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Henry Rzepa's Blog

Henry Rzepa's Blog
Chemistry with a twist
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In 2013, I created an iTunesU library of 115 mechanistic types in organic and organometallic chemistry, illustrated using video animations of the intrinsic reaction coordinate (IRC) computed using a high level quantum mechanical procedure. Many of those examples first derived from posts here. That collection  is still available and is viewable  in the iTunesU app on an iPhone or an iPad.

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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.