Abstract Diffusion and molecular conformation are essential characteristics that could be employed to comprehend the dynamics behaviour of molecules in a nanoporous host-guest system. We have performed here a molecular dynamics simulation on hexadecane-1,16-diol and hexadecane guests in the three-dimensional hexagonal nanoporous structure of urea inclusion compound model system and compared the findings with that of one-dimensional urea model system. The guests’ along urea tunnel exhibited slower diffusion with the value correlating well with experimental findings, as the size of the model systems tend to mimic more the real system. The asymmetrical G- and G+ distortion along the guests’ conformational energies, demonstrated that the influence of urea chirality on the guests was notable on hexadecane-1,16-diol as compared to hexadecane. The variation in the diffusional and conformational properties evaluated in each phase of model systems addressed the significant role of the guests’ functional groups. Rationalisation on the factors affecting the guests’ behavioural properties found that the urea confinement had an important role in manipulating the guests’ conformational properties. The intrinsic conformational property, i.e., the steric constraint associated with hydroxyl and alkyl functional groups of hexadecane-1,16-diol and hexadecane, respectively, was found to have a minor role.

中文翻译：

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十六烷-1,16-二醇和十六烷包合在三维纳米多孔尿素包合物模型系统中的扩散和构象行为通过分子动力学模拟

摘要 扩散和分子构象是可用于理解纳米多孔主客体系统中分子动力学行为的基本特征。我们在这里对尿素包合物模型系统的三维六边形纳米多孔结构中的十六烷-1,16-二醇和十六烷客体进行了分子动力学模拟，并将结果与​​一维尿素模型系统的结果进行了比较。沿着尿素隧道的客人表现出较慢的扩散，该值与实验结果很好地相关，因为模型系统的大小倾向于更多地模仿真实系统。沿着客体构象能量的不对称 G- 和 G+ 畸变表明，与十六烷相比，尿素手性对客体的影响在十六烷-1,16-二醇上更为显着。在模型系统的每个阶段评估的扩散和构象特性的变化解决了客人功能组的重要作用。对影响客人行为特性的因素进行合理化发现，尿素限制在操纵客人的构象特性方面具有重要作用。内在的构象特性，即分别与十六烷-1,16-二醇和十六烷的羟基和烷基官能团相关的空间约束，被发现起次要作用。对影响客人行为特性的因素进行合理化发现，尿素限制在操纵客人的构象特性方面具有重要作用。内在的构象特性，即分别与十六烷-1,16-二醇和十六烷的羟基和烷基官能团相关的空间约束被发现具有次要作用。对影响客人行为特性的因素进行合理化发现，尿素限制在操纵客人的构象特性方面具有重要作用。内在的构象特性，即分别与十六烷-1,16-二醇和十六烷的羟基和烷基官能团相关的空间约束，被发现起次要作用。