Usage of Gaussian Atomic Coordinates in VNL tool bar - reg.

[kala]

Sir,
In many journals i have seen that guassian is used for optimizing molecules and those optimized atomic coordinates are used in atk simulations. I have gaussian optimized atomic coordinates for some molecules. Can i use these atomic coordinates as it is in VNL Builder to attach it to electrode for molecular junction?

[Anders Blom]

If you export the coordinates from Gaussian in XYZ format, you can import them directly in VNL.

[hari16]

i have extracted gaussian Coordinates. How i can import it to VNL tool.

[Anders Blom]

You can drop the xyz file directly on the Builder, or open it inside the Builder from Add>From File.

[hari16]

I want to know whether it is possible to use Nano tubes as electrode in two probe molecular junction, instead of Au electrodes in VNL tool bar. I want to fuse molecule in between nano tubes as i do in molecular junction. If so, what are the steps to be fallowed.

[Anders Blom]

Yes, that's certainly possible, although you should take care to have at least one of the nanotubes metallic, since electrodes normally need to be conducting. That is, choose a (n,n) nanotube for the electrodes.

The first thing to consider is if you want the tube to be capped or not. If you do, you should start by following the tutorial on this - or if you use 12.8 (beta-version is available) you can Add>From Files some existing capped tubes.

After that the procedure is very similar to http://quantumwise.com/publications/tutorials/builder/172, except the "alignment atoms" should be initially inserted as the center point of the hexagon/pentagon on the tip of the capped tube (my suggestion, you can choose differently if you prefer) and then moved out in Z.