{"id":22304,"date":"2020-05-08T09:19:52","date_gmt":"2020-05-08T08:19:52","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=22304"},"modified":"2020-05-10T07:30:59","modified_gmt":"2020-05-10T06:30:59","slug":"choreographing-a-chemical-ballet-what-happens-if-you-change-one-of-the-actors","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=22304","title":{"rendered":"Choreographing a chemical ballet: what happens if you change one of the actors?"},"content":{"rendered":"
\n

Earlier, I explored the choreography<\/a> or “timing”, of what might be described as the curly arrows for a typical taught reaction mechanism, the 1,4-addition of a nucleophile to an unsaturated carbonyl compound (scheme 1). I am now going to explore the consequences of changing one of the actors by adding the nucleophile to an unsaturated imine rather than carbonyl compound (scheme 2).\u00a0<\/p>\n

\"\"<\/a>

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 Scheme 1<\/strong><\/p><\/div>

\"\"<\/a>

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 Scheme 2<\/strong><\/p><\/div><\/p>\n

For the reaction shown in Scheme 1, the maximum energy point along the reaction path involves the formation of an S-C bond (arrow 2<\/strong> in scheme 1) rather than transfer of a proton. Scheme 2 has a new actor in which NH replaces O and which is a better base (i.e.<\/em> has a greater affinity for a proton). The mechanism again starts with arrows 1<\/strong> and 2<\/strong> launching proceedings. If you watch the animation below very carefully, you will notice that arrows 3<\/strong> and 4<\/strong> lag behind them. This means that you have to have the blue arrows\u00a01<\/strong> and\u00a04<\/strong> as distinctly separate arrows. An alternative depiction (and in truth very probably the depiction you would find in pretty much all text books and lecture notes) would be to combine arrows 1<\/strong> and 4<\/strong> into the single red arrow 8<\/strong>. If you do this however, you loose this subtle nuance to the mechanism.<\/p>\n

\"\"

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 Animated\u00a0Reaction coordinate for TS1 (scheme 2)<\/strong> Click to load 3D model<\/p><\/div>

\"\"<\/a>

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0Energy along reaction coordinate for TS1 (Scheme 2)<\/strong><\/p><\/div><\/p>\n

The product of this first step is a zwitterionic (internal ion-pair) compound. This then goes on to form the S-C bond (arrows 5<\/strong>–7<\/strong>) via TS2<\/strong>, with the energy of this second transition state being lower than than TS1<\/strong>.<\/p>\n

\"\"<\/a>

\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 Animated reaction coordinate for TS2 (Scheme 2)<\/strong><\/p><\/div>\n

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

The free energy barrier for this second step is low (\u0394G\u2020<\/sup> 0.6 kcal\/mol) because it is an ion-pair reacting to form a neutral molecule, always a facile process. Because the slowest step in this reaction (TS1<\/strong>) involves a proton transfer, this should now show a primary deuterium kinetic isotope effect. Indeed this is calculated to have the value 4.0 <\/strong>at 298K.\u00a0There is a prediction for an experiment to undertake!<\/p>\n\n\n\n\n\n\n\n\n
Species
\n(FAIR Data: dt5d<\/a>)<\/th>\n		\n

Relative energy<\/p>\n

kcal\/mol<\/p>\n<\/th>\n<\/tr>\n

Reactant<\/td>\n0.0<\/td>\n<\/tr>\n
TS1<\/td>\n7.7<\/td>\n<\/tr>\n
Zwitterion<\/td>\n2.2<\/td>\n<\/tr>\n
TS2<\/td>\n2.8<\/td>\n<\/tr>\n
Product<\/td>\n-12.5<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

To sumarise<\/p>\n

    \n
  1. Changing a C=O group to a C=NH group changes the nature of the mechanism from concerted asynchrous to stepwise.<\/li>\n
  2. As a result of this change, the highest energy step now involves asynchronous proton transfers rather than S-C bond formation.<\/li>\n
  3. The curly arrows can be used to reflect these steps, with two (blue) arrows being preferred to a single (red) one.<\/li>\n<\/ol>\n

    So by expanding the conventional number of curly arrows used to include extra ones capturing asynchronicity in the reaction, one can indeed add further information to the curly arrow formalism.<\/p>\n

    \n

    This post has DOI: dt6v<\/a><\/p>\n

    \n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    Earlier, I explored the choreography or “timing”, of what might be described as the curly arrows for a typical taught reaction mechanism, the 1,4-addition of a nucleophile to an unsaturated carbonyl compound (scheme 1). I am now going to explore the consequences of changing one of the actors by adding the nucleophile to an unsaturated […]<\/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":[2327,1086],"tags":[],"ppma_author":[2661],"class_list":["post-22304","post","type-post","status-publish","format-standard","hentry","category-curl-arrows","category-reaction-mechanism-2"],"yoast_head":"\nChoreographing a chemical ballet: what happens if you change one of the actors? - 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=22304\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Choreographing a chemical ballet: what happens if you change one of the actors? - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"Earlier, I explored the choreography or “timing”, of what might be described as the curly arrows for a typical taught reaction mechanism, the 1,4-addition of a nucleophile to an unsaturated carbonyl compound (scheme 1). 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The arrows in red can be described as firstly addition to the carbonyl group to\u2026","rel":"","context":"In \"Interesting chemistry\"","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=interesting-chemistry"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":8216,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8216","url_meta":{"origin":22304,"position":2},"title":"Secrets revealed for conjugate addition to cyclohexenone using a Cu-alkyl reagent.","author":"Henry Rzepa","date":"November 4, 2012","format":false,"excerpt":"The text books say that cyclohexenone A will react with a Grignard reagent by delivery of an alkyl (anion) to the carbon of the carbonyl (1,2-addition) but if dimethyl lithium cuprate is used, a conjugate 1,4-addition proceeds, to give the product B shown below. The standard explanation is that the\u2026","rel":"","context":"In \"metal\"","block_context":{"text":"metal","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=metal"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/11\/4.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":22153,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=22153","url_meta":{"origin":22304,"position":3},"title":"Choreographing a chemical ballet: a story of the mechanism of 1,4-Michael addition.","author":"Henry Rzepa","date":"April 13, 2020","format":false,"excerpt":"A reaction can be thought of as molecular dancers performing moves. A choreographer is needed to organise the performance into the ballet that is a reaction mechanism. Here I explore another facet of the Michael addition of a nucleophile to a conjugated carbonyl compound. The performers this time are p-toluene\u2026","rel":"","context":"In "crystal_structure_mining"","block_context":{"text":"crystal_structure_mining","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1745"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2020\/04\/SC.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":22011,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=22011","url_meta":{"origin":22304,"position":4},"title":"Substituent effects on the mechanism of Michael 1,4-Nucleophilic addition.","author":"Henry Rzepa","date":"March 29, 2020","format":false,"excerpt":"In the previous post, I looked at the mechanism for 1,4-nucleophilic addition to an activated alkene (the Michael reaction). The model nucleophile was malonaldehyde after deprotonation and the model electrophile was acrolein (prop-2-enal), with the rate determining transition state being carbon-carbon bond formation between the two, accompanied by proton transfer\u2026","rel":"","context":"In "Curly arrows"","block_context":{"text":"Curly arrows","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2327"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":8000,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8000","url_meta":{"origin":22304,"position":5},"title":"How is the bromination of alkenes best represented?","author":"Henry Rzepa","date":"October 14, 2012","format":false,"excerpt":"I occasionally delve into the past I try to understand how we got to our present understanding of chemistry. Thus curly arrow mechanistic notation can be traced back to around 1924, with style that bifurcated into two common types used nowadays (on which I have\u00a0commented\u00a0and about which further historical light\u2026","rel":"","context":"In "Curly arrows"","block_context":{"text":"Curly arrows","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=2327"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/10\/ion-pair-QTAIM.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\/22304","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=22304"}],"version-history":[{"count":44,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/22304\/revisions"}],"predecessor-version":[{"id":22359,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/22304\/revisions\/22359"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=22304"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=22304"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=22304"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=22304"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}