QM/MM: Inorganic linker in organic framework
********************************************

BAND DFTB Hybrid QM/MM QM/QM' Covalent organic framework


Introduction
============

The hybrid engine is about applying different engines or settings to
different regions. There are several different reasons to do so, but
the most common one is performance. We will here look at inserting an
organic linker in a system comprised of otherwise organic material.


Covalent organic frameworks
---------------------------

Covalent organic frameworks are built of small organic units. As
anyone with a little bit of LEGO experience knows: there are infinite
many ways to assemble small units. Understandably this a hot topic in
material science. Organic systems are reasonably well described by the
fast DFTB method. But what if we want to  introduce a new inorganic
block, for which DFTB fails?


Solution
--------

Apply the fast method (DFTB) to most of the system, and only use DFT
for the inorganic linker and its direct surrounding.


Setup with AMSinput
===================

   **1.** Download the "xyz file of the" system
   **2.** In **AMSinput** select **File → Import coordinates** and select the file you just downloaded

This is what the structure looks like

[image]

Most of the rings are made of organic material, except for the
(inorganic) linker in the middle.


Define the QM region
--------------------

In the QM region we want

* our linker, *and*

* the two directly neighboring organic rings.

Make the selection as shown in the picture:

[image]

Using shift and click-dragging you can fairly easily select the three
building blocks. **In the end 21 atoms should be selected**.

Tip:

  When there are bonds sticking out of the QM region, capping atoms
  will be added to the QM region to satisfy dangling bonds. The main
  rule is that you better not break very strong bonds, and it is
  recommended to use the menu item **Selection → Make selection
  cappable**. In this case nothing happens, as the selection was
  already sensible.

Now define the QM region. Use **Model → Regions**, and click on the
plus region, and rename it to "qm"

[image]


Setup the Geometry Optimization
-------------------------------

   On the main panel, set **Task → Geometry Optimization**
   Click on the arrow next to **Geometry Optimization**
   Set **Optimization space → Cartesian**


Setup the Hybrid Engine
-----------------------

Switch the engine from BAND to Hybrid. As you can see there is a
**Method** being either "Energy Terms" or "QMMM". See the hybrid
engine documentation for more details.

   **1.** Click the "QMMM" radio button
   **2.** Set "Embedding" to "Mechanical"
   **3.** Set the engine for the qm region to "Band"
   **4.** Set the engine for the remaining region to "DFTB"

The panel should look like this

[image]

At the bottom you see the names of the two engines.

   **1.** Click at the bottom on "BAND 1"
   **2.** Enable "Unrestricted"
   **3.** Set the basis set to TZP

The panel should look like this

[image]

And that is it.


Results
-------

Running this calculation will take quite a while. It is interesting to
compare the results for three different calculations

* 1. The whole system with the cheap DFTB engine

* 2. The system with the Hybrid engine

* 3. The whole system with the BAND (DFT) engine

The first calculation is quick, the second one a bit more expensive,
and the last one is a lot more expensive.

Here are the final geometries for the three calculations

* "DFTB xyz file"

* "Hybrid xyz file"

* "BAND xyz file"

The **DFTB** result displays a symmetric solution (plane tilted a bit)
From exactly above the linker looks flat.

[image]

The **Hybrid Engine** produces an asymmetric solution

[image]

Also the **Band engine** shows the asymmetric solution.

[image]

   Examine the three geometries (from the xyz files) with either AMSinput or AMSView from several angles


Conclusions
-----------

* For this system full DFTB gives very a different geometry as
  compared to DFT.

* The hybrid result resembles closely the full DFT one (at one tenth
  of the time).

* With the hybrid engine we can fix the inorganic part, wrongly
  described by the DFTB method.
