By: Secrets of a university tutor. An exercise in mechanistic logic: second dénouement. « Henry Rzepa

Mon, 29 Oct 2012 19:40:55 +0000

[...] transition state for each product in a reaction. But one should note that there are increasing claims for reactions whose outcome is determined not by an explicit transition state for each reaction pathway, but [...]

By: The Sn2 reaction and the anomaly of carbon. « Henry Rzepa

The Sn2 reaction and the anomaly of carbon. « Henry Rzepa — Thu, 06 Sep 2012 15:33:21 +0000

[...] find in the research literature and textbooks; the counter-ion (Y=Na+) is also included so as to create a neutral system overall. The method is the usual [...]

By: Henry Rzepa

Henry Rzepa — Wed, 15 Aug 2012 18:31:08 +0000

I noted in a footnote above that the NBO E(2) energies seem sensitive to the basis set used. I also noted that if ωB97XD/6-311+G(d,p)/SCRF=ethanol replaces B3LYP/6-31+G(d,p)/SCRF=ethanol for model (c) the essential features were unchanged.

But the quantatitive aspects do look different:

For example, the gradient norm at IRC +2 takes a different form for B3LYP/6-31+G(d,p) compared with ωB97XD/6-311+G(d,p). The derivative of these gradients also shows differences. This suggests that the latter is perhaps closer to forming a transient intermediate along the path than the former and also hints that the forces acting on the atoms along this path may in turn be quite sensitive to the method used. Another smaller, but intriguing difference is that the gradients for B3LYP/6-31+G(d,p) are quite “bumpy”, whereas ωB97XD/6-311+G(d,p) is much smoother.

We may speculate whether these quantitative differences will impact upon the molecular dynamics calculated using either of these methods, or whether the dynamics turns out to be quite robust to basis set and DFT method.

Oh, you might ask why I use ωB97XD in preference to B3LYP. Well, calibrations on relative energies of a collection of small molecules compared to CCSD(T) calculations suggest that the former matches much better than the latter. For systems where weak interactions between assemblies of molecules matter, ωB97XD does seem to come up with quite realistic simulations. And I believe that dynamics simulations can be sensitive to the potential used.

PS: For proper comparison, the below is the IRC gradient norm computed at ωB97XD/6-31+G(d,p) and ωB97XD/6-311+G(d,p) (no additional counterion or solvent). This shows the the big difference is the functional and not the quality of the basis set, or indeed the presence of counter-ion and solvent.

Comments on: Dynamic effects in nucleophilic substitution at trigonal carbon (with Na+) revisited.

By: Secrets of a university tutor. An exercise in mechanistic logic: second dénouement. « Henry Rzepa

By: The Sn2 reaction and the anomaly of carbon. « Henry Rzepa

By: Henry Rzepa