Henry Rzepa's Blog Chemistry with a twist

August 8, 2018

The “White City Trio” – The formation of an amide from an acid and an amine in non-polar solution (updated).

White City is a small area in west london created as an exhibition site in 1908, morphing over the years into an Olympic games venue, a greyhound track, the home nearby of the BBC (British Broadcasting Corporation) and most recently the new western campus for Imperial College London. The first Imperial department to move into the MSRH (Molecular Sciences Research Hub) building is chemistry. As a personal celebration of this occasion, I here dedicate three transition states located during my first week of occupancy there, naming them the White City trio following earlier inspiration by a string trio and their own instruments.


July 1, 2016

Anomeric effects at boron, silicon and phosphorus.

The anomeric effect occurs at 4-coordinate (sp3) carbon centres carrying two oxygen substituents and involves an alignment of a lone electron pair on one oxygen with the adjacent C-O σ*-bond of the other oxygen. Here I explore whether other centres can exhibit the phenomenon. I start with 4-coordinate boron, using the crystal structure search definition below (along with R < 0.1, no disorder, no errors).[1]anomeric-bo-sq



  1. Henry Rzepa., "Anomeric effects at boron, silicon and phosphorus.", 2016. http://dx.doi.org/10.14469/hpc/696

June 18, 2016

Why is the carbonyl IR stretch in an ester higher than in a ketone: crystal structure data mining.

Filed under: Chemical IT,crystal_structure_mining — Tags: , , — Henry Rzepa @ 9:43 am

In this post, I pondered upon the C=O infra-red spectroscopic properties of esters, and showed three possible electronic influences:


May 11, 2016

What is the approach trajectory of enhanced (super?) nucleophiles towards a carbonyl group?

I have previously commented on the Bürgi–Dunitz angle, this being the preferred approach trajectory of a nucleophile towards the electrophilic carbon of a carbonyl group. Some special types of nucleophile such as hydrazines (R2N-NR2) are supposed to have enhanced reactivity[1] due to what might be described as buttressing of adjacent lone pairs. Here I focus in on how this might manifest by performing searches of the Cambridge structural database for intermolecular (non-bonded) interactions between X-Y nucleophiles (X,Y= N,O,S) and carbonyl compounds OC(NM)2.



  1. G. Klopman, K. Tsuda, J. Louis, and R. Davis, "Supernucleophiles—I", Tetrahedron, vol. 26, pp. 4549-4554, 1970. http://dx.doi.org/10.1016/S0040-4020(01)93101-1

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