{"id":13252,"date":"2015-01-23T07:55:37","date_gmt":"2015-01-23T07:55:37","guid":{"rendered":"http:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=13252"},"modified":"2023-09-16T18:19:23","modified_gmt":"2023-09-16T17:19:23","slug":"fine-tuning-a-hydrogen-bond-into-symmetry","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13252","title":{"rendered":"Fine-tuning a (hydrogen) bond into symmetry."},"content":{"rendered":"
\n

Sometimes you come across a bond in chemistry that just shouts at you. This happened to me in 1989[1]<\/a><\/span> with the molecule shown below. Here is its story and, 26 years later, how I responded.<\/p>\n

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

To start at the beginning, there was a problem with the measured\u00a01<\/sup>H NMR spectrum; specifically (Y=H, Z=O) there are supposedly 16 protons, but only 15 could be located. What had happened to the 16th? To understand how one proton had been “lost”, you should appreciate that on most FT-NMR instruments, one has to specify a spectral window to collect data, and normally for protons, that window ranges from ~14 to -2 ppm. So the standard response to lost signals is to expand the window. When that was done, the offending proton appeared at 19 ppm! You should understand that this is an unusual chemical shift for a proton, and is normally taken as indicating very high acidity. But carboxylic acid protons are not regarded as particularly acidic? The mystery was resolved by recording the crystal structure at low temperatures, and this revealed that this hydrogen was (almost) symmetrically disposed between the oxygen and the nitrogen. The N-H distance was 1.32\u00c5 and the OH 1.17\u00c5. Whilst such symmetric disposition is not that unusual between two atoms of the same type (O-H-O or N-H-N) it was quite unexpected between two different heteroatoms. And such symmetry alone is sufficient to induce very high chemical shifts; acidity per se<\/em> does not come into it.<\/p>\n

That bond clearly shouted at me; so much so that in the text of the original article, we wrote “it is interesting to speculate whether these characteristics could be fine tuned by modification of the pKa values with suitable ring substitution<\/em>“.\u00a0What I had in mind was whether the position of the H could be made perfectly symmetric by adjusting the substituents. But for 26 years this idea lay dormant. Until this post! Rather than make lot of compounds (1-3 years!) I will do it with (lots of) computation (2 days!!).<\/p>\n

So to start we need a reality check. I am using the\u00a0pbe1pbe\/tzvp\/scrf=chloroform<\/strong> method (this functional is often used for hydrogen bonds) and the collected results are shown in the table below.<\/p>\n

    \n
  1. For Y=H, Z=O, the calculation predicts single minimum, with the hydrogen closer to O. Starting from an NH bound hydrogen ends with it on O. It is what is called a single well potential.\u00a0The disposition of that H is not quite correct, but the computed 1<\/sup>H NMR\u00a0shift is pretty close to experiment, and so I will take this method as reasonably good.<\/li>\n
  2. With Y=Li, the polarisation of the N-Li bond enhances the basicity of the second N, and the H now ends up on this atom rather than O (even if it starts on O). Another single well potential. We now know that any symmetric species must occur somewhere between Y=H and Y=Li in terms of the electronegativity of the substituent Y.<\/li>\n
  3. Unsurprisingly, Y=Na does not bracket\u00a0Y=H\/Li and the H moves even closer to the N. Again a single well potential.<\/li>\n
  4. Y=Li.1H2<\/sub>O or 2H2<\/sub>O do not help either (surprisingly?)<\/li>\n
  5. Y=BeH brackets Y=H\/Li, but we also see new behaviour with a double-well potential; the H can be attached to either O or N and the former is slightly\u00a0more stable by 0.22 kcal\/mol in \u0394G. The barrier is tiny, well below the energy of the first vibrational level, and so experimentally this system will manifest as the average of these two isomers and the H will\u00a0similarly manifest with its most probable position being at the average of the two minima, N-H ~1.30, O-H ~1.3\u00c5. Success!\u00a0<\/strong> At this point, the\u00a0NMR shift is at its greatest.<\/span><\/span><\/li>\n
  6. Y=BH2 continues the trend as a double minimum, this time with the H-O species the more stable by\u00a0\u0394G 0.68 kcal\/mol; we are now past the symmetric point.<\/li>\n
  7. By Y=SiH3, the single-well minimum (with H-O) is restored and we emerge with the same result as Y=H.<\/li>\n
  8. And to complete the scan, Y=H, Z=S is the same as Z=O.<\/li>\n
  9. Some second order tuning can be tried by changing the substituent on Y=BeH to Y=BeF, again a double minimum with HO more stable than NH by 0.30 kcal\/mol in \u0394G, and with a \u0394G298<\/sub> barrier from O to N of only 0.02 kcal\/mol! The fine-tuning is again towards symmetrisation.<\/li>\n<\/ol>\n

    I will stop at that point. Unfortunately of course the Y=BeF derivative is unfeasible synthetically and hence unlikely to be tested.<\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
    Y<\/th>\nN-H, \u00c5<\/th>\nO-H, \u00c5<\/th>\n\u03b4, ppm<\/th>\nFAIR Data Citation<\/a><\/th>\n<\/tr>\n
    H (expt)<\/td>\n1.32<\/td>\n1.17<\/td>\n19.0<\/td>\n[1]<\/a><\/span><\/td>\n<\/tr>\n
    H (calc)<\/td>\n1.48<\/td>\n1.04<\/td>\n18.6<\/td>\n[2]<\/a><\/span><\/td>\n<\/tr>\n
    Li<\/td>\n1.06<\/td>\n1.52<\/td>\n16.5<\/td>\n[2]<\/a><\/span><\/td>\n<\/tr>\n
    Na<\/td>\n1.05<\/td>\n1.55<\/td>\n15.6<\/td>\n[3]<\/a><\/span><\/td>\n<\/tr>\n
    Li.H2<\/sub>O<\/td>\n1.06<\/td>\n1.52<\/td>\n16.6<\/td>\n[4]<\/a><\/span><\/td>\n<\/tr>\n
    Li.2H2<\/sub>O<\/td>\n1.06<\/td>\n1.52<\/td>\n16.6<\/td>\n[5]<\/a><\/span><\/td>\n<\/tr>\n
    BeH<\/td>\n1.11<\/td>\n1.39<\/td>\n20.6<\/td>\n[6]<\/a><\/span><\/td>\n<\/tr>\n
    BeH<\/td>\n1.49<\/td>\n1.04<\/td>\n18.7<\/td>\n[7]<\/a><\/span><\/td>\n<\/tr>\n
    BH2<\/sub><\/td>\n1.06<\/td>\n1.56<\/td>\n16.6<\/td>\n[8]<\/a><\/span><\/td>\n<\/tr>\n
    BH2<\/sub><\/td>\n1.53<\/td>\n1.03<\/td>\n17.6<\/td>\n[7]<\/a><\/span><\/td>\n<\/tr>\n
    SiH3<\/sub><\/td>\n1.48<\/td>\n1.04<\/td>\n18.8<\/td>\n[9]<\/a><\/span><\/td>\n<\/tr>\n
    Z=S<\/td>\n1.50<\/td>\n1.03<\/td>\n18.8<\/td>\n[10]<\/a><\/span><\/td>\n<\/tr>\n
    BeF<\/td>\n1.12<\/td>\n1.38<\/td>\n20.9<\/td>\n[11]<\/a><\/span><\/td>\n<\/tr>\n
    BeF (TS)<\/td>\n1.15<\/td>\n1.32<\/td>\n22.5<\/td>\n[12]<\/a><\/span><\/td>\n<\/tr>\n
    BeF<\/td>\n1.48<\/td>\n1.04<\/td>\n18.7<\/td>\n[13]<\/a><\/span><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

    Another reality check, a search of crystal structures. DIST2 = OH, DIST1 = NH, for structures recorded below 140K, R < 0.05%, no errors, no disorder. The structure above is shown as a blue dot. They do tend to show asymmetry, but it is interesting how many such structures have emerged since our own 1989 report; the effect is not that rare any more.
    \n<\/a>    \"H-bond\"<\/a><\/p>\n

    The above plot shows lots more systems that might be subjected to the sort of tuning above, and who knows one of them may even yield to experimental validation.<\/p>\n

    \n

    DOI: 10.14469\/hpc\/10731<\/a><\/p>\n

    \n

    Acknowledgments<\/h4>\n

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

    References<\/h2>\n
    1. P. Camilleri, C.A. Marby, B. Odell, H.S. Rzepa, R.N. Sheppard, J.J.P. Stewart, and D.J. Williams, \"X-Ray crystallographic and NMR evidence for a uniquely strong OH ? N hydrogen bond in the solid state and solution\", Journal of the Chemical Society, Chemical Communications<\/i>, pp. 1722, 1989. https:\/\/doi.org\/10.1039\/c39890001722<\/a>\n\n<\/li>\n
    2. H.S. Rzepa, \"C 13 H 14 Li 1 N 3 O 3\", 2015. https:\/\/doi.org\/10.14469\/ch\/189475<\/a>\n\n<\/li>\n
    3. H.S. Rzepa, \"C 13 H 14 N 3 Na 1 O 3\", 2015. https:\/\/doi.org\/10.14469\/ch\/189477<\/a>\n\n<\/li>\n
    4. H.S. Rzepa, \"C 13 H 16 Li 1 N 3 O 4\", 2015. https:\/\/doi.org\/10.14469\/ch\/189478<\/a>\n\n<\/li>\n
    5. H.S. Rzepa, \"C 13 H 18 Li 1 N 3 O 5\", 2015. https:\/\/doi.org\/10.14469\/ch\/189480<\/a>\n\n<\/li>\n
    6. H.S. Rzepa, \"C 13 H 15 Be 1 N 3 O 3\", 2015. https:\/\/doi.org\/10.14469\/ch\/189476<\/a>\n\n<\/li>\n
    7. H.S. Rzepa, \"C 13 H 15 Be 1 N 3 O 3\", 2015. https:\/\/doi.org\/10.14469\/ch\/189492<\/a>\n\n<\/li>\n
    8. H.S. Rzepa, \"C 13 H 16 B 1 N 3 O 3\", 2015. https:\/\/doi.org\/10.14469\/ch\/189479<\/a>\n\n<\/li>\n
    9. H.S. Rzepa, \"C 13 H 17 N 3 O 3 Si 1\", 2015. https:\/\/doi.org\/10.14469\/ch\/189481<\/a>\n\n<\/li>\n
    10. J.S. Dawson, \"Cl 4 Ni 1 -2\", 2016. https:\/\/doi.org\/10.14469\/ch\/193726<\/a>\n\n<\/li>\n
    11. H.S. Rzepa, \"C 13 H 14 Be 1 F 1 N 3 O 3\", 2015. https:\/\/doi.org\/10.14469\/ch\/189489<\/a>\n\n<\/li>\n
    12. C. Townsend, \"Cl 4 Ni 1 -2\", 2016. https:\/\/doi.org\/10.14469\/ch\/193727<\/a>\n\n<\/li>\n
    13. H.S. Rzepa, \"C 13 H 14 Be 1 F 1 N 3 O 3\", 2015. https:\/\/doi.org\/10.14469\/ch\/189488<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      Sometimes you come across a bond in chemistry that just shouts at you. This happened to me in 1989 with the molecule shown below. Here is its story and, 26 years later, how I responded. To start at the beginning, there was a problem with the measured\u00a01H NMR spectrum; specifically (Y=H, Z=O) there are supposedly […]<\/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_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},"jetpack_post_was_ever_published":false},"categories":[565,4],"tags":[24,1315,1047,1145],"ppma_author":[2661],"class_list":["post-13252","post","type-post","status-publish","format-standard","hentry","category-historical","category-interesting-chemistry","tag-energy","tag-high-chemical-shifts","tag-new-hampshire","tag-unusual-chemical-shift"],"yoast_head":"\nFine-tuning a (hydrogen) bond into symmetry. - 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=13252\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Fine-tuning a (hydrogen) bond into symmetry. - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"Sometimes you come across a bond in chemistry that just shouts at you. 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This happened to me in 1989 with the molecule shown below. Here is its story and, 26 years later, how I responded. 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Now a new report and\u00a0commented upon by\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\/2017\/06\/201-1024x987.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":10839,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=10839","url_meta":{"origin":13252,"position":1},"title":"Hexacoordinate hydrogen.","author":"Henry Rzepa","date":"July 8, 2013","format":false,"excerpt":"A feature of a blog which is quite different from a journal article is how rapidly a topic might evolve.\u00a0Thus I started a few days ago with the theme of dicarbon (C2), identifying a metal carbide that showed C2 as a ligand, but which also entrapped a single carbon in\u2026","rel":"","context":"In "Hypervalency"","block_context":{"text":"Hypervalency","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=7"},"img":{"alt_text":"Click for 3D.","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/07\/6-H.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":11450,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=11450","url_meta":{"origin":13252,"position":2},"title":"The NMR spectra of methano[10]annulene and its dianion. 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But\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":"Click for 3D","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2013\/10\/dianion.jpeg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":6044,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=6044","url_meta":{"origin":13252,"position":3},"title":"Secrets of a university tutor: tetrahedral intermediates.","author":"Henry Rzepa","date":"January 8, 2012","format":false,"excerpt":"The tetrahedral intermediate is one of those iconic species on which the foundation of reaction mechanism in organic chemistry is built. It refers to a (normally undetected and hence merely inferred) species formed initially when a nucleophilic reagent attacks a carbonyl compound. Its importance to understanding the activity of enzymes\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\/01\/acetylcyanide.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":4930,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=4930","url_meta":{"origin":13252,"position":4},"title":"Molecular Matryoshka dolls","author":"Henry Rzepa","date":"September 20, 2011","format":false,"excerpt":"A Matryoshka doll is better known as a Russian nesting doll. They can have up to eight layers. Molecules can only emulate two layers, although see here for a good candidate for making a three-layered example (the inside layer is C60, which itself might\u00a0encapsulate\u00a0a small molecule. See also \u00a0DOI: 10.1021\/ja991747w).\u2026","rel":"","context":"In "General"","block_context":{"text":"General","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1"},"img":{"alt_text":"","src":"https:\/\/i0.wp.com\/www.ch.imperial.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2011\/09\/rebek.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":275,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=275","url_meta":{"origin":13252,"position":5},"title":"A molecule with an identity crisis: Aromatic or anti-aromatic?","author":"Henry Rzepa","date":"April 13, 2009","format":false,"excerpt":"In 1988, Wilke reported molecule 1 It was a highly unexpected outcome of a nickel-catalyzed reaction and was described as a 24-annulene with an unusual 3D shape. Little attention has been paid to this molecule since its original report, but the focus has now returned! The reason is that a\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":"A [24] annulene. 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