A multi-component molecular orbital (MC-MO) theory is developed for a combined quantum system of electrons and nuclei with the full configuration interaction (CI) scheme of Cartesian Gaussian-type functions. The technique of graphical unitary group approach (GUGA) is modified to obtain the CI matrix elements for many kinds of quantum particles efficiently. The optimum basis sets for quantum nuclei are proposed with the fully variational procedure. The average internuclear distances, dipole polarizabilities, and nuclear vibrational excitation energies for isotopic hydrogen molecules calculated with optimized basis sets are found to adequately reproduce the corresponding experimental values. (C) 2002 Elsevier Science B.V. All rights reserved.