In this paper the interaction of hydrogen molecules with atomic-sized superconducting nanojunctions is studied. It is demonstrated by conductance histogram measurements that the superconductors niobium, tantalum and aluminum show a strong interaction with hydrogen, whereas for lead a slight interaction is observed, and for tin and indium no significant interaction is detectable. For Nb, Ta and Pb subgap method is applied to determine the transmission eigenvalues of the nanojunctions in hydrogen environment. It is shown, that in Nb and Ta the mechanical behavior of the junction is spectacularly influenced by hydrogen reflected by extremely long conductance traces, but the electronic properties based on the transmission eigenvalues are similar to those of pure junctions. Evidences for the formation of a single-molecule bridge between the electrodes -- as in recently studied platinum hydrogen system -- were not found.
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