{"id":9320,"date":"2013-02-03T14:10:24","date_gmt":"2013-02-03T14:10:24","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=9320"},"modified":"2013-02-12T06:46:31","modified_gmt":"2013-02-12T06:46:31","slug":"secrets-of-a-university-tutor-conformational-analysis-and-spectroscopy","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9320","title":{"rendered":"Secrets of a university tutor: conformational analysis and NMR spectroscopy."},"content":{"rendered":"
\n

In a previous post<\/a>, I set out how to show how one can reduce a\u00a01<\/sup>H NMR spectrum to the structure [A] below. I speculated how a further test could be applied to this structure; back predicting its spectrum using just quantum mechanics. Overkill I know, but how well might the two match?<\/p>\n

\"4nmr\"<\/a><\/p>\n

    \n
  1. The process must start by considering the conformational possibilities of [A]. Each will have a different predicted spectrum. There are six rotatable bonds in the system, which if each bond has up to three rotamers would be 729 conformations potentially possible. A nightmare to explore (but do-able if you really needed to). I will try to reduce this by searching for the most probable for each bond (which may not of course lead to the final best conformation).<\/li>\n
  2. Bonds 1 and 2 can be subjected to a search of the Cambridge database. The search criteria are the same as described in this post<\/a>. The most probable dihedral angle around this type of bond is\u00a0\u00b1 110\u00b0.\"C=C-C-S\"<\/a><\/li>\n
  3. Bond 3 has few entries, but they show as:\"O=C-S-C\"<\/a><\/li>\n
  4. Bonds 4\/5 are also the one that controls the conformation of esters, and is known as S-cis. All examples show the lone pair on the sulfur as anti to the axis of the C=O bond.\"SCC=O\"<\/a><\/li>\n
  5. Bond 6 has just two conformations, anti and gauche.\"CC-C-S\"<\/a><\/li>\n
  6. We have reduced the possible 729 to just two, which are then subjected to a \u03c9B97XD\/6-311G(d,p)\/SCRF=chloroform calculation. Some faith in this combination can be obtained by inspecting the (remarkably accurate) result obtained for a\u00a0Matryoshka doll<\/a>. A\u00a0suitable model can be invoked using a keyword NMR(mixed.spinspin)<\/a>.\u00a0The method recovers at least a proportion of the effects on conformation induced by the weak dispersion forces present. The prediction comes in two forms:\n
      \n
    1. The magnetic shieldings relative to TMS (chemical shifts). One might expect these to be predicted with an error of around 0.3ppm, but if the actual NMR population comprises more than one rotamer, then one does need to take the Boltzmann average. For this molecule, predicting how the magnetic anisotropy induced from the double or triple bonds will perturb the chemical shifts will depend critically on the conformation of the molecule. In other words, this is actually a pretty challenging system to get right!\u00a0<\/li>\n
    2. The spin-spin couplings. These have an expected predictability of ~1 Hz.\u00a0<\/li>\n<\/ol>\n<\/li>\n
    3. The calculation comes up with essentially identical free energies for the two selected conformations:
      \n\n\n\n\n
      Anti<\/a>\u00a0(0.1)<\/td>\nGauche<\/a>\u00a0(0.0)<\/td>\n<\/tr>\n
      \"14-a\"<\/td>\n\"Click<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n
    4. The experimental spectrum was \u03b4 1.70 (3H,d,6Hz), 2.23 (1H, t, 3Hz), 3.73 (2H, d, 3Hz), 4.84 (1H, dd, 7,8Hz), 5.15 (1H, d, 10Hz), 5.27 (1H, d, 17Hz), 5.51 (1H, dd, 8,16.5 Hz), 5.77 (1H, dq, 6,16.5 Hz), 5.88 (1H, ddd, 7,10,17Hz).\u00a0<\/li>\n
    5. To compare with the computed one, firstly I note that the values for the three hydrogens of the methyl group have to be averaged over both conformations. The predicted chemical shifts are shown below. For the anti<\/em> conformation, they all come within about 0.3ppm of the measured value.
      \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
      –<\/th>\nChemical shifts<\/th>\n<\/tr>\n
      Proton<\/td>\nExpt<\/td>\nanti<\/td>\nGauche<\/td>\n<\/tr>\n
      1<\/td>\n\u00a01.70<\/td>\n\u00a01.68<\/td>\n\u00a01.66<\/td>\n<\/tr>\n
      2<\/td>\n\u00a05.77<\/td>\n\u00a06.15<\/td>\n\u00a06.17<\/td>\n<\/tr>\n
      3<\/td>\n\u00a05.51<\/td>\n\u00a05.76<\/td>\n\u00a05.76<\/td>\n<\/tr>\n
      4<\/td>\n\u00a04.84<\/td>\n\u00a04.66<\/td>\n\u00a04.76<\/td>\n<\/tr>\n
      5<\/td>\n\u00a05.88<\/td>\n\u00a06.15<\/td>\n\u00a06.19<\/td>\n<\/tr>\n
      6<\/td>\n\u00a05.15<\/td>\n\u00a05.59<\/td>\n\u00a05.58<\/td>\n<\/tr>\n
      6<\/td>\n\u00a05.27<\/td>\n\u00a05.76<\/td>\n\u00a05.84<\/td>\n<\/tr>\n
      11<\/td>\n\u00a03.73<\/td>\n\u00a03.40<\/td>\n\u00a03.01<\/td>\n<\/tr>\n
      11<\/td>\n\u00a03.73<\/td>\n\u00a03.49<\/td>\n\u00a03.01<\/td>\n<\/tr>\n
      13<\/td>\n\u00a02.23<\/td>\n\u00a02.19<\/td>\n\u00a02.05<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n
    6. The spin-spin couplings are shown below. Several differ by about 3Hz, but most are better. Notice how the sign of the coupling from H-11 to H-13 is identified as negative, and how the methylene group at C-11 is identified as slightly diastereotopic (from the presence of the chiral centre). The 2<\/sup>JHH<\/sub> coupling is not detected in the (first order) measured spectrum.
      \n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
      –<\/th>\nCouplings, Hz<\/th>\n<\/tr>\n
      Proton<\/td>\nExpt<\/td>\nanti<\/td>\nGauche<\/td>\n<\/tr>\n
      1<\/td>\n6<\/td>\n6.6<\/td>\n6.6<\/td>\n<\/tr>\n
      2<\/td>\n6,16.5<\/td>\n6.6,13.6<\/td>\n6.6,13.6<\/td>\n<\/tr>\n
      3<\/td>\n16.5,8<\/td>\n13.6,9.2<\/td>\n13.6,9.2<\/td>\n<\/tr>\n
      4<\/td>\n8,7<\/td>\n9.2,10.2<\/td>\n9.2,10.2<\/td>\n<\/tr>\n
      5<\/td>\n7,10,17<\/td>\n10.2,10.4,15.4<\/td>\n10.210.4,15.4<\/td>\n<\/tr>\n
      6<\/td>\n10<\/td>\n10.4<\/td>\n10.4<\/td>\n<\/tr>\n
      6<\/td>\n17<\/td>\n15.4<\/td>\n15.4<\/td>\n<\/tr>\n
      11<\/td>\n\u00b13<\/td>\n-15.5,-3.7,-3.7<\/td>\n-17.3,-3.5,-3.3<\/td>\n<\/tr>\n
      11<\/td>\n\u00b13<\/td>\n-3.7,-3.7<\/td>\n-3.5<\/td>\n<\/tr>\n
      13<\/td>\n\u00b13<\/td>\n-3.7, -3.7<\/td>\n-3.3<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n<\/ol>\n

      We might conclude from this analysis that the match between the measured spectrum of [A] and that calculated entirely from quantum mechanical principles is pretty good. We may be reasonably confident that the conformations we have identified are realistic. Of course, if we want to be sure there is none better, then the few hundred other possible conformations would have to be calculated. I am not about to try!<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      In a previous post, I set out how to show how one can reduce a\u00a01H NMR spectrum to the structure [A] below. I speculated how a further test could be applied to this structure; back predicting its spectrum using just quantum mechanics. Overkill I know, but how well might the two match? The process must […]<\/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":[],"tags":[993,17,994,373],"ppma_author":[2661],"class_list":["post-9320","post","type-post","status-publish","format-standard","hentry","tag-1h-nmr","tag-conformational-analysis","tag-spin-spin-coupling","tag-tutorial-material"],"yoast_head":"\nSecrets of a university tutor: conformational analysis and NMR spectroscopy. - 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=9320\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Secrets of a university tutor: conformational analysis and NMR spectroscopy. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"In a previous post, I set out how to show how one can reduce a\u00a01H NMR spectrum to the structure [A] below. 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I speculated how a further test could be applied to this structure; back predicting its spectrum using just quantum mechanics. Overkill I know, but how well might the two match? The process must […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9320","og_site_name":"Henry Rzepa's Blog","article_published_time":"2013-02-03T14:10:24+00:00","article_modified_time":"2013-02-12T06:46:31+00:00","og_image":[{"url":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/02\/4nmr.svg","type":"","width":"","height":""}],"author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"3 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9320#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9320"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Secrets of a university tutor: conformational analysis and NMR spectroscopy.","datePublished":"2013-02-03T14:10:24+00:00","dateModified":"2013-02-12T06:46:31+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9320"},"wordCount":648,"commentCount":0,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9320#primaryimage"},"thumbnailUrl":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/02\/4nmr.svg","keywords":["1H NMR","conformational analysis","spin-spin coupling","Tutorial material"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9320#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9320","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=9320","name":"Secrets of a university tutor: conformational analysis and NMR spectroscopy. - 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It fits into the last lecture of a series on pericyclic mechanisms, and just before the first lecture on conformational analysis. This is how they join. The experiment it relates to may well be a\u2026","rel":"","context":"In \"conformational analysis\"","block_context":{"text":"conformational analysis","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=conformational-analysis"},"img":{"alt_text":"Click for 3D.","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/01\/14me.gif?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":17333,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=17333","url_meta":{"origin":9320,"position":1},"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 "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":18742,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18742","url_meta":{"origin":9320,"position":2},"title":"(another) WATOC 2017 report.","author":"Henry Rzepa","date":"August 29, 2017","format":false,"excerpt":"Another selection (based on my interests, I have to repeat) from WATOC 2017 in Munich. Odile Eisenstein gave a talk about predicted\u00a013C chemical shifts in transition metal (and often transient) complexes, with the focus on metallacyclobutanes. These calculations include full spin-orbit\/relativistic corrections, essential when the carbon is attached to an\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\/2017\/08\/276-1024x760.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":5796,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5796","url_meta":{"origin":9320,"position":3},"title":"Validating the chemical literature heritage. Eudesma-1,3-dien-6,13-olide.","author":"Henry Rzepa","date":"December 8, 2011","format":false,"excerpt":"Previously, I had noted that Corey\u00a0reported\u00a0in 1963\/65 the total synthesis of\u00a0the sesquiterpene dihydrocostunolide. Compound 16, known as\u00a0Eudesma-1,3-dien-6,13-olide was represented as shown below in black; the hydrogen shown in red was implicit in Corey's representation, as was its stereochemistry. As of this instant, this compound is just one of 64,688,893 molecules\u2026","rel":"","context":"In "Chemical IT"","block_context":{"text":"Chemical IT","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2"},"img":{"alt_text":"","src":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/12\/p34a1.svg","width":350,"height":200},"classes":[]},{"id":11331,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11331","url_meta":{"origin":9320,"position":4},"title":"A short non-bonding H…H interaction (continued)","author":"Henry Rzepa","date":"October 2, 2013","format":false,"excerpt":"This is a continuation of the discussion started on Steve Bachrach's blog about a molecule with a very short H...H interaction involving two Si-H groups with enforced proximity. It had been inferred from the X-ray structure that the H...H distance was in the region of 1.50\u00c5. It's that cis-butene all\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":"Si","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/10\/Si.jpeg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":4930,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4930","url_meta":{"origin":9320,"position":5},"title":"Molecular Matryoshka dolls","author":"Henry Rzepa","date":"September 20, 2011","format":false,"excerpt":"A Matryoshka doll is better known as a Russian nesting doll. They can have up to eight layers. Molecules can only emulate two layers, although see here for a good candidate for making a three-layered example (the inside layer is C60, which itself might\u00a0encapsulate\u00a0a small molecule. See also \u00a0DOI: 10.1021\/ja991747w).\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\/2011\/09\/rebek.jpg?resize=350%2C200","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\/9320","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=9320"}],"version-history":[{"count":30,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/9320\/revisions"}],"predecessor-version":[{"id":9509,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/9320\/revisions\/9509"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=9320"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=9320"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=9320"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=9320"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}