{"id":18121,"date":"2017-04-13T10:17:30","date_gmt":"2017-04-13T09:17:30","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=18121"},"modified":"2017-04-13T10:17:30","modified_gmt":"2017-04-13T09:17:30","slug":"the-%cf%80-%cf%80-stacking-of-aromatic-rings-what-is-their-closest-parallel-approach","status":"publish","type":"post","link":"https:\/\/www.rzepa.net\/blog\/?p=18121","title":{"rendered":"The \u03c0-\u03c0 stacking of aromatic rings: what is their closest parallel approach?"},"content":{"rendered":"
\n

Layer stacking in structures such as graphite<\/a> is well-studied. The separation between the \u03c0-\u03c0 planes\u00a0is\u00a0~3.35\u00c5, which is close to twice the estimated van der Waals (vdW) radius of carbon (1.7\u00c5). But how much closer could such layers get, given that many other types of relatively weak interaction such as hydrogen bonding can contract the vdW distance sum by up to ~0.8\u00c5 or even more? This question was prompted by the separation calculated for the ion-pair cyclopropenium cyclopentadienide<\/a> (~2.6-2.8\u00c5).<\/p>\n

The search query for the Cambridge structure database is shown below.<\/p>\n

\"\"
\n The query (dataDOI: 10.14469\/hpc\/2471<\/a>) defines centroids for two benzenoid\u00a0rings, both comprising only 3-coordinated carbons. The sine of an angle subtended at each centroid to the other and to one ring carbon attempts to track how parallel the two rings are (strictly speaking, 12 such angles should be included). If the sines of both angles are 1.00, then the two centroids overlap orthogonally.\u00a0A search constrained to no disorder, no errors and R < 0.05 reveals 1107 hits at a centroid-centroid distance of < 3.5\u00c5. The colour code (red) indicates the distances in the range 3.4-3.5\u00c5, which matches that of\u00a0graphite, while distances down to 3.2\u00c5 (yellow-green) are\u00a0not uncommon.\u00a0<\/p>\n

\"\"<\/p>\n

Here is another way of representing these results, in which the centroid-centroid distances (measured from the positions of 12 carbon atoms and hence statistically more reliable than any individual atom pair distance) are multiplied by either sin(ANGa) or\u00a0sin(ANGb). The number of occurrences\u00a0with distances < 3.2\u00c5 is less than 32 (out of 1107).\"\"<\/p>\n

Taking a look at some of these outliers, PAZJEG has two entries, one with a short distance (dataDOI: 10.5517\/ccsffzl<\/a>) and one with a normal distance[1]<\/a><\/span>, which does tend to cast doubt on the former.\"\" \"\"<\/p>\n

ZOMSEB[2]<\/a><\/span>,\u00a0DataDOI:\u00a010.5517\/CCZS2MF<\/a>) appears to have the planes of the molecules stacked ~2.5\u00c5 apart.\"\"<\/p>\n

OXUDES02[cite10.1016\/j.poly.2016.09.046[\/cite], DataDOI:\u00a010.5517\/CCDC.CSD.CC1MBBFQ<\/a>) has a separation\u00a0of ~2.6\u00c5.\"\"<\/p>\n

Verifying these and other outliers\u00a0would require expert\u00a0inspection of the crystallographic data and its refinement. This might require access to the\u00a0hkl<\/em>\u00a0 structure factors, data which are now being “strongly encouraged”\u2021<\/sup>\u00a0for deposition with the CSD, but which are not present for most structures deposited before ~2016. In extreme cases, the original diffraction images collected by the cameras would allow for a fully independent re-analysis, data which however is rarely if ever deposited.<\/p>\n

So the separation of \u03c0-\u03c0 stacked six-membered benzenoid\u00a0rings is only\u00a0infrequently\u00a0less than ~3.2\u00c5 in measured crystal structures. There are hints it might reach as short as ~2.6\u00c5, but \u00a0such examples with values significantly\u00a0less than 3.2\u00c5\u00a0do require expert validation before they can be called real.\u00a0<\/p>\n

\n

\u2021See structuredepositioninformation\/<\/a>\u00a0“We strongly encourage data to be deposited either with imbedded structure factor data or with an associated FCF or HKL structure factor file.”<\/i><\/p>\n

References<\/h2>\n
  1. J. Rogan, D. Poleti, and L. Karanovi\u0107, \"Synthesis, Structure, and Thermal Properties of Two New Inorganic\u2010organic Framework Compounds: Hexaaqua(<i>\u03bc<\/i><sub>2<\/sub>\u20101,2,4,5\u2010benzenetetracarboxylato)\u2010bis(<i>N<\/i>,<i>N\u2032<\/i>\u20101,10\u2010phenathroline)dicobalt(II) Dihydrate and Hexaaqua(<i>\u03bc<\/i><sub>2<\/sub>\u20101,2,4,5\u2010benzenetetracarboxylato)\u2010bis(<i>N<\/i>,<i>N\u2032<\/i>\u20102,2\u2032\u2010dipyridylamine)dinickel(II) Tetrahydrate\", Zeitschrift f\u00fcr anorganische und allgemeine Chemie<\/i>, vol. 632, pp. 133-139, 2005. https:\/\/doi.org\/10.1002\/zaac.200500292<\/a>\n\n<\/li>\n
  2. P. Das, C.K. Jain, S.K. Dey, R. Saha, A.D. Chowdhury, S. Roychoudhury, S. Kumar, H.K. Majumder, and S. Das, \"Synthesis, crystal structure, DNA interaction and in vitro anticancer activity of a Cu(<scp>ii<\/scp>) complex of purpurin: dual poison for human DNA topoisomerase I and II\", RSC Adv.<\/i>, vol. 4, pp. 59344-59357, 2014. https:\/\/doi.org\/10.1039\/c4ra07127a<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    Layer stacking in structures such as graphite is well-studied. The separation between the \u03c0-\u03c0 planes\u00a0is\u00a0~3.35\u00c5, which is close to twice the estimated van der Waals (vdW) radius of carbon (1.7\u00c5). But how much closer could such layers get, given that many other types of relatively weak interaction such as hydrogen bonding can contract the vdW […]<\/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":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"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":[1754],"tags":[1412,510,1416,2149,2160,1459,1979,1881,1491,733,2196,1842,2202],"class_list":["post-18121","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining","tag-carbon","tag-chemical-bonding","tag-chemistry","tag-cyclopentadienyl-anion","tag-graphite","tag-hydrogen-bond","tag-intermolecular-forces","tag-nature","tag-organic-chemistry","tag-search-query","tag-stacking","tag-supramolecular-chemistry","tag-vdw"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/p1gPyz-4Ih","jetpack_likes_enabled":true,"_links":{"self":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/posts\/18121","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=18121"}],"version-history":[{"count":0,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/posts\/18121\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=18121"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=18121"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=18121"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}