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

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

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.

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 (+) in D-(+)-glyceraldehyde means it has a positive optical rotation? Wrong!

December 6th, 2019

Text books often show the following diagram, famously consolidated over many years by Emil Fischer from 1891 onwards. At the top sits D-(+)-glyceraldehyde, to which all the monosaccharides below are connected by painstaking chemical transformations.

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Prediction preceding experiment in chemistry – how unlucky was John Kirkwood?

November 30th, 2019

Some areas of science progressed via very famous predictions that were subsequently verified by experiments. Think of Einstein and gravitational waves or of Dirac and the positron. There are fewer well-known examples in chemistry; perhaps Watson and Crick’s prediction of the structure of DNA, albeit based on the interpretation of an existing experimental result. Here I take a look at a what if, that of John Kirkwood’s prediction of the absolute configuration of a small molecule based entirely on matching up the sign of a measured optical rotation with that predicted by (his) theory.

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

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

The Structure of Tetrodotoxin as a free base.

November 9th, 2019

The notorious neurotoxin Tetrodotoxin is often chemically represented as a zwitterion, shown below as 1. This idea seems to originate from a famous article written in 1964 by the legendary organic chemist, Robert Burns Woodward.[1] This structure has propagated on to Wikipedia and is found in many other sources.
With the elegance and the unique style that is typical Woodward, his article is a tour de force because of the way in which he deploys a large armoury of spectroscopic (X-ray crystal, NMR, IR) as well as physicochemical (pKa) tools to infer this structure; an approach that has been subsequently widely emulated. The article a well worth a read for the elegant logic that slowly builds to a climax on page 73 (sic!) of the article, when he unveils his final structure (XXXVIII, or 38). The lecture(s) from which the article is apparently derived must have been one hell of an occasion.

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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