{"id":5796,"date":"2011-12-08T11:05:20","date_gmt":"2011-12-08T11:05:20","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=5796"},"modified":"2012-01-14T09:39:43","modified_gmt":"2012-01-14T09:39:43","slug":"validating-the-chemical-literature-heritage-eudesma-13-dien-613-olide","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5796","title":{"rendered":"Validating the chemical literature heritage. Eudesma-1,3-dien-6,13-olide."},"content":{"rendered":"
\n

Previously<\/a>, I had noted that Corey\u00a0reported<\/a>\u00a0in 1963\/65 the total synthesis of\u00a0the sesquiterpene dihydrocostunolide. Compound 16<\/strong>, known as\u00a0Eudesma-1,3-dien-6,13-olide<\/em> was represented as shown below in black; the hydrogen shown in red<\/span> was implicit in Corey’s representation, as was its stereochemistry. As of this instant, this compound is just one of 64,688,893 molecules recorded by Chemical Abstracts. How can we, in 2011, validate this particular entry, and resolve the stereochemical ambiguity? Here I discuss one approach (a vision if you like of the semantic web).<\/p>\n

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

The following facts are asserted about 16<\/strong>;<\/p>\n

    \n
  1. Its connection table, namely what atoms are connected by at least a single bond.<\/li>\n
  2. The (presumed) absolute stereochemistry at four stereogenic centres, leaving the 5th (in red) either unknown or implicit. I say presumed because often when it is not known which of two possible enantiomers a scalemic molecule exists in; just one is often drawn, in essence as a guess.<\/li>\n
  3. The 1<\/sup>H NMR chemical shifts of 13 of the 20 hydrogen atoms present in the molecule (the solvent used is unreported, and may be implicitly chloroform).<\/li>\n
  4. [\u03b1]D<\/sub> +375\u00b0 (no solvent reported)<\/li>\n
  5. m.p. 69.5-70.5\u00b0 (note by the way that the units represented by the symbol \u00b0 are quite different for these two facts! A scientist of course can easily recognise the implicit difference)<\/li>\n
  6. \u03bbmax<\/sub> (methanol) 265 m\u00b5, \u03b5 4800 (note again the ambiguity in the units, in fact 265 m\u00b5 is nowadays written 265 nm and the\u00a0molar extinction coefficient\u00a0\u03b5 is assumed to be expressed in units of L mol\u22121<\/sup>\u00a0cm\u22121<\/sup>).<\/li>\n<\/ol>\n
    Can we use these facts to validate the structure of 16<\/strong> and to resolve its stereochemical ambiguity? Well, modern computational quantum chemistry can (inter alia<\/em>) \u00a0supply the following:<\/div>\n
    \n
      \n
    1. From a given connection table, an accurate prediction of the 3D coordinates of all the atoms for, in this case, either of the stereoisomers involving the hydrogen shown in red.<\/li>\n
    2. The 1<\/sup>H NMR shifts relative to TMS, to an accuracy of better than 0.5ppm (often very much better).<\/li>\n
    3. [\u03b1]D<\/sub><\/li>\n
    4. \u03bbmax<\/sub>\u00a0(methanol) and an approximate estimate of \u03b5.<\/li>\n<\/ol>\n
      How do things pan out? We model the more specific stereoisomer shown below, with complete stereochemical notation (CIP) now annotated in.<\/div>\n
      \"\"<\/div>\n<\/div>\n

      \n<\/span><\/div>\n
        \n
      1. The 1<\/sup>H NMR was calculated<\/a>\u00a0at a \u03c9B97XD\/6-311G(d,p) optimised geometry and a single point 6-311++G(d,p) wavefunction. I have linked the “DOI” identified for this calculation to this post so that the calculation itself can be verified by others. It comes out (in ppm) \u03b4 1.02 [0.98, 3H,s], 1.17 [1.15, 3H, d], 2.11 [1.95, 3H, s], 3.85 [3.79, 1H, dd], 5.75, 6.13, 6.30 [5.2-6.0, vinyl], the reported experimental values being in square brackets […].<\/li>\n
      2. The spin spin couplings were calculated using the NMR(spinspin,mixed)<\/strong> model implemented in Gaussian (a specification for which is found in the online documentation of the NMR<\/a> keyword). For\u00a0\u03b4 3.79, two couplings of 10 Hz are reported. The calculation predicts 9.77 and 9.53 Hz (for assignments, click on the image above to get a 3D model).<\/li>\n
      3. [\u03b1]D<\/sub>\u00a0+391\u00b0 (calculated<\/a> for chloroform)<\/li>\n
      4. \u00a0\u03bbmax<\/sub>\u00a0265 nm (calculated<\/a> for methanol;\u00a0\u03b5 ~4800 for a linewidth of 3600 cm-1<\/sup>).<\/li>\n
      5. Strictly speaking, all of the above should be repeated for the other possible stereoisomer, and the results for the two together analysed statistically.<\/li>\n<\/ol>\n
        Can we add data to the original information (a process which might be called curation)? Well, we can using the above calculations to;<\/div>\n
        \n
          \n
        1. provide estimated chemical shifts and coupling constants for ALL the protons in the molecule, not just the 13 reported by Corey, and for all the carbons (no 13<\/sup>C spectrum was reported). Advances in spectrometer sensitivity and resolution mean that if these spectra were ever to be (re)measured, the additional protons could probably be easily identified, and both homo and heteronuclear spin-spin couplings measured.<\/li>\n
        2. predict the electronic circular dichroism spectrum for 16 <\/strong>(not previously measured)\u00a0and in particular the Cotton effect on the\u00a0\u03bbmax<\/sub>\u00a0265 nm absorption as being positive (\u0394\u03b5 ~+20). This would allow the absolute configuration of this scalemic molecule to be independently validated. We could add to this a prediction of the vibrational circular dichroism spectrum if need be.<\/li>\n
        3. What we cannot easily do is predict the melting point (or indeed the crystal packing), although no doubt this will become more reliable in the future.<\/li>\n<\/ol>\n<\/div>\n
          So what is the big picture? In the earlier post, I had identified a key article in the development of the electronic theory of pericyclic reactions, and in particular how the inferred stereochemistry of 10<\/strong>, 13<\/strong> and 16<\/strong> could have been used as the spark that ignited that theory. It would have been essential to ensure that these stereochemical foundations were absolutely sound. In this case of course, the compounds were related to many others by synthetic transformations, and the very fabric of the connections between these molecules served as a validation of the nature of the molecules.<\/div>\n
          \n

          But think how many (millions) of such molecules have been discovered, and how the majority of these have probably not been subjected to such rigorous scrutiny. It is entirely possible that much of the chemical literature is sprinkled with errors in assignments (and many more have unresolved ambiguities, such as the stereochemistry of the hydrogen shown in red at the top of this post). However, for the first time in the history of chemistry, we can now (almost routinely) use quantum modelling to provide independent validation of the chemical literature, as illustrated above. Of course, the validation is not absolute, merely probable to some degree (the above example we might agree shows a very high level of probability that the structure shown is in fact correct). More importantly, in computational validation, we have the potential for automation. One might strive for an infra-structure where much of the validation can be performed automatically, by tireless machines that operate 24\/7, and that only flag probable errors when they discover them. This is the vision of the chemical semantic web!<\/p>\n<\/div>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

          Previously, I had noted that Corey\u00a0reported\u00a0in 1963\/65 the total synthesis of\u00a0the sesquiterpene dihydrocostunolide. Compound 16, known as\u00a0Eudesma-1,3-dien-6,13-olide was represented as shown below in black; the hydrogen shown in red was implicit in Corey’s representation, as was its stereochemistry. As of this instant, this compound is just one of 64,688,893 molecules recorded by Chemical Abstracts. How […]<\/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":[2],"tags":[779,778,777,218,373],"ppma_author":[2661],"class_list":["post-5796","post","type-post","status-publish","format-standard","hentry","category-chemical-it","tag-13-olide","tag-3-dien-6","tag-eudesma-1","tag-semantic-web","tag-tutorial-material"],"yoast_head":"\nValidating the chemical literature heritage. Eudesma-1,3-dien-6,13-olide. - 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=5796\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Validating the chemical literature heritage. Eudesma-1,3-dien-6,13-olide. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"Previously, I had noted that Corey\u00a0reported\u00a0in 1963\/65 the total synthesis of\u00a0the sesquiterpene dihydrocostunolide. Compound 16, known as\u00a0Eudesma-1,3-dien-6,13-olide was represented as shown below in black; the hydrogen shown in red was implicit in Corey’s representation, as was its stereochemistry. As of this instant, this compound is just one of 64,688,893 molecules recorded by Chemical Abstracts. 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Eudesma-1,3-dien-6,13-olide. - 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=5796","og_locale":"en_GB","og_type":"article","og_title":"Validating the chemical literature heritage. Eudesma-1,3-dien-6,13-olide. - Henry Rzepa's Blog","og_description":"Previously, I had noted that Corey\u00a0reported\u00a0in 1963\/65 the total synthesis of\u00a0the sesquiterpene dihydrocostunolide. Compound 16, known as\u00a0Eudesma-1,3-dien-6,13-olide was represented as shown below in black; the hydrogen shown in red was implicit in Corey’s representation, as was its stereochemistry. As of this instant, this compound is just one of 64,688,893 molecules recorded by Chemical Abstracts. 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Here I apply the principle to the polar azulene 4 explored in an earlier post, taking m-benzyne as a lower homologue of azulene as my starting point. m-Benzyne is a less\u00a0stable\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":10145,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10145","url_meta":{"origin":5796,"position":1},"title":"Feist’s acid. Stereochemistry galore.","author":"Henry Rzepa","date":"April 4, 2013","format":false,"excerpt":"Back in the days (1893) when few compounds were known, new ones could end up being named after the discoverer. Thus Feist is known for the compound bearing his name; the 2,3 carboxylic acid of methylenecyclopropane (1, with Me replaced by CO2H). Compound 1 itself nowadays is used to calibrate\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":"methylene-cyclopropane","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/04\/methylene-cyclopropane.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":1937,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1937","url_meta":{"origin":5796,"position":2},"title":"Semantically rich molecules","author":"Henry Rzepa","date":"May 2, 2010","format":false,"excerpt":"Peter Murray-Rust in his blog asks for examples of the Scientific Semantic Web, a topic we have both been banging on about for ten years or more (DOI: 10.1021\/ci000406v). What we are seeking of course is an example of how scientific connections have been made using inference logic from semantically\u2026","rel":"","context":"In "Chemical IT"","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/05\/DULSAE.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":9894,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9894","url_meta":{"origin":5796,"position":3},"title":"To be cyclobutadiene, or not to be, that is the question? You decide.","author":"Henry Rzepa","date":"March 21, 2013","format":false,"excerpt":"A quartet of articles has recently appeared on the topic of cyclobutadiene.,,,. You will find a great deal discussed there, but I can boil it down to this essence. Do the following coordinates (obtained from a (disordered) previously published x-ray refinement) correspond to a van der Waals complex of 1,3-dimethyl\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":1516,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1516","url_meta":{"origin":5796,"position":4},"title":"Semantic Blogs","author":"Henry Rzepa","date":"January 17, 2010","format":false,"excerpt":"A Semantic blog is one in which the system at least in part understands about (some of the) concepts and topics that are in the content. The idea is that this content can be more intelligently (is that the correct word?) and importantly, automatically searched, harvested, and connected to the\u2026","rel":"","context":"In "Chemical IT"","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":745,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=745","url_meta":{"origin":5796,"position":5},"title":"Spotting the unexpected: Anomeric effects","author":"Henry Rzepa","date":"September 18, 2009","format":false,"excerpt":"Chemistry can be very focussed nowadays. This especially applies to target-driven synthesis, where the objective is to make a specified molecule, in perhaps as an original manner as possible. A welcome, but not always essential aspect of such syntheses is the discovery of new chemistry. In this blog, I will\u2026","rel":"","context":"In "Chemical IT"","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"A cyano-substituted cis decalin","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/09\/anomeric-cn.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\/5796","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=5796"}],"version-history":[{"count":37,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/5796\/revisions"}],"predecessor-version":[{"id":5827,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/5796\/revisions\/5827"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=5796"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=5796"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=5796"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=5796"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}