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Incorrect structures for molecules.

Posted 9 years ago

In the demonstration "Isomer Generator for Organic Molecules", the program generates the incorrect 3D structure for ethylene. Although the bond connectivity is essentially right, ethylene is a planar molecule with the hydrogens all in the same plane as the carbon atoms, and not as a staggered conformation as shown. This geometry arises form the energetic consequences of the bonding interaction between the carbon atoms in a multiple bond and sp2 hybridization. Students use programs like this when they are learning organic chemistry, and are frequently asked questions on exams about the geometry of molecules because it has important consequences in the reactivity pattern and resulting stereochemistry. KP 9/18/15

POSTED BY: Keith Pope
3 Replies

Other molecules with double bonds show the same problem, for instance C3H6. But just because the problem is systematic doesn't mean it's easy to fix... Especially because the plot itself is a Graph3D object where the atoms are the vertices and the bonds are the edges or connections in the graph. The actual position of the atoms in space is dictated by some underlying graph display algorithm that makes its decisions based on criteria such as maximizing visual clarity. Such an algorithm simply has no idea that connections in a graph aren't allowed to rotate. (Actually, I'm quite impressed that the bond lengths and angles are so reasonable overall, which means that GraphLayout->"SpringEmbedding" is pretty awesome at its job.)

I know that using graph theory for molecular modelling and structure prediction is "a thing", which means there should be plenty of publications in the field by now. Maybe someone has already developed an algorithm that can handle pi and delta bonds.

One thing you can always do to get correct molecules is just to look them up in ChemicalData[] (or any other database, for that matter) and get the plots from there. For plotting molecules with multiple bonds from such a source, please feel free to make use of my code. Maybe you can write a little program where you can enter the graph connections returned by William Zhang's Demonstrations, then look up the configuration in ChemicalData[] and get the correct plot from there.

That said, I understand your frustration. If you do improve the Demonstration, I'm sure there's a way to submit a new version even if you're not the original author... I suppose someone at Wolfram can contact the author for you and set something up, but I've never tried that.

~ Bianca

POSTED BY: Bianca Eifert
Posted 9 years ago

To Glen: Thanks for the reply. In the case of propane, butane, and other saturated hydrocarbons the atoms can rotate around the C-C bonds and C-H bonds, so those structures can adopt a series of "conformations", so it doesn't matter as much which conformer is displayed. The problem with C-C multiple bonds is that they can't rotate so they really do have to be in the plane to be considered correct. It is the rigidity of C=C double bonds that gives rise to cis- trans isomerism. Those isomers have different physical properties as well. -KP 9-19-15

POSTED BY: Keith Pope
Posted 9 years ago

I see what you mean.

It's been years since my organic chemistry days. But I do recall some things such as steric interaction that influenced the overall 3D structure. And, yes, I see that molecular orbitals would also affect the structure.

I tried propane and that gave an incorrect result as well: one of the "methyl" ends was not oriented correctly. And both isomers of butane look disfigured.

The best thing to do is to contact the author. However, I did not see the author's name in the Wolfram Community. Very cool demonstration, though!

--Glen

POSTED BY: Glen Deering
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