A peak behind the (hosting) scenes of this blog.

June 15th, 2024

I should start by saying that the server on which this blog is posted was set up in June 1993. Although the physical object has been replaced a few times, and had been “virtualised” about 15 years ago, a small number of the underlying software base components may well date way back, perhaps even to 1993. This system had begun to get unreliable in recent years, and it was decided about 6 months ago to build an entirely new virtual server and then migrate stuff to it.

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The 100th Anniversary year of Curly Arrows.

June 14th, 2024

Chemists now use the term “curly arrows” as a language to describe the electronic rearrangements that occur when a (predominately organic) molecule transforms to another – the so called chemical reaction. It is also used to infer, via valence bond or resonance theory, what the mechanistic implications of that reaction are. It was in this latter context that the very first such usage occured in 1924[cite]bx4svt[/cite] taking the form of a letter by Robert Robinson to the secretary of the Chemical Society and “read” on December 18th 1924. The following diagram was included:

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Data Discoverability as a feature of Journal Articles.

June 11th, 2024

I can remember a time when journal articles carried selected data within their body as e.g. Tables, Figures or Experimental procedures, with the rest consigned to a box of paper deposited (for UK journals) at the British library. Then came ESI or electronic supporting information. Most recently, many journals are now including what is called a “Data availability” statement at the end of an article, which often just cites the ESI, but can increasingly  point to so-called FAIR data. The latter is especially important in the new AI-age (“FAIR is AI-Ready”). One attribute of FAIR data is that it can be associated with a DOI in addition to that assigned to the article itself, and we have been promoting the inclusion of that Data DOI in the citation list of the article.[cite]10.59350/g2p77-78m14[/cite] Since the data can also cite the article, a bidirectional link between data and article is established. ESI itself can exceed 1000 “pages” of a PDF document and examples of chemical FAIR data exceeding 62 Gbytes[cite]10.1021/acs.inorgchem.3c01506[/cite] (Also see DOI: 10.14469/hpc/10386) are known. Finding the chemical needle in that data haystack can become a serious problem. So here I illustrate a recent suggestion for moving to the next stage, namely the inclusion of a “Data Availability and Discovery” statement. The below is the text of such a statement in a recently published article.[cite]10.1039/D3DD00246B[/cite]

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Possible Formation of an Impossible Molecule?

May 20th, 2024

In the previous post, I explored the so-called “impossible” molecule methanetriol. It is regarded as such because the equilbrium resulting in loss of water is very facile, being exoenergic by ~14 kcal/mol in free energy. Here I explore whether changing the substituent R could result in suppressing the loss of water and stabilising the triol.

I started (as I usually do) with a search for crystal structures, in this case containing the motif shown below (trisubstituted carbon, disubstituted oxygen and  R = H or C and any type of connecting bond), which is the species resulting from loss of R to form a trihydroxycarbenium cation.

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Exploring Methanetriol – “the Formation of an Impossible Molecule”

May 16th, 2024

What constitutes an “impossible molecule”? Well, here are two, the first being the topic of a recent article[cite]10.1021/jacs.4c02637[/cite]. The second is a favourite of organic chemistry tutors, to see if their students recognise it as an unusual (= impossible) form of a much better known molecule.

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Detecting anomeric effects in tetrahedral boron bearing four oxygen substituents.

April 30th, 2024

In an earlier post, I discussed[cite]10.59350/dfkt5-k2b20[/cite] a phenomenon known as the “anomeric effect” exhibited by tetrahedral carbon compounds with four C-O bonds. Each oxygen itself bears two bonds and has two lone pairs, and either of these can align with one of three other C-O bonds to generate an anomeric effect. Here I change the central carbon to a boron to explore what happens, as indeed I promised earlier.

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Internet Archeology: reviving a 2001 article published in the Internet Journal of Chemistry.

March 21st, 2024

In the mid to late 1990s as the Web developed, it was becoming more obvious that one area it would revolutionise was of scholarly journal publishing. Since the days of the very first scientific journals in the 1650s, the medium had been firmly rooted in paper. Even printed colour only became common (and affordable) from the 1980s. An opportunity to move away from these restrictions was provided by the Web. Early adopters of this medium in chemistry were the CLIC pilot project[cite]10.1080/13614579509516846[/cite] in 1995 and the Internet Journal of Chemistry (IJC), the latter offering “enhanced chemical publication which permits the publication of materials which cannot be published on paper and end-use customization which permits the readers to read articles prepared for their specific needs“.[cite]10.1590/S0100-40421999000200020[/cite] Publication of the latter started in January 1998, offering “authors the opportunity to enhance their articles by fully incorporating multimedia, large data sets, Java applets, color images and interactive tools.” The journal remained online for seven years, after which it was closed and the articles became inaccessible. By then many major chemistry journals had started evolving along some of the same lines, and it could be argued this journal had served its purpose of alerting both publishers and authors to these new opportunities. Here I describe how an IJC article published in 2001 was brought back to life in more or less the enhanced manner intended.[cite]10.59350/9c769-34y25[/cite]

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Detecting anomeric effects in tetrahedral carbon bearing four oxygen substituents.

March 18th, 2024

I have written a few times about the so-called “anomeric effect“, which relates to stereoelectronic interactions in molecules such as sugars bearing a tetrahedral carbon atom with at least two oxygen substituents. The effect can be detected when the two C-O bond lengths in such molecules are inspected, most obviously when one of these bonds has a very different length from the other. The effect originates when one of the lone pair of electrons on one oxygen atom uniquely overlaps with the C-O antibonding σ* on another oxygen, thus shortening the length of the donating oxygen-carbon length and lengthening the length of accepting C-O bond. Here I take a look at tetra-substituted versions of this (C(OR)4), where in theory there are up to eight lone pairs, interacting with any of three C-O bonds, giving a total of 24 possible anomeric effects in one molecule.

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Data Citation – a snapshot of the chemical landscape.

February 26th, 2024

The recent release of the DataCite Data Citation corpus, which has the stated aim of providing “a trusted central aggregate of all data citations to further our understanding of data usage and advance meaningful data metrics” made me want to investigate what the current state of citing data in the area of chemistry might be. Chemistry is known to be a “data rich” science (as most of the physical sciences are) and  here on this very blog I try to cite whenever possible the source(s) of the data that  I often use when discussing a topic. Such citations are not necessarily the same as citing a journal source via e.g. its DOI, although of course one is very likely to find data associated with most articles nowadays, albeit almost entirely via any associated supporting information document. However the latter is often presented in a relatively unstructured (PDF) form, which does not adhere to what are called the “FAIR” guidelines of being findable, accessible, interoperable and reusable. Directly citing data is a way of improving its FAIR-characteristics. So what insights does the Data citation corpus reveal? Read the rest of this entry »

Mechanistic templates computed for the Grubbs alkene-metathesis reaction.

February 19th, 2024

Following on from my template exploration of the Wilkinson hydrogenation catalyst, I now repeat this for the Grubbs variant of the Alkene metathesis reaction. As with the Wilkinson, here I focus on the stereochemistry of the mechanism as first suggested by Chauvin[cite]https://doi.org/10.1002/macp.1971.021410112[/cite], an aspect lacking in eg the Wikipedia entry. As before, the diagram below is hyperlinked to the appropriate data repository identifier so that you can go straight from the scheme to the data (Top level Data DOI: 10.14469/hpc/13796).

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