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The methods currently used to calculate atomic pair distribution functions (PDFs) from organic structural models do not distinguish between the intramolecular and intermolecular distances. Owing to the stiff bonding between atoms within a molecule, the PDF peaks arising from intramolecular atom–atom distances are much sharper than those of the intermolecular atom–atom distances. This work introduces a simple approach to calculate PDFs of molecular systems without building a supercell model by using two different isotropic displacement parameters to describe atomic motion: one parameter is used for the intramolecular, the other one for intermolecular atom–atom distances. Naphthalene, quinacridone and paracetamol were used as examples. Calculations were done with the DiffPy-CMI complex modelling infrastructure. The new modelling approach produced remarkably better fits to the experimental PDFs, confirming the higher accuracy of this method for organic materials.

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