{"id":2594,"date":"2010-10-30T10:00:12","date_gmt":"2010-10-30T09:00:12","guid":{"rendered":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2594"},"modified":"2017-04-12T15:04:31","modified_gmt":"2017-04-12T14:04:31","slug":"rate-enhancement-of-the-diels-alder-reaction-inside-a-cavity-2","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2594","title":{"rendered":"Rate enhancement of the Diels-Alder reaction inside a cavity"},"content":{"rendered":"
\n

Reactions in cavities<\/a> can adopt quite different characteristics from those in solvents. Thus first example of the catalysis of the Diels-Alder reaction inside an organic scaffold was reported by Endo, Koike, Sawaki, Hayashida, Masuda, and Aoyama[1]<\/a><\/span>, where the reaction shown below is speeded up very greatly in the presence of a crystalline lattice of the anthracene derivative shown below.<\/p>\n\n\n\n\n
\n
\"\"

A Diels-Alder reaction. Click for animation.<\/p><\/div>\n<\/td>\n<\/tr>\n

\n
\"\"

Organic scaffold based on an anthracene derivative. Click for crystal structure.<\/p><\/div>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

Its difficult to be precise about how much faster, since the kinetics depend on reorganisation of the scaffold, the actual reaction kinetics, and diffusion of the products in and out of the cavity. It does however mean that a poor solution reaction (reflux, many hours, modest yield) can be accomplished in an hour or so at room temperature in high yield.<\/p>\n

Some idea of what is going on can be probed using calculation. Because the host and the guest interact though van der Waals or dispersion forces, a new breed of density functional theory which takes these into account is used (\u03c9B97XD). The basic assemblage comprises the reactants shown below, enclosed in a cage formed by four of the anthracene units. A total of 236 atoms. This is a pretty challenging size for a full-blown quantum mechanical calculation. Here, its been done using a reasonable basis set, 6-31G(d) and with a continuum solvation model applied (dichloromethane). If you are interested in this sort of thing, that is 2292 basis functions. I started the calculations in mid September, and its taken more than six weeks to optimise (on 8-processor computers).<\/p>\n

Firstly, the results for a control calculation<\/a> in dichloromethane.\u00a0The energies of activation of the two isolated reactants coming together at the transition state are calculated as:
\u0394G<\/span>298<\/span><\/sub> 29.5, \u0394H 15.5, T.\u0394S \u00a0-13.98 kcal mol<\/span>-1<\/span><\/sup>
(\u0394S -46.9 cal K<\/span>-1<\/span><\/sup>mol<\/span>-1<\/span><\/sup>)<\/span><\/strong><\/p>\n

which are of course the various contributions to the equation \u0394G = \u0394H – T.\u0394S<\/strong>. Note in particular how the last term increases<\/strong> the free energy barrier by ~14 kcal mol-1<\/sup>!\u00a0Using the equation
Ln k\/T = 23.76 – \u0394G\/RT
one can estimate a rate constant of ~4 x 10-6<\/sup> hour-1<\/sup> at 298K (i.e.<\/em> very slow at room temperatures). If the unfavourable -T.\u0394S term is ignored (\u0394G = \u0394H), the rate constant increases to ~9 x 104<\/sup> hour-1<\/sup> at 298K (i.e.<\/em> fast), quite a difference. What about the values when the reactants<\/a> and transition state<\/a> are surrounded by the host?<\/p>\n

\u0394G<\/span>298<\/span><\/sub> 20.0, \u0394H 16.5, T.\u0394S -3.49 kcal mol<\/span>-1<\/span><\/sup>
(\u0394S -11.7 cal K<\/span>-1<\/span><\/sup> mol<\/span>-1<\/span><\/sup>)<\/span><\/strong><\/p>\n

The key difference is that the last term is now \u00a0much smaller, this reduces the free energy of activation and the estimated rate constant at 298K is now ~ 0.01 s-1<\/sup> (42.5 hour-1<\/sup>). \u00a0This magnitude of rate constant corresponds to a reasonably fast reaction at room temperatures.<\/p>\n

\"\"

Transition state for \u00a0Diels Alder inside a cavity. Click for 3D.<\/p><\/div>\n

This post demonstrates that the fascinating area of supermolecular chemistry can be just as amenable to computational exploration as the more conventional reaction.<\/p>\n

 <\/p>\n

References<\/h2>\n
  1. K. Endo, T. Koike, T. Sawaki, O. Hayashida, H. Masuda, and Y. Aoyama, \"Catalysis by Organic Solids. Stereoselective Diels\u2212Alder Reactions Promoted by Microporous Molecular Crystals Having an Extensive Hydrogen-Bonded Network\", Journal of the American Chemical Society<\/i>, vol. 119, pp. 4117-4122, 1997. https:\/\/doi.org\/10.1021\/ja964198s<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    Reactions in cavities can adopt quite different characteristics from those in solvents. Thus first example of the catalysis of the Diels-Alder reaction inside an organic scaffold was reported by Endo, Koike, Sawaki, Hayashida, Masuda, and Aoyama, where the reaction shown below is speeded up very greatly in the presence of a crystalline lattice of the […]<\/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":[4],"tags":[152,1138,40,206,304,2648,305,2650],"ppma_author":[2661],"class_list":["post-2594","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-animation","tag-catalysis","tag-free-energy","tag-free-energy-barrier","tag-grt","tag-interesting-chemistry","tag-organic-scaffold","tag-pericyclic"],"yoast_head":"\nRate enhancement of the Diels-Alder reaction inside a cavity - 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=2594\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Rate enhancement of the Diels-Alder reaction inside a cavity - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"Reactions in cavities can adopt quite different characteristics from those in solvents. 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Thus first example of the catalysis of the Diels-Alder reaction inside an organic scaffold was reported by Endo, Koike, Sawaki, Hayashida, Masuda, and Aoyama, where the reaction shown below is speeded up very greatly in the presence of a crystalline lattice of the […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2594","og_site_name":"Henry Rzepa's Blog","article_published_time":"2010-10-30T09:00:12+00:00","article_modified_time":"2017-04-12T14:04:31+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/09\/res_scheme.jpg","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=2594#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2594"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Rate enhancement of the Diels-Alder reaction inside a cavity","datePublished":"2010-10-30T09:00:12+00:00","dateModified":"2017-04-12T14:04:31+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2594"},"wordCount":534,"commentCount":7,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2594#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/09\/res_scheme.jpg","keywords":["animation","catalysis","free energy","free energy barrier","G\/RT","Interesting chemistry","Organic scaffold","pericyclic"],"articleSection":["Interesting chemistry"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2594#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2594","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2594","name":"Rate enhancement of the Diels-Alder reaction inside a cavity - 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The topic has been reviewed here.\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":"NCI surface. Click for 3D.","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/01\/benzidinenci.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":11110,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11110","url_meta":{"origin":2594,"position":3},"title":"Coarctate reactions as a third fundamental organic-mechanistic type.","author":"Henry Rzepa","date":"September 4, 2013","format":false,"excerpt":"According to Herges, the mechanism of single-step (concerted) reactions can be divided into three basic types; linear (e.g. substitution, elimination etc), pericyclic (e.g. Diels Alder) and a third much rarer, and hence very often overlooked type that was named coarctate. This is based on the topology of\u00a0bond redistribution patterns, an\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":"Click for 3D","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/09\/coarctate-ts.jpeg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":17633,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17633","url_meta":{"origin":2594,"position":4},"title":"George Olah and the norbornyl cation.","author":"Henry Rzepa","date":"March 10, 2017","format":false,"excerpt":"George Olah passed away on March 8th. He was part of the generation of scientists in the post-war 1950s who had access to chemical instrumentation that truly revolutionised chemistry. In particular he showed how the then newly available NMR spectroscopy illuminated structures of cations in solvents such \"Magic acid\". 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":"","width":0,"height":0},"classes":[]},{"id":5087,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5087","url_meta":{"origin":2594,"position":5},"title":"cis-Butene: a reaction coordinate dissected and methyl flags.","author":"Henry Rzepa","date":"October 12, 2011","format":false,"excerpt":"In two previous posts, I have looked at why cis-butene adopts conformation (a) rather than (b). I suggested it boiled down to electronic interactions between the methyl groups and the central alkene resulting in the formation of a H...H \"topological\" bond, rather than attraction between the H...H region to form\u2026","rel":"","context":"In "General"","block_context":{"text":"General","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/cis-butene2.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\/2594","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=2594"}],"version-history":[{"count":7,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/2594\/revisions"}],"predecessor-version":[{"id":18129,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/2594\/revisions\/18129"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2594"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2594"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2594"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=2594"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}