Metal oxides, both simple and complex, are essential for catalysis and energy conversion due to their versatile physicochemical properties. To improve their functionality, they are often enhanced through ion modifications. Nevertheless, challenges remain, particularly in accurately characterizing the surface stability of such oxides beyond idealized conditions and in understanding the thermodynamics and kinetics associated with ion doping and migration. This thesis combines first-principle methods, including density functional theory, with molecular dynamics and enhanced sampling techniques to provide atomic-level insights into intrinsic and dopant ionic behaviors and dynamics within metal oxides. Additionally, in the context of heterogeneous catalysis, it aims to establish a pathway to guide future design improvements and enhance their chemical properties. The composition and stability of metal oxide surfaces are essential in shaping their properties. This thesis focuses on SrTiO3 and examines entropic effects by incorporating phonon contributions and utilizing established thermodynamic principles. It maps the free energies of different surface structures across temperatures, finding that phonon effects on surface morphology at higher temperatures cannot be ignored. This discovery strengthens the link between experiments and theory.Furthermore, the interplay between titanate-based perovskite oxides and transition metal ions through doping and surface adsorption forms a central focus of this work. Although these interactions are generally examined for their bulk doping properties, surface compositions can differ significantly. Through a systematic evaluation of the thermodynamics of 4d-transition metal doping, migration, and segregation with and without host strain effects, this research provides a high-throughput initial assessment of their thermal stability and synthesis feasibility. Another aspect of ion-perovskite interaction involves the thermodynamics of Ni egress and ingress across different SrTiO3 facets. The findings reveal a pronounced egress propensity from the (110) facet, which is uniquely significant for advancing novel catalyst synthesis methods like exsolution. Similarly, the thermodynamic impacts of Pd, Pt, and Rh migrating to the surface of LaFeO3 are explored, revealing that these metal ions can form surface alloys and alter the reducibility of surface oxygens, thereby modifying surface properties compared to the bulk material. Beyond thermodynamic analysis, ion surface migration and dissolution dynamics are explored through ab initio molecular dynamics and enhanced sampling methods. Modeling the exsolution of Pt from various perovskite titanate hosts reveals that Pt diffusion to the surface varies with the host material and specific exposed facets, with distinct temperatures required to overcome the kinetic barriers for exsolution. These insights inform predictions for the synthesis of supported metal catalysts. Additionally, ion dissolution dynamics and surface stability at oxide-solvent interfaces are investigated using metadynamics, focusing on a CaO-water interface to provide insights into phenomena such as catalyst surface leaching contributing to catalyst degradation. Collectively, these analyses provide a comprehensive atomistic understanding of complex metal oxides and establish a framework for furthering their strategic design.