Saturday, December 11, 2010

Computational chemistry exercises

Someone (I'll call him N. O'Boyle ... no, too obvious ... Noel O.) wrote me asking if I had any computational exercises I'd be willing to share. Since I took the trouble of writing him back, it occurred to me that I had free blog material. Here's my reply in a slightly edited form.

When I taught a computational chemistry course in Iowa I used exercises from "A Laboratory Book of Computational Organic Chemistry" by Warren Hehre et al., and Spartan in those pre-Avogadro days. Specifically experiments 4, 11, 34 and 76.  See here for an example.  The computational component of the other half of the course was individual research projects.

I would assign an experiment on a Monday, discuss it the following Monday, and have a write-up due  the Monday after that. I graded the first write-up (of exp 4) very lightly and then gave the student this example write-up of exp 4 so they could see how how to do it.  I also made this check list for a report and a list of questions for each experiment (taken from the book): exp 4, exp 11, exp 34, and exp 76.

Here in Copenhagen I co-teach a similar course with 5 other people, so I just get 1-2 exercises a year, and here I try to fit the content of the exercises in with the other instructors and the topic I cover. I teach the chapter on DFT and here I have developed an exercise using bond energies.

Sometimes I also teach the chapter on geometry optimization and then I use exp 76. Other instructors use Gaussian/Gaussview so that's what the student tend to use here too, so I have made no tutorials to go with the exercises.

"Exercises" in Molecular Modeling Basics: In Chapter 4 I illustrate applications of QM to various chemical problems, and Chapter 5 gives you some details of the underlying GAMESS input and output files (and there are now several blog posts with even more information on the various examples). The intent is that people can reproduce the results I present in Chapter 4 relatively easily.  Depending on the level of the course, reproducing these example may be challenging enough. Otherwise, one could easily come up with additional related problems. Let me know if that is of interest.

Many of the molecules and concepts are very P-chem oriented, i.e. uses small non-organic molecules to illustrate P-chem concepts, but there are some organic molecule/concept examples too: steric strain, hydrogen bonding, amide hydrolysis.  


Anonymous said...

Dear Prof. Jan,

I've used your blog to quick-learn how to use GAMESS.

Now, I've a question, are you aware (or any of your followers) of any GAMESS-related tool that will allow me to obtain the "fukui function" of a given molecule?

Jan said...

Hi, Glad to hear you found the blog useful.

Googlin "GAMESS and Fukui function" lead to Chemissian as a possibility.

Anonymous said...

Prof. Jan,

Thanks for your response. Yes, I've seen the Chemissian tool; but, you may need to pay for that GUI.

I've found that the freeware GABEDIT can also plot the fukui-parameters of a given molecule.

However, I was wondering if you guys as experts of the GAMESS code could have an analytic-tool that could help me to calculate the fukui-parameters for each atom in a given molecule. I guess, I'm searching for a piece of code that could help to calculate the fukui-fuction and not for GUI that can only plot the fukui functions. Something that can say the fukui-function for the C-atom is 2.54, for the H-atom is 0.78, etc (assuming that my molecule is composed of C and H atoms).

I'll be glad to know if you have heard of something like this!


Jan said...

Sorry, but I haven't heard about anything like that. My only other advice is to try the Google GAMESS list