Posts Tagged ‘Much software’

Data galore! 134 kilomolecules.

Wednesday, August 6th, 2014

I do go on a lot about the importance of having modern access to data. And so the appearance of this article[1] immediately struck me as important. It is appropriately enough in the new journal Scientific Data. The data contain computed properties at the B3LYP/6-31G(2df,p) level for 133,885 species with up to nine heavy atoms, and the entire data set has its own DOI[2]. The data is generated by subjecting a molecule set to a number of validation protocols, including obtaining relaxed (optimised) geometries at the B3LYP/6-31G(2df,p) level. It would be good to replicate this set with inclusion of a functional that also includes dispersion, and of course making the coordinates all available in this manner greatly facilitates this. The collection also includes data for e.g. 6095 constitutional isomers of C7H10O2, which reminds me of an early, delightfully entitled, article adopting such an approach in quantum chemistry[3]. Such collections are an important part of the process of validating computational methods[4] This way of publishing data does raise some interesting discussion points.

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References

  1. R. Ramakrishnan, P.O. Dral, M. Rupp, and O.A. von Lilienfeld, "Quantum chemistry structures and properties of 134 kilo molecules", Scientific Data, vol. 1, 2014. http://dx.doi.org/10.1038/sdata.2014.22
  2. Raghunathan Ramakrishnan., Pavlo Dral., Pavlo O. Dral., Matthias Rupp., and O. Anatole von Lilienfeld., "Quantum chemistry structures and properties of 134 kilo molecules", 2015. http://dx.doi.org/10.6084/m9.figshare.978904
  3. P.P. Bera, K.W. Sattelmeyer, M. Saunders, H.F. Schaefer, and P.V.R. Schleyer, "Mindless Chemistry", The Journal of Physical Chemistry A, vol. 110, pp. 4287-4290, 2006. http://dx.doi.org/10.1021/jp057107z
  4. P. Murray-Rust, H.S. Rzepa, J.J.P. Stewart, and Y. Zhang, "A global resource for computational chemistry", Journal of Molecular Modeling, vol. 11, pp. 532-541, 2005. http://dx.doi.org/10.1007/s00894-005-0278-1