Archive for February, 2021

The chemistry of scents: Vetifer oil.

Sunday, February 28th, 2021

I have occasionally covered the topic of colours here, such as those of flowers and minerals, since it is at least possible to illustrate these using photographs or colour charts to illustrate the theme. But when Derek Lowe took a break from his remarkable coverage of the COVID pandemic to highlight a recent article on the active smelling principle in Vetifer oil[1] I could not resist adding a tiny amount to his must-read story.



  1. J. Ouyang, H. Bae, S. Jordi, Q.M. Dao, S. Dossenbach, S. Dehn, J.B. Lingnau, C. Kanta De, P. Kraft, and B. List, "The Smelling Principle of Vetiver Oil, Unveiled by Chemical Synthesis", Angewandte Chemie International Edition, vol. 60, pp. 5666-5672, 2021.

Non-covalent-interaction (NCI) surfaces for two large annulenes (revisited).

Sunday, February 7th, 2021

The last post addressed the concept of “steric clashes” in a pericyclic reaction transition state as an extension of the time honoured practice of building molecular models to analyse reaction outcomes. A modern computer generated model might express this in terms of a NCI (non-covalent-interaction) surface. A few posts ago, I had looked at some “molecules of the year” for 2020, one of which was a “figure-eight” twisted dodecaporphyrin in which an aspect of the reported[1] geometry had struck me as potentially lacking features due to the so-called non-covalent dispersion or van der Waals attractions. So I am revisiting here by adding the NCI surface for this molecule and one other.



  1. M. Rickhaus, M. Jirasek, L. Tejerina, H. Gotfredsen, M.D. Peeks, R. Haver, H. Jiang, T.D.W. Claridge, and H.L. Anderson, "Global aromaticity at the nanoscale", Nature Chemistry, vol. 12, pp. 236-241, 2020.

The thermal reactions … took precisely the opposite stereochemical course to that which we had predicted. A non-covalent-interaction view of the model.

Wednesday, February 3rd, 2021

Another foray into one of the more famous anecdotal chemistry “models”, the analysis of which led directly to the formulation of the WoodWard-Hoffmann (stereochemical) rules for pericyclic reactions. Previously, I tried to produce a modern computer model of what Woodward might have had to hand when discovering that the stereochemical outcome of a key reaction in his vitamin B12 synthesis was opposite to that predicted using his best model of the reaction.