Building Frameworks and Reticular Compounds

In this tutorial we show to the user how to generate a framework compound through the GUI. These compounds are issued from reticular chemistry, and have received a considerable amount of attention from the scientific community. Well-known families of these compounds are Metal-Organic Frameworks (MOFs), Covalent-Organic Frameworks (COFs), Zeolites, etc.

If you are not interested in periodic structures (for example, if you only use ADF), you can skip this tutorial.

The instruments at your disposal are:

  • Autografs Framework builder.
  • The export tool for custom building blocks.

The Export Fragment tool

While a small database of building units is shipped in the ADF suite, you might need to generate your own collection of parts from which to generate you frameworks. The first step is to create a directory in which these parts will be stored. In the following tutorial, it will be the “~/Desktop/my_database/” directory. Then we start the process of creating and exporting the units.

Start ADFinput and create the molecule you desire to export, capped with hydrogens. here, we’ll use a benzene molecule
Next make sure to maximize the symmetry of the molecule using the star button.
Check that the bonding information is correct.
Switch to the UFF -> Model -> Atom Types menu, and fill out the corresponding UFF atomic types. These will be used in the post-processing optimization of the frameworks.

Finally, specify the connectivity of your fragment using dummy atoms.

replace the hydrogens in para positions with dummy atoms using Atoms -> Change Atom Type -> Xx

You can now export the fragment to your database.

Edit -> Framework -> Export Fragment
Select the corresponding geometry. Here, linear.
Save in the directory my_database/ under “benzene”

Do the same for bipyridine, and export a zinc paddlewheel with the octahedral shape. Note the importance of correctly assigning UFF types to dummies in the bipyridine and the paddlewheel, to specify the exclusive type of connectivity in pillared objects. Dummies connecting to nitrogen should have a nitrogen type, and those connected to carbon a carbon type. Guess Types can be used for a good initial guess.

../_images/bipy.png ../_images/pw.png

You are now set up for generation of at least one cubic MOF, with three files in my_database : benzene.inp, znpw.inp and bipy.inp .

Framework builder : Build a pillared, functionalized MOF

Edit -> Framework -> Builder
Select the my_database directory in the path field
Choose the pcu topology
Select the center
Select the linkers in any order
Select the pillar
The building units are displayed on the left. Any modification will be carried on to the MOF.
Replace a hydrogen on the benzene linker with an amine group.
Hit the “Generate” button (answer No when asked if you want to save the linker 1)
Activate View -> Periodic -> Repeat Unit Cells
Close the framework builder

Set the type for the added nitrogen atoms from the NH2 groups to N_3
Select the UFF4MOF force field library
Optimize (only the framework) using UFF for parts to snap into place, do not forget to optimize the lattice vectors also!

Once the optimization is ready, use SCM -> Movie to see the results of the optimization
Activate View -> Periodic -> Repeat Unit Cells
Hit the Play button