Embedding Guest Molecules in Host Matrix

Introduction

For some studies it is helpful to have morphologies of single (or a couple of) isolated molecules embedded in a film of host material, e.g. when studying the impact of doping materials on energy levels of transport layers, or the orientation of isolated emitters in the host matrix. In this tutorial, we explain step by step how such morphologies are generated using Deposit.

In preparation to this tutorial, please check out our webinars on Deposit to understand the basic functionality:

Single Guest in Host Matrix

One (suboptimal) way to generate the desired morphology is to simply follow the above webinars, specify two molecules in the "Molecules" tab of the Deposit WaNo and choose the concentration of the guest molecule so low (i.e. 0.001 for a total of 1000 molecules) that statistically only one guest molecule is deposited during the run. We do not recommend to follow this approach, as the species to be deposited is picked randomly according to the concentration before each deposition. Therefore, it may happen that no (or two) guest molecule is deposited, or that the molecule(s) are placed at the bottom or top of the structure and are therefore not quite useful for the analysis you aim at.

Deposit Guest

We therefore recommend to do the following: Set up a small workflow consisting of three sequential depositions, as depcited in the figure on the right, where a host baselayer is deposited in the first step, a single guest molecule in the second step, followed by another layer of host molecules in the third step. Please regard the following:

  • The Simulation Box settings in the "Simulation parameters" tab need to be the exact same in all three WaNos, and PBC should be enabled. We also recommend to use the same temperatures, numbers of steps and SA cycles. Dihedral moves can be turned on or off in either WaNo depending on the rigidity of your compound.
  • Set the number of molecules in the "Simulation parameters" tab to 1 in the middle "Deposit3_1" WaNo, and to a larger number, e.g. 200 or 500, depending on the desired morphology size, in the first and third WaNos "Deposit3" and "Deposit3_2".
  • As the single guest molecule may be deposited at the edge of the film, we recommend to check the "Extend morphology" option in the "Postprocessing" tab. In this case, periodic copies are added on all sides of the thin film in x-y-direction and guest molecules at the edge have sufficient host environment for electronic structure analysis.
  • In the "Molecules" tabs:
    • define your molecular input at a concentration of 1 in each of the three WaNos, but use the host-molecule input for the first and last WaNo and the guest-molecule input in the middle WaNo "Deposit3_1".
    • In the second and third WaNo, check the "Restart from existing morphology" checkbox. An additional field "Restartfile" will appear. Click on the blue icon to the right of it, as illustrated in the figure on the right. From the drop down menue you can chose the output of previous modules as input morphology and continue the growth. Use "Deposit3/restartfile.zip" as input morphology of the middle WaNo "Deposit3_1", and in the last WaNo "Deposit3_2", chose the output of the middle WaNo where the guest molecule was Deposited, i.e. "Deposit3_1/restartfile.zip".

The output of the last module then provides the desired morphology. Remember to allocate resources for all three WaNos (e.g. 32 cores, 64GB ram).

Multiple isolated guest molecules

If you wish to have multiple isolated guest molecules for statistics, you can either

  • run the above workflow multiple times and perform the analysis on each generated morphology, or
  • Extend the workflow to 5, 7, 9, etc. sequential depositions, alternately depositing a host layer and a single guest molecule.

The results of the search are