Molecular dynamics simulation of guest diffusional and conformational behaviour of hexadecane-1,16-diol and hexadecane in urea inclusion compound models

Abstract

Urea inclusion compounds are organic crystalline complexes that are potential candidates for molecular separator of long chain alkanes. A well-defined structure of the crystalline tunnel systems constructed from hydrogen bonding arrangement of urea molecules can be used to comprehend the fundamental aspects of processes involving ions or molecules transportation which play an important role in many physical, chemical and biological process taking place in a wide range of materials. This work endeavours to explore the diffusional behaviour of hexadecane-1,16-diol and hexadecane enclathration in urea tunnel architecture. The correlation of the diffusion mechanism with the guest’s structural and conformational properties was obtained using molecular dynamics simulation approach. Three-stage of model systems have been developed in this work. In the first phase, a single urea tunnel with inclusion of only one guest molecule was constructed. In the second phase, eleven guest molecules were included inside a single tunnel of rigid and nonrigid urea host molecules to observe the influence of the existence neighbours, i.e. the guest-guest intratunnel molecular interaction. In the third phase, four urea tunnels were constructed to take into account the effect of intertunnel interaction on the guests’ behavioural properties. It was found that hexadecane along the urea tunnel diffuse more rapidly than hexadecane-1,16-diol. The diffusion coefficients of hexadecane-1,16-diol in phase I, phase II of rigid and nonrigid and phase III model systems were 2.69 × 10-9 m2s-1, 1.83 × 10-10 m2s-1, 8.9 × 10-11 m2s-1, and 3.2 × 10-11 m2s-1, respectively, whilst those for hexadecane 1.96 × 10-8 m2s-1, 2.58 × 10-9 m2s-1, 7.15 × 10-10 m2s-1, and 5.36 × 10-10 m2s-1, respectively. The guests’ along urea tunnel exhibited slower diffusion with the value correlated well with experimental findings, as the size of the model systems tended to mimic the real system. Elucidation on the guest rotational pattern as the molecule translated within the confinement of urea tunnel found that the guest preferred to follow the right-handed spirals of the chiral urea hydrogen-bonded structure. Besides, the translational and rotational properties of the guests are much more pronounced in the nonrigid urea systems. It was suggested that restriction imposed on the rigid urea systems constrained the molecules from being in their best conformation, thus contributed to the overall observation on the guest structural and conformational behaviour. The asymmetrical G- and G+ distortion along the guest’s conformational energy which demonstrated the influence of urea chirality on the guest was notable on hexadecane-1,16-diol as compared to hexadecane. The variation in the diffusional and conformational properties evaluated in phase I, II and phase III model systems has highlighted the significant role of the guests’ functional groups, which in turn are associated to guest-guest intratunnel and intertunnel molecular interactions as well as the host-guest interaction. Molecular dynamics method offered significant fundamental knowledge associated with the structures and dynamics of the guest molecules in a well-defined urea nanoporous model systems that have important application in molecular separation and enantiomeric discrimination area.