Encouraging Submission of FAIR Data at the Journal of Organic Chemistry and Organic Letters

February 14th, 2020

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.[1]. 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.

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References

  1. A.M. Hunter, E.M. Carreira, and S.J. Miller, "Encouraging Submission of FAIR Data at The Journal of Organic Chemistry and Organic Letters", Organic Letters, 2020. http://dx.doi.org/10.1021/acs.orglett.0c00383

Molecules of the year 2019: Hexagonal planar crystal structures.

January 23rd, 2020

Here is another selection from the Molecules-of-the-Year shortlist published by C&E News, in which hexagonal planar transition metal coordination is identified. This was a mode of metal coordination first mooted more than 100 years ago,[1] but with the first examples only being discovered recently. The C&E News example comprises a central palladium atom surrounded by three hydride and three magnesium atoms, all seven atoms being in the same plane.

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References

  1. M. Garçon, C. Bakewell, G.A. Sackman, A.J.P. White, R.I. Cooper, A.J. Edwards, and M.R. Crimmin, "A hexagonal planar transition-metal complex", Nature, vol. 574, pp. 390-393, 2019. http://dx.doi.org/10.1038/s41586-019-1616-2

Comment on “Resolving the Quadruple Bonding Conundrum in C2 Using Insights Derived from Excited State Potential Energy Surfaces”: The 7Σ heptet excited states for related molecules.

January 2nd, 2020

I noted in an earlier blog, a potential (if difficult) experimental test of the properties of the singlet state of dicarbon, C2. Now, just a few days ago, a ChemRxiv article has been published suggesting another (probably much more realistic) test.[1] This looks at the so-called 7Σ open shell state of the molecule where three electrons from one σ and two π orbitals are excited into the corresponding σ* and π* unoccupied orbitals. The argument is presented that these states are not dissociative, showing a deep minimum and hence a latent quadruple bonding nature. They also note that the isoelectronic BN molecule IS dissociative. Thus to quote: “Hence, the proof of existence of a minimum in the 7Σu+ for C2 and the absence of such a minimum in the equivalent case for BN is likely to corroborate our findings on quadruple bonding in these two cases.

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References

  1. I. Bhattacharjee, D. Ghosh, and A. Paul, "Resolving the Quadruple Bonding Conundrum in C2 Using Insights Derived from Excited State Potential Energy Surfaces: A Molecular Orbital Perspective", 2019. http://dx.doi.org/10.26434/chemrxiv.11446224.v1

Can a carbon radical act as a hydrogen bond acceptor?

December 28th, 2019

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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Carbon as a hydrogen bond acceptor: can dicarbon (C2) act in this manner?

December 27th, 2019

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? 

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Hydrogen bonds: carbon as an acceptor rather than as a donor?

December 23rd, 2019

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. This led me to ask how many examples are there of carbon as an acceptor rather than as a donor?

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Molecules of the year – 2019: twisty tetracene.

December 22nd, 2019

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.[1]

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References

  1. Y. Xiao, J.T. Mague, R.H. Schmehl, F.M. Haque, and R.A. Pascal, "Dodecaphenyltetracene", Angewandte Chemie International Edition, vol. 58, pp. 2831-2833, 2019. http://dx.doi.org/10.1002/anie.201812418

L-Malic acid: An exercise in conformational analysis impacting upon optical rotatory dispersion (ORD).

December 20th, 2019

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).

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Molecules of the year – 2019: Topological molecular nanocarbons – All-benzene catenane and trefoil knot.

December 15th, 2019

Here is another molecule of the year, on a topic close to my heart, the catenane systems 1 and the trefoil knot 2[1] Such topology is closely inter-twinned with three dimensions (literally) and I always find that the flat pages of a journal are simply insufficient to do them justice. So I set about finding the 3D coordinates.

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References

  1. Y. Segawa, M. Kuwayama, Y. Hijikata, M. Fushimi, T. Nishihara, J. Pirillo, J. Shirasaki, N. Kubota, and K. Itami, "Topological molecular nanocarbons: All-benzene catenane and trefoil knot", Science, vol. 365, pp. 272-276, 2019. http://dx.doi.org/10.1126/science.aav5021

Molecules of the year – 2019: the incredible chloride cage.

December 13th, 2019

Each year, C&E News runs a poll for their “Molecule of the year“. I occasionally comment with some aspect of one of the molecules that catches my eye (I have already written about cyclo[18]carbon, another in the list). Here, it is the Incredible chloride cage, a cryptand-like container with an attomolar (1017 M-1) affinity for a chloride anion.[1] The essence of the binding is six short CH…Cl and one slightly longer interactions to the same chloride (DOI: 10.5517/ccdc.csd.cc1ngqrl) and one further hydrogen bond to a water molecule; eight coordinated chloride anion!

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References