{"id":21726,"date":"2019-12-23T18:24:34","date_gmt":"2019-12-23T18:24:34","guid":{"rendered":"https:\/\/www.ch.imperial.ac.uk\/rzepa\/blog\/?p=21726"},"modified":"2019-12-23T20:29:14","modified_gmt":"2019-12-23T20:29:14","slug":"hydrogen-bonds-carbon-as-an-acceptor-rather-than-as-a-donor","status":"publish","type":"post","link":"https:\/\/www.ch.ic.ac.uk\/rzepa\/blog\/?p=21726","title":{"rendered":"Hydrogen bonds: carbon as an acceptor rather than as a donor?"},"content":{"rendered":"
\n

A hydrogen bond donor<\/a> is considered as an electronegative element carrying a hydrogen that is accepted by an atom carrying a lone pair of electrons, as in X:…H-Y where X: is the acceptor and H-Y the donor. Wikipedia asserts<\/a> that carbon can act as a donor, as we saw in the post on the incredible chloride cage<\/a>, where six Cl:<\/span><\/strong>…H-C interactions trapped the chloride ion inside the cage. This led me to ask how many examples are there of carbon as an acceptor<\/strong> rather than as a donor?<\/p>\n

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

The basic query is constructed as above: in order to act as an acceptor, the carbon must bear a lone pair of electrons, of which a carbene is one example (Query, see DOI: 10.14469\/hpc\/6531<\/a>). Thus we have QA=O,C,S and the central atom has only two connected atoms. When QC is any of C,N,O,F,Cl, we get the following result. The red circle corresponds to QC=O.<\/p>\n

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

The shortest example of these is shown below, with a C:<\/span><\/strong>…HO distance of 1.91\u00c5 nominal but about 0.1\u00c5 shorter if corrected for the over-short H-O bond (Data DOI: 10.5517\/ccvm80q<\/a>)[1]<\/a><\/span><\/p>\n

\"\"

Click image to view 3D<\/p><\/div>\n

The shortest C:<\/span><\/strong>…HN example is shown below with a distance of 2.07\u00c5 (DOI: 10.5517\/ccdc.csd.cc21tzql<\/a>)[2]<\/a><\/span><\/p>\n

\"\"

Click on image to view 3D model<\/p><\/div>\n

Finally C:<\/span><\/strong>…HC, of which there are many in the region of 2.5\u00c5, with the shortest example being 2.17\u00c5[3]<\/a><\/span><\/p>\n

\"\"

Click on image to view 3D model<\/p><\/div>\n

To round this off, N\u2261C:<\/span><\/strong>…HX, of which a nice example is (DOI: 10.5517\/ccs7whc<\/a>)[4]<\/a><\/span><\/p>\n

\"\"

Click on image for 3D model<\/p><\/div>\n

From which we conclude that carbon as a hydrogen bond acceptor exhibits a diversity of forms, often with surprisingly short distances! I guess the wikipedia article needs updating.<\/p>\n

References<\/h2>\n
  1. N.A. Giffin, M. Makramalla, A.D. Hendsbee, K.N. Robertson, C. Sherren, C.C. Pye, J.D. Masuda, and J.A.C. Clyburne, \"Anhydrous TEMPO-H: reactions of a good hydrogen atom donor with low-valent carbon centres\", Organic & Biomolecular Chemistry<\/i>, vol. 9, pp. 3672, 2011. https:\/\/doi.org\/10.1039\/c0ob00999g<\/a>\n\n<\/li>\n
  2. J.M. Kieser, Z.J. Kinney, J.R. Gaffen, S. Evariste, A.M. Harrison, A.L. Rheingold, and J.D. Protasiewicz, \"Three Ways Isolable Carbenes Can Modulate Emission of NH-Containing Fluorophores\", Journal of the American Chemical Society<\/i>, vol. 141, pp. 12055-12063, 2019. https:\/\/doi.org\/10.1021\/jacs.9b04864<\/a>\n\n<\/li>\n
  3. C. Jones, D.P. Mills, and R.P. Rose, \"Oxidative addition of an imidazolium cation to an anionic gallium(I) N-heterocyclic carbene analogue: Synthesis and characterisation of novel gallium hydride complexes\", Journal of Organometallic Chemistry<\/i>, vol. 691, pp. 3060-3064, 2006. https:\/\/doi.org\/10.1016\/j.jorganchem.2006.03.018<\/a>\n\n<\/li>\n
  4. S. Mo, A. Krunic, B.D. Santarsiero, S.G. Franzblau, and J. Orjala, \"Hapalindole-related alkaloids from the cultured cyanobacterium Fischerella ambigua\", Phytochemistry<\/i>, vol. 71, pp. 2116-2123, 2010. https:\/\/doi.org\/10.1016\/j.phytochem.2010.09.004<\/a>\n\n<\/li>\n<\/ol>\n\n<\/div> ","protected":false},"excerpt":{"rendered":"

    A hydrogen bond donor is considered as an electronegative element carrying a hydrogen that is accepted by an atom carrying a lone pair of electrons, as in X:…H-Y where X: is the acceptor and H-Y the donor. 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