ChemSketch on Linux Again

Last year I wrote about using ChemSketch on Linux.  It is about the only Windows program that I regularly use these days.  Since switching to Linux I have not  completely settled on a chemical structure drawing program.  Sometimes I still use ChemSketch on Windows and then copy the image into OpenOffice, sometimes use another program on Linux - usually MarvinSketch.

Thanks to a comment left by Dragly on my original ChemSketch post in January, I can now reliably use ChemSketch on Linux.

ChemSketch is a Windows program, so I have to use Wine in order to run ChemSketch.  The problem was that ChemSketch would run fine the first time it is started after installation, but every other time I tried to run the program it would hang-up without the ChemSketch window ever appearing.

Dragly's comment referred me to:

http://markmail.org/message/grddjlgsn3dh5kqp

And he also pointed out that the program could be run with the window maximized by using this command, provided that the file path to the program is correct:

wine start /MAX C:\\WINDOWS\\TEMP\\ACDFREE12\\CHEMSK.EXE

This works, but it behaves a bit flakey for me running Ubuntu 10.04 and Wine 1.1.42.  First the ACD/Lab Products panel appears (very slowly) - after clicking the "OK" button, the program itself loads on the workspace to the right of the one I am working on. The 3D View program behaves the same way - you need to use:

wine start /MAX C:\\WINDOWS\\TEMP\\ACDFREE12\\SHOW3D.EXE 

to get it to open normally, and then it shifts one workspace to the right.

After digging around a bit, it turns out that the problem is in the Wine registry file, which for me is at

/home/steve/.wine/user.reg

This file is updated every time you close a program that is running under Wine.  The quick and dirty solution would be to delete this file before running ChemSketch.  Except for losing all the settings for every program you run with Wine, this works pretty well.  The program starts normally - if a bit slowly compared to Windows.

The clever thing to do would be to edit user.reg to delete the offending setting, which starts with

[Software\\Advanced Chemistry Development (ACD)\\Size]

and is followed by a bunch of numbers.  Deleting this setting allows you to run ChemSketch and the 3DViewer "normally."    This is a bit tedious but do-able.  To be really clever I should write a program to do it for me every time I run ChemSketch.

Under Windows, you can open the 3DViewer from ChemSketch by using the ACD/Labs menu. Unfortunately, when I run under Linux, this menu does not have any of the labels visible.  The first menu item is the 3DViewer.  Or you can right-click the ACD/Labs icon in the Gnome panel at the top of the screen and select the 3D Viewer to open it.

Copying between the ChemSketch and 3D Viewer windows works, and so do the Database search options.  The only remaining problem is getting the figure into an Open Office document.  You can't simply copy the image, nor can you insert an OLE object the way you would in Windows.  Instead you will need to save the figure as an image and import the image into the Open Office document.  The downsides of this are adding an extra step to save the image, and not being able to edit the image easily unless you also saved the original ChemSketch file.

Finding Buckyballs in Space

When you hear about molecules in interstellar space or on the moons of Saturn they tend to be small molecules like methane, ammonia or water. A big organic molecule would be something like glycine, the simplest amino acid, with only 5 "big" atoms (carbon, oxygen and nitrogen) and 5 Hydrogen atoms.  So finding buckyballs with 60 or 70 carbon atoms is really quite extraordinary.  It's a big difference, and buckyballs contain only carbon atoms - no other elements not even hydrogen, the most common element in the universe.

Buckminsterfullerene - C60

Image via Wikipedia

Using the Spitzer Space Telescope, an international reseach group has recently observed the buckminsterfullerenes C60 and C70 in Tc 1, a young Planetary Nebula (PN) with a white dwarf at the center.  The inner region of the nebula is carbon-rich, hydrogen-poor and dusty and this seems to be an important reason that they were able to see buckyballs there - buckyballs need lots of carbon in order to form, and they don't have any hydrogen in them at all.

The Hourglass Nebula

Image via Wikipedia

Most planetary nebulae have strong emissions from polycyclic aromatic hydrocarbons (PAH's) but not Tc 1.  Also missing, there are almost no simple hydrogen-containing molecules like HCN or C2H2.  A PAH would be like a small piece of a buckyball with hydrogens around the outside edge.  Once a buckyball started to form if there was any hydrogen around, hydrogen atoms could attach to the carbons on the edges resulting in a PAH instead of a buckyball.

from the research article:

On Earth, fullerenes can be synthesized by vaporizing graphite in a hydrogen-poor atmosphere that contains helium as a buffer gas. The fullerene formation process is very efficient, and C60 is by far the dominant and most stable species among the large cluster population formed in these experiments, followed by C70. However, fullerene formation is inhibited by the presence of hydrogen. The circumstellar environment of Tc 1 seems to be the astrophysical analog of such a laboratory setup.

They used Infra-Red (IR) spectroscopy to identify the buckyballs. It's especially useful in this context because it tells you what kinds of bonds there are in a molecule.  Visible light doesn't usually give a lot of useful information except for individual atoms, or maybe certain types of large, complex molecules. But IR gives you a lot of information about the bonds in a molecule.  IR spectra can be quite complex - the nifty thing with C60 is that for as large as it is, it has a very simple IR spectrum.

I had a difficult time finding an IR spectrum for C60 at the usual online chemistry databases (NIST Webbook, ChemSpider, SDBS). But this web page has a small image of the IR spectrum of C60.  It's a very simple spectrum with just 4 absorptions.  The molecular structure of C60 it looks intimidating, but it turns out that there are really only two kinds of bonds:  bonds that are shared between two 6-membered rings, and bonds shared between a 5-membered ring and a 6-membered ring. And the thing about IR spectroscopy is that it is highly dependent on symmetry.  C60 is highly symmetrical, so you only see 4 absorptions for it. C70 is the second most common buckyball.  It's not as symmetrical as C60, and as a result its spectrum is more complex that that of C60.

Cami, J., Bernard-Salas, J., Peeters, E., & Malek, S. (2010). Detection of C60 and C70 in a Young Planetary Nebula Science DOI: 10.1126/science.1192035

The Chemistry of Cthulhu?

I write like
H. P. Lovecraft

I Write Like by Mémoires, Mac journal software. Analyze your writing!

I haven't posted in a while - is this the reason?  

Was I tottering on the brink of cosmic horrors beyond man's power to hear?  

I suppose that some people might say of Organic Chemistry that 

... there is no language for such abysms of shrieking and immemorial lunacy, such eldrich contradictions of all matter, force, and cosmic order.

Image via Wikipedia