I want to model a reaction catalysed by periclase ($\ce{MgO}$) using DFT. I have a good guess on the transition state (TS) of the reaction that goes in gas phase/solvent (produced using MOPAC).

The proposal for this reaction goes by the Eley–Rideal mechanism and I have a good guess on how the reactant adsorbs.

Now comes the question: I would like to optimise the TS on the surface using DFT (either ORCA or NWChem), but in tractable time.

I am tempted to use a simple, fixed model for the surface, e.g., a set of fixed atoms in bulk arrangement. Can this work? How am I supposed to find a structure with just one imaginary frequency using a partially fixed model (maybe using some clever vibrational projections)?

Even though NEB could be applied, the implementation of it in NWChem does not work with fixed atomic coordinates. Besides, I am confident on the TS I found without the catalyst, so I would like to use that instead of starting all over again.

Edit: what about using a very small cluster model, say, 8-16 atoms, and let it relax? Do you think it could work (in the sense of giving a reliable TS in terms of geometry and energy)?

  • 2
    $\begingroup$ It will not be easy because the slab (that's what a cutout of a solid state structure is often called) would need to be optimized in order to supply a decent initial Hessian for the TS search. I doubt that any TS search algorithm deals well with fixed atoms. If you manage that, I would strongly suggest modelling the surrounding Mg/O by pseudopotentials and point charges. My old group did similar work for polarization properties: DOI:10.1002/cphc.201100521. $\endgroup$ – TAR86 Jan 27 '17 at 12:02
  • 1
    $\begingroup$ Several comments: mopac ts maybe qualitatively wrong; surface and vacuum ts-s are generally very different, therefore your approach can easily be wrong; orca cannot calculate slabs; slab calculations takes forever, but you cannot cut corners most cases, and so on $\endgroup$ – Greg Jan 27 '17 at 16:21
  • 1
    $\begingroup$ With a cluster model, you may get an answer. As Greg points out: whether that has much to do with the reality, I have my doubts, but also lack experience: my old group mostly dealt with gas-phase TS. As a first step, you might check whether your cluster relaxes to a reasonable structure when surrounded by the artificial environment (point charges etc.), because without a relaxed geometry, I don't think you will get anywhere. Next, I would look at a trivial model reaction and test the remaining approach. Given those results, I would assess the feasibility. And don't forget dispersion/vdW. $\endgroup$ – TAR86 Jan 27 '17 at 17:04
  • 2
    $\begingroup$ I would question if there is a fast/easy/cheap solution that does not require experience (or even just a fast one) $\endgroup$ – Greg Jan 27 '17 at 17:09
  • 2
    $\begingroup$ The standard scheme here is to take a slab and keep 2-4 atom layers outermost from the reaction center fixed in crystallographic positions while letting everything else to relax naturally. There is a plenty of works done in this fashion. The size of the model used (i.e. how much atomic layers counting from the reaction center) to be used is ideally a matter of trial and asymptotic analysis, but in my experience in published works usually 2-4 layers from reaction center are relaxed and 2-4 more are fixed. $\endgroup$ – permeakra Feb 20 '17 at 12:43

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Browse other questions tagged or ask your own question.