The list of molecules of the year is out now at C&E News (but you have to have an account to view the list, unlike previous years).♣ These three caught my eye:
The last two are examples of large three-dimensional molecules with unusual properties. The second is an example of a trefoil-of-trefoils, called a triskelion knot and I was very keen to get hold of its coordinates so that I could inspect the knotting. I thought I might summarise here the hierarchical procedures one might try for acquiring such data.
Now for the Megalo-Cavitands (or not). Just as above, one ends up in a 49-page PDF file looking for coordinates. There one gets pictures of PM6-computed models starting on p 28, but alas apparently no associated coordinates.†
So no 3D models to show here then (sorry, clicking on the image above will not produce them†).
My concluding remark should be that when an interesting molecule is selected for inclusion in eg the molecules of the year – 2022, one of the criteria for its inclusion is that the availability of full and FAIR data describing its properties should be one of the essential criteria for selection.
‡I note the method used to generate these coordinates (PM6) is perhaps not ideal; it contains no dispersion attraction terms, which are probably important if modelling host-guest complexation. The PM7 method which does is far better for this sort of thing! This highlights the importance of providing data, in this case 3D coordinates. It would be interesting to recompute the dimensions of these molecules using a method that does allow for dispersion attractions to be included. For just such an example, see here.
† I have contacted the authors of [3] and it turns out a reference to a Data repository submission was omitted from the article. The data is at DOI: 10.5281/zenodo.6953961 and I will report separately on my analysis of the effect of replacing PM6 with PM7.
♣See this open letter about changes at C&EN.
This post has DOI: 10.14469/hpc/12028
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