Archive for the ‘Interesting chemistry’ Category

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.

Thursday, 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?

Saturday, 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?

Friday, 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?

Monday, 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.

Sunday, 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

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

Sunday, 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.

Friday, 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

Sign inversions in optical rotation as a function of wavelength (ORD spectra)

Monday, December 9th, 2019

I have been discussing some historical aspects of the absolute configuration of molecules and how it was connected to their optical rotations. The nomenclature for certain types of molecules such as sugars and less commonly amino acids includes the notation (+) to indicate that the specific optical rotation of the molecule has a positive (rather than a negative) value. What is rarely mentioned is the implicit wavelength at which the rotation is measured. Historically polarimeters operated at the so-called sodium Fraunhofer D-line (588.995nm, hence the name [α]D) and only much more recently at the mercury e-line (546.073nm). The former was used for uncoloured organic molecules, since it was realised early on that colour and optical rotation did not mix well. Here I take a closer look at this aspect by constructing the hypothetical molecule shown below.

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What effect do explicit solvent molecules have on calculated optical rotation: D-(“+”)-Glyceraldehyde.

Saturday, December 7th, 2019

In this series of posts on optical rotations, I firstly noted Kirkwood’s 1937 attempt to correlate the optical rotation of butan-2-ol with its absolute configuration. He had identified as essential knowing the relative orientation (the term conformation was not yet in common use) of the two methyl groups (the modern terms are gauche vs anti) and also that of the hydroxyl group, noting that anisotropy from this group could influence his result (he had assumed it was linear, or axially symmetric). I then looked at D-(+)-glyceraldehyde, noting that this species itself has a strongly negative rotation and that it is the hydrated diol that results in a positive rotation and hence the (+) designation. Here I take another look at this latter system to see what effect adding explicit water molecules to the unhydrated form of glyceraldehyde might have on its computed rotation, on the premise that strong hydrogen bonds can also contribute anisotropy to the system.

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The Structure of Tetrodotoxin as a free base – with a better solvation model.

Tuesday, November 26th, 2019

In the previous post, I discussed the structure of the free base form of tetrodotoxin, often represented as originally suggested by Woodward[1] below in an ionic form:

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References

  1. R.B. Woodward, "The structure of tetrodotoxin", Pure and Applied Chemistry, vol. 9, pp. 49-74, 1964. http://dx.doi.org/10.1351/pac196409010049