Posts Tagged ‘simulation’

Thalidomide. The role of water in the mechanism of its aqueous racemisation.

Saturday, November 10th, 2012

Thalidomide is a chiral molecule, which was sold in the 1960s as a sedative in its (S,R)-racemic form. The tragedy was that the (S)-isomer was tetragenic, and only the (R) enantiomer acts as a sedative. What was not appreciated at the time is that interconversion of the (S)- and (R) forms takes place quite quickly in aqueous media. Nowadays, quantum modelling can provide good in-silico estimates of the (free) energy barriers for such processes, which in this case is a simple keto-enol tautomerism. In a recently published article[1], just such a simulation is reported. By involving two explicit water molecules in the transition state, an (~enthalpic) barrier of 27.7 kcal/mol was obtained. The simulation was conducted just with two water molecules acting as solvent, and without any additional continuum solvation applied. So I thought I would re-evaluate this result by computing it at the ωB97XD/6-311G(d,p)/SCRF=water level (a triple-ζ basis set rather than the double-ζ used before[1]), and employing a dispersion-corrected DFT method rather than B3LYP.



  1. C. Tian, P. Xiu, Y. Meng, W. Zhao, Z. Wang, and R. Zhou, "Enantiomerization Mechanism of Thalidomide and the Role of Water and Hydroxide Ions", Chemistry - A European Journal, vol. 18, pp. 14305-14313, 2012.

Secrets revealed for conjugate addition to cyclohexenone using a Cu-alkyl reagent.

Sunday, November 4th, 2012

The text books say that cyclohexenone A will react with a Grignard reagent by delivery of an alkyl (anion) to the carbon of the carbonyl (1,2-addition) but if dimethyl lithium cuprate is used, a conjugate 1,4-addition proceeds, to give the product B shown below. The standard explanation is that the alkyl copper is a “soft” nucleophile attacking the soft conjugate carbon, whereas the alkyl magnesium is a “hard” nucleophile attacking the hard carbonyl carbon. Is this the best explanation? 


Dynamic effects in nucleophilic substitution at trigonal carbon (with Na+).

Thursday, July 19th, 2012

In the preceding post, I described a fascinating experiment and calculation by Bogle and Singleton, in which the trajectory distribution of molecules emerging from a single transition state was used to rationalise the formation of two isomeric products 2 and 3.  In the present post, I explore possible consequences of including a sodium cation (X=Na+ below) in the computational model.


Computers 1967-2011: a personal perspective. Part 4. Moore’s Law and Molecules.

Friday, October 28th, 2011

Moore’s law describes a long-term trend in the evolution of computing hardware, and it is often interpreted in terms of processing speed. Here I chart this rise in terms of the size of computable molecules. By computable I mean specifically how long it takes to predict the geometry of a given molecule using a quantum mechanical procedure.