We report a combined experimental and theoretical study of the Kondo effect in a series of binuclear metal-organic complexes of the form [(Me(hfacac)_2)_2(bpym)]^0, with Me = Nickel (II), Manganese(II), Zinc (II); hfacac = hexafluoroacetylacetonate, and bpym = bipyrimidine, adsorbed on Cu(100) surface. While Kondo-features did not appear in the scanning tunneling spectroscopy spectra of non-magnetic Zn_2, a zero bias resonance was resolved in magnetic Mn_2 and Ni_2 complexes. The case of Ni_2 is particularly interesting as the experiments indicate two adsorption geometries with very different properties. For Ni_2-complexes we have employed density functional theory to further elucidate the situation. Our simulations show that one geometry with relatively large Kondo temperatures T_K ~ 10K can be attributed to distorted Ni_2 complexes, which are chemically bound to the surface via the bipyrimidine unit. The second geometry, we assign to molecular fragmentation: we suggest that the original binuclear molecule decomposes into two pieces, including Ni(hexafluoroacetylacetonate)_2, when brought into contact with the Cu-substrate. For both geometries our calculations support a picture of the (S=1)-type Kondo effect emerging due to open 3d shells of the individual Ni^{2+} ions.
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