{"id":18205,"date":"2017-04-17T08:13:18","date_gmt":"2017-04-17T07:13:18","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=18205"},"modified":"2017-05-30T07:37:46","modified_gmt":"2017-05-30T06:37:46","slug":"%cf%80-facial-hydrogen-bonds-to-alkynes-revisited-how-close-can-an-acidic-hydrogen-approach","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18205","title":{"rendered":"\u03c0-Facial hydrogen bonds to alkynes (revisited): how close can an acidic hydrogen approach?"},"content":{"rendered":"
\n

Following on from my re-investigation of close hydrogen bonding contacts to the \u03c0-face of alkenes<\/a>, here now is an updated scan for H-bonds to alkynes. The search query (dataDOI: 10.14469\/hpc\/2478<\/a>) is similar to the previous one:<\/p>\n

    \n
  1. QA is any of N,O,F,Cl.<\/li>\n
  2. X is any atom, including metals and non-metals.<\/li>\n
  3. The carbon atoms are both specified as 2-coordinate, and the C-C bond type as any<\/strong>.<\/li>\n
  4. The distance is from the hydrogen (normalised) to the C-C centroid, restricted to < 2.5\u00c5 to capture just the shortest examples.<\/li>\n
  5. The mean of the sines of the two angles subtended at the centroid is calculated to indicate whether the approach is orthogonal.<\/li>\n
  6. The mean of the absolute value of the sines of the two angles subtended at each carbon is calculated to indicate how non-linear the\u00a0 X-C-C angle is.<\/li>\n
  7. Other constraints are no disorder, no errors and R < 0.05.<\/li>\n<\/ol>\n

    \"\"<\/p>\n

    First the intermolecular hits (38). Prominent short examples include:<\/p>\n\n\n\n\n\n\n\n
    Entry<\/th>\nArticle DOI<\/th>\nDataDOI<\/th>\nH-centroid distance<\/th>\n<\/tr>\n
    NOXHAJ<\/td>\n[1]<\/a><\/span><\/td>\n\u2021<\/sup><\/td>\n2.16\u00c5<\/td>\n<\/tr>\n
    KESDAO<\/td>\n[2]<\/a><\/span>\u2020<\/sup><\/td>\n10.5517\/CC9YHJ7<\/a>\u2020<\/sup><\/td>\n2.11\u00c5<\/td>\n<\/tr>\n
    ICUTAC<\/td>\n[3]<\/a><\/span><\/td>\n10.5517\/CC9PNSD<\/a><\/td>\n2.19\u00c5<\/td>\n<\/tr>\n
    \"\"<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

    In most of the stronger examples (blue), the approach of the hydrogen is perpendicular to the C-C bond centroid (X-axis of plot above).\u00a0Many\u00a0however exhibit significant bending (Y-axis of plot above)\u00a0from linearity at the two carbons (~173\u00b0), mostly away from the H but in some examples towards the H!<\/p>\n

    Selected entries from the intra-molecular search (34 hits) are shown below.\u00a0Perhaps due to the intra-molecular nature, the angle of approach of the H is more variable than the intermolecular examples and the bending of the erstwhile X-C-C angle is again prominent.\u00a0<\/p>\n\n\n\n\n\n\n\n\n
    Entry<\/th>\nArticle DOI<\/th>\nH-centroid distance<\/th>\n<\/tr>\n
    KIXFOO<\/a><\/td>\n[4]<\/a><\/span><\/td>\n2.11\u00c5<\/td>\n<\/tr>\n
    KEMVOP<\/a><\/td>\n[5]<\/a><\/span><\/td>\n2.16\u00c5<\/td>\n<\/tr>\n
    BEMPUF<\/a><\/td>\n[6]<\/a><\/span><\/td>\n2.14\u00c5<\/td>\n<\/tr>\n
    VEWMIV<\/a><\/td>\n[7]<\/a><\/span><\/td>\n2.14\u00c5<\/td>\n<\/tr>\n
    \"\"<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

    \u03c9B97XD\/Def2-TZVPP calculations\u00a0of\u00a0one intermolecular example,\u00a0ICUTAC (two molecules, dataDOI: 10.14469\/hpc\/2482<\/a>) and one intramolecular case, KIXFOO (dataDOI: 10.14469\/hpc\/2481<\/a>). For the former, crystal packing compressions perhaps provide some shortening of the hydrogen bond\u00a0and the molecule also includes an example of a short C-H to\u00a0\u03c0 interaction (obs[3]<\/a><\/span> 2.63\u00c5).<\/p>\n

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

    What is noticeable from reading the abstracts of the articles cited above is that these hydrogen bonds\u00a0are rarely commented upon by the authors and it does seem that most of these close contacts are serendipitous (they were not designed). All are somewhat longer than the shortest distances encountered for alkenes and it would be interesting to establish if this is an intrinsic property of the triple bond or whether less effort has hitherto been expended on designing closer\u00a0approaches.<\/p>\n

    \n

    \u2021<\/sup> Not all entries have an assigned dataDOI at CCDC.<\/p>\n

    \u2020<\/sup>CrossRef DOIs here are collected as a citation at the bottom of the post using the WordPress KCite<\/a> plugin. Unfortunately for a few months now, this plugin has stopped recognising DataCite DOIs, which is why here they are treated differently from CrossRef DOIs. This is purely a current attribute of the KCite plugin and does not imply any fundamental difference in the two types of DOI, other than one tends to be used as persistent identifiers of journal articles and the other of datasets.<\/p>\n

    References<\/h2>\n
    1. M. Akita, M. Chung, A. Sakurai, S. Sugimoto, M. Terada, M. Tanaka, and Y. Moro-oka, \"Synthesis and Structure Determination of the Linear Conjugated Polyynyl and Polyynediyl Iron Complexes Fp*\u2212(C\u22eeC)<i><sub>n<\/sub><\/i>\u2212X (X = H (<i>n<\/i>= 1, 2); X = Fp* (<i>n<\/i>= 1, 2, 4); Fp* = (\u03b7<sup>5<\/sup>-C<sub>5<\/sub>Me<sub>5<\/sub>)Fe(CO)<sub>2<\/sub>)<sup>1<\/sup>\", Organometallics<\/i>, vol. 16, pp. 4882-4888, 1997. https:\/\/doi.org\/10.1021\/om970538m<\/a>\n\n<\/li>\n
    2. J. Forni\u00e9s, S. Fuertes, A. Mart\u00edn, V. Sicilia, E. Lalinde, and M.T. Moreno, \"Homo\u2010 and Heteropolynuclear Platinum Complexes Stabilized by Dimethylpyrazolato and Alkynyl Bridging Ligands: Synthesis, Structures, and Luminescence\", Chemistry \u2013 A European Journal<\/i>, vol. 12, pp. 8253-8266, 2006. https:\/\/doi.org\/10.1002\/chem.200600139<\/a>\n\n<\/li>\n
    3. R. Banerjee, R. Mondal, J.A.K. Howard, and G.R. Desiraju, \"Synthon Robustness and Solid-State Architecture in Substituted <i>g<\/i><i>em<\/i>-Alkynols\", Crystal Growth & Design<\/i>, vol. 6, pp. 999-1009, 2006. https:\/\/doi.org\/10.1021\/cg050598s<\/a>\n\n<\/li>\n
    4. B. Xu, K. Bussmann, R. Fr\u00f6hlich, C.G. Daniliuc, J.G. Brandenburg, S. Grimme, G. Kehr, and G. Erker, \"An Enamine\/HB(C<sub>6<\/sub>F<sub>5<\/sub>)<sub>2<\/sub> Adduct as a Dormant State in Frustrated Lewis Pair Chemistry\", Organometallics<\/i>, vol. 32, pp. 6745-6752, 2013. https:\/\/doi.org\/10.1021\/om4004225<\/a>\n\n<\/li>\n
    5. M.J. Pouy, S.A. Delp, J. Uddin, V.M. Ramdeen, N.A. Cochrane, G.C. Fortman, T.B. Gunnoe, T.R. Cundari, M. Sabat, and W.H. Myers, \"Intramolecular Hydroalkoxylation and Hydroamination of Alkynes Catalyzed by Cu(I) Complexes Supported by <i>N<\/i>-Heterocyclic Carbene Ligands\", ACS Catalysis<\/i>, vol. 2, pp. 2182-2193, 2012. https:\/\/doi.org\/10.1021\/cs300544w<\/a>\n\n<\/li>\n
    6. R.D. Dewhurst, A.F. Hill, and M.K. Smith, \"Heterobimetallic C<sub>3<\/sub> Complexes through Silylpropargylidyne Desilylation\", Angewandte Chemie International Edition<\/i>, vol. 43, pp. 476-478, 2004. https:\/\/doi.org\/10.1002\/anie.200352693<\/a>\n\n<\/li>\n
    7. T. Holtrichter-R\u00f6\u00dfmann, C. R\u00f6sener, J. Hellmann, W. Uhl, E. W\u00fcrthwein, R. Fr\u00f6hlich, and B. Wibbeling, \"Generation of Weakly Bound Al\u2013N Lewis Pairs by Hydroalumination of Ynamines and the Activation of Small Molecules: Phenylethyne and Dicyclohexylcarbodiimide\", Organometallics<\/i>, vol. 31, pp. 3272-3283, 2012. https:\/\/doi.org\/10.1021\/om3001179<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      Following on from my re-investigation of close hydrogen bonding contacts to the \u03c0-face of alkenes, here now is an updated scan for H-bonds to alkynes. The search query (dataDOI: 10.14469\/hpc\/2478) is similar to the previous one: QA is any of N,O,F,Cl. X is any atom, including metals and non-metals. The carbon atoms are both specified […]<\/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":[1745],"tags":[663,855,1412,2194,734],"ppma_author":[2661],"class_list":["post-18205","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining","tag-alkene","tag-alkyne","tag-functional-groups","tag-intra-molecular-search","tag-search-query"],"yoast_head":"\n\u03c0-Facial hydrogen bonds to alkynes (revisited): how close can an acidic hydrogen approach? - 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=18205\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"\u03c0-Facial hydrogen bonds to alkynes (revisited): how close can an acidic hydrogen approach? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"Following on from my re-investigation of close hydrogen bonding contacts to the \u03c0-face of alkenes, here now is an updated scan for H-bonds to alkynes. The search query (dataDOI: 10.14469\/hpc\/2478) is similar to the previous one: QA is any of N,O,F,Cl. X is any atom, including metals and non-metals. The carbon atoms are both specified […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18205\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2017-04-17T07:13:18+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2017-05-30T06:37:46+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/04\/SQ-triple.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=\"3 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"\u03c0-Facial hydrogen bonds to alkynes (revisited): how close can an acidic hydrogen approach? - 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=18205","og_locale":"en_GB","og_type":"article","og_title":"\u03c0-Facial hydrogen bonds to alkynes (revisited): how close can an acidic hydrogen approach? - Henry Rzepa's Blog","og_description":"Following on from my re-investigation of close hydrogen bonding contacts to the \u03c0-face of alkenes, here now is an updated scan for H-bonds to alkynes. The search query (dataDOI: 10.14469\/hpc\/2478) is similar to the previous one: QA is any of N,O,F,Cl. X is any atom, including metals and non-metals. 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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":18277,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18277","url_meta":{"origin":18205,"position":1},"title":"How does carbon dioxide coordinate to a metal?","author":"Henry Rzepa","date":"May 6, 2017","format":false,"excerpt":"Mention carbon dioxide (CO2) to most chemists and its properties as a metal ligand are not the first aspect that springs to mind. Here thought I might take a look at how it might act as such. There are up to\u00a0five binding modes with one metal that one might envisage:\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\/05\/078.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":18121,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18121","url_meta":{"origin":18205,"position":2},"title":"The \u03c0-\u03c0 stacking of aromatic rings: what is their closest parallel approach?","author":"Henry Rzepa","date":"April 13, 2017","format":false,"excerpt":"Layer stacking in structures such as graphite is well-studied. The separation between the \u03c0-\u03c0 planes\u00a0is\u00a0~3.35\u00c5, which is close to twice the estimated van der Waals (vdW) radius of carbon (1.7\u00c5). But how much closer could such layers get, given that many other types of relatively weak interaction such as hydrogen\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\/ring-distances-1024x709.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":18399,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18399","url_meta":{"origin":18205,"position":3},"title":"CH\u22c5\u22c5\u22c5\u03c0 Interactions between methyl and carbonyl groups in proteins: a small molecule check.","author":"Henry Rzepa","date":"May 29, 2017","format":false,"excerpt":"Derek Lowe highlights a recent article postulating\u00a0CH\u22c5\u22c5\u22c5\u03c0 interactions in proteins. Here I report a quick check using the small molecule crystal structure database (CSD). The search query (DOI:\u00a010.14469\/hpc\/2594)\u00a0is shown below. The distance refers to that between the (normalised) position of a hydrogen on a 4-coordinated carbon atom and the centroid\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\/05\/152-1024x637.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":18205,"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":17579,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17579","url_meta":{"origin":18205,"position":5},"title":"Ammonium tetraphenylborate and the mystery of its \u03c0-facial hydrogen bonding.","author":"Henry Rzepa","date":"March 10, 2017","format":false,"excerpt":"A few years back, I did a post about the Pirkle reagent and the unusual \u03c0-facial hydrogen bonding structure it exhibits. For the Pirkle reagent, this bonding manifests as a close contact between the acidic OH hydrogen and the edge of a phenyl ring; the hydrogen bond is off-centre from\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\/03\/142-1024x770.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\/18205","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=18205"}],"version-history":[{"count":30,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/18205\/revisions"}],"predecessor-version":[{"id":18256,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/18205\/revisions\/18256"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=18205"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=18205"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=18205"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=18205"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}