Wednesday, June 24, 2009

Nicking transition states from Nick Greeves

Nick Greeves has made a wonderful website called ChemTube3D. And I mean this quite literally, the site is full of wonders: Jmol-animated reaction mechanisms for the most important organic reactions.

I especially like the way the usual 2D representations of reactions are tied to the 3D animation: you click on 2D structures to see 3D structures and "electron pushing", and on arrows to animate the reaction. This really drives home to the point that the static 2D pictures is meant to represent a dynamic 3D model. I wish this has been available when I took organic chemistry, which, somehow, wasn't made any easier by the fact that half the reactions hadn't been discovered yet.

In case you are curious how Nick obtained the structures along the reaction path, you can find the detailed instructions here. Generally speaking, they are obtained by finding the TS of the reaction and then following the atomic forces downhill to reactant and products using the intrinsic reaction coordinate method. This is done in the absence of solvent so for some reactions involving ions there is no barrier (and hence no TS) in the gas phase.

Because Jmol is used, the user can interact with the model, rotate, zoom, measure distances, and access the coordinates! That's right, ChemTube3D is also a transition state (TS) repository, and in the screencast I show how use Avogadro to extract the TS structure. But because the "TS part" of a TS is usually confined to a few bonds, one can use Avogadro to add substituents and create more complex TSs as well.

When I run the input file (which you can find here) that I make at the end of the screencast, GAMESS finds the TS in 20 steps (though I had to remove the $FORCE group which is inserted erroneously by Avogadro).

Finally, Steven Bachrachs blog is another good source for TS structures (many images link to a Jmol display of the structure). Look under the Reactions category in the left-hand column.


Jan Jensen said...

Jacob Lerche from Portland State Uniiversity writes

Hi Jan, I hope you don't mind me asking you a couple questions. I recently started reading your blog because I became interested in the possibilities of molecular modeling. I wanted to ask if you've been able to load a GAMESS output file into Avogadro and successfully generate electrostatic potential maps, MOs, or other such things. I am seemingly able to do so with MacMolPlt, but I have yet been able to do it in Avogadro. The other question is if you would be willing to explain to me how to access GAMESS from the command line. I've had to resort to using the bundled queuing program, gamessq, which might be the basis for my troubles.

Thanks for your time, I'm looking forward to hearing from you.


Jan Jensen said...

Glad to hear it!

Unfortunately Avogadro is not yet able to extract the required information from the GAMESS output file. I use MacMolPlt.
I use the gms script that comes with GAMESS: "./gms xxx" where xxx is the input file xxx.inp.
You have to be in the gamess directory for this to work.

The Avogadro people assure me that a GAMESS queueing system will be part of Avogadro soon.

Jan Jensen said...

Jacob Lerche from Portland State University writes:

Also, thank you for your reply. Avogadro is a really nice program but its lack of documentation is quite frustrating sometimes.


Jan Jensen said...

Agreed. Writing documentation is the least fun part of developing software.

But remember Avogadro is a community effort and you can help. For example, when you figure out how to do something (or discover some limitation) that is not documented, why not update the Avogadro wiki?

Anyone can make a login.

Paco said...

Hi Jan,

First of all congratulation for your blog, I believe it's very instructive and helpful for the non-initiated in the computational chemistry, as is my case. Following your post, I'm trying to calculate TS's for some molecules using a MacBook intelCD2 and Avogadro's latest version (0.9.6), unfortunately the program does not recognise the .xyz file when I try to load the animation.
I've tried with several .xyz files from ChemTube3D with the same results. Do you think you could give me a clue about what I'm doing wrong? I would really appreciate it.

Thanks a lot in advance,


Jan Jensen said...


Glad to hear you find the blog useful.

Can you reproduce the example in the screencast?

If yes, give me an example of one that fails, so I can try it.

If no, then the problem is with your version of Avogadro. Try upgrading to 0.9.7.

If it still fails, post your question on the Avogadro discussion list.

Paco said...

Thanks for the quick answer!

I'm afraid I can not reproduce the example in the screencast and I am using Avogadro's latest version (0.9.7.). Strangely, when I load the .xyz file I do not receive the message informing that I am about to open a file with multiple molecules.

In any case I've also tried with version 0.9.5. and I do have the same problem.

As you suggested, I'll try to post a message at the Avogadro discussion list. I'll let you know if I, eventually,can solve the problem. Thanks again.


Jan Jensen said...


Yes, I don't get the message any more with 0.9.7, but I can load all 21 structures fine.