There is a very convenient "Custom builder" for constructing metal-molecule-metal junctions in VNL. This mini-tutorial explores variations on the Au-DTB-Au system, using this tool.
The basic idea with the Molecular Device Builder - and for that matter all Custom builders - is not to provide a full-blow set of functionalities for setting up geometries, but rather to make it quick and simple to build a particular class of systems. For more specialized molecular junctions, one should use the more generic Builder tool.
First of all we need to construct the dithiole-bezene (DTB, sometimes referred to as bezene-dithiole, BDT) molecule.
Open the Database tool by clicking its icon on the main toolbar, and switch to the Molecule database using the menu "Databases".
Select benzene, and use the "Send to" icon in the lower right-hand corner of the window to transfer it to the Builder.
Change two hydrogen atoms, on opposite sides of the molecule, to sulphur by selecting them and changing the element in the "Basis" panel (double-click "Hydrogen" to display the drop-down list of elements).
Click the Z-matrix button to display the Z-matrix tool.
Adjust the C-S bond lengths by selecting first the nearest carbon atom and then the sulphur atom (hold down Ctrl when clicking the second atom) and adjust the bond length in the Z-matrix to 1.75 Å.
Do this, separately, for both S atoms.
Note that if you first select S and then C, the C atom will be moving inwards, instead of, as we want, the S atom moving outwards.
Have a look at the list of atoms (the "Basis" panel), and write down the atom numbers for the two sulphur atoms. We will need this information later.
Leave the Builder window open, and return to the main VNL window.
Putting the junction together
Next we insert the molecule in the junction.
Open the Custom builder tool ol by clicking its icon on the main toolbar, and open the Molecular Junction builder using the menu "Builders".
Now go back to the open Builder window. Drag-and-drop the molecule, by using the icon in the lower right-hand corner, from the Builder to the drop-zone next to the label "New molecule?".
Enter the atom numbers for the two sulphur atoms (taken from step 6 above) in the two boxes "Left/Right adsorption boxes".
Position the S atoms in an fcc site by setting the alignment layers (left and right) to 2.
Set the "Adsorption height" (the distance from the sulphur atoms to the gold surface) to 1.71 Å. This will give a distance Au-S of 2.39 Å, as in the article.
In principle we are now done, and we can proceed to compute the transmission spectrum etc by sending the geometry to the Script Generator. However, that is not within the scope of this tutorial. Instead, we will continue to explore the various options given by the Molecular Device Builder.
Variations
Changing the electrode element/surface
If another element than gold is desired as the electrode element, you can drop any (cubic) crystal from e.g. the Database on the drop-zone next to "New Electrode?".
It is also really easy to alter the surface orientation by changing the Miller indices (hkl). The image below shows the same molecule on a bcc Li (100) surface, obtained by selecting lithium in the crystal Database and dropping it to the junction builder, and then just setting (hkl)=(100). Note how the bcc (100) surface cell has two repeated layers, where as the fcc (111) above had 3. We get 4 layers because the minimal electrode unit cell length is set to 7 Å.
Another way to modify the electrodes is to increase the repetition from the default value of 3, at least in some direction. This may be needed if the molecule is wide across and so might interface electrostatically with its repeated neighbors (remember ATK normally applies periodic boundary conditions in the XY plane).
Changing the orientation of the molecule
There are two parameters for the orientation of the molecule.
Setting the "Bonding angle" provides a powerful way to investigate how the conductance depends on the angle the molecule makes to the surface plane. The parameter you specify is the angle between the molecular axis and the surface plane normal, and the builder will automatically adjust the junction geometry. In the image below we have taken the Li-DTB-Li system and specified a 30 degree bonding angle.
Note carefully how the surface coordination is unchanged; the sulphur atoms are still sitting above the atoms in the second surface layer (see below). The second parameter is the "Rotation angle". This provides a simple and obvious way to rotate the molecule around its axis, defined as the line that runs through the two adsorption atoms. Below we see the same image as above (same view), with a rotation angle of 90 degrees.
Changing the surface coordination
In the configurations above, the suplhur atoms sit above an atom in the first layer below the surface. This is specified by the parameter "Alignment layer", which can be different for the two surfaces. The adsorption atoms are placed on top an atom in the specified surface layer, where 0 means the top layer, 1 the next layer below, etc.
To change the surface coordination to place the S atoms "on top" an atom in the top-most surface layer, set the alignment layer to 0.
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on the main toolbar, and switch to the Molecule database using the menu "Databases".
in the lower right-hand corner of the window to transfer it to the Builder.
on the main toolbar, and open the Molecular Junction builder using the menu "Builders".
The second parameter is the "Rotation angle". This provides a simple and obvious way to rotate the molecule around its axis, defined as the line that runs through the two adsorption atoms. Below we see the same image as above (same view), with a rotation angle of 90 degrees.
