{"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":"2015-08-25T14:35:18","modified_gmt":"2015-08-25T13:35:18","slug":"a-visualisation-of-the-effects-of-conjugation-dienes-and-biaryls","status":"publish","type":"post","link":"https:\/\/www.rzepa.net\/blog\/?p=14485","title":{"rendered":"A visualisation of the effects of conjugation; dienes and biaryls."},"content":{"rendered":"
\n

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?<\/p>\n

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

The search of the CSD (Cambridge structure database) is constrained to R < 5%, no errors and no disorder and the central \u00a0C-C bond is specific to be acyclic.\u2021<\/sup><\/p>\n

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

    \n
  1. Note first that the hotspot occurs for a torsion angle of 180\u00b0, a trans diene.<\/li>\n
  2. There 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.<\/li>\n
  3. There is a gentle curve illustrating that the C-C distance is indeed a maximum at 90\u00b0<\/li>\n
  4. The C-C bond extends from ~1.445\u00c5 when the two double bonds are coplanar (fully conjugated) to ~1.48\u00c5 when orthogonal. Not much of a change, but statistically highly significant.<\/li>\n<\/ol>\n

    Here is another search, this time of the C=C-C=C motif embedded into a biaryl, of which there\u00a0are far more examples. This time, the (red) hotspot is actually at\u00a090\u00b0, with local (green) hotspots at 0 and 180\u00b0 but also at 45 and 135\u00b0. Again, you can easily spot the maximum in C-C bond length at 90\u00b0 but notice how much smaller the bond lengthening is (~ 0.01\u00c5). 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 \u00a0C-C bond at torsions of 0 or 180\u00b0 appear to be no shorter than the values at\u00a045 and 135\u00b0.<\/p>\n

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

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

    Both these searches took about \u00a05 minutes each, and serve to illustrate just how many basic chemical concepts can be teased out of a statistical analysis of crystal structures.<\/p>\n

    \n

    \u2021<\/sup>The analogous diagram for O=C-C=C is shown below;<\/p>\n

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

    That for \u00a0O=C-C=O is different however;<\/p>\n

    \"arm1\"<\/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 \u00a0C-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,"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":[3,1754],"tags":[1561,59,1414,1564,1500],"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"],"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/p1gPyz-3LD","jetpack_likes_enabled":true,"_links":{"self":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14485","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=14485"}],"version-history":[{"count":0,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14485\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=14485"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=14485"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.rzepa.net\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=14485"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}