{"id":17829,"date":"2017-03-25T08:14:53","date_gmt":"2017-03-25T08:14:53","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=17829"},"modified":"2017-08-07T08:57:59","modified_gmt":"2017-08-07T07:57:59","slug":"first-hexacoordinate-carbon-now-pentacoordinate-nitrogen","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17829","title":{"rendered":"First, hexacoordinate carbon – now pentacoordinate nitrogen?"},"content":{"rendered":"
\n

A few years back I followed<\/a> a train of thought here which ended with hexacoordinate carbon, then a hypothesis rather than a demonstrated reality. That reality was recently confirmed via<\/em> a crystal structure,\u00a0DOI:10.5517\/CCDC.CSD.CC1M71QM<\/a>[1]<\/a><\/span>. Here is a\u00a0similar proposal for\u00a0penta-coordinate nitrogen.<\/p>\n

First, a search of the CSD (Cambridge structure database) for such\u00a0nitrogen. There are only three hits[2]<\/a><\/span>, [3]<\/a><\/span>, [4]<\/a><\/span> all of which relate to RN bonded to four borons as part of a boron cage. There are none which relate to RN bonded to four carbon atoms.\u00a0<\/p>\n

The original argument was based on cyclopentadienyl anion and its symmetric coordination to RC3+<\/sup> to achieve six coordination for one carbon. Morphing C to the iso-electronic N+\u00a0<\/sup>gets one to\u00a0the ligand RN4+\u00a0<\/sup>and this can now be coordinated to the di-anion of cyclobutadiene, also iso-electronic in the 6\u03c0 sense to cyclopentadienyl mono-anion.<\/p>\n

\"\"<\/a><\/p>\n

The optimised structure of the methylated system (\u03c9B97XD\/Def2-TZVPP) as shown below (DOI: 10.14469\/hpc\/2348<\/a>) is a true minimum and reveals a 5-coordinate nitrogen. It is the dication of an isomer of pentamethyl pyrrole.<\/p>\n

\"\"<\/p>\n

One of the normal modes for this molecule is the so-called Kekule vibration, which elongates two C-C bonds and shortens the other two. The value (1266 cm-1<\/sup>) is typical of aromatic systems.<\/p>\n

\"\"<\/p>\n

A QTAIM analysis shows four line (bond) critical points (LCP, magenta) connecting the 4-carbon base of the system and four further LCPs connecting each carbon to the nitrogen. Significantly, the four carbons are not themselves characterised by a ring critical point (RCP, green), these being confined to the rings formed between two carbons and the nitrogen. The value of the electron density \u03c1(r) at the basal bond is typical of a single bond; the value to the nitrogen indicates the bond has a smaller order.<\/p>\n

\"\"<\/p>\n

An ELF (electron localisation function) analysis is similar, showing basal C-C electron basins of 2.12e and C-N basins of 1.25e.<\/p>\n

\"\"<\/p>\n

In hunting for examples of hyper-coordination in the second row of the periodic table, the focus has tended largely towards identifying carbon examples. Perhaps that might now right-shift to the adjacent element nitrogen?<\/p>\n

References<\/h2>\n
  1. M. Malischewski, and K. Seppelt, \"Crystal Structure Determination of the Pentagonal\u2010Pyramidal Hexamethylbenzene Dication C<sub>6<\/sub>(CH<sub>3<\/sub>)<sub>6<\/sub><sup>2+<\/sup>\", Angewandte Chemie International Edition<\/i>, vol. 56, pp. 368-370, 2016. https:\/\/doi.org\/10.1002\/anie.201608795<\/a>\n\n<\/li>\n
  2. U. Doerfler, J.D. Kennedy, L. Barton, C.M. Collins, and N.P. Rath, \"Polyhedral azadirhodaborane chemistry. Reaction of [{RhCl2(\u03b75-C5Me5) }2] with [EtH2NB8H11NHEt] to give contiguous ten-vertex [1-Et-6,7-(\u03b75-C5Me5)2- closo-6,7,1-Rh2NB7H7 ]\", Journal of the Chemical Society, Dalton Transactions<\/i>, pp. 707-708, 1997. https:\/\/doi.org\/10.1039\/a700132k<\/a>\n\n<\/li>\n
  3. L. Schneider, U. Englert, and P. Paetzold, \"Die Kristallstruktur von Aza\u2010<i>closo<\/i>\u2010decaboran NB<sub>9<\/sub>H<sub>10<\/sub>\", Zeitschrift f\u00fcr anorganische und allgemeine Chemie<\/i>, vol. 620, pp. 1191-1193, 1994. https:\/\/doi.org\/10.1002\/zaac.19946200711<\/a>\n\n<\/li>\n
  4. M. Mueller, U. Englert, and P. Paetzold, \"X-ray Crystallographic Structure of a 7-Aza-nido-undecaborane Derivative: (NB2tBu3H)NB10H12\", Inorganic Chemistry<\/i>, vol. 34, pp. 5925-5926, 1995. https:\/\/doi.org\/10.1021\/ic00127a034<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    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. There are only three hits, […]<\/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":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}},"categories":[2237,1745,7,4],"tags":[214,1395,2086,2085,1431,1630,1560],"ppma_author":[2661],"class_list":["post-17829","post","type-post","status-publish","format-standard","hentry","category-bond-slam","category-crystal_structure_mining","category-hypervalency","category-interesting-chemistry","tag-aromatic-systems","tag-chemistry","tag-hexacoordinate","tag-hypotheses","tag-matter","tag-molecular-geometry","tag-stereochemistry"],"yoast_head":"\nFirst, hexacoordinate carbon - now pentacoordinate nitrogen? - 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=17829\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"First, hexacoordinate carbon - now pentacoordinate nitrogen? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"A few years back I followed a train of thought here which ended with hexacoordinate carbon, then a hypothesis rather than a demonstrated reality. 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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. 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This was a mode of metal coordination first mooted more than 100 years ago, but with the first examples only being discovered recently.\u00a0The C&E News example comprises a central\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\/2020\/01\/norloy-300x263.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":23686,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23686","url_meta":{"origin":17829,"position":1},"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":[]},{"id":16758,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16758","url_meta":{"origin":17829,"position":2},"title":"What’s in a name? Carbenes: a reality check.","author":"Henry Rzepa","date":"September 11, 2016","format":false,"excerpt":"To quote from Wikipedia: in chemistry, a carbene is a molecule containing a neutral carbon atom with a valence of two and two unshared valence electrons. The most ubiquitous type of carbene of recent times is the one shown below as 1, often referred to as a resonance stabilised or\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":"","width":0,"height":0},"classes":[]},{"id":20010,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=20010","url_meta":{"origin":17829,"position":3},"title":"Tetrahedral carbon and cyclohexane.","author":"Henry Rzepa","date":"August 22, 2018","format":false,"excerpt":"Following the general recognition of carbon as being tetrahedrally tetravalent in 1869 (Paterno) and 1874 (Van't Hoff and Le Bell), an early seminal exploitation of this to the conformation of cyclohexane was by Hermann Sachse in 1890. This was\u00a0verified when the Braggs in 1913, followed by an oft-cited article by\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\/2018\/08\/diamond.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\/2018\/08\/diamond.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2018\/08\/diamond.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2018\/08\/diamond.jpg?resize=700%2C400&ssl=1 2x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2018\/08\/diamond.jpg?resize=1050%2C600&ssl=1 3x"},"classes":[]},{"id":10733,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10733","url_meta":{"origin":17829,"position":4},"title":"Is dicarbon (C2) a molecule of chemical interest?","author":"Henry Rzepa","date":"July 3, 2013","format":false,"excerpt":"C2\u00a0(dicarbon) is certainly interesting from a theoretical point of view. Whether or not it can be described as having a quadruple bond has induced much passionate discussion,,,. Its occurrence in space and in flames is also well-known. But does it have what might be called a conventional chemistry? Other highly\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":"Click for 3D","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/07\/LaOsC1.jpeg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":22971,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=22971","url_meta":{"origin":17829,"position":5},"title":"A new example of a quadruple bond from carbon – to Fe.","author":"Henry Rzepa","date":"November 7, 2020","format":false,"excerpt":"Way back in 2010, I was writing about an experience I had just had during an organic chemistry tutorial, which morphed into speculation as to whether a carbon atom might sustain a quadruple bond to nitrogen. A decade on, and possibly approaching 100 articles by many authors on the topic,\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\/11\/NMn_33a-1024x839.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\/17829","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=17829"}],"version-history":[{"count":21,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/17829\/revisions"}],"predecessor-version":[{"id":17857,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/17829\/revisions\/17857"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=17829"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=17829"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=17829"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=17829"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}