how to construct the 2-probe sys whsoe molecule has 2 dangling bonds

[kay]

i'm calculating the transport properties of a 2-probe system with atk 2008.10, the problem is that the central molecule has two dangling bonds.but the whole molecule is neutral.I don't know how to construct the model and calculate the properties.I hope someone can help me.

[zh]

You can construct it by following the usual way.

[kay]

you mean i can neglect the dangling bond when i construct the model and set the element neutral,or i can truely construct the model with dangling bond by using ATK 2008.10?

[kstokbro]

The dangling bond is just for visual, the molecule is only defined by its elements.
We recommend upgrading to the latest version 12.8.2, it is several times faster, more accurate, and have more features.

[Anders Blom]

It depends a lot on your system, but if it's really a dangling bond you may need to passivate it with e.g. Hydrogen.