Structural properties of carboxylic acid dimers confined within the urea tunnel structure: an MD simulation study.

Large-scale molecular dynamics simulations have been performed on solid inclusion compounds formed between urea and alkane (dodecane) and alkanoic acid (dodecanoic acid) guest molecules. The incommensurate nature of the guest and host substructures means that simulations of these systems are challenging, and our results call into question some of the simplifying assumptions made in earlier simulations on the urea inclusion compounds. Detailed information is obtained on the structural properties of the carboxylic acid dimers and alkyl chains confined within the nanoscale tunnels of the urea host structure, including the chirality of the guest conformation induced by the chiral nature of the urea tunnels. Diffusion coefficients (at 300 K) of the guest molecules along the tunnel axis were determined to be 0.091 ± 0.031 (dodecane) and 0.0063 ± 0.0013 Å(2) ps(-1) (dodecanoic acid), in good agreement with experimental measurements on alkane/urea systems. Weak ordering is observed between guests in neighboring tunnels, which is compatible with experimental measurements on the alkane/urea systems, although the simulations provide more detailed molecular-level insights into the nature of this supramolecular ordering.