{"id":9894,"date":"2013-03-21T13:12:48","date_gmt":"2013-03-21T13:12:48","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=9894"},"modified":"2014-01-17T07:40:37","modified_gmt":"2014-01-17T07:40:37","slug":"to-be-cyclobutadiene-or-not-to-be-that-is-the-question-you-decide","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9894","title":{"rendered":"To be cyclobutadiene, or not to be, that is the question? You decide."},"content":{"rendered":"
\n

A quartet of articles has recently appeared on the topic of cyclobutadiene.[1]<\/a><\/span>,[2]<\/a><\/span>,[3]<\/a><\/span>,[4]<\/a><\/span>. 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<\/a> published[5]<\/a><\/span> x-ray refinement) correspond to a van der Waals complex<\/em><\/strong> of 1,3-dimethyl cyclobutadiene and carbon dioxide, or do they instead represent a covalent interaction<\/strong><\/em> between these two components resulting in a compound with the chemical name 2-oxabicyclo[2.2.0]hex-5-en-3-one (i.e.<\/em> not a cyclobutadiene)?<\/p>\n

\"Click

Click for 3D. The unconnected atoms are the result of disordered partial occupancy.<\/p><\/div>\n

The two bonds to concentrate on are shown in gold; a O…C pair with a distance of 1.61\u00c5 as obtained from the x-ray refinement and a C…C pair with a distance of 1.5\u00c5 (and if you want to go further, the O=C=O bond angle). I list below values obtained from the wonderful Webelements<\/a> site. Using these values, this makes a van der Waals O…C contact 3.22\u00c5 and a C…C contact 3.40\u00c5 and covalent values of respectively 1.38\u00c5 and 1.5\u00c5.<\/p>\n\n\n\n\n\n
Element<\/td>\nCovalent radius, \u00c5<\/td>\nvan der Waals radius<\/td>\n<\/tr>\n
C<\/td>\n0.75<\/td>\n1.70<\/td>\n<\/tr>\n
O<\/td>\n0.63<\/td>\n1.52<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

According to chemistry convention, we classify the interaction between a pair of atoms according to which category best fits the observed distance. So this should allow you to decide if the molecule is a van der Waals complex of 1,3-dimethyl cyclobutadiene and carbon dioxide or the covalent system 2-oxabicyclo[2.2.0]hex-5-en-3-one.\u00a0<\/p>\n

Oh, if the observed\u00a0O…C pair with a distance of 1.61\u00c5 does not seem to perfectly fit either category above, one of the quartet of articles above[1]<\/a><\/span> offers the explanation of an unusual\u00a0\u03c0-anomeric effect lengthening the C…O bond in 2-oxabicyclo[2.2.0]hex-5-en-3-one\u00a0slightly beyond the standard covalent distance. Of course, if the system were to be a van der Waals complex, that explanation cannot apply.<\/p>\n

References<\/h2>\n
  1. H.S. Rzepa, \"A Computational Evaluation of the Evidence for the Synthesis of 1,3\u2010Dimethylcyclobutadiene in the Solid State and Aqueous Solution\", Chemistry \u2013 A European Journal<\/i>, vol. 19, pp. 4932-4937, 2013. https:\/\/doi.org\/10.1002\/chem.201102942<\/a>\n\n<\/li>\n
  2. M. Shatruk, and I.V. Alabugin, \"Reinvestigation of \u201cSingle\u2010Crystal X\u2010ray Structure of 1,3\u2010dimethylcyclobutadiene\u201d\", Chemistry \u2013 A European Journal<\/i>, vol. 19, pp. 4942-4945, 2013. https:\/\/doi.org\/10.1002\/chem.201103017<\/a>\n\n<\/li>\n
  3. Y. Legrand, D. Dumitrescu, A. Gilles, E. Petit, A. van\u2005der\u2005Lee, and M. Barboiu, \"A Constrained Disorder Refinement: \u201cReinvestigation of \u201cSingle\u2010Crystal X\u2010ray Structure of 1,3\u2010Dimethylcyclobutadiene\u201d by M. Shatruk and I.\u2005V. Alabugin\u201d\", Chemistry \u2013 A European Journal<\/i>, vol. 19, pp. 4946-4950, 2013. https:\/\/doi.org\/10.1002\/chem.201203234<\/a>\n\n<\/li>\n
  4. Y. Legrand, D. Dumitrescu, A. Gilles, E. Petit, A. van\u2005der\u2005Lee, and M. Barboiu, \"Reply to A Computational Evaluation of the Evidence for the Synthesis of 1,3\u2010Dimethylcyclobutadiene in Solid State and Aqueous Solution\u2014Beyond the Experimental Reality\", Chemistry \u2013 A European Journal<\/i>, vol. 19, pp. 4938-4941, 2013. https:\/\/doi.org\/10.1002\/chem.201203235<\/a>\n\n<\/li>\n
  5. 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<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    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 cyclobutadiene and carbon dioxide, or […]<\/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":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[4],"tags":[1014,272,1029,42],"ppma_author":[2661],"class_list":["post-9894","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-crystallography","tag-cyclobutadiene","tag-waals-complex","tag-x-ray"],"yoast_head":"\nTo be cyclobutadiene, or not to be, that is the question? You decide. - 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=9894\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"To be cyclobutadiene, or not to be, that is the question? You decide. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"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. 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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":2828,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2828","url_meta":{"origin":9894,"position":1},"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":10498,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10498","url_meta":{"origin":9894,"position":2},"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":10733,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10733","url_meta":{"origin":9894,"position":3},"title":"Is dicarbon (C2) a molecule of chemical interest?","author":"Henry Rzepa","date":"July 3, 2013","format":false,"excerpt":"C2\u00a0(dicarbon) is certainly interesting from a theoretical point of view. Whether or not it can be described as having a quadruple bond has induced much passionate discussion,,,. Its occurrence in space and in flames is also well-known. But does it have what might be called a conventional chemistry? Other highly\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":"Click for 3D","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/07\/LaOsC1.jpeg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":17829,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17829","url_meta":{"origin":9894,"position":4},"title":"First, hexacoordinate carbon – now pentacoordinate nitrogen?","author":"Henry Rzepa","date":"March 25, 2017","format":false,"excerpt":"A few years back I followed a train of thought here which ended with hexacoordinate carbon, then a hypothesis rather than a demonstrated reality. That reality was recently confirmed via a crystal structure,\u00a0DOI:10.5517\/CCDC.CSD.CC1M71QM. Here is a\u00a0similar proposal for\u00a0penta-coordinate nitrogen. First, a search of the CSD (Cambridge structure database) for such\u00a0nitrogen.\u2026","rel":"","context":"In "Bond slam"","block_context":{"text":"Bond slam","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2237"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":8246,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8246","url_meta":{"origin":9894,"position":5},"title":"Thalidomide. The role of water in the mechanism of its aqueous racemisation.","author":"Henry Rzepa","date":"November 10, 2012","format":false,"excerpt":"Thalidomide is a chiral molecule, which was sold in the 1960s as a sedative in its (S,R)-racemic form. The tragedy was that the (S)-isomer was tetragenic, and only the (R) enantiomer acts as a sedative. What was not appreciated at the time is that interconversion of the (S)- and (R)\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\/2012\/11\/thal1.jpg?resize=350%2C200","width":350,"height":200},"classes":[]}],"jetpack_likes_enabled":false,"authors":[{"term_id":2661,"user_id":1,"is_guest":0,"slug":"admin","display_name":"Henry Rzepa","avatar_url":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/9894","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=9894"}],"version-history":[{"count":11,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/9894\/revisions"}],"predecessor-version":[{"id":11930,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/9894\/revisions\/11930"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=9894"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=9894"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=9894"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=9894"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}