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?
