{"id":14601,"date":"2015-10-01T10:50:19","date_gmt":"2015-10-01T09:50:19","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=14601"},"modified":"2015-10-01T11:37:19","modified_gmt":"2015-10-01T10:37:19","slug":"yes-no-yes-computational-mechanistic-exploration-of-nickel-catalysed-cyclopropanation-using-tetramethylammonium-triflate","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=14601","title":{"rendered":"Yes, no, yes. Computational mechanistic exploration of (nickel-catalysed) cyclopropanation using tetramethylammonium triflate."},"content":{"rendered":"
\n

A fascinating re-examination has appeared[1]<\/a><\/span> of a reaction first published[2]<\/a><\/span> in 1960 by Wittig and then[3]<\/a><\/span> repudiated by him in 1964 since it could not be replicated by a later student. According to the new work, the secret to a successful replication seems to be the presence of traces of a nickel catalyst (originally coming from e.g.<\/em> a nickel spatula?). In this recent article[1]<\/a><\/span> a mechanism for the catalytic cycle is proposed. Here I thought I might explore this mechanism using calculations to see if any further insights might emerge.<\/p>\n

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

In the mechanism above (I have retained the original numbering shown in the article itself), Ln<\/sub> is set to 2PH3<\/sub> as an initial approximation and the solvent thf is approximated only by a continuum solvation field, with no explicit thf molecules involved at this stage. At this level and using \u03c9B97XD\/Def2-SVPD\/SCRF=thf free energies, one can explore the cycle quite quickly (~2-3 days). It is also interesting that this reaction unusually involved nine different elements (I wonder what the record is? Not much greater I suspect).<\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n
Species<\/th>\n\u0394\u0394G298<\/sub><\/th>\nDataDOI<\/th>\n<\/tr>\n
4+CH2<\/sub>NMe3<\/sub>+LiOTf + ethene<\/td>\n+23.9<\/td>\n[4]<\/a><\/span>,[5]<\/a><\/span><\/td>\n<\/tr>\n
5<\/td>\n0.0<\/td>\n[6]<\/a><\/span><\/td>\n<\/tr>\n
TS (5\u2192 9)<\/td>\n12.7<\/td>\n[7]<\/a><\/span>,[8]<\/a><\/span><\/td>\n<\/tr>\n
9 + LiOTf + NMe3<\/sub><\/td>\n0.2<\/td>\n[9]<\/a><\/span><\/td>\n<\/tr>\n
TS (9 + ethene \u2192 6)<\/td>\n7.2<\/td>\n[10]<\/a><\/span>,[11]<\/a><\/span><\/td>\n<\/tr>\n
6<\/td>\n4.8<\/td>\n[12]<\/a><\/span><\/td>\n<\/tr>\n
TS (6 \u2192 7)<\/td>\n11.2<\/td>\n[13]<\/a><\/span>,[14]<\/a><\/span><\/td>\n<\/tr>\n
7<\/td>\n-36.3<\/td>\n[15]<\/a><\/span><\/td>\n<\/tr>\n
TS (7 \u2192 4+8)<\/td>\n-18.8<\/td>\n[16]<\/a><\/span>,[17]<\/a><\/span><\/td>\n<\/tr>\n
4+8 + LiOTf + NMe3<\/sub><\/td>\n-29.7<\/td>\n[4]<\/a><\/span><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

The structure of the complex 5<\/strong> is more or less as shown in the article. The mean single bonded Ni-C length in the Cambridge structure database (CSD) is ~1.9\u00c5, and (formally at least) Ni=C lengths are shorter at ~1.80-1.85. There is one reasonable analogy to the sub-structure shown below[18]<\/a><\/span>,[19]<\/a><\/span> with a C-Ni length of 1.90, Ni-Li = 2.51 and Li-C = 2.40 which is reasonably similar to what is shown below. <\/p>\n

T<\/p>\n

\"Click

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

The elimination of NMe3<\/sub> reveals a reasonable thermal barrier, resulting in the formation of the nickel-carbene product and the complex between NMe3<\/sub> and LiOTf. <\/p>\n

\"5a\"<\/a>\"5-9\"<\/a><\/p>\n

The Ni-carbene then reacts with alkene (modelled here by ethene) to form a Ni-alkene \u03c0-complex, with a very low barrier to the exo-energic reaction.<\/p>\n

\"9-6a\"<\/a>\"9-6\"<\/a><\/p>\n

This complex then rearranges, again with a small barrier, to the metallocyclobutane, with considerable release of energy.<\/p>\n

\"6-7a\"<\/a>\"6-7\"<\/a><\/p>\n

Finally, the metallocyclobutane extrudes the nickel to form cyclopropane bound to the Ni(PH3<\/sub>)2<\/sub> as a pseudo-\u03c0\/agostic complex, with this step of the reaction being somewhat endo-energic (+6.6 kcal\/mol). As modelled, it produces a low-coordination Ni product 4<\/b>, which also causes the initial reactants to be relatively high in energy (+23.9 relative to 5<\/b>). This suggests that the entire cycle should optimally be repeated by including say two explicit thf solvent molecules, which could coordinate to 4<\/b>, thus lowering its energy relative to the rest of the cycle. <\/p>\n

\"7-4a\"<\/a>\"7-4\"<\/a><\/p>\n

Below is shown the NCI (non-covalent-interactions) surface for the Ni-cyclopropane complex, revealing the relatively high density between the Ni and the edge of the cyclopropane (high enough indeed to be considered on the verge of being covalent density). No examples of this motif are found in the CSD.<\/p>\n

\"Click

Click for 3D<\/p><\/div>
\nOverall, the reaction as shown shows entirely reasonable energetics and activation free energy barriers (with the caveat that inclusion of explicit solvent molecules might improve things, see above). We might conclude from this that the catalytic cycle as proposed is entirely reasonable. What we cannot comment on of course is the relative energetics of any of the competing side reaction shown in the original scheme,[1]<\/a><\/span> but it would be really easy to include them in a more complete analysis if needed. I wanted to show here that a simple reality check<\/i> on a proposed reaction mechanism can be quick to perform, and perhaps nowadays should be regarded as a sine qua non<\/i> of mechanistic speculation.<\/p>\n

References<\/h2>\n
  1. S.A. K\u00fcnzi, J.M. Sarria\u2005Toro, T. den\u2005Hartog, and P. Chen, \"Nickel\u2010Catalyzed Cyclopropanation with NMe<sub>4<\/sub>OTf and <i>n<\/i>BuLi\", Angewandte Chemie International Edition<\/i>, vol. 54, pp. 10670-10674, 2015. https:\/\/doi.org\/10.1002\/anie.201505482<\/a>\n\n<\/li>\n
  2. V. Franzen, and G. Wittig, \"Trimethylammonium\u2010methylid als Methylen\u2010Donator\", Angewandte Chemie<\/i>, vol. 72, pp. 417-417, 1960. https:\/\/doi.org\/10.1002\/ange.19600721210<\/a>\n\n<\/li>\n
  3. G. Wittig, and D. Krauss, \"Cyclopropanierungen bei Einwirkung von <i>N<\/i>\u2010Yliden auf Olefine\", Justus Liebigs Annalen der Chemie<\/i>, vol. 679, pp. 34-41, 1964. https:\/\/doi.org\/10.1002\/jlac.19646790106<\/a>\n\n<\/li>\n
  4. H.S. Rzepa, \"C 4 H 9 F 3 Li 1 N 1 O 3 S 1\", 2015. https:\/\/doi.org\/10.14469\/ch\/191545<\/a>\n\n<\/li>\n
  5. H.S. Rzepa, \"C 5 H 11 F 3 Li 1 N 1 O 3 S 1\", 2015. https:\/\/doi.org\/10.14469\/ch\/191553<\/a>\n\n<\/li>\n
  6. H.S. Rzepa, and H.S. Rzepa, \"C 5 H 17 F 3 Li 1 N 1 Ni 1 O 3 P 2 S 1\", 2015. https:\/\/doi.org\/10.14469\/ch\/191554<\/a>\n\n<\/li>\n
  7. H.S. Rzepa, \"C 5 H 17 F 3 Li 1 N 1 Ni 1 O 3 P 2 S 1\", 2015. https:\/\/doi.org\/10.14469\/ch\/191536<\/a>\n\n<\/li>\n
  8. H.S. Rzepa, \"C5H17F3LiNNiO3P2S\", 2015. https:\/\/doi.org\/10.14469\/ch\/191550<\/a>\n\n<\/li>\n
  9. H.S. Rzepa, and H.S. Rzepa, \"C 5 H 17 F 3 Li 1 N 1 Ni 1 O 3 P 2 S 1\", 2015. https:\/\/doi.org\/10.14469\/ch\/191555<\/a>\n\n<\/li>\n
  10. H.S. Rzepa, \"C 3 H 12 Ni 1 P 2\", 2015. https:\/\/doi.org\/10.14469\/ch\/191547<\/a>\n\n<\/li>\n
  11. H.S. Rzepa, \"C3H12NiP2\", 2015. https:\/\/doi.org\/10.14469\/ch\/191546<\/a>\n\n<\/li>\n
  12. H.S. Rzepa, \"C 3 H 12 Ni 1 P 2\", 2015. https:\/\/doi.org\/10.14469\/ch\/191541<\/a>\n\n<\/li>\n
  13. H.S. Rzepa, \"C 3 H 12 Ni 1 P 2\", 2015. https:\/\/doi.org\/10.14469\/ch\/191540<\/a>\n\n<\/li>\n
  14. H.S. Rzepa, \"C3H12NiP2\", 2015. https:\/\/doi.org\/10.14469\/ch\/191548<\/a>\n\n<\/li>\n
  15. H.S. Rzepa, \"C 3 H 12 Ni 1 P 2\", 2015. https:\/\/doi.org\/10.14469\/ch\/191542<\/a>\n\n<\/li>\n
  16. H.S. Rzepa, \"C 3 H 12 Ni 1 P 2\", 2015. https:\/\/doi.org\/10.14469\/ch\/191537<\/a>\n\n<\/li>\n
  17. H.S. Rzepa, \"C3H12NiP2\", 2015. https:\/\/doi.org\/10.14469\/ch\/191538<\/a>\n\n<\/li>\n
  18. Buchalski, P.., Grabowska, I.., Kaminska, E.., and Suwinska, K.., \"CCDC 650794: Experimental Crystal Structure Determination\", 2008. https:\/\/doi.org\/10.5517\/ccpv6c2<\/a>\n\n<\/li>\n
  19. P. Buchalski, I. Grabowska, E. Kami\u0144ska, and K. Suwi\u0144ska, \"Synthesis and Structures of 9-Nickelafluorenyllithium Complexes\", Organometallics<\/i>, vol. 27, pp. 2346-2349, 2008. https:\/\/doi.org\/10.1021\/om701275u<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    A fascinating re-examination has appeared of a reaction first published in 1960 by Wittig and then repudiated by him in 1964 since it could not be replicated by a later student. According to the new work, the secret to a successful replication seems to be the presence of traces of a nickel catalyst (originally coming from e.g. […]<\/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":[4,1086],"tags":[1582,144,24,1583,1581],"ppma_author":[2661],"class_list":["post-14601","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","category-reaction-mechanism-2","tag-activation-free-energy-barriers","tag-cambridge","tag-energy","tag-energy-relative","tag-nickel-carbene-product"],"yoast_head":"\nYes, no, yes. 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Here the key intermediate proposed is a thiirenium cation (labelled 8 in the article) and labelled\u00a0Int3 below. The model chosen is the same\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":12115,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=12115","url_meta":{"origin":14601,"position":1},"title":"Aromatic electrophilic substitution. A different light on the bromination of benzene.","author":"Henry Rzepa","date":"March 12, 2014","format":false,"excerpt":"My previous post related to the aromatic electrophilic substitution of benzene using as electrophile phenyl diazonium chloride. Another prototypical reaction, and again one where benzene is too inactive for the reaction to occur easily, is the catalyst-free bromination of benzene to give bromobenzene and HBr.\u00a0 The \"text-book\" mechanism involves nucleophilic\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":"br2+benzene","src":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2014\/03\/br2+benzene.svg","width":350,"height":200},"classes":[]},{"id":24380,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=24380","url_meta":{"origin":14601,"position":2},"title":"More examples of crystal structures containing embedded linear chains of iodines.","author":"Henry Rzepa","date":"October 17, 2021","format":false,"excerpt":"The previous post described the fascinating 170-year history of a crystalline compound known as Herapathite and its connection to the mechanism of the Finkelstein reaction via the complex of Na+I2- (or Na22+I42-). Both compounds exhibit (approximately) linear chains of iodine atoms in their crystal structures, a connection which was discovered\u2026","rel":"","context":"In "Chiroptics"","block_context":{"text":"Chiroptics","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2644"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2021\/10\/Screenshot-925-1024x248.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":19180,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19180","url_meta":{"origin":14601,"position":3},"title":"FAIR data \u21cc Raw data.","author":"Henry Rzepa","date":"December 7, 2017","format":false,"excerpt":"FAIR data is increasingly accepted as a description of what research data should aspire to; Findable, Accessible, Inter-operable and Re-usable, with Context added by rich metadata (and also that it should be Open). But there are two sides to data, one of which is the raw data emerging from say\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":"","width":0,"height":0},"classes":[]},{"id":19499,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19499","url_meta":{"origin":14601,"position":4},"title":"Never mind main group “hypervalency”, what about transition metal “hypervalency”?","author":"Henry Rzepa","date":"March 18, 2018","format":false,"excerpt":"I have posted often on the chemical phenomenon known as hypervalency, being careful to state that as defined it applies just to \"octet excess\" in main group elements. But what about the next valence shell, occurring in transition metals and known as the \"18-electron rule\"? You rarely hear the term\u2026","rel":"","context":"In "Hypervalency"","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2018\/03\/NiPP-987x1024.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":10145,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10145","url_meta":{"origin":14601,"position":5},"title":"Feist’s acid. Stereochemistry galore.","author":"Henry Rzepa","date":"April 4, 2013","format":false,"excerpt":"Back in the days (1893) when few compounds were known, new ones could end up being named after the discoverer. Thus Feist is known for the compound bearing his name; the 2,3 carboxylic acid of methylenecyclopropane (1, with Me replaced by CO2H). Compound 1 itself nowadays is used to calibrate\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":"methylene-cyclopropane","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/04\/methylene-cyclopropane.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\/14601","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=14601"}],"version-history":[{"count":53,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14601\/revisions"}],"predecessor-version":[{"id":14669,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/14601\/revisions\/14669"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=14601"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=14601"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=14601"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=14601"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}