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Henry Rzepa's Blog

Henry Rzepa's Blog
Chemistry with a twist
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A PID or persistent identifier has been in common use in scientific publishing for around 20 years now. It was introduced as a DOI (Digital Object Identifier), and the digital object in this case was the journal article. From 2000 onwards, DOIs started appearing for most journal articles, journals having obtained them from a registration agency, CrossRef.

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In a welcome move, one of the American chemical society journals has published an encouragement to submit what is called FAIR data to the journal.[cite]10.1021/acs.orglett.0c00383[/cite]. A reminder that FAIR data is data that can be Found (F), Accessed (A), Interoperated(I) and Re-used( R). I thought I might try to explore this new tool here. You start at the ACS Research Data Center

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I noted in an earlier blog, a potential (if difficult) experimental test of the properties of the singlet state of dicarbon, C 2 . Now, just a few days ago, a ChemRxiv article has been published suggesting another (probably much more realistic) test.[cite]10.26434/chemrxiv.11446224.v1[/cite] This looks at the so-called 7 Σ open shell state of the molecule where three electrons from one σ and two π orbitals are excited

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Having shown that carbon as a carbene centre, C**:** can act as a hydrogen bond acceptor, as seen from a search of crystal structures, I began to wonder if there is any chance that carbon as a radical centre, C• could do so as well. Definitely a subversive thought, since radical centres are supposed to abstract hydrogens rather than to hydrogen bond to them.

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In the previous post, I showed that carbon can act as a hydrogen bond acceptor (of a proton) to form strong hydrogen bond complexes. Which brings me to a conceptual connection: can singlet dicarbon form such a hydrogen bond?  Dicarbon can be variously represented as above. The first form shows it as a bis-carbene, with an unbonded lone pair of electrons at each end of a carbon double bond.

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A hydrogen bond donor is considered as an electronegative element carrying a hydrogen that is accepted by an atom carrying a lone pair of electrons, as in X:…H-Y where X: is the acceptor and H-Y the donor. Wikipedia asserts that carbon can act as a donor, as we saw in the post on the incredible chloride cage, where six Cl**:**…H-C interactions trapped the chloride ion inside the cage.

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All of the molecules in this year’s C&EN list are fascinating in their very different ways. Here I take a look at the twisty tetracene (dodecaphenyltetracene) which is indeed very very twisty.[cite]10.1002/anie.201812418[/cite] Click on image to view 3D model Unfortunately, the authors point that the twisty-ness does not lead to a stable helical configuration at room temperatures and so separate enantiomers cannot be isolated.

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My momentum of describing early attempts to use optical rotation to correlate absolute configuration of small molecules such as glyceraldehyde and lactic acid with their optical rotations has carried me to L-Malic acid (below labelled as ( S )-Malic acid). The measured optical rotatory dispersion curve at low wavelengths is shown below (dashed line for Malic acid, solid line for Lactic acid). A sign inversion