Zeolites are microporous aluminosilicate materials with well-defined channels and cavities. Cu-exchanged zeolites have remarkable catalytic properties due to the unique redox properties of Cu, as has been inferred in selective catalytic reduction (SCR) of NOx with ammonia and in partial methane oxidation to methanol (PMO). The precise identity and quantity of Cu species and their sensitivity to zeolite framework compositions and synthesis conditions remain obscure. In this dissertation, I describe my usage of supercell density functional theory (DFT) models to determine site- and condition-dependent composition of Cu species in Cu-CHA zeolites. In addition, I show how ab initio molecular dynamics (AIMD) and Monte Carlo simulations are used to explore the thermodynamics of heteroatom (i.e. Al) distributions in CHA and to predict Al distributions. Lastly, I introduce the investigation of the Cu(II) reduction mechanism in NOx SCR and propose reaction pathways for dimeric Cu(II) intermediates being reduced in Cu-CHA. Our work bridges the knowledge of microscopic details of Cu cations to the macroscopic composition of the zeolites. The approaches used here can be applied broadly to other zeolites to find optimal zeolite compositions and synthesis conditions for catalysis applications.