Molecular junctions – whether actual single molecules in nanowire break junctions or artificial molecules realized in coupled quantum dot devices – offer unique functionality due to their orbital complexity, strong electron interactions, gate control, and many-body effects from hybridization with the external electronic circuit. Inverse design involves finding candidate structures that perform a desired function optimally. Here we develop an inverse design strategy for generalized quantum impurity models describing molecular junctions, and as an example, use it to demonstrate that many-body quantum interference can be leveraged to realize the two-channel Kondo critical point in simple 4- or 5-site molecular moieties. We show that remarkably high Kondo temperatures can be achieved, meaning that entropy and transport signatures should be experimentally accessible.

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