{"id":16468,"date":"2016-05-30T08:16:10","date_gmt":"2016-05-30T07:16:10","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=16468"},"modified":"2016-06-26T08:22:00","modified_gmt":"2016-06-26T07:22:00","slug":"the-geometries-of-5-coordinate-compounds-of-group-14-elements","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16468","title":{"rendered":"The geometries of 5-coordinate compounds of group 14 elements."},"content":{"rendered":"
\n

\n\tThis is a follow-up to one aspect of the previous two posts dealing with nucleophilic substitution reactions at silicon. Here I look at the geometries of 5-coordinate compounds containing as a central atom 4A = Si, Ge, Sn, Pb and of the specific formula C3<\/sub>4AO2<\/sub> with a trigonal bipyramidal geometry. This search arose because of a casual comment I made in the earlier post<\/a> regarding possible cooperative effects between the two axial ligands (the ones with an angle of ~180 degrees subtended at silicon). Perhaps the geometries might expand upon this comment?\n<\/p>\n

\n\t\"\"\n<\/p>\n

\n\tThe search query is shown above results in 394 hits (May 2016) and is presented with the three variables in the query plotted as below, with the O-4A-O angle indicated by colour (red ~ 180°; blue ~90° and green ~120°).\n<\/p>\n

\n\t\"\"\n<\/p>\n

    \n
  1. \n\t\tThe cluster at distances of 4A-O of ~1.9Å represents silicon compounds, and tends to suggest that the pair of distances 4A-O are quite similar in value. The angles correspond to a di-axial arrangement around the silicon. In this scenario, one might imagine a stereoelectronic effect similar to the anomeric effect when 4A = C operates and which has the potential to strengthen both di-axial oxygens.\n\t<\/li>\n
  2. \n\t\tThe bulk of the points come at higher 4A-O distances of > 2.1Å and consist mostly of 4A = Sn. There are two a clear-cut distributions, one for angles of ~180° and a separate one for angles of ~90° and both are qualitatively different from the Si distribution. The 180° set corresponds to a di-axial arrangement for the oxygens, whereas the 90° set suggests an axial-equatorial geometry. Both distributions have prominent tails which reveal that as one 4A-O distance shortens, the other lengthens, equivalent to asymmetric anomeric effects at  O-C-O.\n\t<\/li>\n
  3. \n\t\tNoticeably absent are any green points; these would correspond to bond angles of ~120° and hence would correspond to di-equatorial ligands.\n\t<\/li>\n<\/ol>\n

    \n\tThis quick exploration (with potential variations that I have not explored above) can be added to the collection of "ten minute explorations" I have described elsewhere.[1]<\/a><\/span><\/p>\n

    References<\/h2>\n
    1. H.S. Rzepa, \"Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases\", Journal of Chemical Education<\/i>, vol. 93, pp. 550-554, 2015. https:\/\/doi.org\/10.1021\/acs.jchemed.5b00346<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      This is a follow-up to one aspect of the previous two posts dealing with nucleophilic substitution reactions at silicon. Here I look at the geometries of 5-coordinate compounds containing as a central atom 4A = Si, Ge, Sn, Pb and of the specific formula C34AO2 with a trigonal bipyramidal geometry. This search arose because of […]<\/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":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},"jetpack_post_was_ever_published":false},"categories":[2,1745],"tags":[1469,260,1465,1466,1552,1630,1442,1560,1776,1775],"ppma_author":[2661],"class_list":["post-16468","post","type-post","status-publish","format-standard","hentry","category-chemical-it","category-crystal_structure_mining","tag-anomer","tag-anomeric-effect","tag-carbohydrate-chemistry","tag-carbohydrates","tag-ligand","tag-molecular-geometry","tag-physical-organic-chemistry","tag-stereochemistry","tag-stereoelectronic-effect","tag-trigonal-bipyramidal-molecular-geometry"],"yoast_head":"\nThe geometries of 5-coordinate compounds of group 14 elements. - 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=16468\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The geometries of 5-coordinate compounds of group 14 elements. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"This is a follow-up to one aspect of the previous two posts dealing with nucleophilic substitution reactions at silicon. Here I look at the geometries of 5-coordinate compounds containing as a central atom 4A = Si, Ge, Sn, Pb and of the specific formula C34AO2 with a trigonal bipyramidal geometry. This search arose because of […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16468\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2016-05-30T07:16:10+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2016-06-26T07:22:00+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/05\/XC3O2-sq.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=\"2 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"The geometries of 5-coordinate compounds of group 14 elements. - 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=16468","og_locale":"en_GB","og_type":"article","og_title":"The geometries of 5-coordinate compounds of group 14 elements. - Henry Rzepa's Blog","og_description":"This is a follow-up to one aspect of the previous two posts dealing with nucleophilic substitution reactions at silicon. Here I look at the geometries of 5-coordinate compounds containing as a central atom 4A = Si, Ge, Sn, Pb and of the specific formula C34AO2 with a trigonal bipyramidal geometry. This search arose because of […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16468","og_site_name":"Henry Rzepa's Blog","article_published_time":"2016-05-30T07:16:10+00:00","article_modified_time":"2016-06-26T07:22:00+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/05\/XC3O2-sq.jpg","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=16468#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16468"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"The geometries of 5-coordinate compounds of group 14 elements.","datePublished":"2016-05-30T07:16:10+00:00","dateModified":"2016-06-26T07:22:00+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16468"},"wordCount":349,"commentCount":3,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16468#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/05\/XC3O2-sq.jpg","keywords":["Anomer","Anomeric effect","Carbohydrate chemistry","Carbohydrates","Ligand","Molecular geometry","Physical organic chemistry","Stereochemistry","Stereoelectronic effect","Trigonal bipyramidal molecular geometry"],"articleSection":["Chemical IT","crystal_structure_mining"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16468#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16468","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16468","name":"The geometries of 5-coordinate compounds of group 14 elements. - 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Such displacement at silicon famously proceeds by a quite different mechanism, which\u00a0I here quantify with\u2026","rel":"","context":"In "reaction mechanism"","block_context":{"text":"reaction mechanism","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1086"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":11165,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11165","url_meta":{"origin":16468,"position":1},"title":"The dimer of SF2: small is beautiful (and weird).","author":"Henry Rzepa","date":"September 12, 2013","format":false,"excerpt":"Andy Extance at the Chemistry World blog has picked up on a fascinating article on the dimer of SF2. This molecule has three F atoms on one S, and only one on the other; FSSF3. But all four S-F bonds are of different length. Lindquist and Dunning\u00a0claim that the minimum\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\/09\/S2F4.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":12500,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12500","url_meta":{"origin":16468,"position":2},"title":"Trigonal bipyramidal or square pyramidal: Another ten minute exploration.","author":"Henry Rzepa","date":"May 2, 2014","format":false,"excerpt":"This is rather cranking the handle, but taking my previous post and altering the search definition of the crystal structure database from 4- to 5-coordinate metals, one gets the following. Trigonal bipyramidal coordination has angles of 90, 120 and 180\u00b0. Square pyramidal has no 120\u00b0 angles, and the 180\u00b0 angles\u2026","rel":"","context":"In "Chemical IT"","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":10937,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10937","url_meta":{"origin":16468,"position":3},"title":"VSEPR Theory: A closer look at chlorine trifluoride, ClF3.","author":"Henry Rzepa","date":"July 27, 2013","format":false,"excerpt":"Valence shell electron pair repulsion theory is a simple way of rationalising the shapes of many compounds in which a main group element is surrounded by ligands. ClF3 is a good illustration of this theory. The standard application of VSEPR theory to this molecule is as follows: Central atom: chlorine\u2026","rel":"","context":"In "Hypervalency"","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"VSEPR","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/07\/VSEPR.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":23777,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23777","url_meta":{"origin":16468,"position":4},"title":"A suggestion for a molecule with a M\u2a78C quadruple bond with trigonal metal coordination.","author":"Henry Rzepa","date":"May 13, 2021","format":false,"excerpt":"The proposed identification of molecules with potential metal to carbon quadruple bonds, in which the metal exhibits trigonal bipyramidal coordination rather than the tetrahedral modes which have been proposed in the literature,, leads on to asking whether simple trigonal coordination at the metal can also sustain this theme? 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Thus in 1977, quantum molecular modelling, even at the semi-empirical level, was beset 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.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/09\/cbdzw1.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\/16468","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=16468"}],"version-history":[{"count":7,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16468\/revisions"}],"predecessor-version":[{"id":16501,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16468\/revisions\/16501"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=16468"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=16468"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=16468"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=16468"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}