{"id":9056,"date":"2013-01-08T14:09:18","date_gmt":"2013-01-08T14:09:18","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=9056"},"modified":"2014-06-06T09:52:52","modified_gmt":"2014-06-06T08:52:52","slug":"nci-non-covalent-interaction-analysis-for-some-%cf%80-hydrogen-bonded-systems","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9056","title":{"rendered":"NCI (non-covalent-interaction) analysis for some \u03c0-hydrogen bonded systems."},"content":{"rendered":"
\n

In this post<\/a>, I looked at some hydrogen bonds formed by interaction of a\u00a0\u03c0-system with an acidic hydrogen. Unlike normal lone pair donors, \u03c0-systems can involve more than two electrons, most commonly four or six. Here I look at examples of both these higher-order donors.<\/p>\n

FIMNEU<\/span><\/strong><\/a><\/p>\n

\"FIMNEU.

FIMNEU. Click for 3D.<\/p><\/div>\n

The NCI surface<\/a> for this 4-electron hydrogen bonded interaction shows four interesting features:<\/p>\n

    \n
  1. Arrow 1 points to the interaction between the OH group and the diene unit below. The surface is coded light blue, which indicates a moderately strong attraction. This surface is curved, and spans all four carbons of the diene, indicating it truly is a\u00a0\u03b7-4 hydrogen bond.<\/span><\/li>\n
  2. Arrow 2 points to a conventional OH…O hydrogen bond; it is deep blue (strong), and the surface is circular,\u00a0\u03b7-1.<\/li>\n
  3. Arrow 3 is a less conventional attraction, between an oxygen lone pair and an alkene, here only pale blue.<\/li>\n
  4. Arrow 4 is a H…H zone, with pale blue immediately adjacent to yellow (weakly repulsive) and so overall this contact is probably not very attractive.<\/li>\n<\/ol>\n
    \"FINMEU.

    FINMEU. Click for 3D.<\/p><\/div>\n

    AKACAQ<\/span><\/strong><\/a><\/p>\n

    \"AKACAQ.

    AKACAQ. Click for 3D.<\/p><\/div>\n

      \n
    1. Arrows 1 and 2 in the NCI surface<\/a> point to the two cone-shaped surfaces comprising an \u03b7-6 hydrogen bond. It is coloured pale blue around most of the rim of the cone, but not entirely evenly.<\/li>\n
    2. There are lots else going on which I leave you to explore.<\/li>\n<\/ol>\n
      \"AKACAQ.

      AKACAQ. Click for 3D.<\/p><\/div>\n

      WULSUS<\/strong><\/span><\/p>\n

      \"WULSUS.

      WULSUS. Click for 3D<\/p><\/div>\n

        \n
      1. Arrow 1 is the cone-shaped NCI<\/a> zone for the OH group interacting \u03b7-6 with the \u03c0-face, but rather asymmetrically and weakly (no blue, only green).\u00a0<\/li>\n
      2. Arrow 2 is a more conventional OH…O bond, but as part of a 5-membered ring. As we saw before<\/a>, these types of hydrogen bond are quite weak, and you can see this reflected in the blue attractive circle being adjacent to a yellow repulsive zone. The two cancel each other to some extent.<\/li>\n
      3. The same is seen for arrow 3, which is a 5-ring now bearing an O…H-C interaction, again overall weak (despite the blue).<\/li>\n<\/ol>\n
        \"WULSUS.

        WULSUS. Click for 3D.<\/p><\/div>\n

        To sum up, the NCI method (which has been used elsewhere<\/a> in this blog) seems to be teasing out some interesting zones of intramolecular interaction in hydrogen bonded molecules. I end again with the same speculation; have any\u00a0\u03c0-face hydrogen bonds that are >\u00a0\u00a0\u03b7-6 been discovered?\u00a0<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

        In this post, I looked at some hydrogen bonds formed by interaction of a\u00a0\u03c0-system with an acidic hydrogen. Unlike normal lone pair donors, \u03c0-systems can involve more than two electrons, most commonly four or six. Here I look at examples of both these higher-order donors. FIMNEU The NCI surface for this 4-electron hydrogen bonded interaction […]<\/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":[4],"tags":[1179,980],"ppma_author":[2661],"class_list":["post-9056","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag--hydrogen-bonded-systems","tag--systems"],"yoast_head":"\nNCI (non-covalent-interaction) analysis for some \u03c0-hydrogen bonded systems. - 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=9056\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"NCI (non-covalent-interaction) analysis for some \u03c0-hydrogen bonded systems. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"In this post, I looked at some hydrogen bonds formed by interaction of a\u00a0\u03c0-system with an acidic hydrogen. Unlike normal lone pair donors, \u03c0-systems can involve more than two electrons, most commonly four or six. Here I look at examples of both these higher-order donors. FIMNEU The NCI surface for this 4-electron hydrogen bonded interaction […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9056\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2013-01-08T14:09:18+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2014-06-06T08:52:52+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/01\/FIMNEU.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":"NCI (non-covalent-interaction) analysis for some \u03c0-hydrogen bonded systems. - 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=9056","og_locale":"en_GB","og_type":"article","og_title":"NCI (non-covalent-interaction) analysis for some \u03c0-hydrogen bonded systems. - Henry Rzepa's Blog","og_description":"In this post, I looked at some hydrogen bonds formed by interaction of a\u00a0\u03c0-system with an acidic hydrogen. Unlike normal lone pair donors, \u03c0-systems can involve more than two electrons, most commonly four or six. Here I look at examples of both these higher-order donors. FIMNEU The NCI surface for this 4-electron hydrogen bonded interaction […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9056","og_site_name":"Henry Rzepa's Blog","article_published_time":"2013-01-08T14:09:18+00:00","article_modified_time":"2014-06-06T08:52:52+00:00","og_image":[{"url":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/01\/FIMNEU.jpg","type":"","width":"","height":""}],"author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"2 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9056#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9056"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"NCI (non-covalent-interaction) analysis for some \u03c0-hydrogen bonded systems.","datePublished":"2013-01-08T14:09:18+00:00","dateModified":"2014-06-06T08:52:52+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9056"},"wordCount":437,"commentCount":0,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9056#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/01\/FIMNEU.jpg","keywords":["\u03c0-hydrogen bonded systems","\u03c0-systems"],"articleSection":["Interesting chemistry"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9056#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9056","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9056","name":"NCI (non-covalent-interaction) analysis for some \u03c0-hydrogen bonded systems. - Henry Rzepa's Blog","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#website"},"primaryImageOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9056#primaryimage"},"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9056#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/01\/FIMNEU.jpg","datePublished":"2013-01-08T14:09:18+00:00","dateModified":"2014-06-06T08:52:52+00:00","author":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"breadcrumb":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9056#breadcrumb"},"inLanguage":"en-GB","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9056"]}]},{"@type":"ImageObject","inLanguage":"en-GB","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9056#primaryimage","url":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/01\/FIMNEU.jpg","contentUrl":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/01\/FIMNEU.jpg"},{"@type":"BreadcrumbList","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9056#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog"},{"@type":"ListItem","position":2,"name":"NCI (non-covalent-interaction) analysis for some \u03c0-hydrogen bonded systems."}]},{"@type":"WebSite","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#website","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/","name":"Henry Rzepa's Blog","description":"Chemistry with a twist","potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-GB"},{"@type":"Person","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281","name":"Henry Rzepa","image":{"@type":"ImageObject","inLanguage":"en-GB","@id":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g370be3a7397865e4fd161aefeb0a5a85","url":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","contentUrl":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","caption":"Henry Rzepa"},"description":"Henry Rzepa is Emeritus Professor of Computational Chemistry at Imperial College London.","sameAs":["https:\/\/orcid.org\/0000-0002-8635-8390"],"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?author=1"}]}},"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/pDef7-2m4","jetpack-related-posts":[{"id":8925,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8925","url_meta":{"origin":9056,"position":0},"title":"\u03c0-hydrogen bonds as a function of ring size.","author":"Henry Rzepa","date":"January 5, 2013","format":false,"excerpt":"A simple correlation between a ring size and the hydrogen bonding as quantified by the O(Lp)\/H-O \u03c3* NBO interaction in that ring,\u00a0indicated a 7- or 8-membered ring was preferred over smaller ones. Here is the same study, but this time using the \u03c0-electrons of an alkene as the electron donor.\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":"WAK","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/01\/WAK.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":24452,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=24452","url_meta":{"origin":9056,"position":1},"title":"Biotin\u2019s biggest lesson is the importance of nonclassical H-bonds in protein\u2212ligand complexes.","author":"Henry Rzepa","date":"November 27, 2021","format":false,"excerpt":"The title comes from the abstract of an article analysing why Biotin (vitamin B7) is such a strong and effective binder to proteins, with a free energy of (non-covalent) binding approaching 21 kcal\/mol. The author argues that an accumulation of both CH-\u03c0 and CH-O together with more classical hydrogen bonds\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":13506,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13506","url_meta":{"origin":9056,"position":2},"title":"How many water molecules does it take to ionise HCN\/HNC? An NCI exploration.","author":"Henry Rzepa","date":"March 2, 2015","format":false,"excerpt":"HCN is a weak acid (pKa +9.2, weaker than e.g. HF), although it does have an isomer, isocyanic\u00a0acid or HNC (pka < +9.2 ?) which is simultaneously stronger and less stable. I conclude my halide acid series\u00a0by investigating how many water molecules (in gas phase clusters) are required for ionisation\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":[]},{"id":18165,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18165","url_meta":{"origin":9056,"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":2230,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2230","url_meta":{"origin":9056,"position":4},"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":21798,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21798","url_meta":{"origin":9056,"position":5},"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":[]}],"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\/9056","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=9056"}],"version-history":[{"count":22,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/9056\/revisions"}],"predecessor-version":[{"id":12600,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/9056\/revisions\/12600"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=9056"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=9056"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=9056"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=9056"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}