{"id":21883,"date":"2020-01-23T10:21:32","date_gmt":"2020-01-23T10:21:32","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=21883"},"modified":"2020-01-23T12:33:57","modified_gmt":"2020-01-23T12:33:57","slug":"molecules-of-the-year-2019-hexagonal-planar-crystal-structures","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21883","title":{"rendered":"Molecules of the year 2019: Hexagonal planar crystal structures."},"content":{"rendered":"
\n

Here is another selection from the Molecules-of-the-Year shortlist<\/a> published by C&E News, in which hexagonal planar transition metal coordination is identified. This was a mode of metal coordination first mooted more than 100 years ago,[1]<\/a><\/span> but with the first examples only being discovered recently.\u00a0The C&E News example comprises a central palladium atom surrounded by three hydride and three magnesium atoms,\u00a0all seven atoms being in the same plane.<\/p>\n

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

As the original article makes clear,[1]<\/a><\/span> the relative orbital simplicity of these early main group based ligands allows the bonding to be better understood, hence itself allowing “additional design principles” to be introduced for transition metal complexes.\u00a0Here I thought I might extend the scope of this motif by a generalised crystal search for any other hexagonal planar structures to be found in the Cambridge crystal structure database.<\/p>\n

\"\"<\/p>\n

A search query can be constructed by defining a plane using the six ligand atoms and then constraining the perpendicular distance between this plane and the transition metal atom at the centre to\u00a0< 0.1\u00c5. Six angles between adjacent ligands are then themselves constrained to the range 0-70\u00b0 and the coordination of the central atom can also be constrained to either 6, 7 or\u00a08.\u00a0All searches are also defined by no disorder and no errors. The search queries can be found at DOI:\u00a010.14469\/hpc\/6731<\/a><\/p>\n

I carried out a number of separate searches. The least constrained (any coordination number at the central atom, and any type of attached ligand atom) produced 62 hits, exhibiting a variety of sometimes complex coordination modes. To simplify the search, I separated the searches into specific types. You can view 3D models of any of the molecules below by clicking on the static image.<\/p>\n

    \n
  1. The first restricted the transition metal atom to 6-coordinate and for which the ligands all derive from the early main group periods (1A, 2A and H). The sole example (NORLOY[[1]<\/a><\/span>, DOI: 10.5517\/ccdc.csd.cc2235v7<\/a>) is the one noted above.<\/li>\n
  2. The next search restricted all the ligands to a transition metal connected to the central atom, along with 6-coordination. Again just one hit (RISQEP[2]<\/a><\/span> dating from 1997 and comprising a central Au atom surrounded by four Au-based ligands and two\u00a0Fe-based ligands. This type of molecule is a member of a class known as a hexagonal planar metal cluster.\n

    \"\"<\/p>\n<\/li>\n

  3. This search now constrains all six ligands as comprising late main group atoms bonding to the central metal.\u00a0Two hits, VOVZOV, dating from 1992[3]<\/a><\/span> with a P-based ligand Ni central atom and ZUDWUQ from 1996[4]<\/a><\/span> using As and\u00a0Ni.\n

    \"\"<\/p>\n<\/li>\n

  4. The next category combines the previous two, with ligands either from the transition series or the late main group series, resulting in four more hits (HACBOF and\u00a0HACBUL[5]<\/a><\/span> (DOI:\u00a010.5517\/ccdc.csd.cc1n26pm<\/a>\u00a0and 10.5517\/ccdc.csd.cc1n26qn<\/a>)\u00a0using a combination of three carbons (as acetylide) \u00a0and three Ag ligands,\u00a0with Cu as the central ligand.\n

    \"\"<\/p>\n<\/li>\n

  5. Next,\u00a0any ligand is allowed, together with\u00a0a 7-coordinate central atom. Three examples, including \u00a0VAPZEU (2016, [6]<\/a><\/span>, DOI: 10.5517\/ccdc.csd.cc1md045<\/a>)\u00a0with three Pd and three Si hexagonal ligands, with an additional 7th Cu surrounding a central Pd.\n

    \"\"\u00a0<\/p>\n<\/li>\n

  6. One example (of eight found) with 8-coordination at central atom (1996, NANPOH[7]<\/a><\/span>), a central\u00a0Cd, six oxygen ligands and two further cyanide axial ligands.\n

    \"\"<\/p>\n<\/li>\n

  7. To finish, a rather wacky polymeric example with Ti at the centre, six hydrogens deriving from a terminal borane as the hexacoordinate planar motif and two axial P ligands (PEDJOY[8]<\/a><\/span>, DOI: 10.5517\/ccb0d6x<\/a>).\n

    \"\"<\/p>\n<\/li>\n<\/ol>\n

    I hope this short journey through\u00a0hexacoordinate planar transition metal complexes has revealed at least a flavour of the diversity in this category. I am also going to take some gentle issue with the\u00a0C&E News reporting<\/a> of this molecule,\u00a0“Scientists proposed a hexagonal planar geometry more than 100 years ago, but it has never been captured in crystal form until now<\/em>”\u00a0(referring to the 2019 article which inspired this blog[1]<\/a><\/span>). As I hope\u00a0I have shown, a number of the examples above in crystal form actually emerged rather earlier than 2019!<\/p>\n

    References<\/h2>\n
    1. M. Gar\u00e7on, C. Bakewell, G.A. Sackman, A.J.P. White, R.I. Cooper, A.J. Edwards, and M.R. Crimmin, \"A hexagonal planar transition-metal complex\", Nature<\/i>, vol. 574, pp. 390-393, 2019. https:\/\/doi.org\/10.1038\/s41586-019-1616-2<\/a>\n\n<\/li>\n
    2. V.G. Albano, M.C. Iapalucci, G. Longoni, L. Manzi, and M. Monari, \"Synthesis of [Au<sub>3<\/sub>Fe<sub>2<\/sub>(CO)<sub>8<\/sub>(dppm)]<sup>-<\/sup> and [Au<sub>5<\/sub>Fe<sub>2<\/sub>(CO)<sub>8<\/sub>(dppm)<sub>2<\/sub>]<sup>+<\/sup>:\u2009 X-ray Structures of [NEt<sub>4<\/sub>][Au<sub>3<\/sub>Fe<sub>2<\/sub>(CO)<sub>8<\/sub>(dppm)] and [Au<sub>5<\/sub>Fe<sub>2<\/sub>(CO)<sub>8<\/sub>(dppm)<sub>2<\/sub>][BF<sub>4<\/sub>]\", Organometallics<\/i>, vol. 16, pp. 497-499, 1997. https:\/\/doi.org\/10.1021\/om960850g<\/a>\n\n<\/li>\n
    3. R. Ahlrichs, D. Fenske, H. Oesen, and U. Schneider, \"Synthesis and Structure of [Ni(P<i>t<\/i>Bu<sub>6<\/sub>)] and [Ni<sub>5<\/sub>(P<i>t<\/i>Bu)<sub>6<\/sub>(CO)<sub>5<\/sub>] and Calculations on the Electronic Structure of [Ni(P<i>t<\/i>Bu)<sub>6<\/sub>] and (PR)<sub>6<\/sub>, R = <i>t<\/i>Bu,Me\", Angewandte Chemie International Edition in English<\/i>, vol. 31, pp. 323-326, 1992. https:\/\/doi.org\/10.1002\/anie.199203231<\/a>\n\n<\/li>\n
    4. E. Hey\u2010Hawkins, M. Pink, H. Oesen, and D. Fenske, \"Synthesen und Charakterisierung von [Ni(<i>t<\/i>BuAs)<sub>6<\/sub>] und [Pd(<i>t<\/i>BuAs)<sub>6<\/sub>]\", Zeitschrift f\u00fcr anorganische und allgemeine Chemie<\/i>, vol. 622, pp. 689-691, 1996. https:\/\/doi.org\/10.1002\/zaac.19966220420<\/a>\n\n<\/li>\n
    5. S.C.K. Hau, M.C. Yeung, V.W. Yam, and T.C.W. Mak, \"Assembly of Heterometallic Silver(I)\u2013Copper(I) Alkyl-1,3-diynyl Clusters via Inner-Core Expansion\", Journal of the American Chemical Society<\/i>, vol. 138, pp. 13732-13739, 2016. https:\/\/doi.org\/10.1021\/jacs.6b08674<\/a>\n\n<\/li>\n
    6. M. Tanabe, R. Yumoto, T. Yamada, T. Fukuta, T. Hoshino, K. Osakada, and T. Tanase, \"Planar PtPd<sub>3<\/sub> Complexes Stabilized by Three Bridging Silylene Ligands\", Chemistry \u2013 A European Journal<\/i>, vol. 23, pp. 1386-1392, 2016. https:\/\/doi.org\/10.1002\/chem.201604502<\/a>\n\n<\/li>\n
    7. J. Kim, and K. Kim, \"NEW THREE DIMENSIONAL [Cd(CN)<sub>2<\/sub>]<sub>n<\/sub> FRAMEWORK FORMED WITH CADMIUM CYANIDE AND Cd(CN)<sub>2<\/sub>\u00b7(18-CROWN-6): CRYSTAL STRUCTURE OF [Cd(CN)<sub>2<\/sub>]\u00b71\/2[Cd(CN)<sub>2<\/sub> (18-CROWN-6)]\u00b73\/2EtOH<sup>+<\/sup>\", Journal of Coordination Chemistry<\/i>, vol. 37, pp. 7-15, 1996. https:\/\/doi.org\/10.1080\/00958979608023536<\/a>\n\n<\/li>\n
    8. D.M. Goedde, and G.S. Girolami, \"Titanium(II) and Titanium(III) Tetrahydroborates. Crystal Structures of [Li(Et<sub>2<\/sub>O)<sub>2<\/sub>][Ti<sub>2<\/sub>(BH<sub>4<\/sub>)<sub>5<\/sub>(PMe<sub>2<\/sub>Ph)<sub>4<\/sub>], Ti(BH<sub>4<\/sub>)<sub>3<\/sub>(PMe<sub>2<\/sub>Ph)<sub>2<\/sub>, and Ti(BH<sub>4<\/sub>)<sub>3<\/sub>(PEt<sub>3<\/sub>)<sub>2<\/sub>\", Inorganic Chemistry<\/i>, vol. 45, pp. 1380-1388, 2006. https:\/\/doi.org\/10.1021\/ic051556w<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      Here is another selection from the Molecules-of-the-Year shortlist published by C&E News, in which hexagonal planar transition metal coordination is identified. 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 palladium atom surrounded by three […]<\/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_feature_clip_id":0,"_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":[1745],"tags":[],"ppma_author":[2661],"class_list":["post-21883","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining"],"yoast_head":"\nMolecules of the year 2019: Hexagonal planar crystal structures. - 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=21883\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Molecules of the year 2019: Hexagonal planar crystal structures. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"Here is another selection from the Molecules-of-the-Year shortlist published by C&E News, in which hexagonal planar transition metal coordination is identified. 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 palladium atom surrounded by three […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21883\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2020-01-23T10:21:32+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2020-01-23T12:33:57+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2020\/01\/norloy-300x263.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=\"4 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Molecules of the year 2019: Hexagonal planar crystal structures. - 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=21883","og_locale":"en_GB","og_type":"article","og_title":"Molecules of the year 2019: Hexagonal planar crystal structures. - Henry Rzepa's Blog","og_description":"Here is another selection from the Molecules-of-the-Year shortlist published by C&E News, in which hexagonal planar transition metal coordination is identified. 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For 2024 the list is (in order of votes cast for each) Mirror-image cyclodextrin Molecular shuttle in a box Rule-bending strained alkene First soluble promethium complex Single-electron carbon-carbon bond Hot MOF for capturing carbon I\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":20778,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=20778","url_meta":{"origin":21883,"position":1},"title":"Imaging normal vibrational modes of a single molecule of CoTPP: a mystery about the nature of the imaged species.","author":"Henry Rzepa","date":"April 25, 2019","format":false,"excerpt":"Previously, I explored (computationally) the normal vibrational modes of Co(II)-tetraphenylporphyrin (CoTPP) as a \"flattened\" species on copper or gold surfaces for comparison with those recently imaged. The initial intent was to estimate the \"flattening\" energy. There are six electronic possibilities for this molecule on a metal surface. Respectively positively, or\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":26601,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26601","url_meta":{"origin":21883,"position":2},"title":"Molecules of the year: 2023","author":"Henry Rzepa","date":"December 28, 2023","format":false,"excerpt":"The Science education unit at the ACS publication C&EN publishes its list of molecules of the year (as selected by the editors and voted upon by the readers) in December. Here are some observations about three of this year's batch. Diberyllocene with its unusual Be-Be bond has already beeen covered\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2023\/12\/CF.gif?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":21407,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21407","url_meta":{"origin":21883,"position":3},"title":"Does Kekulene have Kekul\u00e9 vibrational modes? Yes!","author":"Henry Rzepa","date":"October 19, 2019","format":false,"excerpt":"Increasingly, individual small molecules are having their structures imaged using STM, including cyclo[18]carbon that I recently discussed. The latest one receiving such treatment is Kekulene. As with cyclo[18]carbon, the point of interest was which of the two resonance structures shown below most closely resembled the measured structure. The one on\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\/2019\/10\/b3-1423-B2u-1024x575.gif?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":23187,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23187","url_meta":{"origin":21883,"position":4},"title":"Dispersion attraction effects on the computed geometry of a leminscular dodecaporphyrin.","author":"Henry Rzepa","date":"January 1, 2021","format":false,"excerpt":"In the previous post, I showed the geometries of three large cyclic porphyrins, as part of an article on exploring the aromaticity of large 4n+2 cyclic rings. One of them had been induced into a \"figure-eight\" or lemniscular conformation, as shown below. Any initial inspection of the geometries of these\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\/12\/c-P12b12_T6f.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":28233,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=28233","url_meta":{"origin":21883,"position":5},"title":"Molecules of the Year 2024: Molecular shuttle in a box.","author":"Henry Rzepa","date":"January 25, 2025","format":false,"excerpt":"This is another in the C&E News list of candidates for the Molecule of the Year, Molecular shuttle in a box Mirror-image cyclodextrin Molecular shuttle in a box Rule-bending strained alkene First soluble promethium complex Single-electron carbon-carbon bond Hot MOF for capturing carbon The molecule shown below inside the cavity\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","author_category":"1","first_name":"Henry","last_name":"Rzepa","user_url":"https:\/\/orcid.org\/0000-0002-8635-8390","job_title":"","description":"Henry Rzepa is Emeritus Professor of Computational Chemistry at Imperial College London."}],"_links":{"self":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/21883","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=21883"}],"version-history":[{"count":22,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/21883\/revisions"}],"predecessor-version":[{"id":21924,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/21883\/revisions\/21924"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=21883"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=21883"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=21883"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=21883"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}