experiments in collaboration at Purdue University,
and the computational studies on Oberlin’s new supercomputer.
We also investigate the thermodynamics of co-crystals by experimentally deriving enthalpies of
formation and measuring heat capacities of different co-crystals. For these experiments, we use
the Department’s new high-precision bomb calorimeter and the new differential scanning
calorimeter. These measurements allow us to assess the thermodynamic stability of a co-crystal
relative to its input materials.
Research Project: Michael Nee
Towards the Synthesis of Cucurbit[9]uril
Cucurbit[n]urils (CB[n] where n=5-8 or 10) are barrel-shaped, class of cyclic compounds all of
which have a cavity in the middle that can act as a nanovessel or molecular container,
especially for cationic organic species. While the reaction chemistry of molecules in solution are
well known, their behavior inside of nanovessels has only recently been begun to be explored.
Also nanovessels can be used for other purposes such as binding drug molecules for slow
release in the body or selective extraction of molecules. A significant downside of CB[n]s is their
relatively low solubility in water or any other solvents. The goal of this project is to synthesize
CB[9], an undiscovered cucurbituril. The odd number of subunits of CB[9] should be more
soluble in water and the larger cavity size will make it potentially more useful as a nanovessel.
O
O
O
N
N
N
N
O
N
NO N
N
N
O
N
n
N
N
NO
N
N
N
O
O
n = 6: Cucurbit[6]uril or CB6
O
n = 5, 6, 7, 8, or 10
N
N
N
O
N
O
O
N
N
O
Research Projects: Oertel Lab
Synthesis and Structural Chemistry of Lead Oxide Carboxylates
Lead oxide carboxylates are hybrid inorganic-organic
compounds in which Pb2+ ions are coordinated by both oxide
anions and carboxylate ligands. Some members of this family
occur as products of the corrosion of lead, which is important
in the conservation of historic lead-rich objects such as organ
pipes. Others have the potential to exhibit noncentrosymmetric structures that give rise to novel optical
properties. Students in the lab have recently synthesized and
determined structures for several new compounds in this
family. In each, edge-sharing Pb4O tetrahedra make up
extended inorganic substructures, the condensation and
topology of which differ with the identity of the ligand. For
example, compounds based on some functionalized benzoate
ligands include helical Pb2O2+ chains (see figure) that are not found
Helical Pb2O2+ features in
in other members of the family. Goals of this year’s work will
Pb2O(C6H5COO)2
include synthesis and structural characterization of new lead oxide
carboxylate phases with chiral organic ligands and application of the partial charge model to
understanding factors governing formation of extended inorganic motifs in these compounds.
Synthesis and Structural Chemistry of Hybrid Lead Halides
Hybrid lead halide perovskites are promising materials for use in solar cells, with
reported efficiencies that have advanced rapidly to rival that of silicon. These perovskites are
solid state compounds of the form ABX3 (A = organic cation, B = Pb2+, X = Cl–, Br–, I–). The
identity of the metal and halide ions are understood to be most important to the electronic
properties of the materials, which determine the ability of the compounds to absorb light.
However, the identity of the organic cation is now thought to have an important role in
secondary properties of the materials including stability and charge transport efficiencies. Goals
of this project are to synthesize and structurally characterize new hybrid lead halides that
incorporate
organic
cations
such
as
pyridinium,
ethylenediammonium,
and
tetramethylammonium. Because there is interest in making analogues that use metals other
than lead, we will also prepare compounds including Sn2+ and Sn4+. Using newly synthesized
compounds as well as those reported in the literature, we will probe the role of ligand volume in
influencing the dimensionality of the compounds that form.
Both projects involve solution synthesis and crystal growth, including solvothermal
synthesis. In addition to synthetic techniques, students will gain experience in methods of
materials characterization including powder and single-crystal X-ray diffraction, thermal
analysis, optical and electron microscopy, and diffuse reflectance UV-Vis spectroscopy.
Students who have completed Chem 213 will be good candidates to join these projects. There
are openings for two new students in the laboratory in fall 2016.
Research Projects: Ryno Lab
Lisa Ryno
Not offered Fall 2016
Next offered: Winter Term 2017
Project 1: Our lab has been working on the careful expression and purification of the bacterial
protein SurA, a chaperonethatactsasagatekeeperbetweentheinteriorofabacteriumandthe
externalenvironment.SurAisresponsiblefortheproperfoldingofsecretedproteinsandtoxinsas
wellastheoverallmaintenanceofthecellmembrane.Weplantostudythebindingofsmall
moleculesSurAinvitrothroughthedevelopmentofafluorescenceanisotropyassay,andhavethe
long-termgoalofdiscoveringnewsmallmoleculesthatmightinhibitthenormalactivityofSurA
and,therefore,compromisethefitnessofthebacteriastudied.
Project2:Weareinterestedintheconnectionbetweenstress-responsivesignalingpathwaysand
biofilmformation.Weareoverexpressingtranscriptionfactorsresponsibleforcontrollingstressspecificpathways,andmonitoringtheirimpactonbiofilmgrowth(viaacolorimetricassay)and
composition.Thebiofilmiscomposedofcellsandamatrixcalledtheextracellularpolymeric
substance(EPS).Wearestudyingtheprotein,carbohydrateandextracellularDNAcompositionof
theextracellularpolymericsubstanceafteroverexpressionofthesetranscriptionfactorsusing
well-establishedmethods.
Project3:OurlabhasbeenexploringthebindingofsmallmoleculestoSurA,abacterial
periplasmicchaperoneprotein,usingcomputationaldockingmethods.TheinhibitionofSurA
functionbysmallmoleculeswillresultindecreasedfitnessofabacterialpopulation,andgreater
susceptibilitytocurrentlyusedantibacterialdrugs.Wehavecompletedinsilicoscreensofsmall
moleculelibraries,andarenowcurrentlyfollowingupinvivoonthemostpromisingsmall
moleculecandidatesdiscoveredinourscreens.Wearestudyingthese“hit”moleculesinminimum
inhibitoryconcentration(MIC)screens,whichdeterminetheminimumconcentrationofan
antimicrobialrequiredtoinhibitvisiblegrowth.Wearealsocontinuingtoscreenlargerlibrariesof
smallmoleculesinsilico,alongwithfragmentlibrariesfordenovodesignofinhibitorsofSurA.
TheRynoLabwillnotbeseekingnewstudentsduringtheFallSemester2016,butmayhave
opportunitiesfornewstudentsduringWinterTerm2017.
Research Projects: Thompson Research Lab
EnvironmentalAnalyticalChemistry
Project1
O
Arsenic, with both natural and human sources, is of concern as a toxic
As
agentinwaterandfood.Inparticular,arsenicinricehasreceivedmuchrecent
OH
H3C
attention. The element arsenic comes in four major forms in rice: arsenite
OH
3–
3–
AsO3 ,arsenateAsO4 ,monomethylarsonicacid,anddimethylarsinicacid(both
O
organic forms shown at right). The pKa values of the parent acids are 9.2, (2.2,
6.9,11.5),(4.1,9.0),and1.57respectively.Inorganicarsenicismuchmoretoxic
As
CH3
H
C
thanorganicarsenic.Thus,speciationisimportant.
3
OH
Wewilldevelopamethodtodeterminethetotalamountofarsenicand
thefractionsofinorganicandorganicarsenicincommercialricecakesandricecereals.Arsenic
is extracted from rice by treatment with an oxidizing mixture of nitric acid and hydrogen
peroxideatelevatedtemperature.Theextractcontainsarsenateandmonomethylarsonicacid.
By passing the mixture, its pH adjusted to 6.0, through an anion exchange resin and then
washingwithincreasinglyacidicaqueoussolutions,organicarsenicandinorganicarseniccanbe
separatelyeluted.Eachfractionispre-reducedusingoneoftworeagentsandisthensubjected
to hydride generation atomic absorption spectrophotometry (HG-AAS). In this technique, the
arsenic is converted to arsine AsH3 gas, the arsine is swept into a hot optical cell where it
decomposestoarsenicatoms,andtheatomicabsorbanceismeasured.
We will determine the most important of the many variables in the method and
optimizethoseusingarational,design-of-experimentsapproach.Withaneffectiveandrobust
experimental procedure in hand, we will determine the arsenic content of some commercial
ricecakesandotherriceproductsavailableinOberlin.
Project2
Organochlorine pesticides (OCPs) and polychlorinated biphenyls
(PCBs),whilelargelybannedintheU.S.andEuropeyearsago,persistinthe
environmentandcontinuetobeconcerningtoxicpollutants.Thesechemicals
canbefoundinwater,soil,andfood.Representativestructures(dieldrinand
ageneralizedPCB)areshownatright.
WewilladaptU.S.EPAmethodsandotherliteraturetoquantify
these pollutants in soil samples. We will find ways to transfer the
chlorinatedcompoundsfromsoilintoorganicsolvent,removeinterfering
matrix components from the liquid extract by solid phase extraction
(SPE),andpreparetheSPEeluateforanalysisbyGCwithelectroncapturedetection.
We will determine the most important of the many variables in the method and
optimizethoseusingarational,design-of-experimentsapproach.Withaneffectiveandrobust
experimentalprocedureinhand,wewillanalyzelocalsoils,suchasthosefromOberlinathletics
fields,ponds,andriverbanks,fortheirOCPandPCBcontent.Sincetherearesomanydifferent
OCP compounds and PCB congeners, one or two chlorinated compounds from each category
willbechosenforstudy.
Research Project Descriptions
Rebecca Whelan
(contact Rebecca Whelan to discuss these projects)
Project 1: Computational analysis. The Whelan lab is invested in identifying new ways to
detect ovarian cancer at its early, most treatable stages. One approach we have investigated is
the selection of nucleic acid aptamers to act as affinity probes for ovarian cancer biomarker
proteins. We have conducted numerous aptamer selection processes. Some have been
successful, but others have been undermined by systematic methodological problems. This fall,
one or two students will be recruited to use the Oberlin supercomputer to conduct computational
characterization of our aptamer selection processes, by sorting through the gigabytes of
sequence data that result from each selection process looking for evidence of contamination or
other method errors. The ideal candidate will have completed at least one semester each of
analytical chemistry and computer science, have some familiarity with basics of molecular
biology, and be fearless about troubleshooting.
Project 2: Selection of ovarian cancer aptamers using novel methods. The Whelan lab
recently reported our selection and characterization of DNA aptamers with moderate binding
affinity for the ovarian cancer biomarkers CA125 and HE4. The goal for this year is to conduct
the selection process again, using methods that have been shown by other investigators to yield
aptamers with more favorable binding properties. Capillary electrophoresis, polymerase chain
reaction, and gel electrophoresis will be the central methods used in this project. Familiarity with
the scientific literature on aptamer selection and ovarian cancer will be developed. The ideal
candidate will have completed at least one semester of organic chemistry and analytical
chemistry, have some familiarity with basics of molecular biology, and be comfortable with
troubleshooting.
Project 3: Analysis of bowerbird paint. This project is a collaboration with Professor Gerald
Borgia of the University of Maryland Biology Department. As part of the mate selection process,
male Satin Bowerbirds build elaborate structures (bowers) out of sticks and decorative objects.
Females decide on their mates based on the awesomeness of the bowers. A poorly understood
aspect of bower construction is the use of “paint” in decorating the bower sticks. The paint
appears to be derived from plant material, and females have been observed to taste bowerpaint
as part of the assessment process. Recently, members of the Whelan lab conducted extensive
GC-MS of paint found on sticks collected from bowers in Australia to determine its composition.
A comprehensive study of one bower indicates that the chemical profile of the bower may
change over time. One or two students will be hired this semester to complete the examination
of the GC-MS data and identify chemical constituents in the paint. The ideal candidate will have
completed organic and analytical chemistry and have interest in evolutionary biology.
Project 4: Visual communication of science concepts. This is a non-laboratory project ideal
for a student (not necessarily a CHEM or BCHM major) interested in the communication of
science concepts through visual images and text. The intended product is a set of Powerpoint
slides to be included in the display case in the Chemistry department. Effective visuals and
engaging content are the goal, and the student will have considerable freedom to exercise
creativity in conducting the work.
Research Preferences
There is also an optional Online Form available at
https://goo.gl/forms/WF5ulHoUDxEXlc9t1
Your Name_____________________________
Graduation year__________________ T# __________________
Major_________________________________
Please indicate your choice(s)
Rank Preferences
Faculty
List top 3 choices
#1 is first choice
Did you meet
with this
faculty
member?
Yes
No
___________
Jason Belitsky
___________
___________
___________
Matt Elrod
___________
___________
___________
Michael Nee
___________
___________
___________
Catherine Oertel
___________
___________
___________
Rob Thompson
___________
___________
___________
Rebecca Whelan
___________
___________
___________
___________
Will you be participating in the Honors Program?
(Eligible students were invited in Spring 2015)
Please provide any comments regarding your strengths of preferences, and/or choices among
multiple projects on the back of this form.
IMPORTANT
Please return this form by 4:00 pm on Friday, September 2, 2016
to the Chemistry Department Office A263, Science Center