{"id":16557,"date":"2016-06-18T09:43:30","date_gmt":"2016-06-18T08:43:30","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=16557"},"modified":"2016-06-26T08:19:16","modified_gmt":"2016-06-26T07:19:16","slug":"why-is-the-carbonyl-ir-stretch-in-an-ester-higher-than-in-a-ketone-crystal-structure-data-mining","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16557","title":{"rendered":"Why is the carbonyl IR stretch in an ester higher than in a ketone: crystal structure data mining."},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"16557\">\n<p>\n\t<a href=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=9606\" target=\"_blank\">In this post<\/a>, I pondered upon the C=O infra-red spectroscopic&nbsp;properties of esters, and showed three possible electronic influences:\n<\/p>\n<p>\n\t<img decoding=\"async\" alt=\"s-cis-ester1\" class=\"aligncenter size-full wp-image-9607\" src=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/02\/s-cis-ester1.svg\" \/>\n<\/p>\n<p>\n\tThe red (and blue) arrows imply the C-O bond might shorten and the C=O bond would lengthen; the green the reverse. So time for a search of the crystal structure database as a reality check. The query is as follows:\n<\/p>\n<p>\n\t<img decoding=\"async\" alt=\"s-cis-ester1\" class=\"aligncenter size-full wp-image-9607\" src=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/06\/amides-sq.jpg\" width=\"400\" \/>\n<\/p>\n<p>\n\tThe response shows the bimodal distribution with as expected the<em> s-cis<\/em> conformation dominating. There is indeed a hint that for the <em>s-cis<\/em>, the C-O distance is rather shorter than for the <em>s-trans<\/em> conformation.\n<\/p>\n<p>\n\t<img decoding=\"async\" alt=\"s-cis-ester1\" class=\"aligncenter size-full wp-image-9607\" src=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/06\/amides-all.jpg\" width=\"440\" \/>\n<\/p>\n<p>\n\tRepeating the search, but specifying that the temperature of data acquisition is &lt; 90K, one gets a much clearer indication of the difference in bond lengths.\n<\/p>\n<p>\n\t<img decoding=\"async\" alt=\"s-cis-ester1\" class=\"aligncenter size-full wp-image-9607\" src=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/06\/amides-90.jpg\" width=\"440\" \/>\n<\/p>\n<p>\n\tThis alternative representation shows the C-O and the C=O distances, with red indicating <em>s-trans<\/em> and blue indicating <em>s-cis<\/em> conformations (T &lt; 140K). The red dots occupy a bottom right cluster for which the C-O distance is longer and the C=O shorter than the corresponding blue cluster.\n<\/p>\n<p>\n\t<img decoding=\"async\" alt=\"s-cis-ester1\" class=\"aligncenter size-full wp-image-9607\" src=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/06\/amides-1vs2-140.jpg\" width=\"440\" \/>\n<\/p>\n<p>\n\tAgain reducing the temperature of data collection to &lt; 90K shows a rather weak inverse correlation between the two distances for eg the blue dots.\n<\/p>\n<p>\n\t<img decoding=\"async\" alt=\"s-cis-ester1\" class=\"aligncenter size-full wp-image-9607\" src=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/06\/amides-1vs2-90.jpg\" width=\"440\" \/>\n<\/p>\n<p>\n\tA shame however that this database does not hold IR values for the carbonyl stretches. I am sure correlations must exist, but how to get at them (other than manual collection of data).<\/p>\n<!-- kcite active, but no citations found -->\n<\/div> <!-- kcite-section 16557 -->","protected":false},"excerpt":{"rendered":"<p>In this post, I pondered upon the C=O infra-red spectroscopic&nbsp;properties of esters, and showed three possible electronic influences: The red (and blue) arrows imply the C-O bond might shorten and the C=O bond would lengthen; the green the reverse. So time for a search of the crystal structure database as a reality check. The query [&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":true,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[2,1745],"tags":[1756,1412,1755],"ppma_author":[2661],"class_list":["post-16557","post","type-post","status-publish","format-standard","hentry","category-chemical-it","category-crystal_structure_mining","tag-ester","tag-functional-groups","tag-infra-red"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.5 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Why is the carbonyl IR stretch in an ester higher than in a ketone: crystal structure data mining. - 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=16557\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Why is the carbonyl IR stretch in an ester higher than in a ketone: crystal structure data mining. - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"In this post, I pondered upon the C=O infra-red spectroscopic&nbsp;properties of esters, and showed three possible electronic influences: The red (and blue) arrows imply the C-O bond might shorten and the C=O bond would lengthen; the green the reverse. So time for a search of the crystal structure database as a reality check. The query [&hellip;]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16557\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"article:published_time\" content=\"2016-06-18T08:43:30+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2016-06-26T07:19:16+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/02\/s-cis-ester1.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=\"1 minute\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Why is the carbonyl IR stretch in an ester higher than in a ketone: crystal structure data mining. - 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=16557","og_locale":"en_GB","og_type":"article","og_title":"Why is the carbonyl IR stretch in an ester higher than in a ketone: crystal structure data mining. - Henry Rzepa&#039;s Blog","og_description":"In this post, I pondered upon the C=O infra-red spectroscopic&nbsp;properties of esters, and showed three possible electronic influences: The red (and blue) arrows imply the C-O bond might shorten and the C=O bond would lengthen; the green the reverse. So time for a search of the crystal structure database as a reality check. The query [&hellip;]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16557","og_site_name":"Henry Rzepa&#039;s Blog","article_published_time":"2016-06-18T08:43:30+00:00","article_modified_time":"2016-06-26T07:19:16+00:00","og_image":[{"url":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/02\/s-cis-ester1.svg","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=16557#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16557"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Why is the carbonyl IR stretch in an ester higher than in a ketone: crystal structure data mining.","datePublished":"2016-06-18T08:43:30+00:00","dateModified":"2016-06-26T07:19:16+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16557"},"wordCount":245,"commentCount":1,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16557#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/02\/s-cis-ester1.svg","keywords":["Ester","Functional groups","Infra-Red"],"articleSection":["Chemical IT","crystal_structure_mining"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16557#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16557","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16557","name":"Why is the carbonyl IR stretch in an ester higher than in a ketone: crystal structure data mining. - 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As before, I start with a search definition, the ester being restricted to one bearing only sp3 carbon centers. The result of such a search is pretty clear-cut; they all exist in just one conformation, the s-cis,\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":"s-cis-ester-torsion-search","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/02\/s-cis-ester-torsion-search.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":9500,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9500","url_meta":{"origin":16557,"position":1},"title":"The conformational preference of s-cis amides. Ramachandran plots.","author":"Henry Rzepa","date":"February 11, 2013","format":false,"excerpt":"This is really just a postscript to the previous post. There I showed how a search of the (small molecule) crystal database revealed the s-cis conformation about the N-C amide bond (the one with partial double bond character that prevents rotation) and how this conformation means that a C-H approaches\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":[]},{"id":9459,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9459","url_meta":{"origin":16557,"position":2},"title":"The conformational preference of s-cis amides.","author":"Henry Rzepa","date":"February 10, 2013","format":false,"excerpt":"Amides with an H-N group are a component of the peptide linkage\u00a0(O=C-NH). Here I ask what the conformation (it could also be called a configuration) about the C-N bond is. A search of the following type can be defined: The dihedral shown is for H-N-C=O (but this is equivalent to\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":"cis-amide","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/02\/cis-amide.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":5087,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5087","url_meta":{"origin":16557,"position":3},"title":"cis-Butene: a reaction coordinate dissected and methyl flags.","author":"Henry Rzepa","date":"October 12, 2011","format":false,"excerpt":"In two previous posts, I have looked at why cis-butene adopts conformation (a) rather than (b). I suggested it boiled down to electronic interactions between the methyl groups and the central alkene resulting in the formation of a H...H \"topological\" bond, rather than attraction between the H...H region to form\u2026","rel":"","context":"In &quot;General&quot;","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\/10\/cis-butene2.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":16557,"position":4},"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":[]},{"id":9606,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9606","url_meta":{"origin":16557,"position":5},"title":"Why is the carbonyl IR stretch in an ester higher than in a ketone?","author":"Henry Rzepa","date":"February 28, 2013","format":false,"excerpt":"Infra-red spectroscopy of molecules was introduced 110 years ago by Coblentz as the first functional group spectroscopic method (\"\u00a0The structure of the compound has a great influence on the absorption spectra. In many cases it seems as though certain bonds are due to certain groups.\"). It hangs on in laboratories\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\/16557","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=16557"}],"version-history":[{"count":6,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16557\/revisions"}],"predecessor-version":[{"id":16590,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/16557\/revisions\/16590"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=16557"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=16557"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=16557"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=16557"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}