Saturday, December 10, 2011

Bond lengths, Avogadro, Google Docs, and gamification

Recently a colleague of mine, Henrik, lamented that at a recent oral exam many first year students had no clue what a typical bond length in a molecule is.  I am not a big fan of memorizing something that can be easily Googled, but we're talking order of magnitude here, not the last decimal place.

This is a place where molecular modeling tools such as Avogadro can help, but how to do this exactly?  Knowing an approximate bond length by heart comes from looking at many, many molecular structures, and imagining a worksheet with dozens of fill-in-the-blank bond lengths already puts me to sleep.

But how about something like: use Avogadro to build a molecule with the longest CC single bond possible.  This sounds a bit more fun and I bet a few strategies are already popping into your mind. 

Based on my recent excellent experience with Google Docs, I would then have student collect answers on a common Google spreadsheet.  Students could either collect their work on a single sheet or one sheet per student/team. This allows students to learn different design principles from each other and adds an element of competition (gamification) since you can now compare results.

Would this actually work?  I challenge you to find out!
By work I mean: engage students enough to build a large number of molecules and think about bond lengths?  I don't know, but how about testing it out here?  I have started a spreadsheet with a few entriesIf you can do better, feel free to add your entries.

Some ground rules: 
1. The bond length must come from the lowest energy conformation
2. To beat a current entry the CC bond length must be longer by 0.005 Å
3. You must use the MMFFs force field (which will limit the number of elements at your disposal).
4. For now I'll leave the maximum number of atoms open, but the fewer atoms you use, the more impressed I will be.

You might have the students figure these issues out by themselves. Explaining why they are important could be very teachable moments.

Practical tips
1. As the molecules get more complicated, naming them becomes difficult.  In that case I suggest using SMILES, which you can generate with this GUI.  It would be nice if Avogadro has a "Copy SMILES" option.
2. You can build your molecule using SMILES.

Tuesday, December 6, 2011

Using Google Docs spreadsheets when teaching molecular modeling

Every year I teach DFT in the Computational Chemistry course here at the University of Copenhagen, where I give a 2 hour lecture one day, and give them an assignment to complete another day in the computer lab across the hall from my office.

I typically start them off around 10 am and they typically finish around 2 or 3 pm, when I then lead them through a discussion of the data.  In past years this has been pretty chaotic: computed energies are missing or wrong, and relative energies had to be converted to kcal/mol on the fly.

This year, inspired by Luca De Vico, I set up a Google spreadsheet where they could collect their data (they work in pairs) on separate sheets.  This worked great:

The students where able to see each others data, and they quickly discovered when they made mistakes (which I then helped them fix).

A "best practice" with respect to organization and presentation of the data was quickly adopted.

Discussion of the data was made much easier since I could just show the spreadsheet on the projector.

Finally, I could follow their progress from my computer and figure out when most people had finished, so we could start discussion.

Highly recommended!

Thursday, December 1, 2011

Reinventing Discovery: Practical steps toward open science

What can you do if you're a scientist?

I recently finished reading Michael Nielsen's book Reinventing Discovery.  This is not another review of the book (there are many: Google it).  I'll just say it is a well written book on a very important topic, so go buy it now.

Towards the end of the book there is a section entitled "Practical steps toward open science" and one subsection is about what you can do if you're a scientist.  There are some good suggestions, some of which I'd like to expand on here, and I'd like to add some new suggestions as well.  The suggestions are roughly ordered in increasing effort (though not necessarily impact!), together with my own examples (where applicable).

Read the rest of the post over at Proteins and Wave Functions

"Missing" MOPAC parameters

A long, long time ago in a land far, far away I implemented MNDO, AM1, and PM3 in GAMESS.  This was done by taking chunks of code from MOPAC that contained contained the parameters, integral code, and Fock matrix builder.  In doing so, I never noticed that the parameter file contained more parameters than where published in the papers describing the method.  This conundrum came back to haunt us recently as we're trying to implement PM6.

Read the rest of the post over at Proteins and Wave Functions