Fragment Orbitals in DFTB

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

Build Guanine-Cytosine and set the DFTB parameters

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

Start AMSinput
Switch to DFTB: ADFPanel → DFTBPanel
Click on the Structure tool StructTool 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
/scm-uploads/doc.2023/Tutorials/_images/GC.png /scm-uploads/doc.2023/Tutorials/_images/model.png

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
/scm-uploads/doc.2023/Tutorials/_images/atmultilevel.png
Save and Run
Wait for the calculation to finish
SCM → Levels
/scm-uploads/doc.2023/Tutorials/_images/atlevels.png

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.

Panel bar Model → Regions
Select all atoms of Guanine, click the AddButton button next to Regions, rename Region_1 to Guanine
Select all atoms of Cytosine, click the AddButton button next to Regions, rename Region_2 to Cytosine
/scm-uploads/doc.2023/Tutorials/_images/GCregions.png /scm-uploads/doc.2023/Tutorials/_images/regions.png
Panel bar MultiLevel → Fragments
Check the ‘Use fragments’ check box
/scm-uploads/doc.2023/Tutorials/_images/multilevel.png

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
/scm-uploads/doc.2023/Tutorials/_images/levels.png

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.

/scm-uploads/doc.2023/Tutorials/_images/homoinfo.png /scm-uploads/doc.2023/Tutorials/_images/lumoinfo.png
Right-click on the HOMO level of Guanine-Cytosine, and select 49
/scm-uploads/doc.2023/Tutorials/_images/selecthomo.png

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

/scm-uploads/doc.2023/Tutorials/_images/homo.png

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.