{"id":2046,"date":"2010-05-31T15:51:00","date_gmt":"2010-05-31T14:51:00","guid":{"rendered":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2046"},"modified":"2019-10-12T16:38:39","modified_gmt":"2019-10-12T15:38:39","slug":"chemistry-with-a-super-twist-a-molecular-trefoil-knot","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2046","title":{"rendered":"Chemistry with a super-twist: A molecular trefoil knot, part 1."},"content":{"rendered":"
\n

Something important happened in chemistry for the first time about 100 years ago. A molecule was built (nowadays we would say synthesized) specifically for the purpose of investigating a theory. It was cyclo-octatetraene or (CH)8<\/sub>, and it was made by Willst\u00e4tter and Waser[1]<\/a><\/span> to try to find out if benzene, (CH)6<\/sub>, was an aromatic<\/strong> one-off or whether it might be a member of a series, envisaged as (CH)n<\/sub>. Of course, a hell of a surprise was in store for Willst\u00e4tter and Waser[1]<\/a><\/span>!\u00a0Prior to this synthesis, (CH)8<\/sub> had never existed; nature had not gotten there first. In that sense, chemistry became much like mathematics had before it; it was OK to make molecules because they might be interesting<\/em>, and for the purpose of\u00a0investigating possible patterns in nature. So it is in this spirit that I suggest an interesting molecule here. It is a molecular trefoil, constructed by joining 15 pyrrole units together into a ring with appropriate linkers and in effect tying a knot in that ring. A trefoil knot to be specific.<\/p>\n

\"\"

A molecular trefoil knot, shown with a Mg at the centre. Click to view in 3D<\/p><\/div>\n

Why might such a molecule be interesting? These are ten reasons<\/strong>:<\/p>\n

    \n
  1. It would make an interesting ligand for a metal<\/li>\n
  2. It has lots of interesting groves and dimples for transition states to nest in<\/li>\n
  3. It would be an extended porphyrin (a pentadecaphyrin to be precise). Nature likes to make molecules out of tetraphyrins (chlorophyll, haemoglobin, etc), and so we are pushing beyond nature’s own boundaries. Both a penta and a hexadecaphyrin have already been made[2]<\/a><\/span>,[2]<\/a><\/span>,[3]<\/a><\/span><\/li>\n
  4. The trefoil knot is a most interesting object in a branch of mathematics called knot theory<\/strong>, and it is also related to another fascinating object, the M\u00f6bius band<\/strong>.<\/li>\n
  5. The pyrrole units in such a molecule are conjugated<\/em> via the \u03c0-system, and the molecule above is potentially fully conjugated across its entire length. This could make it aromatic, and hence it is interesting for the same reason that Willst\u00e4tter[1]<\/a><\/span> found cyclo-octatetraene\u00a0so.<\/li>\n
  6. The system above, if carefully counted, would have 74 \u03c0-electrons in cyclic conjugation. This would make it a 4n+2 aromatic (n=18), just like benzene, but not at all like (CH)8 <\/sub>(which as Willst\u00e4tter and Wases[1]<\/a><\/span> found, is not aromatic).<\/li>\n
  7. It seems highly twisted. Indeed the title of this post is super-twisted. But is it really? We learn from topology that twist is not the only property that cyclic bands or strips can have. They can also exhibit writhe<\/strong>. So is it writhed as well as twisted?<\/li>\n
  8. Aromatic molecules have one rather mysterious behaviour. The ring bonds in in such systems resemble neither double nor single bonds, but aromatic bonds, and in this they have a length intermediate between the single and the double, and this applies to all of the bonds. The origins of this delocalization<\/em> continue to provoke controversy (see this post<\/a>). Thus it is thought that only (planar) carbon rings with around 26 or less \u03c0-electrons can exhibit such equal lengths (boron rings can apparently go much further.[4]<\/a><\/span>.\u00a0More than that, and distortion sets in which makes the lengths alternate. The molecule above has 74 \u03c0-electrons. What will its bonds do, and is what they do related to the twist (or the writhe) of the system?<\/li>\n
  9. The trefoil is chiral<\/strong>. It cannot be superimposed upon its mirror image. But how chiral (whatever that means)?<\/li>\n
  10. The system has many design handles, including the number of pyrrole (or thiophene) units, the number of\u00a0N-H\u00a0vs =N motifs, and the scope for templating using a metal cation (Mg in the example above).<\/li>\n<\/ol>\n

    So what might be the properties of our trefoil knot? I am going to list only two here.<\/p>\n

      \n
    1. A theorem emerged from mathematics in the 1970s known as the White, C\u00e3lug\u00e3reanu, Fuller Theorem. It defines the topological properties of bands in terms of a quantity known as the linking number (Lk). The theorem states that: Lk = Tw + Wr<\/strong>, where Lk is an integer, being the sum of two properties Tw<\/strong> (the total twist of the band) and Wr<\/strong> (the total writhe of the band). This theory was recently extended to the analysis of twisted conjugated molecular rings[5]<\/a><\/span>, for which Lk adopts integer values (in units of \u03c0). Thus a conjugated M\u00f6bius \u03c0-cycle has a value Lk = 1\u03c0 (specifically when describing the band formed by the \u03c0-electrons). Most of this value is composed of twist rather than writhe. What of our molecule? Well, it has Lk =6\u03c0, and this comprises Tw = ~-0.8\u03c0\u00a0and Wr ~+6.8\u03c0\u00a0(yes the two can be either positive or negative, and do not have to be the same sign). The surprise is that it is (overall) hardly twisted! The knot is composed almost entirely of writhe. So much for the title of this post!<\/li>\n
    2. What about the bond lengths? The best way of analyzing these[6]<\/a><\/span> is to compare pairs of so-called meso<\/em>-bonds, being the coupler unit connecting any two pyrrole rings. Around the cycle, all the C-C meso-pairs are ~1.4\u00c5 and the C-N pairs are both ~1.34\u00c5. That characteristic of benzene, in having all its (C-C) bonds equal, seems true here as well (at least at the B3LYP\/6-311G(d,p) level, see e.g.10042\/to-2109<\/a>. There are reasons for thinking that in fact the B3LYP method does predict this behaviour more or less realistically). By the way, a molecule with a \u03c0-linking number of\u00a0six is indeed classified by the same selection rule as benzene, ie 4n+2 (odd numbers of \u00a0Lk are governed by a 4n rule instead).[7]<\/a><\/span><\/li>\n<\/ol>\n

      It is tempting to conclude that perhaps the extended conjugation of this molecule (shown by the bond length equality) is somehow connected to the dominance of writhe over twist in this trefoil.<\/p>\n

      I will follow this post up with another relating to the predicted chiro-optical properties. For now, I leave its synthesis to be contemplated by a present day Willst\u00e4tter or Waser.<\/p>\n

      \n

      Webcite archive:. Chemistry with a super-twist: A molecular trefoil knot, part 1. . 2010-06-01. URL:http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2046. Accessed: 2010-06-01. (Archived by WebCite\u00ae at http:\/\/www.webcitation.org\/5qA81X8qW<\/a>)<\/p>\n

      References<\/h2>\n
      1. R. Willst\u00e4tter, and E. Waser, \"\u00dcber Cyclo\u2010octatetraen\", Berichte der deutschen chemischen Gesellschaft<\/i>, vol. 44, pp. 3423-3445, 1911. https:\/\/doi.org\/10.1002\/cber.191104403216<\/a>\n\n<\/li>\n
      2. S. Shimizu, W. Cho, J. Sessler, H. Shinokubo, and A. Osuka, \"<i>meso<\/i>\u2010Aryl Substituted Rubyrin and Its Higher Homologues: Structural Characterization and Chemical Properties\", Chemistry \u2013 A European Journal<\/i>, vol. 14, pp. 2668-2678, 2008. https:\/\/doi.org\/10.1002\/chem.200701909<\/a>\n\n<\/li>\n
      3. J. Setsune, and S. Maeda, \"Bis(azafulvene) as a Versatile Building Block for Giant Cyclopolypyrroles:\u2009 X-ray Crystal Structure of [64]Hexadecaphyrin(1.0.1.0.1.0.1.0.1.0.1.0.1.0.1.0)\", Journal of the American Chemical Society<\/i>, vol. 122, pp. 12405-12406, 2000. https:\/\/doi.org\/10.1021\/ja005588o<\/a>\n\n<\/li>\n
      4. H.S. Rzepa, \"The distortivity of \u03c0-electrons in conjugated boron rings\", Physical Chemistry Chemical Physics<\/i>, vol. 11, pp. 10042, 2009. https:\/\/doi.org\/10.1039\/b911817a<\/a>\n\n<\/li>\n
      5. S.M. Rappaport, and H.S. Rzepa, \"Intrinsically Chiral Aromaticity. Rules Incorporating Linking Number, Twist, and Writhe for Higher-Twist M\u00f6bius Annulenes\", Journal of the American Chemical Society<\/i>, vol. 130, pp. 7613-7619, 2008. https:\/\/doi.org\/10.1021\/ja710438j<\/a>\n\n<\/li>\n
      6. H.S. Rzepa, \"Lemniscular Hexaphyrins as Examples of Aromatic and Antiaromatic Double-Twist M\u00f6bius Molecules\", Organic Letters<\/i>, vol. 10, pp. 949-952, 2008. https:\/\/doi.org\/10.1021\/ol703129z<\/a>\n\n<\/li>\n
      7. P.L. Ayers, R.J. Boyd, P. Bultinck, M. Caffarel, R. Carb\u00f3-Dorca, M. Caus\u00e1, J. Cioslowski, J. Contreras-Garcia, D.L. Cooper, P. Coppens, C. Gatti, S. Grabowsky, P. Lazzeretti, P. Macchi, ?. Mart\u00edn Pend\u00e1s, P.L. Popelier, K. Ruedenberg, H. Rzepa, A. Savin, A. Sax, W.E. Schwarz, S. Shahbazian, B. Silvi, M. Sol\u00e0, and V. Tsirelson, \"Six questions on topology in theoretical chemistry\", Computational and Theoretical Chemistry<\/i>, vol. 1053, pp. 2-16, 2015. https:\/\/doi.org\/10.1016\/j.comptc.2014.09.028<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

        Something important happened in chemistry for the first time about 100 years ago. A molecule was built (nowadays we would say synthesized) specifically for the purpose of investigating a theory. It was cyclo-octatetraene or (CH)8, and it was made by Willst\u00e4tter and Waser to try to find out if benzene, (CH)6, was an aromatic one-off […]<\/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":[4],"tags":[2648,264,236,263,265],"ppma_author":[2661],"class_list":["post-2046","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-interesting-chemistry","tag-linking-number","tag-metal-cation","tag-trefoil-knot","tag-writhe"],"yoast_head":"\nChemistry with a super-twist: A molecular trefoil knot, part 1. - 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=2046\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Chemistry with a super-twist: A molecular trefoil knot, part 1. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"Something important happened in chemistry for the first time about 100 years ago. 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