Thursday, 22 May 2008

Generating structures

I just heard of a pretty cool tool for generating structures.

Imagine the following problem. You have the structural formula of some molecule, let's say

And now you are wondering what the molecule actually looks like. If you have a "real" molecule model kit, you could use that. But you probably don't carry that around with you everywhere, it may not have enough atoms and it does not give you quantitative information and so on. The alternative is the Online SMILES Translator.

First you draw your molecule in a standard molecular editor (e.g. ChemSketch) and save it as a .mol file. Then you upload it to that tool and create a 3D mol file. Open the result in a 3D molecular editor: for example Pymol if you want nice pictures; Arguslab if you want some quantitative information and do computations.

The structure I just mentioned looks like this.

I did not really find any special information in this case. But for example it is interesting to notice that the part of the ring with the double bonds is planar.

The side remark is that there are of course more interesting things than just the global minimum (assuming that the tool even finds this minimum). For example other stable structures and the barriers to get a feeling of the dynamics. But I think it's still quite a bit of information for how fast it is and for how little input it needs.

Add on: At this site you can use the CORINA structure generating tool without the need of any other software. "Create molecule" opens a java applet editor, the result is shown in another applet, both in your webbrowser.


Geoff H said...

Alternatively you could open that .mol file in something like Avogadro, do a quick geometry optimization with MMFF94, then a quick conformer search. One-stop shopping...

I suspect ArgusLab also reads mol files -- it can certainly do the geometry optimization with UFF.

Ψ*Ψ said...

Cool! Would be useful for people like me who can't do that third dimension...except I already live in Flatland. :)

Felix said...

Ψ*Ψ: well time to leave flatland! but on the other hand: all of us are missing 5 of the 8 dimensions really existing ...

Geoff: what I like about this tool is that it is so fast and simple. arguslab will do the same. but you have to do things like creating a reasonable starting geometry and checking the hybridisations for the force field.
avogadro seems nice on first glance, i'll take a look at it