{"id":14161,"date":"2015-06-12T13:13:04","date_gmt":"2015-06-12T12:13:04","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=14161"},"modified":"2015-06-13T12:51:32","modified_gmt":"2015-06-13T11:51:32","slug":"the-formation-of-tetrahedral-intermediates","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14161","title":{"rendered":"The formation of tetrahedral intermediates."},"content":{"rendered":"
\n

In the preceding post, I discussed<\/a>\u00a0the reaction between mCPBA (meta-chloroperbenzoic acid) and cyclohexanone, resulting in Baeyer-Villiger oxidation via<\/em> a tetrahedral intermediate (TI). Dan Singleton, in whose group the original KIE (kinetic isotope measurements) were made, has kindly\u00a0pointed out<\/a>\u00a0on this blog that his was a mixed-phase reaction, and that mechanistic comparison with homogenous solutions\u00a0may not be justified. An intriguing aspect of\u00a0the (solution) mechanism would be whether the TI forms quickly and\/or reversibly and what the position of any equilibrium between it and the starting ketone is. This reminded me of work we did some years ago<\/a>,[1]<\/a><\/span> and here I discuss that.<\/p>\n

It involved the addition of phenyl hydroxylamine, PhNHOH to acetyl cyanide at 215K. Because the CN group is poor at leaving, the tetrahedral intermediates do not collapse and instead accumulate in seconds to the point of becoming detectable by NMR (both N-C and O-C isomers). The position of the equilibrium clearly favours the TI rather than the starting materials. In another context, both the rate of reaction and the equilibrium can be driven towards the TI by the application of pressure.[2]<\/a><\/span> Hydroxylamines are known to be super nucleophiles, enhanced by the so-called \u03b1-effect from buttressing of adjacent lone pairs on the N and O. This reminds that a peracid also should exhibit a related \u03b1-effect; it should be a better nucleophile than a normal carboxylic acid. So I decided to take the TI formed from cyclohexanone and mcPBA and look at the NBO orbitals, which should tell us about the anomeric effects present in this TI, and in particular if they might be larger than normal (which could be equated with greater stability for the TI). Here are the relevant NBO energies.[3]<\/a><\/span><\/p>\n

\"TI-NBO\"<\/a><\/p>\n

    \n
  1. The conventional anomeric effect in O-C-O manifests as a E(2) perturbation energy of ~16-18 kcal\/mol between one oxygen lone pair and the antibonding C-O orbital. There are two combinations, and these are normally similar in energy.<\/li>\n
  2. For the system above,\u00a0the O1-C2-O6 interaction is 25.6 kcal\/mol, much\u00a0larger than normal, but partially counterbalanced by:<\/li>\n
  3. O6-C1-O2 =13.0 kcal\/mol which is a little lower than normal. This is overall an unusually strong anomeric effect for the O-C-O motif!<\/li>\n
  4. The energetic asymmetry is matched by the two computed bond lengths, 1.381\u00c5 for the larger interaction and 1.455\u00c5 for the smaller. The pseudo-\u03b1-effect has desymmetrized the anomeric effect, but nevertheless\u00a0strengthened it overall.<\/li>\n<\/ol>\n
    \"NBO

    NBO 103 for O1(Lp)<\/p><\/div>\n

    \"NBO

    NBO 97 for O6(Lp)<\/p><\/div>\n

    \"NBO

    NBO 123 for C2-O6 antibonding \u03c3*<\/sup>orbital<\/p><\/div>\n

    One concludes that the asymmetric anomeric effect makes the TI resemble the reactants. The transition state leading to the TI must be even earlier. In this context, I note that the (mixed phase) 13<\/sup>C effect reported for the carbonyl by Singleton and Szymanski[4]<\/a><\/span> was quite a large one for carbon (1.045-1.051), a magnitude which argues against a very early transition state under these conditions. But the calculated value for a homogenous solution state model of ~1.023 is certainly more in accord with an early transition state.<\/p>\n

    Finally, a search of the CSD reveals 12 molecules containing either a O-O-C-O-O or a O-C-O-O sub unit This one[5]<\/a><\/span> shows a bis HO-C-O-O-C-OH structure at room temperature; these species need not be unstable! There are none however with Ac-O-O-C-O. And of course the potent antimalarial artemisinin<\/a> contains a O-O-C-O-C-O-Ac unit, for which stereoelectronic effects may also be important.<\/p>\n

    References<\/h2>\n
    1. A.M. Lobo, M.M. Marques, S. Prabhakar, and H.S. Rzepa, \"Tetrahedral intermediates formed by nitrogen and oxygen attack of aromatic hydroxylamines on acetyl cyanide\", The Journal of Organic Chemistry<\/i>, vol. 52, pp. 2925-2927, 1987. https:\/\/doi.org\/10.1021\/jo00389a050<\/a>\n\n<\/li>\n
    2. N.S. Isaacs, H.S. Rzepa, R.N. Sheppard, A.M. Lobo, S. Prabhakar, and A.E. Merbach, \"Volumes of reaction for the formation of some analogues of tetrahedral intermediates\", Journal of the Chemical Society, Perkin Transactions 2<\/i>, pp. 1477, 1987. https:\/\/doi.org\/10.1039\/p29870001477<\/a>\n\n<\/li>\n
    3. H.S. Rzepa, \"C 20 H 20 Cl 2 O 6\", 2015. https:\/\/doi.org\/10.14469\/ch\/191327<\/a>\n\n<\/li>\n
    4. D.A. Singleton, and M.J. Szymanski, \"Simultaneous Determination of Intermolecular and Intramolecular <sup>13<\/sup>C and <sup>2<\/sup>H Kinetic Isotope Effects at Natural Abundance\", Journal of the American Chemical Society<\/i>, vol. 121, pp. 9455-9456, 1999. https:\/\/doi.org\/10.1021\/ja992016z<\/a>\n\n<\/li>\n
    5. A. Kobayashi, Y. Ikeda, K. Kubota, and Y. Ohashi, \"Syntheses and crystalline structures of several aldehyde peroxides as new flavor compounds\", Journal of Agricultural and Food Chemistry<\/i>, vol. 41, pp. 1297-1299, 1993. https:\/\/doi.org\/10.1021\/jf00032a025<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      In the preceding post, I discussed\u00a0the reaction between mCPBA (meta-chloroperbenzoic acid) and cyclohexanone, resulting in Baeyer-Villiger oxidation via a tetrahedral intermediate (TI). Dan Singleton, in whose group the original KIE (kinetic isotope measurements) were made, has kindly\u00a0pointed out\u00a0on this blog that his was a mixed-phase reaction, and that mechanistic comparison with homogenous solutions\u00a0may not be […]<\/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":[1469,260,1465,1466,1395,1457,1470,1428,1468,1410,1467],"ppma_author":[2661],"class_list":["post-14161","post","type-post","status-publish","format-standard","hentry","category-reaction-mechanism-2","tag-anomer","tag-anomeric-effect","tag-carbohydrate-chemistry","tag-carbohydrates","tag-chemistry","tag-dan-singleton","tag-homogenous-solutions","tag-ketone","tag-meta-chloroperoxybenzoic-acid","tag-organic-chemistry","tag-tetrahedral-carbonyl-addition-compound"],"yoast_head":"\nThe formation of tetrahedral intermediates. - 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=14161\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The formation of tetrahedral intermediates. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"In the preceding post, I discussed\u00a0the reaction between mCPBA (meta-chloroperbenzoic acid) and cyclohexanone, resulting in Baeyer-Villiger oxidation via a tetrahedral intermediate (TI). Dan Singleton, in whose group the original KIE (kinetic isotope measurements) were made, has kindly\u00a0pointed out\u00a0on this blog that his was a mixed-phase reaction, and that mechanistic comparison with homogenous solutions\u00a0may not be […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14161\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2015-06-12T12:13:04+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2015-06-13T11:51:32+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/06\/TI-NBO.jpg\" \/>\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 formation of tetrahedral intermediates. - 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=14161","og_locale":"en_GB","og_type":"article","og_title":"The formation of tetrahedral intermediates. - Henry Rzepa's Blog","og_description":"In the preceding post, I discussed\u00a0the reaction between mCPBA (meta-chloroperbenzoic acid) and cyclohexanone, resulting in Baeyer-Villiger oxidation via a tetrahedral intermediate (TI). Dan Singleton, in whose group the original KIE (kinetic isotope measurements) were made, has kindly\u00a0pointed out\u00a0on this blog that his was a mixed-phase reaction, and that mechanistic comparison with homogenous solutions\u00a0may not be […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14161","og_site_name":"Henry Rzepa's Blog","article_published_time":"2015-06-12T12:13:04+00:00","article_modified_time":"2015-06-13T11:51:32+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/06\/TI-NBO.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=14161#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14161"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"The formation of tetrahedral intermediates.","datePublished":"2015-06-12T12:13:04+00:00","dateModified":"2015-06-13T11:51:32+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14161"},"wordCount":602,"commentCount":2,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14161#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/06\/TI-NBO.jpg","keywords":["Anomer","Anomeric effect","Carbohydrate chemistry","Carbohydrates","Chemistry","Dan Singleton","homogenous solutions","Ketone","Meta-Chloroperoxybenzoic acid","Organic chemistry","Tetrahedral carbonyl addition compound"],"articleSection":["reaction mechanism"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14161#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14161","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14161","name":"The formation of tetrahedral intermediates. - 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It refers to a (normally undetected and hence merely inferred) species formed initially when a nucleophilic reagent attacks a carbonyl compound. Its importance to understanding the activity of enzymes\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\/01\/acetylcyanide.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":14112,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14112","url_meta":{"origin":14161,"position":1},"title":"Natural abundance kinetic isotope effects: mechanism of the Baeyer-Villiger reaction.","author":"Henry Rzepa","date":"June 10, 2015","format":false,"excerpt":"I have blogged before about the mechanism of this classical oxidation reaction. Here I further explore computed models, and whether they match the observed kinetic isotope effects (KIE) obtained using the natural-abundance method described in the previous post. There is much previous study of this rearrangement, and the issue can\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":10184,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10184","url_meta":{"origin":14161,"position":2},"title":"Intermediates in oxime formation from hydroxylamine and propanone: now you see them, now you don’t.","author":"Henry Rzepa","date":"April 14, 2013","format":false,"excerpt":"A recent theme here has been to subject to scrutiny well-known mechanisms supposedly involving intermediates. These transients can often involve the creation\/annihilation of charge separation resulting from \u00a0proton transfers, something that a cyclic mechanism can avoid. Here I revisit the formation of an oxime from hydroxylamine and propanone, but with\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":"N-pre","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/04\/N-pre.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":7822,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7822","url_meta":{"origin":14161,"position":3},"title":"Oxime formation from hydroxylamine and ketone. Part 2: Elimination.","author":"Henry Rzepa","date":"September 25, 2012","format":false,"excerpt":"This is the follow-up to the previous post exploring a typical nucleophilic addition-elimination reaction. Here is the elimination step, which as before requires proton transfers. We again adopt a cyclic mechanism to try to avoid the build up of charge separation during those proton movements. Overall, the transition state for\u2026","rel":"","context":"In \"Reaction Mechanism\"","block_context":{"text":"Reaction Mechanism","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=reaction-mechanism"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/09\/N-2H2O-8-ring-2.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":546,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=546","url_meta":{"origin":14161,"position":4},"title":"Molecular toys: Tetrahedral cavities","author":"Henry Rzepa","date":"July 4, 2009","format":false,"excerpt":"An earlier post described how a (spherical) halide anion fitted snugly into a cavity generated by the simple molecule propanone, itself assembled by sodium cations coordinating to the oxygen. A recent elaboration of this theme, reminiscent of the children's toys where objects have to be fitted into the only cavity\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":"P4 inside a Tetrahedral cavity. ","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/07\/P4.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":13047,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13047","url_meta":{"origin":14161,"position":5},"title":"A computed mechanistic pathway for the formation of an amide from an acid and an amine in non-polar solution.","author":"Henry Rzepa","date":"November 12, 2014","format":false,"excerpt":"In London, one has the pleasures of attending occasional one day meetings at the Burlington House, home of the Royal Society of Chemistry. 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":[]}],"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\/14161","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=14161"}],"version-history":[{"count":11,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14161\/revisions"}],"predecessor-version":[{"id":14190,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14161\/revisions\/14190"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=14161"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=14161"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=14161"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=14161"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}