{"id":10883,"date":"2013-07-14T10:37:21","date_gmt":"2013-07-14T09:37:21","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=10883"},"modified":"2023-09-16T18:16:32","modified_gmt":"2023-09-16T17:16:32","slug":"the-butterfly-effect-in-chemistry-bimodal-ms-bonds","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10883","title":{"rendered":"The butterfly effect in chemistry: Bimodal M~S bonds?"},"content":{"rendered":"
\n

I noted previously<\/a> that some 8-ring cyclic compounds could exist in either a planar-aromatic or a non-planar-non-aromatic mode, the mode being determined by apparently quite small changes in a ring substituent. Hunting for other examples of such chemistry on the edge, I did a search of the Cambridge crystal database for metal sulfides.\u00a0<\/p>\n

The search was specified as following:<\/p>\n

    \n
  1. Any element from one of the three transition metal series, TS1, TS2 or TS3<\/span><\/li>\n
  2. to contain a M-S bond (any type of bond)<\/li>\n
  3. with the restriction that the sulfur has only one atom attached (the metal)<\/li>\n
  4. R < 0.05<\/li>\n
  5. No errors and no disorder<\/li>\n<\/ol>\n

    The results for the three transition series were quite different. The first row indicated a distribution with a single maximum (~2.3\u00c5), albeit with a very long tail reaching out to 3.2\u00c5. The second row had a very clear bimodel distribution, with two peaks, at ~2.2\u00c5 and ~2.55\u00c5, the latter having the greater number of examples. The third row showed an inverse distribution, with the prominent peak at ~2.2\u00c5 and the smaller peak at 2.55\u00c5.\u00a0<\/p>\n

    \"TS1\"\"TS2\" \"TS3\"<\/p>\n

    A search for the possible reasons for the bimodal distributions is now needed. This could be done in two ways; (a) to refine the search, or (b) to individually scrutinize each example to identify if any chemical reasons can be found. Since there are 100s of examples, I will concentrate on the first tactic. The most obvious is that the compounds cluster into neutral and ionic, as below, which allows the search to be constrained to only entries where a negative charge has been assigned to the sulfur.<\/p>\n

    \"MS\"<\/p>\n

    \"TS2m\" \"TS3m\"<\/p>\n

    This reveals such entries are a fraction of the total, and for these the C-S bond length clusters around 2.2\u00c5. Which leaves us with a mystery. This would mean that the neutral systems, presumably with a formal M=S bond, would have to be responsible for the entries at ~2.55\u00c5. Could it really be that a higher bond order results in a longer bond?\u00a0<\/p>\n

    What the search does not allow us to do (or I am unaware of how to do it) is to identify whether there are any pair of examples where the ligands surrounding M are identical but where one of the pair has a short and the other a long M-S bond. Or indeed such a pair where the differences between the ligands are small (however that is defined). Similarly, one cannot constrain the searches by spin state to see if that might be responsible. It would also be nice to have the system automatically evaluate whether the valence shell on the metal is full (18) or not (16, 17) to see if that is related to the bond length. Indeed, an example of needing to count the valence shell was recently brought to my attention by a student, and it will be the subject of a future post.\u00a0<\/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":"

    I noted previously that some 8-ring cyclic compounds could exist in either a planar-aromatic or a non-planar-non-aromatic mode, the mode being determined by apparently quite small changes in a ring substituent. Hunting for other examples of such chemistry on the edge, I did a search of the Cambridge crystal database for metal sulfides.\u00a0 The search […]<\/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":[4],"tags":[144,1107,157,1105,1106,1381],"ppma_author":[2661],"class_list":["post-10883","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-cambridge","tag-chemical-reasons","tag-metal","tag-metal-sulfides","tag-neutral-systems","tag-transition-metal-series"],"yoast_head":"\nThe butterfly effect in chemistry: Bimodal M~S bonds? - 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=10883\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The butterfly effect in chemistry: Bimodal M~S bonds? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"I noted previously that some 8-ring cyclic compounds could exist in either a planar-aromatic or a non-planar-non-aromatic mode, the mode being determined by apparently quite small changes in a ring substituent. Hunting for other examples of such chemistry on the edge, I did a search of the Cambridge crystal database for metal sulfides.\u00a0 The search […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10883\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2013-07-14T09:37:21+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2023-09-16T17:16:32+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/07\/TS1.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":"The butterfly effect in chemistry: Bimodal M~S bonds? - 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=10883","og_locale":"en_GB","og_type":"article","og_title":"The butterfly effect in chemistry: Bimodal M~S bonds? - Henry Rzepa's Blog","og_description":"I noted previously that some 8-ring cyclic compounds could exist in either a planar-aromatic or a non-planar-non-aromatic mode, the mode being determined by apparently quite small changes in a ring substituent. 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This was a mode of metal coordination first mooted more than 100 years ago, but with the first examples only being discovered recently.\u00a0The C&E News example comprises a central\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\/2020\/01\/norloy-300x263.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":16758,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16758","url_meta":{"origin":10883,"position":1},"title":"What’s in a name? Carbenes: a reality check.","author":"Henry Rzepa","date":"September 11, 2016","format":false,"excerpt":"To quote from Wikipedia: in chemistry, a carbene is a molecule containing a neutral carbon atom with a valence of two and two unshared valence electrons. The most ubiquitous type of carbene of recent times is the one shown below as 1, often referred to as a resonance stabilised or\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":"","width":0,"height":0},"classes":[]},{"id":12482,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12482","url_meta":{"origin":10883,"position":2},"title":"Tetrahedral or square planar? A ten minute exploration.","author":"Henry Rzepa","date":"April 30, 2014","format":false,"excerpt":"I love experiments where the insight-to-time-taken ratio is high. This one pertains to exploring the coordination chemistry of the transition metal region of the periodic table; specifically the tetra-coordination of the series headed by\u00a0Mn-Ni. Is the geometry tetrahedral, square planar, or other? One can get a statistical answer in about\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":"Tet-SP.jpg","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/04\/Tet-SP.jpg.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":15992,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15992","url_meta":{"origin":10883,"position":3},"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":2046,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2046","url_meta":{"origin":10883,"position":4},"title":"Chemistry with a super-twist: A molecular trefoil knot, part 1.","author":"Henry Rzepa","date":"May 31, 2010","format":false,"excerpt":"Something important happened in chemistry for the first time about 100 years ago. A molecule was built (nowadays we would say synthesized) specifically for the purpose of investigating a theory. It was cyclo-octatetraene or (CH)8, and it was made by Willst\u00e4tter and Waser to try to find out if benzene,\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\/2010\/05\/metallatrefoil.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":7721,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7721","url_meta":{"origin":10883,"position":5},"title":"Predicted properties of a candidate for a frozen semibullvalene.","author":"Henry Rzepa","date":"September 17, 2012","format":false,"excerpt":"I am following up on one unfinished thread in my previous post; a candidate was proposed in which the transition state for [3,3] sigmatropic rearrangement in a semibullvalene might be frozen out to become instead a stable minimum. The hypothesis was that such a species would be aromatic, a bis-homoaromatic\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.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/09\/dicyano-diaza-aim.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\/10883","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=10883"}],"version-history":[{"count":8,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/10883\/revisions"}],"predecessor-version":[{"id":26461,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/10883\/revisions\/26461"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=10883"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=10883"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=10883"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=10883"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}