Least squares modeling was applied to gain insights into changes that occur in the structure of Nafion polymer membrane during hydration. Transmission infrared spectra followed changes in the strong polymer bands in the range of 1400–950 cm<sup>−1</sup> during water uptake by initially dry membrane upon exposure to 100% relative humidity atmosphere. Spectra recorded during hydration were fit to a rate equation that modeled the loss of a dry state accompanied by the development of a hydrated state. The evolution of the two states was described by an equation for diffusion in a cylindrical pore in the long time limit. Comparison of the experimental spectra in a data set to spectra calculated from the pure components derived by least squares modeling gave an excellent match for bands of the −CF<sub>2</sub> and C–O–C group modes, but agreement was not as close for bands arising from modes of the hydrophilic −SO<sub>3</sub><sup>−</sup> group and (modeled separately) water. The differences are discussed in terms of the likelihood that the −SO<sub>3</sub><sup>−</sup> groups have stronger interactions with bulk-like water condensed in the membrane and therefore undergo more complex changes than do more hydrophobic polymer regions during hydration. A different model is necessary to describe the evolution of spectral features for water and −SO<sub>3</sub><sup>−</sup> end groups during water uptake into Nafion thin films.
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