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This paper describes the molecular dynamic (MD) simulation investigation on the 3, 4, 9, 10-perylene tetracarboxylate (PTCB) dye anion intercalated Mg-Al-layered double hydroxide (PTCB/Mg-A1-LDH).The simulation results show that the intercalated PTCB exhibit a tendency from tilted to vertical orientation with respect to the layers as the interlayer water content increases, furthermore, the H and J-type dimer species are most likely populated under low and high hydration conditions, respectively.