October 14th, 2021
On October 13, 2021, the historical group of the Royal Society of Chemistry organised a symposium celebrating ~150 years of the history of (molecular) chirality. We met for the first time in person for more than 18 months and were treated to a splendid and diverse program about the subject. The first speaker was Professor John Steeds from Bristol, talking about the early history of light and the discovery of its polarisation. When a slide was shown about herapathite[1] my “antennae” started vibrating. This is a crystalline substance made by combining elemental iodine with quinine in acidic conditions and was first discovered by William Herapath as long ago as 1852[2] in unusual circumstances. Now to the serendipity!
Read the rest of this entry »
References
- B. Kahr, J. Freudenthal, S. Phillips, and W. Kaminsky, "Herapathite", Science, vol. 324, pp. 1407-1407, 2009. https://doi.org/10.1126/science.1173605
- W.B. Herapath, "XXVI. <i>On the optical properties of a newly-discovered salt of quinine, which crystalline substance possesses the power of polarizing a ray of light, like tourmaline, and at certain angles of rotation of depolarizing it, like selenite</i>", The London, Edinburgh, and Dublin Philosophical Magazine and Journal of Science, vol. 3, pp. 161-173, 1852. https://doi.org/10.1080/14786445208646983
Posted in Chiroptics, crystal_structure_mining, Historical, Interesting chemistry | No Comments »
September 28th, 2021
In the previous blog post, I looked at the metadata records registered with DataCite for some chemical computational modelling files as published in three different repositories. Here I take it one stage further, by looking at how searches of the DataCite metadata store for three particular values of the metadata associated with this dataset compare.
Read the rest of this entry »
Posted in Chemical IT | No Comments »
September 28th, 2021
The number of repositories which accept research data across a wide spectrum of disciplines is on the up. Here I report the results of conducting an experiment in which chemical modelling data was deposited in six such repositories and comparing the richness of the metadata describing the essential properties of the six depositions.
Read the rest of this entry »
Posted in Chemical IT | No Comments »
September 13th, 2021
You might have noticed if you have read any of my posts here is that many of them have been accompanied since 2006 by supporting calculations, normally based on density functional theory (DFT) and these calculations are accompanied by a persistent identifier pointer‡ to a data repository publication. I have hitherto not gone into the detail here of the infrastructures required to do this sort of thing, but recently one of the two components has been updated to V2, after being at V1 for some fourteen years[1] and this provides a timely opportunity to describe the system a little more.
Read the rest of this entry »
References
- M.J. Harvey, N.J. Mason, and H.S. Rzepa, "Digital Data Repositories in Chemistry and Their Integration with Journals and Electronic Notebooks", Journal of Chemical Information and Modeling, vol. 54, pp. 2627-2635, 2014. https://doi.org/10.1021/ci500302p
Posted in Chemical IT | No Comments »
August 17th, 2021
The homologous hydrocarbon series R4C is known for R=Me as neopentane and for R=Et as 3,3-diethylpentane. The next homologue, R=iPr bis(3,3-isopropyl)-2,4-dimethylpentane is also a known molecule[1] for which a crystal structure has been reported (DOI: https://doi.org/10.5517/cc4wvnh). The final member of the series, R= tbutyl is unknown. Here I have a look at some properties of the last two of these highly hindered hydrocarbons.
Read the rest of this entry »
References
- S.I. Kozhushkov, R.R. Kostikov, A.P. Molchanov, R. Boese, J. Benet-Buchholz, P.R. Schreiner, C. Rinderspacher, I. Ghiviriga, and A. de Meijere, "Tetracyclopropylmethane: A Unique Hydrocarbon with S4 Symmetry", Angewandte Chemie International Edition, vol. 40, pp. 180-183, 2001. https://doi.org/10.1002/1521-3773(20010105)40:1<180::aid-anie180>3.0.co;2-k
Posted in Interesting chemistry | No Comments »
August 15th, 2021
Whilst I was discussing the future of scientific publication in the last post, a debate was happening behind the scenes regarding the small molecule cyclopropenylidene. This is the smallest known molecule displaying π-aromaticity, but its high reactivity means that it is unlikely to be isolated in the condensed phase. A question in the discussion asked if substituting it with a large sterically hindering group such as R=Et3C might help prevent its dimerisation and hence allow for isolation of the monomer so that its properties can be studied.
Read the rest of this entry »
Posted in crystal_structure_mining, Interesting chemistry | 2 Comments »
August 13th, 2021
In 2011, I suggested that the standard monolith that is the conventional scientific article could be broken down into two separate, but interlinked components, being the story or narrative of the article and the data on which the story is based. Later in 2018 the bibliography in the form of open citations were added as a distinct third component.[1] Here I discuss an approach that has taken this even further, breaking the article down into as many as eight components and described as “Octopus publishing” for obvious reasons. These are;
Read the rest of this entry »
References
- D. Shotton, "Funders should mandate open citations", Nature, vol. 553, pp. 129-129, 2018. https://doi.org/10.1038/d41586-018-00104-7
Posted in Chemical IT | No Comments »
July 22nd, 2021
In the earlier post on the topic of anomeric effects, I identified a number of outliers associated with large differences in the lengths of two carbon-oxygen bonds sharing a common carbon atom.
Read the rest of this entry »
Posted in crystal_structure_mining | No Comments »
July 21st, 2021
In another post, a discussion arose about whether it might be possible to trap cyclopropenylidene to form a small molecule with a large dipole moment. Doing so assumes that cyclopropenylidene has a sufficiently long lifetime to so react, before it does so with itself to e.g. dimerise. That dimerisation has an energy profile shown below, with a free energy of activation of 14.4 kcal/mol, so a facile reaction that will indeed compete with reaction with Ph-I+-CC–. 
Read the rest of this entry »
Posted in Curly arrows, reaction mechanism | 4 Comments »