{"id":2902,"date":"2010-12-01T16:48:28","date_gmt":"2010-12-01T15:48:28","guid":{"rendered":"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2902"},"modified":"2023-09-16T18:22:14","modified_gmt":"2023-09-16T17:22:14","slug":"anatomy-of-an-arrow-pushing-tutorial-reducing-a-carboxylic-acid","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2902","title":{"rendered":"Anatomy of an arrow-pushing tutorial: reducing a carboxylic acid."},"content":{"rendered":"<div class=\"kcite-section\" kcite-section-id=\"2902\">\n<p>Arrow pushing (why never pulling?) is a technique learnt by all students of organic chemistry (inorganic chemistry seems exempt!). 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 as a tutor,  its subtle and nuanced character starts to dawn. An example of such a mechanism is illustrated below, and in this post I attempt to tease out some of these nuances.<\/p>\n<p>The example chosen is the reduction of a carboxylic acid to an alcohol by borane (diborane). Lecture notes present this reaction as being specific to carboxylic acids, even in the presence of carboxylic esters. The tutor is then faced with how to explain this selectivity to students in a tutorial, using arrow pushing.<\/p>\n<div id=\"attachment_2903\" style=\"width: 481px\" class=\"wp-caption aligncenter\"><a href=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/12\/acyloxyborane.jpg\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-2903\" class=\"size-full wp-image-2903\" title=\"acyloxyborane\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/12\/acyloxyborane1.jpg\" alt=\"\" width=\"471\" height=\"418\" \/><\/a><p id=\"caption-attachment-2903\" class=\"wp-caption-text\">Scheme for reduction of a carboxylic acid by borane.<\/p><\/div>\n<p>I start with grouping the arrow pushing into three sets:<\/p>\n<ol>\n<li>The <strong>essential<\/strong> arrows (red). These will attempt to describe the key mechanistic step for which an answer is sought, in this example why the reaction is so selective for the carboxylic acid. A cruder, but perhaps pragmatic description is that these are the arrows needed to pass examinations in the subject (music to students&#8217; ears).<\/li>\n<li>The <strong>lazy<\/strong> arrows (blue). In this case, these arrows are essential to &#8220;prep the patient&#8221;, but they will not of themselves carry much insight into the operation of the mechanism.<\/li>\n<li>The <strong>workup<\/strong> arrows (green). To continue the medical analogy, this is a post operative &#8220;closing the patient up&#8221; stage.<\/li>\n<\/ol>\n<p>This tutorial actually starts with <strong>non-arrows<\/strong>. Process <strong>1<\/strong> involves converting the actual real structure of diborane (a bridged dimer) into its monomer, which is thought to be the active ingredient of this reagent. Because the bridging hydrogens are bound by three-centre-two-electron bonds, it is actually difficult to represent this process with conventional (two-centre-two-electron) arrows. So we do not even try!<\/p>\n<p>Process <strong>3<\/strong> is the one which involves the essential\u00a0(red) arrow pushing. It encapsulates the reason why only a carboxylic acid reacts in this process, and these arrows can be formalised by computing the transition state quantum mechanically (below). In fact there are two ways of illustrating this essential process. Process <strong>2<\/strong> involves first forming a O-B bond before the essential arrows. Process <strong>4<\/strong> involves another B-O bond AFTER the key transition state; the outcome of either process is identical. This illustrates another subtle behaviour in arrow pushing; the detailed timing or choreography of the arrows. In this example, the animated form of the reaction coordinate indicates relatively little B-O bond formation, so we will go with <strong>2 <\/strong>and then<strong> 5<\/strong> as the more realistic representation. In fact, the QM transition state is fascinating in its own right; note for example how one of the two extruding hydrogen atoms is moving far less (the hydridic one) than the other (the proton-like one; full details available at <a href=\"http:\/\/hdl.handle.net\/10042\/to-5725\" target=\"_blank\" rel=\"noopener\">10042\/to-5725<\/a>).<\/p>\n<div id=\"attachment_2915\" style=\"width: 315px\" class=\"wp-caption aligncenter\"><img loading=\"lazy\" decoding=\"async\" aria-describedby=\"caption-attachment-2915\" class=\"size-full wp-image-2915\" title=\"acyloxyborane-ts\" onclick=\"jmolInitialize('..\/Jmol\/');jmolSetAppletColor('green');jmolApplet([600,600],'load wp-content\/uploads\/2010\/12\/acyloxyborane-ts.log;frame 43;set measurementUnits Angstroms;delay 5;vectors on;vectors 4;vectors scale 5.0; color vectors purple; vibration 15;animation mode loop;');\" src=\"http:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/12\/acyloxyborane-ts1.jpg\" alt=\"\" width=\"305\" height=\"207\" srcset=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/12\/acyloxyborane-ts1.jpg 915w, https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2010\/12\/acyloxyborane-ts1-300x203.jpg 300w\" sizes=\"auto, (max-width: 305px) 100vw, 305px\" \/><p id=\"caption-attachment-2915\" class=\"wp-caption-text\">Key transition state?  Click for 3D.<\/p><\/div>\n<p>Process <strong>6<\/strong> is a lazy category. The preceding steps are simply repeated twice more to form a triacyloxyborane. There are many other forms of lazy arrow. Proton transfers are often thought of in this category, and double headed arrows involved in addition\/elimination to e.g. carbonyl groups.<\/p>\n<p>Process <strong>7<\/strong> and <strong>8<\/strong> are in an awkward category. Of themselves, they do not explain the selectivity of borane for this functional group, but they do represent another essential operation; namely the actual reduction of the carbonyl group. They are also somewhat speculative, and it is quite possible other routes could be devised.<\/p>\n<p>Finally, with <strong>9<\/strong>, we arrive at a resting phase which now requires workup (green). Thus <strong>10<\/strong> and <strong>11<\/strong> represent hydrolysis of the borate esters to the reduced alcohol and something starting to resemble boric acid. Clearly, more arrows are needed after <strong>11<\/strong>, but few tutors (or examination graders) would begrudge a student if these were to be omitted. Step <strong>11<\/strong> also contains some lazy arrows, since a proton is transferred between oxygen atoms, but no arrows are shown for this process.<\/p>\n<p>Clearly, there are plenty of nuances here, and it is perfectly possible that other arrow-pushers may even disagree with some of the ones I have shown above. But perhaps the above analysis might give you some ideas of your own on how to communicate the essential of reaction mechanisms to others.<\/p>\n<hr \/>\n<h4>Acknowledgments<\/h4>\n<p>This post has been cross-posted in PDF format at <a href=\"https:\/\/doi.org\/10.15200\/winn.142795.57337\" rel=\"noopener\" target=\"_blank\">Authorea<\/a>.<\/p>\n<!-- kcite active, but no citations found -->\n<\/div> <!-- kcite-section 2902 -->","protected":false},"excerpt":{"rendered":"<p>Arrow pushing (why never pulling?) is a technique learnt by all students of organic chemistry (inorganic chemistry seems exempt!). 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 as a tutor, its subtle [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_feature_clip_id":0,"_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},"jetpack_post_was_ever_published":false},"categories":[4],"tags":[332,333,2648,331,330],"ppma_author":[2661],"class_list":["post-2902","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry","tag-acyloxyborane","tag-arrow-pushing","tag-interesting-chemistry","tag-post-operative","tag-tutor"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v27.8 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Anatomy of an arrow-pushing tutorial: reducing a carboxylic acid. - Henry Rzepa&#039;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=2902\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Anatomy of an arrow-pushing tutorial: reducing a carboxylic acid. - Henry Rzepa&#039;s Blog\" \/>\n<meta property=\"og:description\" content=\"Arrow pushing (why never pulling?) is a technique learnt by all students of organic chemistry (inorganic chemistry seems exempt!). 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We are now\u2026","rel":"","context":"In &quot;reaction mechanism&quot;","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":18091,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18091","url_meta":{"origin":2902,"position":1},"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 &quot;crystal_structure_mining&quot;","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":[]},{"id":6816,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=6816","url_meta":{"origin":2902,"position":2},"title":"The mechanism (in 4D) of the reaction between thionyl chloride and a carboxylic acid.","author":"Henry Rzepa","date":"May 25, 2012","format":false,"excerpt":"If you have not previously visited, take a look at Nick Greeves' ChemTube3D\u00a0, an\u00a0ever-expanding gallery of reactions and their mechanisms. The 3D is because all molecules are offered with X, Y and z coordinates. You also get arrow pushing\u2021\u00a0in 3D. Here, I argue that we should adopt Einstein, and go\u2026","rel":"","context":"In \"acetic acid\"","block_context":{"text":"acetic acid","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=acetic-acid"},"img":{"alt_text":"","src":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/05\/thionyl.svg","width":350,"height":200},"classes":[]},{"id":5114,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=5114","url_meta":{"origin":2902,"position":3},"title":"Mechanism of the reduction of a carboxylic acid by borane: revisited and revised.","author":"Henry Rzepa","date":"October 16, 2011","format":false,"excerpt":"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\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","block_context":{"text":"Interesting chemistry","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=4"},"img":{"alt_text":"","src":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/10\/acyloxy1-page001.svg","width":350,"height":200},"classes":[]},{"id":2017,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=2017","url_meta":{"origin":2902,"position":4},"title":"Anatomy of an asymmetric reaction. The Strecker synthesis, part 2.","author":"Henry Rzepa","date":"May 26, 2010","format":false,"excerpt":"In the first part of the post on this topic, I described how an asymmetric sulfoxide could be prepared as a pure enantiomer using a chiral oxygen transfer reagent. In the second part, we now need to deliver a different group, cyano, to a specific face of the previously prepared\u2026","rel":"","context":"In &quot;Interesting chemistry&quot;","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\/05\/strecker4.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":19828,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=19828","url_meta":{"origin":2902,"position":5},"title":"The &#8220;White City Trio&#8221; &#8211; 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 &quot;Interesting chemistry&quot;","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":[]}],"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","author_category":"1","first_name":"Henry","last_name":"Rzepa","user_url":"https:\/\/orcid.org\/0000-0002-8635-8390","job_title":"","description":"Henry Rzepa is Emeritus Professor of Computational Chemistry at Imperial College London."}],"_links":{"self":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/2902","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=2902"}],"version-history":[{"count":2,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/2902\/revisions"}],"predecessor-version":[{"id":26467,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/2902\/revisions\/26467"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=2902"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=2902"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=2902"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=2902"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}