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The assumption here is that the geometries of the molecules studied are largely independent of the functional. This is widely recognized to be the case by the DFT community. To quote a recent review on DFT caculations on bioinorganic systems (Neese, F. J. Biol. Inorg. Chem. 2006, 11, 702-711, Geometries predicted by DFT methods tend to be quite reliable. Moreover, the predicted geometries converge quickly with basis set size, Different DFT functionals behave quite similarly as long as at least gradient corrections are taken into account e.g. one has to go beyond the local density approximation, LDA
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