{"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":"2022-12-15T09:14:51","modified_gmt":"2022-12-15T09:14:51","slug":"molecules-of-the-year-2022-a-closer-look-at-the-megalo-cavitands","status":"publish","type":"post","link":"https:\/\/www.rzepa.net\/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,"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":[1],"tags":[],"class_list":["post-25785","post","type-post","status-publish","format-standard","hentry","category-uncategorized"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/p1gPyz-6HT","jetpack_likes_enabled":true,"_links":{"self":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/posts\/25785","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=25785"}],"version-history":[{"count":0,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/posts\/25785\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=25785"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=25785"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=25785"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}