Two influential textbooks – “Mee” and “Mellor”.

November 11th, 2023

I am a member of the  Royal Society of  Chemistry’s Historical group. Amongst other activities, it publishes two editions of a newsletter each year for its members. A new theme was recently launched asking for contributions on the topic of  “two influential books” and shortly to appear in the winter 2023 edition will be the following recollections by myself (reprinted here with permission).

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More examples of “double-headed” curly arrows: S and C Nucleophiles attacking acetyl chloride

October 12th, 2023

In an earlier post on this topic,[1] I described how the curly-arrows describing the mechanism of a nucleophilic addition at a carbonyl group choreograph in two distinct ways, as seen in red or blue below. The arrows in red can be described as firstly addition to the carbonyl group to form either a transient intermediate (a two-step process) or instead a formal transition state state as a concerted single-step mechanism. The blue arrows do the reverse; firstly elimination and then followed by addition. I will use the shorthand AE for the first type and EA for the second type. Here I explore some more nucleophiles to see which of these two mechanisms they follow. Data for these results can be found at 10.14469/hpc/13171
N- carbon ylid: This is a very facile (low-barrier) reaction with a C-O bond length response that initially increases steeply, followed by a more modest decline and hence corresponds to an AE mechanism.

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  1. H. Rzepa, "The “double-headed” curly arrow as used in mechanistic representations.", 2023.

Improving the Science blog – The Rogue Scholar service.

September 12th, 2023

Some 13 years ago, I speculated about the longevity of the type of science communication then (and still now) represented by Blogs. I noted one new project called ArchivePress that was looking into providing solutions equivalent to what scientific journals have done for some 350 years of science communication. The link to ArchivePress no longer works, but details of the project can still be found here. Since then the technology and infrastructure has moved on, with a new backbone provided by the use of persistent identifiers (PIDs) in the form of DOIs. The PID ecosystem is now extensive and so a revival of the concept has recently been launched called The Rogue Scholar. Here I take a look at some of is features and illustrate these with application to this blog.

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The “double-headed” curly arrow as used in mechanistic representations.

August 29th, 2023

The schematic representation of a chemical reaction mechanism is often drawn using a palette of arrows connecting or annotating the various molecular structures involved. These can be selected from a chemical arrows palette, taken for this purpose from the commonly used structure drawing program Chemdraw. Explanations of how to apply the individual arrows are not always easy to find however! Circled in red are the ones to be discussed here, although most carry fascinating and often subtle meanings!

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Pre-mechanism for the Swern Oxidation: formation of chlorodimethylsulfonium chloride.

August 25th, 2023

The Swern oxidation[1] is a class of “activated” dimethyl sulfoxide (DMSO) reaction in which the active species is a chlorodimethylsulfonium chloride salt. The mechanism of this transformation as shown in e.g. Wikipedia is illustrated below. However, an interesting and important aspect of chemistry is not apparent in this schematic mechanism and to rectify this, a full computed mechanism is laid out below, for which the FAIR data has a DOI: 10.14469/hpc/13151
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  1. K. Omura, and D. Swern, "Oxidation of alcohols by “activated” dimethyl sulfoxide. a preparative, steric and mechanistic study", Tetrahedron, vol. 34, pp. 1651-1660, 1978.

Blue blood.

August 7th, 2023

Respiratory pigments are metalloproteins that transport O2, the best known being the bright red/crimson coloured hemoglobin in human blood. The colour derives from Fe2+ at the core of a tetraporphyrin ring. But less well known is blue blood, and here the colour derives from an oxyhemocyanin unit based on Cu1+ (the de-oxy form is colourless) rather than iron. See below for the carapace of a red rock crab.

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Physical Sample identifiers – the future?

July 12th, 2023

I have variously talked about persistent identifiers on this blog. These largely take the form of DOIs (Digital object identifiers), and here they relate to either journal articles or datasets associated with either the article or the blog post or both. Other disciplines, particularly the earth sciences, have long used persistent identifiers (PIDs) to identify physical objects rather than digital ones. One of my ambitions is to assign such identifiers to a small but highly historical collection of physical objects in my possession, as described at this post. As a prelude to this project, here I describe some ways of searching for physical objects that have been assigned a PID. Thanks Rorie for providing these! 

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Diberyllocene — and Lithioborocene?

June 18th, 2023

Sometimes, the properties of a molecule are predicted long before it is synthesised. One such is diberyllocene. I first encountered a related molecule, beryllocene itself, many moons ago.[1] This was unusual because unlike the original metallocenes, the metal atom was not symmetrically disposed between the two cyclopentadienyl faces. Now diberyllocene is finally reported in which replacing one Be by Be-Be induces (according to calculation, D2) symmetry[2]. I will not repeat the excellent analysis of the wavefunction reported in this article, but confine myself to showing two molecular orbitals which examplify its bonding.

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  1. M.J.S. Dewar, and H.S. Rzepa, "Ground states of molecules. 45. MNDO results for molecules containing beryllium", Journal of the American Chemical Society, vol. 100, pp. 777-784, 1978.
  2. J.T. Boronski, A.E. Crumpton, L.L. Wales, and S. Aldridge, "Diberyllocene, a stable compound of Be(I) with a Be–Be bond", Science, vol. 380, pp. 1147-1149, 2023.

The Pinacol rearrangement.

June 13th, 2023

This is a venerable organic reaction, which curiously I have not previously covered here. First described in 1859, its nature was only properly elucidated in 1873. It is a member of a class of reaction I have previously named “solvolytically assisted pericyclic”, or “perisolvolytic“. Here I explore some of the subtle stereoelectronic effects observed for this apparently simple reaction.

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“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 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.