{"id":29799,"date":"2025-10-27T12:23:18","date_gmt":"2025-10-27T12:23:18","guid":{"rendered":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=29799"},"modified":"2025-10-28T16:15:23","modified_gmt":"2025-10-28T16:15:23","slug":"short-b-h-h-o-interactions-in-crystal-structures-a-short-dft-exploration-using-b3lypd4-and-r2scan-3c","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=29799","title":{"rendered":"Short B-H…H-O Interactions in crystal structures – a short DFT Exploration using B3LYP+D4 and r2scan-3c"},"content":{"rendered":"
\n

In the previous post,[1]<\/a><\/span> I was commenting that the transition state for borohydride reduction of a ketone contained some close contacts between the hydrogen of the borohydride and the hydrogen of water. A systematic search of the CSD reveals a modest number of such contacts have been observed in crystal structures (Table). \u00a0Since it is always good to have a reality check for constructed transition states, here I take a look at some of compounds showing the closest H…H contacts in the experimental database of structures.<\/p>\n

The DFT procedures I used to calculate the geometries of the examples tabled below[2]<\/a><\/span> were<\/p>\n

    \n
  1. the classical B3LYP\/Def2-TZVPP method, but enhanced with the D4 dispersion correction – the latter developed as a successor to the often used D3+BJ predecessor.<\/li>\n
  2. The DFT method named \u00a0r2<\/sup>scan-3c<\/strong>, a composite described by its developers as the “Swiss army knife of DFT methods<\/em>” and \u00a0“r2<\/sup>SCAN-3c Works Well On Everything”.[3]<\/a><\/span> rather grandly quotes<\/em>The specific features are described as \u00a0“The unaltered r2SCAN functional is combined with a tailor-made triple-\u03b6 Gaussian atomic orbital basis set as well as with refitted D4 and geometrical counter-poise corrections for London-dispersion and basis set superposition error<\/em>“.[4]<\/a><\/span> The method scales efficiently to several hundred atoms. Results for both types of DFT calculation are \u00a0collected here.[2]<\/a><\/span><\/li>\n<\/ol>\n\n\n\n\n\n\n\n\n\n\n\n\n
    Table. Calculated and observed BH…HO interactions<\/th>\n<\/tr>\n
    Molecule<\/th>\nrH…H<\/sub> using B3LYP+D4\/
    \nDef2-TZVPP<\/th>\n    		rH…H<\/sub> using r2SCAN-3c\/
    \nDef2-mTZVPP<\/th>\n    		Crystal structure,
    \nrH…H<\/sub>, \u00c5<\/th>\n    		angle, BH…H, \u00b0<\/th>\nangle, OH…H, \u00b0<\/th>\n<\/tr>\n
    JATMUN<\/td>\n1.531<\/td>\n1.544<\/td>\n1.519 (1.513)
    \n[5]<\/a><\/span>,[6]<\/a><\/span><\/td>\n    		95.1<\/td>\n158.6<\/td>\n<\/tr>\n
    OLEVIL<\/td>\n1.612<\/td>\n1.654<\/td>\n1.806 (1.67)
    \n[7]<\/a><\/span>,[8]<\/a><\/span><\/td>\n    		107.7<\/td>\n171.4<\/td>\n<\/tr>\n
    OLEVEH<\/td>\n1.623<\/td>\n1.666<\/td>\n1.857 (1.757)
    \n[7]<\/a><\/span>,[9]<\/a><\/span><\/td>\n    		105.1<\/td>\n176.6<\/td>\n<\/tr>\n
    OWUKID<\/td>\n1.685<\/td>\n1.770<\/td>\n1.871 (1.778)
    \n[10]<\/a><\/span>,[11]<\/a><\/span><\/td>\n    		131.7<\/td>\n157.8<\/td>\n<\/tr>\n
    SASVAS<\/td>\n1.757<\/td>\n1.872<\/td>\n1.901 (1.807)
    \n[12]<\/a><\/span>,[13]<\/a><\/span><\/td>\n    		94.3<\/td>\n155.0<\/td>\n<\/tr>\n
    BOTFOJ<\/td>\n1.741<\/td>\n1.810<\/td>\n1.976 (1.856)
    \n[14]<\/a><\/span><\/td>\n    		129.6<\/td>\n171.0<\/td>\n<\/tr>\n
    MOPXOG<\/td>\n1.888<\/td>\n1.966<\/td>\n1.990 (1.872)
    \n[15]<\/a><\/span>,[16]<\/a><\/span><\/td>\n    		95.4<\/td>\n159.5<\/td>\n<\/tr>\n
    FOLREF<\/td>\n1.881<\/td>\n1.966<\/td>\n1.998 (1.908)
    \n[17]<\/a><\/span>,[18]<\/a><\/span><\/td>\n    		110.2<\/td>\n160.8<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

    \"\"
    \nOLEVIL@r2SCAN-3c\"\"
    \nOLEVIL @B3LYP+D4<\/p>\n

    In general, the B3LYP+D4 method predicts slightly shorter H…H contacts than does r2<\/sup>SCAN-3c. <\/em>Comparison with experiment is tricky, since OH and BH distances obtained directly from a classical crystal structure refinement tend to emerge as ~0.1A too short (see eg [19]<\/a><\/span> for more detailed discussion). A simple correction for these values is shown in parentheses in the table above. However, given that the angle subtended at the hydrogen atom varies \u00a0enormously, this correction may too simplistic.\u00a0Better would be if the original crystallographic data could be re-refined using the non-spherical atom model model described in [19]<\/a><\/span> \u00a0A provisional conclusion without such treatment might be that r2<\/sup>SCAN-3c<\/em> is somewhat more accurately predicting the\u00a0H…H distances.<\/p>\n

    OLEVIL is interesting because it contains two OH groups, with only one interacting with a proximate BH group. Calculating (r2scan-3c) \u03bdOH<\/sub> gives values of 3477 cm-1 <\/sup>as perturbed by the close BH vs a BH unperturbed value of 3801 cm-1 <\/sup>\u00a0or \u0394\u03bd 324 cm-1<\/sup>. The corresponding values using B3LYP+D4 are 3700 vs 3803, \u0394\u03bd 103 cm-1<\/sup>. This large difference in perturbation predicted by these two DFT methods could be easily tested experimentally. Unfortunately, the experimental information reported for this compound[7]<\/a><\/span> does not contain the OH stretching values, which might have been a good test of the claim that “r2<\/sup>SCAN-3c Works Well On Everything”.<\/em><\/p>\n

    This selection of compounds illustrates how one aspect of a transition state can be given a reality check by comparing a key interaction with experimentally determined crystal structures.<\/p>\n

    References<\/h2>\n
    1. H. Rzepa, \"The mechanism of borohydride reductions. Part 2: 4-t-butyl-cyclohexanone \u2013 Dispersion induced stereochemistry.\", 2025. https:\/\/doi.org\/10.59350\/x5k75-t2m40<\/a>\n\n<\/li>\n
    2. H. Rzepa, \"Short B-H...H-O Interactions in crystal structures - a short DFT Exploration using B3LYP+D4 and r2scan-3c\", 2025. https:\/\/doi.org\/10.14469\/hpc\/15566<\/a>\n\n<\/li>\n
    3. S. Grimme, A. Hansen, S. Ehlert, and J. Mewes, \"r2SCAN-3c: An Efficient \u201cSwiss Army Knife\u201d Composite Electronic-Structure Method\", 2020. https:\/\/doi.org\/10.26434\/chemrxiv.13333520.v2<\/a>\n\n<\/li>\n
    4. S. Grimme, A. Hansen, S. Ehlert, and J. Mewes, \"r2SCAN-3c: A \u201cSwiss army knife\u201d composite electronic-structure method\", The Journal of Chemical Physics<\/i>, vol. 154, 2021. https:\/\/doi.org\/10.1063\/5.0040021<\/a>\n\n<\/li>\n
    5. S. Hoffmann, E. Justus, M. Ratajski, E. Lork, and D. Gabel, \"B12H11-containing guanidinium derivatives by reaction of carbodiimides with H3N\u2013B12H11(1\u2212). A new method for connecting boron clusters to organic compounds\", Journal of Organometallic Chemistry<\/i>, vol. 690, pp. 2757-2760, 2005. https:\/\/doi.org\/10.1016\/j.jorganchem.2005.02.037<\/a>\n\n<\/li>\n
    6. Hoffmann, S.., Justus, E.., Ratajski, M.., Lork, E.., and Gabel, D.., \"CCDC 252153: Experimental Crystal Structure Determination\", 2006. https:\/\/doi.org\/10.5517\/cc8gcz1<\/a>\n\n<\/li>\n
    7. M. Stephan, B. Modec, and B. Mohar, \"Asymmetric synthesis of SMS-Phos series\u2019 precursor and a naphthalene analogue\", Tetrahedron Letters<\/i>, vol. 52, pp. 1086-1089, 2011. https:\/\/doi.org\/10.1016\/j.tetlet.2010.12.106<\/a>\n\n<\/li>\n
    8. Stephan, M.., Modec, B.., and Mohar, B.., \"CCDC 791282: Experimental Crystal Structure Determination\", 2011. https:\/\/doi.org\/10.5517\/ccvkd70<\/a>\n\n<\/li>\n
    9. Stephan, M.., Modec, B.., and Mohar, B.., \"CCDC 791281: Experimental Crystal Structure Determination\", 2011. https:\/\/doi.org\/10.5517\/ccvkd6z<\/a>\n\n<\/li>\n
    10. A.M.W. Dufter, T.M. Klap\u00f6tke, M. Rusan, A. Schweiger, and J. Stierstorfer, \"Comparison of Functionalized Lithium Dihydrobis(azolyl)borates with Their Corresponding Azolates as Environmentally Friendly Red Pyrotechnic Coloring Agents\", ChemPlusChem<\/i>, vol. 85, pp. 2044-2050, 2020. https:\/\/doi.org\/10.1002\/cplu.202000427<\/a>\n\n<\/li>\n
    11. Dufter, Alicia M. W.., Klap\u00f6tke, Thomas M.., Rusan, Magdalena., Schweiger, Alexander., and Stierstorfer, J\u00f6rg., \"CCDC 1998250: Experimental Crystal Structure Determination\", 2021. https:\/\/doi.org\/10.5517\/ccdc.csd.cc252bp9<\/a>\n\n<\/li>\n
    12. H. Fern\u00e1ndez\u2010P\u00e9rez, S. Donald, I. Munslow, J. Benet\u2010Buchholz, F. Maseras, and A. Vidal\u2010Ferran, \"Highly Modular P\uf8ffOP Ligands for Asymmetric Hydrogenation: Synthesis, Catalytic Activity, and Mechanism\", Chemistry \u2013 A European Journal<\/i>, vol. 16, pp. 6495-6508, 2010. https:\/\/doi.org\/10.1002\/chem.200902915<\/a>\n\n<\/li>\n
    13. Fernandez-Perez, H.., Donald, S.M.A.., Munslow, I.J.., Benet-Buchholz, J.., Maseras, F.., and Vidal-Ferran, A.., \"CCDC 752671: Experimental Crystal Structure Determination\", 2012. https:\/\/doi.org\/10.5517\/cct86qz<\/a>\n\n<\/li>\n
    14. Daniliuc, Constantin G.., Neumann, Markus., Fr\u00f6hlich, Roland., and Erker, Gerhard., \"CCDC 2362258: Experimental Crystal Structure Determination\", 2024. https:\/\/doi.org\/10.5517\/ccdc.csd.cc2k93ww<\/a>\n\n<\/li>\n
    15. R. Bigler, E. Otth, and A. Mezzetti, \"Chiral Macrocyclic N<sub>2<\/sub>P<sub>2<\/sub> Ligands and Iron(II): A Marriage of Interest\", Organometallics<\/i>, vol. 33, pp. 4086-4099, 2014. https:\/\/doi.org\/10.1021\/om5005989<\/a>\n\n<\/li>\n
    16. Bigler, Raphael., Otth, Elisabeth., and Mezzetti, Antonio., \"CCDC 1019093: Experimental Crystal Structure Determination\", 2014. https:\/\/doi.org\/10.5517\/cc136fzq<\/a>\n\n<\/li>\n
    17. S. Rast, B. Mohar, and M. Stephan, \"Efficient Asymmetric Syntheses of 1-Phenyl-phosphindane, Derivatives, and 2- or 3-Oxa Analogues: Mission Accomplished\", Organic Letters<\/i>, vol. 16, pp. 2688-2691, 2014. https:\/\/doi.org\/10.1021\/ol500970x<\/a>\n\n<\/li>\n
    18. Rast, Slavko., Mohar, Barbara., and Stephan, Michel., \"CCDC 1007629: Experimental Crystal Structure Determination\", 2014. https:\/\/doi.org\/10.5517\/cc12tj5l<\/a>\n\n<\/li>\n
    19. H. Rzepa, \"Crystallography meets DFT Quantum modelling.\", 2025. https:\/\/doi.org\/10.59350\/5dy8w-0zs92<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      In the previous post, I was commenting that the transition state for borohydride reduction of a ketone contained some close contacts between the hydrogen of the borohydride and the hydrogen of water. A systematic search of the CSD reveals a modest number of such contacts have been observed in crystal structures (Table). \u00a0Since it is […]<\/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":"federated","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":[4],"tags":[],"ppma_author":[2661],"class_list":["post-29799","post","type-post","status-publish","format-standard","hentry","category-interesting-chemistry"],"yoast_head":"\nShort B-H...H-O Interactions in crystal structures - a short DFT Exploration using B3LYP+D4 and r2scan-3c - 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=29799\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Short B-H...H-O Interactions in crystal structures - a short DFT Exploration using B3LYP+D4 and r2scan-3c - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"In the previous post, I was commenting that the transition state for borohydride reduction of a ketone contained some close contacts between the hydrogen of the borohydride and the hydrogen of water. A systematic search of the CSD reveals a modest number of such contacts have been observed in crystal structures (Table). \u00a0Since it is […]\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=29799\" \/>\n<meta property=\"og:site_name\" content=\"Henry Rzepa's Blog\" \/>\n<meta property=\"article:published_time\" content=\"2025-10-27T12:23:18+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2025-10-28T16:15:23+00:00\" \/>\n<meta name=\"author\" content=\"Henry Rzepa\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Henry Rzepa\" \/>\n\t<meta name=\"twitter:label2\" content=\"Estimated reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"3 minutes\" \/>\n<!-- \/ Yoast SEO plugin. -->","yoast_head_json":{"title":"Short B-H...H-O Interactions in crystal structures - a short DFT Exploration using B3LYP+D4 and r2scan-3c - Henry Rzepa's Blog","robots":{"index":"index","follow":"follow","max-snippet":"max-snippet:-1","max-image-preview":"max-image-preview:large","max-video-preview":"max-video-preview:-1"},"canonical":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=29799","og_locale":"en_GB","og_type":"article","og_title":"Short B-H...H-O Interactions in crystal structures - a short DFT Exploration using B3LYP+D4 and r2scan-3c - Henry Rzepa's Blog","og_description":"In the previous post, I was commenting that the transition state for borohydride reduction of a ketone contained some close contacts between the hydrogen of the borohydride and the hydrogen of water. A systematic search of the CSD reveals a modest number of such contacts have been observed in crystal structures (Table). \u00a0Since it is […]","og_url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=29799","og_site_name":"Henry Rzepa's Blog","article_published_time":"2025-10-27T12:23:18+00:00","article_modified_time":"2025-10-28T16:15:23+00:00","author":"Henry Rzepa","twitter_card":"summary_large_image","twitter_misc":{"Written by":"Henry Rzepa","Estimated reading time":"3 minutes"},"schema":{"@context":"https:\/\/schema.org","@graph":[{"@type":"Article","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=29799#article","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=29799"},"author":{"name":"Henry Rzepa","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"headline":"Short B-H…H-O Interactions in crystal structures – a short DFT Exploration using B3LYP+D4 and r2scan-3c","datePublished":"2025-10-27T12:23:18+00:00","dateModified":"2025-10-28T16:15:23+00:00","mainEntityOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=29799"},"wordCount":631,"commentCount":2,"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=29799#primaryimage"},"thumbnailUrl":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2025\/10\/OLEVIL.jpg","articleSection":["Interesting chemistry"],"inLanguage":"en-GB","potentialAction":[{"@type":"CommentAction","name":"Comment","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=29799#respond"]}]},{"@type":"WebPage","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=29799","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=29799","name":"Short B-H...H-O Interactions in crystal structures - a short DFT Exploration using B3LYP+D4 and r2scan-3c - Henry Rzepa's Blog","isPartOf":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#website"},"primaryImageOfPage":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=29799#primaryimage"},"image":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=29799#primaryimage"},"thumbnailUrl":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2025\/10\/OLEVIL.jpg","datePublished":"2025-10-27T12:23:18+00:00","dateModified":"2025-10-28T16:15:23+00:00","author":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281"},"breadcrumb":{"@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=29799#breadcrumb"},"inLanguage":"en-GB","potentialAction":[{"@type":"ReadAction","target":["https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=29799"]}]},{"@type":"ImageObject","inLanguage":"en-GB","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=29799#primaryimage","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2025\/10\/OLEVIL.jpg","contentUrl":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/wp-content\/uploads\/2025\/10\/OLEVIL.jpg","width":1594,"height":1203},{"@type":"BreadcrumbList","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=29799#breadcrumb","itemListElement":[{"@type":"ListItem","position":1,"name":"Home","item":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog"},{"@type":"ListItem","position":2,"name":"Short B-H…H-O Interactions in crystal structures – a short DFT Exploration using B3LYP+D4 and r2scan-3c"}]},{"@type":"WebSite","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#website","url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/","name":"Henry Rzepa's Blog","description":"Chemistry with a twist","potentialAction":[{"@type":"SearchAction","target":{"@type":"EntryPoint","urlTemplate":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?s={search_term_string}"},"query-input":{"@type":"PropertyValueSpecification","valueRequired":true,"valueName":"search_term_string"}}],"inLanguage":"en-GB"},{"@type":"Person","@id":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/#\/schema\/person\/2b40f7b9c872a4dc1547e040a11b6281","name":"Henry Rzepa","image":{"@type":"ImageObject","inLanguage":"en-GB","@id":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g370be3a7397865e4fd161aefeb0a5a85","url":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","contentUrl":"https:\/\/secure.gravatar.com\/avatar\/897b6740f7f599bca7942cdf7d7914af5988937ae0e3869ab09aebb87f26a731?s=96&d=blank&r=g","caption":"Henry Rzepa"},"description":"Henry Rzepa is Emeritus Professor of Computational Chemistry at Imperial College London.","sameAs":["https:\/\/orcid.org\/0000-0002-8635-8390"],"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?author=1"}]}},"jetpack_publicize_connections":[],"jetpack_featured_media_url":"","jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/pDef7-7KD","jetpack-related-posts":[{"id":29725,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=29725","url_meta":{"origin":29799,"position":0},"title":"The mechanism of borohydride reductions. Part 2: 4-t-butyl-cyclohexanone – Dispersion induced stereochemistry.","author":"Henry Rzepa","date":"October 21, 2025","format":false,"excerpt":"Part one of this topic was posted more than ten years ago. I clearly forgot about it, so belatedly, here is part 2 - dealing with the stereochemistry of the reduction of tert-butyl-cyclohexanone by borohydride in water. The known stereochemistry is nicely summarised in this article, along with an extensive\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":29892,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=29892","url_meta":{"origin":29799,"position":1},"title":"Reinvestigating the reported transition state structure of a concerted triple H-tunneling mechanism.","author":"Henry Rzepa","date":"November 21, 2025","format":false,"excerpt":"Substituting a deuterium isotope (2H) for a normal protium hydrogen isotope can slow the rate of a chemical reaction if this atom is involved in the reaction mode. The magnitude of the effect,\u00a0referred to as a kinetic isotope effect or KIE is normally 2-7, but higher values of 20 or\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\/2025\/11\/FOTBAR.jpg?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":21407,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21407","url_meta":{"origin":29799,"position":2},"title":"Does Kekulene have Kekul\u00e9 vibrational modes? Yes!","author":"Henry Rzepa","date":"October 19, 2019","format":false,"excerpt":"Increasingly, individual small molecules are having their structures imaged using STM, including cyclo[18]carbon that I recently discussed. The latest one receiving such treatment is Kekulene. As with cyclo[18]carbon, the point of interest was which of the two resonance structures shown below most closely resembled the measured structure. The one on\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\/2019\/10\/b3-1423-B2u-1024x575.gif?resize=350%2C200&ssl=1","width":350,"height":200},"classes":[]},{"id":30746,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=30746","url_meta":{"origin":29799,"position":3},"title":"Quantum crystallography: The structure and C-C bond length alternation of [18]-annulene.","author":"Henry Rzepa","date":"February 13, 2026","format":false,"excerpt":"In my story about one of the molecules of the year, cyclo[48]carbon, I noted that the DFT method used in the literature to model the C-C bond length alternation around the ring (OX B3LYP30) had been re-calibrated against a remeasured crystal structure of C18H18 or [18]-annulene (below) in order to\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":"","width":0,"height":0},"classes":[]},{"id":18165,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=18165","url_meta":{"origin":29799,"position":4},"title":"\u03c0-Facial hydrogen bonds to alkenes (revisited): how close can an acidic hydrogen approach?","author":"Henry Rzepa","date":"April 15, 2017","format":false,"excerpt":"Back in the early 1990s, we first discovered the delights of searching crystal structures\u00a0for unusual\u00a0bonding features. One of the first cases was a search for hydrogen bonds formed to the\u00a0\u03c0-faces of alkenes and alkynes. In those days the CSD database of crystal structures was a lot smaller (<80,000 structures; it's\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\/SQ-H-pi-1024x783.jpg?resize=350%2C200","width":350,"height":200},"classes":[]},{"id":13899,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13899","url_meta":{"origin":29799,"position":5},"title":"The mechanism of borohydride reductions. Part 1: ethanal.","author":"Henry Rzepa","date":"April 12, 2015","format":false,"excerpt":"Sodium borohydride is the tamer cousin of lithium aluminium hydride (LAH). It is used in aqueous solution to e.g. reduce aldehydes and ketones, but it leaves acids, amides and esters alone. Here I start an exploration of why it is such a different reducing agent. Initially, I am using Li,\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":[]}],"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\/29799","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=29799"}],"version-history":[{"count":67,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/29799\/revisions"}],"predecessor-version":[{"id":29890,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/29799\/revisions\/29890"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=29799"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=29799"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=29799"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=29799"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}