{"id":12482,"date":"2014-04-30T20:16:14","date_gmt":"2014-04-30T19:16:14","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=12482"},"modified":"2023-09-16T18:18:24","modified_gmt":"2023-09-16T17:18:24","slug":"tetrahedral-or-square-planar-a-ten-minute-exploration","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12482","title":{"rendered":"Tetrahedral or square planar? A ten minute exploration."},"content":{"rendered":"
\n

\n\tI love experiments where the insight-to-time-taken ratio is high. This one pertains to exploring the coordination chemistry of the transition metal region of the periodic table; specifically the tetra-coordination of the series headed by Mn-Ni. Is the geometry tetrahedral, square planar, or other? One can get a statistical answer in about ten minutes.
\n\t\"Tet-SP.jpg\"<\/a>The (CCDC database) search definition required is shown above. The central atom defines the column of the period table, it is specified to have precisely four other atoms bonded to it, which can be any other element. These four bonds are specified as acyclic (to avoid any bias introduced by rings). And two angles are defined subtending the central atom. And off we go, defining on the way that the hits must be refined to an R-factor of < 0.05, have no disorder, and no errors.\n<\/p>\n

\"Mn,

Mn, (Tc), Re<\/p><\/div>\n

\"Fe,

Fe, Ru, Os<\/p><\/div>\n

\"Co,

Co, Rh, Ir<\/p><\/div>\n

\"Ni,

Ni, Pd, Pt<\/p><\/div>\n

\n\tSquare planar coordination will manifest with pairs of angles of either 90° or 180°, whilst tetrahedral coordination will reveal only 109°.\n<\/p>\n

    \n
  1. \n\t\tBoth the Mn and the Fe series show a (red) hotspot at the tetrahedral value.\n\t<\/li>\n
  2. \n\t\tThe Co series shows a tetrahedral hot spot AND a somewhat less abundant square planar double-hot spot for the combination 90\/180 and 180\/90.\n\t<\/li>\n
  3. \n\t\tThe Ni series reveals the hottest spots to correspond to square planar, but with a significant tetrahedral cluster.\n\t<\/li>\n<\/ol>\n

    \n\tThis quick survey can be followed up by more detailed explorations of the clusters. For example, can one go to the literature and find out the typical spin state for e.g.<\/em> the Ni series in each of the geometries. Unfortunately, the CCDC database does not record what the spin state of any individual compound is; one will have to go to the original literature to find out. What a shame that the linkage between two quite different properties is (as far as I know) not available in any easily searchable form. Alternatively, one can narrow down the searches to individual searches of row 1, 2 or 3 of the transition series and then compare the behaviour. The possibilities are considerable.\n<\/p>\n

    \n\tThen there are the outliers in each plot. Some (many?) may prove to be due to faulty data (whilst we have specified no errors, they can still occur) but others may be due to an unusual structural feature, or perhaps even an as yet unrecognized phenomenon! Set as a student experiment, one might ask each student to explore say 3 outliers and express an opinion as to what causes them to deviate. Enjoy!\n<\/p>\n

    \n

    Acknowledgments<\/h4>\n

    This post has been cross-posted in PDF format at Authorea<\/a>.<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    I love experiments where the insight-to-time-taken ratio is high. This one pertains to exploring the coordination chemistry of the transition metal region of the periodic table; specifically the tetra-coordination of the series headed by Mn-Ni. Is the geometry tetrahedral, square planar, or other? One can get a statistical answer in about ten minutes. The (CCDC database) […]<\/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":[2,1745,1],"tags":[1211,1209,1001,1210],"ppma_author":[2661],"class_list":["post-12482","post","type-post","status-publish","format-standard","hentry","category-chemical-it","category-crystal_structure_mining","category-general","tag-data","tag-ptcaption-square","tag-search-definition","tag-transition-metal-region"],"yoast_head":"\nTetrahedral or square planar? A ten minute exploration. - 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=12482\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Tetrahedral or square planar? A ten minute exploration. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"I love experiments where the insight-to-time-taken ratio is high. This one pertains to exploring the coordination chemistry of the transition metal region of the periodic table; specifically the tetra-coordination of the series headed by Mn-Ni. Is the geometry tetrahedral, square planar, or other? One can get a statistical answer in about ten minutes. 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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":14548,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14548","url_meta":{"origin":12482,"position":1},"title":"Deviations from tetrahedral four-coordinate carbon: a statistical exploration.","author":"Henry Rzepa","date":"September 6, 2015","format":false,"excerpt":"An article entitled \"Four Decades of the Chemistry of Planar Hypercoordinate Compounds\" was recently reviewed by Steve Bacharach on his blog, where you can also see comments. Given the recent crystallographic themes here, I thought I might try a search of the CSD (Cambridge structure database) to see whether anything\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":17702,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17702","url_meta":{"origin":12482,"position":2},"title":"How does methane invert (its configuration)?","author":"Henry Rzepa","date":"March 16, 2017","format":false,"excerpt":"This is a spin-off from the table I constructed here for further chemical examples of the classical\/non-classical norbornyl cation conundrum. One possible entry would include the transition state for inversion of methane via a square planar geometry as compared with e.g. NiH4 for which the square planar motif is its\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":14560,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14560","url_meta":{"origin":12482,"position":3},"title":"Deviations from planarity of trigonal carbon and from linearity of digonal carbon.","author":"Henry Rzepa","date":"September 13, 2015","format":false,"excerpt":"Previously, I explored deviation from ideal tetrahedral arrangements of four carbon ligands around a central (sp3) carbon using crystal structures. Now it is the turn of digonal (sp1) and trigonal (sp2) carbons.\u00a0 Firstly, the digonal C\u2261C case. Attached to each carbon of the C\u2261C unit are two saturated carbon ligands;\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":18277,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18277","url_meta":{"origin":12482,"position":4},"title":"How does carbon dioxide coordinate to a metal?","author":"Henry Rzepa","date":"May 6, 2017","format":false,"excerpt":"Mention carbon dioxide (CO2) to most chemists and its properties as a metal ligand are not the first aspect that springs to mind. Here thought I might take a look at how it might act as such. There are up to\u00a0five binding modes with one metal that one might envisage:\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\/2017\/05\/078.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":10883,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10883","url_meta":{"origin":12482,"position":5},"title":"The butterfly effect in chemistry: Bimodal M~S bonds?","author":"Henry Rzepa","date":"July 14, 2013","format":false,"excerpt":"I noted previously that some 8-ring cyclic compounds could exist in either a planar-aromatic or a non-planar-non-aromatic mode, the mode being determined by apparently quite small changes in a ring substituent. Hunting for other examples of such chemistry on the edge, I did a search of the Cambridge crystal database\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\/12482","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=12482"}],"version-history":[{"count":9,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/12482\/revisions"}],"predecessor-version":[{"id":26463,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/12482\/revisions\/26463"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=12482"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=12482"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=12482"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=12482"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}