Molecular cluster models, developed for an exfoliated kaolinite, provide a structural description comparable to that of periodic slab models for a fraction of the computational cost. These models include both the octahedral and the tetrahedral sheets of kaolinite. The first-generation model (G1) contains the inner and outer coordination sphere of the Al- and Si-honeycombs as the preferred sites for adsorption of small organic molecules. Since no experimental information is available to date at the atomic level for exfoliated kaolinite, we carried out a systematic density functional theory evaluation for establishing the most reasonable coordinates of the ions and groups. The results of molecular cluster and periodic calculations were utilized for evaluating semi-empirical Hamiltonians on larger models. Using a PM7 Hamiltonian, the structure of cluster models containing 1 + 6 (second generation) and 1 + 6 + 12 (third generation) Al- and Si-honeycombs which are out of reach for ab initio calculations, were determined. These molecular slab models offer a structural platform for adsorption, intercalation and delamination studies.