{"id":7580,"date":"2012-09-06T16:31:08","date_gmt":"2012-09-06T15:31:08","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=7580"},"modified":"2012-09-06T16:40:45","modified_gmt":"2012-09-06T15:40:45","slug":"the-sn2-reaction-and-the-anomaly-of-carbon","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7580","title":{"rendered":"The Sn2 reaction and the anomaly of carbon."},"content":{"rendered":"
\n

It was three years ago that I first blogged on the topic of the Sn2 reaction<\/a>. Matthias Bickelhaupt<\/a> had suggested that the Sn2 reaction involving displacement at a carbon atom was an anomaly; the true behaviour was in fact exhibited by the next element down in the series, silicon. The pentacoordinate species shown below (X=Si) is naturally a minimum<\/strong>, and the fact that for carbon (X=C) one gets instead a transition state<\/strong> resulting in a significant thermal barrier (~ 20 kcal\/mol) was a manifestation of abnormal<\/em> behaviour.<\/p>\n

\"\"<\/p>\n

The argument was that carbon as an atom was too small to fit snugly into a box of width ~5\u00c5 defined by the positions of two e.g. bromine atoms at more or less their closest possible approach, and instead rattled around between the two halogens, needing to surmount a barrier at the midpoint of the box. Silicon on the other hand being larger, fitted nicely into this box at the centre, and thus being unable to rattle around represented instead a minimum in the potential energy surface. I note (parenthetically) that a similar reason is often used to explain why hydrogen bonds to F are both rare and weak, whereas those to O are common and strong.<\/p>\n

As part of a project to create a library of reaction mechanism animations<\/a>, I calculated the IRC for the reaction<\/a> above (X=C). This one is slightly different from those one may find in the research literature and textbooks; the counter-ion (Y=Na+<\/sup>) is also included so as to create a neutral system<\/a> overall. The method is the usual \u03c9B97XD\/6-311+G(d,p)\/SCRF=water.<\/p>\n

\"\"<\/p>\n

If you watch carefully, you will see that at the early and late stages of the reaction, the bromine moves, but during the middle part of the reaction both bromine atoms are absolutely stationary and it is the carbon now that adopts the motion, rattling between the two bromine atoms. This aspect can also be seen very clearly in the two plots below:\"\" \"\"<\/p>\n

Note in particular how the gradient norm plot changes in character at IRC\u00a0\u00b1 3; the central region represents motion of carbon inside the “box”, the region outside of the box that of the bromine. I think its fascinating how such an apparently simple reaction can carry such insight into molecular behaviour.<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

It was three years ago that I first blogged on the topic of the Sn2 reaction. Matthias Bickelhaupt had suggested that the Sn2 reaction involving displacement at a carbon atom was an anomaly; the true behaviour was in fact exhibited by the next element down in the series, silicon. The pentacoordinate species shown below (X=Si) […]<\/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":[4],"tags":[141,142,843],"ppma_author":[2661],"class_list":["post-7580","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-matthias-bickelhaupt","tag-potential-energy-surface","tag-reaction-mechanism"],"yoast_head":"\nThe Sn2 reaction and the anomaly of carbon. - 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=7580\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The Sn2 reaction and the anomaly of carbon. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"It was three years ago that I first blogged on the topic of the Sn2 reaction. Matthias Bickelhaupt had suggested that the Sn2 reaction involving displacement at a carbon atom was an anomaly; the true behaviour was in fact exhibited by the next element down in the series, silicon. The pentacoordinate species shown below (X=Si) […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7580\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2012-09-06T15:31:08+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2012-09-06T15:40:45+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/09\/sn2.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":"The Sn2 reaction and the anomaly of carbon. - 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=7580","og_locale":"en_GB","og_type":"article","og_title":"The Sn2 reaction and the anomaly of carbon. - Henry Rzepa's Blog","og_description":"It was three years ago that I first blogged on the topic of the Sn2 reaction. Matthias Bickelhaupt had suggested that the Sn2 reaction involving displacement at a carbon atom was an anomaly; the true behaviour was in fact exhibited by the next element down in the series, silicon. 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This is a difficult question to answer with any precision, largely because our concept of a bond derives from trying to define what the properties of\u2026","rel":"","context":"In "Hypervalency"","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"The Sn2 transition state","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/09\/sn2.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":7580,"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":5166,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5166","url_meta":{"origin":7580,"position":4},"title":"The perception of stereochemistry. A challenging case.","author":"Henry Rzepa","date":"October 18, 2011","format":false,"excerpt":"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\u2026","rel":"","context":"In \"Cahn-Ingold-Prelog\"","block_context":{"text":"Cahn-Ingold-Prelog","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=cahn-ingold-prelog"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/13.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":845,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=845","url_meta":{"origin":7580,"position":5},"title":"It’s penta-coordinate carbon Spock- but not as we know it!","author":"Henry Rzepa","date":"September 30, 2009","format":false,"excerpt":"In the previous two posts, I noted the recent suggestion of how a stable frozen SN2 transition state might be made. This is characterised by a central carbon with five coordinated ligands. 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