{"id":5166,"date":"2011-10-18T21:45:41","date_gmt":"2011-10-18T20:45:41","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=5166"},"modified":"2011-10-19T07:38:02","modified_gmt":"2011-10-19T06:38:02","slug":"the-perception-of-stereochemistry-a-challenging-case","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5166","title":{"rendered":"The perception of stereochemistry. A challenging case."},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"5166\">\n<p>Most representational chemistry generated on a computer requires the viewer to achieve a remarkably subtle transformation in their mind from two to three dimensions (we are not quite yet in the era of the 3D iPad!). The <a href=\"http:\/\/en.wikipedia.org\/wiki\/Cahn\u2013Ingold\u2013Prelog_priority_rules\" target=\"_blank\">Cahn-Ingold-Prelog<\/a> convention was a masterwork (which won the Nobel prize). It is shown in action for the molecule on the left below. The CIP notation was actually generated by Chemdraw, and required a fair sprinkling of wedged and hashed bonds to (try to) remove stereoambiguity and generate the labels (try it for yourself). As part of a lecture course on pericyclic reactions, I tell the students that the reaction involves a [1,3] sigmatropic migration of the red carbon and that this migration proceeds with <strong><em>inversion of configuration<\/em><\/strong> at this migrating carbon (as the selection rules require). Perceiving what the correct CIP product label should be (with inferred stereochemical labels, resolving ? into either R or S) is IMHO one of the most difficult conceptual experiences in all of organic chemistry. I have over the years struggled to find a way of revealing this in lecture notes (these struggles with the &#8220;lecture notes&#8221; will be the topic of a future post here). However, I think I may have finally cracked it; my solution is set out below!<\/p>\n<div id=\"attachment_5167\" style=\"width: 320px\" class=\"wp-caption aligncenter\"><a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/13.jpg\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-5167\" class=\"size-full wp-image-5167  \" title=\"13\" src=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/13.jpg\" alt=\"\" width=\"310\" height=\"164\" \/><\/a><p id=\"caption-attachment-5167\" class=\"wp-caption-text\">A 1,3 sigmatropic methyl migration.<\/p><\/div>\n<p>A short-cut to the answer might be to reason that if the CIP label for the reactant is (S), and we are told that the carbon migrates with inversion, we should label the product (R). Unfortunately, CIP does not work like that. Because the key carbon in the product is not connected to <em>exactly the same four surrounding ligands<\/em> as the reactant, all bets are off! Having got that one out of the way, I now uncover my new diagram.<\/p>\n<p><div id=\"attachment_5176\" style=\"width: 317px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-5176\" class=\"size-full wp-image-5176 \" title=\"13Me\" onclick=\"jmolInitialize('..\/Jmol\/');jmolSetAppletColor('yellow');jmolApplet([450,450],'load wp-content\/uploads\/2011\/10\/13Me.log; frame 3; zoom 100; connect (atomno=12) (atomno=4) PARTIAL;connect (atomno=12) (atomno=2) PARTIAL;vectors on;vectors 4;vectors scale 5.0; color vectors green; vibration 20;animation mode loop;');\" src=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/13Me.gif\" alt=\"\" width=\"307\" height=\"311\" \/><p id=\"caption-attachment-5176\" class=\"wp-caption-text\">Intrinsic reaction coordinate (IRC) for the 1,3 carbon migration. Click for transition state mode.<\/p><\/div>Keep an eye out for the CIP labels, which are generated dynamically as the IRC proceeds. It starts (S), but then the label goes as the <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=5104\" target=\"_blank\">bond<\/a> to the atom gets disconnected (formally), and reappears as (R) when the atom is reconnected to its new home. If you look carefully at the breaking and forming bond, you will perceive in effect an S<sub>N<\/sub>2 reaction taking place, with the required inversion at the carbon. The hydrogen on that carbon conveniently swings around to reinforce the perception of an inversion.<\/p>\n<p>It is worth considering how the <a href=\"http:\/\/hdl.handle.net\/10042\/to-9510\" target=\"_blank\">IRC representation<\/a> might improve upon the perception compared with the <a href=\"http:\/\/hdl.handle.net\/10042\/to-9509\" target=\"_blank\">imaginary (transition state) vibrational mode<\/a>. The latter in effect represents only a small part of that IRC, the so-called harmonic part. Most reactions deviate from such a <a href=\"http:\/\/en.wikipedia.org\/wiki\/Harmonic_oscillator\" target=\"_blank\">harmonic oscillator<\/a>, and the IRC captures that deviation. The stereochemical perception can be enhanced by showing the full (<a href=\"http:\/\/en.wikipedia.org\/wiki\/Anharmonicity\" target=\"_blank\">anharmonic<\/a>) motion of the atoms during the reaction.<\/p>\n<p>Finally, a bonus. Below you can see a [1,9] sigmatropic methyl migration. It proceeds both with inversion at the methyl, and from top to bottom faces \u00a0(antarafacially)\u00a0of the nonatetraene. A double-twist M\u00f6bius transition state.<\/p>\n<div id=\"attachment_5186\" style=\"width: 294px\" class=\"wp-caption aligncenter\"><a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/19.gif\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-5186\" class=\"size-full wp-image-5186\" title=\"19\" src=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/19.gif\" alt=\"\" width=\"284\" height=\"208\" \/><\/a><p id=\"caption-attachment-5186\" class=\"wp-caption-text\">1,9 methyl migration with double antarafaciality.<\/p><\/div>\n<!-- kcite active, but no citations found -->\n<\/div> <!-- kcite-section 5166 -->","protected":false},"excerpt":{"rendered":"<p>Most representational chemistry generated on a computer requires the viewer to achieve a remarkably subtle transformation in their mind from two to three dimensions (we are not quite yet in the era of the 3D iPad!). The Cahn-Ingold-Prelog convention was a masterwork (which won the Nobel prize). It is shown in action for the molecule [&hellip;]<\/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_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},"jetpack_post_was_ever_published":false},"categories":[],"tags":[695,694,328,2650,696,373],"ppma_author":[2661],"class_list":["post-5166","post","type-post","status-publish","format-standard","hentry","tag-cahn-ingold-prelog","tag-cip","tag-ipad","tag-pericyclic","tag-sigmatropic","tag-tutorial-material"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.7 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>The perception of stereochemistry. A challenging case. - Henry Rzepa&#039;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=5166\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The perception of stereochemistry. A challenging case. - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"Most representational chemistry generated on a computer requires the viewer to achieve a remarkably subtle transformation in their mind from two to three dimensions (we are not quite yet in the era of the 3D iPad!). The Cahn-Ingold-Prelog convention was a masterwork (which won the Nobel prize). It is shown in action for the molecule [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5166\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"article:published_time\" content=\"2011-10-18T20:45:41+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2011-10-19T06:38:02+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/13.jpg\" \/>\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=\"3 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"The perception of stereochemistry. 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From an entirely different area of chemistry, another example of this behaviour emerges; Schreiner's trapping and reactions of t-butyl-hydroxycarbene, as\u2026","rel":"","context":"In &quot;pericyclic&quot;","block_context":{"text":"pericyclic","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=559"},"img":{"alt_text":"H-mig","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/11\/H-mig.gif?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":5716,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5716","url_meta":{"origin":5166,"position":1},"title":"A modern take on pericyclic sigmatropic migrations.","author":"Henry Rzepa","date":"November 29, 2011","format":false,"excerpt":"Another common type of pericyclic reaction is the migration of hydrogen or carbon along a conjugated chain, as in the [1,3] migration of a carbon as shown below. As before, I explore the stereochemistry of the thermal and photochemical reactions. The reaction is known to proceed thermally\u00a0with inversion of configuration\u2026","rel":"","context":"In \"pericyclic\"","block_context":{"text":"pericyclic","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=pericyclic"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/11\/s.gif?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":23434,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23434","url_meta":{"origin":5166,"position":2},"title":"Deltamethrin &#8211; a polymorphed insecticide.","author":"Henry Rzepa","date":"March 24, 2021","format":false,"excerpt":"Deltamethin is a pyrethroid insecticide for control of malaria which has been used for a little while. Perhaps inevitably, mosquitoes are developing resistance to it. So what could be done about countering this? Well, perhaps surprisingly, form a polymorph!\u00a0These crystal structure isomers are often highly undesirable; thus\u00a0Ritonavir, which changed its\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","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\/2021\/03\/Screenshot-643-1024x716.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":7756,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7756","url_meta":{"origin":5166,"position":3},"title":"The ten-electron homologue of semibullvalene.","author":"Henry Rzepa","date":"September 21, 2012","format":false,"excerpt":"Semibullvalene is a molecule which undergoes a facile [3,3] sigmatropic shift. So facile that it appears this equilibrium can be frozen out at the transition state if suitable substituents are used. This is a six-electron process, which leads to one of those homologous questions; what happens with ten electrons? The\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/09\/55.svg","width":350,"height":200},"classes":[]},{"id":9090,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9090","url_meta":{"origin":5166,"position":4},"title":"A conflation of concepts: Conformation and pericyclic.","author":"Henry Rzepa","date":"January 10, 2013","format":false,"excerpt":"This is an interesting result I got when studying the [1,4] sigmatropic rearrangement of\u00a0heptamethylbicyclo-[3.1.0]hexenyl cations. It fits into the last lecture of a series on pericyclic mechanisms, and just before the first lecture on conformational analysis. This is how they join. The experiment it relates to may well be a\u2026","rel":"","context":"In \"conformational analysis\"","block_context":{"text":"conformational analysis","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=conformational-analysis"},"img":{"alt_text":"Click for  3D.","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/01\/14me.gif?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":23281,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23281","url_meta":{"origin":5166,"position":5},"title":"The Stevens rearrangement: how history gives us new insights.","author":"Henry Rzepa","date":"January 29, 2021","format":false,"excerpt":"In a recent post, I told the story of how in the early 1960s, Robert Woodward had encountered an unexpected stereochemical outcome to the reaction of a hexatriene, part of his grand synthesis of vitamin B12. He had constructed a model of the reaction he wanted to undertake, perhaps with\u2026","rel":"","context":"In &quot;Historical&quot;","block_context":{"text":"Historical","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=565"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2021\/01\/sden.jpg?resize=350%2C200&ssl=1","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\/5166","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=5166"}],"version-history":[{"count":0,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/5166\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=5166"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=5166"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=5166"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=5166"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}