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.

Reconstruction of the most common pristine and hydrolyzed surfaces of quartz was investigated with periodic density functional theory calculations. Surface energies of reconstructed pristine faces, pertinent to quartz growth morphologies in melts, are found to range from 0.071 eV/A2 for the (101) surface to 0.139 eV/A2 for the (001) surface, and they increase as (101) < (102) < (112) < [(100), (111)] < (110) < (001). Four types of reconstruction reactions are observed: (1) formation of two-membered rings from vicinal silyl and siloxy sites, (2) formation of a pair of tricoordinated/unicoordinated oxygen atoms, (3) formation of three-membered rings, and (4) transformation of silanone sites into siloxane sites. The main features of reconstructed pristine quartz surfaces are two-membered rings formed from bridged siloxy and silyl sites on all investigated surfaces, a stable site complex with geminal positively charged tricoordinated and negatively charged unicoordinated oxygen atoms revealed on the (112) surface, and charged nonbridged siloxy/silyl sites, which are more stable than radical siloxy/silyl sites. Hydrolyzed surface energies range from -0.010 eV/A2 for the (001) surface to 0.002 eV/A2 for the (101) surface and increase as (001) < (110) < (102) < (111) < (100) < (112) < (101). The hydrolyzed surface stability is found to depend strongly on inter-site silanol hydrogen bonding. Observed networks of hydrogen bonds are important for interactions between silica surfaces and biomolecules in an aqueous environment.