about building a molecular junction

[FlyFlower]

hello, everyone. i'm new to vnl 10.8. when i'm building a molecular junction, my goal molecule is like pic.1.

but in vnl 10.8 (pic.2) i can't make the two sulfur atoms align with z-axis. how can i do that? also how to change the number of layers in surfaces and electrode? much thanks.

[Anders Blom]

Use the Custom builder "Molecular junction" and make sure to align the right-hand sulphur atom to the same surface layer as the left one.

[FlyFlower]

Use the Custom builder "Molecular junction" and make sure to align the right-hand sulphur atom to the same surface layer as the left one.

i just did it in "molecular junction" tool, 8 and 10 atoms are sulfur atoms, and the alignment layer for left and right surface are both 2. But it still can't make the two S atoms align in z-axis.

[Anders Blom]

The right-hand alignment layer should be equivalent to the left. Since the structure is not mirror symmetric, this means it's not necessarily the same layer number when counted from the surface. Try setting the right alignment layer to 3!

[FlyFlower]

The right-hand alignment layer should be equivalent to the left. Since the structure is not mirror symmetric, this means it's not necessarily the same layer number when counted from the surface. Try setting the right alignment layer to 3!

no matter setting the right alignment layer to any number, it does not make any influence on the orientation of the molecule.

[Anders Blom]

Can you attach the molecule (only!) as a Python file, then I can try.

[FlyFlower]

Can you attach the molecule (only!) as a Python file, then I can try.

Thank you !

[Anders Blom]

The key is to set the "Bonding angle" to 30 degrees. Also note that the top layer is 0.

[FlyFlower]

The key is to set the "Bonding angle" to 30 degrees. Also note that the top layer is 0.

i have tried that, but it still didnot work.

[Anders Blom]

I did one thing differently compared to you, didn't realize it was critical. I first rotated your molecule 90 degrees about the Y axis (in the Builder). The idea with this was to have the two S atoms along Z already to begin with.

[FlyFlower]

I did one thing differently compared to you, didn't realize it was critical. I first rotated your molecule 90 degrees about the Y axis (in the Builder). The idea with this was to have the two S atoms along Z already to begin with.

Thank you very much !