Layer-type Mn oxides are common minerals in soils. They greatly influence the fate of trace elements through the high sorption capacity. Synchrotron-based experimental techniques have provided molecular-level insights into the sorption phenomena. However, the relationship between structure and chemical reactivity remains ambiguous as little variation in the structural and chemical composition exhibits significant changes in the reactivity. Molecular modeling is essential to reduce the ambiguity. Indeed first-principle calculations based on density functional theory (DFT) have resolved many ambiguities in the metal sorption mechanisms, in particular, related to Mn(IV) vacancies. Nevertheless, the dynamic features of interlayer structures are challenging to explore with DFT only. Classical molecular dynamic (MD) simulations using interatomic pair potentials is an alternative method to examine the dynamic features. This talk introduces a newly developed set of pair-potentials for classical MD simulations that can deal with more realistic Mn oxide models. MD simulation results are presented as to the relationship among the interlayer cation/water content and structures and the Mn octahedral sheet stacking modes.