{"id":15141,"date":"2015-12-20T10:13:31","date_gmt":"2015-12-20T10:13:31","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=15141"},"modified":"2023-09-17T07:10:14","modified_gmt":"2023-09-17T06:10:14","slug":"could-anyone-comment-on-any-recent-calculated-results-on-the-planarity-or-lack-thereof-of-azobenzene","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15141","title":{"rendered":"Could anyone comment on any recent calculated results on the planarity, or lack thereof, of azobenzene?"},"content":{"rendered":"
\n

\n\tThis question was posted<\/a> on the CCL<\/a> (computational chemistry list) by John McKelvey. Here, I give an answer in the form of a search of the CSD (crystal structure database).\n<\/p>\n

\n\tI was not sure if the question related purely to the geometries obtained using computational methods or to comparisons with experimentally determined structures. Or indeed whether it related to azobenzene specifically or to azobenzenes in general. Here, I comment only in respect of the latter two. The search was defined as below, with the following specifications:\n<\/p>\n

    \n
  1. \n\t\tThe absolute value of the central torsion (TOR1) was constrained to 0-60° for cis azobenzenes and to 120-180° for trans azobenzenes.\n\t<\/li>\n
  2. \n\t\tTwo further torsions (TOR2, TOR3) specify the torsion angle about the aryl to N bond.\n\t<\/li>\n
  3. \n\t\tThe R factor is < 0.1, and there are no errors or disorder.\n\t<\/li>\n
  4. \n\t\tThe C-N bonds were specified as acyclic.\n\t<\/li>\n<\/ol>\n

    \n\t\"search<\/a>\n<\/p>\n\n\n\n\n\n\n
    \n\t\t\t\tTrans Azobenzenes, 1111 examples\n\t\t\t<\/th>\n<\/tr>\n
    \n\t\t\t\t\"trans<\/a>\n\t\t\t<\/td>\n<\/tr>\n
    \n\t\t\t\tCis Azobenzenes, 42 examples\n\t\t\t<\/th>\n<\/tr>\n
    \n\t\t\t\t\"cis<\/a>\n\t\t\t<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

    \n\tThe results show that by and large, trans azo-benzenes are co-planar to ± 30°, but there are some interesting points in the centre with dihedral angles of ~90°. Cis azobenzenes on the other hand are mostly NOT planar, with red hotspots at about 50 or 130° of twist.\n<\/p>\n

    \n\tThese results took about 20 minutes to define, search, and plot as per above. I hope it provides John with an answer<\/a>, even if it's not the one he might have meant!\n<\/p>\n

    \n

    Acknowledgments<\/h4>\n

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

    This question was posted on the CCL (computational chemistry list) by John McKelvey. 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 experimentally determined structures. Or indeed […]<\/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":[1610,1611,1612],"ppma_author":[2661],"class_list":["post-15141","post","type-post","status-publish","format-standard","hentry","category-chemical-it","category-crystal_structure_mining","tag-azobenzene","tag-john-mckelvey","tag-search-azobenzene"],"yoast_head":"\nCould anyone comment on any recent calculated results on the planarity, or lack thereof, of azobenzene? - 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=15141\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Could anyone comment on any recent calculated results on the planarity, or lack thereof, of azobenzene? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"This question was posted on the CCL (computational chemistry list) by John McKelvey. 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Unfortunately the calculated barrier for this simple process was\u2026","rel":"","context":"In "reaction mechanism"","block_context":{"text":"reaction mechanism","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1086"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2020\/12\/CNAl-1024x889.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":19483,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19483","url_meta":{"origin":15141,"position":2},"title":"How FAIR are the data associated with the 2017 Molecules-of-the-Year?","author":"Henry Rzepa","date":"March 7, 2018","format":false,"excerpt":"C&EN has again run a vote for the 2017 Molecules of the year. Here I take a look not just at these molecules, but at how FAIR (Findable, Accessible, Interoperable and Reusable) the data associated with these molecules actually is. 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