# The Role of Metal Ions in the Electron Transport through Azurin-Based Junctions
## 3 Results and Discussion
Figure 4 (left) shows a comparison for the transmission curves obtained for the four proteins at the shortest tip-ion distance in a narrow energy range around the Fermi level. The transmission curve for the Apo (the protein deprived of the metal ion) is also shown in the same graph. It mainly differs from the other curves in the obvious absence of the peaks which derive, in the case of the other four proteins, from the d states of the metal ions. Quite strikingly, the transmission at the Fermi level for the metal-substituted azurins and the Apo is almost identical. This is due to the extreme sharpness of the HOMO-related resonances deriving from the metal ions. Similar conclusions can be drawn for the other three tip-protein distance values (see Figure 4 (right) for a comparison of the transmission values at the Fermi level at all distances for all proteins). In the case of Co, Ni and Cu, these results suggest that, despite these metal ions contributing to levels close to the Fermi level, their role in a fully-coherent electron transport is certainly important but not so dominant as one might naively expect. A large part of the contribution seems instead to be given by the rest of the protein, which provides the same background transmission for the Apo and for the other proteins analyzed in this study. For the short-distance structure corresponding to the curves shown in Figure 4, the main role seems to be played by the LUMO (this is less visible in the case of the curves of Figure 3 corresponding to larger distances, which seem to rather indicate an equal contribution between HOMO and LUMO). In any case, one has to bear in mind that the occupied energy range immediately below the Fermi level includes the contribution of several residues (mostly glutamic and aspartic acids: for a detailed analysis in the case of the Cu-azurin, we refer the reader to the work of [PERSON] et al. [34]). In the case of the Zn-azurin and for the Apo, part of the contribution to the transmission at the Fermi level seems indeed to be provided by these residues as well. As an aside, it is worth mentioning that recent experiments on protoporphyrins have revealed that the metal redox center has no role in the electron transfer, which was instead found to be mediated solely by the conjugated backbone of the molecule [68]. Our results are based on DFT, which is known to be affected by uncertainties concerning the size of the HOMO-LUMO gap because of self-interaction errors in the standard exchange-correlation functionals and image charge effects [69; 70; 71; 72; 73; 74]. Nevertheless, it is hard to foresee that the main conclusions would change upon use of a more sophisticated exchange-correlation functional. Although in this study we focused on sideways approach of the tip, other mechanisms would be possible such as indentation from the top. Geometries obtained  
via this kind of simulation, however, would probably lead to similar conclusions as those drawn for the geometries discussed above. Such a prediction is based on the fact that, for the Cu-azurin for instance, the main features of the transmission curves (concerning coupling and energetic alignment) were found to be quite similar [34]. We now turn to comparing our results with the experimental ones reported in [15]. There, the current density was found to follow the trend Cu \(>\) Ni \(>\) Co \(>\) Zn. This is at odds with our results which, as explained above, did not show significant changes for the transmission at the Fermi level. However, our findings, based on single-protein junctions, cannot be directly compared with those experiments, which were carried out on self-assembled monolayers; the latter are affected by dipole-dipole interaction and other effects [75] which are not present in our systems. Moreover, the electrodes which were there used (a highly-doped Si substrate and, in certain cases, a top electrode made of Hg) are very different from the gold electrodes employed in our simulations. [PERSON] et al.