The PUPIL system is a combination of software and protocols for the systematic linkage and interoperation of molecular dynamics and quantum mechanics codes to perform QM/MD (sometimes called QM/MM) calculations. The Gaussian-03 and Amber packages were added to the Pupil suite recently. However, efficient parallel QM codes are critical because calculation of the QM forces is the overwhelming majority of the computational load. Here we report details of incorporation of the deMon2k density functional suite as a new parallel QM code. An additional motivation is to add a highly optimized, purely DFT code. We illustrate with a demonstration study of the influence of perchlorate as a dopant ion of the poly(3,4-ethylenedioxythiophene) conducting polymer in explicit acetonitrile solvent using Amber and deMon2k. We discuss unanticipated requirements for use of a scheme for semi-empirical correction of Kohn-Sham eigenvalues to give physically meaningful one-electron gap energies. We provide comparison of both geometric parameters and electronic properties for non-doped and doped systems. We also present results comparing deMon2k and Gaussian03 calculation of forces for a short sequence of steps. And we discuss briefly some difficult problems of quantum zone scf convergence for the anionically doped system. The difficulties seem to be caused by well-know deficiencies in simple approximate exchange-correlation functionals.