{"id":18165,"date":"2017-04-15T17:33:24","date_gmt":"2017-04-15T16:33:24","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=18165"},"modified":"2017-04-16T09:17:32","modified_gmt":"2017-04-16T08:17:32","slug":"%cf%80-facial-hydrogen-bonds-to-alkenes-revisited-how-close-can-an-acidic-hydrogen-approach","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18165","title":{"rendered":"\u03c0-Facial hydrogen bonds to alkenes (revisited): how close can an acidic hydrogen approach?"},"content":{"rendered":"
\n

Back in the early 1990s, we first discovered the delights of searching crystal structures\u00a0for unusual\u00a0bonding features.[1]<\/a><\/span> 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 now ten times larger) and the search software less powerful. So here is an update.\u00a0<\/p>\n

The search query (dataDOI:10.14469\/hpc\/2473<\/a>)\u00a0is shown below:<\/p>\n

    \n
  1. A mid-point (centroid) of a C-C bond (of any type) is defined, but the carbons are each restricted to being 3-coordinate, with the substituents R being either C or H.<\/li>\n
  2. The distance to a hydrogen (attached to group QA, where QA is any one of N,O,F,Cl, i.e.<\/em> acidic H) is defined.<\/li>\n
  3. The properties of the alkene are defined by the sines of the two angles subtended at the centroid. This defines how perpendicular the QA-H hydrogen bond is to the C-C bond.<\/li>\n
  4. Four torsions R-C-centroid-H are defined by their sines. The mean of the absolute values of these will define how\u00a0orthogonal the approach of the hydrogen to the\u00a0\u03c0-\u03c0 plane is.<\/li>\n
  5. Further constraints in the search are no disorder, no errors, R < 0.05, \u00a0the H atom position is normalised and this position is defined as being <2.5\u00c5 from the C-C bond centroid, which is ~0.3\u00c5 < the sum of the van der Waals values for C and H.
    \n \"\"<\/li>\n<\/ol>\n

    The first search is limited to intermolecular contacts between the C-C bond and the H and reveals that for most of the 18 hits, the H approach is close to perpendicular to the centroid but the inclination to the\u00a0\u03c0-\u03c0 plane is more scattered. The most interesting (shortest H…centroid contact of ~2.22\u00c5, orthogonal approach) can be inspected as KANYAA (dataDOI: 10.5517\/CC8JRQ7<\/a>).\u00a0
    \n \"\"When the search is repeated for intramolecular contacts, rather shorter distances are obtained for 88 hits and with more variation in the angles of approach. The most interesting candidate (blue dots) is IGELAJ    [2]<\/a><\/span> (dataDOI:\u00a010.5517\/CC14PBW1 <\/a>) which has the very short intramolecular H approach of 1.90\u00c5 to the C-C centroid corresponding to ~2.04\u00c5 to the carbons,\u00a0 a contraction of ~0.8\u00c5 from the van der Waals sum.<\/p>\n

    \"\"<\/p>\n

    The authors\u00a0remarked[2]<\/a><\/span>\u00a0 “that it possesses a better defined intramolecular hydrogen bond compared to the usual molecules for which it is noted<\/em>“.\u00a0They also note JOCQEX, which is present in the above plot, but for which there is\u00a0\u00a0a\u00a0non-orthogonal approach of the hydrogen bond to the \u03c0-\u03c0 plane. The authors do not<\/strong>\u00a0mention\u00a0TIBCUD[3]<\/a><\/span> (dataDOI: 10.5517\/CCPL0FP<\/a>), which has a similar close approach of 1.92\u00c5 to the C-C centroid, but at an angle inclined to the C-C axis.<\/p>\n

    IGELAJ, as an intramolecular H-bond, was amenable to calculation of its geometry and properties (inter-molecular interactions would ideally require the periodic lattice to be computed), with the observation[3]<\/a><\/span> that “another test was to compare the energy calculation of\u00a0IGELAJ\u00a0to a non-hydrogen-bound version where the OH bond is\u00a0rotated 180\u00b0” <\/em>and “the\u00a0results predict IGELAJ to be 7.30<\/strong> kcal more stable\u00a0than the non-hydrogen-bound version”.\u00a0<\/em>This value, \u00a0if correct, \u00a0is indeed typical of a very\u00a0strong hydrogen bond!<\/p>\n

    Pedant (curious?) as I am, I wanted to be clear what kind of calculated energy was being reported. Was it the\u00a0difference in total energies, or the energies corrected for ZPE (zero-point-energy) as \u0394H or the free energies for which entropy is included as \u0394G? The article[3]<\/a><\/span> itself is unclear on this aspect and no energies are reported in the\u00a0\u00a0supporting information. This is an illustration that “supporting information<\/em>” in most current incarnations may often not provide crucial information; only a full deposition as the management of research (RDM) of\u00a0FAIR\u00a0data can provide. This process is\u00a0illustrated for my own calculations of this system (\u03c9B97XD\/Def2-TZVPP, dataDOIs: 10.14469\/hpc\/2474<\/a>, 10.14469\/hpc\/2475<\/a>), which reveals that \u00a0\u0394G298<\/sub> 4.8 kcal\/mol and\u00a0\u03bd 3761 cm-1<\/sup>.\u00a0In comparison when the\u00a0OH bond is\u00a0rotated 180\u00b0 <\/em>the wavenumber goes up 3956 cm-1<\/sup>, a difference of 195 cm-1\u00a0<\/sup>is calculated, which is indeed a large red-shift.\u00a0But the “non-hydrogen-bound version where the OH bond is\u00a0rotated 180\u00b0”<\/i> is not<\/strong><\/span> a valid reference point for a non-hydrogen bonded isomer, since it manifests instead as a transition state for OH rotation with \u03bdi<\/i><\/sub> 166 cm-1<\/sup>, there being no minimum other than the \u03c0-facially hydrogen bonded one (dataDOI: 10.14469\/hpc\/2476<\/a>).\u00a0So, for the lack of a suitable reference system, we cannot conclude what the strength of this particular hydrogen bond is, nor make any conclusions about it being unusually strong.<\/p>\n

    So IGELAJ holds the current record for the shortest\u00a0\u03c0-facial hydrogen bond to an alkene, but not necessarily the strongest! I wonder if this record might be broken with the aid of further computational design and prediction?<\/p>\n

    References<\/h2>\n
    1. H.S. Rzepa, M.H. Smith, and M.L. Webb, \"A crystallographic AM1 and PM3 SCF-MO investigation of strong OH \u22ef\u03c0-alkene and alkyne hydrogen bonding interactions\", J. Chem. Soc., Perkin Trans. 2<\/i>, pp. 703-707, 1994. https:\/\/doi.org\/10.1039\/p29940000703<\/a>\n\n<\/li>\n
    2. M.D. Struble, M.G. Holl, G. Coombs, M.A. Siegler, and T. Lectka, \"Synthesis of a Tight Intramolecular OH\u00b7\u00b7\u00b7Olefin Interaction, Probed by IR,<sup>1<\/sup>H NMR, and Quantum Chemistry\", The Journal of Organic Chemistry<\/i>, vol. 80, pp. 4803-4807, 2015. https:\/\/doi.org\/10.1021\/acs.joc.5b00470<\/a>\n\n<\/li>\n
    3. B. Ndjakou Lenta, K.P. Devkota, B. Neumann, E. Tsamo, and N. Sewald, \"4-(1,1-Dimethylprop-2-enyl)-1,3,5-trihydroxy-2-(3-methylbut-2-enyl)-9<i>H<\/i>-xanthen-9-one\", Acta Crystallographica Section E Structure Reports Online<\/i>, vol. 63, pp. o1629-o1631, 2007. https:\/\/doi.org\/10.1107\/s1600536807009907<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      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 now ten times larger) and […]<\/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":[2130,557,1395,2128,1014,24,2129,1959,1871,734,1554,1746],"ppma_author":[2661],"class_list":["post-18165","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining","tag-calculated-energy","tag-chemical-bonding","tag-chemistry","tag-crystal","tag-crystallography","tag-energy","tag-energy-calculation","tag-intermolecular-forces","tag-nature","tag-search-query","tag-search-software","tag-supramolecular-chemistry"],"yoast_head":"\n\u03c0-Facial hydrogen bonds to alkenes (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=18165\" \/>\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 alkenes (revisited): how close can an acidic hydrogen approach? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"Back in the early 1990s, we first discovered the delights of searching crystal structures\u00a0for unusual\u00a0bonding features. 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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\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\/triple-inter-1024x672.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":17992,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17992","url_meta":{"origin":18165,"position":1},"title":"The conformation of enols: revealed and explained.","author":"Henry Rzepa","date":"April 6, 2017","format":false,"excerpt":"Enols are simple compounds with an OH group as a substituent on a C=C double bond and with a very distinct conformational preference for the OH group. Here I take a look at this preference as revealed by crystal structures, with the theoretical explanation. First, a search of the Cambridge\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\/All-1024x948.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":20576,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=20576","url_meta":{"origin":18165,"position":2},"title":"The shortest known CF…HO hydrogen bond.","author":"Henry Rzepa","date":"March 24, 2019","format":false,"excerpt":"There is a predilection amongst chemists for collecting records; one common theme is the length of particular bonds, either the shortest or the longest. A particularly baffling type of bond is that between the very electronegative F atom and an acid hydrogen atom such as that in OH. Thus short\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\/2019\/03\/F-inter-300x189.png?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":18121,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18121","url_meta":{"origin":18165,"position":3},"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":21798,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21798","url_meta":{"origin":18165,"position":4},"title":"Can a carbon radical act as a hydrogen bond acceptor?","author":"Henry Rzepa","date":"December 28, 2019","format":false,"excerpt":"Having shown that carbon as a carbene centre, C:\u00a0can act as a hydrogen bond acceptor, as seen from a search of crystal structures, I began to wonder if there is any chance that carbon as a radical centre, C\u2022 could do so as well.\u00a0Definitely a subversive thought, since radical centres\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\/2019\/12\/CH-1024x940.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":16573,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16573","url_meta":{"origin":18165,"position":5},"title":"How does an OH or NH group approach an aromatic ring to hydrogen bond with its \u03c0-face?","author":"Henry Rzepa","date":"June 22, 2016","format":false,"excerpt":"I previously used data mining of crystal structures to explore the directing influence of substituents on aromatic and heteroaromatic rings. Here\u00a0I explore, quite literally, a different angle to the hydrogen bonding interactions between a benzene ring and\u00a0OH or NH groups. I start by defining a benzene ring with a centroid.\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":"aromatic-pi-query","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/06\/aromatic-pi-query-1-e1466580253270.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\/18165","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=18165"}],"version-history":[{"count":37,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/18165\/revisions"}],"predecessor-version":[{"id":18225,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/18165\/revisions\/18225"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=18165"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=18165"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=18165"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=18165"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}