Earlier this year, Molnupiravir hit the headlines as a promising antiviral drug. This is now followed by Paxlovid, which is the first small molecule to be aimed by design at the SAR-CoV-2 protein and which is reported as reducing greatly the risk of hospitalization or death when given within three days of symptoms appearing in high risk patients.
First came Molnupiravir – now there is Paxlovid as a SARS-CoV-2 protease inhibitor. An NCI analysis of the ligand.
November 13th, 2021More examples of crystal structures containing embedded linear chains of iodines.
October 17th, 2021The previous post described the fascinating 170-year history of a crystalline compound known as Herapathite and its connection to the mechanism of the Finkelstein reaction via the complex of Na+I2– (or Na22+I42-). Both compounds exhibit (approximately) linear chains of iodine atoms in their crystal structures, a connection which was discovered serendipitously. Here I pursue a rather more systematic way of tracking down similar compounds.
Herapathite: an example of (double?) serendipity.
October 14th, 2021On 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[cite]10.1126/science.1173605[/cite] 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[cite]10.1080/14786445208646983[/cite] in unusual circumstances. Now to the serendipity!
A comparison of searches based on metadata records from three (update: five) research repositories.
September 28th, 2021In 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.
A comparison of descriptive metadata across different data repositories.
September 28th, 2021The 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.
HPC Access and Metadata Portal (CHAMP).
September 13th, 2021You 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[cite]10.1021/ci500302p[/cite] and this provides a timely opportunity to describe the system a little more.
More record breakers for the anomeric effect involving C-N bonds.
September 4th, 2021An earlier post investigated large anomeric effects involving two oxygen atoms attached to a common carbon atom.
Tetra-isopropylmethane and tetra-t-butylmethane.
August 17th, 2021The 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[cite]10.1002/1521-3773(20010105)40:1%3C180::AID-ANIE180%3E3.3.CO;2-B[/cite] 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.
Sterically stabilized cyclopropenylidenes. An example of Octopus publishing?
August 15th, 2021Whilst 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.
Octopus publishing: dis-assembling the research article into eight components.
August 13th, 2021In 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.[cite]10.1038/d41586-018-00104-7[/cite] 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;