{"id":2828,"date":"2010-11-19T07:49:54","date_gmt":"2010-11-19T06:49:54","guid":{"rendered":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2828"},"modified":"2017-04-08T08:21:19","modified_gmt":"2017-04-08T07:21:19","slug":"can-a-cyclobutadiene-and-carbon-dioxide-co-exist-in-a-calixarene-cavity","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2828","title":{"rendered":"Can a cyclobutadiene and carbon dioxide co-exist in a calixarene cavity?"},"content":{"rendered":"
\n

On 8th August this year, I posted<\/a> on a fascinating article that had just appeared in Science[1]<\/a><\/span> in which the crystal structure was reported of two small molecules,\u00a01,3-dimethyl cyclobutadiene\u00a0and\u00a0carbon dioxide, entrapped together inside a calixarene cavity. Other journals (e.g.\u00a0Nature Chemistry<\/em>[2]<\/a><\/span> ran the article as a research highlight <\/em>(where the purpose is not a critical analysis but more of an alerting service).\u00a0A 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[3]<\/a><\/span> and also those of another independent group, Igor Alabugin and colleagues[4]<\/a><\/span>. The original authors have in turn responded [5]<\/a><\/span>. My own article on the topic will appear very shortly[6]<\/a><\/span>. You can see quite a hornet’s nest has been stirred up!<\/p>\n

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\u00a0and\u00a0carbon dioxide can co-exist as separate species inside the cavity. The first would argue that they have reacted to form a different molecule.\u00a0You can inspect the 3D coordinates<\/a> by clicking on the diagram below.<\/p>\n

\"\"

Reported X-Ray structure. Click for 3D<\/p><\/div>Barboiu et al<\/em> originally argued that these two bonds were strong<\/em> van der Waals contacts, with C-C and C-O distances of 1.5 and 1.6\u00c5 respectively, and with a OCO angle of \u00a0120\u00b0. 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<\/strong> be described as 1,3-dimethyl cyclobutadiene\u00a0and\u00a0carbon 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<\/a> based on the articles cited above and if it helps, the \u00a0original 3D coordinates, for your convenience made available above!<\/p>\n

References<\/h2>\n
  1. Y. Legrand, A. van der Lee, and M. Barboiu, \"Single-Crystal X-ray Structure of 1,3-Dimethylcyclobutadiene by Confinement in a Crystalline Matrix\", Science<\/i>, vol. 329, pp. 299-302, 2010. https:\/\/doi.org\/10.1126\/science.1188002<\/a>\n\n<\/li>\n
  2. A. Pichon, \"Structure of a strained ring\", Nature Chemistry<\/i>, 2010. https:\/\/doi.org\/10.1038\/nchem.823<\/a>\n\n<\/li>\n
  3. D. Scheschkewitz, \"Comment on \u201cSingle-Crystal X-ray Structure of 1,3-Dimethylcyclobutadiene by Confinement in a Crystalline Matrix\u201d\", Science<\/i>, vol. 330, pp. 1047-1047, 2010. https:\/\/doi.org\/10.1126\/science.1195752<\/a>\n\n<\/li>\n
  4. I.V. Alabugin, B. Gold, M. Shatruk, and K. Kovnir, \"Comment on \u201cSingle-Crystal X-ray Structure of 1,3-Dimethylcyclobutadiene by Confinement in a Crystalline Matrix\u201d\", Science<\/i>, vol. 330, pp. 1047-1047, 2010. https:\/\/doi.org\/10.1126\/science.1196188<\/a>\n\n<\/li>\n
  5. Y. Legrand, A. van der Lee, and M. Barboiu, \"Response to Comments on \u201cSingle-Crystal X-ray Structure of 1,3-Dimethylcyclobutadiene by Confinement in a Crystalline Matrix\u201d\", Science<\/i>, vol. 330, pp. 1047-1047, 2010. https:\/\/doi.org\/10.1126\/science.1195846<\/a>\n\n<\/li>\n
  6. H.S. Rzepa, \"Can 1,3-dimethylcyclobutadiene and carbon dioxide co-exist inside a supramolecular cavity?\", Chem. Commun.<\/i>, vol. 47, pp. 1851-1853, 2011. https:\/\/doi.org\/10.1039\/c0cc04023a<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

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Other journals (e.g.\u00a0Nature Chemistry ran the article as a research highlight (where the purpose is not a critical analysis […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"activitypub_content_warning":"","activitypub_content_visibility":"","activitypub_max_image_attachments":5,"activitypub_interaction_policy_quote":"anyone","activitypub_status":"","footnotes":"","jetpack_publicize_message":"","jetpack_publicize_feature_enabled":true,"jetpack_social_post_already_shared":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[4],"tags":[314,315,2648,2650,572,42],"ppma_author":[2661],"class_list":["post-2828","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-david-scheschkewitz","tag-igor-alabugin","tag-interesting-chemistry","tag-pericyclic","tag-watoc11","tag-x-ray"],"yoast_head":"\nCan a cyclobutadiene and carbon dioxide co-exist in a calixarene cavity? - Henry Rzepa's Blog<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2828\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Can a cyclobutadiene and carbon dioxide co-exist in a calixarene cavity? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"On 8th August this year, I posted on a fascinating article that had just appeared in Science in which the crystal structure was reported of two small molecules,\u00a01,3-dimethyl cyclobutadiene\u00a0and\u00a0carbon dioxide, entrapped together inside a calixarene cavity. 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