{"id":7601,"date":"2012-09-12T10:49:20","date_gmt":"2012-09-12T09:49:20","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=7601"},"modified":"2012-09-12T11:26:33","modified_gmt":"2012-09-12T10:26:33","slug":"the-sn2-reaction-followed-up","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7601","title":{"rendered":"The Sn2 reaction: followed up."},"content":{"rendered":"
\n

An obvious issue to follow-up my last post on the (solvated) intrinisic reaction coordinate for the Sn2 reaction is how variation of the halogen (X) impacts upon the nature of the potential.<\/p>\n

\"\"<\/p>\n\n\n\n\n\n\n\n\n\n\n
X=F<\/th>\nX=Cl<\/th>\n<\/tr>\n
\"\"<\/td>\n\"\"<\/td>\n<\/tr>\n
X=Br<\/th>\nX=I<\/th>\n<\/tr>\n
\"\"<\/td>\n\"\"<\/td>\n<\/tr>\n
X=F<\/th>\nX=Cl<\/th>\n<\/tr>\n
\"\"<\/td>\n\"\"<\/td>\n<\/tr>\n
X=Br<\/th>\nX=I<\/th>\n<\/tr>\n
\"\"<\/td>\n\"\"<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

The change in slope of the gradient norm along the IRC is hardly noticeable for\u00a0Y=Na,\u00a0X=F, but increases up to X=I. The distance between the two halogens varies as 3.74, 4.68, 4.98, 5.40\u00c5 at the point where the gradients change character (all at the \u03c9B97XD\/6-311+G(d,p)\/SCRF=methanol level). This nicely reinforces the explanation given before<\/a>, that the dimensions of the box defined by the two halogens is too large for the small central CH3<\/sub> to fit in snugly for X=Cl,Br and I, but is not an issue with the very much smaller box with X=F.\u00a0One more variation; replacing\u00a0CH3<\/sub> with the slightly smaller NH3<\/sub>(+)<\/sup> results in the box contracting to 4.74\u00c5 (X=Br) and again the very characteristic behaviour.<\/p>\n\n\n\n
\"\"<\/td>\n\"\"<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

I should end with a quick comment on the form of the potential energy surfaces. That for the last example above is typical and looks like as below. But this shape is not what many textbooks show. These indicate that as the halide (anion) approaches the (neutral) molecule, an initial ion-dipole complex is form as a minimum, before surmounting the barrier and forming a similar complex the other side. The diagram below (and all the others) show no sign of these minima. This is because all the systems are computed as neutral ion-pairs and a solvation correction has been applied to the potential. Under these conditions, the classical form of the potential found in text books does not pertain.<\/p>\n

\"\"<\/p>\n

\n\n\n\n\n\n\n\n\n\n
Digital repository entries<\/a><\/th>\n<\/tr>\n
system<\/th>\nDspace<\/th>\nChempound<\/th>\nFigshare<\/th>\n<\/tr>\n
NH3<\/sub>(+)<\/sup>, X=Br<\/td>\n10042\/20313<\/a><\/td>\na25daa67-d409-4d38-8d35-8a009f449bc9<\/a><\/td>\n10.6084\/m9.figshare.95816<\/a><\/td>\n<\/tr>\n
CH3<\/sub>, X=F<\/td>\n10042\/20314<\/a><\/td>\ndfccf382-8c60-459c-8da0-c6efdd2b0931<\/a><\/td>\n10.6084\/m9.figshare.95817<\/a><\/td>\n<\/tr>\n
CH3<\/sub>, X=Cl<\/td>\n10042\/20315<\/a><\/td>\nd5ab33c2a-9e92-49a0-b488-f0559bbc2061<\/a><\/td>\n10.6084\/m9.figshare.95818<\/a><\/td>\n<\/tr>\n
CH3<\/sub>, X=Br<\/td>\n10042\/20316<\/a><\/td>\n5b1995f1-fef0-451b-a467-80a592081119<\/a><\/td>\n–<\/td>\n<\/tr>\n
CH3<\/sub>, X=I<\/td>\n10042\/20317<\/a><\/td>\nd9149e4e-466e-4358-9de5-67a47950eff1<\/a><\/td>\n10.6084\/m9.figshare.95819<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n
\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

An obvious issue to follow-up my last post on the (solvated) intrinisic reaction coordinate for the Sn2 reaction is how variation of the halogen (X) impacts upon the nature of the potential. X=F X=Cl X=Br X=I X=F X=Cl X=Br X=I The change in slope of the gradient norm along the IRC is hardly noticeable for\u00a0Y=Na,\u00a0X=F, […]<\/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":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":[876,843,373],"ppma_author":[2661],"class_list":["post-7601","post","type-post","status-publish","format-standard","hentry","tag-potential-energy-surfaces","tag-reaction-mechanism","tag-tutorial-material"],"yoast_head":"\nThe Sn2 reaction: followed up. - 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=7601\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The Sn2 reaction: followed up. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"An obvious issue to follow-up my last post on the (solvated) intrinisic reaction coordinate for the Sn2 reaction is how variation of the halogen (X) impacts upon the nature of the potential. X=F X=Cl X=Br X=I X=F X=Cl X=Br X=I The change in slope of the gradient norm along the IRC is hardly noticeable for\u00a0Y=Na,\u00a0X=F, […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7601\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2012-09-12T09:49:20+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2012-09-12T10:26:33+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/09\/sn2-X.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: followed up. - 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=7601","og_locale":"en_GB","og_type":"article","og_title":"The Sn2 reaction: followed up. - Henry Rzepa's Blog","og_description":"An obvious issue to follow-up my last post on the (solvated) intrinisic reaction coordinate for the Sn2 reaction is how variation of the halogen (X) impacts upon the nature of the potential. X=F X=Cl X=Br X=I X=F X=Cl X=Br X=I The change in slope of the gradient norm along the IRC is hardly noticeable for\u00a0Y=Na,\u00a0X=F, […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7601","og_site_name":"Henry Rzepa's Blog","article_published_time":"2012-09-12T09:49:20+00:00","article_modified_time":"2012-09-12T10:26:33+00:00","og_image":[{"url":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/09\/sn2-X.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=7601#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7601"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"The Sn2 reaction: followed up.","datePublished":"2012-09-12T09:49:20+00:00","dateModified":"2012-09-12T10:26:33+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7601"},"wordCount":376,"commentCount":1,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7601#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/09\/sn2-X.svg","keywords":["potential energy surfaces","Reaction Mechanism","Tutorial material"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7601#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7601","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7601","name":"The Sn2 reaction: followed up. - 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=7601#primaryimage"},"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7601#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/09\/sn2-X.svg","datePublished":"2012-09-12T09:49:20+00:00","dateModified":"2012-09-12T10:26:33+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=7601#breadcrumb"},"inLanguage":"en-GB","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7601"]}]},{"@type":"ImageObject","inLanguage":"en-GB","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7601#primaryimage","url":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/09\/sn2-X.svg","contentUrl":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/09\/sn2-X.svg"},{"@type":"BreadcrumbList","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7601#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog"},{"@type":"ListItem","position":2,"name":"The Sn2 reaction: followed up."}]},{"@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\/pDef7-1YB","jetpack-related-posts":[{"id":7580,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7580","url_meta":{"origin":7601,"position":0},"title":"The Sn2 reaction and the anomaly of carbon.","author":"Henry Rzepa","date":"September 6, 2012","format":false,"excerpt":"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\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\/09\/sn2-Na1.gif?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":783,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=783","url_meta":{"origin":7601,"position":1},"title":"Capturing penta-coordinate carbon! (Part 1).","author":"Henry Rzepa","date":"September 22, 2009","format":false,"excerpt":"The bimolecular nucleophilic substitution reaction at saturated carbon is an icon of organic chemistry, and is better known by its mechanistic label, SN2. It is normally a slow reaction, with half lives often measured in hours. This implies a significant barrier to reaction (~15-20 kcal\/mol) for the transition state, shown\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":20560,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=20560","url_meta":{"origin":7601,"position":2},"title":"Smoke and mirrors. All is not what it seems with this Sn2 reaction!","author":"Henry Rzepa","date":"April 4, 2019","format":false,"excerpt":"Previously, I explored the Graham reaction to form a diazirine. The second phase of the reaction involved an Sn2' displacement of N-Cl forming C-Cl. Here I ask how facile the simpler displacement of C-Cl by another chlorine might be and whether the mechanism is Sn2 or the alternative Sn1. The\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":25338,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25338","url_meta":{"origin":7601,"position":3},"title":"Unexpected Isomerization of Oxetane-Carboxylic Acids \u2013 a viable mechanism","author":"Henry Rzepa","date":"August 12, 2022","format":false,"excerpt":"In the previous post, I looked at the intramolecular rearrangement of the oxetane carboxylic acid to a lactone, finding the barrier to the Sn2 reaction with retention was unfeasibly high. Here I explore alternatives. This first attempt uses a second molecule of a carboxylic acid (modelled as formic acid for\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/08\/Rtn.gif?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/08\/Rtn.gif?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/08\/Rtn.gif?resize=525%2C300&ssl=1 1.5x"},"classes":[]},{"id":4002,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4002","url_meta":{"origin":7601,"position":4},"title":"The Sn1…Sn2 mechanistic continuum. The special case of neopentyl bromide","author":"Henry Rzepa","date":"May 9, 2011","format":false,"excerpt":"Introductory organic chemistry invariably features the mechanism of haloalkane solvolysis, and introduces both the Sn1 two-step mechanism, and the Sn2 one step mechanism to students. They are taught to balance electronic effects (the stabilization of carbocations) against steric effects in order to predict which mechanism prevails. It was whilst preparing\u2026","rel":"","context":"In \"free energy\"","block_context":{"text":"free energy","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=free-energy"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/05\/neopentyl-ts.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":25313,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25313","url_meta":{"origin":7601,"position":5},"title":"Unexpected Isomerization of Oxetane-Carboxylic Acids – a first look at the mechanism","author":"Henry Rzepa","date":"August 7, 2022","format":false,"excerpt":"Derek Lowe's blog has a recent post entitled A Downside to Oxetane Acids which picks up on a recent article describing how these acids are unexpectedly unstable, isomerising to a lactone at a significant rate without the apparent need for any catalyst. This is important because these types of compound\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":[]}],"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\/7601","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=7601"}],"version-history":[{"count":19,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/7601\/revisions"}],"predecessor-version":[{"id":7632,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/7601\/revisions\/7632"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=7601"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=7601"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=7601"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=7601"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}