{"id":11110,"date":"2013-09-04T14:52:03","date_gmt":"2013-09-04T13:52:03","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=11110"},"modified":"2013-09-13T06:41:42","modified_gmt":"2013-09-13T05:41:42","slug":"coarctate-reactions-as-a-third-fundamental-organic-mechanistic-type","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11110","title":{"rendered":"Coarctate reactions as a third fundamental organic-mechanistic type."},"content":{"rendered":"
\n

According to Herges[1]<\/a><\/span>,[2]<\/a><\/span> the mechanism of single-step (concerted) reactions can be divided into three basic types; linear<\/strong> (e.g.<\/em> substitution, elimination etc), pericyclic<\/strong> (e.g.<\/em> Diels Alder) and a third much rarer, and hence very often overlooked type that was named coarctate<\/strong>. This is based on the topology of\u00a0bond redistribution patterns, an explicit real example[3]<\/a><\/span> illustrating:<\/p>\n

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

It happens that this reaction bears a close similarity to epoxidation using peracid<\/a>, the characteristic feature being that the central (spiro) atom has two bonds forming to it and two bonds breaking from it in both reactions.\u2020,\u2021<\/sup> I had noted for the latter reaction that in fact the bond redistribution, although concerted, was asynchronous. This asynchrony was represented by the green arrows preceding the blue ones (or vice-versa<\/em> for the reverse reaction).<\/p>\n

\"peracid1\"<\/a><\/p>\n

So here I decided to investigate if the same might be true of the coarctate reaction shown above (\u03c9B97XD\/6-311G(d,p)\/SCRF=water.[4]<\/a><\/span><\/p>\n

\"Click

Click for 3D<\/p><\/div>\n

The transition state is indeed interestingly asynchronous. The O-O bond (shown green above) is clearly the first to break; neither of the C-C bonds has really started to do so at the transition state. But the process remains resolutely concerted.<\/p>\n

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

\"coarc-IRC\"<\/p>\n

\"coarc-IRCG\"\u00a0<\/p>\n

The IRC above shows clearly that the reaction has a room-temperature barrier (i.e.<\/em> it is a very facile process). But missing really from this process is any hidden intermediate either (there is the merest hint at IRC = -2). So this reaction is interesting for<\/p>\n

    \n
  1. its classification apart from the normal two types of organic mechanism, as a coarctate type<\/li>\n
  2. Its asynchrony in the bond redistributions<\/li>\n
  3. but this asynchrony not resulting in any hidden intermediates.<\/li>\n<\/ol>\n
    \n

    \u2020<\/sup> Another example was the topic of this post<\/a>.<\/p>\n

    \u2021<\/sup> One can contrive an even higher-order reaction<\/a> (thus far un-named) in which (formally) three bonds break and three bonds form at a single atom.<\/p>\n

    References<\/h2>\n
    1. R. Herges, \"Coarctate transition states: the discovery of a reaction principle\", Journal of Chemical Information and Computer Sciences<\/i>, vol. 34, pp. 91-102, 1994. https:\/\/doi.org\/10.1021\/ci00017a011<\/a>\n\n<\/li>\n
    2. B.S. Young, R. Herges, and M.M. Haley, \"Coarctate cyclization reactions: a primer\", Chemical Communications<\/i>, vol. 48, pp. 9441, 2012. https:\/\/doi.org\/10.1039\/c2cc34026g<\/a>\n\n<\/li>\n
    3. C. Berger, C. Bresler, U. Dilger, D. Geuenich, R. Herges, H. R\u00f6ttele, and G. Schr\u00f6der, \"A Spontaneous Fragmentation: From the Criegee Zwitterion to Coarctate M\u00f6bius Aromaticity\", Angewandte Chemie International Edition<\/i>, vol. 37, pp. 1850-1853, 1998. https:\/\/doi.org\/10.1002\/(sici)1521-3773(19980803)37:13\/14<1850::aid-anie1850>3.0.co;2-b<\/a>\n\n<\/li>\n
    4. H.S. Rzepa, \"Gaussian Job Archive for C4H6O3\", 2013. https:\/\/doi.org\/10.6084\/m9.figshare.787693<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      According to Herges, the mechanism of single-step (concerted) reactions can be divided into three basic types; linear (e.g. substitution, elimination etc), pericyclic (e.g. Diels Alder) and a third much rarer, and hence very often overlooked type that was named coarctate. This is based on the topology of\u00a0bond redistribution patterns, an explicit real example illustrating: It […]<\/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":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_feature_clip_id":0,"_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":[1086],"tags":[1127],"ppma_author":[2661],"class_list":["post-11110","post","type-post","status-publish","format-standard","hentry","category-reaction-mechanism-2","tag-ozonolysis"],"yoast_head":"\nCoarctate reactions as a third fundamental organic-mechanistic type. - 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=11110\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Coarctate reactions as a third fundamental organic-mechanistic type. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"According to Herges, the mechanism of single-step (concerted) reactions can be divided into three basic types; linear (e.g. substitution, elimination etc), pericyclic (e.g. Diels Alder) and a third much rarer, and hence very often overlooked type that was named coarctate. This is based on the topology of\u00a0bond redistribution patterns, an explicit real example illustrating: It […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11110\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2013-09-04T13:52:03+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2013-09-13T05:41:42+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/09\/coarctate.svg\" \/>\n<meta name=\"author\" content=\"Henry Rzepa\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Henry Rzepa\" \/>\n\t<meta name=\"twitter:label2\" content=\"Estimated reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"2 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Coarctate reactions as a third fundamental organic-mechanistic type. - Henry Rzepa's Blog","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11110","og_locale":"en_GB","og_type":"article","og_title":"Coarctate reactions as a third fundamental organic-mechanistic type. - Henry Rzepa's Blog","og_description":"According to Herges, the mechanism of single-step (concerted) reactions can be divided into three basic types; linear (e.g. substitution, elimination etc), pericyclic (e.g. Diels Alder) and a third much rarer, and hence very often overlooked type that was named coarctate. This is based on the topology of\u00a0bond redistribution patterns, an explicit real example illustrating: It […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11110","og_site_name":"Henry Rzepa's Blog","article_published_time":"2013-09-04T13:52:03+00:00","article_modified_time":"2013-09-13T05:41:42+00:00","og_image":[{"url":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/09\/coarctate.svg","type":"","width":"","height":""}],"author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"2 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11110#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11110"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Coarctate reactions as a third fundamental organic-mechanistic type.","datePublished":"2013-09-04T13:52:03+00:00","dateModified":"2013-09-13T05:41:42+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11110"},"wordCount":337,"commentCount":2,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11110#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/09\/coarctate.svg","keywords":["Ozonolysis"],"articleSection":["reaction mechanism"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11110#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11110","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11110","name":"Coarctate reactions as a third fundamental organic-mechanistic type. - 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This molecule has three F atoms on one S, and only one on the other; FSSF3. But all four S-F bonds are of different length. Lindquist and Dunning\u00a0claim that the minimum\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\/09\/S2F4.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":20354,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=20354","url_meta":{"origin":11110,"position":1},"title":"Epoxidation of ethene: a new substituent twist.","author":"Henry Rzepa","date":"December 21, 2018","format":false,"excerpt":"Five years back,\u00a0I speculated about the mechanism of the epoxidation of ethene by a peracid, concluding that kinetic isotope effects provided interesting evidence that this mechanism is highly asynchronous and involves a so-called \"hidden intermediate\". Here I revisit this reaction in which a small change is applied to the atoms\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\/2018\/12\/imine2.gif?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":13174,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13174","url_meta":{"origin":11110,"position":2},"title":"Cyclopropanation: the mechanism of the Simmons\u2013Smith reaction.","author":"Henry Rzepa","date":"December 14, 2014","format":false,"excerpt":"These posts contain the computed potential energy surfaces for a fair few \"text-book\" reactions. Here I chart the course of the cyclopropanation of alkenes using the Simmons-Smith reagent, as\u00a0prepared from di-iodomethane using zinc metal insertion into a C-I bond. Two reactions it can be compared with are the epoxidation of\u2026","rel":"","context":"In "reaction mechanism"","block_context":{"text":"reaction mechanism","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1086"},"img":{"alt_text":"Click for 3D","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/12\/SS-react1.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":16402,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16402","url_meta":{"origin":11110,"position":3},"title":"The mechanism of silylether deprotection using a tetra-alkyl ammonium fluoride.","author":"Henry Rzepa","date":"May 25, 2016","format":false,"excerpt":"The substitution of a nucleofuge (a good leaving group) by a nucleophile at a carbon centre\u00a0occurs with inversion\u00a0of configuration at the carbon, the mechanism being known by\u00a0the term\u00a0SN2\u00a0(a story I have also told\u00a0in this post). Such displacement at silicon famously proceeds by a quite different mechanism, which\u00a0I here quantify with\u2026","rel":"","context":"In "reaction mechanism"","block_context":{"text":"reaction mechanism","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1086"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":10743,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10743","url_meta":{"origin":11110,"position":4},"title":"Mechanism of the Boekelheide rearrangement","author":"Henry Rzepa","date":"June 26, 2013","format":false,"excerpt":"A reader asked me about the mechanism of\u00a0the reaction of 2-picoline N-oxide with acetic anhydride to give 2-acetoxymethylpyridine (the\u00a0Boekelheide Rearrangement). He wrote \"\u00a0I don't understand why the system should prefer to go via fragmentation-recombination (... the evidence being that\u00a0oxygen labelling shows scrambling)\u00a0when there is an easy concerted pathway available (...\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":"Boek1","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/06\/Boek1.gif?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":8375,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8375","url_meta":{"origin":11110,"position":5},"title":"The regiospecificity of di-imide reduction of an alkene.","author":"Henry Rzepa","date":"November 25, 2012","format":false,"excerpt":"Not a few posts on this blog dissect the mechanisms of well known text-book reactions. But one reaction type where there are few examples on these pages are reductions. These come in three types; using electrons, using a hydride anion and using di-hydrogen. Here I first take a closer look\u2026","rel":"","context":"In \"free energy discrimination\"","block_context":{"text":"free energy discrimination","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=free-energy-discrimination"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/11\/diimide.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","author_category":"1","first_name":"Henry","last_name":"Rzepa","user_url":"https:\/\/orcid.org\/0000-0002-8635-8390","job_title":"","description":"Henry Rzepa is Emeritus Professor of Computational Chemistry at Imperial College London."}],"_links":{"self":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/11110","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=11110"}],"version-history":[{"count":32,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/11110\/revisions"}],"predecessor-version":[{"id":11195,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/11110\/revisions\/11195"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=11110"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=11110"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=11110"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=11110"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}