Having shown that carbon as a carbene centre, C: can act as a hydrogen bond acceptor, as seen from a search of crystal structures, I began to wonder if there is any chance that carbon as a radical centre, C• could do so as well. Definitely a subversive thought, since radical centres are supposed to abstract hydrogens rather than to hydrogen bond to them.
Archive for the ‘crystal_structure_mining’ Category
Can a carbon radical act as a hydrogen bond acceptor?
Saturday, December 28th, 2019CH…O hydrogen bonding competing with layered dispersion attractions.
Friday, July 19th, 2019I have previously looked at the topic of hydrogen bonding interactions from the hydrogen of chloroform Here I generalize C-H…O interactions by conducting searches of the CSD (Cambridge structure database) as a function of the carbon hybridisation. I am going to jump straight to a specific molecule XEVJIR (DOI: 10.5517/cc5fgpq) identified from the searches appended to this post as interesting for further inspection.[1]
References
- K.S. Huang, M.J. Haddadin, M.M. Olmstead, and M.J. Kurth, "Synthesis and Reactions of Some Heterocyclic Azacyanines1", The Journal of Organic Chemistry, vol. 66, pp. 1310-1315, 2001. http://dx.doi.org/10.1021/jo001484k
The shortest known CF…HO hydrogen bond.
Sunday, March 24th, 2019There is a predilection amongst chemists for collecting records; one common theme is the length of particular bonds, either the shortest or the longest. A particularly baffling type of bond is that between the very electronegative F atom and an acid hydrogen atom such as that in OH. Thus short C-N…HO hydrogen bonds are extremely common, as are C-O…HO.‡ But F atoms in C-F bonds are largely thought to be inert to hydrogen bonding, as indicated by the use of fluorine in many pharmaceuticals as inert isosteres.[1] Here I do an up-to-date search of the CSD crystal structure database, which is now on the verge of accumulating 1 million entries, to see if any strong C-F…HO hydrogen bonding may have been recently discovered.
References
- S. Purser, P.R. Moore, S. Swallow, and V. Gouverneur, "Fluorine in medicinal chemistry", Chem. Soc. Rev., vol. 37, pp. 320-330, 2008. http://dx.doi.org/10.1039/B610213C
Elongating an N-B single bond is much easier than stretching a C-C single bond.
Tuesday, October 24th, 2017An N-B single bond is iso-electronic to a C-C single bond, as per below. So here is a simple question: what form does the distribution of the lengths of these two bonds take, as obtained from crystal structures?
Dispersion “bonds” not involving hydrogen. A Cl…Cl candidate?
Thursday, June 29th, 2017In the previous post, I noted the crystallographic detection of an unusually short non-bonded H…H contact of ~1.5Å, some 0.9Å shorter than twice the van der Waals radius of hydrogen (1.2Å, although some sources quote 1.1Å which would make the contraction ~0.7Å). This was attributed to dispersion attractions accumulating in the rest of the molecule. I asked myself what the potential might be for other elements to reveal significantly contracted non-bonded distances as a result of dispersive attractions.
Tautomeric polymorphism.
Thursday, June 1st, 2017Conformational polymorphism occurs when a compound crystallises in two polymorphs differing only in the relative orientations of flexible groups (e.g. Ritonavir).[1] At the Beilstein conference, Ian Bruno mentioned another type; tautomeric polymorphism, where a compound can crystallise in two forms differing in the position of acidic protons. Here I explore three such examples.
References
- G.J.O. Beran, I.J. Sugden, C. Greenwell, D.H. Bowskill, C.C. Pantelides, and C.S. Adjiman, "How many more polymorphs of ROY remain undiscovered", Chemical Science, vol. 13, pp. 1288-1297, 2022. http://dx.doi.org/10.1039/D1SC06074K
CH⋅⋅⋅π Interactions between methyl and carbonyl groups in proteins: a small molecule check.
Monday, May 29th, 2017Derek Lowe highlights a recent article[1] postulating CH⋅⋅⋅π interactions in proteins. Here I report a quick check using the small molecule crystal structure database (CSD).
References
- F.A. Perras, D. Marion, J. Boisbouvier, D.L. Bryce, and M.J. Plevin, "Observation of CH⋅⋅⋅π Interactions between Methyl and Carbonyl Groups in Proteins", Angewandte Chemie International Edition, vol. 56, pp. 7564-7567, 2017. http://dx.doi.org/10.1002/anie.201702626