Department of Chemistry, Faculty of Sciences, Ferdowsi University of Mashhad, Mashhad, Iran.
Phys Chem Chem Phys. 2015 May 7;17(17):11382-91. doi: 10.1039/c5cp00973a.
Molecular dynamic simulations were performed to investigate the stability of heterocyclic peptide nanotubes composed of 1,4-disubstituted-1,2,3-triazol ε-amino acid. 45 ns MD simulations were conducted on the cyclic peptide nanotube (CPNT) and cyclic peptide dimer in methanol, chloroform, and water and revealed that these structures are more stable in nonpolar solvents. MM-PBSA and MM-GBSA calculations were employed to analyze the solvent effect on the stability and length of the CPNT. These calculations showed that CPNT in chloroform was more stable and longer as compared to other solvents. In addition, the effect of the guest molecule (ethanol) inside the dimer and CPNT was investigated. The obtained results confirmed that guest molecule(s) stabilized the dimer and CPNT in all solvents. Quantum chemistry calculations on the cyclic peptide dimer were performed at the M06-2X/6-31G(d) level in the gas phase and three solvents. The obtained results from the quantum chemistry study were in good agreement with the MD simulation results. DFT calculations showed that the guest molecule stabilized the dimer structure and electrostatically interacted with the cyclic peptide dimer. Finally, for investigation of the solvent effects on the hydrogen bonds of the cyclic peptide dimer, NBO and AIM analysis were performed.
采用分子动力学模拟研究了由 1,4-二取代-1,2,3-三唑 ε-氨基酸组成的杂环肽纳米管的稳定性。在甲醇、氯仿和水中对环状肽纳米管 (CPNT) 和环状肽二聚体进行了 45 ns 的 MD 模拟，结果表明这些结构在非极性溶剂中更稳定。采用 MM-PBSA 和 MM-GBSA 计算分析了溶剂对 CPNT 稳定性和长度的影响。这些计算表明，与其他溶剂相比，CPNT 在氯仿中更稳定且更长。此外，还研究了二聚体和 CPNT 内客体分子（乙醇）的影响。所得结果证实，客体分子（s）在所有溶剂中稳定了二聚体和 CPNT。在气相和三种溶剂中，对环状肽二聚体进行了 M06-2X/6-31G(d)水平的量子化学计算。量子化学研究的结果与 MD 模拟结果吻合较好。DFT 计算表明，客体分子稳定了二聚体结构并与环状肽二聚体静电相互作用。最后，为了研究溶剂对环状肽二聚体氢键的影响，进行了 NBO 和 AIM 分析。
