Imperial College London

Henry Rzepa

On 8th August this year, [I
posted](http://www.ch.ic.ac.uk/rzepa/blog/?p=2355){target="_blank"} on a
fascinating article that had just appeared in
Science\[cite\]10.1126/science.1188002\[/cite\] in which the crystal
structure was reported of two small molecules, 1,3-dimethyl
cyclobutadiene and carbon dioxide, entrapped together inside a
calixarene cavity. Other journals (e.g. N*ature
Chemistry*\[cite\]10.1038/nchem.823\[/cite\] ran the article as a
*research highlight* (where the purpose is not a critical analysis but
more of an alerting service). A colleague, David Scheschkewitz, pointed
me to the article. We both independently analyzed different aspects, and
first David, and then I then submitted separate articles for publication
describing what we had found. Science today published both David's
thoughts\[cite\]10.1126/science.1195752\[/cite\] and also those of
another independent group, Igor Alabugin and
colleagues\[cite\]10.1126/science.1196188\[/cite\]. The original authors
have in turn responded \[cite\]10.1126/science.1195846\[/cite\]. My own
article on the topic will appear very
shortly\[cite\]10.1039/C0CC04023A\[/cite\]. You can see quite a hornet's
nest has been stirred up!

At issue is whether the two bonds (indicated with arrows below) are best
described as normally covalent, or very much weaker van der Waals
contacts, or essentially non-interacting atoms. The last two
interpretations would sustain the claim that 1,3-dimethyl
cyclobutadiene and carbon dioxide can co-exist as separate species
inside the cavity. The first would argue that they have reacted to form
a different molecule. You can [inspect the 3D
coordinates](http://www.ch.ic.ac.uk/rzepa/blog/?p=3154){target="_blank"}
by clicking on the diagram below.

::: {#attachment_2830 .wp-caption .aligncenter style="width: 304px"}
![](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2010/11/cbd.jpg "cbd"){.size-full
.wp-image-2830 loading="lazy" decoding="async"
aria-describedby="caption-attachment-2830"
onclick="jmolInitialize('../Jmol/',true);jmolSetAppletColor('yellow');jmolApplet([600,600],'load wp-content/uploads/2010/11/764868.cif;');"
width="294" height="228"}

Reported X-Ray structure. Click for 3D
:::

Barboiu *et al* originally argued that these two bonds were *strong* van
der Waals contacts, with C-C and C-O distances of 1.5 and 1.6Å
respectively, and with a OCO angle of  120°. The various responses to
this claim tend to the view that these distances/angles clearly
represent new covalent (or partially ionic-covalent) bonds, and that the
combined species **cannot** be described as 1,3-dimethyl
cyclobutadiene and carbon dioxide. There is obviously much more to it
than that (including a detailed analysis of the errors present in a
partially disordered crystal structure). So [make your own minds
up](http://quixote.wikispot.org/The_Cyclobutadiene_mysteries){target="_blank"}
based on the articles cited above and if it helps, the  original 3D
coordinates, for your convenience made available above!

::: {.wp_orcid_field}
[https://orcid.org/0000-0002-8635-8390](https://orcid.org/0000-0002-8635-8390){target="_blank"
rel="author"}
:::


On 8th August this year, I posted on a fascinating article that had just appeared in Science[cite]10.1126/science.1188002[/cite] in which the crystal structure was reported of two small molecules, 1,3-dimethyl cyclobutadiene and carbon dioxide, entrapped together inside a calixarene cavity.

Publicaciones de Rogue Scholar

Can a cyclobutadiene and carbon dioxide co-exist in a calixarene cavity?