Dynamics in crystals of rigid organic molecules: contrasting the phonon frequencies calculated by molecular dynamics with harmonic lattice dynamics for imidazole and 5-azauracil

Gray, A.E., Day, G.M., Leslie, M. and Price, S.L. (2004) Dynamics in crystals of rigid organic molecules: contrasting the phonon frequencies calculated by molecular dynamics with harmonic lattice dynamics for imidazole and 5-azauracil. Molecular Physics, 102 (9-10), 1067-1083. (doi:10.1080/00268970412331284208).

Abstract

Molecular dynamics simulations have been performed on crystalline imidazole at 100?K and 5-azauracil at 310?K with a model intermolecular potential that includes a distributed multipole representation of the molecular charge distribution using the program DL_MULTI. The anisotropic atom–atom electrostatic model enabled the experimental crystal structures to be reproduced well in a constant pressure simulation and the simulations showed a physically reasonable thermal expansion relative to the minimum in the static lattice energy. The rigid-body molecular motions in a subsequent constant volume simulation were analysed to obtain the k?=?0 frequencies corresponding to different symmetry representations, via the translational and rotational velocity autocorrelation functions. These frequencies were contrasted with the corresponding harmonic lattice modes calculated with the same molecular model and intermolecular potential. The agreement was good, with most, but not all, modes decreasing in frequency in the finite temperature simulation, by generally less than 5?cm?1 in the case of imidazole (reducing the rms error in comparison with experimental frequencies to 18.8?cm?1) and by less than 20?cm?1 for 5-azauracil. Quasi-harmonic calculations using experimental unit cell parameters and analyses of the modes in terms of the different hydrogen bonding motifs were unable to give any clear insight into the causes of the significant variations in the effects of temperature on the different motions.

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Contributors

Author: G.M. Day

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