Today’s cyclic peptide nanotubes (CPN) have found many applications in different fields of biology, chemistry and material sciences. The interest is largely related to their technological possibilities as biosensors, photosensitive materials, antimicrobial agents, selective transporter systems and molecular electronic components. In this work, molecular dynamics (MD) and quantum chemistry calculations (QC) have been performed for investigation of the stability of heterocyclic peptide nanotube (1,4-disubstituted-1,2,3-triazole amino acid) and its analysis as a channel for molecules transportation. Starting from the X-ray structures, MD simulations of nanotubes were performed in water, methanol and chloroform using the Amber 12.0 software with FF12SB force filed. All of systems were partially optimized, thermalized and equilibrated in 10 ns and production MD has been done in 45 ns. The dimer of heterocyclic peptide has been optimized by M062X/6-31G(d). MD simulations showed that the CPN is not stable in water. Because hydrogen bond formation between the cyclic peptide nanotube and water molecules makes the CPN unstable. But CPN individually is more stable in chloroform than water and methanol. Ethanol molecules were inserted into CPN and MD simulations were repeated. According to obtained results, the CPN was stable after 45 ns in water, methanol and chloroform. RMSD analysis for these structures (with ethanol and without ethanol) in water confirmed that the CPN in water without guest molecule is not stable. Based on these investigations, it is confirmed that this CPN has great potential for using as a channel for molecules transportation such as drugs and ions. Finally, according to QC data, dimer structure is more stable in polar than non-polar solvents.

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