Archive for August, 2023

The “double-headed” curly arrow as used in mechanistic representations.

Tuesday, August 29th, 2023

The schematic representation of a chemical reaction mechanism is often drawn using a palette of arrows connecting or annotating the various molecular structures involved. These can be selected from a chemical arrows palette, taken for this purpose from the commonly used structure drawing program Chemdraw. Explanations of how to apply the individual arrows are not always easy to find however! Circled in red are the ones to be discussed here, although most carry fascinating and often subtle meanings!


Pre-mechanism for the Swern Oxidation: formation of chlorodimethylsulfonium chloride.

Friday, August 25th, 2023

The Swern oxidation[1] is a class of “activated” dimethyl sulfoxide (DMSO) reaction in which the active species is a chlorodimethylsulfonium chloride salt. The mechanism of this transformation as shown in e.g. Wikipedia is illustrated below. However, an interesting and important aspect of chemistry is not apparent in this schematic mechanism and to rectify this, a full computed mechanism is laid out below, for which the FAIR data has a DOI: 10.14469/hpc/13151


  1. K. Omura, and D. Swern, "Oxidation of alcohols by “activated” dimethyl sulfoxide. a preparative, steric and mechanistic study", Tetrahedron, vol. 34, pp. 1651-1660, 1978.

Blue blood.

Monday, August 7th, 2023

Respiratory pigments are metalloproteins that transport O2, the best known being the bright red/crimson coloured hemoglobin in human blood. The colour derives from Fe2+ at the core of a tetraporphyrin ring. But less well known is blue blood, and here the colour derives from an oxyhemocyanin unit based on Cu1+ (the de-oxy form is colourless) rather than iron. See below for the carapace of a red rock crab.