QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: pervanem on October 4, 2016, 17:32

Title: electrical conductivity of metal-DNA for single nanowires?
Post by: pervanem on October 4, 2016, 17:32

 Hi,
I want to calculate electrical condutivities of complexes (m -DNA).
What should I do for it?
For this, is it suitable following devices? :-\
can you help me?
thanks you.

note: complex was optimized in gausian 09 (LANL2DZ and 6-311G++dp basis sets  was used for metal and other atoms, respectively)

Title: Re: electrical conductivity of metal-DNA for single nanowires?
Post by: zh on October 5, 2016, 02:29

Your case is a typical  study for the electronic transport properties of molecular device. Please follow the tutorial of AKT for your general question:
http://quantumwise.com/support/tutorials/item/103-building-a-molecular-junction-au-dtb-au
http://quantumwise.com/documents/tutorials/latest/MolecularDevice/index.html/

Title: Re: electrical conductivity of metal-DNA for single nanowires?
Post by: pervanem on October 5, 2016, 17:02

http://quantumwise.com/support/tutorials/item/103-building-a-molecular-junction-au-dtb-au
I watched it. https://www.youtube.com/watch?v=aoErF-WpU0c
in this video,
 S atom is used because of Di-thiol benzene (SH-benzene-SH).
my complex binds from N atom to DNA.
in my device,  is it must be carbon-Au bond?

Title: Re: electrical conductivity of metal-DNA for single nanowires?
Post by: zh on October 6, 2016, 04:20

To find out which atom in the molecule should be bonded with gold, it is better to first check the electronic structure of molecule, particularly for the distribution of HOMO or LUMO states.  Other information  such as the relative difference of the HOMO and LUMO levels of molecule with respect to the work function of gold is also needed.

 

Title: Re: electrical conductivity of metal-DNA for single nanowires?
Post by: pervanem on October 7, 2016, 12:29

thank you for reply Zh :)

let's say, C atom binds Au atom.
in this case, what should be Au-C bond lenght and Au-C Z-matrix distance ? or Au-X atom?
Is it that calculated by ATK?
or , How do we find  this distance (As shown picture, Au-X bond lenght or Au-X   Z-matris distance) ?

Title: Re: electrical conductivity of metal-DNA for single nanowires?
Post by: zh on October 8, 2016, 03:08

The distance between the Au atom in electrode and the C atom in molecule should be optimized by yourself with the ATK.

No comments for your attached figure, because it isn't related to the molecule and the electrode.
 

Title: Re: electrical conductivity of metal-DNA for single nanowires?
Post by: pervanem on October 11, 2016, 21:30

I dont know how I will  optimize the Au-structure-Au (or Au-C structure) please can you help me?

Title: Re: electrical conductivity of metal-DNA for single nanowires?
Post by: Petr Khomyakov on October 12, 2016, 09:44

Have a look at the tutorial, http://docs.quantumwise.com/tutorials/device_relaxation/device_relaxation.html, where the geometry optimization for a device configuration is discussed.