Interactions of pulverized crystalline silica with biological systems, including the lungs, cause cell damage, inflammation, and apoptosis. To allow computational atomistic modeling of these pathogenic processes, including interactions between silica surfaces and biological molecules, new parameters for quartz, compatible with the CHARMM empirical force field were developed. Parameters were optimized to reproduce the experimental geometry of α-quartz, ab initio vibrational spectra and interactions between model compounds and water. The newly developed force field was used to study interactions of water with two singular surfaces of α-quartz, (011) and (100). Properties monitored and analyzed include the variation of the density of water molecules in the plane perpendicular to the surface, disruption of the water H-bond network upon adsorption, and spacetime correlations of water oxygen atoms in terms of Van Hove self correlation functions. The Vibrational Density of States (VDOS) spectra of water in confined compartments were also computed and compared with experimental neutron-scattering results. Both the attenuation and shifting to higher frequencies of the hindered translational peaks upon confinement are clearly reproduced by the model. However, an upshift of librational peaks under the conditions of model confinement still remains underrepresented at the current empirical level.

The vibrational normal modes of the free base porphine (FBP) have been investigated within the framework of the density functional theory (DFT). The scaling of the internal force constants has been performed using a least-squares method, and a general valence force field was deduced for the free base porphine with D 2 h symmetry. To check the vibrational assignments for the normal modes having the Ag symmetry, the resonance Raman intensities have been predicted. It is shown that the A term part of the scattering tensor is able to explain most of the observed resonance Raman enhancements for the electronic transitions lying in the Q band.