We present a basis-set-free approach to the variational quantum eigensolver using an adaptive representation of the spatial part of molecular wavefunctions. Our approach directly determines system-specific representations of qubit Hamiltonians while fully omitting globally defined basis sets. In this work, we use directly determined pair-natural orbitals on the level of second-order perturbation theory. This results in compact qubit Hamiltonians with high numerical accuracy. We demonstrate initial applications with compact Hamiltonians on up to 20 qubits where conventional representation would for the same systems require 40-100 or more qubits.