Molecular dynamics simulations can provide the means to visualize and understand the role of intermolecular interactions in the mechanisms involved in molecular aggregation. Along these lines, simulations can allow the study of how surface chemical modifications can influence nanomaterial assembly at the molecular level. Layered silicate clays have been of significant interest for some time, particularly with regard to their use in organic/inorganic nanocomposites. However, despite numerous reports on the covalent linkage of organic moieties via silanol condensation, the theoretical understanding of these systems has heretofore been limited to noncovalent interactions, specifically ionic interactions at the charged basal surfaces. Herein, a model for edge-functionalized layered aluminosilicate clay, based on the siloxane linkage, is presented. In addition to reproducing experimentally observed degrees of molecular aggregation of clay-linked perylene diimide derivatives with different terminal functional groups as a function of solvent composition, a molecular-level understanding of the role of van der Waals interactions and hydrogen bonding of the different end-groups on the aggregation state in different water/N,N-dimethylformamide mixtures is obtained. The reported model provides a means to simulate organic moieties covalently bound to the layered silicate edge, which will enable future simulations of nanocomposites and organic/inorganic hybrids based on this system.