none 10.1039/D3DD00246B Royal Society of Chemistry (RSC) The Royal Society of Chemistry 292 161378000 457443 20240807143813 10.1039 2024-08-07T10:40:34Z 2024-06-05T02:01:18Z 12 10.1039/D3DD00246B/v1/decision1 10.26434/chemrxiv-2023-vcmcl 10.1039/D3DD00246B/v2/review2 10.1039/D3DD00246B/v2/response1 10.1039/D3DD00246B/v1/review3 10.1039/D3DD00246B/v1/review2 10.1039/D3DD00246B/v2/decision1 10.1039/D3DD00246B/v1/review1 10.1039/D3DD00246B/v2/review1 Digital Discovery Digital Discovery 2635-098X DDIIAI 08 07 2024 3 8 D. Christopher Braddock Department of Chemistry, Molecular Sciences Research Hub, White City Campus, Imperial College London, 82 Wood Lane, London W12 0BZ, UK http://orcid.org/0000-0002-4161-7256 Siwoo Lee Department of Chemistry, Molecular Sciences Research Hub, White City Campus, Imperial College London, 82 Wood Lane, London W12 0BZ, UK Henry S. Rzepa Department of Chemistry, Molecular Sciences Research Hub, White City Campus, Imperial College London, 82 Wood Lane, London W12 0BZ, UK http://orcid.org/0000-0002-8635-8390 Kinetic isotope effects (KIEs) computed using DFT theory for the intramolecular hydrogen transfer step of the Swern oxidation compare well with experiment if basis sets of triple- or quadruple-ζ rather than double-ζ quality are used. We investigate the model reported by Giagou and Meyer in 2010 for comparing deuterium kinetic isotope effects (KIEs) computed using density functional theory (DFT) for the intramolecular hydrogen transfer step in the mechanism of the Swern oxidation of alcohols to aldehydes, with those measured by experiment. Whereas the replication of the original computed values for the gas-phase reaction proved entirely successful, several issues were discovered when a continuum solvent model was used. These included uncertainty regarding the parameters and methods used for the calculations and also the coordinates for the original reactant and transition structures, via their provision as data in the ESI. The original conclusions, in which a numerical mis-match between the magnitude of the computed and experimentally measured KIE was attributed to significant deviations from transition structure theory, are here instead rationalised as a manifestation of basis-set effects in the computation. Transition state theory appears to be operating successfully. We now recommend the use of basis sets of triple- or quadruple-ζ quality, rather than the split-valence level previously employed, that dispersion energy corrections be included and that a continuum solvent model using smoothed reaction cavities is essential for effective geometry optimisation and hence accurate normal coordinate analysis. An outlying experimental KIE obtained for chloroform as solvent is attributed to a small level of an explicit hydrogen bonded interaction with the substrate. A temperature outlier for the measured KIE at 195 K is suggested for further experimental investigation, although it may also be an indication of an unusually abrupt incursion of hydrogen tunnelling which would need non-Born–Oppenheimer methods in which nuclear quantum effects are included to be more accurately modelled. We predict KIEs for new substituents, of which those for R = NMe 2 are significantly larger than those for R = H. This approach could be useful in designing variations of the Swern reagent that could lead to synthesis of aldehydes incorporating much higher levels of deuterium. The use of FAIR data rather than the traditional model of its inclusion in the ESI is discussed, and two data discovery tools exploiting these FAIR attributes are suggested. 2024 1496 1508 1 10.1039/rsc_crossmark_policy rsc.org true http://creativecommons.org/licenses/by/3.0/ 10.1039/D3DD00246B 20240807143813 https://xlink.rsc.org/?DOI=D3DD00246B http://pubs.rsc.org/en/content/articlepdf/2024/DD/D3DD00246B Chem. Commun. Braddock 58 2022 4981 10.1039/D2CC01136K RSC Adv. Okamura 11 2021 28530 10.1039/D1RA05405H Org. Lett. Kardile 21 2019 6452 10.1021/acs.orglett.9b02343 Org. Lett. Kulandai Raj 23 2021 1378 10.1021/acs.orglett.1c00038 Nat. Catal. Geng 2 2019 1071 10.1038/s41929-019-0370-z Coord. Chem. Rev. Guo 263 2022 214525 10.1016/j.ccr.2022.214525 Tetrahedron Omura 34 1978 1651 10.1016/0040-4020(78)80197-5 Synthesis Mancuso 1981 165 10.1055/s-1981-29377 J. Org. Chem. Giagou 75 2010 8088 10.1021/jo101636w ChemRxiv Braddock 2023 10.26434/chemrxiv-2023-vcmcl For a preprint, see, D. C.Braddock , S.Lee and H. S.Rzepa , SWERN Oxidation. transition structure Theory is OK , ChemRxiv , 2023 , preprint, 10.26434/chemrxiv-2023-vcmcl Gaussian 16, Revisions C.01 and C.02 Frisch 2016 M. J.Frisch , G. W.Trucks , H. B.Schlegel , G. E.Scuseria , M. A.Robb , J. R.Cheeseman , G.Scalmani , V.Barone , G. A.Petersson , H.Nakatsuji , X.Li , M.Caricato , A. V.Marenich , J.Bloino , B. G.Janesko , R.Gomperts , B.Mennucci , H. P.Hratchian , J. V.Ortiz , A. F.Izmaylov , J. L.Sonnenberg , D.Williams-Young , F.Ding , F.Lipparini , F.Egidi , J.Goings , B.Peng , A.Petrone , T.Henderson , D.Ranasinghe , V. G.Zakrzewski , J.Gao , N.Rega , G.Zheng , W.Liang , M.Hada , M.Ehara , K.Toyota , R.Fukuda , J.Hasegawa , M.Ishida , T.Nakajima , Y.Honda , O.Kitao , H.Nakai , T.Vreven , K.Throssell , J. A.Montgomery Jr , J. E.Peralta , F.Ogliaro , M. J.Bearpark , J. J.Heyd , E. N.Brothers , K. N.Kudin , V. N.Staroverov , T. A.Keith , R.Kobayashi , J.Normand , K.Raghavachari , A. P.Rendell , J. C.Burant , S. S.Iyengar , J.Tomasi , M.Cossi , J. M.Millam , M.Klene , C.Adamo , R.Cammi , J. W.Ochterski , R. L.Martin , K.Morokuma , O.Farkas , J. B.Foresman and D. J.Fox , Gaussian 16, Revisions C.01 and C.02 , Gaussian, Inc. , Wallingford CT , 2016 GaussView, Version 6.1 Dennington 2016 R.Dennington , T. A.Keith and J. M.Millam , GaussView, Version 6.1 , Semichem Inc. , Shawnee Mission, KS , 2016 Sci. Data Wilkinson 3 2016 160018 10.1038/sdata.2016.18 J. Cheminf. Harvey 9 2017 4 10.1186/s13321-017-0190-6 Isr. J. Chem. Rzepa 62 2022 e202100034 10.1002/ijch.202100034 Can. J. Chem. Rzepa 101 2023 725 10.1139/cjc-2022-0255 Chemistry with a Twist blog Rzepa 2022 10.59350/mzs83-g6218 H. S.Rzepa , Quantum chemistry interoperability (library): another step towards FAIR data , Chemistry with a Twist blog , 2022 , 10.59350/mzs83-g6218 J. Open Source Softw. Cave-Ayland 7 2022 3824 10.21105/joss.03824 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/13108 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/13108 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/12407 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/12407 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/13239 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/13239 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/12902 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/12902 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/13176 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/13176 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/13177 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/13177 J. Chem. Phys. Scalmani 2010 114110 10.1063/1.3359469 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/13186 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/13186 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/13188 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/13188 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/13223 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/13223 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/13242 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/13242 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/13225 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/13225 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/13246 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/13246 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/13084 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/13084 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/12396 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/12396 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/13090 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/13090 Chemistry with a twist blog Rzepa 2023 10.59350/vmtgs-0gw62 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/12404 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/12404 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/12379 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/12379 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/13337 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/13337 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/13355 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/13355 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/13337 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/13337 J. Chem. Phys. Bigeleisen 15 1947 261 10.1063/1.1746492 Kinisot Paton 2022 10.5281/zenodo.6831009 R.Paton , Kinisot , V2.0.1, Zenodo , 2022 , 10.5281/zenodo.6831009 KINISOT. A basic program to calculate kinetic isotope effects using normal coordinate analysis of transition structure and reactants Rzepa 2015 10.5281/zenodo.19272 H. S.Rzepa , KINISOT. A basic program to calculate kinetic isotope effects using normal coordinate analysis of transition structure and reactants , Zenodo , 2015 , 10.5281/zenodo.19272 J. Am. Chem. Soc. Brown 100 1978 7832 10.1021/ja00493a008 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/13256 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/13256 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/12902 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/12902 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/13189 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/13189 Phys. Chem. Chem. Phys. Weigend 7 2005 3297 10.1039/B508541A J. Comput. Chem. Grimme 32 2011 1456 10.1002/jcc.21759 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/13261 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/13261 Phys. Chem. Chem. Phys. Chai 10 2008 6615 10.1039/B810189B Phys. Chem. Chem. Phys. Schwabe 9 2007 3397 10.1039/B704725H Imperial College Research Data Repository Braddock 2023 10.14469/hpc/12928 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/12928 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/13370 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/13370 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/13276 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/13276 Philos. Trans. R. Soc., A Hammes-Schiffer 380 2022 20200377 10.1098/rsta.2020.0377 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/13327 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/13327 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/13326 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/13326 Imperial College Research Data Repository Braddock 2023 10.14469/hpc/13320 D. C.Braddock , H. S.Rzepa and S.Lee , Imperial College Research Data Repository , 2023 , 10.14469/hpc/13320 J. Am. Chem. Soc. Frenklach 146 2024 11823 10.1021/jacs.4c00608 https://www.crossref.org , accessed 15/11/2023 Patterns Cousijn 2 2020 100180 10.1016/j.patter.2020.100180 Chemistry with a Twist Blog Rzepa 2020 10.59350/7jq8v-z4p56 Further examples can be found at e.g. , H. S.Rzepa , Chemistry with a Twist Blog , 2020 , 10.59350/7jq8v-z4p56