High fluence ion implantation with silicon-28 into natural silicon substrates has been shown to result in the depletion of the nuclear spin 1/2 silicon-29 isotope to below 3 ppm resulting in a close to spin-free matrix for donor-based quantum computer architectures. Optimisation of this enrichment process requires a detailed understanding of the atomic dynamics during the deposition process. Given that previous binary collision Monte Carlo simulations, employed to model experimental settings, lack the mechanistic detail needed for process optimisation, a more exhaustive description of the ion implantation process remains to be addressed. In this context, we employ molecular dynamics (MD) simulations, to examine the enrichment process by performing overlapping depositions of silicon-28 ions across a wide range of energies followed by a post-irradiation annealing, resulting in the overall enrichment of the sample with silicon-28, and reduced silicon-29 and silicon-30 isotopes. Our results show how the key variables, such as the deposition energy and angle of impact can influence factors including the enrichment depth and sputtering yield. By comparing with experimental outcomes, we aim to validate and enhance the understanding of the silicon-28 enrichment process for future quantum computing architectures.