3D numerical simulations of the interaction of a powerful CO2 laser with hydrogen jets demonstrating the role of ionization in the characteristics of induced wakes are presented. Simulations using SPACE, a parallel relativistic particle-in-cell code, are performed in support of the plasma wakefield accelerator experiments being conducted at the Brookhaven National Laboratory (BNL) Accelerator Test Facility (ATF). A novelty of the SPACE code is its set of efficient atomic physics algorithms that compute ionization and recombination rates on the grid and transfer them to particles. The influence of ionization on the spectrum of the pump laser has been studied for a range of gas densities. Simulations reproduce both Stokes and antiStokes shifts in the spectrum of the pump laser, similar to those observed in experiments in the spectrum of the probe. Good agreement has been achieved with the experiments on the effect of variation in gas density on Stokes/antiStokes intensity. In addition, self-injection and trapping of electrons into the self-modulated wakes have been observed and analyzed. The experimentally validated code SPACE will be used for predictive simulations to guide future experiments at BNL ATF.