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Friday, March 24, 2023

Molecules of the yr -2022. Knowledge points!

The record of molecules of the yr is out now at C&E Information (however it’s important to have an account to view the record, not like earlier years). These three caught my eye:

  1. Electron in a dice: Synthesis and characterization of perfluorocubane as an electron acceptor,[1]. I’ve already written about this technique and won’t focus on it additional, besides to notice this one topped the ballot!
  2. Vernier template synthesis of molecular knots[2]
  3. Megalo-Cavitands: Synthesis of Acridane[4]arenes and Formation of Giant, Deep Cavitands for Selective C70 Uptake[3]

The final two are examples of huge three-dimensional molecules with uncommon properties. The second is an instance of a trefoil-of-trefoils, referred to as a triskelion knot and I used to be very eager to pay money for its coordinates in order that I might examine the knotting. I believed I would summarise right here the hierarchical procedures one may strive for buying such knowledge.

  • Probably the most trendy methodology of buying knowledge related to an article is to examine the quotation record on the finish of the article. The pattern inspired by the FAIR knowledge ideas means that if such knowledge has an related DOI (as certainly the article itself does), then this DOI ought to be cited within the citations similar to articles themselves. This idea is also referred to as treating knowledge as a first-class citizen of the scholarly processes. On this case no knowledge was related to the 81 citations listed at 10.1126/science.abm9247
  • The prevalent methodology since ~1996 has been to subsequent obtain any ESI. That’s linked right here. I can’t assist however observe that the PDF format isn’t one optimised for knowledge, however its higher than nothing. This PDF has 114 pages, and one finally finds the next on p 103: buildings and corresponding energies uploaded to the Github database (https://github.com/kjhstenlid/AshbridgeVernier2022/). Github is called a software program repository, however its use as a knowledge repository is uncommon. Thus no DOI is assigned this knowledge (which might clarify why its not listed within the article citations). Right here one learns from the readme that it accommodates Molecular knot buildings in cif-file format for the Verner and Sheild knots.
  • To get this knowledge one has to faux it’s code, and obtain the ZIP code archive. The CIF file discovered there nonetheless offers a deadly error when attempting to load right into a CIF viewer comparable to Mercury: Studying cell from Cif failed, couldn’t retrieve ‘_cell_length+a’. The CIF is clearly not generated from a crystallographic evaluation program however a modelling program and is clearly invalid as a CIF.
  • One now has to fall again seeing if the CIF file could be rescued utilizing a textual content editor. That is non-trivial however about 10 minutes of enhancing lastly produces a file that may be seen.
  • Right here is the 3D construction (click on on the picture to view).

Now for the Megalo-Cavitands (or not). Simply as above, one leads to a 49-page PDF file in search of coordinates. There one will get photos of PM6-computed fashions beginning on p 28, however alas apparently no related coordinates.

So no 3D fashions to indicate right here then (sorry, clicking on the picture above is not going to produce them).

My concluding comment ought to be that when an fascinating molecule is chosen for inclusion in eg the molecules of the yr – 2022, one of many standards for its inclusion is that the supply of full and FAIR knowledge describing its properties ought to be one of many important standards for choice.

I observe the strategy used to generate these coordinates (PM6) is maybe not ultimate; it accommodates no dispersion attraction phrases, that are most likely essential if modelling host-guest complexation. The PM7 methodology which does is much better for this form of factor! This highlights the significance of offering knowledge, on this case 3D coordinates. It will be fascinating to recompute the scale of those molecules utilizing a way that does permit for dispersion sights to be included. For simply such an instance, see right here.
I’ve contacted the authors of [3] and it seems a reference to a Knowledge repository submission was omitted from the article. The information is at DOI: 10.5281/zenodo.6953961 and I’ll report individually on my evaluation of the impact of changing PM6 with PM7.
See this open letter about modifications at C&EN.

This publish has DOI: 10.14469/hpc/12028

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