{"id":4254,"date":"2011-05-31T13:05:16","date_gmt":"2011-05-31T13:05:16","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=4254"},"modified":"2011-11-29T15:08:09","modified_gmt":"2011-11-29T15:08:09","slug":"conformational-restriction-involving-formyl-ch-f-hydrogen-bonds","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4254","title":{"rendered":"Conformational restriction involving formyl CH&#8230;F hydrogen bonds."},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"4254\">\n<p>The title of this post paraphrases E. J. Corey&#8217;s article in 1997 (DOI:\u00a0<a href=\"http:\/\/dx.doi.org\/10.1016\/S0040-4039(96)02248-4\" target=\"_blank\">10.1016\/S0040-4039(96)02248-4<\/a>) which probed the origins of conformation restriction in aldehydes. The proposal was of (then) unusual hydrogen bonding between the O=C-H&#8230;F-B groups. Here I explore whether the NCI (non-covalent-interaction) method can be used to cast light on this famous example of how unusual interactions might mediate selectivity in organic reactions.<\/p>\n<p><div id=\"attachment_4255\" style=\"width: 410px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-4255\" class=\"size-full wp-image-4255\" title=\"RUGYEX-x\" onclick=\"jmolInitialize('..\/Jmol\/',true);jmolSetAppletColor('white');jmolApplet([600,600],'load wp-content\/uploads\/2011\/05\/RUGYEX.cif;zoom 140;');\" src=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/05\/RUGYEX-x.jpg\" alt=\"\" width=\"400\" height=\"317\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/05\/RUGYEX-x.jpg 814w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/05\/RUGYEX-x-300x237.jpg 300w\" sizes=\"auto, (max-width: 400px) 100vw, 400px\" \/><p id=\"caption-attachment-4255\" class=\"wp-caption-text\">Crystal structure of RUGYEX. Click for 3D<\/p><\/div>The crystal structure revealed a fixed syn orientation between one B-F bond and the formyl C-H bond, with a distance of ~2.36\u00c5 (using un-normalised C-H lengths), compared with a value of 2.55\u00c5 for the vdW sum. Since hydrogen bonds to fluorine are quite rare, it seems worth applying the NCI method (<a href=\"http:\/\/hdl.handle.net\/10042\/to-8522\" target=\"_blank\">DOI for calculation<\/a>).<\/p>\n<p><div id=\"attachment_4257\" style=\"width: 410px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-4257\" class=\"size-full wp-image-4257\" title=\"RUGYEX\" onclick=\"jmolInitialize('..\/Jmol\/',true);jmolSetAppletColor('white');jmolApplet([600,600],'load wp-content\/uploads\/2011\/05\/RUGYEX.xyz;isosurface wp-content\/uploads\/2011\/05\/RUGYEX.jvxl colorscheme translucent bgyor;select atomno=5,atomno=4,atomno=1,atomno=16,atomno=19;halo on;measure 5 4;measure 1 16;measure 16 19;zoom 140;');\" src=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/05\/RUGYEX.jpg\" alt=\"\" width=\"400\" height=\"306\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/05\/RUGYEX.jpg 513w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/05\/RUGYEX-300x229.jpg 300w\" sizes=\"auto, (max-width: 400px) 100vw, 400px\" \/><p id=\"caption-attachment-4257\" class=\"wp-caption-text\">NCI surfaces for RUGYEX. click for 3D.<\/p><\/div>The result indeed shows a strongly blue (= attractive) interaction surface for the CH&#8230;F region, and only a tiny one for the adjacent \u00a0H&#8230;H region. A welcome surprise however is the \u00a0O&#8230;O region, which also shows a distinct (strong) attraction. Perhaps this is due to the presence of the electron withdrawing BF3 group on one of the oxygens. This could also be regarded as a through-space anomeric effect, from one oxygen donating into the \u00a0O-B \u03c3* orbital. Such <em>through space<\/em>anomeric effects (they are normally propagated through bonds, as in sugars) are probably more common than we believe.<\/p>\n<p>This result nicely illustrates the utility of the NCI method; it brings an immediate visual impact, which serves to highlight interactions which otherwise might be ignored.<\/p>\n<!-- kcite active, but no citations found -->\n<\/div> <!-- kcite-section 4254 -->","protected":false},"excerpt":{"rendered":"<p>The title of this post paraphrases E. J. Corey&#8217;s article in 1997 (DOI:\u00a010.1016\/S0040-4039(96)02248-4) which probed the origins of conformation restriction in aldehydes. The proposal was of (then) unusual hydrogen bonding between the O=C-H&#8230;F-B groups. Here I explore whether the NCI (non-covalent-interaction) method can be used to cast light on this famous example of how unusual [&hellip;]<\/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":[17,545,546,249],"ppma_author":[2661],"class_list":["post-4254","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-conformational-analysis","tag-corey","tag-formyl-hydrogen","tag-julia-contreras-garcia"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Conformational restriction involving formyl CH...F hydrogen bonds. - Henry Rzepa&#039;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=4254\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Conformational restriction involving formyl CH...F hydrogen bonds. - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"The title of this post paraphrases E. J. Corey&#8217;s article in 1997 (DOI:\u00a010.1016\/S0040-4039(96)02248-4) which probed the origins of conformation restriction in aldehydes. The proposal was of (then) unusual hydrogen bonding between the O=C-H&#8230;F-B groups. Here I explore whether the NCI (non-covalent-interaction) method can be used to cast light on this famous example of how unusual [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4254\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"article:published_time\" content=\"2011-05-31T13:05:16+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2011-11-29T15:08:09+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/05\/RUGYEX-x.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=\"1 minute\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Conformational restriction involving formyl CH...F hydrogen bonds. - Henry Rzepa&#039;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=4254","og_locale":"en_GB","og_type":"article","og_title":"Conformational restriction involving formyl CH...F hydrogen bonds. - Henry Rzepa&#039;s Blog","og_description":"The title of this post paraphrases E. J. Corey&#8217;s article in 1997 (DOI:\u00a010.1016\/S0040-4039(96)02248-4) which probed the origins of conformation restriction in aldehydes. The proposal was of (then) unusual hydrogen bonding between the O=C-H&#8230;F-B groups. Here I explore whether the NCI (non-covalent-interaction) method can be used to cast light on this famous example of how unusual [&hellip;]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4254","og_site_name":"Henry Rzepa&#039;s Blog","article_published_time":"2011-05-31T13:05:16+00:00","article_modified_time":"2011-11-29T15:08:09+00:00","og_image":[{"url":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/05\/RUGYEX-x.jpg","type":"","width":"","height":""}],"author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"1 minute"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4254#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4254"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Conformational restriction involving formyl CH&#8230;F hydrogen bonds.","datePublished":"2011-05-31T13:05:16+00:00","dateModified":"2011-11-29T15:08:09+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4254"},"wordCount":281,"commentCount":2,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4254#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/05\/RUGYEX-x.jpg","keywords":["conformational analysis","Corey","formyl hydrogen","Julia Contreras-Garcia"],"articleSection":["Interesting chemistry"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4254#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4254","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4254","name":"Conformational restriction involving formyl CH...F hydrogen bonds. - 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Each oxygen itself bears two bonds and has two lone pairs, and either of these can align with one of three other C-O bonds to generate an anomeric\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/04\/Screenshot-304.jpg?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/04\/Screenshot-304.jpg?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/04\/Screenshot-304.jpg?resize=525%2C300&ssl=1 1.5x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2024\/04\/Screenshot-304.jpg?resize=700%2C400&ssl=1 2x"},"classes":[]},{"id":1856,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=1856","url_meta":{"origin":4254,"position":1},"title":"Conformational analysis of biphenyls: an upside-down view","author":"Henry Rzepa","date":"April 2, 2010","format":false,"excerpt":"One of the (not a few) pleasures of working in a university is the occasional opportunity that arises to give a new lecture course to students. New is not quite the correct word, since the topic I have acquired is Conformational analysis. The original course at Imperial College was delivered\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","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\/04\/biphenyl-1.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":4254,"position":2},"title":"The shortest known CF&#8230;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 &quot;crystal_structure_mining&quot;","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":5500,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5500","url_meta":{"origin":4254,"position":3},"title":"The peroxidation of alkynes: things are not always what they seem.","author":"Henry Rzepa","date":"November 16, 2011","format":false,"excerpt":"The epoxidation of an alkene to give an oxirane is taught in introductory organic chemistry. Formulating an analogous mechanism for such reaction of an alkyne\u00a0sounds straightforward, but one gradually realises that it requires raiding knowledge from several other areas of (perhaps slightly more advanced) chemistry to achieve a joined up\u2026","rel":"","context":"In &quot;Curly arrows&quot;","block_context":{"text":"Curly arrows","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2327"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/11\/1.gif?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":17992,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17992","url_meta":{"origin":4254,"position":4},"title":"The conformation of enols: revealed and explained.","author":"Henry Rzepa","date":"April 6, 2017","format":false,"excerpt":"Enols are simple compounds with an OH group as a substituent on a C=C double bond and with a very distinct conformational preference for the OH group. Here I take a look at this preference as revealed by crystal structures, with the theoretical explanation. First, a search of the Cambridge\u2026","rel":"","context":"In &quot;crystal_structure_mining&quot;","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\/All-1024x948.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":17333,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17333","url_meta":{"origin":4254,"position":5},"title":"Ritonavir: a look at a famous example of conformational polymorphism.","author":"Henry Rzepa","date":"January 2, 2017","format":false,"excerpt":"Here is an inside peek at another one of Derek Lowe's 250 milestones in chemistry, the polymorphism of Ritonavir.\u00a0The story in a nutshell concerns one of a pharma company's worst nightmares; a drug which has been successfully brought to market unexpectedly\u00a0\"changes\" after a few years on market to a less\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","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":[]}],"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\/4254","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=4254"}],"version-history":[{"count":1,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/4254\/revisions"}],"predecessor-version":[{"id":5749,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/4254\/revisions\/5749"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=4254"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=4254"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=4254"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=4254"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}