Molecular dynamics investigation of nanotube diameter and wall thickness of cyclic hexa-, octa-, deca- and dodeca-peptide

Cyclic hexa-, octa-, deca- and dodeca-peptide nanotubes are investigated to insight their wall thickness and diameter with molecular dynamics based on a COMPASS force field. Single nanotube model of cyclo[(-D-Ala-L-Ala) _n=3,4,5,6-] and cyclo[(-D-Ala-L-Ala R)_n=3-] with side chain R = CH_2N+1 are built. Molecular modeling results indicate that cyclic peptide nanotubes of cyclo[(-DAla- L-Ala)_n=3,4,5,6-] have the internal diameters of 6.5 Å, 8.5 Å, 10.9 Å and 13.1 Å and the outer diameters of 13.5 Å, 15.5 Å, 17.9 Å and 20.1 Å respectively, as well as the same wall thickness of 3.5 Å. The nanotubes with 1∼6 side chain carbon atoms have the thickness wall of 3.5 Å, 4.7 Å, 5.5 Å, 6.6 Å, 7.5 Å, and 9.1 Å.