Geometry Optimization of the two Probe System(organic molecule between 2 electro

[hendchem2024]

I am having difficulty in performing a geometry optimization for a two-probe system. So I would like to have a sound methodology to properly perform a two-probe system geometry optimization, especially when studying the rectification properties of an organic molecule when placed between two gold electrodes.

[Jahanzaib]

The way I approach the two-probe system optimization is by dividing it into smaller parts.  Instead of optimizing the entire device at once, which is a massive task, I find it faster and more efficient to build the device from optimized components.

I first separately optimize the central region, which in this case includes the organic molecules and similarly, optimize the gold electrodes. Then, place the optimized organic molecules between the optimized gold electrodes.

Each part is already optimized, then no need to optimize complete device again.

If you want expert comments, you should wait for a response from @Anders Blom.

[Anders Blom]

Yes, this is the correct approach: optimize it in steps. The molecule does not affect the electrodes, but only the gold atoms near the molecule, so a full-blown device optimization is often unnecessarily cumbersome (but necessary in some cases).

Also note that in almost all cases, the bias does not influence the geometry, unless you are specifically looking at such effects.