{"id":25761,"date":"2022-12-13T15:34:49","date_gmt":"2022-12-13T15:34:49","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=25761"},"modified":"2023-03-12T08:28:45","modified_gmt":"2023-03-12T08:28:45","slug":"molecules-of-the-year-2022-data-issues","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25761","title":{"rendered":"Molecules of the year -2022.  Data issues!"},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"25761\">\n<p>The list of molecules of the year is out now at <a href=\"https:\/\/cen.acs.org\/synthesis\/Check-CENs-molecules-year-2022\/100\/i44\">C&amp;E News<\/a> (but you have to have an account to view the list, unlike previous years).<sup>&clubs;<\/sup> These three caught my eye:<\/p>\n<ol>\n<li><em>Electron in a cube: Synthesis and characterization of perfluorocubane as an electron acceptor<\/em>,<span id=\"cite_ITEM-25761-0\" name=\"citation\"><a href=\"#ITEM-25761-0\">[1]<\/a><\/span>. I have already <a href=\"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=25486\">written about this system<\/a> and will not discuss it further, except to note this one topped the poll!<\/li>\n<li><em>Vernier template synthesis of molecular knots<\/em><span id=\"cite_ITEM-25761-1\" name=\"citation\"><a href=\"#ITEM-25761-1\">[2]<\/a><\/span><\/li>\n<li><em>Megalo-Cavitands: Synthesis of Acridane[4]arenes and Formation of Large, Deep Cavitands for Selective C70 Uptake<\/em><span id=\"cite_ITEM-25761-2\" name=\"citation\"><a href=\"#ITEM-25761-2\">[3]<\/a><\/span><\/li>\n<\/ol>\n<p>The last two are examples of large three-dimensional molecules with unusual properties. The second is an example of a trefoil-of-trefoils, called a triskelion knot and I was very keen to get hold of its coordinates so that I could inspect the knotting. I thought I might summarise here the hierarchical procedures one might try for acquiring such data.<\/p>\n<ul>\n<li>The most modern method of acquiring data associated with an article is to inspect the citation list at the end of the article. The trend encouraged by the FAIR data principles suggests that if such data has an associated DOI (as indeed the article itself does), then this DOI should be cited in the citations just like articles themselves. This concept is also known as treating data as a <strong>first class citizen<\/strong> of the scholarly processes. In this case no data was associated with the 81 citations listed at\u00a0<a href=\"https:\/\/doi.org\/10.1126\/science.abm9247\">10.1126\/science.abm9247<\/a><\/li>\n<li>The prevalent method since ~1996 has been to next download any ESI. That is linked <a href=\"https:\/\/www.science.org\/doi\/suppl\/10.1126\/science.abm9247\/suppl_file\/science.abm9247_sm.pdf\">here<\/a>. I cannot help but note that the PDF format is not one optimised for data, but its better than nothing. This PDF has 114 pages, and one eventually finds the following on p 103: structures and corresponding energies uploaded to the Github database (<a href=\"https:\/\/github.com\/kjhstenlid\/AshbridgeVernier2022\/\">https:\/\/github.com\/kjhstenlid\/AshbridgeVernier2022\/<\/a>). Github is known as a software repository, but its use as a data repository is unusual. Thus no DOI is assigned this data (which would explain why its not listed in the article citations). Here one learns from the readme that it contains <em>Molecular knot structures in cif-file format for the Verner and Sheild knots<\/em>.<\/li>\n<li>To get this data one has to pretend it is code, and download the ZIP code archive. The CIF file found there however gives a fatal error when trying to load into a CIF viewer such as Mercury: <em>Reading cell from Cif failed, could not retrieve &#8216;_cell_length+a&#8217;. <\/em>The CIF is clearly not generated from a crystallographic analysis program but a modelling program and is clearly invalid as a CIF.<\/li>\n<li>One now has to fall back seeing if the CIF file can be rescued using a text editor. This is non-trivial but about 10 minutes of editing finally produces a file that can be viewed.<\/li>\n<li>Here is the 3D structure (click on the image to view).<br \/>\n<img decoding=\"async\" onclick=\"jmolApplet([540,540],'load wp-content\/uploads\/2022\/12\/Vernier.mol2; zoom 130;spin 3;','c1');\"  class=\"alignnone size-full wp-image-25767\" src=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/12\/vernier.jpg\" alt=\"\" width=\"500\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/12\/vernier.jpg 1177w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/12\/vernier-271x300.jpg 271w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/12\/vernier-926x1024.jpg 926w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/12\/vernier-768x850.jpg 768w\" sizes=\"(max-width: 1177px) 100vw, 1177px\" \/><\/li>\n<\/ul>\n<p>Now for the Megalo-Cavitands (or not). Just as above, one ends up in a <a href=\"https:\/\/onlinelibrary.wiley.com\/action\/downloadSupplement?doi=10.1002%2Fanie.202209885&amp;file=anie202209885-sup-0001-misc_information.pdf\">49-page PDF file<\/a> looking for coordinates. There one gets pictures of PM6-computed models starting on p 28, but alas apparently no associated coordinates.<sup>&dagger;<\/sup><\/p>\n<p><img decoding=\"async\" class=\"alignnone size-full wp-image-25772\" src=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/12\/Screenshot-1351.jpg\" alt=\"\" width=\"500\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/12\/Screenshot-1351.jpg 1307w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/12\/Screenshot-1351-300x275.jpg 300w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/12\/Screenshot-1351-1024x940.jpg 1024w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/12\/Screenshot-1351-768x705.jpg 768w\" sizes=\"(max-width: 1307px) 100vw, 1307px\" \/><\/p>\n<p>So no 3D models to show here then (sorry, clicking on the image above will not produce them<sup>&dagger;<\/sup>).<\/p>\n<p>My concluding remark should be that when an interesting molecule is selected for inclusion in <em>eg<\/em> the molecules of the year &#8211; 2022, one of the criteria for its inclusion is that the availability of full and FAIR data describing its properties should be one of the essential criteria for selection.<\/p>\n<hr \/>\n<p><sup>\u2021<\/sup>I note the method used to generate these coordinates (PM6) is perhaps not ideal;\u00a0it contains no dispersion attraction terms, which are probably important if modelling host-guest complexation.\u00a0The PM7 method which does is far better for this sort of thing! This highlights the importance of providing data, in this case 3D coordinates. It would be interesting to recompute the dimensions of these molecules using a method that does allow for dispersion attractions to be included. For just such an example, see <a href=\"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=23187\">here<\/a>.<br \/>\n<sup>&dagger;<\/sup> I have contacted the authors of <span id=\"cite_ITEM-25761-2\" name=\"citation\"><a href=\"#ITEM-25761-2\">[3]<\/a><\/span> and it turns out a reference to a Data repository submission was omitted from the article. The data is at DOI: <a href=\"https:\/\/doi.org\/10.5281\/zenodo.6953961\">10.5281\/zenodo.6953961<\/a> and I will report separately on my analysis of the effect of replacing PM6 with PM7. <br \/>\n<sup>&clubs;<\/sup>See this <a href=\"https:\/\/kitchenchemistry.substack.com\/p\/an-open-letter-to-the-membership\" rel=\"noopener\" target=\"_blank\">open letter<\/a> about changes at C&#038;EN.<\/p>\n<hr \/>\n<p>This post has DOI: 10.14469\/hpc\/12028<\/p>\n<hr \/>\n<h2>References<\/h2>\n    <ol class=\"kcite-bibliography csl-bib-body\"><li id=\"ITEM-25761-0\">M. Sugiyama, M. Akiyama, Y. Yonezawa, K. Komaguchi, M. Higashi, K. Nozaki, and T. Okazoe, \"Electron in a cube: Synthesis and characterization of perfluorocubane as an electron acceptor\", <i>Science<\/i>, vol. 377, pp. 756-759, 2022. <a href=\"https:\/\/doi.org\/10.1126\/science.abq0516\">https:\/\/doi.org\/10.1126\/science.abq0516<\/a>\n\n<\/li>\n<li id=\"ITEM-25761-1\">Z. Ashbridge, E. Kreidt, L. Pirvu, F. Schaufelberger, J.H. Stenlid, F. Abild-Pedersen, and D.A. Leigh, \"Vernier template synthesis of molecular knots\", <i>Science<\/i>, vol. 375, pp. 1035-1041, 2022. <a href=\"https:\/\/doi.org\/10.1126\/science.abm9247\">https:\/\/doi.org\/10.1126\/science.abm9247<\/a>\n\n<\/li>\n<li id=\"ITEM-25761-2\">J. Pfeuffer\u2010Roosch\u00fcz, S. Heim, A. Prescimone, and K. Tiefenbacher, \"Megalo\u2010Cavitands: Synthesis of Acridane[4]arenes and Formation of Large, Deep Cavitands for Selective C70 Uptake\", <i>Angewandte Chemie International Edition<\/i>, vol. 61, 2022. <a href=\"https:\/\/doi.org\/10.1002\/anie.202209885\">https:\/\/doi.org\/10.1002\/anie.202209885<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> <!-- kcite-section 25761 -->","protected":false},"excerpt":{"rendered":"<p>The list of molecules of the year is out now at C&amp;E News (but you have to have an account to view the list, unlike previous years).&clubs; These three caught my eye: Electron in a cube: Synthesis and characterization of perfluorocubane as an electron acceptor,. I have already written about this system and will not [&hellip;]<\/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":[],"tags":[],"ppma_author":[2661],"class_list":["post-25761","post","type-post","status-publish","format-standard","hentry"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.9 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Molecules of the year -2022. Data issues! - Henry Rzepa&#039;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=25761\" \/>\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 -2022. Data issues! - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"The list of molecules of the year is out now at C&amp;E News (but you have to have an account to view the list, unlike previous years).&clubs; These three caught my eye: Electron in a cube: Synthesis and characterization of perfluorocubane as an electron acceptor,. 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I have already written about this system and will not [&hellip;]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25761","og_site_name":"Henry Rzepa&#039;s Blog","article_published_time":"2022-12-13T15:34:49+00:00","article_modified_time":"2023-03-12T08:28:45+00:00","og_image":[{"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/12\/vernier.jpg","type":"","width":"","height":""}],"author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"4 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25761#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25761"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Molecules of the year -2022. 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For 2024 the list is (in order of votes cast for each) Mirror-image cyclodextrin Molecular shuttle in a box Rule-bending strained alkene First soluble promethium complex Single-electron carbon-carbon bond Hot MOF for capturing carbon I\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","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":3908,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=3908","url_meta":{"origin":25761,"position":1},"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 &quot;Interesting chemistry&quot;","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":25785,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25785","url_meta":{"origin":25761,"position":2},"title":"Molecules of the year -2022. A closer look at the Megalo-Cavitands.","author":"Henry Rzepa","date":"December 15, 2022","format":false,"excerpt":"In the previous post, I discussed how data associated with two of the candidates for molecules of the year - 2022 could be retrieved and then used to inspect their three dimensional structures. Here I focus on the ultra large cavitands recently reported. As I noted, these have an associated\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/12\/cavitand.png?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":30276,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=30276","url_meta":{"origin":25761,"position":3},"title":"Molecules of the year 2025: Cyclo[48]carbon and others &#8211; the onset of bond alternation and the Raman Activity Spectrum.","author":"Henry Rzepa","date":"December 29, 2025","format":false,"excerpt":"The annual \"Molecules of the Year\" selections are available for the year 2025. A theme was elemental allotropes and one such was carbon in the form of C48\u00a0stabilised by formation of a catenane C48.M3 (M = red ligand below) - it was not possible however to crystallise C48.M3. When \"unmasked\"\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","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":1985,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1985","url_meta":{"origin":25761,"position":4},"title":"Anatomy of an asymmetric reaction. The Strecker synthesis, part 1.","author":"Henry Rzepa","date":"May 24, 2010","format":false,"excerpt":"The assembly of a molecule for a purpose has developed into an art form, one arguably (chemists always argue) that is approaching its 100th birthday celebrating Willst\u00e4tter's report of the synthesis of cyclo-octatetraene. Most would agree it reached its most famous achievement with Woodward's synthesis of quinine in 1944. To\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","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\/strecker0.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":9973,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9973","url_meta":{"origin":25761,"position":5},"title":"A (very) short history of shared-electron bonds.","author":"Henry Rzepa","date":"March 26, 2013","format":false,"excerpt":"The concept of a shared electron bond and its property of an order is almost 100 years old in modern form, when G. N. Lewis suggested a model for single and double bonds that involved sharing either 2 or 4 electrons between a pair of atoms. We tend to think\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"Click for  3D","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/03\/PYRDRE.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\/25761","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=25761"}],"version-history":[{"count":23,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/25761\/revisions"}],"predecessor-version":[{"id":25826,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/25761\/revisions\/25826"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=25761"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=25761"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=25761"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=25761"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}