{"id":25785,"date":"2022-12-15T09:14:51","date_gmt":"2022-12-15T09:14:51","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=25785"},"modified":"2023-03-12T08:28:32","modified_gmt":"2023-03-12T08:28:32","slug":"molecules-of-the-year-2022-a-closer-look-at-the-megalo-cavitands","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25785","title":{"rendered":"Molecules of the year -2022. A closer look at the Megalo-Cavitands."},"content":{"rendered":"
\n

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[1]<\/a><\/span>. As I noted, these have an associated data coordinate archive published on Zenodo (DOI: 10.5281\/zenodo.6953961<\/a>) although this is not cited in the article itself.<\/p>\n

\"\"<\/p>\n

Shown below are the coordinates of the A4-T molecule containing C70<\/sub>, the first being optimized at the\u00a0PM6 level and the second at the PM7 level.\u00a0The most obvious difference is that all the close\u00a0C-H…H-C contacts of the host molecule shrink from between ~4\u00c5 to 2.6\u00c5 at PM6 geometries, down to about 2.1\u00c5 for PM7, a contraction of at least 0.5\u00c5. Also, the gap between the host and the guest reduces from around 4.2Å to 3.45 Å (a distance typical of π-π stacking by the way), a significant reduction of ~0.75Å. Click on the two images below to view this model.<\/p>\n

\"\"<\/p>\n

\"\"<\/p>\n

The difference in the dispersion terms for these two geometries emerges as 36.6 kcal\/mol lower for the PM7 optimised geometry compared to the original PM6 geometry, a significant stabilisation. FAIR data is at DOI: 10.14469\/hpc\/12022<\/a> if you want to analyse the cavity sizes further.<\/p>\n

Shown below is the NCI (non-covalent-interaction) surface, computed at the PM7 geometry and using the MNDO wavefunction. This illustrates the stabilisations occuring from the non-covalent density (takes a little while to load). <\/p>\n

\"\"<\/p>\n

\n

This post has DOI: 10.14469\/hpc\/12027<\/p>\n

\n

References<\/h2>\n
  1. 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\", Angewandte Chemie International Edition<\/i>, vol. 61, 2022. https:\/\/doi.org\/10.1002\/anie.202209885<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    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 data coordinate archive published on […]<\/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":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[],"tags":[],"ppma_author":[2661],"class_list":["post-25785","post","type-post","status-publish","format-standard","hentry"],"yoast_head":"\nMolecules of the year -2022. A closer look at the Megalo-Cavitands. - 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=25785\" \/>\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. A closer look at the Megalo-Cavitands. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"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 data coordinate archive published on […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25785\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2022-12-15T09:14:51+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2023-03-12T08:28:32+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/12\/A4-T.jpg\" \/>\n<meta name=\"author\" content=\"Henry Rzepa\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Henry Rzepa\" \/>\n\t<meta name=\"twitter:label2\" content=\"Estimated reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"1 minute\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Molecules of the year -2022. 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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":23187,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23187","url_meta":{"origin":25785,"position":1},"title":"Dispersion attraction effects on the computed geometry of a leminscular dodecaporphyrin.","author":"Henry Rzepa","date":"January 1, 2021","format":false,"excerpt":"In the previous post, I showed the geometries of three large cyclic porphyrins, as part of an article on exploring the aromaticity of large 4n+2 cyclic rings. One of them had been induced into a \"figure-eight\" or lemniscular conformation, as shown below. Any initial inspection of the geometries of these\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\/12\/c-P12b12_T6f.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":23134,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23134","url_meta":{"origin":25785,"position":2},"title":"Global aromaticity at the nanoscale.","author":"Henry Rzepa","date":"December 31, 2020","format":false,"excerpt":"Here is another of the \"large\" molecules in the c&e news shortlist for molecule-of-the-year, 2020. This one is testing the H\u00fcckel 4n+2 rule out to a value never before seen (n = 40, or 162 \u03c0-electrons). The take-home message is that this rule seems to behave well in predicting global\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\/12\/c-P6e6_neutral.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":28233,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=28233","url_meta":{"origin":25785,"position":3},"title":"Molecules of the Year 2024: Molecular shuttle in a box.","author":"Henry Rzepa","date":"January 25, 2025","format":false,"excerpt":"This is another in the C&E News list of candidates for the Molecule of the Year, Molecular shuttle in a box 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 The molecule shown below inside the cavity\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":30276,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=30276","url_meta":{"origin":25785,"position":4},"title":"Molecules of the year 2025: Cyclo[48]carbon and others – 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 "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":23360,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23360","url_meta":{"origin":25785,"position":5},"title":"Non-covalent-interaction (NCI) surfaces for two large annulenes (revisited).","author":"Henry Rzepa","date":"February 7, 2021","format":false,"excerpt":"The last post addressed the concept of \"steric clashes\" in a pericyclic reaction transition state as an extension of the time honoured practice of building\u00a0molecular models to analyse reaction outcomes. A modern computer generated model might express this in terms of a NCI (non-covalent-interaction) surface. A few posts ago, I\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":[]}],"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\/25785","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=25785"}],"version-history":[{"count":27,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/25785\/revisions"}],"predecessor-version":[{"id":25825,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/25785\/revisions\/25825"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=25785"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=25785"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=25785"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=25785"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}