{"id":19828,"date":"2018-08-08T07:41:36","date_gmt":"2018-08-08T06:41:36","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=19828"},"modified":"2022-12-11T10:30:05","modified_gmt":"2022-12-11T10:30:05","slug":"the-white-city-trio-the-formation-of-an-amide-from-an-acid-and-an-amine-in-non-polar-solution-updated","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19828","title":{"rendered":"The “White City Trio” – The formation of an amide from an acid and an amine in non-polar solution (updated)."},"content":{"rendered":"
\n

White City is a small area in west london created as an exhibition site in 1908, morphing over the years into an Olympic games venue, a greyhound track, the home nearby of the BBC (British Broadcasting Corporation) and most recently the new western campus for Imperial College London.\u2663<\/sup> The first Imperial department to move into the MSRH (Molecular Sciences Research Hub) building is chemistry. As a personal celebration of this occasion, I here dedicate three transition states located during my first week of occupancy there, naming them the White City trio following earlier\u00a0inspiration<\/a> by a string trio<\/a> and their own instruments.<\/p>\n

The chemistry revisits the mechanism of amide formation from an acid and an amine, which I first described<\/a> on this blog about four years ago. I had constructed a model of one amine and one carboxylic acid, to which I added a further acid in recognition that proton transfers are a key aspect of the mechanism. When the model is quantified using quantum calculations (\u03c9B97XD\/6-311G(d,p)\/SCRF=p-toluene) it resulted in a free energy barrier\u00a0\u0394G298<\/sub>\u2021<\/sup> of about 22 kcal\/mol. Re-reading what I wrote, I see I did rather gloss over this value, which implies a decently rapid reaction! In fact, the reaction occurs relatively slowly at the temperature of refluxing toluene. Perhaps some alarm bells should have been tinkling at this stage (although\u00a0the sluggish reaction might for example instead be due to poor solubility) and so here I have a rethink of the model used to see if that modest barrier really is correct.<\/p>\n

The new premise is to test if the required proton transfers can instead be mediated using a second molecule of amine instead of acid; thus two molecules of carboxylic acid are now accompanied by two of amine, one of which will be used to transfer protons. The second acid is retained to facilitate comparison. As before, the mechanism is characterised by three transition states and two tetrahedral intermediates. The new mechanism is summarised below, with TS1-3<\/strong><\/span> being the White City Trio.\"\"<\/p>\n

The free energies are summarised in the table below.\u00a0TS3, the rate limiting step, is slightly lower in energy if the amine is used for the proton transfer than via<\/em> carboxylic acid. This is the wrong direction; we really want the barrier to increase to explain the relative difficulty of the reaction as observed in refluxing toluene! Fear not however, the new barrier is indeed a much more sluggish 28.6 kcal\/mol (30.5 using a larger basis set).<\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
\n

Species<\/p>\n

(FAIR Data DOI\u00a010.14469\/hpc\/4598<\/a>)<\/p>\n<\/th>\n

\n

\u0394G298<\/sub> (\u0394G298<\/sub>\u2021<\/sup>)<\/p>\n

kcal\/mol<\/p>\n<\/th>\n

\n

Structure<\/p>\n<\/th>\n<\/tr>\n

Ionic reactants<\/td>\n-649.737562<\/a>\u2665<\/sup> (0.0)<\/td>\n\"\"<\/td>\n<\/tr>\n
TS1 (N-C bond formation via acid PT)<\/td>\n-649.702436<\/a> (22.0)<\/td>\n\"\"<\/td>\n<\/tr>\n
TS1 (N-C bond formation via amine PT),\u00a0the “White City”<\/td>\n-649.702307<\/a> (22.1)<\/td>\n\"\"<\/td>\n<\/tr>\n
TI1 from TS1<\/td>\n-649.709938<\/a> (17.3)<\/td>\n\"\"<\/td>\n<\/tr>\n
TS2 (PT from N to O via acid PT)<\/td>\n-649.713027<\/a> (15.4)<\/td>\n\"\"<\/td>\n<\/tr>\n
TS2 (PT from N to O via amine PT),\u00a0the “White City”<\/td>\n-649.706042<\/a><\/td>\n\"\"<\/td>\n<\/tr>\n
TI2 from TS2<\/td>\n-649.711481<\/a> (16.4)<\/td>\n\"\"<\/td>\n<\/tr>\n
TS3 (O-C bond cleavage via amine PT), the “White City”<\/td>\n-649.691918<\/a> (28.6) [30.5]\u2021<\/sup><\/td>\n\"\"<\/td>\n<\/tr>\n
TS3 (O-C bond cleavage via acid PT)<\/td>\n-649.689910<\/a> (29.9)<\/td>\n\"\"<\/td>\n<\/tr>\n
Non-ionic product from TS3<\/td>\n-649.732417<\/a> (+3.2)<\/td>\n\"\"<\/td>\n<\/tr>\n
Ionic product after PT<\/td>\n-649.741246<\/a> (-2.3)<\/td>\n\"\"<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

How did this happen? It’s the reactants<\/a>! The original reactant model was based on the known structure of acetic acid dimer, with an amine weakly hydrogen bonded. Adding an extra amine now allows an entirely new motif to form, in which the amine disrupts the acetic dimer to form a cyclic system with a pair of very strong (-)O-H-N(+)-H-O(-) hydrogen bond units.\u2020 The original model did not have sufficient components to fully allow this to happen.<\/p>\n

\"\"So the White City Trio achieve a performance which helps explain why a reaction is sluggish rather than facile (normally one strives to show the opposite). Perhaps however it should be the White City quartet, in recognition that the reactant also had a role to play?<\/p>\n

\n

\u2663<\/sup>A photograph of the building under construction can be seen here<\/a>. \u2021<\/sup>Def2-TZVPPD basis set. \u2020<\/sup>There does not appear to be a recorded structure for methylammonium acetate. We hope to obtain one to check what the extended structure actually is. \u2665<\/sup>I will elaborate an interesting new use of this value in a separate post<\/a>.<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

White City is a small area in west london created as an exhibition site in 1908, morphing over the years into an Olympic games venue, a greyhound track, the home nearby of the BBC (British Broadcasting Corporation) and most recently the new western campus for Imperial College London.\u2663 The first Imperial department to move into […]<\/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":true,"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":[284,1617,1556,1738,233,1395,2421,2419,24,1756,2420,206,1412,1449,37,449,2417,2415,2418,2416,1410,2422],"ppma_author":[2661],"class_list":["post-19828","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-acetic-acid","tag-acid","tag-amide","tag-amine","tag-carboxylic-acid","tag-chemistry","tag-company-bbc","tag-company-british-broadcasting-corporation","tag-energy","tag-ester","tag-exhibition-site","tag-free-energy-barrier","tag-functional-groups","tag-hydrogen-bond","tag-imperial-college","tag-imperial-college-london","tag-ionic-product","tag-newspaper-magazine-printing-services","tag-non-ionic-product","tag-olympic-games","tag-organic-chemistry","tag-white-city-trio"],"yoast_head":"\nThe "White City Trio" - The formation of an amide from an acid and an amine in non-polar solution (updated). - 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=19828\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The "White City Trio" - The formation of an amide from an acid and an amine in non-polar solution (updated). - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"White City is a small area in west london created as an exhibition site in 1908, morphing over the years into an Olympic games venue, a greyhound track, the home nearby of the BBC (British Broadcasting Corporation) and most recently the new western campus for Imperial College London.\u2663 The first Imperial department to move into […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19828\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2018-08-08T06:41:36+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2022-12-11T10:30:05+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2018\/08\/thewhitecity-page001.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":"The \"White City Trio\" - 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On November 5th this year, there was an excellent\u00a0meeting on the topic of Challenges in Catalysis,\u00a0and you can see the speakers and (some of) their slides here.\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":16031,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16031","url_meta":{"origin":19828,"position":1},"title":"Ways to encourage water to protonate an amine: superbasing.","author":"Henry Rzepa","date":"April 8, 2016","format":false,"excerpt":"Previously, I looked at\u00a0models of how\u00a0ammonia could be protonated by water to form ammonium hydroxide. The energetic outcome of my\u00a0model matched the known equilbrium in water as favouring the unprotonated form (pKb ~4.75). I add here two amines for which\u00a0R=Me3Si and R=CN. The idea is that the first will assist\u2026","rel":"","context":"In "General"","block_context":{"text":"General","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":248,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=248","url_meta":{"origin":19828,"position":2},"title":"Conformational analysis and enzyme activity: models for amide hydrolysis.","author":"Henry Rzepa","date":"April 12, 2009","format":false,"excerpt":"The diagram below summarizes an interesting result recently reported by Hanson and co-workers (DOI: 10.1021\/jo800706y. At ~neutral pH, compound 13 hydrolyses with a half life of 21 minutes, whereas 14 takes 840 minutes. Understanding this difference in reactivity may allow us to understand why some enzymes can catalyze the hydrolysis\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":"Models for peptide cleavage.","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/04\/amide-cleavage.png?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":19522,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19522","url_meta":{"origin":19828,"position":3},"title":"The dark satanic mills (of the industrial revolution?)","author":"Henry Rzepa","date":"March 18, 2018","format":false,"excerpt":"Around the time of the 2012 olympic games, the main site for which was Stratford in east London, I heard a fascinating talk about the \"remediation\" of the site from the pollution caused by its industrial chemical heritage. Here I visit another, arguably much more famous and indeed older industrial\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.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2018\/03\/IMG_2723-1024x768.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":4719,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4719","url_meta":{"origin":19828,"position":4},"title":"A stable borylene. An exercise in lateral thinking.","author":"Henry Rzepa","date":"August 7, 2011","format":false,"excerpt":"I have often heard the question posed \"how much of chemistry has been discovered?\" Another might be \"has most of chemistry, like low-hanging fruit, already been picked?\". Well, time and time again, one comes across examples which are only a simple diagram or so away from what might be found\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\/08\/borylene.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":20452,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=20452","url_meta":{"origin":19828,"position":5},"title":"The Chemistry of the Book of Kells","author":"Henry Rzepa","date":"January 22, 2019","format":false,"excerpt":"The Book of Kells is a spectacularly illuminated gospel manuscript dating from around 800AD and held in Trinity College library in Dublin. Some idea of the colours achieved can be seen below.\u00a0 I thought it would be of interest to list how these colours were achieved. Black ink was made\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.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2019\/01\/KellsDecoratedInitial-150x150.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2019\/01\/KellsDecoratedInitial-150x150.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2019\/01\/KellsDecoratedInitial-150x150.jpg?resize=525%2C300&ssl=1 1.5x"},"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\/19828","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=19828"}],"version-history":[{"count":75,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/19828\/revisions"}],"predecessor-version":[{"id":25760,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/19828\/revisions\/25760"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=19828"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=19828"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=19828"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=19828"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}