Molecular modeling of diphenylalanine peptide nanotubes (FF PNT) is performed using PM3 method in HyperChem. The study focuses on the polar properties of FF PNT structures having different chiralities (L, D) and conformations (alpha-helix, beta-sheet). The results show that the optimized structures for L-PNT possess higher polarization in both conformations (0.023 C/m(2) - alpha, 0.04 C/m(2) - beta) compared with D-PNT (0.016 C/m(2) - alpha, 0.014 C/m(2) - beta). The water structures inside PNT are investigated, too. The hexagonal ice/water structures used for these models are analyzed in respect to the XRD data recently obtained.