We report a combined Non-Equilibrium Green's Function - Density Functional Theory study of molecular junctions made of photochromic diarylethenes between gold electrodes. The impact of derivatization of the molecule on the transmission spectrum is assessed by introducing: (i) substituents on the diarylethene core; and (ii) linker substituents between the gold surface and the diarylethene. We illustrate that substituents on the core shift considerably the HOMO/LUMO level energies in gas phase but do not change the I-V characteristics of the molecular junctions; this behaviour has been rationalized by establishing links between the transmission spectrum and interfacial electronic reorganization upon chemisorption. In contrast, the different linker substituents under study modulate the conductivity of the junction by changing the degree of orbital hybridization with the metallic electrodes and the degree of orbital polarization.
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