  Stable organic radicals integrated into molecular junctions represent a
practical realization of the single-orbital Anderson impurity model. Motivated
by recent experiments for perchlorotriphenylmethyl (PTM) molecules contacted to
gold electrodes, we develop a method that combines density functional theory
(DFT), quantum transport theory, numerical renormalization group (NRG)
calculations and renormalized super-perturbation theory (rSPT) to compute both
equilibrium and non-equilibrium properties of strongly correlated nanoscale
systems at low temperatures effectively from first principles. We determine the
possible atomic structures of the interfaces between the molecule and the
electrodes, which allow us to estimate the Kondo temperature and the
characteristic transport properties, which compare well with experiments. By
using the non-equilibrium rSPT results we assess the range of validity of
equilibrium DFT+NRG-based transmission calculations for the evaluation of the
finite voltage conductance. The results demonstrate that our method can provide
qualitative insights into the properties of molecular junctions when the
molecule-metal contacts are amorphous or generally ill-defined, and that it can
further give a fully quantitative description when the experimental contact
structures are well characterized.
