{"id":18091,"date":"2017-04-11T15:54:34","date_gmt":"2017-04-11T14:54:34","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=18091"},"modified":"2017-04-16T08:30:45","modified_gmt":"2017-04-16T07:30:45","slug":"the-conformation-of-carboxylic-acids-revealed","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18091","title":{"rendered":"The conformation of carboxylic acids revealed."},"content":{"rendered":"
\n

Following my conformational exploration<\/a> of enols, here is one about a much more common molecule, a carboxylic acid.<\/p>\n

\"\"<\/a>The components of the search are shown as four queries below, which will be combined in various Boolean senses (DOI:\u00a010.14469\/hpc\/2462<\/a>).<\/p>\n

    \n
  1. Query one defines the carboxylic acid, with 3-coordinate carbon specified at the carbonyl along with 1-coordinate for the carbonyl oxygen. Then the HO-C=O torsion (o\u00b0 for the syn<\/em> conformation shown on the left above and 180\u00b0 for the anti<\/em>-conformation shown on the right) and the length of the O-C bond as variables.<\/li>\n
  2. Query two defines a contact as \u2264 the sum of van der Waals radii between QA (=N,O,F,Cl) and the hydrogen of the carboxylic acid (pink).<\/li>\n
  3. Query three defines a contact as \u2264 the sum of van der Waals radii between\u00a0QA-H (QA=N,O,F,Cl) and the oxygen of the acid (pink).<\/li>\n
  4. Query four defines a temperature of <100K for the data collection temperature.
    \n \"\"<\/li>\n<\/ol>\n

    The first search uses just Query 1, with additional constraints of no errors, no disorder and R < 0.05.<\/p>\n

    \"\"<\/p>\n

    This can then be focused by combining Query 1 + Query 4, which shows a clear preference for the syn<\/em> conformation.<\/p>\n

    \"\"<\/p>\n

    Next, Query 1 with NOT<\/strong> query 2, which restricts the search to carboxylic acids that do not have contacts to the hydrogen of the OH group. This excludes carboxylic acid dimers, as shown above. The predominant hot-spot now corresponds to the anti\u00a0<\/em>conformation.<\/p>\n

    \"\"<\/p>\n

    Again this is narrowed using Query 4, which removes almost all the syn\u00a0<\/em>examples.<\/p>\n

    \"\"<\/p>\n

    Now using Query 3 (as shown above), which restricts the search to examples where the oxygen of the HO group is itself not in contact with an acidic hydrogen. This allows carboxylic acid dimers. This now reveals the syn<\/em> preference again.<\/p>\n

    \"\"<\/p>\n

    At <100K reinforces this effect.<\/p>\n

    \"\"<\/p>\n

    Finally, Query 1 and NOT<\/strong> query 2 (no dimers) and NOT<\/strong> query 3, where a smaller preference for anti<\/em> is seen.<\/p>\n

    \"\"<\/p>\n

    So it seems that an interesting difference emerges between enols and carboxylic acids in that when no hydrogen bonding to the HO group is allowed, an anti<\/em> preference emerges. The electronic origins of this effect will be probed in a future post.<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    Following my conformational exploration of enols, here is one about a much more common molecule, a carboxylic acid. The components of the search are shown as four queries below, which will be combined in various Boolean senses (DOI:\u00a010.14469\/hpc\/2462). Query one defines the carboxylic acid, with 3-coordinate carbon specified at the carbonyl along with 1-coordinate for […]<\/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":[1745],"tags":[1617,2123,233,1395,2120,1412,1410,2124],"ppma_author":[2661],"class_list":["post-18091","post","type-post","status-publish","format-standard","hentry","category-crystal_structure_mining","tag-acid","tag-alcohols","tag-carboxylic-acid","tag-chemistry","tag-enol","tag-functional-groups","tag-organic-chemistry","tag-search-uses"],"yoast_head":"\nThe conformation of carboxylic acids revealed. - 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=18091\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"The conformation of carboxylic acids revealed. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"Following my conformational exploration of enols, here is one about a much more common molecule, a carboxylic acid. The components of the search are shown as four queries below, which will be combined in various Boolean senses (DOI:\u00a010.14469\/hpc\/2462). Query one defines the carboxylic acid, with 3-coordinate carbon specified at the carbonyl along with 1-coordinate for […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18091\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2017-04-11T14:54:34+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2017-04-16T07:30:45+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2017\/04\/carboxylic-acids-page001.svg\" \/>\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":"The conformation of carboxylic acids revealed. - 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=18091","og_locale":"en_GB","og_type":"article","og_title":"The conformation of carboxylic acids revealed. - Henry Rzepa's Blog","og_description":"Following my conformational exploration of enols, here is one about a much more common molecule, a carboxylic acid. The components of the search are shown as four queries below, which will be combined in various Boolean senses (DOI:\u00a010.14469\/hpc\/2462). 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The rules are easily learnt (supposedly) and it can be used across a broad spectrum of mechanism. But, as one both becomes more experienced, and in time teaches the techniques oneself\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\/acyloxyborane1.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":5114,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5114","url_meta":{"origin":18091,"position":1},"title":"Mechanism of the reduction of a carboxylic acid by borane: revisited and revised.","author":"Henry Rzepa","date":"October 16, 2011","format":false,"excerpt":"I asked a while back\u00a0whether blogs could be considered a serious form of scholarly scientific communication (and so has Peter Murray-Rust more recently). A case for doing so might be my post of about a year ago, addressing why borane reduces a carboxylic acid, but not its ester, where I\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":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/acyloxy1-page001.svg","width":350,"height":200},"classes":[]},{"id":6750,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=6750","url_meta":{"origin":18091,"position":2},"title":"Mechanism of the diazomethane alkylation of a carboxylic acid.","author":"Henry Rzepa","date":"May 19, 2012","format":false,"excerpt":"Many reaction mechanisms involve a combination of bond formation\/cleavage between two non-hydrogen atoms and those involving reorganisation of proximate hydrogens. The Baeyer-Villiger discussed previously illustrated a complex dance between the two types. Here I take a look at another such mechanism, the methylation of a carboxylic acid by diazomethane. Text-books\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\/2012\/05\/diazomethane12.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":25391,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25391","url_meta":{"origin":18091,"position":3},"title":"Unexpected Isomerization of Oxetane-Carboxylic Acids \u2013 catalyst design.","author":"Henry Rzepa","date":"August 13, 2022","format":false,"excerpt":"Previously, a mechanism with a reasonable predicted energy was modelled for the isomerisation of an oxetane carboxylic acid to a lactone by using two further molecules of acid to transfer the proton and in the process encouraging an Sn2 reaction with inversion to open the oxetane ring. We are now\u2026","rel":"","context":"In "reaction mechanism"","block_context":{"text":"reaction mechanism","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1086"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":6816,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=6816","url_meta":{"origin":18091,"position":4},"title":"The mechanism (in 4D) of the reaction between thionyl chloride and a carboxylic acid.","author":"Henry Rzepa","date":"May 25, 2012","format":false,"excerpt":"If you have not previously visited, take a look at Nick Greeves' ChemTube3D\u00a0, an\u00a0ever-expanding gallery of reactions and their mechanisms. The 3D is because all molecules are offered with X, Y and z coordinates. You also get arrow pushing\u2021\u00a0in 3D. Here, I argue that we should adopt Einstein, and go\u2026","rel":"","context":"In \"acetic acid\"","block_context":{"text":"acetic acid","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=acetic-acid"},"img":{"alt_text":"","src":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/05\/thionyl.svg","width":350,"height":200},"classes":[]},{"id":26962,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26962","url_meta":{"origin":18091,"position":5},"title":"Detecting anomeric effects in tetrahedral boron bearing four oxygen substituents.","author":"Henry Rzepa","date":"April 30, 2024","format":false,"excerpt":"In an earlier post, I discussed a phenomenon known as the \"anomeric effect\" exhibited by tetrahedral carbon compounds with four C-O bonds. 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":[]}],"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\/18091","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=18091"}],"version-history":[{"count":10,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/18091\/revisions"}],"predecessor-version":[{"id":18112,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/18091\/revisions\/18112"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=18091"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=18091"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=18091"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=18091"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}