Missing double and triple bonds in Molecules 2.0
Tue, 05/10/2011 - 14:00
Hey Brad, I am immensely impressed by the update to Molecules. I'm really looking forward to teaching organic chemistry with it now, with the additions of small molecules and PubChem support. I downloaded a few molecules that should have had double bonds (acetone, benzene) and triple bonds (benzyne, ethyne), but every bond was displayed as a single bond. I downloaded cyclohexane for comparison against benzene, and the geometries for both are definitely right, the bonds are all just displayed as single bonds. Thanks for all your hard work, Molecules is an amazing program (especially for free).
Wed, 05/11/2011 - 15:36
#2
Ah, I guess I didn't even realize that, since with previous versions they were mostly large biomolecules. It will still be useful to see geometry of smaller molecules, but double and triple bonds are relatively important to see along with the changes in geometry that accompany those bond types. I've actually been watching your advanced iphone programming class from itunes, but i'm nowhere near really being able to program efficiently, otherwise i would attempt to contribute to this great project.
Yes, I only represent bonds with a single cylinder right now, with no indication of them being single, double, or triple bonds. The previous versions never made this distinction either.
I had to ship this at some point, so this was a feature that didn't quite make it in. It's on my list of improvements for the application, though.
Thanks for the kind words about the application. Hopefully the lack of these bonds won't be too much of an issue for your students until I get them added in.