How do I graphically represent a chemical compound?

May 1, 2006 6:45 AM

Calling all Organic Chemists! Please help me with my next tattoo!

Here goes... I basically have decided that for my next tattoo, I want to have a molecular diagram of Venlafaxine Hcl (also known as the drug Effexor). I have been googling this for ages and asked doctor friends, to no avail, so I turn to my ever trusty bastion of truth, AskMe.

Now I understand that the chemical compound when drawn out traditionally in the drug literature looks like this

However, what I am looking for is something like this

(links go to google image results)

This is actually going to be the foundation for a larger piece, and I think the 3-d look would suit it much better. If anyone knows of any other ways that you can represent chemical compounds graphically, I would love to see some examples.

The problem though is that I have no idea how to get this type of Imagery for this specific compound. Even if I could get some sort of 3-d representation, I need to be able to rotate it somehow to the best angle, as well as get a printout to give to the artist... Friends have told me that they have software at their places of work that can do this, but would not be able to get something for me. Where should I turn? I am located in Melbourne, Australia if that means anything.

Thanking you as always.

posted by LongDrive to clothing, beauty, & fashion (7 comments total)

No real answer for you, but the first image you linked to is a Lewis structure. If you want the spatial configuration of the molecule, you venture in the field of molecular modelling (or computational chemistry). For some molecules, it is trivial to find the spatial structure. Other (e.g. proteins) need lots of CPU power to find the correct folding. There's a list of software that might be useful here. I've played with software like this ages ago and with most packages you can zoom/rotate, etc.

On preview: a google image search yields this.
posted by swordfishtrombones at 7:02 AM on May 1, 2006

Perhaps try ChemFinder? They have a free plug-in that lets you view molecular structures. You probably want something like the cylindrical-bond or colour by element structure.
posted by greatgefilte at 7:08 AM on May 1, 2006

Googling found two programs which (to my completely untrained eye) look like they should do what you want. One of them, ChemSketch, is free for academic use, and the other, Chem3D, has a 2 week free trial.
posted by jacalata at 7:09 AM on May 1, 2006

There's a linux OpenGL screensaver (don't remember the actual name) that'll display what you want.
posted by NucleophilicAttack at 7:15 AM on May 1, 2006

I've sketched the base structure Longbaugh, check your mail. I'm sending you a couple of pictures and the geometry file which you can import into one of the programs listed above. The structure I've produced is geometry optimized, that is how the chemical would organize itself most of the time, but that may not be the best configuration for display.

Venlafaxine is the base structure, the acid would not be represented on the same diagram, typically. I've left the acid part off.

As you've discovered, there are many representations of molecular structure. The one you want is called ball and tube, normally. You've got the choice of showing it with and without hydrogens. For larger molecules, the hydrogens are often left off (they were left off your Lewis structure). I've sent you examples of both.

Feel free to drop me a line if you want anything else.
posted by bonehead at 7:58 AM on May 1, 2006

There's a linux OpenGL screensaver (don't remember the actual name) that'll display what you want.

It's called molecule, and it's part of xscreensaver. It will render arbitrary molecules given Protein Data Bank files that include both atoms and bonds. If you can come up with a PDB file I'd be happy to render it for you.

One problem with 3d renderings of molecules is that they won't be flat -- some of the atoms will be in front of or behind others. I don't know how well that would render into a tattoo.
posted by mendel at 9:21 AM on May 1, 2006

Another option: you can buy or borrow an organic chem modelling set for cheap, put your structure together (or have someone help you do so), and then photograph it from whatever angle seems most pleasing to you.
posted by ikkyu2 at 11:46 AM on May 1, 2006