Quantum mechanical energy levels are computed for the hydrogen molecule and its homonuclear isotopes confined within nanotubes of various sizes and structures. A realistic many-body potential is used to compute the interactions between the atoms of the diatomic and the nanotube carbons. Two translational and two rotational degrees of freedom are treated explicitly. Zero-pressure quantum sieving selectivities are computed from the energy levels. The effects of including both translation and rotation are discussed. The effect of confinement on the ortho/para splitting of hydrogen is also discussed.