Density functional theory (DFT) calculations were performed to study the crystallographic properties of the cis-vacant form of dioctahedral 2:1 phyllosilicates. Samples with different layer charges are studied; only tetrahedrally charged, only octahedrally charged, or mixed octahedrally/tetrahedrally charged. The isomorphous cation substitutions were explored in different relative positions with substitutions of octahedral Al3+ by Mg2+ or Fe3+, tetrahedral substitution of Si4+ by Al3+, and different interlayer cations (IC) (Na+, K+, and Ca2+). X-ray diffraction patterns of cis-vacant and trans-vacant forms of phyllosilicates were simulated and compared. The experimental observation of clustering tendency of Fe3+ and dispersion tendency of Mg2+ in the octahedral sheet is reproduced and explained with reference to the relative energies of the octahedral cation arrangements observing the same tendency that in the trans-vacant forms. These energies are higher than those due to the IC/tetrahedral and IC/octahedral cations relative arrangements. The tetrahedral and octahedral substitutions that generate charged layers tend also to be dispersed. The energy difference between the cis-vacant and trans-vacant polymorphs is smaller than that of cation arrangements.