Spectroscopic Case-Based Studies in a Flipped
Quantum Mechanics Course
Steve Shipman
New College of Florida
June 23, 2015
New College of Florida
• Public liberal arts college in the state university system
• Enrollment of 825 students, 80 faculty
• No letter grades or GPAs – narrative evaluations instead
Flipped Course Implementation
Course Background
• Textbook: McQuarrie, 2nd edition
• Typical size: about 15 students, primarily 3rd and 4th years
• Meets twice a week for 80 minutes (TR, 10:30 – 11:50)
Notes are distributed each week
Students are assigned three
problems for each class period
Students write questions on a
notecard. To reduce stigma,
those without questions write “I
don’t have any questions” so it’s
hard to tell whether or not
someone is asking something.
Case Studies in General
• Used in many fields as a way for students to apply knowledge
from class to practical / realistic situations.
• Scenario is presented and an objective is described (identify
the pathogen, figure out the unknown, decide what to do)
• Depending on structure, all information could be made
available at once or given out in stages.
• Can be formative (students find their own gaps and weak
spots) and summative (do students understand concept X?)
Modified graphical abstract from Donaldson, D.J. et al.,
“Standard States and Thermochemical Kinetics in
Heterogeneous Atmospheric Chemistry,” J. Phys. Chem.
A 116, 6312 (2012).
Case Studies With Spectroscopy
Six case studies (two sets of three).
Discussed scenario, requested data, interpreted, discussed again,
made second request (two class periods). Each group explained
reasoning to class and answered questions / listened to suggestions.
First set: single unknown molecule. Students could request two of:
IR, NMR, UV-vis, Mass Spec, Microwave.
Second set: all were mixtures of three components.
One was complicated – all data available on each component,
basically like three of first set
One was moderate – all data available but of mixture, not
separated components
One was all simple molecules (small linear cations) – could only
request IR and microwave
Data Sources
Mass spectra were from NIST Chemistry WebBook (http://webbook.nist.gov).
All other spectra were calculated via Gaussian 09.
For NMR (H- and C-), I simulated TMS at the same level of theory to get the
chemical shifts and determined the splitting patterns myself.
Example Case Study
In a small town to the southwest of Greenwich, CT, the air has started to smell
strange and people are concerned. People who have been exposed to the air do
not appear to be suffering from any acute respiratory distress, but are worried
just the same. Given its volatility, the source of the smell is almost certainly a
small molecule with a reasonable vapor pressure. An air sample has been
collected and initial analysis indicates that it does not contain any phosphorous,
which is a relief (this means it can't be sarin or a related organophosphorousbased nerve agent). It is up to you to figure out what the compound is and to
relay that information to the local community.
Students conferred and chose mass spec. They used
that to estimate the molecular formula and some of
the fragments, but could only narrow things down so
far. They requested NMR next, and were able to
determine the unknown compound.
What Happened?
First set of case studies (single compounds):
The groups correctly identified all of the unknowns. For each case,
NMR + either IR or mass spec was sufficient.
Background said it was
an organic cation
Background said it was
an amino acid
NMR first, nearly got it
(symmetry helps)
IR gave information on
side chain
MS used to confirm ID
of central atom
NMR confirmed side
chain identity
Background said small
molecule with vapor
pressure
MS gave total mass and
some fragment IDs
NMR showed how to
link fragments together
What Happened?
Second set of case studies (mixtures):
In the one with the most information, students correctly identified
two of the three species and were very close on the third.
In the other two, students identified one of the three compounds but
only had vague guesses about the other two.
#4
#5
#6
What Worked Well?
•
•
•
•
Learned about structure determination via several spectroscopic techniques.
Learned that NMR is not enough without the chemical formula!
Learned why complex mixtures are hard to characterize.
Practiced articulating reasoning behind choices of data to request and what it
would tell them, as well as explaining the logic in final structures.
What Worked Poorly?
• Second round of case studies felt rushed, students didn’t have enough time
to deeply think about data
• Students did not understand how to use microwave data to narrow down
possibilities (case study with small linear cations)
Things to Change
• Simulated data could have been more realistic: IR spectra with linewidths,
simulate in solvents, conformational / temperature effects
• Could have spent more time afterwards discussing alternate routes of solving
the problem, what techniques are more efficient, etc.
• Groups were a little too big (six people), and coordinating at the end of the
academic year was challenging
Conclusions
•
•
•
•
Reinforced student understanding and appreciation of spectroscopy
Students enjoyed them, called them “innovative” and “fun”
Doing them helped me more easily spot student weak areas
Will definitely do again, with modifications mentioned above
Acknowledgements
• Dr. Rebekah Ward, Georgia Gwinnett College
• Anastasia Edsell
• Students in my Spring 2015 Quantum Mechanics course
Typical Class
• 10:30 – 10:45: students form 6 small groups (2-3 per group,
2 groups per problem), come to consensus within group,
then reach consensus with other group on the same
problem.
• 10:45 – 11:00: one person per bigger group explains their
problem to the class and answers questions
• 11:00 – 11:20: I answer questions from note cards
• 11:20 – 11:50: Students work in small groups on new
questions, some of which may become the questions for the
next class period
Case Study #1: Poison
You work in a pharmaceutical company, as part of a team applying green
chemistry methods to drug synthesis. Two of your co-workers, who you've had
several heated public arguments with, become gravely ill and experience
several seizures not long after one of these disputes and people suspect you of
poisoning them. You maintain your innocence and insist that your co-workers
must not have been following proper lab safety protocols. In a catastrophic
failure of impartiality, it's been decided that you should determine the
structure of the molecular culprit, which preliminary tests have revealed to be
an organic cation.
Solution: Tetraethylammonium cation
This is a real phase-transfer catalyst used for
green chemistry. It’s also the same size as
hydrated K+ and is toxic because it can block
potassium ion channels.
Case Study #2: Aliens!
You're a scientist at a biotech firm in San Diego. One morning, before you start your
hour-long commute to work, your neighbor catches you on your way out the door.
Looking a bit confused and exhausted, he tells that he was abducted by aliens with
purple, curly hair late last night and teleported back into his bed just before his
alarm went off. While you're used to hearing strange things from him, this time it
seems different somehow. He mentions as part of his story that he brought back
one of their hairs from the alien craft, and he was wondering if you could use the
equipment at your company to confirm his story. You're skeptical, but the hair is
indeed purple, at least. It also has a faint smell almost but not quite like garlic. At
work, you quickly confirm that the primary component of the hair is more or less
typical protein, but one amino acid in particular is both prevalent and strange. You
need to figure out what it is and decide whether or not your neighbor's story is true.
Solution: Selenocysteine
(My hair was dyed purple at the time…)
Case Study #3: Strange Smell
In a small town to the southwest of Greenwich, CT, the air has started to smell
strange and people are concerned. People who have been exposed to the air do
not appear to be suffering from any acute respiratory distress, but are worried
just the same. Given its volatility, the source of the smell is almost certainly a
small molecule with a reasonable vapor pressure. An air sample has been
collected and initial analysis indicates that it does not contain any phosphorous,
which is a relief (this means it can't be sarin or a related organophosphorousbased nerve agent). It is up to you to figure out what the compound is and to
relay that information to the local community.
Solution: Sotolon
(3-Hydroxy-4,5-dimethylfuran-2(5H)-one)
This scenario was based on a real event, the
“Maple Syrup Event” in 2005. The “small town”
was New York City.
Case Study #4: Contaminated Drinking Water
Things are going well in the city of Townsville. Corporate tax incentives have led to oil and
gas companies building refineries in the area, adding new jobs and accelerating the rate of
local resource extraction. However, in the last year, there have been a number of small
earthquakes (3.0-ish), despite the fact that Townsville is not near any fault lines and even
the oldest residents had never previously experienced earthquakes. If that weren't
enough, the local water has started to take on a strange taste and smell. As the local
chemist, residents of the town have interrupted your research on “Chemical X” to ask you
to investigate. You've acquired a sample of the contaminated water. Unfortunately, even
though you can smell and taste the difference, the concentrations in the sample are
sufficiently low that you are not able to separate individual components out by anything
other than GC/MS, which immediately destroys the components it has isolated. Hopefully
you can quickly figure out what's going on so that you can get back to your research!
Solution: Ethylene glycol, isopropanol, 2-butoxyethanol.
All are molecules used in the fracking process.
Case Study #5: Democratization of Perfumery
Thieves! Corporate thieves broke into your grandmother's house during her funeral and stole a
safe containing a perfume recipe that she had crafted and perfected over many long years. Her
dying wish, whispered urgently to you, was that you would spread her recipe far and wide so
that any who wanted could make her particular perfume directly, without needing to purchase
it from unsavory corporations. You were never able to prove that they stole the recipe, but the
scent of one of their new product lines, “The Negation of Consumption”, is unmistakable.
Because reverse engineering a product is legal in the U.S. as long as the product was obtained
legally, and, moreover, because it is an ethically correct thing to do in this case, you have
purchased a sample of “The Negation of Consumption” to figure out what it contains and
reconstruct your beloved grandmother's recipe so that all may benefit. With careful
chromatography work, you have been able to isolate three main organic components from the
bottle, each of which bears a strong scent.
Solution: Methyl propionate (sweet
fruity rum), 4-anisaldehyde (floral and
almond), furan-2-ylmethanethiol
(roasted coffee)
These all have strong scents.
Case Study #6: Ions in SPAAAACE!
As part of an astrochemistry research group, one of your goals is to produce ions
in the lab that are present in the interstellar medium and then study them in a
molecular beam instrument with a microwave/mm-wave spectrometer and an IR
laser source. In a gas mixture of acetylene, hydrogen, and nitrogen, you apply a
strong electric discharge while screaming “It's alive!”. In addition to annoying your
lab mates, this produces several different cationic species, which you need to
characterize. Given the fragile nature of the sample and the special conditions
under which the molecules in the mixture were created, it is not possible to do
NMR or mass spec on the products.
Solution: N2H+, HCNH+, HC3NH+
All of these ions have been detected
in the interstellar medium.