Author Topic: Modelling charged molecules in molecular junctions  (Read 517 times)

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Offline paullapham95

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Hello,

I was hoping you could help clarify something. I'm currently doing transport studies on a series of molecular junctions (Image attached for reference). The molecule in question(POM) is easily reduced and so I am trying to compare the transport of the -3 through -9 redox states of the molecule.  To do so, I optimise the molecule (with DFT)  with different charges. I then build the device with the optimised molecule. I assumed that as the optimisation has taken into account the charge, and the number of electrons ( checked by MES) is consistent ( increases by 1 as charge increases), when placed between electrodes, although you can't specify the charge of the molecule in the device, the number of electrons (in the molecule) should be consistent with its redox state.

However, when I calculate the MES(focusing only on the molecule) for the different devices the number of electrons is consistently 628 ( which is the number for the -4 state). The transmission spectra, HOMO-LUMO gap are all different for all devices, suggesting that the same molecule is not being modelled. But I want to be sure that the charge of the molecule is being modelled correctly and that it is a result of it reaching equilibrium with the electrodes or something else physical rather than an error in the modelling of the device.

If this is erroneous, is there a way I can specify the charge of the molecule within the device?

Offline Daniele Stradi

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Re: Modelling charged molecules in molecular junctions
« Reply #1 on: April 27, 2020, 11:56 »
Unfortunately, you cannot specify the charge of the molecule in a device calculation. This is because in a DFT-NEGF calculation the charge state of the molecule will be a consequence of the electronic density of the central region reaching equilibrium with the Au electrodes.

There is no unique way of fixing the charge state of the molecule in a DFT-NEGF calculation. If you want to calculate the transport in a charged molecule, that will be in the Coulomb blockade regime, and therefore I would suggest to simulate as documented in the paper linked here below:

https://pubs.acs.org/doi/abs/10.1021/jp104811r

Best,
Daniele