{"id":14070,"date":"2015-06-03T18:11:29","date_gmt":"2015-06-03T17:11:29","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=14070"},"modified":"2023-09-17T07:26:12","modified_gmt":"2023-09-17T06:26:12","slug":"natural-abundance-kinetic-isotope-effects-expt-vs-theory","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14070","title":{"rendered":"Natural abundance kinetic isotope effects: expt. vs theory."},"content":{"rendered":"
\n

My PhD thesis involved determining kinetic isotope effects (KIE) for aromatic electrophilic substitution reactions in an effort to learn more about the nature of the transition states involved.[1]<\/a><\/span> I learnt relatively little, mostly because a transition state geometry is defined by 3N-6 variables (N = number of atoms) and its force constants by even more and you get only one or two measured KIE per reaction; a rather under-defined problem in terms of data! So I decided to spend a PostDoc learning how to invert the problem by computing the anticipated isotope effects using quantum mechanics and then comparing the predictions with measured KIE.[2]<\/a><\/span> Although such computation allows access to ALL possible isotope effects, the problem is still under-defined because of the lack of measured KIE to compare the predictions with. In 1995 Dan Singleton and Allen Thomas reported an elegant strategy\u00a0to this very problem by proposing a remarkably simple method for obtaining KIE using natural isotopic abundances.[3]<\/a><\/span> It allows isotope effects to be measured for all<\/strong> the positions in one of the reactant molecules by running the reaction close to completion and then recovering unreacted reactant and measuring the changes in its isotope abundances using NMR. The method has since been widely applied[4]<\/a><\/span>,[5]<\/a><\/span> and improved.[6]<\/a><\/span> Here I explore how measured and calculated KIE can be reconciled.<\/p>\n

The original example uses the Diels-Alder cycloaddition as an example, with the 2-methylbutadiene component being subjected to the isotopic abundance. Although comparison with calculation on related systems was done at the time[7]<\/a><\/span> the computational methods in use then did not allow effects such as solvation to be included. I thought it might be worth re-investigating this specific reaction using more modern methodology (\u03c9B97XD\/Def2-TZVPP\/SCRF=xylenes), giving an opportunity for testing one key assumption made by Singleton and Allen, viz<\/em> the use of an internal isotope reference for a site where the KIE is assumed to be exactly 1.000 (the 2-methyl group in this instance). This assumption made me recollect my post on\u00a0how methyl groups might not be entirely passive<\/a>\u00a0by rotating (methyl “flags”) in the Diels-Alder reaction between cis<\/em>-butene and 1,4-dimethylbutadiene. I had concluded that post by remarking\u00a0that\u00a0Rotating methyl groups should be looked at more often as harbingers of interesting effects<\/em>, which in this context may mean that such rotations may\u00a0not be entirely isotope agnostic.<\/p>\n

\"DA\"<\/a><\/p>\n

To start, I note that the endo<\/em> (closed shell, i.e.<\/i> non-biradical; the wavefunction is STABLE to open shell solutions) transition state obtained for this reaction[8]<\/a><\/span>,[9]<\/a><\/span> has a computed dipole moment of 6.1D, just verging into the region where solvation starts to make an impact. Perhaps the most important conclusion drawn from Singleton and Allen’s original article[2]<\/a><\/span> was that the presence\u00a0of an apparently innocuous 2-methyl substituent is sufficient to render the reaction asynchronous, which means that one C-C bond forms faster than\u00a0the other. They drew this conclusion from observing that the\u00a0inverse deuterium isotope effect was larger at C1 than C4, the difference being well outside of their estimated errors. The calculations indicate that the two bonds have predicted lengths of 2.197 (to C1) and 2.294\u00c5 (to C4) at the transition state. This means that an asynchronicity as small as \u03940.1\u00c5 can be picked up in measured isotope effects!<\/p>\n

The calculated activation free energy is 19.2 kcal\/mol (0.044M), which is entirely reasonable for a reaction occurring slowly at room temperature. The barrier for the exo<\/i> isomer is 21.0 kcal\/mol, 1.8 kcal\/mol higher in free energy.\u2020<\/sup> The measured isotope effects are shown below with the predicted values in brackets. The colour code is green=within the estimated experimental error, red=outside the error.<\/p>\n

\"DA1\"<\/a><\/p>\n

The following observations can be made:<\/p>\n

    \n
  1. The internal isotope reference assumed as 1.000 is reasonable for carbon, but the “rotating methyl groups” resulting from hyper conjugation between the C-H groups and the \u03c0 system do have a small effect resulting in a predicted KIE of\u00a00.996 rather than the assumed 1.000. This will impact upon all the other measured values to some extent.<\/li>\n
  2. All the predicted\u2021<\/sup>\u00a013<\/sup>C isotope effects agree with experiment within the error estimated for the latter.\u00a0The calculation also has its errors, of which the most obvious is that harmonic frequencies are used rather than the more correct anharmonic values.<\/li>\n
  3. The 2<\/sup>H isotope effects show more deviation.\u00a0This might be a combination of the assumption that the internal\u00a0Me reference has no isotope effect coupled with the use of harmonic frequencies for the calculation.<\/li>\n
  4. Although the 2<\/sup>H values differ\u00a0somewhat beyond the experimental error, the\u00a0E\/Z effects are well reproduced by calculation.\u00a0The inverse isotope effect for the (Z) configuration is significantly larger in magnitude than for the (E) form, as was indeed noted by\u00a0Singleton and Thomas.<\/li>\n
  5. So too is the asymmetry induced by the methyl group. The inverse isotope effects are greater for the more completely formed bond (to\u00a0C1) than for the lagging bond (to C4).\u00a0They are indeed a very sensitive measure of reaction synchronicity.<\/li>\n<\/ol>\n

    The pretty good agreement between calculation and experiment provides considerable reassurance that the calculated properties of transition states can indeed be subjected to reality checks using experiment<\/i>. Indeed, it takes little more than a day to compute a complete set of KIEs, far less than it takes to measure them. One could easily argue that such a computation should accompany measured KIE whenever possible.<\/p>\n

    \n

    \u2021<\/sup>This gives me an opportunity to extol the virtues of effective RDM (research data management). The two DOIs for the data include files containing the full coordinates and force constant matrices for both reactant and TS. Using these, one can obtain frequencies for any isotopic substitution you might wish to make in <1 second each, and hence isotope effects not computed here. One option might be to e.g.<\/i> invert the reactant from the 2-methylbutadiene to the maleic anhydride and hence compute the isotope effects expected on this species (not reported in the original article) or to monitor instead the product.[10]<\/a><\/span><\/p>\n

    \n

    \u2020<\/sup>The KIE have only subtle small differences to the endo<\/i> isomer; too small to assign the stereochemistry with certainty.<\/p>\n

    \n

    Acknowledgments<\/h4>\n

    This post has been cross-posted in PDF format at Authorea<\/a>.<\/p>\n

    References<\/h2>\n
    1. B.C. Challis, and H.S. Rzepa, \"The mechanism of diazo-coupling to indoles and the effect of steric hindrance on the rate-limiting step\", Journal of the Chemical Society, Perkin Transactions 2<\/i>, pp. 1209, 1975. https:\/\/doi.org\/10.1039\/p29750001209<\/a>\n\n<\/li>\n
    2. M.J.S. Dewar, S. Olivella, and H.S. Rzepa, \"Ground states of molecules. 49. MINDO\/3 study of the retro-Diels-Alder reaction of cyclohexene\", Journal of the American Chemical Society<\/i>, vol. 100, pp. 5650-5659, 1978. https:\/\/doi.org\/10.1021\/ja00486a013<\/a>\n\n<\/li>\n
    3. D.A. Singleton, and A.A. Thomas, \"High-Precision Simultaneous Determination of Multiple Small Kinetic Isotope Effects at Natural Abundance\", Journal of the American Chemical Society<\/i>, vol. 117, pp. 9357-9358, 1995. https:\/\/doi.org\/10.1021\/ja00141a030<\/a>\n\n<\/li>\n
    4. Y. Wu, R.P. Singh, and L. Deng, \"Asymmetric Olefin Isomerization of Butenolides via Proton Transfer Catalysis by an Organic Molecule\", Journal of the American Chemical Society<\/i>, vol. 133, pp. 12458-12461, 2011. https:\/\/doi.org\/10.1021\/ja205674x<\/a>\n\n<\/li>\n
    5. J. Chan, A.R. Lewis, M. Gilbert, M. Karwaski, and A.J. Bennet, \"A direct NMR method for the measurement of competitive kinetic isotope effects\", Nature Chemical Biology<\/i>, vol. 6, pp. 405-407, 2010. https:\/\/doi.org\/10.1038\/nchembio.352<\/a>\n\n<\/li>\n
    6. J.W. Storer, L. Raimondi, and K.N. Houk, \"Theoretical Secondary Kinetic Isotope Effects and the Interpretation of Transition State Geometries. 2. The Diels-Alder Reaction Transition State Geometry\", Journal of the American Chemical Society<\/i>, vol. 116, pp. 9675-9683, 1994. https:\/\/doi.org\/10.1021\/ja00100a037<\/a>\n\n<\/li>\n
    7. H.S. Rzepa, \"C 9 H 10 O 3\", 2015. https:\/\/doi.org\/10.14469\/ch\/191299<\/a>\n\n<\/li>\n
    8. H.S. Rzepa, \"C 9 H 10 O 3\", 2015. https:\/\/doi.org\/10.14469\/ch\/191301<\/a>\n\n<\/li>\n
    9. D.E. Frantz, D.A. Singleton, and J.P. Snyder, \"<sup>13<\/sup>C Kinetic Isotope Effects for the Addition of Lithium Dibutylcuprate to Cyclohexenone. Reductive Elimination Is Rate-Determining\", Journal of the American Chemical Society<\/i>, vol. 119, pp. 3383-3384, 1997. https:\/\/doi.org\/10.1021\/ja9636348<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      My PhD thesis involved determining kinetic isotope effects (KIE) for aromatic electrophilic substitution reactions in an effort to learn more about the nature of the transition states involved. I learnt relatively little, mostly because a transition state geometry is defined by 3N-6 variables (N = number of atoms) and its force constants by even more […]<\/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":[1086],"tags":[1458,1460,1395,1457,1459,1455,1454,1456,1453,1452,1442,1461],"ppma_author":[2661],"class_list":["post-14070","post","type-post","status-publish","format-standard","hentry","category-reaction-mechanism-2","tag-allen-thomas","tag-calculated-activation-free-energy","tag-chemistry","tag-dan-singleton","tag-deuterium","tag-diels-alder-reaction","tag-isotope","tag-isotopes","tag-kinetic-isotope-effect","tag-nuclear-physics","tag-physical-organic-chemistry","tag-shell-solutions"],"yoast_head":"\nNatural abundance kinetic isotope effects: expt. vs theory. - 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=14070\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Natural abundance kinetic isotope effects: expt. vs theory. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"My PhD thesis involved determining kinetic isotope effects (KIE) for aromatic electrophilic substitution reactions in an effort to learn more about the nature of the transition states involved. 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Computed kinetic isotope effects.","author":"Henry Rzepa","date":"January 11, 2013","format":false,"excerpt":"Kinetic isotope effects have become something of a lost art when it comes to exploring reaction mechanisms. But in their heyday they were absolutely critical for establishing the mechanism of the benzidine rearrangement. This classic mechanism proceeds via bisprotonation of diphenyl hydrazine, but what happens next was the crux. Does\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":15505,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15505","url_meta":{"origin":14070,"position":1},"title":"Kinetic isotope effect models as a function of ring substituent for indole-3-carboxylic acids and indolin-2-ones.","author":"Henry Rzepa","date":"January 20, 2016","format":false,"excerpt":"The original strategic objective of my PhD researches in 1972-74 was to explore how primary kinetic hydrogen isotope effects might be influenced by the underlying structures of the transition states involved. Earlier posts dealt with how\u00a0one can\u00a0construct quantum-chemical\u00a0models of these transition states that fit the known properties of the reactions.\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":14112,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14112","url_meta":{"origin":14070,"position":2},"title":"Natural abundance kinetic isotope effects: mechanism of the Baeyer-Villiger reaction.","author":"Henry Rzepa","date":"June 10, 2015","format":false,"excerpt":"I have blogged before about the mechanism of this classical oxidation reaction. Here I further explore computed models, and whether they match the observed kinetic isotope effects (KIE) obtained using the natural-abundance method described in the previous post. There is much previous study of this rearrangement, and the issue can\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":15295,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15295","url_meta":{"origin":14070,"position":3},"title":"I\u2019ve started so I\u2019ll finish. Mechanism and kinetic isotope effects for protiodecarboxylation of indoles.","author":"Henry Rzepa","date":"January 2, 2016","format":false,"excerpt":"Another mechanistic study we\u00a0started in\u00a01972 is\u00a0here 40+ years on\u00a0subjected to quantum mechanical scrutiny. The kinetics are again complex, the mechanism involving protonation\u2021 of the indole carboxylate (by a general acid), followed by the presumption of a zwitterionic Wheland intermediate that then loses carbon dioxide in a second step (blue arrows).\u2026","rel":"","context":"In "Historical"","block_context":{"text":"Historical","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=565"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":15395,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=15395","url_meta":{"origin":14070,"position":4},"title":"I\u2019ve started so I\u2019ll finish. Kinetic isotope effect models for a general acid as a catalyst in the protiodecarboxylation of indoles.","author":"Henry Rzepa","date":"January 10, 2016","format":false,"excerpt":"Earlier I explored models for the heteroaromatic electrophilic protiodecarboxylation of an 3-substituted indole, focusing on the role of water as the proton transfer and delivery agent. Next, came\u00a0models for both water and the general base catalysed\u00a0ionization of indolinones. Here I\u00a0explore\u00a0general acid\u00a0catalysis by evaluating the properties of two possible models for\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":14327,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14327","url_meta":{"origin":14070,"position":5},"title":"Reproducibility in science: calculated kinetic isotope effects for cyclopropyl carbinyl radical.","author":"Henry Rzepa","date":"July 11, 2015","format":false,"excerpt":"Previously on the kinetic isotope effects for the Baeyer-Villiger reaction, I was discussing whether a realistic computed model could be constructed for the mechanism. The measured KIE or kinetic isotope effects (along with the approximate rate of the reaction) were to be our\u00a0reality check. I had used \u0394\u0394G energy differences\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":[]}],"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\/14070","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=14070"}],"version-history":[{"count":30,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14070\/revisions"}],"predecessor-version":[{"id":26503,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14070\/revisions\/26503"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=14070"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=14070"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=14070"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=14070"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}