{"id":17858,"date":"2017-03-25T17:28:11","date_gmt":"2017-03-25T17:28:11","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=17858"},"modified":"2017-08-07T08:58:27","modified_gmt":"2017-08-07T07:58:27","slug":"first-hexacoordinate-carbon-now-pentacoordinate-oxygen","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17858","title":{"rendered":"First, hexacoordinate carbon \u2013 now pentacoordinate oxygen?"},"content":{"rendered":"
\n

The previous post<\/a> demonstrated the simple iso-electronic progression from six-coordinate carbon to five coordinate nitrogen. Here, a further progression to oxygen is investigated computationally.<\/p>\n

The systems are formally constructed from a cyclobutadienyl di-anion and firstly the HO5+<\/sup> cation, giving a tri-cationic complex. There are no examples of the resulting motif\u00a0in the Cambridge structure database. A \u03c9B97XD\/Def2-TZVPP calculation (DOI: 10.14469\/hpc\/2350<\/a>) shows it is again a stable minimum, with a Kekule mode of 1203 cm-1<\/sup>.\"\"<\/p>\n

A QTAIM\u00a0\u00a0topological analysis of the electron density shows it differs from the nitrogen analogue in now having the ring topological feature for the basal four carbons, which in turn gives rise to a cage critical point (blue dot). The values of the electron density are lower than for N.\"\"<\/p>\n

The ELF basin analysis shows the C-C bonds are regular single ones (2.01e), whereas the C-O bonds have a slightly greater electron population\u00a0than the C-N bonds discussed in the previous post.<\/p>\n

\"\"<\/p>\n

I suspect the prospects of making a stable tri-cation in such a small molecule are lower than the crystal di-cation achieved with carbon as the apical atom. But the charge can be reduced to a di-cation by replacing the HO5+<\/sup>\u00a0 above with S–<\/sup>-O5+<\/sup>;\u00a0the animation below showing the Kekule mode (1140 cm-1<\/sup>, DOI:\u00a010.14469\/hpc\/2356<\/a>).<\/p>\n

\"\"<\/p>\n

\"\"<\/p>\n

And for some (negative) loose ends.<\/p>\n

    \n
  1. The P equivalent constructed from\u00a0cyclobutadienyl di-anion and HP4+<\/sup> is now unremarkably 5-coordinate. But in fact it is not a stable minimum (DOI: 10.14469\/hpc\/2357<\/a>), having two negative force constants.<\/li>\n
  2. as does the system \u00a0from\u00a0cyclobutadienyl di-anion and O=P4+<\/sup>(DOI:\u00a010.14469\/hpc\/2358<\/a>)<\/li>\n
  3. and the system from cyclobutadienyl di-anion and HS5+<\/sup>(DOI:\u00a010.14469\/hpc\/2360<\/a>).<\/li>\n
  4. Transposition of S\/O to give O–<\/sup>-S5+\u00a0<\/sup>likewise (DOI:\u00a010.14469\/hpc\/2359<\/a>).<\/li>\n<\/ol>\n

    So the family of hyper-coordinate 2nd row main group elements now comprises the experimentally verified\u00a0C, with N and O now open to such\u00a0verification.<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    The previous post demonstrated the simple iso-electronic progression from six-coordinate carbon to five coordinate nitrogen. Here, a further progression to oxygen is investigated computationally. The systems are formally constructed from a cyclobutadienyl di-anion and firstly the HO5+ cation, giving a tri-cationic complex. There are no examples of the resulting motif\u00a0in the Cambridge structure database. A […]<\/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":true,"_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},"jetpack_post_was_ever_published":false},"categories":[2237,7],"tags":[152,1402,1395,1431,1885,1512],"ppma_author":[2661],"class_list":["post-17858","post","type-post","status-publish","format-standard","hentry","category-bond-slam","category-hypervalency","tag-animation","tag-chemical-bond","tag-chemistry","tag-matter","tag-nitrogen","tag-quantum-chemistry"],"yoast_head":"\nFirst, hexacoordinate carbon \u2013 now pentacoordinate oxygen? - 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=17858\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"First, hexacoordinate carbon \u2013 now pentacoordinate oxygen? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"The previous post demonstrated the simple iso-electronic progression from six-coordinate carbon to five coordinate nitrogen. Here, a further progression to oxygen is investigated computationally. The systems are formally constructed from a cyclobutadienyl di-anion and firstly the HO5+ cation, giving a tri-cationic complex. There are no examples of the resulting motif\u00a0in the Cambridge structure database. A […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17858\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2017-03-25T17:28:11+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2017-08-07T07:58:27+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/03\/5-O.gif\" \/>\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=\"2 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"First, hexacoordinate carbon \u2013 now pentacoordinate oxygen? - 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=17858","og_locale":"en_GB","og_type":"article","og_title":"First, hexacoordinate carbon \u2013 now pentacoordinate oxygen? - Henry Rzepa's Blog","og_description":"The previous post demonstrated the simple iso-electronic progression from six-coordinate carbon to five coordinate nitrogen. Here, a further progression to oxygen is investigated computationally. The systems are formally constructed from a cyclobutadienyl di-anion and firstly the HO5+ cation, giving a tri-cationic complex. There are no examples of the resulting motif\u00a0in the Cambridge structure database. A […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17858","og_site_name":"Henry Rzepa's Blog","article_published_time":"2017-03-25T17:28:11+00:00","article_modified_time":"2017-08-07T07:58:27+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/03\/5-O.gif","type":"","width":"","height":""}],"author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"2 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17858#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17858"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"First, hexacoordinate carbon \u2013 now pentacoordinate oxygen?","datePublished":"2017-03-25T17:28:11+00:00","dateModified":"2017-08-07T07:58:27+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17858"},"wordCount":309,"commentCount":4,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17858#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/03\/5-O.gif","keywords":["animation","Chemical bond","Chemistry","Matter","Nitrogen","Quantum chemistry"],"articleSection":["Bond slam","Hypervalency"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17858#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17858","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17858","name":"First, hexacoordinate carbon \u2013 now pentacoordinate oxygen? 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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":16610,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16610","url_meta":{"origin":17858,"position":1},"title":"Anomeric effects at carbon involving lone pairs originating from one or two nitrogens.","author":"Henry Rzepa","date":"July 8, 2016","format":false,"excerpt":"The previous post looked at anomeric effects set up on centres such as B, Si or P, and involving two oxygen groups attached to these atoms. Here I vary the attached groups to include either one or two nitrogen atoms..The\u00a0plot below shows aminols, C(NHR)(OR\"). A torsion along either the C-O\u2026","rel":"","context":"In "crystal_structure_mining"","block_context":{"text":"crystal_structure_mining","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1745"},"img":{"alt_text":"aminol","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/07\/aminol-1-1024x773.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":7779,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7779","url_meta":{"origin":17858,"position":2},"title":"Oxime formation from hydroxylamine and ketone: a (computational) reality check on stage one of the mechanism.","author":"Henry Rzepa","date":"September 23, 2012","format":false,"excerpt":"The mechanism of forming an oxime from nucleophilic addition of a hydroxylamine to a ketone is taught early on in most courses of organic chemistry. Here I subject the first step of this reaction to form a tetrahedral intermediate to quantum mechanical scrutiny. The first decision is to decide which\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.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/09\/hydroxylamine%2Bacetone-O-1H2O-6-ring_small.gif?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":16601,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16601","url_meta":{"origin":17858,"position":3},"title":"Anomeric effects at boron, silicon and phosphorus.","author":"Henry Rzepa","date":"July 1, 2016","format":false,"excerpt":"The anomeric effect occurs at 4-coordinate (sp3) carbon centres carrying two oxygen substituents and involves an alignment of a lone electron pair\u00a0on one oxygen with the adjacent C-O \u03c3*-bond of the other oxygen. Here I explore whether other centres can exhibit the phenomenon. I start with 4-coordinate boron, using the\u2026","rel":"","context":"In "crystal_structure_mining"","block_context":{"text":"crystal_structure_mining","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1745"},"img":{"alt_text":"anomeric-bo-sq","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/06\/anomeric-bo-sq-1024x644.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":26199,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26199","url_meta":{"origin":17858,"position":4},"title":"Blue blood.","author":"Henry Rzepa","date":"August 7, 2023","format":false,"excerpt":"Respiratory pigments are metalloproteins that transport O2, the best known being the bright red\/crimson coloured hemoglobin in human blood. The colour derives from Fe2+ at the core of a tetraporphyrin ring. But less well known is blue blood, and here the colour derives from an oxyhemocyanin unit based on Cu1+\u2026","rel":"","context":"In "crystal_structure_mining"","block_context":{"text":"crystal_structure_mining","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1745"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2023\/08\/Screenshot57.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2023\/08\/Screenshot57.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2023\/08\/Screenshot57.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2023\/08\/Screenshot57.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2023\/08\/Screenshot57.jpg?resize=1050%2C600&ssl=1 3x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2023\/08\/Screenshot57.jpg?resize=1400%2C800&ssl=1 4x"},"classes":[]},{"id":23686,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23686","url_meta":{"origin":17858,"position":5},"title":"A reality-based suggestion for a molecule with a metal M\u2a78N quadruple bond.","author":"Henry Rzepa","date":"May 13, 2021","format":false,"excerpt":"I noted in an earlier post the hypothesized example of (CO)3Fe\u2a78C as exhibiting a carbon to iron quadruple bond and which might have precedent in known five-coordinate metal complexes where one of the ligands is a \"carbide\" or C ligand. I had previously mooted that the Fe\u2a78C combination might be\u2026","rel":"","context":"In "crystal_structure_mining"","block_context":{"text":"crystal_structure_mining","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1745"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2021\/05\/Screenshot-703-1024x818.jpg?resize=350%2C200&ssl=1","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\/17858","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=17858"}],"version-history":[{"count":14,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/17858\/revisions"}],"predecessor-version":[{"id":17877,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/17858\/revisions\/17877"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=17858"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=17858"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=17858"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=17858"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}