{"id":21631,"date":"2019-12-15T09:06:52","date_gmt":"2019-12-15T09:06:52","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=21631"},"modified":"2019-12-17T09:13:28","modified_gmt":"2019-12-17T09:13:28","slug":"molecules-of-the-year-2019-topological-molecular-nanocarbons-all-benzene-catenane-and-trefoil-knot","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21631","title":{"rendered":"Molecules of the year – 2019: Topological molecular nanocarbons – All-benzene catenane and trefoil knot."},"content":{"rendered":"
\n

Here is another molecule of the year, on a topic close to my heart<\/a>, the catenane systems 1<\/strong> and the trefoil knot 2<\/strong>[1]<\/a><\/span> Such topology is closely inter-twinned with three dimensions (literally) and I always find that the flat pages of a journal are simply insufficient to do them justice. So I set about finding the 3D coordinates.<\/p>\n

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

The most obvious place to start is the supporting information. I show below a little snippet of what I found, which is fairly typical of such data in the PDF-based SI documents accompanying most articles.<\/p>\n

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

A bit of knowledgeable text-editing is needed to convert these into something that can be displayed as a rotatable 3D model.‡<\/sup> For this example, the three-column mode did not actually prove too problematic (but sometimes you have to work very hard to reduce it to the single column mode required for coordinates) and one has to remember to notice and remove the pagination text from the coordinates. Here I include the structure as a static 2D image which when clicked expands to a 3D model. Sadly, I know of no journal that offers up this relatively simple service as part of its “added-value” to the publication processes; it has been possible to do this since 1994![2]<\/a><\/span>,[3]<\/a><\/span> I also found that the provided coordinates could be symmetrised to D2<\/sub>.<\/p>\n

\"\"

1a, which are here symmetrised to D2<\/sub> symmetry.<\/p><\/div>\n

Molecule 2<\/strong> posed a new challenge. The coordinates when extracted from the SI had 480 atoms, double that of 1a<\/strong>. When displayed they overlayed each other. Clearly two sets of 240 atoms was the answer (the first probably in error) only the second set of which displays as a trefoil knot. The coordinates here can be symmetrised to D3<\/sub>, as appropriate for a trefoil knot.<\/p>\n

\"\"

2, which here are symmetrised to D3<\/sub> symmetry<\/p><\/div>\n

The above coordinates are computed using quantum mechanics at the B3LYP-D3\/6-31G(d) level. What about the crystallographic coordinates? Here again a little expertise is needed to obtain these.<\/p>\n

    \n
  1. Just after the article acknowledgements, the CCDC identifiers are given as 1860595-7 and 1908693. These values are resolved using www.ccdc.cam.ac.uk\/structures\/<\/a> which allows the download of a CIF file.<\/li>\n
  2. These files reveal that a number of solvent and other molecules have been occluded into the structures, and for clarity it helps to edit all these out as well as disordered atoms with partial occupancy.<\/li>\n<\/ol>\n
    \"\"

    Crystallographic coordinates for 1a. DOI:\u00a010.5517\/ccdc.csd.cc20g36t<\/a><\/p><\/div>\n

    \"\"

    Crystallographic coordinates for 2. DOI:\u00a010.5517\/ccdc.csd.cc20g37v<\/a><\/p><\/div>\n

    Each of these experimental structures is also allocated a DOI of its own, which can be accessed from the captions above, if you want to view the un-edited coordinates. I have also made available my coordinates produced for the display here as a FAIR dataset (DOI: 10.14469\/hpc\/6470<\/a>), together with metadata such as the InChI descriptors to improve its discoverability.<\/p>\n

    Having acquired and displayed both the calculated and the measured coordinates, I noticed one oddity. The calculated structure for 2<\/b> symmetrises to D3<\/sub> symmetry, but the measured crystal structure only to C2<\/sub> symmetry. This is due to a “kink” in the twists for the latter coordinates, a single region where the Ar-Ar single bond is twisted by 66°. This kink is absent in the calculated coordinates, where the largest dihedral angle at the Ar-Ar bond is only 37°. Is this effect real? What does it tell us about the conjugations and extended aromaticity of this system? Such twist localisation has been previously noticed in cyclacenes.[4]<\/a><\/span> I think this observation highlights the need to have readily accessible 3D structures of such novel systems, if only to allow readers to spot such apparently anomalies.<\/p>\n

    So, with a little bit of knowledge and effort, one can indeed proceed from a published article to viewing aspects of the three-dimensional topology of the molecules discussed. I just feel it would be good if these aspects could be better integrated into the article itself, since I suspect that the additional effort and knowledge required to go further is probably not going to appeal to most readers.‡<\/sup><\/p>\n

    \n

    ‡<\/sup>Tidying up the PDF cartesian coordinates into a list of atomic number and a set of three coordinates per line of text is relatively simple. To coerce this format into a visualisation program takes more knowledge. Direct conversion to eg a standard molfile is not possible. I instead add a header to the coordinates to make it suitable for visualisation using the Gaussview program. Another good program for handling this is wxMacMolPlot<\/a> which supports the veritable Xmol XYZ format, but again a correct header at the top of the file is needed for this program to recognise the file. As I noted, only a knowledgeable user would be able to do this, and the average reader is unlikely to go down this road.<\/p>\n

    References<\/h2>\n
    1. Y. Segawa, M. Kuwayama, Y. Hijikata, M. Fushimi, T. Nishihara, J. Pirillo, J. Shirasaki, N. Kubota, and K. Itami, \"Topological molecular nanocarbons: All-benzene catenane and trefoil knot\", Science<\/i>, vol. 365, pp. 272-276, 2019. https:\/\/doi.org\/10.1126\/science.aav5021<\/a>\n\n<\/li>\n
    2. H.S. Rzepa, B.J. Whitaker, and M.J. Winter, \"Chemical applications of the World-Wide-Web system\", Journal of the Chemical Society, Chemical Communications<\/i>, pp. 1907, 1994. https:\/\/doi.org\/10.1039\/c39940001907<\/a>\n\n<\/li>\n
    3. O. Casher, G.K. Chandramohan, M.J. Hargreaves, C. Leach, P. Murray-Rust, H.S. Rzepa, R. Sayle, and B.J. Whitaker, \"Hyperactive molecules and the World-Wide-Web information system\", Journal of the Chemical Society, Perkin Transactions 2<\/i>, pp. 7, 1995. https:\/\/doi.org\/10.1039\/p29950000007<\/a>\n\n<\/li>\n
    4. S. Mart\u00edn-Santamar\u00eda, and H.S. Rzepa, \"Twist localisation in single, double and triple twisted M\u00f6bius cyclacenes\u2020\", Journal of the Chemical Society, Perkin Transactions 2<\/i>, pp. 2378-2381, 2000. https:\/\/doi.org\/10.1039\/b005560n<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      Here is another molecule of the year, on a topic close to my heart, the catenane systems 1 and the trefoil knot 2 Such topology is closely inter-twinned with three dimensions (literally) and I always find that the flat pages of a journal are simply insufficient to do them justice. So I set about finding […]<\/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_feature_clip_id":0,"_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-21631","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry"],"yoast_head":"\nMolecules of the year - 2019: Topological molecular nanocarbons - All-benzene catenane and trefoil knot. - 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=21631\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Molecules of the year - 2019: Topological molecular nanocarbons - All-benzene catenane and trefoil knot. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"Here is another molecule of the year, on a topic close to my heart, the catenane systems 1 and the trefoil knot 2 Such topology is closely inter-twinned with three dimensions (literally) and I always find that the flat pages of a journal are simply insufficient to do them justice. 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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,\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\/2010\/05\/metallatrefoil.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":17366,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17366","url_meta":{"origin":21631,"position":1},"title":"Braiding a molecular knot with eight crossings.","author":"Henry Rzepa","date":"January 20, 2017","format":false,"excerpt":"This is one of those posts of a molecule whose very structure is interesting enough to merit a picture and a 3D model. The study reports a molecular knot with the remarkable number of eight crossings. The DOI for the 3D model is 10.5517\/CCDC.CSD.CC1M85Y0\u00a0(or click on the image above). Such\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\/2017\/01\/085-1021x1024.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":2084,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2084","url_meta":{"origin":21631,"position":2},"title":"Chemistry with a super-twist: A molecular trefoil knot, part 2.","author":"Henry Rzepa","date":"June 1, 2010","format":false,"excerpt":"A conjugated, (apparently) aromatic molecular trefoil might be expected to have some unusual, if not extreme properties. Here some of these are explored. The first is the vibrational spectrum. With 144 atoms for this molecule, it has 426 vibrational modes, but one is highlighted below. This is the mode that\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\/2010\/06\/trefoil-kekule.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":25761,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25761","url_meta":{"origin":21631,"position":3},"title":"Molecules of the year -2022. Data issues!","author":"Henry Rzepa","date":"December 13, 2022","format":false,"excerpt":"The list of molecules of the year is out now at C&E News (but you have to have an account to view the list, unlike previous years).\u2663 These three caught my eye: Electron in a cube: Synthesis and characterization of perfluorocubane as an electron acceptor,. I have already written about\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":30975,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=30975","url_meta":{"origin":21631,"position":4},"title":"The first “half-M\u00f6bius” molecule: A question about its twist?","author":"Henry Rzepa","date":"March 13, 2026","format":false,"excerpt":"The recent report of what is termed a \"half-M\u00f6bius\" molecule is generating a lot of excitement. It has its origins in a project to make odd-numbered cyclocarbons on STM (scanning tunnelling microscope) surfaces. I had discussed even-numbered cyclocarbons in another post, where I also happened to include several odd-numbered examples,\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":17142,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17142","url_meta":{"origin":21631,"position":5},"title":"Molecule of the year (month\/week)?","author":"Henry Rzepa","date":"December 12, 2016","format":false,"excerpt":"Chemical and engineering news (C&EN) is asking people to vote for their molecule of the year from six highlighted candidates. This reminded me of the history of internet-based \"molecules of the moment\". It is thought that the concept originated in December 1995 here at Imperial and in January 1996 at\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\/2016\/12\/ferris.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","author_category":"1","first_name":"Henry","last_name":"Rzepa","user_url":"https:\/\/orcid.org\/0000-0002-8635-8390","job_title":"","description":"Henry Rzepa is Emeritus Professor of Computational Chemistry at Imperial College London."}],"_links":{"self":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/21631","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=21631"}],"version-history":[{"count":48,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/21631\/revisions"}],"predecessor-version":[{"id":21693,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/21631\/revisions\/21693"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=21631"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=21631"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=21631"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=21631"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}