Archive for the ‘Interesting chemistry’ Category

How should data be cited in journal articles? A Crossref request for public comment!

Thursday, July 18th, 2024

Metadata is something that goes on behind the scenes and is rarely of concern to either author or readers of scientific articles. Here I tell a story where it has rather greater exposure. For journals in science and chemistry, each article published has a corresponding metadata record, associated with the persistent identifier of the article and known to most as its DOI. The metadata contains information about the article such as its authors and their affiliations, the title of the article and its abstract, and is submitted to/registered with Crossref –  an organisation set up in 1999 on behalf of publishers, libraries, research institutions and funders. Relatively recent additions to Crossref metadata are the citations included in the article, so-called Open Citations. Doing so has helped to create the new area of article metrics, used by e.g. Altmetrics or Dimensions  to help identify the impacts that science publications have. Basically, if one article is cited by another, it is making an impact. Many citations of a given article by other articles means a larger impact. Most researchers love to have a high – and of course positive – impact and perhaps for better or worse, academic careers to some extent depend on such impacts.


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

Saturday, 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.


The 100th Anniversary year of Curly Arrows.

Friday, 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:


Data Discoverability as a feature of Journal Articles.

Tuesday, 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]


3-Methyl-5-phenylpyrazole: a crystallographic enigma?

Thursday, May 19th, 2022

Previously, I explored the unusual structure of a molecule with a hydrogen bonded interaction between a phenol and a pyridine. The crystal structure name was RAKQOJ and it had been reported as having almost symmetrical N…H…O hydrogen bonds. This feature had been determined using neutron diffraction crystallography, which is thought very reliable at determining proton positions. Another compound with these characteristics is 3-methyl-5-phenylpyrazole or MEPHPY01.[cite]10.1039/p29750001068[/cite] Here the neutron study showed it to apparently have the structure represented below, where the solid N-H lines indicate a proton equidistant between two nitrogens.


C2N2: a 10-electron four-atom molecule displaying both Hückel 4n+2 and Baird 4n selection rules for ring aromaticity.

Thursday, April 7th, 2022

The previous examples of four atom systems displaying two layers of aromaticity illustrated how 4 (B4), 8 (C4) and 12 (N4) valence electrons were partitioned into 4n+2 manifolds (respectively 2+2, 6+2 and 6+6). The triplet state molecule B2C2 with 6 electrons partitioned into 2π and 4σ electrons, with the latter following Baird’s aromaticity rule.[cite]10.1021/ja00769a025[/cite],[cite]10.1021/cr300471v[/cite]. Now for the final missing entry; as a triplet C2N2 has 10 electrons, which now partition into 4 + 6. But would that be 4π + 6σ or 4σ + 6π? Well, in a way neither! Read on.


Sir Geoffrey Wilkinson: An anniversary celebration. 23 March, 2022, Burlington House, London.

Thursday, March 24th, 2022

The meeting covered the scientific life of Professor Sir Geoffrey Wilkinson from the perspective of collaborators, friends and family and celebrated three anniversaries, the centenary of his birth (2021), the half-century anniversary of the Nobel prize (2023) and 70 years almost to the day (1 April) since the publication of the seminal article on Ferrocene (2022).[cite]10.1021/ja01128a527[/cite]


A four-atom molecule exhibiting simultaneous compliance with Hückel 4n+2 and Baird 4n selection rules for ring aromaticity.

Tuesday, March 22nd, 2022

Normally, aromaticity is qualitatively assessed using an electron counting rule for cyclic conjugated rings. The best known is the Hückel 4n+2 rule (n=0,1, etc) for inferring diatropic aromatic ring currents in singlet-state π-conjugated cyclic molecules and a counter 4n rule which infers an antiaromatic paratropic ring current for the system. Some complex rings can sustain both types of ring currents in concentric rings or regions within the molecule, i.e. both diatropic and paratropic regions. Open shell (triplet state) molecules have their own rule; this time the molecule has a diatropic ring current if it follows a 4n rule, often called Baird’s rule. But has a molecule which simultaneously follows both Hückel’s AND Baird’s rule ever been suggested? Well, here is one, as indeed I promised in the previous post.


More aromatic species with four atoms. B4 and N4.

Saturday, March 19th, 2022

I discussed in the previous post the small molecule C4 and how of the sixteen valence electrons, eight were left over after forming C-C σ-bonds which partitioned into six σ and two π. So now to consider B4. This has four electrons less, and now the partitioning is two σ and two π (CCSD(T)/Def2-TZVPPD calculation, FAIR DOI: 10.14469/hpc/10157). Again both these sets fit the Hückel 4n+2 rule (n=0).

Molecule of the year 2021: Infinitene.

Thursday, December 16th, 2021

The annual “molecule of the year” results for 2021 are now available … and the winner is Infinitene.[cite]10.33774/chemrxiv-2021-pcwcc[/cite],[cite]10.1021/jacs.1c10807[/cite] This is a benzocirculene in the form of a figure eight loop (the infinity symbol), a shape which is also called a lemniscate [cite]10.1021/jo801022b[/cite] after the mathematical (2D) function due to Bernoulli. The most common class of molecule which exhibits this (well known) motif are hexaphyrins (hexaporphyrins; porphyrin is a tetraphyrin)[cite]10.1039/b502327k[/cite],[cite]10.1021/ol0521937[/cite],[cite]10.1002/chem.200600158[/cite], many of which exhibit lemniscular topology as determined from a crystal structure. Straightforward annulenes have also been noted to display this[cite]10.1107/S1600536811048604[/cite] (as first suggested here for a [14]annulene[cite]10.1021/ol0518333[/cite]) and other molecules show higher-order Möbius forms such as trefoil knots.[cite]10.1038/NCHEM.1955[/cite],[cite]10.1039/D0CC04190D[/cite] This new example uses twelve benzo groups instead of six porphyrin units to construct the lemniscate. So the motif is not new, but this is the first time it has been constructed purely from benzene rings. (more…)