Posts Tagged ‘Ammonium’

Organocatalytic cyclopropanation of an enal: (computational) mechanistic understanding.

Saturday, August 25th, 2018

Symbiosis between computation and experiment is increasingly evident in pedagogic journals such as J. Chemical Education. Thus an example of original laboratory experiments[1],[2] that later became twinned with a computational counterpart.[3] So when I spotted this recent lab experiment[4] I felt another twinning approaching.



  1. A. Burke, P. Dillon, K. Martin, and T.W. Hanks, "Catalytic Asymmetric Epoxidation Using a Fructose-Derived Catalyst", Journal of Chemical Education, vol. 77, pp. 271, 2000.
  2. J. Hanson, "Synthesis and Use of Jacobsen's Catalyst: Enantioselective Epoxidation in the Introductory Organic Laboratory", Journal of Chemical Education, vol. 78, pp. 1266, 2001.
  3. K.K.(. Hii, H.S. Rzepa, and E.H. Smith, "Asymmetric Epoxidation: A Twinned Laboratory and Molecular Modeling Experiment for Upper-Level Organic Chemistry Students", Journal of Chemical Education, vol. 92, pp. 1385-1389, 2015.
  4. M. Meazza, A. Kowalczuk, S. Watkins, S. Holland, T.A. Logothetis, and R. Rios, "Organocatalytic Cyclopropanation of (E)-Dec-2-enal: Synthesis, Spectral Analysis and Mechanistic Understanding", Journal of Chemical Education, vol. 95, pp. 1832-1839, 2018.

Ammonide: an alkalide formed from ammonia and resembling an electride.

Sunday, December 17th, 2017

Alkalides are anionic alkali compounds containing e.g. sodide (Na), kalide (K), rubidide (Rb) or caeside (Cs). Around 90 examples can be found in the Cambridge structure database (see DOI: 10.14469/hpc/3453  for the search query and results). So what about the ammonium analogue, ammonide (NH4)? A quick search of Scifinder drew a blank! So here I take a look at this intriguingly simple little molecule.


Ammonium tetraphenylborate and the mystery of its π-facial hydrogen bonding.

Friday, March 10th, 2017

A few years back, I did a post about the Pirkle reagent[1] and the unusual π-facial hydrogen bonding structure[2] it exhibits. For the Pirkle reagent, this bonding manifests as a close contact between the acidic OH hydrogen and the edge of a phenyl ring; the hydrogen bond is off-centre from the middle of the aryl ring. Here I update the topic, with a new search of the CSD (Cambridge structure database), but this time looking at the positional preference of that bond and whether it is on or off-centre. 



  1. H.S. Rzepa, M.L. Webb, A.M.Z. Slawin, and D.J. Williams, "? Facial hydrogen bonding in the chiral resolving agent (S)-2,2,2-trifluoro-1-(9-anthryl)ethanol and its racemic modification", Journal of the Chemical Society, Chemical Communications, pp. 765, 1991.
  2. H.S. Rzepa, M.H. Smith, and M.L. Webb, "A crystallographic AM1 and PM3 SCF-MO investigation of strong OH ⋯π-alkene and alkyne hydrogen bonding interactions", J. Chem. Soc., Perkin Trans. 2, pp. 703-707, 1994.

Ways to encourage water to protonate an amine: superbasing.

Friday, April 8th, 2016

Previously, I looked at models of how ammonia could be protonated by water to form ammonium hydroxide. The energetic outcome of my model matched the known equilbrium in water as favouring the unprotonated form (pKb ~4.75). I add here two amines for which R=Me3Si and R=CN. The idea is that the first will assist nitrogen protonation by stabilising the positive centre and the second will act in the opposite sense; an exploration if you like of how one might go about computationally designing a non-steric superbasic amine that becomes predominantly protonated when exposed to water (pKb <1) and is thus more basic than hydroxide anion in this medium.


How many water molecules does it take to form ammonium hydroxide from ammonia and water?

Sunday, March 20th, 2016

This is a corollary to the previous post exploring how many molecules are needed to ionise HCl. Here I am asking how many water molecules are required to form the ionic ammonium hydroxide from ammonia and water.