Building Frameworks and Reticular Compounds
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ForceField AMSinput Building structures MOF COF Zeolite Autografs UFF

In this tutorial we demonstrate how to generate a framework compound
with AMSinput. 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.

In this tutorial we will learn how to use:

* The export tool for custom building blocks.

* Autografs Framework builder.


The Export Fragment tool
========================

While a small database of building units is shipped with AMS, you
might need to generate your own collection of parts from which to
generate you frameworks. By default the ".scm_gui/autografs/custom"
directory in your home directory is used for modified or custom units.
You can also choose to use any other location and point the builder to
there. We first start the process of creating and exporting the units.

   **1.** Start AMSinput and create the molecule you desire to export. Here, we'll use a benzene molecule.
   **2.** Next make sure to maximize the symmetry of the molecule using the star button.
   **3.** Check that the bonding information is correct.
   **4.** Switch to the force field engine: [image: ADFPanel][image] **→** [image: ForceFieldPanel][image].
   **5.** **Model → Atom Details** menu and click **Guess FF Types, Charges and Parameters**. These will be used in the post-processing optimization of the framework.

   [image]

Make sure that the guessed FF types are correct.

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**

   [image]

You can now export the fragment to your database.

   Click **Builders → MOFs, ... → Export Fragment** in the menu bar.
   Save in the default directory, ".scm_gui/autografs/custom/", as "benzene".

We will use the other building units from the default database. You
are now set up for generation of at least one cubic MOF.


AuToGraFS Builder : Build a functionalized MOF with defects
===========================================================

   Click **Builders → MOFs, ... → AuToGraFS Builder** in the menu bar.

In the builder you can choose to use a different database location.
Since we saved in the default location, you can keep it as is. The
input options can be chosen from the dropdown lists. The lists only
contain options that are still possible. For example, only centers
that match the chosen topology will be in that list. The lists can be
further filtered by typing in part of the name.

   **1.** Choose the **pcu** topology.
   **2.** Select the **Zn_mof5_octahedral** center.
   **3.** Select the **benzene** linker we just created.
   **4.** Click the **+** button next to the linker to add a defect.
   **5.** Select the **benzene** linker again for the defect.

   [image]

The building units are displayed on the left. Any modification will be
carried on to the MOF.

   Replace a hydrogen on the benzene linker defect with an amine group.

   [image]

You can modify the ratio between the defects. We will keep the ratios
equal for this tutorial. The Reduce sites option can be disabled for
some topologies to also choose units for equivalent sites.

   **1.** Set the **Super cell** to "2", "2", "2".
   **2.** Press the **Generate** button. Answer **No** when asked if you want to save the linker 1 defect 1.

Now we optimize the structure of the MOF we just generated using UFF:

   **1.** Close the AuToGraFS builder.

   **2.** Select **UFF4MOF** as **Force field library**.
   **3.** On the **Details → Geometry Optimization** panel, enable the **Optimize lattice** option.
   **4.** Save and run the calculation. When asked to run all, choose **No**.

   [image]

   Once the optimization is ready, use **SCM → Movie** to see the results of the optimization.

   [image]
