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The space-filling model, while useful for visualizing molecular structures, has several limitations. It can obscure important details about molecular geometry and functionality by depicting atoms as spheres without regard to their specific bonding angles or orientations. Additionally, this model does not effectively represent electron cloud distributions or the effects of intermolecular forces, potentially leading to misinterpretations of molecular interactions. Lastly, it can be challenging to discern the actual arrangement of atoms when complex molecules are represented, limiting its effectiveness for detailed analysis.

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