{"id":21436,"date":"2019-11-09T07:00:49","date_gmt":"2019-11-09T07:00:49","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=21436"},"modified":"2019-11-10T09:09:25","modified_gmt":"2019-11-10T09:09:25","slug":"the-structure-of-tetrodotoxin-as-a-free-base","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21436","title":{"rendered":"The Structure of Tetrodotoxin as a free base."},"content":{"rendered":"
\n

The notorious neurotoxin Tetrodotoxin is often chemically represented as a zwitterion, shown below as 1<\/strong>. This idea seems to originate from a famous article written in 1964 by the legendary organic chemist, Robert Burns Woodward.[1]<\/a><\/span> This structure has propagated on to Wikipedia<\/a> and is found in many other sources. \"\"<\/a>
\nWith the elegance and the unique style that is typical Woodward, his article is a tour de force<\/em> because of the way in which he deploys a large armoury of spectroscopic (X-ray crystal,\u2020<\/sup> NMR, IR) as well as physicochemical (pKa) tools to infer this structure; an approach that has been subsequently widely emulated. The article a well worth a read for the elegant logic that slowly builds to a climax on page 73 (sic!) of the article, when he unveils his final structure (XXXVIII<\/strong>, or 38). The lecture(s) from which the article is apparently derived must have been one hell of an occasion.\u2021<\/sup><\/p>\n

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

One technique not available in 1964 to Woodward was quantitative quantum calculation of the molecular free energies. This property is now routinely computable,\u00a0but is still only rarely used for structural problems even today.\u00a0Here I add this property to Woodward’s collection (FAIR data DOI: 10.14469\/hpc\/6278<\/a>, method=\u03c9B97XD\/Def2-TZVPP, SCRF=chloroform).<\/p>\n

My initial hypothesis was based on the observation of a rather large separation of the charges in the zwitterion. The surface below is the computed molecular electrostatic potential (value 0.1 au),\u00a0which indeed shows large charge separation. The computed dipole moment is 18D.<\/p>\n

\"\"<\/a>

MEP isosurface; orange = -ve, \u00a0yellow = +ve.<\/p><\/div>\n

Charges by and large do not much like being separated, even though of course the actual separation is often misleadingly indicated by simple Lewis structures such as the above. So I started by moving one proton to produce 2<\/strong> to see if that improved the free energy, by reducing charge separation. The dipole moment was indeed smaller at\u00a014.6D (although the energy was not lower).<\/p>\n

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

I then included three neutral forms (3<\/strong>–5<\/strong>) where the nominal charge separation is eliminated entirely.<\/p>\n\n\n\n\n\n\n\n\n
Structure<\/th>\nDiagram<\/th>\n\n

\u0394\u0394G<\/p>\n

kcal\/mol<\/p>\n<\/th>\n

Dipole moment<\/th>\n<\/tr>\n
1<\/td>\n\"\"<\/td>\n+10.4<\/td>\n18.0<\/td>\n<\/tr>\n
2<\/td>\n\"\"<\/td>\n+21.1<\/td>\n14.6<\/td>\n<\/tr>\n
3<\/td>\n\"\"<\/td>\n0.0<\/td>\n3.9<\/td>\n<\/tr>\n
4<\/td>\n\"\"<\/td>\n+1.8<\/td>\n6.0<\/td>\n<\/tr>\n
5<\/td>\n\"\"<\/td>\n+4.2<\/td>\n6.5<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

This computed model suggests 3<\/strong> is the predominant species present (in chloroform solutions), although of course all the species are in a prototropic equilibrium. 3<\/strong> also happens to have the smallest calculated dipole moment. Species 5<\/strong>\u00a0was also a front-runner in 1964[2]<\/a><\/span> (as 1c<\/strong> in that article). Certainly the zwitterion 1<\/strong> as suggested by\u00a0Woodward,\u00a0with its large degree of charge separation, is unlikely to feature and 5<\/strong> is also less likely to be the dominant species.<\/p>\n

The computed free energy for such molecules takes < 1 day of elapsed time to produce, and so I here argue that this should be a mandatory reported property for such structural problems.<\/p>\n

\n

\u2020<\/sup>The crystal structure is recorded[3]<\/a><\/span> for the protonated species, as the HCl or HBr salt. These of course do not indicate where the protons are for the deprotonated neutral base. \u2021<\/sup>I only ever attended one lecture by Woodward. It lasted the typical two hours and was indeed hugely\u00a0memorable in several regards. I also note the parsimony of stereochemical notation (just one dashed bond),\u00a0presumably on the grounds that omitting such notation does not actually result in ambiguity. Disambiguation does depend of course on perceived “hidden line” removal.<\/p>\n

References<\/h2>\n
  1. R.B. Woodward, \"The structure of tetrodotoxin\", Pure and Applied Chemistry<\/i>, vol. 9, pp. 49-74, 1964. https:\/\/doi.org\/10.1351\/pac196409010049<\/a>\n\n<\/li>\n
  2. T. Goto, Y. Kishi, S. Takahashi, and Y. Hirata, \"Further studies on the structure of tetrodotoxin\", Tetrahedron Letters<\/i>, vol. 5, pp. 779-786, 1964. https:\/\/doi.org\/10.1016\/0040-4039(64)83035-5<\/a>\n\n<\/li>\n
  3. A. Furusaki, Y. Tomiie, and I. Nitta, \"The Crystal and Molecular Structure of Tetrodotoxin Hydrobromide\", Bulletin of the Chemical Society of Japan<\/i>, vol. 43, pp. 3332-3341, 1970. https:\/\/doi.org\/10.1246\/bcsj.43.3332<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    The notorious neurotoxin Tetrodotoxin is often chemically represented as a zwitterion, shown below as 1. This idea seems to originate from a famous article written in 1964 by the legendary organic chemist, Robert Burns Woodward. This structure has propagated on to Wikipedia and is found in many other sources. With the elegance and the unique […]<\/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":[4],"tags":[],"ppma_author":[2661],"class_list":["post-21436","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry"],"yoast_head":"\nThe Structure of Tetrodotoxin as a free base. - 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=21436\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The Structure of Tetrodotoxin as a free base. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"The notorious neurotoxin Tetrodotoxin is often chemically represented as a zwitterion, shown below as 1. This idea seems to originate from a famous article written in 1964 by the legendary organic chemist, Robert Burns Woodward. This structure has propagated on to Wikipedia and is found in many other sources. 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This idea seems to originate from a famous article written in 1964 by the legendary organic chemist, Robert Burns Woodward. This structure has propagated on to Wikipedia and is found in many other sources. 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Niels Bohr was one such and four decades later Robert Woodward wrote \"The conservation of orbital symmetry\" (Chem. Soc. Special Publications (Aromaticity), 1967, 21, 217-249; it is not online and so no doi\u2026","rel":"","context":"In "pericyclic"","block_context":{"text":"pericyclic","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=559"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":3908,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=3908","url_meta":{"origin":21436,"position":2},"title":"Ferrocene","author":"Henry Rzepa","date":"April 17, 2011","format":false,"excerpt":"The structure of ferrocene was famously analysed by Woodward and Wilkinson in 1952,, symmetrically straddled in history by Pauling (1951) and Watson and Crick (1953). Quite a trio of Nobel-prize winning molecular structural analyses, all based on a large dose of intuition. The structures of both proteins and DNA succumbed\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\/2011\/04\/ferrocene-aim.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":6859,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=6859","url_meta":{"origin":21436,"position":3},"title":"Streptomycin: a case study in the progress of science.","author":"Henry Rzepa","date":"May 28, 2012","format":false,"excerpt":"Streptomycin is an antibiotic active against tuberculosis, and its discovery has become something of a cause c\u00e9l\u00e8bre. It was first isolated on October 19, 1943 by a graduate student Albert Schatz in the laboratory of Selman Waksman at Rutgers University. I want to concentrate in this post on its molecular\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\/05\/streptomycin.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":23203,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23203","url_meta":{"origin":21436,"position":4},"title":"The thermal reactions … took precisely the opposite stereochemical course to that which we had predicted","author":"Henry Rzepa","date":"January 20, 2021","format":false,"excerpt":"The quote of the post title comes from R. B. Woodward explaining the genesis of the discovery of what are now known as the Woodward-Hoffmann rules for pericyclic reactions. I first wrote about this in 2012, noting that \"for (that) blog, I do not want to investigate the transition states\".\u00a0Here\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\/01\/Screenshot-515-300x215.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":10611,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10611","url_meta":{"origin":21436,"position":5},"title":"Another Woodward pericyclic example dissected: all is not what it seems.","author":"Henry Rzepa","date":"May 22, 2013","format":false,"excerpt":"Here is another example gleaned from that Woodward essay of 1967 (Chem. Soc. Special Publications (Aromaticity), 1967, 21, 217-249), where all might not be what it seems. Woodward notes that the reaction between the (highly reactive) 1 does not occur. This is attributed to it being a disallowed \u03c06 +\u2026","rel":"","context":"In \"free energy barrier\"","block_context":{"text":"free energy barrier","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=free-energy-barrier"},"img":{"alt_text":"w2+2+2","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/05\/w2%2B2%2B2.gif?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\/21436","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=21436"}],"version-history":[{"count":25,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/21436\/revisions"}],"predecessor-version":[{"id":21468,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/21436\/revisions\/21468"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=21436"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=21436"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=21436"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=21436"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}