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.

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.

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.

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.

If, as a synthetic chemist, you want to invert the configuration of an alcohol in which the OH group is at a chiral centre, then the Mitsunobu reaction has been a stalwart for many years. Now a catalytic version has been published, [cite]10.1126/science.aax3353[/cite] along with a proposed mechanism.

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.