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In the present work the role of the thermal treatment on the reorganization of gold nanoparticles (AuNPs) functionalized with a π-conjugated dithiol ligand, namely 9,9-didodecyl-2,7-bis-thiofluorene, is studied by grazing incidence X-ray diffraction technique. For a detailed investigation of the structural changes and reorganization occurring in the AuNPs network and of the monitoring of complex interactions between nanoparticles, the line profiles are analyzed in out-of-plane and in-plane directions. The obtained data support the idea of the formation of a uniform network of nanoparticles that after annealing are extended from hexagonal to cubic arrangement. [ABSTRACT FROM AUTHOR]