{"id":5114,"date":"2011-10-16T16:59:44","date_gmt":"2011-10-16T15:59:44","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=5114"},"modified":"2023-09-16T18:13:10","modified_gmt":"2023-09-16T17:13:10","slug":"mechanism-of-the-reduction-of-a-carboxylic-acid-by-borane-revisited-and-revised","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5114","title":{"rendered":"Mechanism of the reduction of a carboxylic acid by borane: revisited and revised."},"content":{"rendered":"
\n

I asked a while back<\/a>\u00a0whether blogs could be considered a serious form of scholarly scientific communication (and so has Peter Murray-Rust <\/a>more recently). A case for doing so might be my post of about a year ago<\/a>, addressing why borane reduces a carboxylic acid, but not its ester, where I suggested a possible mechanism. Well, colleagues have raised some interesting questions, both on the blog itself<\/a>\u00a0and more silently by email to me. As a result, I have tried to address some of these questions, and accordingly my original scheme needs some revision! This sort of iterative process of getting to the truth with the help of the community (a kind of crowd-sourced chemistry) is where I feel blogs do have a genuine role to play.
\n

\"\"<\/a>

The reduction of a carboxylic acid by borane<\/p><\/div><\/p>\n

TS1<\/a><\/strong> in this scheme is modified from before to include an extra borane coordinating to the oxygen of the O-R group. I will include here the intrinsic reaction coordinate<\/a> [computed at \u03c9B97XD\/6-311G(d,p)], since it shows some fascinating features.<\/p>\n

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

One notes that the barrier for extrusion (R=H) is lower than before, due to the effect of the extra coordinated BH3<\/sub> group. But notice the “bump” at an IRC value of ~4.0. If one inspects the gradients along the IRC, they reveal that the ejecting H-H molecule is tempted to coordinate to the boron to form a 5-coordinate species (a “hidden intermediate”) before abruptly changing direction and flying off into space!<\/p>\n

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

You can see an animation by invoking this link<\/a>\u00a0 or below:<\/p>\n

\"acyloxy+bh3-irc\"<\/p>\n

What happens if R=Me<\/a> (an ester)? Well, the activation energy is now closer to 40 kcal\/mol, which means the rate of the reaction would be very slow. Notice the bump corresponding to 5-coordinate boron has now vanished!<\/p>\n

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

Again, a link<\/a> for IRC<\/a> animation of the reaction (it is rather nice, even if a say so myself).\u00a0QED? Well, not quite. One still has to show that TS2 – TS4 do not control things! The IRC <\/a>for TS2<\/a>\u00a0(the first addition of a hydrogen to the carbon) is shown below, again with fascinating bumps along the way.\u00a0The TS2\u00a0animation is here<\/a>.\u00a0The free energy of TS2 is 6.9 kcal\/mol\u00a0lower<\/strong>\u00a0than TS1 (even though the actual activation barrier is higher), which makes the latter the rate determining step. Note the bumps at \u00a0IRC = -8 and +5. These are due to rotations<\/a> setting up the reaction.<\/p>\n

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

TS3<\/a>,\u00a0a ring closing reaction (animation<\/a>) shows an unexpected feature <\/a>which I leave you to discover for yourself.\u00a0TS4<\/a>\u00a0is the second and final addition of a hydrogen to the carbon<\/a>, with\u00a0animation<\/a>\u00a0and\u00a0resembling an SN<\/sub>2 inversion. The reaction is completed by hydrolysis.<\/p>\n\n\n\n
\"\"<\/a><\/td>\n\"\"<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

The relative free energies of TS1<\/strong>, 2, 3 and 4 are respectively 0.0<\/strong>, -6.9<\/strong>, -35.0<\/strong> and -19.4<\/strong> kcal\/mol, which makes the overall rate limiting step TS1<\/strong>. If that is the case, then this explains why borane reduces only a carboxylic acid and not an ester.<\/p>\n

Now all I have to do is explain all of this to my tutorial group! Mind you, this is a deceptively complex mechanism, and who knows if it may yet spring surprises.<\/p>\n

Acknowledgments<\/h4>\n

This post has been cross-posted in PDF format at Authorea<\/a>.<\/p>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

I asked a while back\u00a0whether blogs could be considered a serious form of scholarly scientific communication (and so has Peter Murray-Rust more recently). A case for doing so might be my post of about a year ago, addressing why borane reduces a carboxylic acid, but not its ester, where I suggested a possible mechanism. Well, […]<\/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":false,"jetpack_social_options":{"image_generator_settings":{"template":"highway","default_image_id":0,"font":"","enabled":false},"version":2}},"categories":[4],"tags":[693,152,233,692,690,40,2650,31,843,691,373],"ppma_author":[2661],"class_list":["post-5114","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-activation-energy","tag-animation","tag-carboxylic-acid","tag-carboxylic-ester","tag-diborane","tag-free-energy","tag-pericyclic","tag-peter-murray-rust","tag-reaction-mechanism","tag-reduction","tag-tutorial-material"],"yoast_head":"\nMechanism of the reduction of a carboxylic acid by borane: revisited and revised. - 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=5114\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Mechanism of the reduction of a carboxylic acid by borane: revisited and revised. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"I asked a while back\u00a0whether blogs could be considered a serious form of scholarly scientific communication (and so has Peter Murray-Rust more recently). 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The rules are easily learnt (supposedly) and it can be used across a broad spectrum of mechanism. But, as one both becomes more experienced, and in time teaches the techniques oneself\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":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/12\/acyloxyborane1.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":25391,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25391","url_meta":{"origin":5114,"position":1},"title":"Unexpected Isomerization of Oxetane-Carboxylic Acids \u2013 catalyst design.","author":"Henry Rzepa","date":"August 13, 2022","format":false,"excerpt":"Previously, a mechanism with a reasonable predicted energy was modelled for the isomerisation of an oxetane carboxylic acid to a lactone by using two further molecules of acid to transfer the proton and in the process encouraging an Sn2 reaction with inversion to open the oxetane ring. We are now\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":25338,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25338","url_meta":{"origin":5114,"position":2},"title":"Unexpected Isomerization of Oxetane-Carboxylic Acids \u2013 a viable mechanism","author":"Henry Rzepa","date":"August 12, 2022","format":false,"excerpt":"In the previous post, I looked at the intramolecular rearrangement of the oxetane carboxylic acid to a lactone, finding the barrier to the Sn2 reaction with retention was unfeasibly high. Here I explore alternatives. This first attempt uses a second molecule of a carboxylic acid (modelled as formic acid for\u2026","rel":"","context":"Similar post","block_context":{"text":"Similar post","link":""},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/08\/Rtn.gif?resize=350%2C200&ssl=1","width":350,"height":200,"srcset":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/08\/Rtn.gif?resize=350%2C200&ssl=1 1x, https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/08\/Rtn.gif?resize=525%2C300&ssl=1 1.5x"},"classes":[]},{"id":19828,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19828","url_meta":{"origin":5114,"position":3},"title":"The “White City Trio” – The formation of an amide from an acid and an amine in non-polar solution (updated).","author":"Henry Rzepa","date":"August 8, 2018","format":false,"excerpt":"White City is a small area in west london created as an exhibition site in 1908, morphing over the years into an Olympic games venue, a greyhound track, the home nearby of the BBC (British Broadcasting Corporation) and most recently the new western campus for Imperial College London.\u2663 The first\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":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2018\/08\/reactants-1024x719.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":25439,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=25439","url_meta":{"origin":5114,"position":4},"title":"Unexpected Isomerization of Oxetane-Carboxylic Acids \u2013 an alternative autocatalytic mechanism evaluated.","author":"Henry Rzepa","date":"August 17, 2022","format":false,"excerpt":"Previously, I looked at autocatalytic mechanisms where the carboxyl group of an oxetane-carboxylic acid could catalyse its transformation to a lactone, finding that a chain of two such groups were required to achieve the result. Here I look at an alternative mode where the oxetane-carboxylate itself acts as the transfer\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":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2022\/08\/saddle.gif?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":18091,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18091","url_meta":{"origin":5114,"position":5},"title":"The conformation of carboxylic acids revealed.","author":"Henry Rzepa","date":"April 11, 2017","format":false,"excerpt":"Following my conformational exploration of enols, here is one about a much more common molecule, a carboxylic acid. The components of the search are shown as four queries below, which will be combined in various Boolean senses (DOI:\u00a010.14469\/hpc\/2462). Query one defines the carboxylic acid, with 3-coordinate carbon specified at the\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\/2017\/04\/051-1024x676.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\/5114","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=5114"}],"version-history":[{"count":9,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/5114\/revisions"}],"predecessor-version":[{"id":26458,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/5114\/revisions\/26458"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=5114"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=5114"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=5114"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=5114"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}