The monomer and dimer structures of cyclo[(-L-Phe(1)-D-Ala(2))(n)-] and cyclo[(-L-Phe(1)-D-N-Me-Ala(2))(n)-] (n = 3-6) were studied by using the semiempirical molecular orbital AM1 method and the density functional B3LYP method. The structural characteristics of these molecules were revealed, some of which are not yet confirmed experimentally. The influences of the substituents and ring size on molecular structure and the self-assembly process are discussed in detail. The inherent impetus for these molecules to self-assemble to polypeptide nanotubes is discussed.