{"id":17579,"date":"2017-03-10T14:20:25","date_gmt":"2017-03-10T14:20:25","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=17579"},"modified":"2017-03-11T16:09:19","modified_gmt":"2017-03-11T16:09:19","slug":"ammonium-tetraphenylborate-and-the-mystery-of-its-%cf%80-facial-hydrogen-bonding","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17579","title":{"rendered":"Ammonium tetraphenylborate and the mystery of its \u03c0-facial hydrogen bonding."},"content":{"rendered":"
\n

A few years back, I did a post about the Pirkle reagent<\/a>[1]<\/a><\/span> and the unusual \u03c0-facial hydrogen bonding structure[2]<\/a><\/span> 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 the middle of the aryl ring. Here I update the topic, with a new search of the CSD (Cambridge structure database), but this time looking at the positional preference of that bond and whether it is on or off-centre. <\/p>\n

\"\"<\/p>\n

The search (February 2017 database, DOI:10.14469\/hpc\/2233<\/a>) is shown above, QA = N, O, F, Cl and other constraints are R < 0.01, no errors, no disorder. Two distances are plotted, one (DIST1) is from the H to the ring centroid and the second (DIST2) from the H to an edge carbon atom. The colour code relates to ANG1, the angle subtended at the centroid. A value of 90\u00b0 would indicate the H is orthogonal to the plane of the aromatic ring.<\/p>\n

\"\"<\/p>\n

You can see from the above that the yellow dots correspond to ~90\u00b0 and that by and large the H…centroid distances are shorter than the H…C distances. <\/p>\n

\"\"<\/p>\n

The above is another representation of this search, again showing that the preferred angle is 90\u00b0, although there is a fair bit of scatter. The extreme outliers may be crystallographic errors, but one point caught my eye and is circled in red above; ammonium tetrafluoroborate (3D model DOI: 10.5517\/CC4V6TZ<\/a>). This has a very short distance from the H to the centroid (2.07\u00c5), shorter than the Pirkle reagent that we looked at all those years back. The authors[3]<\/a><\/span> note that “The N-H…Ph distances, H…M 2.067\u00c5 … are exceptionally short (M = aromatic midpoint)<\/em>” but also that “even at 20 K the ammonium ion performs large amplitude motions which allow the N-H vectors to sample the entire face of the aromatic system.<\/em>” This implies that such bonds are largely agnostic about whether they bind to the centroid of the ring or to its edge and that the most probable position might arise simply because of crystal packing. An interesting variation on this molecule is a crystal that includes a further 5NH3<\/sub> in addition to ammonium tetraphenylborate (3D model DOI: 10.5517\/cc7bly2<\/a>). Here an ammonia intervenes between the ammonium cation and a phenyl ring, resulting in a binding of the ammonia with two NHs closer to the edge of the ring and one NH interacting in parallel mode.<\/p>\n

\"\"<\/p>\n

Time therefore for a calculation, using B3LYP+GD3BJ\/Def2-TZVPP, the functional being chosen because the dispersion contribution is not built in, but uses what is currently thought to be the best representation of these attractions. The issue now is what molecular unit to use? This is an ionic structure and so a periodic boundary model is most appropriate, but given its size I reduced this to two models comprising smaller discrete fragments.<\/p>\n

    \n
  1. A unit just comprising the simple ion pair. This leaves two of the four N-H bonds devoid of hydrogen bonding (DOI:10.14469\/hpc\/2234<\/a>). The optimisation adopts a pose where two NH groups are directed towards a carbon atom rather than the ring centroid. How much of this is due to the smallness of this model?
    \n \"\"<\/li>\n
  2. A unit comprising a double ion pair, which allows one ammonium group to participate with all four NH groups across four phenyl rings and exhibiting six NH interactions in total with six rings (DOI: 10.14469\/hpc\/2235<\/a>). The NH hydrogen vectors all interact with ring carbons rather than the ring centroid.
    \n \"\"<\/li>\n<\/ol>\n

    This brief computational exploration has covered only one method (the B3LYP DFT procedure), albeit with what is thought to be a good dispersion attraction term added and a reasonable basis set. It does seem to show that hydrogen bonds interacting with the centroid of a phenyl ring are not the preferred mode, which is instead an interaction with the edge of the ring. The quote above, “even at 20 K the ammonium ion performs large amplitude motions which allow the N-H vectors to sample the entire face of the aromatic system<\/em>” suggests that whilst the average position might be the centroid, a true hydrogen bond to the centroid might be rarer than thought. Although most of the crystallographic examples located in the searches above deem to show a preference for the ring centroid, this might be more apparent than real. <\/p>\n

    References<\/h2>\n
    1. H.S. Rzepa, M.L. Webb, A.M.Z. Slawin, and D.J. Williams, \"? Facial hydrogen bonding in the chiral resolving agent (S)-2,2,2-trifluoro-1-(9-anthryl)ethanol and its racemic modification\", Journal of the Chemical Society, Chemical Communications<\/i>, pp. 765, 1991. https:\/\/doi.org\/10.1039\/c39910000765<\/a>\n\n<\/li>\n
    2. 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
    3. T. Steiner, and S.A. Mason, \"Short N<sup>+<\/sup>\u2014H...Ph hydrogen bonds in ammonium tetraphenylborate characterized by neutron diffraction\", Acta Crystallographica Section B Structural Science<\/i>, vol. 56, pp. 254-260, 2000. https:\/\/doi.org\/10.1107\/s0108768199012318<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      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 the middle of the aryl […]<\/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":true,"_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":[1713,1712,16,1527,1726,557,1395,1449,2047],"ppma_author":[2661],"class_list":["post-17579","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining","tag-ammonia","tag-ammonium","tag-aromaticity","tag-cations","tag-centroid","tag-chemical-bonding","tag-chemistry","tag-hydrogen-bond","tag-phenyl-group"],"yoast_head":"\nAmmonium tetraphenylborate and the mystery of its \u03c0-facial hydrogen bonding. - 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=17579\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Ammonium tetraphenylborate and the mystery of its \u03c0-facial hydrogen bonding. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"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 the middle of the aryl […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17579\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2017-03-10T14:20:25+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2017-03-11T16:09:19+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/03\/143.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=\"4 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Ammonium tetraphenylborate and the mystery of its \u03c0-facial hydrogen bonding. - 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=17579","og_locale":"en_GB","og_type":"article","og_title":"Ammonium tetraphenylborate and the mystery of its \u03c0-facial hydrogen bonding. - Henry Rzepa's Blog","og_description":"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 the middle of the aryl […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17579","og_site_name":"Henry Rzepa's Blog","article_published_time":"2017-03-10T14:20:25+00:00","article_modified_time":"2017-03-11T16:09:19+00:00","og_image":[{"url":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/03\/143.jpg","type":"","width":"","height":""}],"author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"4 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17579#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17579"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Ammonium tetraphenylborate and the mystery of its \u03c0-facial hydrogen bonding.","datePublished":"2017-03-10T14:20:25+00:00","dateModified":"2017-03-11T16:09:19+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17579"},"wordCount":756,"commentCount":0,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17579#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/03\/143.jpg","keywords":["Ammonia","Ammonium","aromaticity","Cations","Centroid","chemical bonding","Chemistry","Hydrogen bond","Phenyl group"],"articleSection":["crystal_structure_mining"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17579#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17579","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17579","name":"Ammonium tetraphenylborate and the mystery of its \u03c0-facial hydrogen bonding. - 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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":[]},{"id":221,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=221","url_meta":{"origin":17579,"position":1},"title":"How do molecules interact with each other?","author":"Henry Rzepa","date":"April 12, 2009","format":false,"excerpt":"Understanding how molecules interact (bind) with each other when in close proximity is essential in all areas of chemistry. One specific example of this need is for the molecule shown below. This is the so-called Pirkle Reagent and is much used to help resolve the two enantiomers of a racemic\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":"The Pirkle reagent","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2009\/04\/pirkle.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":17311,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17311","url_meta":{"origin":17579,"position":2},"title":"The “hydrogen bond”; its early history.","author":"Henry Rzepa","date":"December 31, 2016","format":false,"excerpt":"My holiday reading has been Derek Lowe's excellent\u00a0Chemistry Book setting out 250 milestones in chemistry, organised by year. An\u00a0entry for 1920 entitled hydrogen bonding\u00a0seemed worth exploring in more detail here. As with many historical concepts, it can often take a few years to coalesce into something we would readily recognise\u2026","rel":"","context":"In "Historical"","block_context":{"text":"Historical","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=565"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/12\/066-1024x91.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":18165,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18165","url_meta":{"origin":17579,"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":20576,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=20576","url_meta":{"origin":17579,"position":4},"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":16118,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16118","url_meta":{"origin":17579,"position":5},"title":"Hydronium hydroxide: the why of pH 7.","author":"Henry Rzepa","date":"April 14, 2016","format":false,"excerpt":"Ammonium hydroxide (NH4+...OH-) can be characterised quantum mechanically when stabilised by water bridges connecting the ion-pairs. It is a small step from there to hydronium hydroxide, or H3O+...OH-. The measured concentrations [H3O+] \u2261 [OH-]\u00a0give\u00a0rise of course to the well-known\u00a0pH 7 of pure water, and converting this ionization constant to a\u2026","rel":"","context":"In "General"","block_context":{"text":"General","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1"},"img":{"alt_text":"","src":"","width":0,"height":0},"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\/17579","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=17579"}],"version-history":[{"count":42,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/17579\/revisions"}],"predecessor-version":[{"id":17632,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/17579\/revisions\/17632"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=17579"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=17579"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=17579"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=17579"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}