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.

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.

Here is another molecule of the year, on a topic close to my heart, the catenane systems 1 and the trefoil knot 2 [cite]10.1126/science.aav5021[/cite] 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.

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 (10 ¹⁷ M ^-1 ) affinity for a chloride anion.[cite]10.1126/science.aaw5145[/cite] The essence of

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.

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.

In the previous post, I discussed the structure of the free base form of tetrodotoxin, often represented as originally suggested by Woodward[cite]10.1351/pac196409010049[/cite] below in an ionic form: Quantum calculations suggested that this form was higher in energy than neutral forms devoid of the zwitterionic charge separation in a relatively non polar solvent such as chloroform. For this, a so-called continuum solvation model was used.

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.[cite]10.1351/pac196409010049[/cite] This structure has propagated on to Wikipedia and is found in many other sources.

Increasingly, individual small molecules are having their structures imaged using STM, including cyclo[18]carbon that I recently discussed. The latest one receiving such treatment is Kekulene.[cite]10.1021/jacs.9b07926[/cite] As with cyclo[18]carbon, the point of interest was which of the two resonance structures shown below most closely resembled the measured structure.

In the previous post, I looked at a class of molecule known as hexaphyrins, inspecting bond length alternation (BLA) at the so-called meso position, the carbon atom joining two pyrrole rings. A search of the difference in bond lengths at this position had shown two significant clusters of crystal structures. Molecules in the bottom left of this diagram shows little or no bond length alternation.