{"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":"2017-04-16T08:31:52","modified_gmt":"2017-04-16T07:31:52","slug":"the-%cf%80-%cf%80-stacking-of-aromatic-rings-what-is-their-closest-parallel-approach","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/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,"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":[1745],"tags":[1440,557,1395,2116,2127,1449,1959,1871,1410,734,2125,1746,2126],"ppma_author":[2661],"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"],"yoast_head":"\nThe \u03c0-\u03c0 stacking of aromatic rings: what is their closest parallel approach? - 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=18121\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The \u03c0-\u03c0 stacking of aromatic rings: what is their closest parallel approach? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"Layer stacking in structures such as graphite is well-studied. 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A search of the Cambridge structure database reveals 52 instances of the cyclopropenium cation with a variety of counter-anions, 77 cyclopentadienide\u00a0anions with a variety of counter-cations and one (SOWMOG,\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\/04\/SOWMOG-1002x1024.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":14423,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14423","url_meta":{"origin":18121,"position":1},"title":"Intermolecular atom-atom bonds in crystals? The O…O case.","author":"Henry Rzepa","date":"July 25, 2015","format":false,"excerpt":"I recently followed this bloggers trail; link1 \u2192 link2 to arrive at this delightful short commentary on atom-atom bonds in crystals by Jack Dunitz. Here he discusses that age-old question (to chemists), what is a bond? Even almost 100 years after Gilbert Lewis' famous analysis, we continue to ponder this\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":"OO-query","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/07\/OO-query.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":16573,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16573","url_meta":{"origin":18121,"position":2},"title":"How does an OH or NH group approach an aromatic ring to hydrogen bond with its \u03c0-face?","author":"Henry Rzepa","date":"June 22, 2016","format":false,"excerpt":"I previously used data mining of crystal structures to explore the directing influence of substituents on aromatic and heteroaromatic rings. Here\u00a0I explore, quite literally, a different angle to the hydrogen bonding interactions between a benzene ring and\u00a0OH or NH groups. I start by defining a benzene ring with a centroid.\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":"aromatic-pi-query","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/06\/aromatic-pi-query-1-e1466580253270.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":18165,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18165","url_meta":{"origin":18121,"position":3},"title":"\u03c0-Facial hydrogen bonds to alkenes (revisited): how close can an acidic hydrogen approach?","author":"Henry Rzepa","date":"April 15, 2017","format":false,"excerpt":"Back in the early 1990s, we first discovered the delights of searching crystal structures\u00a0for unusual\u00a0bonding features. One of the first cases was a search for hydrogen bonds formed to the\u00a0\u03c0-faces of alkenes and alkynes. In those days the CSD database of crystal structures was a lot smaller (<80,000 structures; it's\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\/04\/SQ-H-pi-1024x783.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":18277,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18277","url_meta":{"origin":18121,"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":27788,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=27788","url_meta":{"origin":18121,"position":5},"title":"A carbon-carbon one-electron bond! Or a weak carbon-carbon interaction?","author":"Henry Rzepa","date":"October 1, 2024","format":false,"excerpt":"More than 100 years ago, before the quantum mechanical treatment of molecules had been formulated, G. N. Lewis proposed a simple model for chemical bonding that is still taught today. This is the idea of the three categories of bond we know as single, double and triple, comprising respectively two,\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\/18121","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=18121"}],"version-history":[{"count":25,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/18121\/revisions"}],"predecessor-version":[{"id":18160,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/18121\/revisions\/18160"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=18121"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=18121"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=18121"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=18121"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}