{"id":15885,"date":"2016-03-02T09:41:10","date_gmt":"2016-03-02T09:41:10","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=15885"},"modified":"2023-09-17T07:21:40","modified_gmt":"2023-09-17T06:21:40","slug":"discovery-based-research-experiences-gauche-effects-in-group-16-elements","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15885","title":{"rendered":"Discovery based research experiences: gauche effects in group 16 elements."},"content":{"rendered":"
\n

\n\tThe upcoming ACS national meeting in San Diego has a CHED (chemical education division) session entitled Implementing Discovery-Based Research Experiences in Undergraduate Chemistry Courses<\/a>. I had previously explored<\/a> what I called extreme gauche effects<\/em> in the molecule F-S-S-F. Here I take this a bit further to see what else can be discovered about molecules containing bonds between group 16 elements (QA= O, S, Se, Te). \n<\/p>\n

\n\t\"OO-SQ\"\n<\/p>\n

\n\tThe search definition is shown above, with DIST1 being the QA-QA bond length, the QA-QA bond being acyclic, each QA bearing only two bonded atoms and NM being any non-metal. The first result shown is for QA=S.\n<\/p>\n

\n\t\"S-S\"\n<\/p>\n

    \n
  1. \n\t\tThe first discovery is that the most common torsion (red-hot spot) is about 90°, but there appears to be a statistically significant distortion towards longer<\/strong> S-S distances as the torsion deviates from this angle. For those who are so inclined it would perhaps be worth improving my term "appears to be<\/a>" with a more formal numerical analysis of the distribution shown above and its significance. Any offers?\n\t<\/li>\n
  2. \n\t\tThe other discovery worth exploring is the number of occurences with an angle of 180°. With F-S-S-F itself (not a solid), I had previously noted<\/a> that this angle actually represented a transition state in the torsion! So what might be inferred from these examples?\n\t<\/li>\n<\/ol>\n

    \n\tThe next search includes a further constraint that the temperature the data was recorded at be <140K. This reduces vibrational "noise" and so should increase the significance. \"S-S-140\"\n<\/p>\n

      \n
    1. \n\t\tHere we discover the same "V"-shaped distribution as before, possibly more significant statistically than the previous search. Again, a proper statistical analysis of the significance of this result is desirable.\n\t<\/li>\n<\/ol>\n

      \n\tThe next search is for QA = Se or Te. \"X-X\"\n<\/p>\n

        \n
      1. \n\t\tThe Se and Te distributions can clearly be distinguished, with a weak "V-shape" visible for Se, but absent for Te. Again, those hits at 180!\n\t<\/li>\n
      2. \n\t\tThere are a few instances "in-between" the two distributions, which appear to be  Se-Te systems.\n\t<\/li>\n<\/ol>\n

        \n\tFinally, QA=QB = O.\n<\/p>\n

        \n\t\"O-O\"\n<\/p>\n

          \n
        1. \n\t\tThe discovery here is the apparent absence<\/strong> of any "V-shaped" distribution.\n\t<\/li>\n
        2. \n\t\tThe hot spot now occurs at 180°, but with a tail down to 60° or less. Clearly, the definition of "NM" as any non-metal probably needs to be explored further for specific instances to see what influence the nature of NM has. NM for example could be another O, which might be a severe perturbation. \n\t<\/li>\n<\/ol>\n

          \n\tSo here I have tried to tease out seven directions for further discovery. I am attending\/presenting at the session I noted at the top and will report back on any interesting observations.\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":"

          The upcoming ACS national meeting in San Diego has a CHED (chemical education division) session entitled Implementing Discovery-Based Research Experiences in Undergraduate Chemistry Courses. I had previously explored what I called extreme gauche effects in the molecule F-S-S-F. Here I take this a bit further to see what else can be discovered about molecules containing bonds […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_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},"jetpack_post_was_ever_published":false},"categories":[1745,4],"tags":[1689,157,1688,1686,1687],"ppma_author":[2661],"class_list":["post-15885","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining","category-interesting-chemistry","tag-city-san-diego","tag-metal","tag-non-metal","tag-singular-spectrum-analysis","tag-time-series-analysis"],"yoast_head":"\nDiscovery based research experiences: gauche effects in group 16 elements. - 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=15885\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Discovery based research experiences: gauche effects in group 16 elements. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"The upcoming ACS national meeting in San Diego has a CHED (chemical education division) session entitled Implementing Discovery-Based Research Experiences in Undergraduate Chemistry Courses. I had previously explored what I called extreme gauche effects in the molecule F-S-S-F. 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The components of the search are shown as four queries below, which will be combined in various Boolean senses (DOI:\u00a010.14469\/hpc\/2462). Query one defines the carboxylic acid, with 3-coordinate carbon specified at the\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\/051-1024x676.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":14016,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14016","url_meta":{"origin":15885,"position":2},"title":"The B\u00fcrgi\u2013Dunitz angle revisited: a mystery?","author":"Henry Rzepa","date":"May 12, 2015","format":false,"excerpt":"The B\u00fcrgi\u2013Dunitz angle is one of those memes that most students of organic chemistry remember.\u00a0It hypothesizes the geometry of attack of a\u00a0nucleophile\u00a0on a\u00a0trigonal\u00a0unsaturated (sp2) carbon in a\u00a0molecule\u00a0such as\u00a0ketone, aldehyde,\u00a0ester, and\u00a0amide\u00a0carbonyl. Its value obviously depends on the exact system, but is generally taken to be in the range 105-107\u00b0. A very\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":18165,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18165","url_meta":{"origin":15885,"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":21726,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21726","url_meta":{"origin":15885,"position":4},"title":"Hydrogen bonds: carbon as an acceptor rather than as a donor?","author":"Henry Rzepa","date":"December 23, 2019","format":false,"excerpt":"A hydrogen bond donor is considered as an electronegative element carrying a hydrogen that is accepted by an atom carrying a lone pair of electrons, as in X:...H-Y where X: is the acceptor and H-Y the donor. Wikipedia asserts that carbon can act as a donor, as we saw in\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":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2019\/12\/query-1024x598.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":11279,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11279","url_meta":{"origin":15885,"position":5},"title":"An example of an extreme gauche effect: FSSF.","author":"Henry Rzepa","date":"September 21, 2013","format":false,"excerpt":"The best known example of the gauche effect is 1,2-difluoroethane, which exhibits a relatively small preference of ~0.5 kcal\/mol for this conformer over the anti orientation, which is also a minimum. But FSSF, which I discussed in the previous post, beats this hands down! It also, by the way, must\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":"FSSF-ELF","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/09\/FSSF-ELF.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\/15885","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=15885"}],"version-history":[{"count":17,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/15885\/revisions"}],"predecessor-version":[{"id":26498,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/15885\/revisions\/26498"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=15885"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=15885"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=15885"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=15885"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}