{"id":4224,"date":"2011-05-31T06:51:24","date_gmt":"2011-05-31T06:51:24","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=4224"},"modified":"2011-05-31T09:14:57","modified_gmt":"2011-05-31T09:14:57","slug":"deja-vu-all-over-again-h-h-interactions","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4224","title":{"rendered":"D\u00e9j\u00e0 vu all over again. Are H…H interactions attractive or repulsive?"},"content":{"rendered":"
\n

The Pirkle reagent is a 9-anthranyl derivative (X=OH, Y=CF3<\/sub>). The previous post<\/a> on the topic had highlighted DIST1, the separation of the two hydrogen atoms shown below. The next question to ask is how general this feature is. Here we take a look at the distribution of lengths found in the Cambridge data base, and focus on another interesting example.<\/p>\n

\"\"

9-anthranyl derivatives. Click for Pirkle with normalised C-H lengths.<\/p><\/div>The histogram below shows all 9-anthranyl compounds in the CCDC database distributed by DIST1. The search was conducted with the restrictions of no disorder, no “errors”, and using normalised hydrogen bond lengths. A note of explanation for the latter. Because of the nature of x-ray diffraction, when a C-H distance is obtained from a structural refinement, it tends to emerge ~0.1\u00c5 to short. Normalisation means adjusting that distance to a more correct 1.09\u00c5 (the heavy atom stays put, its the \u00a0H that moves). In our case, this has the effect of actually shortening DIST1. In the Pirkle structure (shortcode SOCLIF) the nominal value for DIST1 is 1.94-1.96\u00c5, but normalisation reduces these to 1.82-1.85\u00c5. This really is an unusually short contact between two hydrogen atoms (the sum of the vdW radii is 2.4\u00c5). So how unusual might this be? Show below is the result of the CCDC search.<\/p>\n

\"\"<\/a>

H...H Contacts in 9-anthranyl derivatives<\/p><\/div>\n

Notice how a maximum in the number of examples is visible at ~1.9\u00c5, but examples all the way down to ~1.7\u00c5 are known! If one restricts the search to examples where X=O, the following plot is obtained. The entry on the bottom left is JARYEG, where Y is sufficiently large to enforce short H…H or O…H contacts on both sides. Click on the histogram picture below to see it. When you do so, you will also see the NCI surface computed at this geometry. Note that both the short H..H (DIST1) and the short O…H (DIST2) interaction surfaces are coloured blue, indicating attractive contacts!<\/p>\n

\"\"

9-anthranyl derivatives, X=O.<\/p><\/div>If you explore the 3D model further, you will notice other blue interaction surfaces, and a number which have both blue AND orange (= repulsive) zones. We see here yet another example of a weak interaction being simultaneously both attractive and repulsive. It is no longer sufficient to say that the interaction between two atoms is either one or the other. Depending on where you measure it, it can be both! In other words, even weak bonds can have internal structure (for a discussion of the internal structure of a strong C-S bond, see DOI 10.1021\/ct100470g<\/a>).<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

The Pirkle reagent is a 9-anthranyl derivative (X=OH, Y=CF3). The previous post on the topic had highlighted DIST1, the separation of the two hydrogen atoms shown below. The next question to ask is how general this feature is. Here we take a look at the distribution of lengths found in the Cambridge data base, 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":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[4],"tags":[544,144,552,249,42],"ppma_author":[2661],"class_list":["post-4224","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-9-anthranyl","tag-cambridge","tag-disorder","tag-julia-contreras-garcia","tag-x-ray"],"yoast_head":"\nD\u00e9j\u00e0 vu all over again. Are H...H interactions attractive or repulsive? - 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=4224\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"D\u00e9j\u00e0 vu all over again. Are H...H interactions attractive or repulsive? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"The Pirkle reagent is a 9-anthranyl derivative (X=OH, Y=CF3). The previous post on the topic had highlighted DIST1, the separation of the two hydrogen atoms shown below. The next question to ask is how general this feature is. Here we take a look at the distribution of lengths found in the Cambridge data base, and […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4224\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2011-05-31T06:51:24+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2011-05-31T09:14:57+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/05\/9-anthranyl1.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":"D\u00e9j\u00e0 vu all over again. 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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":17579,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17579","url_meta":{"origin":4224,"position":1},"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. 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Published recently by Johnson, Keinan, Mori-Snchez, Contreras-Garca, Cohen and Yang, it came to my attention at a conference to celebrate the 20th birthday of ELF when Julia Contreras-Garcia talked about the procedure. It is one\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":4153,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4153","url_meta":{"origin":4224,"position":3},"title":"D\u00e9j\u00e0 vu: Pirkle for a third time!","author":"Henry Rzepa","date":"May 25, 2011","format":false,"excerpt":"This molecule is not leaving me in peace. It and I first met in 1990 (DO:\u00a010.1039\/C39910000765), when we spotted the two unusual \u03c0-facial bonds formed when it forms a loose dimer. The next step was to use QTAIM to formalise this interaction, and this led to spotting a second one\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\/07\/pirkle.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":6998,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=6998","url_meta":{"origin":4224,"position":4},"title":"Connections in chemistry. Anti-malaria drug \u2194 organocatalysis.","author":"Henry Rzepa","date":"July 5, 2012","format":false,"excerpt":"Back in 1994, we published the crystal structure of the molecule below (X=H), a putative anti-malarial drug called halofantrine. Little did we realise that a whole area of organo catalysis based on a thiourea catalyst with a similar motif would emerge a little later. Here is how the two are\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":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/07\/halofantrine.svg","width":350,"height":200},"classes":[]},{"id":2926,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2926","url_meta":{"origin":4224,"position":5},"title":"Morphing an arrow-pushing tutorial into a dihydrogen bond","author":"Henry Rzepa","date":"December 2, 2010","format":false,"excerpt":"My university tutorial yesterday covered selective reductions of functional groups in organic chemistry. My thoughts on that topic have now morphed into something rather different. Scientific research has a habit of having this sort of thing happen. After I completed the blog post (deliberately done whilst the memory of the\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\/12\/acyloxy-beh2.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\/4224","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=4224"}],"version-history":[{"count":0,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/4224\/revisions"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=4224"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=4224"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=4224"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=4224"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}