Spectroscopic Case-Based Studies in a Flipped Quantum Mechanics Course

Steve ShipmanNew 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

• 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)

Course Background

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 SpectroscopySix 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 SourcesMass 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 StudyIn 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 organophosphorous-based 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

NMR first, nearly got it (symmetry helps)

MS used to confirm ID of central atom

Background said it was an amino acid

IR gave information on side chain

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

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.

What Happened?

#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.

• 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)

What Worked Poorly?

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: PoisonYou 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 SmellIn 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 organophosphorous-based 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 WaterThings 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 PerfumeryThieves! 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.