{"id":14485,"date":"2015-08-25T14:35:18","date_gmt":"2015-08-25T13:35:18","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=14485"},"modified":"2023-09-17T07:16:54","modified_gmt":"2023-09-17T06:16:54","slug":"a-visualisation-of-the-effects-of-conjugation-dienes-and-biaryls","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14485","title":{"rendered":"A visualisation of the effects of conjugation; dienes and biaryls."},"content":{"rendered":"
\n

\n\tHere is another exploration of simple chemical concepts using crystal structures. Consider a simple diene: how does the central C-C bond length respond to the torsion angle between the two C=C bonds?\n<\/p>\n

\n\t\"arm1\"\n<\/p>\n

\n\tThe search of the CSD (Cambridge structure database) is constrained to R < 5%, no errors and no disorder and the central  C-C bond is specific to be acyclic.‡<\/sup>\n<\/p>\n

\n\t\"arm1\"\n<\/p>\n

    \n
  1. \n\t\tNote first that the hotspot occurs for a torsion angle of 180°, a trans diene.\n\t<\/li>\n
  2. \n\t\tThere is just a hint that the C-C distance for a cis-diene might be a little shorter than the trans diene, but this might not be significant.\n\t<\/li>\n
  3. \n\t\tThere is a gentle curve illustrating that the C-C distance is indeed a maximum at 90°\n\t<\/li>\n
  4. \n\t\tThe C-C bond extends from ~1.445Å when the two double bonds are coplanar (fully conjugated) to ~1.48Å when orthogonal. Not much of a change, but statistically highly significant.\n\t<\/li>\n<\/ol>\n

    \n\tHere is another search, this time of the C=C-C=C motif embedded into a biaryl, of which there are far more examples. This time, the (red) hotspot is actually at 90°, with local (green) hotspots at 0 and 180° but also at 45 and 135°. Again, you can easily spot the maximum in C-C bond length at 90° but notice how much smaller the bond lengthening is (~ 0.01Å). This lengthening is inhibited by retention of the aromaticity of the two aryl rings; again the statistical effect is highly significant. Perhaps also significant is that the  C-C bond at torsions of 0 or 180° appear to be no shorter than the values at 45 and 135°.\n<\/p>\n

    \n\t\"arm1\"\n<\/p>\n

    \n\t\"arm1\"\n<\/p>\n

    \n\tBoth these searches took about  5 minutes each, and serve to illustrate just how many basic chemical concepts can be teased out of a statistical analysis of crystal structures.\n<\/p>\n

    \n

    \n\t‡<\/sup>The analogous diagram for O=C-C=C is shown below;\n<\/p>\n

    \n\t\"arm1\"\n<\/p>\n

    \n\tThat for  O=C-C=O is different however;\n<\/p>\n

    \n\t\"arm1\"\n<\/p>\n

    Acknowledgments<\/h4>\n

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

    Here is another exploration of simple chemical concepts using crystal structures. Consider a simple diene: how does the central C-C bond length respond to the torsion angle between the two C=C bonds? The search of the CSD (Cambridge structure database) is constrained to R < 5%, no errors and no disorder and the central  C-C […]<\/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":[2,1745],"tags":[1568,144,1402,1569,1512],"ppma_author":[2661],"class_list":["post-14485","post","type-post","status-publish","format-standard","hentry","category-chemical-it","category-crystal_structure_mining","tag-basic-chemical-concepts","tag-cambridge","tag-chemical-bond","tag-chemical-concepts-using-crystal-structures","tag-quantum-chemistry"],"yoast_head":"\nA visualisation of the effects of conjugation; dienes and biaryls. - 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=14485\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"A visualisation of the effects of conjugation; dienes and biaryls. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"Here is another exploration of simple chemical concepts using crystal structures. Consider a simple diene: how does the central C-C bond length respond to the torsion angle between the two C=C bonds? The search of the CSD (Cambridge structure database) is constrained to R < 5%, no errors and no disorder and the central  C-C […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14485\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2015-08-25T13:35:18+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2023-09-17T06:16:54+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2015\/08\/dienes.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":"A visualisation of the effects of conjugation; dienes and biaryls. - 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=14485","og_locale":"en_GB","og_type":"article","og_title":"A visualisation of the effects of conjugation; dienes and biaryls. - Henry Rzepa's Blog","og_description":"Here is another exploration of simple chemical concepts using crystal structures. Consider a simple diene: how does the central C-C bond length respond to the torsion angle between the two C=C bonds? 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Here, I give an answer in the form of a search of the CSD (crystal structure database). I was not sure if the question related purely to the geometries obtained using computational methods or to comparisons with\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":14508,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14508","url_meta":{"origin":14485,"position":2},"title":"A visualization of the anomeric effect from crystal structures.","author":"Henry Rzepa","date":"August 27, 2015","format":false,"excerpt":"The anomeric effect is best known in sugars, occuring in sub-structures such as RO-C-OR. Its origins relate to how the lone pairs on each oxygen atom align with the adjacent C-O bonds. When the alignment is 180\u00b0, one oxygen lone pair can donate into the C-O \u03c3* empty orbital and\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":14537,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14537","url_meta":{"origin":14485,"position":3},"title":"\u03c0-Resonance in amides: a crystallographic reality check.","author":"Henry Rzepa","date":"September 5, 2015","format":false,"excerpt":"The \u03c0-resonance in amides famously helped Pauling to his proposal\u00a0of a helical structure for proteins. Here I explore some geometric properties of amides related to the C-N bond and the torsions about it. The key aspect of amides is that a lone pair of electrons on the nitrogen can conjugate\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":15992,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15992","url_meta":{"origin":14485,"position":4},"title":"Celebrating Paul Schleyer: searching for hidden treasures in the structures of metallocene complexes.","author":"Henry Rzepa","date":"April 2, 2016","format":false,"excerpt":"A celebration of the life and work of the great chemist\u00a0Paul von R. Schleyer was held this week in Erlangen, Germany. There were many fantastic talks given by some great chemists describing fascinating chemistry. Here I highlight the presentation\u00a0given by\u00a0Andy Streitwieser on the topic of organolithium chemistry, also a great\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":5368,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5368","url_meta":{"origin":14485,"position":5},"title":"Spotting the unexpected. Anomeric effects involving alkenes?","author":"Henry Rzepa","date":"November 2, 2011","format":false,"excerpt":"How one might go about answering the question: do alkenes promote anomeric effects? A search of chemical abstracts does not appear to cite any examples (I may have missed them of course, since it depends very much on the terminology you use, and new effects may not yet have any\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":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/11\/query.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\/14485","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=14485"}],"version-history":[{"count":10,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14485\/revisions"}],"predecessor-version":[{"id":26493,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14485\/revisions\/26493"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=14485"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=14485"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=14485"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=14485"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}