{"id":26601,"date":"2023-12-28T18:08:51","date_gmt":"2023-12-28T18:08:51","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=26601"},"modified":"2023-12-28T18:27:11","modified_gmt":"2023-12-28T18:27:11","slug":"molecules-of-the-year-2023","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=26601","title":{"rendered":"Molecules of the year: 2023"},"content":{"rendered":"
\n

The Science education unit at the ACS publication C&EN publishes its list of molecules of the year (as selected by the editors and voted upon by the readers) in December. Here are some observations about three of this year’s batch<\/a>.<\/p>\n

    \n
  1. Diberyllocene[1]<\/a><\/span> with its unusual Be-Be bond has already beeen covered on this blog.[2]<\/a><\/span>, where I commented that lithioborocene should be possible to make as well.
    \n\"\"<\/li>\n
  2. The second in the list is the synthesis of the chiral triaryloxonium ion[3]<\/a><\/span> HICBUU(Crystal DOI: 10.5517\/ccdc.csd.cc2cjynj<\/a>). Curiously, this combines the features of two of our recent publications (with Chris Braddock)[4]<\/a><\/span>,[5]<\/a><\/span>. The first of these speculated upon a mechanism involving an intermediate (and as it happens chiral) oxonium ion and its subsequent rapid fragmentation by nucleophilic attack. This meant it was never isolated, unlike the one reported this year.[3]<\/a><\/span> The second article of ours involved another class of chiral natural product called polysiphenols and their enantiomerisation by a process called atropisomerism via a two stage process. This as it happens is also the feature reported for the the chiral triaryloxonium ion.\n

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

    The atropisomerism involves restricted (high energy) rotation about an axis shown as a dotted red line, accompanied at a separate stage with rotation about the C-C single bond shown in blue. The polysiphenols showed similar two-stage atropisomerism.<\/p>\n

    I show an intrinsic reaction coordinate calculation of this process below, being respectively the energy response and the dihedral angle responses about the 16-17 bond (blue) and the axis 2-18 (dashed red) and ending with an animation of the process.\n<\/p>\n

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

    Note how the C-C rotation is much lower in energy than the about the red axis. It is also interesting to observe that pyramidal inversion at the chiral oxygen centre via<\/em> a trigonal planar unit only happens at an IRC value of ~+30, well after both transition states have passed!\n<\/li>\n

  3. The third topic is represented by the crystal structure NITRUH (Crystal DOI: 10.5517\/ccdc.csd.cc2fcr2n<\/a>),[6]<\/a><\/span>. This is announced at the C&EN page as “carbene breaks octet rule”, in having only four valence electrons at the central carbon atom. The structure is certainly unique, the motif shown below having only one entry in the crystal structure database. Leaving aside the observation that a true carbene also breaks the octet rule with its nominal six valence electrons, how could this arise? Well, shown below are six canonical forms of this species (the original article shows four) of which species 1a<\/strong> is the one referred to as having only four valence electrons at the central atom, whilst 1b<\/strong> is that favoured in the article.\n

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

    What does a calculation reveal (ωB97XD\/Def2-TZVPP; DOI for data 10.14469\/hpc\/13532<\/a>)? The Wiberg bond index calculated for the central carbon atom is 3.8328, which corresponds to 7.67 electrons. Far from four! The Wiberg bond orders along the chain are 1.54, 1.14, 1.83, 1.83, 1.12, 1.58 (the species is calculated as not quite symmetrical as an isolated molecule) which is a close match to structure 1e<\/strong> (not shown in the article). Dare I suggest that the tag line for this entry in the C&EN article is a good example of copywriters hyperbole, something designed to catch the interest and attention of the reader? Well, it certainly succeeded, but I venture to suggest that although the molecule is indeed interesting and unique, it does NOT break the octet rule. A good discussion point perhaps for a chemistry tutorial?\n<\/li>\n<\/ol>\n

    References<\/h2>\n
    1. J.T. Boronski, A.E. Crumpton, L.L. Wales, and S. Aldridge, \"Diberyllocene, a stable compound of Be(I) with a Be\u2013Be bond\", Science<\/i>, vol. 380, pp. 1147-1149, 2023. https:\/\/doi.org\/10.1126\/science.adh4419<\/a>\n\n<\/li>\n
    2. H. Rzepa, \"Diberyllocene \u2014 and Lithioborocene?\", 2023. https:\/\/doi.org\/10.59350\/v1cma-xjk91<\/a>\n\n<\/li>\n
    3. O. Smith, M.V. Popescu, M.J. Hindson, R.S. Paton, J.W. Burton, and M.D. Smith, \"Control of stereogenic oxygen in a helically chiral oxonium ion\", Nature<\/i>, vol. 615, pp. 430-435, 2023. https:\/\/doi.org\/10.1038\/s41586-023-05719-z<\/a>\n\n<\/li>\n
    4. J. Clarke, K.J. Bonney, M. Yaqoob, S. Solanki, H.S. Rzepa, A.J.P. White, D.S. Millan, and D.C. Braddock, \"Epimeric Face-Selective Oxidations and Diastereodivergent Transannular Oxonium Ion Formation Fragmentations: Computational Modeling and Total Syntheses of 12-Epoxyobtusallene IV, 12-Epoxyobtusallene II, Obtusallene X, Marilzabicycloallene C, and Marilzabicycloallene D\", The Journal of Organic Chemistry<\/i>, vol. 81, pp. 9539-9552, 2016. https:\/\/doi.org\/10.1021\/acs.joc.6b02008<\/a>\n\n<\/li>\n
    5. D.C. Braddock, A. Duran-Corbera, M. Nilforoushan, Z. Yang, T. He, G. Santhakumar, K.A. Bahou, H.S. Rzepa, R. Woscholski, and A.J.P. White, \"(\u00b1)-Polysiphenol and Other Analogues via Symmetrical Intermolecular Dimerizations: A Synthetic, Spectroscopic, Structural, and Computational Study\", Journal of Natural Products<\/i>, vol. 85, pp. 2650-2655, 2022. https:\/\/doi.org\/10.1021\/acs.jnatprod.2c00749<\/a>\n\n<\/li>\n
    6. Y.K. Loh, M. Melaimi, M. Gembicky, D. Munz, and G. Bertrand, \"A crystalline doubly oxidized carbene\", Nature<\/i>, vol. 623, pp. 66-70, 2023. https:\/\/doi.org\/10.1038\/s41586-023-06539-x<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

      The Science education unit at the ACS publication C&EN publishes its list of molecules of the year (as selected by the editors and voted upon by the readers) in December. Here are some observations about three of this year’s batch. Diberyllocene with its unusual Be-Be bond has already beeen covered on this blog., where I […]<\/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":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":[],"tags":[],"ppma_author":[2661],"class_list":["post-26601","post","type-post","status-publish","format-standard","hentry"],"yoast_head":"\nMolecules of the year: 2023 - 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=26601\" \/>\n<meta property=\"og:locale\" content=\"en_GB\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Molecules of the year: 2023 - Henry Rzepa's Blog\" \/>\n<meta property=\"og:description\" content=\"The Science education unit at the ACS publication C&EN publishes its list of molecules of the year (as selected by the editors and voted upon by the readers) in December. 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Here I extend that by probing\u00a0the role of water molecules\u00a0in the mechanism of acetal hydrolysis. Water molecules can participate in three ways: One water acts as a nucleophile to\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":13458,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13458","url_meta":{"origin":26601,"position":1},"title":"How many water molecules does it take to ionise HF and HBr?","author":"Henry Rzepa","date":"February 27, 2015","format":false,"excerpt":"No doubt answers to the question posed in the previous post\u00a0are already being obtained by experiment. Just in case that does not emerge in the next day or so, I offer a prediction here. The methodology is the same as before, and I have not tried to look for new\u2026","rel":"","context":"In "General"","block_context":{"text":"General","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?cat=1"},"img":{"alt_text":"","src":"","width":0,"height":0},"classes":[]},{"id":28187,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=28187","url_meta":{"origin":26601,"position":2},"title":"Molecules of the Year 2024: A crystal structure perspective on anti-Bredt olefins.","author":"Henry Rzepa","date":"January 8, 2025","format":false,"excerpt":"Each year C&E News publishes a list of candidates for the Molecule of the Year. For 2024 the list is (in order of votes cast for each) Mirror-image cyclodextrin Molecular shuttle in a box Rule-bending strained alkene First soluble promethium complex Single-electron carbon-carbon bond Hot MOF for capturing carbon I\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":"","width":0,"height":0},"classes":[]},{"id":13618,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13618","url_meta":{"origin":26601,"position":3},"title":"Ionizing ultra-strong acids with water molecules.","author":"Henry Rzepa","date":"March 15, 2015","format":false,"excerpt":"My previous posts have covered the ionization by a small number of discrete water molecules of the series of halogen acids, ranging from HI (the strongest,\u00a0pKa -10) via HF (weaker, pKa 3.1) to the pseudo-halogen HCN (the weakest, pKa 9.2). Here I try out some even stronger acids to see\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":"","width":0,"height":0},"classes":[]},{"id":31140,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=31140","url_meta":{"origin":26601,"position":4},"title":"The fast disappearance of hydroxycarbene through hydrogen tunnelling – or is it really tunnelling?","author":"Henry Rzepa","date":"April 11, 2026","format":false,"excerpt":"In 2008, the previously elusive hydroxycarbene, H-C-OH was finally reported as having been captured by matrix isolation, accompanied by the observation that \"we unexpectedly find that H\u2013C\u2013OH rearranges to formaldehyde with a half-life of only 2h at 11K by pure hydrogen tunnelling through a large energy barrier in excess of\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":"","width":0,"height":0},"classes":[]},{"id":13676,"url":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=13676","url_meta":{"origin":26601,"position":5},"title":"Ionizing yet more ultra-strong acids with water molecules.","author":"Henry Rzepa","date":"March 20, 2015","format":false,"excerpt":"This might be seen as cranking a handle by producing yet more examples of acids ionised by a small number of water molecules. I justify it (probably only to myself) as an exercise in how a scientist might approach a problem, and how it linearly develops with time, not necessarily\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":"","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","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\/26601","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=26601"}],"version-history":[{"count":15,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/26601\/revisions"}],"predecessor-version":[{"id":26622,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=\/wp\/v2\/posts\/26601\/revisions\/26622"}],"wp:attachment":[{"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=26601"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=26601"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=26601"},{"taxonomy":"author","embeddable":true,"href":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/index.php?rest_route=%2Fwp%2Fv2%2Fppma_author&post=26601"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}