{"id":5087,"date":"2011-10-12T08:16:21","date_gmt":"2011-10-12T08:16:21","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=5087"},"modified":"2011-11-28T13:14:23","modified_gmt":"2011-11-28T13:14:23","slug":"cis-butene-a-reaction-coordinate-dissected","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5087","title":{"rendered":"cis-Butene: a reaction coordinate dissected and methyl flags."},"content":{"rendered":"
\n

In two previous posts<\/a>, I have looked at why cis<\/em>-butene adopts conformation (a) rather than (b). I suggested it boiled down to electronic interactions between the methyl groups and the central alkene resulting in the formation of a H…H “topological<\/em>” bond, rather than attraction between the H…H region to form a weak chemical “bond<\/em>“. Here I take a look at what happens when that central C=C bond is gradually removed.<\/p>\n

\"\"<\/a>

Two possible conformations of cis but-2-ene.<\/p><\/div>\n

One reaction that removes this bond (marked with a magenta arrow below) is the Diels Alder \u03c0<\/sub>2s<\/sub> + \u03c0<\/sub>4s<\/sub> cycloaddition to a butadiene.<\/p>\n

\"\"<\/a>

The classic Diels Alder cycloaddition<\/p><\/div>\n

An intrinsic reaction coordinate<\/a> for this reaction looks as below: the barrier is around 25 kcal\/mol and the reaction is exothermic (SVG compatible browser needed to view figure).<\/p>\n

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

But much more interesting are the geometric responses of the two molecules as the reaction proceeds:<\/p>\n

    \n
  1. Watch first the butadiene component. Its resting conformation is gauche rather than eclipsed at the central C-C single bond, with the two double bonds rotated slightly to avoid (in this case) a close H…H contact. The first step in the reaction path is to rotate the butadiene from this gauche orientation into a eclipsed conformation at that bond.<\/li>\n
  2. Next, the action takes place on the cis<\/em>-butene. Unlike the diene, it starts off eclipsed (due to the effects noted previously) in conformation (a) above, but as the alkene starts to weaken (and the electronic effects holding it in this shape lessen), the two methyl groups rotate into conformation (b). In effect, the electronic reorganisation has moved the close H…H contact from the alkene to the diene!<\/li>\n
  3. Finally, the two C-C bonds can proceed to form, and the rest of the reaction proceeds to form the cyclohexene product.<\/li>\n
  4. Keep an eye out as well for the two methyl groups on the butadiene. Watch how they too rotate near the final stages of the reaction.<\/li>\n<\/ol>\n
    \"\"<\/a>

    Geometric responses to the cycloaddition reaction.<\/p><\/div>\n

    I have observed methyl groups in a number of reactions now via intrinsic reaction coordinates, and they do seem to be acting as flags, highlighting subtle effects in the electronic reorganisations. Rotating methyl groups should be looked at more often as harbingers of interesting effects!<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    In two previous posts, I have looked at why cis-butene adopts conformation (a) rather than (b). I suggested it boiled down to electronic interactions between the methyl groups and the central alkene resulting in the formation of a H…H “topological” bond, rather than attraction between the H…H region to form a weak chemical “bond“. Here […]<\/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":[1,4],"tags":[683,2650,373],"ppma_author":[2661],"class_list":["post-5087","post","type-post","status-publish","format-standard","hentry","category-general","category-interesting-chemistry","tag-diels-alder-cycloaddition","tag-pericyclic","tag-tutorial-material"],"yoast_head":"\ncis-Butene: a reaction coordinate dissected and methyl flags. - 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=5087\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"cis-Butene: a reaction coordinate dissected and methyl flags. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"In two previous posts, I have looked at why cis-butene adopts conformation (a) rather than (b). I suggested it boiled down to electronic interactions between the methyl groups and the central alkene resulting in the formation of a H…H “topological” bond, rather than attraction between the H…H region to form a weak chemical “bond“. Here […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5087\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2011-10-12T08:16:21+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2011-11-28T13:14:23+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/cis-butene2.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=\"2 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"cis-Butene: a reaction coordinate dissected and methyl flags. - 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=5087","og_locale":"en_GB","og_type":"article","og_title":"cis-Butene: a reaction coordinate dissected and methyl flags. - Henry Rzepa's Blog","og_description":"In two previous posts, I have looked at why cis-butene adopts conformation (a) rather than (b). I suggested it boiled down to electronic interactions between the methyl groups and the central alkene resulting in the formation of a H…H “topological” bond, rather than attraction between the H…H region to form a weak chemical “bond“. Here […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5087","og_site_name":"Henry Rzepa's Blog","article_published_time":"2011-10-12T08:16:21+00:00","article_modified_time":"2011-11-28T13:14:23+00:00","og_image":[{"url":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/cis-butene2.jpg","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=5087#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5087"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"cis-Butene: a reaction coordinate dissected and methyl flags.","datePublished":"2011-10-12T08:16:21+00:00","dateModified":"2011-11-28T13:14:23+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5087"},"wordCount":408,"commentCount":14,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5087#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/cis-butene2.jpg","keywords":["Diels Alder cycloaddition","pericyclic","Tutorial material"],"articleSection":["General","Interesting chemistry"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5087#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5087","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5087","name":"cis-Butene: a reaction coordinate dissected and methyl flags. - Henry Rzepa's Blog","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#website"},"primaryImageOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5087#primaryimage"},"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5087#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/cis-butene2.jpg","datePublished":"2011-10-12T08:16:21+00:00","dateModified":"2011-11-28T13:14:23+00:00","author":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"breadcrumb":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5087#breadcrumb"},"inLanguage":"en-GB","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5087"]}]},{"@type":"ImageObject","inLanguage":"en-GB","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5087#primaryimage","url":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/cis-butene2.jpg","contentUrl":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/cis-butene2.jpg"},{"@type":"BreadcrumbList","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5087#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog"},{"@type":"ListItem","position":2,"name":"cis-Butene: a reaction coordinate dissected and methyl flags."}]},{"@type":"WebSite","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#website","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/","name":"Henry Rzepa's Blog","description":"Chemistry with a twist","potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-GB"},{"@type":"Person","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281","name":"Henry Rzepa","image":{"@type":"ImageObject","inLanguage":"en-GB","@id":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g370be3a7397865e4fd161aefeb0a5a85","url":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","contentUrl":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","caption":"Henry Rzepa"},"description":"Henry Rzepa is Emeritus Professor of Computational Chemistry at Imperial College London.","sameAs":["https:\/\/orcid.org\/0000-0002-8635-8390"],"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?author=1"}]}},"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/pDef7-1k3","jetpack-related-posts":[{"id":5040,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5040","url_meta":{"origin":5087,"position":0},"title":"Are close H\u2026H contacts bonds? 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This conjugation is more subtle in\u2026","rel":"","context":"In "crystal_structure_mining"","block_context":{"text":"crystal_structure_mining","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1745"},"img":{"alt_text":"C-H\/alkene interaction. Click for 3D.","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/02\/cis-butene-orbitals.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":14070,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14070","url_meta":{"origin":5087,"position":3},"title":"Natural abundance kinetic isotope effects: expt. vs theory.","author":"Henry Rzepa","date":"June 3, 2015","format":false,"excerpt":"My PhD thesis involved determining kinetic isotope effects (KIE) for aromatic electrophilic substitution reactions in an effort to learn more about the nature of the transition states involved. I learnt relatively little, mostly because a transition state geometry is defined by 3N-6 variables (N = number of atoms) and its\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":9296,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9296","url_meta":{"origin":5087,"position":4},"title":"Secrets of a university tutor: unravelling a mechanism using spectroscopy.","author":"Henry Rzepa","date":"January 31, 2013","format":false,"excerpt":"It is always rewarding when one comes across a problem in chemistry that can be solved using a continuous stream of rules and logical inferences from them. The example below is one I have been using as a tutor in organic chemistry for a few years now, and I share\u2026","rel":"","context":"In \"final product\"","block_context":{"text":"final product","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=final-product"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":9424,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9424","url_meta":{"origin":5087,"position":5},"title":"The conformation of acetaldehyde: a simple molecule, a complex explanation?","author":"Henry Rzepa","date":"February 8, 2013","format":false,"excerpt":"Consider acetaldehyde (ethanal for progressive nomenclaturists). What conformation does it adopt, and why? This question was posed of me by a student at the end of a recent lecture of mine. Surely, an easy answer to give? Read on ... There really are only two possibilities, the syn\u00a0and anti. 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