{"id":12705,"date":"2014-07-05T09:42:47","date_gmt":"2014-07-05T08:42:47","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=12705"},"modified":"2014-07-06T07:47:07","modified_gmt":"2014-07-06T06:47:07","slug":"the-5%cf%83-confidence-level-how-much-chemistry-achieves-this","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12705","title":{"rendered":"The 5\u03c3-confidence level: how much chemistry achieves this?"},"content":{"rendered":"
\n

I was lucky enough to attend the announcement made in 2012 of the discovery of the Higgs Boson. It consisted of a hour-long talk mostly about statistics, and how the particle physics community can only claim a discovery when their data has\u00a0achieved a 5\u03c3 confidence level<\/a>. This represents a 1 in 3.5 million probability of the result occurring by chance. I started thinking: how much chemistry is asserted at that level of confidence? Today, I read Steve Bachrach’s post on the structure of Citrinalin B<\/a>\u00a0and how “use of Goodman\u2019s DP4 method indicates a 100% probability that the structure of citrinalin B is (the structure below)”.<\/em>\u00a0Wow, that is even higher than the physicists. Of course, 100% has been obtained by rounding 99.7 (3\u03c3 is 99.73%<\/a>) or whatever (this is one number that should never be so rounded!). \"pc\" But there was one aspect of this that I did want to have a confidence level for; the absolute configuration<\/strong> of citrinalin B. Reading the article Steve quotes[1]<\/a><\/span>,\u00a0one sees this aspect is attributed to ref 5[2]<\/a><\/span>, dating from 2005. There the configuration was assigned on the basis of “comparison of the electronic circular dichroism (ECD) spectra for 1 and 2 with those of known spirooxiindole alkaloids<\/i>“. However, this method can fail[3]<\/a><\/span>. Also, one finds “comparison of the vibrational circular dichroism (VCD) spectra of 1 with those of model compounds<\/i>“[2]<\/a><\/span>. Nowadays, one would say that there is no need for model compounds, why not measure and compute the VCD of the actual compound? Even a determination using the Flack crystallographic method can occasionally be wrong![4]<\/a><\/span>. Which leads to asking what typical confidence levels might be for these three techniques, and indeed whether improving instrumentation means that the confidence level gets higher with time. OK, I am going to guess these.<\/p>\n

    \n
  1. I think the confidence level for assigning absolute configurations on the basis of ECD analogy with other compounds is the lowest of all the methods. Around 1\u03c3 or 68.3% (and this mostly from additional information such as the chemical transforms performed from starting materials of known absolute configuration).<\/li>\n
  2. VCD is higher. If performed on the actual compound, I think it can be as high as 2-3\u03c3 or 95.5-99.7%. It is difficult to know how much of this certainty is lost by using only model compounds.<\/li>\n
  3. Flack analysis (of anomalous X-ray)[5]<\/a><\/span> is probably also at\u00a02-3\u03c3; I suggest however that a fair bit of uncertainly not included in the 2-3\u03c3 probably arises from analysing a tiny crystal (1 \u00b5g) arising from a solution perhaps 10,000 times larger in weight of sample.<\/li>\n
  4. And of course combining the uncertainties from multiple experiments reduces it overall.<\/li>\n<\/ol>\n

    I am not casting any doubts on an assigned absolute configuration on which that of citrinalin B is based, as done in 2005. I have no grounds to think it is wrongly assigned. I am merely suggesting that in 2014, one\u00a0should be able to\u00a0achieve an even greater confidence level. And do what the physicists do, try to estimate the confidence level attained. I wonder how much chemistry would match the physicists\u00a05\u03c3-confidence level (99.99994%)<\/span>?<\/p>\n

    References<\/h2>\n
    1. E.V. Mercado-Marin, P. Garcia-Reynaga, S. Romminger, E.F. Pimenta, D.K. Romney, M.W. Lodewyk, D.E. Williams, R.J. Andersen, S.J. Miller, D.J. Tantillo, R.G.S. Berlinck, and R. Sarpong, \"Total synthesis and isolation of citrinalin and cyclopiamine congeners\", Nature<\/i>, vol. 509, pp. 318-324, 2014. https:\/\/doi.org\/10.1038\/nature13273<\/a>\n\n<\/li>\n
    2. T. Mugishima, M. Tsuda, Y. Kasai, H. Ishiyama, E. Fukushi, J. Kawabata, M. Watanabe, K. Akao, and J. Kobayashi, \"Absolute Stereochemistry of Citrinadins A and B from Marine-Derived Fungus\", The Journal of Organic Chemistry<\/i>, vol. 70, pp. 9430-9435, 2005. https:\/\/doi.org\/10.1021\/jo051499o<\/a>\n\n<\/li>\n
    3. F. Cherblanc, Y. Lo, E. De\u2005Gussem, L. Alcazar\u2010Fuoli, E. Bignell, Y. He, N. Chapman\u2010Rothe, P. Bultinck, W.A. Herrebout, R. Brown, H.S. Rzepa, and M.J. Fuchter, \"On the Determination of the Stereochemistry of Semisynthetic Natural Product Analogues using Chiroptical Spectroscopy: Desulfurization of Epidithiodioxopiperazine Fungal Metabolites\", Chemistry \u2013 A European Journal<\/i>, vol. 17, pp. 11868-11875, 2011. https:\/\/doi.org\/10.1002\/chem.201101129<\/a>\n\n<\/li>\n
    4. F.L. Cherblanc, Y. Lo, W.A. Herrebout, P. Bultinck, H.S. Rzepa, and M.J. Fuchter, \"Mechanistic and Chiroptical Studies on the Desulfurization of Epidithiodioxopiperazines Reveal Universal Retention of Configuration at the Bridgehead Carbon Atoms\", The Journal of Organic Chemistry<\/i>, vol. 78, pp. 11646-11655, 2013. https:\/\/doi.org\/10.1021\/jo401316a<\/a>\n\n<\/li>\n
    5. H.D. Flack, and G. Bernardinelli, \"The use of X\u2010ray crystallography to determine absolute configuration\", Chirality<\/i>, vol. 20, pp. 681-690, 2007. https:\/\/doi.org\/10.1002\/chir.20473<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      I was lucky enough to attend the announcement made in 2012 of the discovery of the Higgs Boson. It consisted of a hour-long talk mostly about statistics, and how the particle physics community can only claim a discovery when their data has\u00a0achieved a 5\u03c3 confidence level. This represents a 1 in 3.5 million probability of […]<\/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":[1],"tags":[27,1242,20,42],"ppma_author":[2661],"class_list":["post-12705","post","type-post","status-publish","format-standard","hentry","category-general","tag-chemical","tag-reading","tag-steve-bachrach","tag-x-ray"],"yoast_head":"\nThe 5\u03c3-confidence level: how much chemistry achieves this? - 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=12705\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The 5\u03c3-confidence level: how much chemistry achieves this? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"I was lucky enough to attend the announcement made in 2012 of the discovery of the Higgs Boson. 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A decade on, and possibly approaching 100 articles by many authors on the topic,\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\/2020\/11\/NMn_33a-1024x839.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":16889,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16889","url_meta":{"origin":12705,"position":1},"title":"More stereoelectronics galore: hexamethylene triperoxide diamine.","author":"Henry Rzepa","date":"September 22, 2016","format":false,"excerpt":"Compounds with O-O bonds often have weird properties. For example, artemisinin, which has some fascinating stereoelectronics. Here is another such, recently in the news\u00a0and\u00a0known as HMTD (hexamethylene triperoxide diamine).\u00a0The crystal structure was reported some time ago and the article included an inspection of the computed wavefunction. 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":14395,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14395","url_meta":{"origin":12705,"position":2},"title":"The structure of naphthalene: 1890-1925, and a modern twist.","author":"Henry Rzepa","date":"July 18, 2015","format":false,"excerpt":"This is a little historical essay into the electronic structure of naphthalene, presented as key dates (and also collects comments made which were appended to other posts). 1890: Henry Armstrong presents the following structure of naphthalene. Three words need translation into modern usage. Where he uses the word nuclei the\u2026","rel":"","context":"In "Historical"","block_context":{"text":"Historical","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=565"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":23777,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23777","url_meta":{"origin":12705,"position":3},"title":"A suggestion for a molecule with a M\u2a78C quadruple bond with trigonal metal coordination.","author":"Henry Rzepa","date":"May 13, 2021","format":false,"excerpt":"The proposed identification of molecules with potential metal to carbon quadruple bonds, in which the metal exhibits trigonal bipyramidal coordination rather than the tetrahedral modes which have been proposed in the literature,, leads on to asking whether simple trigonal coordination at the metal can also sustain this theme? The rational\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":12276,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12276","url_meta":{"origin":12705,"position":4},"title":"Artemisinin: are stereo-electronics at the core of its (re)activity?","author":"Henry Rzepa","date":"April 13, 2014","format":false,"excerpt":"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\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":"artemisinin1","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/04\/artemisinin1.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":17992,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17992","url_meta":{"origin":12705,"position":5},"title":"The conformation of enols: revealed and explained.","author":"Henry Rzepa","date":"April 6, 2017","format":false,"excerpt":"Enols are simple compounds with an OH group as a substituent on a C=C double bond and with a very distinct conformational preference for the OH group. Here I take a look at this preference as revealed by crystal structures, with the theoretical explanation. First, a search of the Cambridge\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\/2017\/04\/All-1024x948.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\/12705","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=12705"}],"version-history":[{"count":9,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/12705\/revisions"}],"predecessor-version":[{"id":12714,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/12705\/revisions\/12714"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=12705"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=12705"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=12705"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=12705"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}