{"id":16573,"date":"2016-06-22T09:15:12","date_gmt":"2016-06-22T08:15:12","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=16573"},"modified":"2016-06-26T08:18:14","modified_gmt":"2016-06-26T07:18:14","slug":"how-does-an-oh-or-nh-group-approach-an-aromatic-ring-to-hydrogen-bond-with-its-%cf%80-face","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16573","title":{"rendered":"How does an OH or NH group approach an aromatic ring to hydrogen bond with its \u03c0-face?"},"content":{"rendered":"
\n

\n\tI previously<\/a> used data mining of crystal structures to explore the directing influence of substituents on aromatic and heteroaromatic rings. Here I explore, quite literally, a different angle to the hydrogen bonding interactions between a benzene ring and OH or NH groups.\n<\/p>\n

\n\t\"aromatic-pi-query\"\n<\/p>\n

\n\tI start by defining a benzene ring with a centroid. The distance is from that centroid to the H atom of an OH or NH group and the angle is C-centroid-H. To limit the search to approach of the OH or NH group more or less orthogonal to the ring, the absolute value of the torsion between the centroid-H vector and the ring C-C vector is constrained to lie between 70-100° (the other constraints being no disorder, no errors, T < 140K and R < 0.05).[1]<\/a><\/span>\n<\/p>\n

\n\t\"aromatic-pi-HN-140\"\n<\/p>\n

\n\tThe above shows the results for NH groups interacting with the aromatic ring. The maximum distance 2.8Å is more or less the van der Waals contact distance between a hydrogen and a carbon and as you can see the contacts "funnel down" to the centroid at < 2.1Å. The shortest distance[2]<\/a><\/span> is for ammonium tetraphenylborate, which you can view in e.g.<\/em> spacefill mode here[3]<\/a><\/span>\n<\/p>\n

\n\t\"390\"\n<\/p>\n

\n\tThe other interesting close contact derives from a protonated pyridine[4]<\/a><\/span>, which can in turn be viewed here.[5]<\/a><\/span> The main message from the distribution shown above is that as the distances between the HN and the centroid get shorter, the "trajectory" of approach remains orthogonal to the ring (the angle defined above remains ~90°) and heads towards the centroid of the π-cloud. The hotspot itself (red, ~2.6Å) also lies along this trajectory.\n<\/p>\n

\n\tRecollect that when I used such hydrogen bonding to see if crystal structures discriminate between the ortho or meta positions of a ring carrying an electron donating substituent, it was the distance from a HO to the carbon that was measured as the discriminator. So it's a faint surprise to find that with HN, and without the necessary perturbation of an electron donating substituent, the intrinsic preference seems to be for the ring centroid and not any specific carbon atom of the ring.\n<\/p>\n

\n\tSo how about the OH group? There are in fact rather fewer examples, and so the statistics are a bit less clear-cut. But there is a tantalising suggestion that this time, the trajectory is not ~90° but rather less, implying that the destination is no longer the centroid of the π-cloud but one of the carbon atoms of the ring itself. For those who like to "read between the lines" and spot things that are absent rather than present, you may have asked yourself why I did not use NH probes in my earlier post<\/a>. Well, it appears that the NH group is less effective at e.g.<\/em> o\/p<\/em> discrimination than is an OH group.\n<\/p>\n

\n\t\"aromatic-pi-OH-140\"\n<\/p>\n

\n\tI can only speculate as to the origins (real or not) of the difference in behaviour between OH and NH groups towards a phenyl π-face. Perhaps it is simply bias in the CSD database? Or might there be electronic origins? Time to end with that phrase "watch this space".\n<\/p>\n

\n\t <\/p>\n

References<\/h2>\n
  1. H. Rzepa, \"How does an OH or NH group approach an aromatic ring to hydrogen bond with its \u00cf\u0080-face?\", 2016. https:\/\/doi.org\/10.14469\/hpc\/673<\/a>\n\n<\/li>\n
  2. 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
  3. Steiner, T.., and Mason, S.A.., \"CCDC 144361: Experimental Crystal Structure Determination\", 2000. https:\/\/doi.org\/10.5517\/cc4v6tz<\/a>\n\n<\/li>\n
  4. O. Danylyuk, B. Le\u015bniewska, K. Suwinska, N. Matoussi, and A.W. Coleman, \"Structural Diversity in the Crystalline Complexes of <i>para<\/i>-Sulfonato-calix[4]arene with Bipyridinium Derivatives\", Crystal Growth & Design<\/i>, vol. 10, pp. 4542-4549, 2010. https:\/\/doi.org\/10.1021\/cg100831c<\/a>\n\n<\/li>\n
  5. Danylyuk, O.., Lesniewska, B.., Suwinska, K.., Matoussi, N.., and Coleman, A.W.., \"CCDC 819118: Experimental Crystal Structure Determination\", 2011. https:\/\/doi.org\/10.5517\/ccwhc5w<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    I previously used data mining of crystal structures to explore the directing influence of substituents on aromatic and heteroaromatic rings. Here I explore, quite literally, a different angle to the hydrogen bonding interactions between a benzene ring and OH or NH groups. I start by defining a benzene ring with a centroid. The distance is from that […]<\/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":[2,1745],"tags":[905,1748,1749,16,387,1726,557,1091,1412,1449,1442,1747,1619,1746],"ppma_author":[2661],"class_list":["post-16573","post","type-post","status-publish","format-standard","hentry","category-chemical-it","category-crystal_structure_mining","tag-10-1021","tag-10-1107","tag-10-5517","tag-aromaticity","tag-benzene","tag-centroid","tag-chemical-bonding","tag-data-mining","tag-functional-groups","tag-hydrogen-bond","tag-physical-organic-chemistry","tag-pyridine","tag-simple-aromatic-rings","tag-supramolecular-chemistry"],"yoast_head":"\nHow does an OH or NH group approach an aromatic ring to hydrogen bond with its \u03c0-face? - 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=16573\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"How does an OH or NH group approach an aromatic ring to hydrogen bond with its \u03c0-face? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"I previously used data mining of crystal structures to explore the directing influence of substituents on aromatic and heteroaromatic rings. 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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":[]},{"id":24483,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=24483","url_meta":{"origin":16573,"position":1},"title":"Protein-Biotin complexes. Crystal structure mining.","author":"Henry Rzepa","date":"December 12, 2021","format":false,"excerpt":"In the previous post, I showed some of the diverse \"non-classical\"interactions between Biotin and a protein where it binds very strongly. Here I take a look at two of these interactions to discover how common they are in small molecule structures. The first search is of a CH hydrogen bond\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\/2021\/12\/Screenshot-983-1024x893.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":30548,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=30548","url_meta":{"origin":16573,"position":2},"title":"Molecules of the year 2025: Benzene-busting inverted sandwich.","author":"Henry Rzepa","date":"January 1, 2026","format":false,"excerpt":"Sandwich compounds are the colloquial term used for molecules where a metal atom such as an iron dication is \"sandwiched\" between two carbon-based rings as ligands, most commonly cyclopentadienyl anion (the \"bread\") as in e.g. Ferrocene - a molecule first discovered in 1951. An \"inverted\" sandwich is where the carbon\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":"","width":0,"height":0},"classes":[]},{"id":15992,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15992","url_meta":{"origin":16573,"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":18121,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18121","url_meta":{"origin":16573,"position":4},"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":9218,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9218","url_meta":{"origin":16573,"position":5},"title":"Aromaticity in the benzidine-like \u03c0-complex formed from PhNHOPh.","author":"Henry Rzepa","date":"January 19, 2013","format":false,"excerpt":"The transient \u03c0-complex formed during the \"[5,5]\" sigmatropic rearrangement of protonated N,O-diphenyl hydroxylamine can be (formally) represented as below, namely the interaction of a six-\u03c0-electron aromatic ring (the phenoxide anion 2) with a\u00a0four-\u03c0-electron phenyl dication-anion pair 1. Can one analyse this interaction in terms of aromaticity? I showed previously that\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":"pi-QTAIM","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/01\/pi-QTAIM.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","author_category":"1","first_name":"Henry","last_name":"Rzepa","user_url":"https:\/\/orcid.org\/0000-0002-8635-8390","job_title":"","description":"Henry Rzepa is Emeritus Professor of Computational Chemistry at Imperial College London."}],"_links":{"self":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16573","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=16573"}],"version-history":[{"count":12,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16573\/revisions"}],"predecessor-version":[{"id":16589,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16573\/revisions\/16589"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=16573"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=16573"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=16573"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=16573"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}