Molecular dynamics of guest radicals in urea inclusion compounds

Molecular dynamics simulations of several radical guests included in urea clathrates have been performed for a period of 1 ns. The starting conformations of the radicals have been obtained by AM1 quantum mechanical computations. The host matrix has been modelled as a single channel formed by 47 or 72 urea molecules, and different constraints imposed on the urea molecule positions have been tested to optimize the effect of the host confinement on the guest radicals. Two kinds of motion have been considered, the internal dynamics of the methylene group beta to the radical centre and the rotation of the guest inside the host channel. The simulation results have been compared with experimental data obtained by electron paramagnetic resonance spectroscopy. Good agreement is found for the internal motion when a finite harmonic constraint is imposed on the urea carbonyl. The correlation time for the molecular rotation is estimated to be longer than the simulation period. The slow reorientation process should be controlled by the concurrent rearrangement of the host matrix.