{"id":546,"date":"2009-07-04T17:16:38","date_gmt":"2009-07-04T16:16:38","guid":{"rendered":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=546"},"modified":"2010-09-02T19:39:21","modified_gmt":"2010-09-02T18:39:21","slug":"molecular-toys-tetrahedral-cavities","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=546","title":{"rendered":"Molecular toys: Tetrahedral cavities"},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"546\">\n<p><script src=\"..\/Jmol\/Jmol.js\" type=\"text\/javascript\"><\/script><br \/>\nAn <a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=439\" target=\"_blank\">earlier post<\/a> described how a  (spherical) halide anion fitted snugly into a cavity generated by the simple molecule propanone, itself assembled by  sodium cations coordinating to the oxygen. A recent elaboration of this theme, reminiscent of the children&#8217;s toys where objects have to be fitted into the only cavity that matches their shape, Nitschke and co-workers report the creation of a molecule with a tetrahedral rather than a spherical cavity (DOI: <a href=\"http:\/\/dx.doi.org\/10.1126\/science.1175313\">10.1126\/science.1175313<\/a> ), into which another but much smaller tetrahedral molecule is fitted. \u00a0The small molecule is\u00a0P<sub>4<\/sub>, in which each of the three valencies of the\u00a0P atom is directed to a corner of the tetrahedron. The large molecule \u00a0comprises four\u00a0Fe atoms.\u00a0These are each octahedrally coordinated with six ligand sites, three of which mimic the P atoms in also being directed towards the remaining three vertices of a tetrahedron.<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"aligncenter size-full wp-image-550\" title=\"P4 inside a  Tetrahedral cavity. \" onclick=\"jmolInitialize('..\/Jmol\/');jmolSetAppletColor('yellow');jmolApplet([450,450],'load wp-content\/uploads\/2009\/07\/P41.mol;select atomno=7,atomno=6,atomno=5,atomno=8; cpk on; color atom orange;zoom 120;spin 3;');\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/07\/P4.jpg\" alt=\"P4 inside a  Tetrahedral cavity. \" width=\"237\" height=\"229\" \/><\/p>\n<p>Needless to say, the properties of the  P<sub>4<\/sub> molecule when entrained into this larger container are nothing like that of  the free molecule. Now it is quite inert, but this is due purely to the snug fit. For example, the normal reaction of  this molecule is to oxidize in air.  But such oxidation would now produce a molecule too big to fit into the cavity. Hence no reaction!<\/p>\n<p>So, now the search is on for a cubic container to include a cubic molecule!<\/p>\n<!-- kcite active, but no citations found -->\n<\/div> <!-- kcite-section 546 -->","protected":false},"excerpt":{"rendered":"<p>An earlier post described how a (spherical) halide anion fitted snugly into a cavity generated by the simple molecule propanone, itself assembled by sodium cations coordinating to the oxygen. A recent elaboration of this theme, reminiscent of the children&#8217;s toys where objects have to be fitted into the only cavity that matches their shape, Nitschke [&hellip;]<\/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":[197,2648,74,196],"ppma_author":[2661],"class_list":["post-546","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-cavity","tag-interesting-chemistry","tag-pence","tag-tetrahedral"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Molecular toys: Tetrahedral cavities - 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=546\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Molecular toys: Tetrahedral cavities - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"An earlier post described how a (spherical) halide anion fitted snugly into a cavity generated by the simple molecule propanone, itself assembled by sodium cations coordinating to the oxygen. A recent elaboration of this theme, reminiscent of the children&#8217;s toys where objects have to be fitted into the only cavity that matches their shape, Nitschke [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=546\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"article:published_time\" content=\"2009-07-04T16:16:38+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2010-09-02T18:39:21+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/07\/P4.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":"Molecular toys: Tetrahedral cavities - Henry Rzepa&#039;s Blog","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=546","og_locale":"en_GB","og_type":"article","og_title":"Molecular toys: Tetrahedral cavities - Henry Rzepa&#039;s Blog","og_description":"An earlier post described how a (spherical) halide anion fitted snugly into a cavity generated by the simple molecule propanone, itself assembled by sodium cations coordinating to the oxygen. A recent elaboration of this theme, reminiscent of the children&#8217;s toys where objects have to be fitted into the only cavity that matches their shape, Nitschke [&hellip;]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=546","og_site_name":"Henry Rzepa&#039;s Blog","article_published_time":"2009-07-04T16:16:38+00:00","article_modified_time":"2010-09-02T18:39:21+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/07\/P4.jpg","type":"","width":"","height":""}],"author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"1 minute"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=546#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=546"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Molecular toys: Tetrahedral cavities","datePublished":"2009-07-04T16:16:38+00:00","dateModified":"2010-09-02T18:39:21+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=546"},"wordCount":242,"commentCount":1,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=546#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/07\/P4.jpg","keywords":["cavity","Interesting chemistry","pence","tetrahedral"],"articleSection":["Interesting chemistry"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=546#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=546","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=546","name":"Molecular toys: Tetrahedral cavities - Henry Rzepa&#039;s Blog","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#website"},"primaryImageOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=546#primaryimage"},"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=546#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/07\/P4.jpg","datePublished":"2009-07-04T16:16:38+00:00","dateModified":"2010-09-02T18:39:21+00:00","author":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"breadcrumb":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=546#breadcrumb"},"inLanguage":"en-GB","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=546"]}]},{"@type":"ImageObject","inLanguage":"en-GB","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=546#primaryimage","url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/07\/P4.jpg","contentUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/07\/P4.jpg"},{"@type":"BreadcrumbList","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=546#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog"},{"@type":"ListItem","position":2,"name":"Molecular toys: Tetrahedral cavities"}]},{"@type":"WebSite","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#website","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/","name":"Henry Rzepa&#039;s Blog","description":"Chemistry with a twist","potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-GB"},{"@type":"Person","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281","name":"Henry Rzepa","image":{"@type":"ImageObject","inLanguage":"en-GB","@id":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g370be3a7397865e4fd161aefeb0a5a85","url":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","contentUrl":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","caption":"Henry Rzepa"},"description":"Henry Rzepa is Emeritus Professor of Computational Chemistry at Imperial College London.","sameAs":["https:\/\/orcid.org\/0000-0002-8635-8390"],"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?author=1"}]}},"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/pDef7-8O","jetpack-related-posts":[{"id":17498,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17498","url_meta":{"origin":546,"position":0},"title":"More tetrahedral fun. Spherical aromaticity (and other oddities) in N4 and C4 systems?","author":"Henry Rzepa","date":"March 2, 2017","format":false,"excerpt":"The thread thus far. The post about Na2He introduced the electride anionic counter-ion to Na+ as corresponding topologically to a rare feature known as a non-nuclear attractor. This prompted speculation about other systems with such a feature, and the focus shifted to a tetrahedral arrangement of four hydrogen atoms as\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":10015,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10015","url_meta":{"origin":546,"position":1},"title":"A sideways look at the mechanism of ester hydrolysis.","author":"Henry Rzepa","date":"March 29, 2013","format":false,"excerpt":"The mechanism of ester hydrolysis is a staple of examination questions in organic chemistry. To get a good grade, one might have to reproduce something like the below. Here, I subject that answer to a reality check. In this scheme, HA is a general acid, R=Me, and the net result\u2026","rel":"","context":"In \"ALSO\"","block_context":{"text":"ALSO","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=also"},"img":{"alt_text":"acyl-ester","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/03\/acyl-ester.gif?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":28233,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=28233","url_meta":{"origin":546,"position":2},"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 &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":17483,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17483","url_meta":{"origin":546,"position":3},"title":"The H4 (2+) dication and its bonding.","author":"Henry Rzepa","date":"February 15, 2017","format":false,"excerpt":"This post arose from a comment attached to the post on Na2He\u00a0and relating to peculiar and rare topological features of the electron density in molecules called non-nuclear attractors. This set me thinking about other molecules that might exhibit this and one of these is shown below. The topology of the\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\/2017\/02\/049-1009x1024.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":1135,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1135","url_meta":{"origin":546,"position":4},"title":"The SN1 Reaction- revisited","author":"Henry Rzepa","date":"November 11, 2009","format":false,"excerpt":"In an earlier post I wrote about the iconic SN1 solvolysis reaction, and presented a model for the transition state involving 13 water molecules. Here, I follow this up with an improved molecule containing 16 water molecules, and how the barrier for this model compares with experiment. This latter is\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":"Transition state for  Sn1 solvolysis of  tert-butyl chloride","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/11\/sn1.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":6044,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=6044","url_meta":{"origin":546,"position":5},"title":"Secrets of a university tutor: tetrahedral intermediates.","author":"Henry Rzepa","date":"January 8, 2012","format":false,"excerpt":"The tetrahedral intermediate is one of those iconic species on which the foundation of reaction mechanism in organic chemistry is built. It refers to a (normally undetected and hence merely inferred) species formed initially when a nucleophilic reagent attacks a carbonyl compound. Its importance to understanding the activity of enzymes\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\/2012\/01\/acetylcyanide.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","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\/546","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=546"}],"version-history":[{"count":0,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/546\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=546"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=546"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=546"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=546"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}