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.

Thursday, September 06, 2012

IUPAC periodic table?

The cover of the latest issue of Chemistry International features a fragment of Homenatge als elements (Hommage to the Elements) by the Catalan artist Eugènia Balcells. The display in the atrium of the Physics and Chemistry Library at the University of Barcelona takes the shape of the periodic table where each chemical element is represented by its emission spectrum [1]. According to the artist’s website, it “was born as a counterpoint” to the video installation Freqüències (Frequencies).

The Periodic Table Project at the University of Waterloo, Canada is another work of art,

designed by chemistry students from all Canadian provinces and territories, 20 U.S. states, and 14 countries. It can be viewed online and is available as a printed poster.
Also, as a free app for iPad or Playbook.

Both the Periodic Table Project and Hommage to the Elements use the medium-long form periodic table. The “IUPAC Periodic Table of the Elements” as published at the back of Chemistry International (in this issue, for the first time it includes flerovium and livermorium) has the same shape. Why the quotes? Because, as a matter of fact, there is no such thing as IUPAC-approved periodic table. Jeffery Leigh wrote three years ago that “there is unlikely to be a definitive IUPAC-recommended form of the periodic table” [2]. In my humble opinion, this is unfortunate that IUPAC refuses to take a position on this matter. Eric Scerri takes a view that “IUPAC should in fact take a stance on the membership of particular groups even if this has not been the practice up to this point” [3]. To illustrate this point, he goes to address the Group 3 question. He argues that the most logical composition of this group is Sc, Y, Lu and Lr (rather than Sc, Y, La and Ac), as shown below.

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
H He
Li Be B C N O F Ne
Na Mg Al Si P S Cl Ar
K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe
Cs Ba La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
Fr Ra Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr Rf Db Sg Bh Hs Mt Ds Rg Cn Fl Lv
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32
In addition to arranging all the elements in a more correct sequence of increasing atomic numbers, the decision to move to a long-form or 32-column table forces the periodic table designer towards just one possible option regarding the question of which elements to place in group 3.

I entirely agree with that. And yet Scerri stops short of proposing that IUPAC should support the 32-column (or “long, long form”, as Leigh put it) periodic table; in fact he explicitly states that he is not suggesting a change of IUPAC policy, viz. that of doing nothing about it. Why? That would be one of the most important and immediately noticeable changes sponsored by IUPAC in decades.

The problem is, sorting out the Group 3 does not resolve the problem how to number the f-block columns. If we stick with 18 groups (blue numbering on the top of the table), that would be really unfair towards the lanthanoids and actinoids. Why don’t we simply number groups from 1 to 32 (red numbers on the bottom of the table)? Sc, Y, Lu and Lr will find themselves in Group 17. So what? It’s not that many people will miss the current Group 17 — nobody really calls these elements anything but “halogens”. And 32 is even more convenient number than 18. I think it’s about time IUPAC took the lead and said how exactly the periodic table should look like.

  1. Alvarez, S. (2012) An artist’s hommage to the elements. Chemistry International 34, 5.
  2. Leigh, J. (2009) Periodic tables and IUPAC. Chemistry International 31, 4—6.
  3. Scerri, E. (2012) Mendeleev’s periodic table is finally completed and what to do about group 3? Chemistry International 34, 28—31.