{"id":25486,"date":"2022-08-29T07:51:50","date_gmt":"2022-08-29T06:51:50","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=25486"},"modified":"2022-09-19T07:19:28","modified_gmt":"2022-09-19T06:19:28","slug":"octafluorocubane-radical-anion-where-does-the-extra-electron-sit","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25486","title":{"rendered":"Octafluorocubane radical anion – where does the extra electron sit?"},"content":{"rendered":"
\n

Derek Lowe<\/a> reports the story[1]<\/a><\/span> that the recently synthesized octafluorocubane can absorb one electron to form a radical anion – an electron in a cube<\/em>. So I thought it would be fun to compute exactly where that electron sits!<\/p>\n

A\u00a0\u03c9B97XD\/Def2-TZVPPD\/SCRF=chloroform\u00a0calculation (DOI: 10.14469\/hpc\/11090<\/a>) is carried out on the neutral system (optimizing its geometry) and then the radical anion at the same geometry. Cubes of total electron density are evaluated for both and then the neutral form is subtracted from the anion. The result is shown below (density isosurface\u00a0value 0.0025 au; click on the image to load a rotatable 3D model of the density difference).<\/p>\n

\"\"<\/p>\n

The below is at the optimised anion geometry for both species;<\/p>\n

\"\"<\/p>\n

The colour code is that blue represents the location of the additional electron, and red indicates reduced<\/strong> electron density compared to the anion. Arrow 1 shows an additional sphere of density inside the cube – yes, an electron in a cube. But you probably would not have anticipated that the outer surface of the cube (arrow 2) is also surrounded by that electron and there is a reduced density layer on the inside surface of the cube. The C-F bonds have regions of both additional density and reduced density.<\/p>\n

\n

Postscript: Perfluorododecahedrane added as per comment<\/p>\n

\"\"<\/p>\n

Postscript: Perfluorotetrahedrane added for completeness<\/p>\n

\"\"<\/p>\n

\n

References<\/h2>\n
  1. 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\", Science<\/i>, vol. 377, pp. 756-759, 2022. https:\/\/doi.org\/10.1126\/science.abq0516<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    Derek Lowe reports the story that the recently synthesized octafluorocubane can absorb one electron to form a radical anion – an electron in a cube. So I thought it would be fun to compute exactly where that electron sits! A\u00a0\u03c9B97XD\/Def2-TZVPPD\/SCRF=chloroform\u00a0calculation (DOI: 10.14469\/hpc\/11090) is carried out on the neutral system (optimizing its geometry) and then the […]<\/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-25486","post","type-post","status-publish","format-standard","hentry"],"yoast_head":"\nOctafluorocubane radical anion - where does the extra electron sit? - 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=25486\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Octafluorocubane radical anion - where does the extra electron sit? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"Derek Lowe reports the story that the recently synthesized octafluorocubane can absorb one electron to form a radical anion – an electron in a cube. 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A\u00a0\u03c9B97XD\/Def2-TZVPPD\/SCRF=chloroform\u00a0calculation (DOI: 10.14469\/hpc\/11090) is carried out on the neutral system (optimizing its geometry) and then the […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25486\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2022-08-29T06:51:50+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2022-09-19T06:19:28+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/08\/radical-anion_den_sub.png\" \/>\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":"Octafluorocubane radical anion - where does the extra electron sit? - Henry Rzepa'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=25486","og_locale":"en_GB","og_type":"article","og_title":"Octafluorocubane radical anion - where does the extra electron sit? - Henry Rzepa's Blog","og_description":"Derek Lowe reports the story that the recently synthesized octafluorocubane can absorb one electron to form a radical anion – an electron in a cube. 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A\u00a0\u03c9B97XD\/Def2-TZVPPD\/SCRF=chloroform\u00a0calculation (DOI: 10.14469\/hpc\/11090) is carried out on the neutral system (optimizing its geometry) and then the […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25486","og_site_name":"Henry Rzepa's Blog","article_published_time":"2022-08-29T06:51:50+00:00","article_modified_time":"2022-09-19T06:19:28+00:00","og_image":[{"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/08\/radical-anion_den_sub.png","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=25486#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25486"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Octafluorocubane radical anion – where does the extra electron sit?","datePublished":"2022-08-29T06:51:50+00:00","dateModified":"2022-09-19T06:19:28+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25486"},"wordCount":233,"commentCount":10,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25486#primaryimage"},"thumbnailUrl":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/08\/radical-anion_den_sub.png","inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25486#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25486","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25486","name":"Octafluorocubane radical anion - where does the extra electron sit? 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A discussion developed in which a molecule isoelectronic with ethane radical cation, namely the methyl-\u03bb1-borane radical (H3B-CH3) was proposed by Jacob. The optimised structure at the\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":14272,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14272","url_meta":{"origin":25486,"position":1},"title":"Electrides (aka solvated electrons).","author":"Henry Rzepa","date":"July 8, 2015","format":false,"excerpt":"Peter Edwards has just given the 2015 Hofmann lecture here at Imperial on the topic of solvated electrons. An organic chemist knows this species as \"e-\" and it occurs in ionic compounds known as electrides; chloride = the negative anion of a chlorine atom, hence electride = the negative anion\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":17829,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17829","url_meta":{"origin":25486,"position":2},"title":"First, hexacoordinate carbon – now pentacoordinate nitrogen?","author":"Henry Rzepa","date":"March 25, 2017","format":false,"excerpt":"A few years back I followed a train of thought here which ended with hexacoordinate carbon, then a hypothesis rather than a demonstrated reality. That reality was recently confirmed via a crystal structure,\u00a0DOI:10.5517\/CCDC.CSD.CC1M71QM. Here is a\u00a0similar proposal for\u00a0penta-coordinate nitrogen. First, a search of the CSD (Cambridge structure database) for such\u00a0nitrogen.\u2026","rel":"","context":"In "Bond slam"","block_context":{"text":"Bond slam","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2237"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":8452,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8452","url_meta":{"origin":25486,"position":3},"title":"The mechanism of the Birch reduction. Part 1: reduction of anisole.","author":"Henry Rzepa","date":"December 1, 2012","format":false,"excerpt":"The Birch reduction is a classic method for partially reducing e.g. aryl ethers using electrons (from sodium dissolved in ammonia) as the reductant rather than e.g. dihydrogen. As happens occasionally in chemistry, a long debate broke out over the two alternative mechanisms labelled O (for ortho protonation of the initial\u2026","rel":"","context":"In \"dielectric\"","block_context":{"text":"dielectric","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=dielectric"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/12\/birch1.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":8540,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8540","url_meta":{"origin":25486,"position":4},"title":"The mechanism of the Birch reduction. Part 3: reduction of benzene","author":"Henry Rzepa","date":"December 4, 2012","format":false,"excerpt":"Birch reduction of benzene itself results in 1,4-cyclohexadiene rather than the more stable (conjugated) 1,3-cyclohexadiene. Why is this? The mechanism, as elaborated in the previous two posts, involves a one-electron transfer from a sodium atom to form the radical anion, which is then protonated in a second step, and this\u2026","rel":"","context":"In \"Birch reduction\"","block_context":{"text":"Birch reduction","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=birch-reduction"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/12\/birch-ip.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":27870,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=27870","url_meta":{"origin":25486,"position":5},"title":"The one-electron carbon-carbon bond: Hexafluoroethane and ethane radical cations.","author":"Henry Rzepa","date":"October 3, 2024","format":false,"excerpt":"In the previous post, I looked at the recently reported hexa-arylethane containing a carbon-carbon one-electron bond, its structure having been determined by x-ray diffraction (XRD). The measured C-C bond length was ~2.9a\u00c5 and my conclusion was that the C...C region represented more of a weak \"interaction\" than of a bond\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\/25486","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=25486"}],"version-history":[{"count":22,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/25486\/revisions"}],"predecessor-version":[{"id":25615,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/25486\/revisions\/25615"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=25486"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=25486"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=25486"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=25486"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}