On 8th August this year, I posted on a fascinating article that had just appeared in Science (DOI: 10.1126/science.1188002), 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. Nature Chemistry, DOI: 10.1038/nchem.823) 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 (DOI:10.1126/science.1195752) and also those of another independent group, Igor Alabugin and colleagues (DOI: 10.1126/science.1196188). The original authors have in turn responded (DOI: 10.1126/science.1195846). My own article on the topic will appear very shortly (DOI: 10.1039/C0CC04023A). 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 by clicking on the diagram below.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 based on the articles cited above and if it helps, the original 3D coordinates, for your convenience made available above!