Unique physical, chemical, and mechanical properties can be engineered into functional nanomaterials via structural control. However, as the hierarchical structural complexity of a nanomaterial increases, so do the challenges associated with generating atomistic models, which are sufficiently realistic that they can be interrogated to reliably predict properties and processes. The structural complexity of a functional nanomaterial necessarily emanates during synthesis. Accordingly, to capture such complexity, we have simulated each step in the synthetic protocol. Specifically, atomistic models of mesoporous ceria were generated by simulating the infusion and confined crystallization of ceria in a mesoporous silica scaffold. After removing the scaffold, the chemical reactivity of the templated mesoporous ceria was calculated and predicted to be more reactive compared to mesoporous ceria generated without template; visual "reactivity fingerprints" are presented. The strategy affords a general method for generating atomistic models, with hierarchical structural complexity, which can be used to predict a variety of properties and processes enabling the nanoscale design of functional materials.