A computational analysis of the vibrational absorption of molecular solids in the teraherz range

Abstract

In this thesis, we deal with the application of transmission terahertz spectroscopy as an analysis tool for the study of molecular solids, in particular organic crystals of pharmaceutical interest. Most of the work has been performed using two computational packages aimed at the interpretation of the spectra, one based on molecular forcefields (DMACRYS), the other on solid state density functional theory (CASTEP). We compare low temperature determinations of several molecular organic crystals to calculated spectra, and attempt to assign calculated modes of vibrations to absorption peaks, based on the similarity in frequency between the measured and calculated peaks. One of the main aims of this work is to establish the limits of our forcefield approach, which is based on the approximation that the intramolecular degrees of freedom can be neglected. We analyse the normal modes of vibration calculated with CASTEP, evaluating the amount of rigid molecule rotational and translational contribution to each eigenvector as a function of frequency, in order to validate our forcefield approach. We also compare the two sets of eigenvectors from the DMACRYS and CASTEP calculations to assess the similarity between the two approaches. We perform the same eigenvectors analysis on several hydrate systems in order to understand the role of water in the lattice dynamics of crystalline hydrates. We attempt a classification of the eigenvectors based on the strength of the forces involved in the molecular vibrations and based on the amount of the water contribution to each normal mode. A set of isostructural crystals is analysed in order to understand the effect that small variations (in the molecular formula and in the unit cell arrangement) have on the measured and calculated absorption spectra of a crystal. Finally, we discuss the use and development of computational methods that allow us to have a more realistic description of the molecular electrostatic in DMACRYS.