{"id":9572,"date":"2013-02-21T10:51:22","date_gmt":"2013-02-21T10:51:22","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=9572"},"modified":"2014-01-17T07:34:22","modified_gmt":"2014-01-17T07:34:22","slug":"a-to-and-fro-of-electrons-operating-in-s-cis-esters","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9572","title":{"rendered":"A to-and-fro of electrons operating in s-cis esters."},"content":{"rendered":"
\n

I conclude my exploration of conformational preferences by taking a look at esters. As before<\/a>, I start with a search definition, the ester being restricted to one bearing only sp3<\/sup> carbon centers.<\/p>\n

\"s-cis-ester-torsion-search\"<\/p>\n

The result of such a search is pretty clear-cut; they all exist in just one conformation, the s-cis<\/em><\/a>, in which a lone pair of electrons on the alkyl-oxygen is aligned quite precisely anti-periplanar with the axis of the C=O bond. This very narrow distribution suggests a relatively large energy preference for this orientation, and we need to seek its origins.<\/p>\n

\"s-cis-ester-torsion\"<\/p>\n

This arises from two electronic alignments. The first orients the in-plane alkyl oxygen lone pair (orange-purple below) anti-periplanar with the C=O \u03c3* empty orbital (red-blue; orange=red, blue=purple), an interaction mapping to 7.7 kcal\/mol in the NBO E(2) energy. The second reinforcement (not shown) aligns the (O=)C-Me donor bond with the antiperiplanar O-Me acceptor (5.3 kcal\/mol). These two interactions are weaker in the s-trans<\/em> ester<\/a>, which is 8.1 kcal\/mol higher in \u0394G298<\/sub> and for which the E(2) terms are respectively 3.0 and 0.6 kcal\/mol.\u00a0<\/p>\n

\"Click

Lp(alkyl-O)\/C=O \u03c3* Click for 3D.<\/p><\/div>\n

But wait, this interaction has electrons moving from the alkyl oxygen to the acyl oxygen (red arrows below) and apparently weakening the C=O bond in the process. But in an entirely different context, we learn that the C=O vibrational stretching wavenumber for an ester (1750 cm-1<\/sup>) is higher than that of a ketone (~1715 cm-1<\/sup>); the C=O is stronger rather than weaker in the ester. So now we have to move the \u03c3-electrons back again (green arrows below).\"s-cis-ester\"<\/p>\n

This strengthening of the C=O bond arises from the following overlap of the \u03c3-lone pair on the carbonyl oxygen with the alkyl-O-C\u00a0\u03c3* empty orbital, for which E(2) is 41.5 kcal\/mol, much larger than the previous effect. It however does NOT discriminate between the s-cis<\/em> and s-trans<\/em>\u00a0 conformations, since this interaction is almost the same in the latter (41.8). So we have a to-of-(red)-electrons<\/em> which promote the s-cis conformation, and rather stronger fro-of-(green)-electrons<\/em> which strengthen the C=O bond. But they do not cancel each-other; each has its own job to do!<\/p>\n

\"Click

Lp(acyl-O)\/C-O \u03c3* Click for 3D.<\/p><\/div>\n

There is one other overlap which may differentiate between s-cis<\/em> and s-trans<\/em>, but a rather less obvious one. That is the alkyl-O\u03c0<\/sub> donating to the acyl C=O\u03c0*<\/sub> which has E(2) 64.7 for the former and 59.4 kcal\/mol for the latter. It is not immediately apparent why this overlap should favour s-cis<\/em>. It is however the effect that induces a significant rotational barrier about the C-O bond (~12 kcal\/mol).<\/p>\n

\"Click

Lp (alkyl-O \u03c0)\/C=O \u03c0* Click for 3D.<\/p><\/div>\n

Here is the result of another search of the crystal database; \u00a0namely the C=O distance (DIST1) vs the \u00a0C-O distance (DIST2). You can see that the red hot spot (~1400 examples) is very isolated (the blue squares represent < 200 hits), and there seems to be no significant correlation between the two lengths and the structure.<\/p>\n<\/p>\n

\"s-cis-ester-distance\"
I will conclude with a brief discussion of the carbonyl lone pairs. There are two, and one of them has been shown above in the\u00a0Lp(acyl-O)\/C-O \u03c3* interaction. There is another, but it plays no role in the conformation, and is of quite a different character. Although a low-lying orbital, it is clearly non bonding; indeed might be slightly anti-bonding along the C=O axis. These two carbonyl lone pairs are quite different in character, since each performs a different role in the molecule.<\/p>\n

\"Click

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

So the conformational analysis of this simple little molecule reveals some interesting toos-and-fros in the electrons. I will deal with the issue of the carbonyl stretching frequencies in another post.<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

I conclude my exploration of conformational preferences by taking a look at esters. 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, in which a lone pair […]<\/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":[17,24,1000,1001,373],"ppma_author":[2661],"class_list":["post-9572","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-conformational-analysis","tag-energy","tag-large-energy-preference","tag-search-definition","tag-tutorial-material"],"yoast_head":"\nA to-and-fro of electrons operating in s-cis esters. - 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=9572\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"A to-and-fro of electrons operating in s-cis esters. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"I conclude my exploration of conformational preferences by taking a look at esters. 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The result of such a search is pretty clear-cut; they all exist in just one conformation, the s-cis, in which a lone pair […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9572\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2013-02-21T10:51:22+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2014-01-17T07:34:22+00:00\" \/>\n<meta property=\"og:image\" content=\"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/02\/s-cis-ester-torsion-search.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=\"3 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"A to-and-fro of electrons operating in s-cis esters. - 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=9572","og_locale":"en_GB","og_type":"article","og_title":"A to-and-fro of electrons operating in s-cis esters. - Henry Rzepa's Blog","og_description":"I conclude my exploration of conformational preferences by taking a look at esters. 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