Archive for March, 2020

Substituent effects on the mechanism of Michael 1,4-Nucleophilic addition.

Sunday, March 29th, 2020

In the previous post, I looked at the mechanism for 1,4-nucleophilic addition to an activated alkene (the Michael reaction). The model nucleophile was malonaldehyde after deprotonation and the model electrophile was acrolein (prop-2-enal), with the rate determining transition state being carbon-carbon bond formation between the two, accompanied by proton transfer to the oxygen of the acrolein.


The mechanism of Michael 1,4-Nucleophilic addition: a computationally derived reaction pathway.

Wednesday, March 25th, 2020

In 2013, I created an iTunesU library of 115 mechanistic types in organic and organometallic chemistry, illustrated using video animations of the intrinsic reaction coordinate (IRC) computed using a high level quantum mechanical procedure. Many of those examples first derived from posts here. That collection  is still available and is viewable  in the iTunesU app on an iPhone or an iPad. The realisation struck me now that one of the types not described in that library was Michael-type 1,4-nucleophilic addition to an activated alkene, as described at Wikipedia. So here is that addition.


The Persistent Identifier ecosystem expands – to instruments!

Saturday, March 21st, 2020

A PID or persistent identifier has been in common use in scientific publishing for around 20 years now. It was introduced as a DOI (Digital Object Identifier), and the digital object in this case was the journal article. From 2000 onwards, DOIs started appearing for most journal articles, journals having obtained them from a registration agency, CrossRef. This is a not-for-profit organisation set up by a publishers association for the purpose. Most readers of journal articles started to use this DOI as an easier way of navigating through invariably different and sometimes confusing metaphors set up by any given journal to navigate through its issues. Readers slowly learnt to prepend the URL to the DOI to “resolve” it directly to what is known as the “landing page” of the article. More recently, the prefix recommendation has changed to the slightly shorter form. Few readers are aware  however that the DOI can serve a much more interesting purpose than just taking you to the article landing page. This post will explore a few of these extras.


The singlet and open shell higher-spin states of [4], [6] and [8]-annulenes and their Kekulé vibrational modes

Wednesday, March 11th, 2020

In 2001, Shaik and co-workers published the first of several famous review articles on the topic A Different Story of π-Delocalization. The Distortivity of π-Electrons and Its Chemical Manifestations[1]. The main premise was that the delocalized π-electronic component of benzene is unstable toward a localizing distortion and is at the same time stabilized by resonance relative to a localized reference structure.  Put more simply, the specific case of benzene has six-fold symmetry because of the twelve C-C σ-electrons and not the six π-electrons. In 2009, I commented here on this concept, via a calculation of the quintet state of benzene in which two of the six π-electrons are excited from bonding into anti-bonding π-orbitals, thus reducing the total formal π-bond orders around the ring from three to one. I focused on a particular vibrational normal mode, which is usefully referred to as the Kekulé mode, since it lengthens three bonds in benzene whilst shortening the other three. In this case the stretching wavenumber increased by ~207 cm-1 when the total π-bond order of benzene was reduced from three to one by spin excitation. In other words, each C-C bond gets longer when the π-electrons are excited, but the C-C bond itself gets stronger (in terms at least of the Kekulé mode). This behaviour is called a violation of Badger’s rule[2] for the relationship between the length of a bond and its stretching force constant. 



  1. S. Shaik, A. Shurki, D. Danovich, and P.C. Hiberty, "A Different Story of π-DelocalizationThe Distortivity of π-Electrons and Its Chemical Manifestations†", Chemical Reviews, vol. 101, pp. 1501-1540, 2001.
  2. R.M. Badger, "A Relation Between Internuclear Distances and Bond Force Constants", The Journal of Chemical Physics, vol. 2, pp. 128-131, 1934.