{"id":5228,"date":"2011-10-25T08:38:38","date_gmt":"2011-10-25T07:38:38","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=5228"},"modified":"2011-11-01T08:52:10","modified_gmt":"2011-11-01T08:52:10","slug":"the-sn1-mechanism-for-a-third-time-exploration-of-the-intrinsic-reaction-coordinate","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5228","title":{"rendered":"The SN1 Mechanism for a third time. Exploration of the intrinsic reaction coordinate."},"content":{"rendered":"
\n

As the title hints, I have been here before<\/a>. The SN<\/sub>1 solvolysis mechanism of t-butyl chloride was central to the flourishing of physical organic chemistry from the 1920s onwards, and it appears early on in most introductory lecture courses and text books. There we teach that it is a two-stage mechanism. Firstly the C-Cl bond heterolyses to form a stable tertiary carbocation intermediate, which in a second stage reacts with nucleophile (water) to form e.g. t-butanol. This is contrasted with the SN<\/sub>2 mechanism<\/a>, where these two stages are conflated into a single concerted process, involving no intermediates. Here I explore an intrinsic reaction coordinate for the hydrolysis of t-butyl chloride which attempts to tease out whether this simple picture is realistic.<\/p>\n

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

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

The basic model comprises t-butyl chloride and 16 water molecules. These are subjected to a wB97XD\/6-311G(d,p) calculation<\/a> with a continuum water solvent field applied throughout. The functional is different from the one I used last time, since \u00a0I wanted one that included dispersion attractions. The basis set is also better.<\/p>\n

    \n
  1. At IRC -5, we see the first stage of the mechanism, the cleavage of the C-Cl bond. Note how the methyl flag<\/a> waves at this point.<\/li>\n
  2. At IRC 0.0 we have the transition state, at which point the gradients of the energy are precisely zero.<\/li>\n
  3. At IRC +5, we have a very slight dip\/inflexion point in the potential, but the gradients do not actually go to zero. This is the point that would correspond to the formation of a carbocation. The SN<\/sub>1 mechanism proper would require a formal intermediate here, with zero gradients.<\/li>\n
  4. At IRC ~+15, we see a new phenomenon, the attack of a water molecule on the “almost” carbocation, reflecting in fact an SN<\/sub>2 mechanism.<\/li>\n
  5. At IRC ~+20, we see a slight blip, which in fact is reorganisation of the hydrogen bonds of the surrounding water molecules, accompanying the formation of an entirely ionic chloride.<\/li>\n
  6. All these processes are animated in the diagram below, where you can see other features:\n
      \n
    1. Note the methyl rotation just after the Cl has started leaving, and another when the C-O bond formation is completing.<\/li>\n
    2. Note the hydrogen bond reorganisation near the end.<\/li>\n<\/ol>\n<\/li>\n<\/ol>\n
      \"\"

      (anharmonic) IRC for hydrolysis of t-butyl chloride. Click to see the (harmonic) transition normal mode.<\/p><\/div>\n

      As I noted in my previous post on the topic, there are other complexities, involving potential proton transfers amongst the water molecules which is not reflected here. As is not unusual in science, sometimes the most apparently simple processes turn out to have hidden complexities.<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      As the title hints, I have been here before. The SN1 solvolysis mechanism of t-butyl chloride was central to the flourishing of physical organic chemistry from the 1920s onwards, and it appears early on in most introductory lecture courses and text books. There we teach that it is a two-stage mechanism. Firstly the C-Cl bond […]<\/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":[],"tags":[2651,665,710,711,373],"ppma_author":[2661],"class_list":["post-5228","post","type-post","status-publish","format-standard","hentry","tag-historical","tag-irc","tag-sn1","tag-sn2","tag-tutorial-material"],"yoast_head":"\nThe SN1 Mechanism for a third time. Exploration of the intrinsic reaction coordinate. - 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=5228\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The SN1 Mechanism for a third time. Exploration of the intrinsic reaction coordinate. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"As the title hints, I have been here before. The SN1 solvolysis mechanism of t-butyl chloride was central to the flourishing of physical organic chemistry from the 1920s onwards, and it appears early on in most introductory lecture courses and text books. There we teach that it is a two-stage mechanism. Firstly the C-Cl bond […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5228\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2011-10-25T07:38:38+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2011-11-01T08:52:10+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/sn11.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 SN1 Mechanism for a third time. Exploration of the intrinsic reaction coordinate. - 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=5228","og_locale":"en_GB","og_type":"article","og_title":"The SN1 Mechanism for a third time. Exploration of the intrinsic reaction coordinate. - Henry Rzepa's Blog","og_description":"As the title hints, I have been here before. The SN1 solvolysis mechanism of t-butyl chloride was central to the flourishing of physical organic chemistry from the 1920s onwards, and it appears early on in most introductory lecture courses and text books. There we teach that it is a two-stage mechanism. Firstly the C-Cl bond […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5228","og_site_name":"Henry Rzepa's Blog","article_published_time":"2011-10-25T07:38:38+00:00","article_modified_time":"2011-11-01T08:52:10+00:00","og_image":[{"url":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/sn11.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=5228#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5228"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"The SN1 Mechanism for a third time. 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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":5888,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5888","url_meta":{"origin":5228,"position":2},"title":"Mechanistic morphemes. Perisolvolysis of a cyclopropyl chloride.","author":"Henry Rzepa","date":"December 13, 2011","format":false,"excerpt":"There are many treasures in Woodward and Hoffmann's (WH)\u00a0classic monograph. One such is acetolysis of \u00a0the endo chloride (green), which is much much faster than that of the exo isomer (red). The explanation given in their article (p 805) confines itself to succinctly stating that only loss of the endo\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\/2011\/12\/cpendo.gif?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":10073,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10073","url_meta":{"origin":5228,"position":3},"title":"The mechanism of ester hydrolysis via alkyl oxygen cleavage under a quantum microscope","author":"Henry Rzepa","date":"April 2, 2013","format":false,"excerpt":"My previous dissection of the mechanism for ester hydrolysis dealt with the acyl-oxygen cleavage route (red bond). There is a much rarer alternative: alkyl-oxygen cleavage (green bond) which I now place under the microscope. Here, guanidine is used as a general acid\/base, which results in a reasonable activation barrier for\u2026","rel":"","context":"In \"acetic acid\"","block_context":{"text":"acetic acid","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=acetic-acid"},"img":{"alt_text":"alkylg","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/03\/alkylg.gif?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":1135,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1135","url_meta":{"origin":5228,"position":4},"title":"The SN1 Reaction- revisited","author":"Henry Rzepa","date":"November 11, 2009","format":false,"excerpt":"In an earlier post I wrote about the iconic SN1 solvolysis reaction, and presented a model for the transition state involving 13 water molecules. Here, I follow this up with an improved molecule containing 16 water molecules, and how the barrier for this model compares with experiment. This latter is\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":"Transition state for Sn1 solvolysis of tert-butyl chloride","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/11\/sn1.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":63,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=63","url_meta":{"origin":5228,"position":5},"title":"The SN-1 Reaction live!","author":"Henry Rzepa","date":"April 3, 2009","format":false,"excerpt":"The ionization of a C-X bond (X=halogen) to form what we call a carbocation and which is known as the SN-1 reaction goes way back in the history of chemistry. Julius Steglitz was probably the first person to suggest such an ionization, back in 1899 (Steglitz, J.; Am. Chem. J.,\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":"SN-1 Reaction. Click on image to see 3D model","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/04\/sn1.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","0":null,"1":"","2":"","3":"","4":"","5":"","6":"","7":"","8":""}],"_links":{"self":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/5228","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=5228"}],"version-history":[{"count":0,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/5228\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=5228"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=5228"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=5228"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=5228"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}