Education 2.0: Leveraging Collaborative Tools for Teaching

On March 25, 2010 I presented at the Drexel E-Learning 2.0 Conference on "Education 2.0: Leveraging Collaborative Tools for Teaching". It was an opportunity to update my slides with what I did and learned from the Chemical Information Retrieval course I taught over the Fall 2009 term.

I described using a wiki to organize course content and to allow students to contribute useful resources. Their assignments were also designed to be useful to other students in the class as well as to the general library and chemistry community.

I covered using wikis and other collaborative tools to mentor students doing laboratory research with Open Notebook Science. At the end I provided a quick overview of using games and Second Life for educational purposes.

Education 2.0: Leveraging Collaborative Tools for Teaching

View more presentations from Jean-Claude Bradley.

We're Gonna Ugi All Night!

Thus begins the CHEM254 lab manual for the week of April 7, 2008 at Dominican University:

“Ugi to the left, Ugi to the right. This is so fun, we’re gonna Ugi all night.”

As I discussed a few days ago, Brent has followed through in a big way in incorporating the UsefulChem project into his teaching lab:

This experiment represents the beginning of collaboration with the UsefulChem Bradley open notebook science group of graduate and undergraduate research at Drexel University. The goal of the UsefulChem project is to use the Ugi 4 component reaction to synthesize possible anti-malarial compounds. Open notebook science allows immediate dissemination of experimental results that invites advice and suggestions as well as complementary experiments that enhance and advance the project. We are going to reproduce some of the Drexel results as well as perform two complementary reactions that have not been done at Drexel.

The procedure is derived from our lab notebook with one interesting vortexing modification :)

Part I.
Add 0.33 g of your aldehyde to 8 mL methanol in a 20 mL scintillation vial.
Screw on a Teflon (green) cap on the vial. Vortex to mix and dissolve the aldehyde.
Add 1 mL of methylamine solution to the vial.
Vortex to mix. Sing the “Ugi song” while vortexing.
Obtain 0.34 g of the carboxylic acid. Add the carboxylic acid to the vial.
Vortex to mix.
Obtain 0.39 g of tosylmethylisocyanide. Add the tosylmethylisocyanide to the vial.
Vortex to mix.
Take a photo of your reaction mixture.
Label the vial and let the reaction mixture sit in the sealed vial.

By taking pictures his students can directly compare the progress of the reaction with our group. The questions for this lab are also excellent and may result in some useful ideas for my students to ponder (this may end up being a realistic way to foster chemistry crowdsourcing):

What could you do to isolate your product if after 7 days if there are no spontaneously formed crystals?

Refer to UsefulChem Experiment 171 . Which reaction most closely corresponds to our experiment? What were the results?

Consider the IR spectrum may reveal that there is unreacted isocyanide in your product mixture. Where does the isonitrile group appear in an IR spectrum? (Refer to appendix 2B in your textbook.)

Consider the possible 1H spectrum of your Ugi product. How many aromatic Hydrogens are there? How many methyl groups are there? Where would you expect to observe the methyl groups?

Consider the possible 13C spectrum of your Ugi product. How many aromatic Carbons are there? How many carbonyl carbons are there? How many methyl carbons are there? Where would you expect to observe the methyl carbons?

If you were given four different compounds for each type of Ugi reactant (16 compounds in all), how many different Ugi products could you attempt to make?

Safety Question: What is the safest way to transfer 1 mL of 2.0 M methamine in methanol from the stock bottle to your reaction vial? Give a reasonable explanation of your choice.

I also really like that he is exposing his students to some handy cheminformatics tools:

Look up “tosylmethyl isocyanide” in chemspider. What is the InChI code? What is an InChI code?

Since Brent and I started the discussion we have a few more precipitates involving the non-stinky tosylmethylisocyanide that may be suitable for his lab. Khalid has been doing some tedious but very necessary data checking and recording and the updated results are available on the Master Table of Ugi reactions.

There are currently 65 reactions, with 20 giving precipitates - and we are now including reactions where the starting materials fail to dissolve. Not all the precipitates have been characterized but they will be over time. In fact the Ugi product that Brent is trying to make in his lab for next week has not yet been fully characterized - all those phenolic groups seem to give rise to solubility issues in CDCl3.

That is a risk associated with using Open Notebook Science for a teaching lab. But it is also one that could pay off because his students could be contributing valuable results to an ongoing research project focussed on making anti-malarial compounds.

Expanding the UsefulChem Collaboration to Teaching Labs

A few weeks ago I received a very interesting email from Brent Friesen at Dominican University. He mused:

I am trying to put together a bridge between the type of opensource research you are instigating and the traditional Sophomore Organic Chemistry lab. There are over 4,000 college and universities in the United States - all of them teach Sophomore Organic Chemistry lab. How can we harness this resource? .....

SOC labs must fulfill 4 criteria:
1) inexpensive reagents and equipment
2) fit into the time constraints of 1 3-hour period per week.
3) Must be a robust reaction with fairly stable products. It doesn’t have to be “foolproof” but that helps.
4) Compatible with equipment, glassware, procedures that student know how to use and do.

Bottom Line: I am definitely interested in developing collaborative projects, especially if they can be performed as part of a Sophomore Organic Chemistry laboratory curriculum.

This is extremely encouraging news for open scientific collaborations and I am very impressed with Brent's initiative! It certainly is more work for him compared to maintaining the status quo.

Kevin Owens and I have discussed this possibility for some time now and he is willing to contribute by carrying out mass spectrometry if required.

Brent and I further discussed the applicability of the Ugi reaction that we perform in my lab because of its simplicity - 4 components are mixed together in methanol at room temperature and a Ugi product often precipitates within days, requiring only filtering to isolate. (see EXP150 for a good example)

However, one major limitation of the Ugi reaction for a teaching lab is the terrible stench of most isonitriles, one of the four key components. One way around this is to use isonitriles that don't stink, such as TOSMIC.

So as a starting point, we would like to start with a Ugi reaction which involves TOSMIC and has lead to a precipitate in our lab. There is only one example so far: 171H.



According to the lab notebook, all starting materials dissolved easily and a precipitate appeared after 2 days. The precipitate has not yet been isolated and characterized. Hopefully it will prove to be pure Ugi product, as other similar Ugi reactions have done.

It turns out that many of the top ranking compounds from Rajarshi's falcipain-2 docking run (V2) contain TOSMIC as the isonitrile. Phil Rosenthal at UCSF is still up for testing compounds for anti-malarial activity. Wouldn't it be a testament to the power of open collaborative science if a decent anti-malarial lead was uncovered through the routine teaching of undergraduate organic chemistry labs?

At the very least I'll bet it would be rewarding for the students involved.

Brent has placed the orders from Sigma-Aldrich and is moving full steam ahead. He recently wrote to me:

You know, I'm ready to dance and you are the only dance partner who seems to be ready and willing. Let's figure out a way to adapt the Ugi reaction to Sophomore Organic Chemistry laboratory and give it a try!

I would like to plan it for the week of April 7 and the following week...
Does not give us much time, but it can be done.

Keep track of Brent's activities on his blog.

Tags
171H InChIKey XRHVBZVCUGMHPN-UHFFFAOYAR
TOSMIC InChIKey CFOAUYCPAUGDFF-UHFFFAOYAC InChI=1/C9H9NO2S/c1-8-3-5-9(6-4-8)13(11,12)7-10-2/h3-6H,7H2,1H3