{"id":14327,"date":"2015-07-11T08:06:04","date_gmt":"2015-07-11T07:06:04","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=14327"},"modified":"2015-07-12T08:07:24","modified_gmt":"2015-07-12T07:07:24","slug":"reproducibility-in-science-calculated-kinetic-isotope-effects-for-cyclopropyl-carbonyl-radical","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14327","title":{"rendered":"Reproducibility in science: calculated kinetic isotope effects for cyclopropyl carbinyl radical."},"content":{"rendered":"
\n

Previously<\/a> 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 and then HRR (harmonic rate ratios) to compute[1]<\/a><\/span> the KIE, and Dan Singleton asked <\/a>if I had included heavy atom tunnelling corrections in the calculation, which I had not. His group has shown these are not negligible for low-barrier reactions such as ring opening of cyclopropyl carbinyl\u00a0radical.[2]<\/a><\/span> As a prelude to configuring his suggested programs for computing tunnelling (GAUSSRATE and POLYRATE<\/a>), it was important I learnt how to reproduce his\u00a0KIE values.[2]<\/a><\/span> Hence the title of this post. Now, read on.<\/p>\n

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

I felt I could contribute to the cause by extending the published results in two respects:<\/p>\n

    \n
  1. The reported[2]<\/a><\/span> calculations are for the model B3LYP\/6-31G(d) but\u00a0the article does not report the tolerance to e.g.<\/em> basis set variation (6-31G(d), a modest basis set by 2015 standards),<\/li>\n
  2. or to the quantum model used (B3LYP, a veritable DFT method).<\/li>\n<\/ol>\n

    These two model chemistries can both be tested by “increasing” their accuracy. The Def2-QZVPP basis set is nearing the CBS, or complete basis set limit. The coupled-cluster CCSD(T) method is regarded as the gold standard for single reference calculations. The CASSCF method tests the response to a multi-reference wave function. Each is applied separately to ensure only one variable is being changed at a time.<\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n
    Method<\/th>\nExpt. KIE[2]<\/a><\/span>\u2021<\/sup><\/th>\nPred. KIE (my result)<\/th>\nPred. \u0394G298<\/sub>\u2021<\/sup><\/th>\nPred. KIE[2]<\/a><\/span><\/th>\nKIE + Tunnelling correction[2]<\/a><\/span><\/th>\n<\/tr>\n
    B3LYP\/6-31G(d)[3]<\/a><\/span>,[4]<\/a><\/span><\/strong><\/span><\/td>\n1.079295<\/sub><\/strong><\/span><\/td>\n1.0582<\/strong><\/span><\/td>\n8.0<\/b><\/span><\/td>\n1.058<\/strong><\/span><\/td>\n1.073<\/strong><\/span><\/td>\n<\/tr>\n
    1.163173<\/sub><\/strong><\/span><\/td>\n1.1067<\/strong><\/span><\/td>\n1.106<\/strong><\/span><\/td>\n1.169<\/strong><\/span><\/td>\n<\/tr>\n
    B3LYP\/Def2-QZVPP[5]<\/a><\/span>,[6]<\/a><\/span><\/span><\/strong><\/td>\n1.079295<\/sub><\/span><\/strong><\/td>\n1.0563<\/span><\/strong><\/td>\n6.6<\/b><\/span><\/td>\n1.058<\/span><\/strong><\/td>\n1.073<\/span><\/strong><\/td>\n<\/tr>\n
    1.163173<\/sub><\/span><\/strong><\/td>\n1.1031<\/span><\/strong><\/td>\n1.106<\/span><\/strong><\/td>\n1.169<\/span><\/strong><\/td>\n<\/tr>\n
    CASSCF(5,5)\/6-31G(d)[7]<\/a><\/span>,[8]<\/a><\/span><\/span><\/strong><\/td>\n1.079295<\/sub><\/span><\/strong><\/td>\n1.0572<\/span><\/strong><\/td>\n8.2<\/b><\/span><\/td>\n1.058<\/span><\/strong><\/td>\n1.073<\/span><\/strong><\/td>\n<\/tr>\n
    1.163173<\/sub><\/span><\/strong><\/td>\n1.1050<\/span><\/strong><\/td>\n1.106<\/span><\/strong><\/td>\n1.169<\/span><\/strong><\/td>\n<\/tr>\n
    CASSCF(5,5)\/Def2-TZVPP[9]<\/a><\/span>,[10]<\/a><\/span><\/strong><\/span><\/td>\n1.079295<\/sub><\/strong><\/span><\/td>\n1.0561<\/strong><\/span><\/td>\n7.9<\/b><\/span><\/td>\n1.058<\/strong><\/span><\/td>\n1.073<\/strong><\/span><\/td>\n<\/tr>\n
    1.163173<\/sub><\/strong><\/span><\/td>\n1.1028<\/strong><\/span><\/td>\n1.106<\/strong><\/span><\/td>\n1.169<\/strong><\/span><\/td>\n<\/tr>\n
    CCSD(T)\/6-31G(d)[11]<\/a><\/span>,[12]<\/a><\/span><\/span><\/strong><\/td>\n1.079295<\/sub><\/span><\/strong><\/td>\n1.0597\u2020<\/sup><\/span><\/strong><\/td>\n9.7<\/b><\/span><\/td>\n1.058<\/span><\/strong><\/td>\n1.073<\/span><\/strong><\/td>\n<\/tr>\n
    1.163173<\/sub><\/span><\/strong><\/td>\n1.1099<\/span><\/strong><\/td>\n1.106<\/span><\/strong><\/td>\n1.169<\/span><\/strong><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

    \u2020Actually separate\u00a0ratios of\u00a013<\/sup>C\/12<\/sup>C(C-4)\/13<\/sup>C\/12<\/sup>C(C-3) since C-3 and C-4 are not equivalent in the reactant species because of the methylene group pyramidalisation. The KIE calculation input and outputs are archived.[13]<\/a><\/span><\/small><\/p>\n

    The first two rows of table<\/span> are my attempt at an\u00a0exact replication of the literature. The start point of such a project would be the supporting information or SI[2]<\/a><\/span> which contains coordinates for the program GAUSSRATE and defines key structures in the form of a double-column, page thrown (broken<\/a> might be a better word)\u00a0PDF file. It was going to be a bit of a struggle<\/a> to reconstitute this format\u00a0into the structure\u00a0required for a Gaussian calculation, so I simply constructed the models\u00a0from scratch\u00a0and optimised to\u00a0the ring-opening\u00a0transition state[4]<\/a><\/span> and reactant.[3]<\/a><\/span> I used a more recent version of the Gaussian program (G09\/D.01 rather than G03\/D.02) to do this, and tightened up some of the criteria\u00a0to modern\u00a0cutoff standards. A\u00a0continuum solvent model\u00a0could have been specified\u00a0\u00a0(the solvent used in the experiments was 1,2-dichlorobenzene) but since no mention was made of solvent, I assumed a gas phase calculation had originally been done.\u00a0\u00a0The starting geometry of the reactant deliberately had no symmetry, but during optimisation it converged to having a plane of symmetry using the\u00a0B3LYP\/6-31G(d) level of theory (the SI does not note this symmetry, it is implicit).\u00a0I then used\u00a0my code[1]<\/a><\/span> to compute the isotope effects. The KIE program used in the original literature calculation was not directly mentioned in the supporting information but is presumed to be Quiver. Dan Singleton has recently sent me these codes, but they still need to be compiled and tested at my end. I ended up with splendid agreement for the KIE as you can see above (top two lines). Its reproducible! Hence the\u00a0various assumptions I made in achieving this\u00a0appear justified.<\/p>\n

    Returning to\u00a0the geometry of the cyclopropyl carbinyl radical as having a plane of symmetry,\u00a0two of the other methods, CCSD(T)\/6-31G(d) and CASSCF(5,5)\/6-31G(d), as well as CASSCF(5,5) at the better Def2-TZVPP basis all predicted that the methylene radical is twisted by about\u00a020\u00b0 with respect to the Cs plane of the ring.<\/p>\n

    \"cp-asymm\"<\/a><\/p>\n

    It is useful to check whether\u00a0this twisting\u00a0has any impact on the predicted KIE. The answer is clear (Table). ALL the methods predict similar\u00a0KIE to \u00b1 0.003,\u2020<\/sup> which is as about as accurate as can be measured experimentally at the\u00a01\u03c3 level of confidence<\/a>. This is a remarkable result; few other computed molecular\u00a0properties turn out to be so insensitive to the quantum procedure used. The next stage will be to check if the tunnelling corrections required to bring the calculation into congruence with the measured values are similarly insensitive.<\/p>\n

    \n

    \u2021<\/sup> The “barrier height” is quoted as 7 kcal\/mol[2]<\/a><\/span>. This is probably NOT the activation free energy.<\/p>\n

    References<\/h2>\n
    1. H.S. Rzepa, \"KINISOT. A basic program to calculate kinetic isotope effects using normal coordinate analysis of transition state and reactants.\", 2015. https:\/\/doi.org\/10.5281\/zenodo.19272<\/a>\n\n<\/li>\n
    2. O.M. Gonzalez-James, X. Zhang, A. Datta, D.A. Hrovat, W.T. Borden, and D.A. Singleton, \"Experimental Evidence for Heavy-Atom Tunneling in the Ring-Opening of Cyclopropylcarbinyl Radical from Intramolecular <sup>12<\/sup>C\/<sup>13<\/sup>C Kinetic Isotope Effects\", Journal of the American Chemical Society<\/i>, vol. 132, pp. 12548-12549, 2010. https:\/\/doi.org\/10.1021\/ja1055593<\/a>\n\n<\/li>\n
    3. H.S. Rzepa, \"C4H7(2)\", 2015. https:\/\/doi.org\/10.14469\/ch\/191357<\/a>\n\n<\/li>\n
    4. H.S. Rzepa, \"C4H7(2)\", 2015. https:\/\/doi.org\/10.14469\/ch\/191358<\/a>\n\n<\/li>\n
    5. H.S. Rzepa, \"C 4 H 7\", 2015. https:\/\/doi.org\/10.14469\/ch\/191353<\/a>\n\n<\/li>\n
    6. H.S. Rzepa, \"C 4 H 7\", 2015. https:\/\/doi.org\/10.14469\/ch\/191352<\/a>\n\n<\/li>\n
    7. H.S. Rzepa, \"C 4 H 7\", 2015. https:\/\/doi.org\/10.14469\/ch\/191361<\/a>\n\n<\/li>\n
    8. H.S. Rzepa, \"C 4 H 7\", 2015. https:\/\/doi.org\/10.14469\/ch\/191364<\/a>\n\n<\/li>\n
    9. H.S. Rzepa, \"C 4 H 7\", 2015. https:\/\/doi.org\/10.14469\/ch\/191363<\/a>\n\n<\/li>\n
    10. H.S. Rzepa, \"C 4 H 7\", 2015. https:\/\/doi.org\/10.14469\/ch\/191362<\/a>\n\n<\/li>\n
    11. H.S. Rzepa, \"C 4 H 7\", 2015. https:\/\/doi.org\/10.14469\/ch\/191367<\/a>\n\n<\/li>\n
    12. H.S. Rzepa, \"C 4 H 7\", 2015. https:\/\/doi.org\/10.14469\/ch\/191356<\/a>\n\n<\/li>\n
    13. H.S. Rzepa, \"Reproducibility In Science: Calculated Kinetic Isotope Effects For Cyclopropyl Carbonyl Radical.\", 2015. https:\/\/doi.org\/10.5281\/zenodo.19949<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      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 and then HRR (harmonic rate […]<\/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":[352,1523,1457,239,283,1453,327,1442],"ppma_author":[2661],"class_list":["post-14327","post","type-post","status-publish","format-standard","hentry","category-reaction-mechanism-2","tag-activation-free-energy","tag-basis-set","tag-dan-singleton","tag-energy-differences","tag-gas-phase-calculation","tag-kinetic-isotope-effect","tag-pdf","tag-physical-organic-chemistry"],"yoast_head":"\nReproducibility in science: calculated kinetic isotope effects for cyclopropyl carbinyl radical. - 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=14327\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Reproducibility in science: calculated kinetic isotope effects for cyclopropyl carbinyl radical. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"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. 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The measured KIE or kinetic isotope effects (along with the approximate rate of the reaction) were to be our\u00a0reality check. 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