Graphene Nanoribbons

Our Angewandte paper just came out: "The Multiradical Character of One- and Two-Dimensional Graphene Nanoribbons."

What we looked at is how open-shell character develops in polyacenes and bigger graphene nanoribbons. Some time ago I learned in basic organic chemistry that phenantren is more stable then anthracene. And interestingly this difference becomes enhanced when you move to longer chains. If you just keep adding rings in a linear fashion (forming polyacenes) you can go until five rings, reaching pentacene, and then things become really unstable. By contrast you can create longer stable phenacenes without any problem. The reason is that unpaired electrons accumulate at the zigzag edges, as shown in this TOC graphic.

Similar things also hold for the 2-dimensional systems and the precise shape of the edge decides whether or not the system obtains open-shell character. Apparently people have been discussing these things a lot. And since the paper is about graphene and contains the word "nano" we decided to try submitting it to Angewandte ...

There is also a German version: "Der Multiradikalcharakter ein- und zweidimensionaler Graphen-Nanobänder." Apparently the Gesellschaft Deutscher Chemiker likes to keep German as an active science language. It was kind of fun to translate it actually. Because the only German papers I ever read were from the very early times, like Hückel, Förster, Kuhn that write like quantum theory is something really new and special. So I felt a little bit like one of them. And actually I also got a free book from Wiley for my translation work: "Relativistic Quantum Chemistry".

Arrows

Arrows in molecular graphics are always pretty. So what can you do?

For molecular vibrations, I prefer Jmol. Turning on the "vectors" can simply be done in the context menu. For the scaling it is usually best to use the console (as described here), e.g.

 vector SCALE 0.03

The result looks something like this (more details about the molecule in this paper):

Another nice feature is that you can export transparent pngs using "PNGT"

write IMAGE width height PNGT n "fileName"

Then you can play around with it a little bit and create more fancy graphics (coming from this paper):

If you have any other kind of arrows you want to draw, like for example (transition) dipole moments, you can just set it up yourself in VMD. For example:

draw delete all

draw color red
draw cylinder {0 0 0} {19.28 -1.42 0.0} radius 0.4
draw cone {19.28 -1.42 0.0} {21.200001 -1.560000 0.000000} radius 0.8

draw color blue
draw cylinder {0 0 0} {-5.60 0.60 0.0} radius 0.4
draw cone {-5.600000 0.600000 0.000000} {-6.160000 0.660000 0.000000} radius 0.8

The nice thing compared to doing it in an external editor is that it also works well in 3D (assuming that you entered proper coordinates for the vector)