{"id":12276,"date":"2014-04-13T17:12:43","date_gmt":"2014-04-13T16:12:43","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=12276"},"modified":"2023-07-02T08:19:30","modified_gmt":"2023-07-02T07:19:30","slug":"artemisinin-are-stereo-electronics-at-the-core-of-its-reactivity","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12276","title":{"rendered":"Artemisinin: are stereo-electronics at the core of its (re)activity?"},"content":{"rendered":"
\n

\n\tAround 100 tons of the potent antimalarial artemisinin is produced annually; a remarkable quantity given its very unusual and fragile looking molecular structure (below). When I looked at this, I was immediately struck by a thought: surely this is a classic molecule for analyzing stereoelectronic effects (anomeric and gauche). Here this aspect is explored.\n<\/p>\n

\n\t\"artemisinin\"<\/a>\n<\/p>\n

\n\tI start by listing the bonds around which interesting things might happen:\n<\/p>\n

    \n
  1. \n\t\tC3-C4 has the gauche motif of a 1,2-diol\n\t<\/li>\n
  2. \n\t\tCarbons 7 and 4 are anomeric centres, with the focus on bonds 1-7\/7-6 and 6-4\/4-5\n\t<\/li>\n
  3. \n\t\tBond 1-2 has the potential for a so-called α-effect, where the lone pairs on adjacent hetero-atoms are buttressed.\n\t<\/li>\n<\/ol>\n

    \n\tThe crystal structure is shown below, annotated with pertinent bond lengths (trivial atom numbering). The dihedral 2-3-4-6 and 2-3-4-6 are respectively -51 and 72° (hence a double gauche at the 3-4 bond).\n<\/p>\n

    \"Click

    Click for 3D<\/p><\/div>\n

    \n\tFirst, an exploration of what might be happening around C4. The following is a search of the Cambridge crystal structure database, plotted for the two C-O bond lengths common to C4.\n<\/p>\n

    \n\t\"artemisinin1\"<\/a> \"artemisinin\"<\/a> Here, DIST1 is C4-O6 and DIST2 is C4-O5. Notice the very pronounced asymmetry; at the red hotspot above, the most frequent occurrence is ~1.39 and 1.46Å respectively; artemisinin is more or less at that hotspot. This can be quantified by the NBO E(2) energies for the interaction of an oxygen lone pair antiperiplanar to the C-O σ* bond;\n<\/p>\n

      \n
    1. \n\t\tLp(O6)-σ*(C4-O5) = 21.2 kcal\/mol which helps to account for the short C4-O6 and the long C4-O5 bonds.\n\t<\/li>\n
    2. \n\t\twhereas the reverse donation of Lp(O5)-σ*(C4-O6) is merely 4.8 kcal\/mol (normally the two donations are more or less equal, and hence so at the two C-O bond lengths).\n\t<\/li>\n
    3. \n\t\tAt the second anomeric centre of C7, Lp(O1)-σ*(C7-O6) = 19.9 kcal\/mol\n\t<\/li>\n
    4. \n\t\twhereas the reverse donation of Lp(O6)-σ*(C7-O1) is 5.7 kcal\/mol, again highly asymmetric, as are the C-O bond lengths (1.413\/1.441Å).\n\t<\/li>\n
    5. \n\t\tNext, the gauche effect at C3-C4. The C4-H to C3-O2 donation is 6.4 kcal\/mol, again contributing to the longer C-O length of 1.447Å.\n\t<\/li>\n<\/ol>\n

      \n\tWhere such stereoelectronic interactions are asymmetric, one might expect enhanced reactivity. A good example of this are two stereoisomeric of a 7-ring herbicide[1]<\/a><\/span> where one anomer with equal anomeric C-O lengths is a stable soil-persistent species, whereas the other with asymmetric lengths has a very short soil residency due to rapid hydrolysis. It might be tempting to speculate that some aspect of the activity of artemisinin may be due to such stereoelectronic asymmetries.\n<\/p>\n

      \n\tFinally, because it is virtually free to do so in a computational sense, I show the computed VCD spectrum[2]<\/a><\/span> (covering the possibility that it is measured at some point). The calculated[3]<\/a><\/span> optical rotation ([α]589<\/sub> is +93° (obs ~+76°). Whilst the absolute configuration is not in any doubt, it is always nice to have further confirmations.\n<\/p>\n

      \n\t\"artemisinin\"<\/a>\n<\/p>\n

      \n

      This post has DOI: 10.14469\/hpc\/12766<\/p>\n

      \n

      References<\/h2>\n
      1. P. Camilleri, D. Munro, K. Weaver, D.J. Williams, H.S. Rzepa, and A.M.Z. Slawin, \"Isoxazolinyldioxepins. Part 1. Structure\u2013reactivity studies of the hydrolysis of oxazolinyldioxepin derivatives\", J. Chem. Soc., Perkin Trans. 2<\/i>, pp. 1929-1933, 1989. https:\/\/doi.org\/10.1039\/p29890001929<\/a>\n\n<\/li>\n
      2. H.S. Rzepa, \"Gaussian Job Archive for C15H22O5\", 2014. https:\/\/doi.org\/10.6084\/m9.figshare.997360<\/a>\n\n<\/li>\n
      3. H.S. Rzepa, \"Gaussian Job Archive for C15H22O5\", 2014. https:\/\/doi.org\/10.6084\/m9.figshare.997463<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

        Around 100 tons of the potent antimalarial artemisinin is produced annually; a remarkable quantity given its very unusual and fragile looking molecular structure (below). When I looked at this, I was immediately struck by a thought: surely this is a classic molecule for analyzing stereoelectronic effects (anomeric and gauche). Here this aspect is explored. I […]<\/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":[1745,4],"tags":[1200,144,1201],"ppma_author":[2661],"class_list":["post-12276","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining","category-interesting-chemistry","tag-c7-lp","tag-cambridge","tag-stereo-electronics"],"yoast_head":"\nArtemisinin: are stereo-electronics at the core of its (re)activity? - 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=12276\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Artemisinin: are stereo-electronics at the core of its (re)activity? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"Around 100 tons of the potent antimalarial artemisinin is produced annually; a remarkable quantity given its very unusual and fragile looking molecular structure (below). When I looked at this, I was immediately struck by a thought: surely this is a classic molecule for analyzing stereoelectronic effects (anomeric and gauche). Here this aspect is explored. I […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12276\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2014-04-13T16:12:43+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2023-07-02T07:19:30+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/04\/artemisinin.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":"Artemisinin: are stereo-electronics at the core of its (re)activity? - 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=12276","og_locale":"en_GB","og_type":"article","og_title":"Artemisinin: are stereo-electronics at the core of its (re)activity? - Henry Rzepa's Blog","og_description":"Around 100 tons of the potent antimalarial artemisinin is produced annually; a remarkable quantity given its very unusual and fragile looking molecular structure (below). When I looked at this, I was immediately struck by a thought: surely this is a classic molecule for analyzing stereoelectronic effects (anomeric and gauche). Here this aspect is explored. 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However this did not\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":"hmtd","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/09\/HMTD-1024x986.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":26962,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26962","url_meta":{"origin":12276,"position":1},"title":"Detecting anomeric effects in tetrahedral boron bearing four oxygen substituents.","author":"Henry Rzepa","date":"April 30, 2024","format":false,"excerpt":"In an earlier post, I discussed a phenomenon known as the \"anomeric effect\" exhibited by tetrahedral carbon compounds with four C-O bonds. Each oxygen itself bears two bonds and has two lone pairs, and either of these can align with one of three other C-O bonds to generate an anomeric\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/04\/Screenshot-304.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\/2024\/04\/Screenshot-304.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/04\/Screenshot-304.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/04\/Screenshot-304.jpg?resize=700%2C400&ssl=1 2x"},"classes":[]},{"id":16601,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16601","url_meta":{"origin":12276,"position":2},"title":"Anomeric effects at boron, silicon and phosphorus.","author":"Henry Rzepa","date":"July 1, 2016","format":false,"excerpt":"The anomeric effect occurs at 4-coordinate (sp3) carbon centres carrying two oxygen substituents and involves an alignment of a lone electron pair\u00a0on one oxygen with the adjacent C-O \u03c3*-bond of the other oxygen. Here I explore whether other centres can exhibit the phenomenon. I start with 4-coordinate boron, using the\u2026","rel":"","context":"In "crystal_structure_mining"","block_context":{"text":"crystal_structure_mining","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1745"},"img":{"alt_text":"anomeric-bo-sq","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/06\/anomeric-bo-sq-1024x644.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":14161,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14161","url_meta":{"origin":12276,"position":3},"title":"The formation of tetrahedral intermediates.","author":"Henry Rzepa","date":"June 12, 2015","format":false,"excerpt":"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\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":24019,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=24019","url_meta":{"origin":12276,"position":4},"title":"More record breakers for the anomeric effect involving C-N bonds.","author":"Henry Rzepa","date":"September 4, 2021","format":false,"excerpt":"An earlier post investigated large anomeric effects involving two oxygen atoms attached to a common carbon atom. A variation is to replace one oxygen by a nitrogen atom, as in N-C-O. Shown below is a scatter plot of the two distances to the common carbon atom derived from crystal structures.\u2026","rel":"","context":"In "crystal_structure_mining"","block_context":{"text":"crystal_structure_mining","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1745"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2021\/07\/N-C-O-distances-1024x758.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":4089,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4089","url_meta":{"origin":12276,"position":5},"title":"The inner secrets of the DNA structure.","author":"Henry Rzepa","date":"May 18, 2011","format":false,"excerpt":"In earlier posts, I alluded to what might make DNA wind into a left or a right-handed helix. Here I switch the magnification of our structural microscope up a notch to take a look at some more inner secrets. The 3D coordinates of this fragment were obtained by taking a\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\/05\/CGCG.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\/12276","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=12276"}],"version-history":[{"count":26,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/12276\/revisions"}],"predecessor-version":[{"id":26196,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/12276\/revisions\/26196"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=12276"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=12276"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=12276"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=12276"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}