How does an anaesthetic work? Surprisingly, it is only recently[cite]10.1038/nchembio.1340[/cite] that the possible binding sites of the anaesthetic propofol (2,6-di-isopropylphenol) have been identified using a technique known as photoaffinity labelling.[cite]10.1016/j.bmc.2011.06.066[/cite] A propofol analogue was constructed[cite]10.1038/nchembio.1340[/cite] by replacing one of the isopropyl groups with a trifluoromethyl diazirine group (R=CF3, X=Y=N below). Upon photolysis, this species looses nitrogen and forms a carbene as a reactive species, which with further chemistry binds covalently[cite]10.1016/j.bmc.2011.06.066[/cite] to adjacent amino acids in the binding pocket.These modified segments could then be analysed by mass spectrometry.[cite]10.1038/nchembio.1340[/cite] An isomer of diazirine is diazomethane, which is some 11 kcal/mol lower in free energy, but fortunately the diazirene is preventing from thermally isomerising to this species by a large kinetic barrier. That was the intro; now for a connection.‡ I recently attended a presentation on another medical topic, the therapeutic uses of carbon monoxide.[cite]10.1038/nrd3228[/cite] In higher concentrations it is notoriously lethal, but with appropriate delivery it can be therapeutic. So, intertwingling, I asked myself what the properties of the carbon monoxide isoelectronic analogue of a diazirine might be (X=C, Y=O below).
Isoelectronic games: the CO analogue of diazirines as an intriguing species?
September 24th, 2015Deviations from planarity of trigonal carbon and from linearity of digonal carbon.
September 13th, 2015Previously, I explored deviation from ideal tetrahedral arrangements of four carbon ligands around a central (sp3) carbon using crystal structures. Now it is the turn of digonal (sp1) and trigonal (sp2) carbons.
π-Resonance in thioamides: a crystallographic “diff” with amides.
September 5th, 2015The previous post explored the structural features of amides. Here I compare the analysis with that for the closely related thioamides.
π-Resonance in amides: a crystallographic reality check.
September 5th, 2015The 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.
A sea-change in science citation? The Wikipedia Science conference.
September 3rd, 2015The 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.
A tourist trip around London Overground with a chemical theme.
August 29th, 2015Most 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.
Mesomeric resonance in substituted benzenes: a crystallographic reality check.
August 26th, 2015Previously, I showed how conjugation in dienes and diaryls can be visualised by inspecting bond lengths as a function of torsions. Here is another illustration, this time of the mesomeric resonance on a benzene ring induced by an electron donating substituent (an amino group) or an electron withdrawing substituent (cyano).
A visualisation of the effects of conjugation; dienes and biaryls.
August 25th, 2015Here 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?