{"id":7779,"date":"2012-09-23T12:18:01","date_gmt":"2012-09-23T11:18:01","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=7779"},"modified":"2023-09-16T18:17:27","modified_gmt":"2023-09-16T17:17:27","slug":"oxime-formation-from-hydroxylamine-and-ketone-a-computational-reality-check-on-stage-one-of-the-mechanism","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7779","title":{"rendered":"Oxime formation from hydroxylamine and ketone: a (computational) reality check on stage one of the mechanism."},"content":{"rendered":"
\n

The mechanism of forming an oxime from nucleophilic addition of a hydroxylamine to a ketone is taught early on in most courses of organic chemistry. Here I subject the first step of this reaction to form a tetrahedral intermediate to quantum mechanical scrutiny.<\/p>\n

\"\"<\/p>\n

    \n
  1. The first decision is to decide which atom of the hydroxylamine acts as the nucleophile. Reaction 1<\/strong> shows the oxygen and reaction 2<\/strong> the nitrogen. The text books will tell you that nitrogen nucleophiles are better than oxygen ones. This is because nitrogen is less electronegative than oxygen (it has a smaller nuclear charge) and so binds its single lone pair less tightly than oxygen does its two lone pairs. Sometimes the Klopman-Salem equation is invoked, which tells you that the reactivity is directly proportional to the overlap between the donor MO and the (empty) acceptor MO, and inversely proportional to the energy gap between these two orbitals. Nitrogen wins out because its lone pair is “larger” and hence overlaps better, and because its donor MO energy is higher than oxygen and hence the energy gap between it and the \u03c0* C=O acceptor is lower.\u00a0<\/li>\n
  2. Reality check:\u00a0<\/strong>We need to construct a suitable transition state for both possibilities, and then compare their free energies. There is a choice of choosing a stepwise pathway (the one shown in all the text books) in which the bond from N or O to C is formed in an initial step, and then followed by a step often just labelled PT to transfer the proton using solvent molecules. These two steps can also be conflated into a single concerted mechanism involving a 6-membered ring transition state. Quantum mechanically, this latter option has the advantage of avoiding any great build up of charge separation at any stage in the mechanism, but has the disadvantage that the entropic loss at the transition state is greater (although “borrowing” a water molecule from a bulk solvent for this purpose is easier than doing so from an infinite distance away).\n
      \n
    1. Shown below is a\u00a0\u03c9B97XD\/6-311G(d,p)\/SCRF=water calculation of the transition state for N-attack<\/a>. It has a dipole moment of 6.2D, which is really quite small, and far from that expected for the zwitterionic intermediate shown in the stepwise mechanism (that would be between 15-30D).
      \n
      \"\"

      Cyclic transition state for N-attack.<\/p><\/div>\n<\/li>\n

    2. The intrinsic reaction coordinate shows a concerted reaction with quite a small barrier. It is small because the nitrogen is in fact a super-nucleophile, its nucleophilicity has been augmented over that of a simple amine by a so-called \u03b1-effect from the adjacent two pairs of lone pairs on the oxygen activating the nitrogen lone pair by lone-pair repulsions.\u00a0\"\"<\/li>\n
    3. The gradient norm along the coordinate also shows an almost synchronous reaction. The only blip occurs at around IRC +1.3, and this corresponds to the transfer of a proton from NH to a water molecule. An earlier proton transfer from water to the carbonyl oxygen was essentially synchronous with formation of the N-C bond. This synchronicity is what helps avoid any large build up of charge separation. For this reason, I cannot help but feel that the text books could absorb this lesson and show a cyclic concerted reaction mechanism as a probable alternative to two stepwise processes.\"\"<\/li>\n<\/ol>\n<\/li>\n
    4. Next, O-attack.\u00a0The IRC for this isomeric mode<\/a> shows a significantly higher barrier compared to N (the computed relative free energies s<\/em>how the O to be higher by 8.3 kcal\/mol than the N)\u00a0and smaller exothermicity. It reveals even greater synchrony of the two proton transfers with the O-C bond formation. So we have a reality check of the text-books on this point in the form of an energy difference, which is always useful.
      \n\n\n\n\n
      \n
      \"\"

      O-attack.<\/p><\/div>\n<\/td>\n<\/tr>\n

      \"\"<\/td>\n\"\"<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n
    5. Now that our proton transfers are involved in the mechanism, it is time to take a closer look at the geometry of these transfers. On this point, the text books tell us that the most favourable geometry for a proton transfer is having the proton co-linear with the two oxygens. Whilst this is largely true for the geometries shown above, the resulting 6-membered ring as a result adopts a triangular shape, which is not ideal for the bond angles. This could be solved by incorporating a second water molecule, to give us model 3\u00a0<\/strong>shown above.\n
        \n
      1. A second water molecule can be placed in two alternative positions. The first simply solvates the 6-ring transition state<\/a>. The second actively participates via<\/em> an enlarged 8-membered ring transition state<\/a>. It turns out that the latter is lower by 4.5 kcal\/mol in free energy, largely due to the far better bond angles and the almost exactly linear proton transfers now possible.
        \n\n\n\n
        \n
        \"\"

        O-Transition state with two water molecules, one merely hydrogen bonding to the 6-ring (magenta arrow).<\/p><\/div>\n<\/td>\n

        		\n
        \"\"

        O-Transition state with two water molecules, both part of a cyclic transition state.<\/p><\/div>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n

      2. So the following is our best model<\/a>. It is 10.4 kcal\/mol lower in free energy than the isomeric O-attack transition state. The timing of the bonds<\/a> shows that N-C formation coincides with the first proton transfer to the carbonyl oxygen, followed by an O to O proton transfer and finally N to O. The dipole moment at the transition state is 5.9D, revealing little explicit charge separation.
        \n\n\n\n\n
        \n
        \"\"

        N-attack via an 8-ring transition state.<\/p><\/div>\n<\/td>\n<\/tr>\n

        \"\"<\/td>\n\"\"<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n<\/ol>\n<\/li>\n<\/ol>\n

        It is worth concluding this exploration by reiterating that the models above are not complete. A bulk solvent would allow (statistical) participation of more than just two solvent molecules, and the dynamics of such a (very complex) process has yet to be explored. But I hope what you see here is a bit closer to “reality” than many a text-book author has when they illustrate their books.<\/p>\n

        \n

        Acknowledgements<\/h4>\n

        This post has been cross-posted in PDF format at Authorea<\/a>.<\/p>\n

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

        The mechanism of forming an oxime from nucleophilic addition of a hydroxylamine to a ketone is taught early on in most courses of organic chemistry. Here I subject the first step of this reaction to form a tetrahedral intermediate to quantum mechanical scrutiny. 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These transients can often involve the creation\/annihilation of charge separation resulting from \u00a0proton transfers, something that a cyclic mechanism can avoid. Here I revisit the formation of an oxime from hydroxylamine and propanone, but with\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":"N-pre","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/04\/N-pre.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":7822,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=7822","url_meta":{"origin":7779,"position":1},"title":"Oxime formation from hydroxylamine and ketone. Part 2: Elimination.","author":"Henry Rzepa","date":"September 25, 2012","format":false,"excerpt":"This is the follow-up to the previous post exploring a typical nucleophilic addition-elimination reaction. Here is the elimination step, which as before requires proton transfers. We again adopt a cyclic mechanism to try to avoid the build up of charge separation during those proton movements. Overall, the transition state for\u2026","rel":"","context":"In \"Reaction Mechanism\"","block_context":{"text":"Reaction Mechanism","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=reaction-mechanism"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/09\/N-2H2O-8-ring-2.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":23410,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=23410","url_meta":{"origin":7779,"position":2},"title":"The small-molecule antiviral compound Molnupiravir: an exploration of its tautomers.","author":"Henry Rzepa","date":"March 14, 2021","format":false,"excerpt":"For obvious reasons, anti-viral molecules are very much in the news at the moment. Thus Derek Lowe highlights Molnupiravir which is shown as a hydroxylamine, the representation originating from the Wikipedia page on the molecule. I like stereocentres more clearly identified using eg R\/S notation and so I went to\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\/2021\/03\/molnupiravir-1024x639.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":8246,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=8246","url_meta":{"origin":7779,"position":3},"title":"Thalidomide. The role of water in the mechanism of its aqueous racemisation.","author":"Henry Rzepa","date":"November 10, 2012","format":false,"excerpt":"Thalidomide is a chiral molecule, which was sold in the 1960s as a sedative in its (S,R)-racemic form. The tragedy was that the (S)-isomer was tetragenic, and only the (R) enantiomer acts as a sedative. What was not appreciated at the time is that interconversion of the (S)- and (R)\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.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2012\/11\/thal1.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":3576,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=3576","url_meta":{"origin":7779,"position":4},"title":"The formation of cyanohydrins: re-writing the text books. ! or ?","author":"Henry Rzepa","date":"March 4, 2011","format":false,"excerpt":"Nucleophilic addition of cyanide to a ketone or aldehyde is a standard reaction for introductory organic chemistry. But is all as it seems? The reaction is often represented as below, and this seems simple enough. But attention to detail suggests that, HCN being a weak acid, there will be only\u2026","rel":"","context":"In \"acidic solutions\"","block_context":{"text":"acidic solutions","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?tag=acidic-solutions"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/03\/cyano1.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":16844,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=16844","url_meta":{"origin":7779,"position":5},"title":"\u03c3 or \u03c0? The ambident nucleophilic reactivity of imines: crystallographic and computational reality checks.","author":"Henry Rzepa","date":"September 21, 2016","format":false,"excerpt":"Nucleophiles are species\u00a0that seek to react with an electron deficient centre by donating a lone or a \u03c0-bond pair of electrons. The ambident variety has two or more such possible sources in the same molecule, an example of which might be hydroxylamine\u00a0or\u00a0H2NOH. I previously discussed how for this example, 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":"imine2","src":"https:\/\/i0.wp.com\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2016\/09\/imine2.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\/7779","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=7779"}],"version-history":[{"count":55,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/7779\/revisions"}],"predecessor-version":[{"id":26462,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/7779\/revisions\/26462"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=7779"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=7779"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=7779"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=7779"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}