“For chemists, the AI revolution has yet to happen”.

May 25th, 2023

This editorial from Nature[1] is a timely reminder of the importance of data. But also, not just any data, but “accurate and accessible training data“. Accessible of course is one of the attributes of FAIR (Findable, Accessible, Interoperable and Re-usable). The editorial also states “data need to be recorded in agreed and consistent formats, which they are not at present“. That is covered by the I and R of FAIR, often applied in conjunction with metadata recording the Media type that the data is held in (See DOI https://doi.org/jvk9 for examples of the use of Media types in chemical computation and chemical NMR). Again, “The best possible training sets would also include data on negative outcomes“. This relates to the separation of the two publication processes, namely the article itself (or the story behind the data) and the data itself as a first class scientific object. Thus when we publish FAIR data in association with articles, the data archive will often contain data that is not used in the article itself (perhaps because it led to a negative outcome), but is nevertheless part of the FAIR data collection for that topic. Even if the data does not lead to journal publication, publishing it in a data repository means it will not be lost. Somebody (or AI software) may still find it useful.

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  1. "For chemists, the AI revolution has yet to happen", Nature, vol. 617, pp. 438-438, 2023. http://dx.doi.org/10.1038/d41586-023-01612-x

Tunable aromaticity? An unrecognized new aromatic molecule?

May 21st, 2023

Some time ago in 2010, I showed a chemical problem I used to set during university entrance interviews. It was all about pattern recognition and how one can develop a hypothesis based on this. In that instance, it involved recognising that a cyclic molecule which appeared to have the cyclohexatriene benzene-aromatic pattern 1 was in fact a trimer of carbon dioxide. Perhaps small amounts of this aromatic molecule exist in solutions of fizzy drinks? Analysing these patterns occupied about 10-20 minutes of an interview, and although you might think I was posing a difficult challenge, many students successfully rose to it! Now I revisit, but with a slightly better reality check on a related molecule 2 (cyanuric acid).

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One vs two bond rotation – An example using Acyl amides

April 3rd, 2023

One of the important aspects of chemical reaction mechanisms is the order in which things happen. More specifically, the order in which bonds make or break when there are more than two involved in undertaking a reaction. So we have:

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A ROR Persistent Identifier for the WATOC organisation – helping to make scientific connections.

March 9th, 2023

Science frequently works by people making connections between related (or even apparently unrelated) concepts or data. There are many ways of helping people make these connections – attending a conference or seminar, searching journals for published articles and nowadays also searching for data are just a few examples. For about 20 years now, one technology which has been helping to enable such discoveries is what are called “Persistent IDentifiers” or PIDs. These are unique labels which can be attached to a (scientific) object such as a journal article, a dataset or a researcher. The PIDs for the first two examples have become better known as DOIs (digital object identifier), the last is known as an ORCID. The PID is registered with a registration authority. Two of the oldest and  best known authorities are CrossRef for journal articles, funders (etc) and DataCite, who specialise in citable identifiers for data. The registration process includes creating and adding a metadata record to the PID, the record is then indexed and can then be used for searching for the objects. The terms of these metadata records are carefully controlled to use specified and standardised vocabularies to describe the objects (one current initiative in chemistry in this area is described here[1]).

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  1. R.M. Hanson, D. Jeannerat, M. Archibald, I.J. Bruno, S.J. Chalk, A.N. Davies, R.J. Lancashire, J. Lang, and H.S. Rzepa, "IUPAC specification for the FAIR management of spectroscopic data in chemistry (IUPAC FAIRSpec) – guiding principles", Pure and Applied Chemistry, vol. 94, pp. 623-636, 2022. http://dx.doi.org/10.1515/pac-2021-2009

Determining absolute configuration: Cylindricine.

February 1st, 2023

Nature has produced most natural molecules as chiral objects, which means the molecule can come in two enantiomeric forms, each being the mirror image of the other. When a natural product is synthesised in a laboratory, a chiral synthesis means just one form is made, and then is compared with the natural product to see if it matches. Just such a process was following in the recent synthesis of cylindricine, a marine alkaloid[1] featured on the ACS molecule-of-the-week site. The authors noted that the absolute configuration of cylindricine as isolated naturally had remained unassigned, and as it happens one way of measuring the properties of the individual enantiomer – its optical rotation – had not been determined. So in part, the purpose of this synthesis was to determine the absolute configuration of this molecule. Here I explore this process.

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  1. M. Piccichè, A. Pinto, R. Griera, J. Bosch, and M. Amat, "Total Synthesis of (−)-Cylindricine H", Organic Letters, vol. 24, pp. 5356-5360, 2022. http://dx.doi.org/10.1021/acs.orglett.2c02004

A look at (one of) the dyes used in the Bayeaux tapestry.

January 3rd, 2023

I have previously looked at the pigments used to colour the Book of Kells, which dates from around 800 AD and which contained arsenic sulfide as the yellow colourant. The Bayeaux tapestry is a later embroidery dating probably from around 1077 and here the colours are based entirely on mordanted natural dyes. These are generally acknowledged to be blue woad (principle component indigo), red madder (principle component alizarin) and the less well-known yellow weld, which comes from the plant Reseda Luteola and the principle component of which is luteolin.

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Molecules of the year -2022. A closer look at the Megalo-Cavitands.

December 15th, 2022

In the previous post, I discussed how data associated with two of the candidates for molecules of the year – 2022 could be retrieved and then used to inspect their three dimensional structures. Here I focus on the ultra large cavitands recently reported[1]. As I noted, these have an associated data coordinate archive published on Zenodo (DOI: 10.5281/zenodo.6953961) although this is not cited in the article itself.

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  1. J. Pfeuffer‐Rooschüz, S. Heim, A. Prescimone, and K. Tiefenbacher, "Megalo‐Cavitands: Synthesis of Acridane[4]arenes and Formation of Large, Deep Cavitands for Selective C70 Uptake", Angewandte Chemie International Edition, vol. 61, 2022. http://dx.doi.org/10.1002/anie.202209885

Molecules of the year -2022. Data issues!

December 13th, 2022

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:

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Gaseous carbon: The energetics of two forms of tetracarbon, C4 and a challenge!

November 29th, 2022

The topic of dicarbon, C2, has been discussed here for a few years now. It undoubtedly would be a gas! This aspect of the species came to the fore recently[1] when further experiments on a potential chemical precursor of dicarbon, the zwitterion X(+)-C≡C(-), showed that different variants of X(+), such as not only X=PhI(+), but also e.g. X=dibenzothiophenium(+) appeared to generate a gaseous species, which could be trapped as “C2” in a solvent-free connected flask experiment.

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  1. H.S. Rzepa, M. Arita, K. Miyamoto, and M. Uchiyama, "A combined DFT-predictive and experimental exploration of the sensitivity towards nucleofuge variation in zwitterionic intermediates relating to mechanistic models for unimolecular chemical generation and trapping of free C2 and alternative bimolecular pathways involving no free C2", Physical Chemistry Chemical Physics, vol. 24, pp. 25816-25821, 2022. http://dx.doi.org/10.1039/D2CP01214F

Derek Lowe asks “What’s a Journal For?” – Knowledge graphs?

October 21st, 2022

What’s a Journal For? This debate has been raging ever since preprint servers were introduced as far back as 1991! Indeed, during my recent submission of a journal article, one of the questions asked was whether the article was already deposited in such a preprint server (in a positive sense, and not one excluding further submission progress). Since my previous comment on this theme was made more than three years ago, I thought I might update it.

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