{"id":4153,"date":"2011-05-25T14:57:20","date_gmt":"2011-05-25T14:57:20","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=4153"},"modified":"2011-05-30T15:37:51","modified_gmt":"2011-05-30T15:37:51","slug":"deja-vu-pirkle-for-a-third-time","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4153","title":{"rendered":"D\u00e9j\u00e0 vu: Pirkle for a third time!"},"content":{"rendered":"
\n

This molecule is not leaving me in peace. It and I first met in 1990 (DO:\u00a010.1039\/C39910000765<\/a>), 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<\/a> one missed the first time round (labelled 2<\/strong> in that post). Then a method known as NCI was tried<\/a>, which revealed an H…H interaction, labelled ?<\/strong> in that post! Here I discuss the origins of the\u00a0?<\/strong><\/p>\n

\"\"<\/a>

The Pirkle reagent<\/p><\/div>\n

What sparked this re-visitation? Firstly, in this post<\/a>, a CH…O interaction in Z-DNA was identified using NCI, and its origins probed using NBO E2 perturbation energies, which revealed that the C-H bond was antiperiplanar to a C-O bond (effects 2 and 3<\/strong> in that<\/strong> post), that could have the effect of acidifying the H, and making it more prone to hydrogen bond to the lone pair of an oxygen. Inspired by this, I worked out how to display NCI colour codes surfaces here on this blog using Jmol (previously, VMD had been used, which cannot be embedded in a blog).<\/p>\n

\"\"

NCI Surface for the Pirkle reagent. Click for 3D<\/p><\/div>The H..H interaction previously alluded to is shown with a magenta arrow (between the two atoms with halos in the 3D model). The colour coding blue<\/strong><\/em> means it is distinctly attractive. In my\u00a0(second) post, I did not mention why it might be special (and also the colour coding covered a large range, which meant the blue tinge did not really stand out visually). Why might that interaction be significant? Well, the C-H bond is perfectly aligned with the C-F\u00a0\u03c3* orbital. The NBO E2 energy is 3.9 kcal\/mol, which represents a modest acidification of the hydrogen.<\/p>\n

 <\/p>\n

You may notice from the above other blue regions. Click on the diagram, and go explore them. The history of this molecule is such that it is bound to hold more surprises!<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

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 missed the first time round […]<\/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":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2},"jetpack_post_was_ever_published":false},"categories":[4],"tags":[24,249,373],"ppma_author":[2661],"class_list":["post-4153","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-energy","tag-julia-contreras-garcia","tag-tutorial-material"],"yoast_head":"\nD\u00e9j\u00e0 vu: Pirkle for a third time! - 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=4153\" \/>\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: Pirkle for a third time! - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"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 missed the first time round […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4153\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2011-05-25T14:57:20+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2011-05-30T15:37:51+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/07\/pirkle.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: Pirkle for a third time! - 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=4153","og_locale":"en_GB","og_type":"article","og_title":"D\u00e9j\u00e0 vu: Pirkle for a third time! - Henry Rzepa's Blog","og_description":"This molecule is not leaving me in peace. 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The next question to ask is how general this feature is. Here we take a look at the distribution of lengths found in\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.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/05\/9-anthranyl1.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":2230,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2230","url_meta":{"origin":4153,"position":2},"title":"Non-covalent interactions (NCI): revisiting Pirkle","author":"Henry Rzepa","date":"July 15, 2010","format":false,"excerpt":"NCI (non-covalent interactions) is the name of a fascinating new technique for identifying exactly these. 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":17579,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17579","url_meta":{"origin":4153,"position":3},"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":[]},{"id":6998,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=6998","url_meta":{"origin":4153,"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":4089,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4089","url_meta":{"origin":4153,"position":5},"title":"The inner secrets of the DNA structure.","author":"Henry Rzepa","date":"May 18, 2011","format":false,"excerpt":"In earlier posts, I alluded to what might make DNA wind into a left or a right-handed helix. Here I switch the magnification of our structural microscope up a notch to take a look at some more inner secrets. The 3D coordinates of this fragment were obtained by taking 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":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/05\/CGCG.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\/4153","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=4153"}],"version-history":[{"count":1,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/4153\/revisions"}],"predecessor-version":[{"id":6278,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/4153\/revisions\/6278"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=4153"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=4153"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=4153"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=4153"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}