{"id":16441,"date":"2016-05-27T15:53:08","date_gmt":"2016-05-27T14:53:08","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=16441"},"modified":"2016-07-14T07:27:54","modified_gmt":"2016-07-14T06:27:54","slug":"an-alternative-mechanism-for-nucleophilic-substitution-at-silicon-using-a-tetra-alkyl-ammonium-fluoride","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16441","title":{"rendered":"An alternative mechanism for nucleophilic substitution at silicon using a tetra-alkyl ammonium fluoride."},"content":{"rendered":"
\n

In the previous post, I explored the mechanism for nucleophilic substitution at a silicon centre proceeding via<\/em> retention of configuration involving a Berry-like pseudorotation.\u00a0Here\u00a0I probe an alternative route involving inversion of configuration at the Si centre. Both stereochemical modes are known to occur, depending on the leaving group, solvent and other factors.[1]<\/a><\/span>,[2]<\/a><\/span>,[3]<\/a><\/span><\/p>\n

\"\"<\/p>\n

This alternative involves attack by F–<\/sup> along the axial trajectory of the trigonal bipyramidal Si centre, with the OR group occupying the other axial position (TS1<\/strong>).\u00a0In order to prepare the OR group for elimination with inversion of stereochemistry, the ion-pair complex has to reorganise (a process replacing the previous Berry pseudorotation necessary with for stereochemical retention) via TS2.<\/strong> And finally the OR is eliminated in TS3<\/strong>. The energetics of this pathway (\u03c9B97XD\/6-31+G(d) or Def2-TZVPPD\/SCRF=thf) are shown below, with the inversion pathway coming out lower in energy than the previously reported retention pathway.\u00a0<\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n
System<\/th>\nRelative free energy<\/th>\nDataDOI<\/th>\n<\/tr>\n
Inversion mechanism<\/th>\n<\/tr>\n
Reactants<\/td>\n0.0<\/td>\n[4]<\/a><\/span><\/td>\n<\/tr>\n
\n

TS1<\/p>\n<\/td>\n

4.9 (4.1)*<\/td>\n[5]<\/a><\/span><\/td>\n<\/tr>\n
TS2<\/td>\n3.1<\/td>\n[6]<\/a><\/span><\/td>\n<\/tr>\n
TS3<\/td>\n0.0 (-0.8)*<\/td>\n[7]<\/a><\/span><\/td>\n<\/tr>\n
Retention mechanism<\/th>\n<\/tr>\n
TS1<\/td>\n7.9 (8.3)*<\/td>\n[8]<\/a><\/span><\/td>\n<\/tr>\n
TS2<\/td>\n9.2 (8.7)*<\/td>\n[9]<\/a><\/span><\/td>\n<\/tr>\n
TS3<\/td>\n5.2 (4.9)*<\/td>\n[10]<\/a><\/span><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

* Values in parentheses are computed for the\u00a0Def2-TZVPPD basis set.<\/p>\n

The key new finding for the inversion mechanism is the ion-pair isomerisation (TS2), which is animated below. Transition states which involve no rearrangement at a bond (either formation\/cleavage or rotation) are quite rare, and it is nice to show one here.<\/p>\n

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

So the nucleophilic displacement reaction at 4-substituted silicon centres is really quite different from carbon.Two distinct associative\/elimination mechanisms proceeding through 5-coordinate silicon seem possible. For the specific case of tetra-alkyl\u00a0ammonium fluoride as nucleophile and an enolate anion as the leaving group, it appears that an inversion <\/span><\/strong>mechanism is favoured, and one gets strong indications of this from crystal structures of such 5-coordinate species. It might be nice to repeat this study with a reaction which is known to strongly favour retention of configuration.<\/p>\n

References<\/h2>\n
  1. L. Wozniak, M. Cypryk, J. Chojnowski, and G. Lanneau, \"Optically active silyl esters of phosphorus. II. Stereochemistry of reactions with nucleophiles\", Tetrahedron<\/i>, vol. 45, pp. 4403-4414, 1989. https:\/\/doi.org\/10.1016\/s0040-4020(01)89077-3<\/a>\n\n<\/li>\n
  2. L.H. Sommer, and H. Fujimoto, \"Stereochemistry of asymmetric silicon. X. Solvent and reagent effects on stereochemistry crossover in alkoxy-alkoxy exchange reactions at silicon centers\", Journal of the American Chemical Society<\/i>, vol. 90, pp. 982-987, 1968. https:\/\/doi.org\/10.1021\/ja01006a024<\/a>\n\n<\/li>\n
  3. D.N. Roark, and L.H. Sommer, \"Dramatic stereochemistry crossover to retention of configuration with angle-strained asymmetric silicon\", Journal of the American Chemical Society<\/i>, vol. 95, pp. 969-971, 1973. https:\/\/doi.org\/10.1021\/ja00784a081<\/a>\n\n<\/li>\n
  4. H. Rzepa, \"enol + Me4N(+).F(-) Reactant\", 2016. https:\/\/doi.org\/10.14469\/hpc\/565<\/a>\n\n<\/li>\n
  5. H. Rzepa, \"Di-axial elimination of F\", 2016. https:\/\/doi.org\/10.14469\/hpc\/570<\/a>\n\n<\/li>\n
  6. H.S. Rzepa, \"C 9 H 24 F 1 N 1 O 1 Si 1\", 2016. https:\/\/doi.org\/10.14469\/ch\/195052<\/a>\n\n<\/li>\n
  7. H. Rzepa, \"Di-axial elimination of O TS\", 2016. https:\/\/doi.org\/10.14469\/hpc\/567<\/a>\n\n<\/li>\n
  8. H. Rzepa, \"trimethyl silyl enol + Me4N(+).F(-) 5-coordinate intermediate F axial TS\", 2016. https:\/\/doi.org\/10.14469\/hpc\/554<\/a>\n\n<\/li>\n
  9. H. Rzepa, \"5-coordinate intermediate Berry pseudorotation TS2 New conf?\", 2016. https:\/\/doi.org\/10.14469\/hpc\/577<\/a>\n\n<\/li>\n
  10. H. Rzepa, \"trimethyl silyl enol + Me4N(+).F(-) TS\", 2016. https:\/\/doi.org\/10.14469\/hpc\/539<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    In the previous post, I explored the mechanism for nucleophilic substitution at a silicon centre proceeding via retention of configuration involving a Berry-like pseudorotation.\u00a0Here\u00a0I probe an alternative route involving inversion of configuration at the Si centre. Both stereochemical modes are known to occur, depending on the leaving group, solvent and other factors.,, This alternative involves […]<\/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":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[1086],"tags":[1782,24,40,1779,1777,1780,1783,1781,1443,1778],"ppma_author":[2661],"class_list":["post-16441","post","type-post","status-publish","format-standard","hentry","category-reaction-mechanism-2","tag-brook-rearrangement","tag-energy","tag-free-energy","tag-leaving-group","tag-nucleophilic-substitution","tag-pseudorotation","tag-si-centre","tag-sni","tag-substitution-reactions","tag-walden-inversion"],"yoast_head":"\nAn alternative mechanism for nucleophilic substitution at silicon using a tetra-alkyl ammonium fluoride. - 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=16441\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"An alternative mechanism for nucleophilic substitution at silicon using a tetra-alkyl ammonium fluoride. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"In the previous post, I explored the mechanism for nucleophilic substitution at a silicon centre proceeding via retention of configuration involving a Berry-like pseudorotation.\u00a0Here\u00a0I probe an alternative route involving inversion of configuration at the Si centre. Both stereochemical modes are known to occur, depending on the leaving group, solvent and other factors.,, This alternative involves […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16441\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2016-05-27T14:53:08+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2016-07-14T06:27:54+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/05\/siax.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":"An alternative mechanism for nucleophilic substitution at silicon using a tetra-alkyl ammonium fluoride. - 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=16441","og_locale":"en_GB","og_type":"article","og_title":"An alternative mechanism for nucleophilic substitution at silicon using a tetra-alkyl ammonium fluoride. - Henry Rzepa's Blog","og_description":"In the previous post, I explored the mechanism for nucleophilic substitution at a silicon centre proceeding via retention of configuration involving a Berry-like pseudorotation.\u00a0Here\u00a0I probe an alternative route involving inversion of configuration at the Si centre. 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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":8085,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8085","url_meta":{"origin":16441,"position":1},"title":"Secrets of a university tutor. An exercise in mechanistic logic: first d\u00e9nouement.","author":"Henry Rzepa","date":"October 28, 2012","format":false,"excerpt":"The reaction described in the previous post (below) is an unusual example of nucleophilic attack at an sp2-carbon centre, reportedly resulting in inversion of configuration. One can break it down to a sequence of up to eight individual steps, which makes teaching it far easier. But how real is that\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\/10\/triflate.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":26272,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26272","url_meta":{"origin":16441,"position":2},"title":"Pre-mechanism for the Swern Oxidation: formation of chlorodimethylsulfonium chloride.","author":"Henry Rzepa","date":"August 25, 2023","format":false,"excerpt":"The Swern oxidation is a class of \"activated\" dimethyl sulfoxide (DMSO) reaction in which the active species is a chlorodimethylsulfonium chloride salt. The mechanism of this transformation as shown in e.g. Wikipedia is illustrated below.\u2021 However, an interesting and important aspect of chemistry is not apparent in this schematic mechanism\u2026","rel":"","context":"In "Curly arrows"","block_context":{"text":"Curly arrows","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2327"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":9917,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9917","url_meta":{"origin":16441,"position":3},"title":"Concerted vs stepwise (Meisenheimer) mechanisms for aromatic nucleophilic substitution.","author":"Henry Rzepa","date":"March 25, 2013","format":false,"excerpt":"My two previous explorations of aromatic substitutions have involved an electrophile (NO+ or Li+). Time now to look at a nucleophile, representing nucleophilic aromatic substitution. The mechanism of this is thought to pass through an intermediate analogous to the Wheland for an electrophile, this time known as the Meisenheimer complex.\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":"Click for 3D.","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/03\/trinitro.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":16468,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16468","url_meta":{"origin":16441,"position":4},"title":"The geometries of 5-coordinate compounds of group 14 elements.","author":"Henry Rzepa","date":"May 30, 2016","format":false,"excerpt":"This is a follow-up to one aspect of the previous two posts dealing with nucleophilic substitution reactions at silicon. Here I look at the geometries of 5-coordinate compounds containing as a central atom 4A = Si, Ge, Sn, Pb and of the specific formula C34AO2 with a trigonal bipyramidal geometry.\u2026","rel":"","context":"In "Chemical IT"","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":10073,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10073","url_meta":{"origin":16441,"position":5},"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":[]}],"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\/16441","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=16441"}],"version-history":[{"count":27,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16441\/revisions"}],"predecessor-version":[{"id":16618,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16441\/revisions\/16618"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=16441"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=16441"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=16441"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=16441"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}