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Highlights • The unusual ClAlPc molecular self-assembled layer on a buffer layer have large deformations compared with the common ClAlPc bilayer. • Almost freestanding environment is provided for the molecules when the influence from the substrate is shielded by the buffer layer. • The dominated intermolecular interaction is likely to be the dispersion forces via Reduced Density Gradient analysis. Abstract We report an unusual self-assembled layer structure of chloroaluminium phthalocyanine (ClAlPc) molecules on highly ordered pyrolytic graphite (HOPG), in which a close-packed well-ordered monolayer is separated from the substrate by a relatively disordered buffer layer, as revealed using scanning tunneling microscopy (STM). Our close-packed monolayer has a nearly rectangular lattice, instead of the distinctly different square lattice for the more commonly observed well-ordered bilayer structure. This may be due to the dominance of intermolecular interactions within the monolayer when the influence from the substrate is shielded by the buffer layer. Density Functional Theory (DFT) calculations and Reduced Density Gradient (RDG) analysis indicate that the dominant intermolecular interaction within the unusual layer is likely the London dispersion force. Graphic abstract Image, graphical abstract [ABSTRACT FROM AUTHOR]