Fragment Orbitals in DFTB
*************************

DFTB Bonding Analysis Fragments AMSlevels

This tutorial will show you how to perform a Fragment orbital Analysis
using DFTB and visualize the results.

Tip:

  This tutorials can also be run from the command-line. See

  * Example: Fragment Orbital analysis Guanine-Cytosine


Build Guanine-Cytosine and set the DFTB parameters
==================================================

For a fragment analysis the Task need to be 'Single Point'.

   Start AMSinput
   Switch to **DFTB**: [image: ADFPanel][image] **→** [image: DFTBPanel][image]
   Click on the **Structure** tool [image: StructTool][image] and select **→ DNA → GC**
   Click somewhere in the empty viewport on the left to create the Guanine-Cytosine base pair
   **Task → Single Point**
   Select **Model → SCC-DFTB**
   Click on the **parameter directory folder** and select **DFTB.org/mio-1-1**
 [image][image]


Atomic fragments
================

Atomic fragments will be used in DFTB if one does not use regions.

   Panel bar **MultiLevel → Fragments**
   Check the 'Use fragments' check box
 [image]

   Save and Run
   Wait for the calculation to finish
   **SCM → Levels**

   [image]

If you move the mouse over a level (orbital) of the Guanine-Cytosine
DNA base pair one can find out more detailed information about the
composition of the level in terms of the atomic orbitals. If one
right-clicks on the HOMO level of Guanine-Cytosine, and select "49",
then a new AMSview window will appear which will show the HOMO. One
can also right-click on atomic fragment orbital levels, and select one
of the SFOs. SFO means symmetrized fragment orbital, which for DFTB is
the same as a fragment orbital (FO), since DFTB does not use symmetry.
Furthermore, in case of atomic fragments the FOs are in fact atomic
orbitals.


Molecular fragments
===================

Fragments that consists of multiple atoms can be used in DFTB if one
uses regions. Note that all atoms should be part of exactly one
region, otherwise one can not do a DFTB fragment analysis.

   In AMSinput:
   Panel bar **Model → Regions**
   Select all atoms of Guanine, click the [image: AddButton][image] button next to Regions, rename Region_1 to "Guanine"
   Select all atoms of Cytosine, click the [image: AddButton][image] button next to Regions, rename Region_2 to "Cytosine"
 [image][image]

   Panel bar **MultiLevel → Fragments**
   Check the 'Use fragments' check box
 [image]

Next you will Save and Run the calculation. When you do this, AMSinput
will actually save three different calculations:

* The Guanine fragment calculation (with matching .ams and .run file)

* The Cytosine fragment calculation (with matching .ams and .run file)

* The Guanine-Cytosine fragment analysis calculation (with matching
  .ams and .run file)

You do not need to run the fragment calculations first, they will
automatically be executed when needed.

   Save and Run
   Wait for the calculation to finish (note that first the fragment calculations are executed, followed by the final fragment analysis)
   **SCM → Levels**

   [image]

If you move the mouse over a level (orbital) of the Guanine-Cytosine
DNA base pair one can find out more detailed information about the
composition of the level in terms of the fragment orbitals (FOs). One
can conclude that the HOMO of Guanine-Cytosine is almost purely on
Guanine, whereas the LUMO is almost purely on Cytosine.

[image][image]

   Right-click on the HOMO level of Guanine-Cytosine, and select "49"

   [image]

Next a new AMSview window will appear that shows a picture the HOMO.

   [image]

Similar one can select fragment orbitals if one right-clicks on a
fragment level in AMSlevels. One can also directly use AMSview to view
(fragment) orbitals, and some other properties.
