The modeling of the barrier properties of semicrystalline polymers has gained interest following the possible application of such materials as protective liners for the safe supply of pressurized hydrogen. The mass transport in such systems is intimately related to the complex intercalation between the crystal and amorphous phases, which was approached in this work through an all-atom representation of high-density polyethylene structures with a tailored fraction of amorphous-crystalline connections (tie-chains). Simulations of the polymer pressure-volume-temperature data and hydrogen sorption were performed by means of molecular dynamics and the Widom test particle insertion method. The discretization of the simulation domains of the semicrystalline structures allowed us to obtain profiles of density, degree of order, and gas solubility. The results indicated that the gas sorption in the crystalline regions is negligible and that the confinement of the amorphous phase between crystals induces a significant increase in density and a drop in the sorption capacity, even in the absence of tie-chains. Adding ties between the crystal and the amorphous phase results in further densification, an increase of the lamella tilt angle, and a decrease in the degree of crystallinity and hydrogen sorption coefficient, in agreement with several literature references.