Friday, September 21, 2012

Visualising hexabenzocoronene

A few years ago, I wrote that we do not know how to draw ferrocene or a nitro group. (Still true.) Is the situation with polycyclic aromatic hydrocarbons any better?

Take hexabenzo[bc,ef,hi,kl,no,qr]coronene, one of the subjects of the single-molecule visualisation study published last week in Science [1]. One way to draw it shown in diagram (a):


I chose this one (out of many other possible Kekulé representations) because I can reproduce it on a paper napkin (beermat, Post-it note, you name it). If you look carefully, you will notice that the central ring and the six outermost rings are connected with single bonds.


Continuing the paper-napkin-doodle argument, it is even easier to draw a circle inside of each ring as in all-delocalised representation (b). However, that would not be a preferred diagram from IUPAC point of view [2, GR-6.5]: for example, benzene is acceptable but is preferred. Moreover, “it is generally not acceptable to use curves in two adjacent fused rings”. Still, I’d stick with circles.

The question is, do I have to draw a circle within each ring? Of course not. If I draw seven aromatic rings and connect the with single bonds as shown in (c), the resulting structure will be the same. In this way, I can even save some ink (graphite, chalk, etc.)


Without the circles, the six rings that surround the central ring in (c) start to look, well, more empty. Using the noncontact atomic force microscopy (NC-AFM), the team behind the study [1] were able to show (and in this case “to show” really means “to show”), that those rings are indeed slightly larger. The C—C bonds in the central ring (i-bonds, 1.417 Å) are 0.03 Å shorter than the bonds connecting that ring with the six outermost rings (j-bonds, 1.447 Å).

  1. Gross, L., Mohn, F., Moll, N., Schuler, B., Criado, A., Guitián, E., Peña, D., Gourdon, A. and Meyer, G. (2012) Bond-order discrimination by atomic force microscopy. Science 337, 1326—1329.
  2. Brecher, J. (2008) Graphical representation standards for chemical structure diagrams (IUPAC Recommendations 2008). Pure Appl. Chem. 80, 277—410.

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