{"id":17543,"date":"2017-03-05T09:07:24","date_gmt":"2017-03-05T09:07:24","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=17543"},"modified":"2017-03-10T11:05:25","modified_gmt":"2017-03-10T11:05:25","slug":"stable-unstable-molecules-a-crystallographic-survey-of-cyclobutadienes-and-cyclo-octatetraenes","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17543","title":{"rendered":"Stable “unstable” molecules: a crystallographic survey of cyclobutadienes and cyclo-octatetraenes."},"content":{"rendered":"
\n

Cyclobutadiene is one of those small iconic molecules, the transience and instability of which was explained theoretically long before it was actually detected in 1965.[1]<\/a><\/span> Given that instability, I was intrigued as to how many crystal structures might have been reported for this ring system, along with the rather more stable congener cyclo-octatetraene. Here is what I found.<\/p>\n

The Conquest search query shown (with no disorder, no errors and R < 0.1 also specified).\u00a0\"\"<\/p>\n

There are 23 instances (February 2017 database; see DOI: 10.14469\/hpc\/2231<\/a>\u00a0for search query) of the supposedly unstable cyclobutadiene motif!<\/p>\n

\"\"<\/a><\/p>\n

The three clusters deserve explanations. The orange cluster reveals a long C-C bond (rather longer than normal C-C bonds), accompanied by short C=C bonds, as indicated by the valence bond form shown below. Take particular note that the arrow connecting the two forms is NOT a resonance arrow but an equilibrium arrow. The “bond shifting” is not fast but slow, allowing long and short bonds to be measured in a crystal structure.<\/p>\n

\"\"<\/p>\n

The rather larger blue cluster exhibits much more equal bonds. These arise from the presence of “push-pull” substituents on the ring which serve to delocalise the unfavourable cyclobutadiene ring and hence decrease the unfavourable anti-aromaticity. A typical example is shown below (EACBUT):<\/p>\n

\"\"<\/p>\n

The small red cluster shows a long C=C bond and a short C-C bond! I have commented previously<\/a> on apparently abnormally long C=C bonds, which in fact all turned out to be errors, and I suspect the same is true here. The bond orders in the indexing in the CSD data base have probably been mis-assigned, as per below for GANBII;<\/p>\n

\"\"<\/p>\n

The Conquest search query is shown (with no disorder, no errors and R < 0.1 specified) for the 8-ring, which further specifies a torsion angle about a C-C bond to determine how planar the ring might be.<\/p>\n

\"\"<\/p>\n

The “normal” cluster in the top left exhibits long C-C bonds and short C=C bonds. The colour code indicates how planar the ring is (red-blue spectrum = twisted\u00a0\u21d2 planar). The majority of examples are twisted about the C-C bond(s),\u00a0but there are a few interesting examples that are not, as shown by the blue dots. There are only a few “bond-equalised” examples in the centre; perhaps “push-pull” induced equalisation is more difficult or perhaps few examples have been made?<\/p>\n

\"\"<\/p>\n

The members of the red cluster in the bottom right all reveal short “C-C” bonds and long “C=C” bonds. Intriguingly they all also have low values of the torsion\u00a0about one C-C bond (although not always about all four C-C bonds).\u00a0A typical example (BAQVUK, DOI: 10.5517\/CC4GWWB <\/a><\/i>) is shown below. These all need careful inspection and possibly reversal of the C-C and C=C indexing.<\/p>\n

\"\" \"\"<\/p>\n

It was interesting to discover how many crystalline examples of this archetypal “unstable” cyclobutadiene motif have been made, and the means by which some of them at least have been stabilized. In the more abundant cyclo-octatetraene system, I learnt that one has to be cautious about blindly accepting the bond order designations in the database. Perhaps we might learn here that some of these have indeed been re-assigned<\/a> in the next release of the database.<\/p>\n

References<\/h2>\n
  1. L. Watts, J.D. Fitzpatrick, and R. Pettit, \"Cyclobutadiene\", Journal of the American Chemical Society<\/i>, vol. 87, pp. 3253-3254, 1965. https:\/\/doi.org\/10.1021\/ja01092a049<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    Cyclobutadiene is one of those small iconic molecules, the transience and instability of which was explained theoretically long before it was actually detected in 1965. Given that instability, I was intrigued as to how many crystal structures might have been reported for this ring system, along with the rather more stable congener cyclo-octatetraene. Here is […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":true,"_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":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2},"jetpack_post_was_ever_published":false},"categories":[1745],"tags":[561,1395,272,2003,1871,1442,1872,734],"ppma_author":[2661],"class_list":["post-17543","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining","tag-antiaromaticity","tag-chemistry","tag-cyclobutadiene","tag-instability","tag-nature","tag-physical-organic-chemistry","tag-physics","tag-search-query"],"yoast_head":"\nStable "unstable" molecules: a crystallographic survey of cyclobutadienes and cyclo-octatetraenes. - 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=17543\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Stable "unstable" molecules: a crystallographic survey of cyclobutadienes and cyclo-octatetraenes. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"Cyclobutadiene is one of those small iconic molecules, the transience and instability of which was explained theoretically long before it was actually detected in 1965. 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The simplest such system would be the triplet state of cyclobutadiene, for which a non or anti-aromatic singlet state is always found to\u2026","rel":"","context":"In "Interesting chemistry"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2019\/01\/CBD-1024x717.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":10498,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10498","url_meta":{"origin":17543,"position":1},"title":"Au and Pt \u03c0-complexes of cyclobutadiene.","author":"Henry Rzepa","date":"May 15, 2013","format":false,"excerpt":"In the preceding post, I introduced Dewar's\u00a0\u03c0-complex theory for alkene-metal compounds, outlining the molecular orbital analysis he presented, in which the filled \u03c0-MO of the alkene donates into a Ag+\u00a0empty metal orbital and back-donation occurs from a filled metal orbital into the alkene \u03c0* MO. Here I play a little\u2026","rel":"","context":"In "Hypervalency"","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"Pt-cbd","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/05\/Pt-cbd.jpeg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":2828,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2828","url_meta":{"origin":17543,"position":2},"title":"Can a cyclobutadiene and carbon dioxide co-exist in a calixarene cavity?","author":"Henry Rzepa","date":"November 19, 2010","format":false,"excerpt":"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. Other journals (e.g.\u00a0Nature Chemistry ran the article as a research highlight (where the purpose\u2026","rel":"","context":"In "Interesting chemistry"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/11\/cbd.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":4893,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4893","url_meta":{"origin":17543,"position":3},"title":"Some fun with no-go areas of chemistry: cyclobutadiene.","author":"Henry Rzepa","date":"September 18, 2011","format":false,"excerpt":"Organic chemistry has some no-go areas, where few molecules dare venture. One of them is described by a concept known as anti-aromaticity. Whereas aromatic molecules are favoured species, their anti-equivalent is avoided. I previously illustrated this (H\u00fcckel rule) with cyclopropenium anion. Now I take a look at cyclobutadiene, for which\u2026","rel":"","context":"In "Interesting chemistry"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/09\/cbdzw.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":9894,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9894","url_meta":{"origin":17543,"position":4},"title":"To be cyclobutadiene, or not to be, that is the question? You decide.","author":"Henry Rzepa","date":"March 21, 2013","format":false,"excerpt":"A quartet of articles has recently appeared on the topic of cyclobutadiene.,,,. You will find a great deal discussed there, but I can boil it down to this essence. Do the following coordinates (obtained from a (disordered) previously published x-ray refinement) correspond to a van der Waals complex of 1,3-dimethyl\u2026","rel":"","context":"In "Interesting chemistry"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":275,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=275","url_meta":{"origin":17543,"position":5},"title":"A molecule with an identity crisis: Aromatic or anti-aromatic?","author":"Henry Rzepa","date":"April 13, 2009","format":false,"excerpt":"In 1988, Wilke reported molecule 1 It was a highly unexpected outcome of a nickel-catalyzed reaction and was described as a 24-annulene with an unusual 3D shape. Little attention has been paid to this molecule since its original report, but the focus has now returned! The reason is that a\u2026","rel":"","context":"In "Interesting chemistry"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"A [24] annulene. 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