Dienstag, 26. Februar 2013

QM 005: Comparing semi-empirical methods

In a recent paper Liao et al. calculated the reaction profile for a newly suggested mechanism of acetylene hydratase. Conveniently, the atomic coordinates of all species along the reaction coordinate have been deposited in the supporting material.

Carrying out some SPE calculations of all species using MOPAC2012, we find the following profiles.

Fig. 1: Calculated Reaction profiles.
In the SPE calculations, a dielectric constant of \(\epsilon=4\) was applied. In the reference ("B3LYP" in Fig. 1), the optimization was done using the LANL2TZ(f) pseudo-potential on W, 6-311+G(d) for S and 6-31G(d,p) for the other elements. The reference SPE calculations were carried out using 6-311+G(2d,2p) on all elements but W.
Apparently, the semi-empirical methods greatly overestimate the interaction energy between W and the acetylene unit (going from 0 to 1) and underestimate the activation energy for the proton transfer in step 4.
However, without reoptimizing the transition state, PM6 is does see a very clear transition state for the hydroxylation at step 2.

Orbital diagram from supplementary material.


  1. That first step is a bit suspicious. Are you sure you have the same electronic state?

  2. I would call it a singlet and I think I have that.