{"id":15395,"date":"2016-01-10T09:00:21","date_gmt":"2016-01-10T09:00:21","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=15395"},"modified":"2023-09-17T07:19:52","modified_gmt":"2023-09-17T06:19:52","slug":"ive-started-so-ill-finish-kinetic-isotope-effect-models-for-a-general-acid-as-a-catalyst-in-the-protiodecarboxylation-of-indoles","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15395","title":{"rendered":"I\u2019ve started so I\u2019ll finish. Kinetic isotope effect models for a general acid as a catalyst in the protiodecarboxylation of indoles."},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"15395\">\n<p>    <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=15295\" target=\"_blank\" rel=\"noopener\">Earlier<\/a> I explored models for the heteroaromatic electrophilic protiodecarboxylation of an 3-substituted indole, focusing on the role of water as the proton transfer and delivery agent. Next, came&nbsp;<a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=15415\" target=\"_blank\" rel=\"noopener\">models<\/a> for both water and the general <strong>base<\/strong> catalysed&nbsp;ionization of indolinones. Here I&nbsp;explore&nbsp;general <strong>acid<\/strong>&nbsp;catalysis by evaluating the properties of two possible models for decarboxylation of 3-indole carboxylic acid,&nbsp;one involving proton transfer (PT) from neutral water in the presence of&nbsp;covalent&nbsp;un-ionized HCl (<strong>1<\/strong>) and one with PT from a protonated water resulting from&nbsp;ionised HCl (<strong>2<\/strong>).<\/p>\n<p>    <a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/01\/decarbox2.svg\"><img decoding=\"async\" alt=\"Indole diazocoupling\" class=\"aligncenter size-full wp-image-14967\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/01\/decarbox2.svg\" style=\"text-align: justify;\" width=\"440\" \/><\/a><\/p>\n<p>    The original study<span id=\"cite_ITEM-15395-0\" name=\"citation\"><a href=\"#ITEM-15395-0\">[1]<\/a><\/span> noted that the rate of decarboxylation fitted well to the kinetic expression: <span style=\"color:#FF0000;\">rate = {a + b[L<sub>3<\/sub>O<sup>+<\/sup>]\/(1 + c[L<sub>3<\/sub>O<sup>+<\/sup>])}[indole]<\/span>, where L can be&nbsp;H or&nbsp;D.&nbsp;Experimentally,&nbsp;[L<sub>3<\/sub>O<sup>+<\/sup>]&nbsp;is controlled by adding a&nbsp;strong general acid such as HCl, which when the <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=13394\" target=\"_blank\" rel=\"noopener\">appropriate<\/a> number of water molecules are added<span id=\"cite_ITEM-15395-1\" name=\"citation\"><a href=\"#ITEM-15395-1\">[2]<\/a><\/span>&nbsp;fully ionizes&nbsp;to H<sub>3<\/sub>O<sup>+<\/sup>.OH<sup>&#8211;<\/sup>. Now for B3LYP+D3\/Def2-TZVPD\/SCRF=water calculations:<\/p>\n<ul>\n<li>\n        Model <strong>1&nbsp;<\/strong>takes the pure&nbsp;water model and adds HCl (blue above) <em>via<\/em> hydrogen bonding to the H<sub>2<\/sub>O&nbsp;that is transferring the proton to the indole ring. Three&nbsp;water molecules are hydrogen bonding to the carboxylate oxygens to&nbsp;create a bicyclic network in which a ring of either 8 or 10 atoms can act as the proton relay structure. The question now arises whether the proton relay takes the longer&nbsp;(red) route or the slightly shorter green route.\n    <\/li>\n<li>\n        Isomeric model <strong>2<\/strong>&nbsp;uses&nbsp;H<sub>3<\/sub>O<sup>+<\/sup>&nbsp;for&nbsp;proton transfer, with an adjacent Cl<sup>&#8211;<\/sup> to complete the ion-pair.\n    <\/li>\n<\/ul>\n<table border=\"1\">\n<tbody>\n<tr>\n<th>\n                Model\n            <\/th>\n<th>\n                &Delta;G<sup>&Dagger;<\/sup><sub>298<\/sub>&nbsp;(0.044M)\n            <\/th>\n<th>\n                DataDOIs\n            <\/th>\n<th>\n                k<sup>H<\/sup>\/k<sup><span style=\"font-size: 11px;\">D<\/span><\/sup><span id=\"cite_ITEM-15395-2\" name=\"citation\"><a href=\"#ITEM-15395-2\">[3]<\/a><\/span>\n            <\/th>\n<\/tr>\n<tr>\n<td>\n                1\n            <\/td>\n<td>\n                27.4\n            <\/td>\n<td>\n                <span id=\"cite_ITEM-15395-3\" name=\"citation\"><a href=\"#ITEM-15395-3\">[4]<\/a><\/span>,<sup>&Dagger;<\/sup><span id=\"cite_ITEM-15395-4\" name=\"citation\"><a href=\"#ITEM-15395-4\">[5]<\/a><\/span>,<sup>&dagger;<\/sup><span id=\"cite_ITEM-15395-5\" name=\"citation\"><a href=\"#ITEM-15395-5\">[6]<\/a><\/span>,<span id=\"cite_ITEM-15395-6\" name=\"citation\"><a href=\"#ITEM-15395-6\">[7]<\/a><\/span>\n            <\/td>\n<td>\n                5.69\n            <\/td>\n<\/tr>\n<tr>\n<td>\n                2\n            <\/td>\n<td>\n                16.8<sup>&Dagger;<\/sup> (14.8)<sup>&dagger;<\/sup>\n            <\/td>\n<td>\n                <span id=\"cite_ITEM-15395-4\" name=\"citation\"><a href=\"#ITEM-15395-4\">[5]<\/a><\/span>,<span id=\"cite_ITEM-15395-7\" name=\"citation\"><a href=\"#ITEM-15395-7\">[8]<\/a><\/span>,<span id=\"cite_ITEM-15395-8\" name=\"citation\"><a href=\"#ITEM-15395-8\">[9]<\/a><\/span>\n            <\/td>\n<td>\n                2.45\n            <\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>    <sup>&Dagger;<\/sup><span style=\"font-size:10px;\">Reactant as a non-ionised covalent HCl.<\/span> <sup>&dagger;<\/sup><span style=\"font-size:10px;\">reactant as an isomeric ionized H<sub>3<\/sub>O<sup>+<\/sup>.Cl<sup>&#8211;&nbsp;<\/sup>&nbsp;beng 2.0 kcal\/mol higher in energ within this solvation model. <span style=\"color:#FF0000;\">Note added in proof. A significantly lower form of the reactant has subsequently been located which increases the free energy barrier to 22.1 kcal (vis 22.0 actually measured!). Diacussion of this can be seen in the <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=15505\" target=\"_blank\" rel=\"noopener\">associated post here<\/a>.<\/span><\/span><\/p>\n<ol>\n<li>\n        An IRC for Model 1&nbsp;shows that the proton relay takes the red&nbsp;path, whereas without the HCl the green path is followed.<\/p>\n<p>            &nbsp;<\/p>\n<p>            &nbsp;<\/p>\n<p>            &nbsp;<\/p>\n<p>            <a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/01\/HCL-cova.gif\"><img decoding=\"async\" alt=\"Indole diazocoupling\" class=\"aligncenter size-full wp-image-14967\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/01\/HCL-cova.gif\" style=\"text-align: justify;\" width=\"440\" \/><\/a><\/p>\n<p>            The transition state free energy however is ..<\/p>\n<\/li>\n<li>\n        10.6<sup>&Dagger;&nbsp;<\/sup>or 12.6<sup>&dagger;<\/sup> kcal\/mol <strong>higher<\/strong> than&nbsp;model <strong>2&nbsp;<\/strong>(click on the image below to load a&nbsp;3D model).&nbsp;The general acid catalysed model is therefore preferred. The difference in free energy between the two models corresponds to a rate acceleration of &gt;10<sup>6<\/sup>,<sup>&nbsp;<\/sup>which is indeed similar to that observed<span id=\"cite_ITEM-15395-0\" name=\"citation\"><a href=\"#ITEM-15395-0\">[1]<\/a><\/span>.\n    <\/li>\n<\/ol>\n<p>    <img decoding=\"async\" alt=\"Decarboxylation using a general acid catalyst\" class=\"aligncenter size-full wp-image-14967\" onclick=\"jmolInitialize('..\/Jmol\/','JmolAppletSigned.jar');jmolSetAppletColor('white');jmolApplet([450,450],'load wp-content\/uploads\/2016\/01\/model2.log;frame 3;vectors on;vectors 4;vectors scale 8.0;color vectors green;vibration 6;');\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/01\/Model2.jpg\" style=\"text-align: justify;\" width=\"400\" \/><\/p>\n<p>    The clincher comes with calculation<span id=\"cite_ITEM-15395-2\" name=\"citation\"><a href=\"#ITEM-15395-2\">[3]<\/a><\/span> of the kinetic isotope effects (KIE).&nbsp;For general acid catalysis, they were measured as&nbsp;k<sup>H<\/sup>\/k<sup>D<\/sup> ~2.5.<span id=\"cite_ITEM-15395-0\" name=\"citation\"><a href=\"#ITEM-15395-0\">[1]<\/a><\/span><\/p>\n<ul>\n<li>\n        For model 1, using an un-ionised reactant and un-ionised transition state, the calculated KIE is 5.69 (very similar to that <a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=15295\" target=\"_blank\" rel=\"noopener\">calculated for the water catalysed reaction<\/a>, 5.66) but not a good fit to experiment.\n    <\/li>\n<li>\n        For model 2,&nbsp;using the same un-ionised reactant but an ionised transition state, KIE = 2.04, a much better fit.\n    <\/li>\n<li>\n        For model 2, using ionised reactant&nbsp;AND transition state, KIE = <span style=\"font-size:14px;\"><span style=\"color:#FF0000;\"><strong>2.45<\/strong><\/span><\/span>, an even better fit to experiment.\n    <\/li>\n<\/ul>\n<p>    So we now have&nbsp;a model for the general acid catalysed decarboxylation of a 3-indole carboxylate which agrees with both the kinetic behaviours&nbsp;and the isotope effects measured for this reaction.&nbsp;Since the barrier is a relatively large one,&nbsp;proton tunnelling may play a lesser role in this interpretation,&nbsp;and the stage is set to use this model to <em>e.g.<\/em> explore how isotope effects are indeed influenced by tuning the reactivity using ring substitutents, the original purpose of my researches all those years ago. Perhaps the catch phrase&nbsp;<em>I&rsquo;ve started so I&rsquo;ll start<\/em> is now more apposite.<\/p>\n<hr \/>\n<h4>Acknowledgments<\/h4>\n<p>This post has been cross-posted in PDF format at <a href=\"https:\/\/doi.org\/10.15200\/winn.145337.72789\" rel=\"noopener\" target=\"_blank\">Authorea<\/a>.<\/p>\n<h2>References<\/h2>\n    <ol class=\"kcite-bibliography csl-bib-body\"><li id=\"ITEM-15395-0\">B.C. Challis, and H.S. Rzepa, \"Heteroaromatic hydrogen exchange reactions. Part 9. Acid catalysed decarboxylation of indole-3-carboxylic acids\", <i>Journal of the Chemical Society, Perkin Transactions 2<\/i>, pp. 281, 1977. <a href=\"https:\/\/doi.org\/10.1039\/p29770000281\">https:\/\/doi.org\/10.1039\/p29770000281<\/a>\n\n<\/li>\n<li id=\"ITEM-15395-1\">A. Vargas\u2010Caamal, J.L. Cabellos, F. Ortiz\u2010Chi, H.S. Rzepa, A. Restrepo, and G. Merino, \"How Many Water Molecules Does it Take to Dissociate HCl?\", <i>Chemistry \u2013 A European Journal<\/i>, vol. 22, pp. 2812-2818, 2016. <a href=\"https:\/\/doi.org\/10.1002\/chem.201504016\">https:\/\/doi.org\/10.1002\/chem.201504016<\/a>\n\n<\/li>\n<li id=\"ITEM-15395-2\">H. Rzepa, \"Ionic model for general acid catalysed decarboxylation\", 2016. <a href=\"https:\/\/doi.org\/10.14469\/hpc\/204\">https:\/\/doi.org\/10.14469\/hpc\/204<\/a>\n\n<\/li>\n<li id=\"ITEM-15395-3\">H.S. Rzepa, \"C 9 H 16 Cl 1 N 1 O 6\", 2016. <a href=\"https:\/\/doi.org\/10.14469\/ch\/191792\">https:\/\/doi.org\/10.14469\/ch\/191792<\/a>\n\n<\/li>\n<li id=\"ITEM-15395-4\">H.S. Rzepa, \"C 9 H 16 Cl 1 N 1 O 6\", 2016. <a href=\"https:\/\/doi.org\/10.14469\/ch\/191795\">https:\/\/doi.org\/10.14469\/ch\/191795<\/a>\n\n<\/li>\n<li id=\"ITEM-15395-5\">H.S. Rzepa, \"C 9 H 16 Cl 1 N 1 O 6\", 2016. <a href=\"https:\/\/doi.org\/10.14469\/ch\/191794\">https:\/\/doi.org\/10.14469\/ch\/191794<\/a>\n\n<\/li>\n<li id=\"ITEM-15395-6\">H.S. Rzepa, \"C9H16ClNO6\", 2016. <a href=\"https:\/\/doi.org\/10.14469\/ch\/191767\">https:\/\/doi.org\/10.14469\/ch\/191767<\/a>\n\n<\/li>\n<li id=\"ITEM-15395-7\">H.S. Rzepa, \"C 9 H 16 Cl 1 N 1 O 6\", 2016. <a href=\"https:\/\/doi.org\/10.14469\/ch\/191790\">https:\/\/doi.org\/10.14469\/ch\/191790<\/a>\n\n<\/li>\n<li id=\"ITEM-15395-8\"><a href=\"https:\/\/doi.org\/\">https:\/\/doi.org\/<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> <!-- kcite-section 15395 -->","protected":false},"excerpt":{"rendered":"<p>Earlier I explored models for the heteroaromatic electrophilic protiodecarboxylation of an 3-substituted indole, focusing on the role of water as the proton transfer and delivery agent. Next, came&nbsp;models for both water and the general base catalysed&nbsp;ionization of indolinones. Here I&nbsp;explore&nbsp;general acid&nbsp;catalysis by evaluating the properties of two possible models for decarboxylation of 3-indole carboxylic acid,&nbsp;one [&hellip;]<\/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":[4],"tags":[1617,1626,1618,233,40,1412,1449,1608,1627],"ppma_author":[2661],"class_list":["post-15395","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-acid","tag-acids","tag-bicyclic-network","tag-carboxylic-acid","tag-free-energy","tag-functional-groups","tag-hydrogen-bond","tag-indole","tag-transition-state-free-energy"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.3 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>I\u2019ve started so I\u2019ll finish. Kinetic isotope effect models for a general acid as a catalyst in the protiodecarboxylation of indoles. - Henry Rzepa&#039;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=15395\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"I\u2019ve started so I\u2019ll finish. Kinetic isotope effect models for a general acid as a catalyst in the protiodecarboxylation of indoles. - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"Earlier I explored models for the heteroaromatic electrophilic protiodecarboxylation of an 3-substituted indole, focusing on the role of water as the proton transfer and delivery agent. Next, came&nbsp;models for both water and the general base catalysed&nbsp;ionization of indolinones. Here I&nbsp;explore&nbsp;general acid&nbsp;catalysis by evaluating the properties of two possible models for decarboxylation of 3-indole carboxylic acid,&nbsp;one [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15395\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"article:published_time\" content=\"2016-01-10T09:00:21+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2023-09-17T06:19:52+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/01\/decarbox2.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=\"3 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"I\u2019ve started so I\u2019ll finish. Kinetic isotope effect models for a general acid as a catalyst in the protiodecarboxylation of indoles. - Henry Rzepa&#039;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=15395","og_locale":"en_GB","og_type":"article","og_title":"I\u2019ve started so I\u2019ll finish. Kinetic isotope effect models for a general acid as a catalyst in the protiodecarboxylation of indoles. - Henry Rzepa&#039;s Blog","og_description":"Earlier I explored models for the heteroaromatic electrophilic protiodecarboxylation of an 3-substituted indole, focusing on the role of water as the proton transfer and delivery agent. Next, came&nbsp;models for both water and the general base catalysed&nbsp;ionization of indolinones. Here I&nbsp;explore&nbsp;general acid&nbsp;catalysis by evaluating the properties of two possible models for decarboxylation of 3-indole carboxylic acid,&nbsp;one [&hellip;]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15395","og_site_name":"Henry Rzepa&#039;s Blog","article_published_time":"2016-01-10T09:00:21+00:00","article_modified_time":"2023-09-17T06:19:52+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/01\/decarbox2.svg","type":"","width":"","height":""}],"author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"3 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15395#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15395"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"I\u2019ve started so I\u2019ll finish. 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