Computer modelling studies of 18-crown-6 with urea and thiourea

Abstract

Computer modelling studies have been carried out on the interaction of 18-crown-6 with a variety of guest molecules, including urea, thiourea and substituted ureas. The five known crystal structures of these host/guest systems were used as models. We were interested to establish whether the arrangement of guest molecules around a host molecule in the crystal was indicative of the lowest energy configuration for a host/guest fragment or was a consequence of packing effects. Two models were therefore considered for each structure and the structures minimised via molecular mechanics. In the first mode, the structure consisted of one unit cell and periodic boundary conditions were used in the calculation. Coulombic effects were calculated using the Ewald summation. In the second model, the structure consisted of an 18-crown-6 molecule surrounded by two hydrogen-bonded guest molecules. Both models were minimised using the CERIUS package using the DreidingII forcefield.

The crystal structure minimisations reproduced the structures very well with an average change in cell volume of 3.6% and a mean r.m.s. positional deviation of 0.20 Å. The fits for the fragment models were significantly larger for all structures (mean 0.30 Å) but even so it can be concluded that the arrangement in the crystal gave a good indication of the lowest energy configuration of the host/guest in vacuo.