Previously, I explored deviation from ideal tetrahedral arrangements of four carbon ligands around a central (sp ³ ) carbon using crystal structures. Now it is the turn of digonal (sp ¹ ) and trigonal (sp ² ) carbons.  Firstly, the digonal C≡C case. Attached to each carbon of the C≡C unit are two saturated carbon ligands; this to prevent conjugation from influencing our result.

An article entitled " Four Decades of the Chemistry of Planar Hypercoordinate Compounds "[cite]10.1002/anie.201410407[/cite] was recently reviewed by Steve Bacharach on his blog, where you can also see comments. Given the recent crystallographic themes here, I thought I might try a search of the CSD (Cambridge structure database) to see whether anything interesting might emerge for tetracoordinate carbon.

The previous post explored the structural features of amides. Here I compare the analysis with that for the closely related thioamides. Here is the torsional analysis around the C-N bond. The “diff” (difference) is that almost all the hits are concentrated into angles of 0° or 180°; the twist about the C-N bond from co-planarity is much less if S is present.

The π-resonance in amides famously helped Pauling to his proposal of a helical structure for proteins. Here I explore some geometric properties of amides related to the C-N bond and the torsions about it. The key aspect of amides is that a lone pair of electrons on the nitrogen can conjugate with the C=O carbonyl only if the lone pair orbital is parallel to the C-O π-system.

The first conference devoted to scientific uses of Wikipedia has just finished; there was lots of fascinating stuff but here I concentrate on one report that I thought was especially interesting. To introduce it, I need first to introduce WikiData. This is part of the WikiMedia ecosystem, and one of the newest. The basic concept is really simple. It is a repository for data objects; 14,757,419 of them as I write this to be precise.

Most visitors to London use the famous underground trains (the “tube”) or a* double-decker bus* to see the city (one can also use rivers and canals). So I thought, during the tourism month of August, I would show you an alternative overground circumnavigation of the city using the metaphor of benzene. Benzene you see is a ring, comprising three “HCCH” segments.

The anomeric effect is best known in sugars, occuring in sub-structures such as RO-C-OR. Its origins relate to how the lone pairs on each oxygen atom align with the adjacent C-O bonds. When the alignment is 180°, one oxygen lone pair can donate into the C-O σ* empty orbital and a stabilisation occurs. Here I explore whether crystal structures reflect this effect.

Previously, I showed how conjugation in dienes and diaryls can be visualised by inspecting bond lengths as a function of torsions.

Here is another exploration of simple chemical concepts using crystal structures. Consider a simple diene: how does the central C-C bond length respond to the torsion angle between the two C=C bonds?

Management of research (data) outputs is a hot topic in the UK at the moment, although the topic has been rumbling for five years or more.

This post is prompted by the appearance of a retrospective special issue of C&E news, with what appears to be its very own Website: internet.cenmag.org.