Structural properties of bioinorganic composites are of contemporary research interest in fields such as drug delivery, bone repair and biomimetics. While being a key material in bio-engineering applications, silica may be either hazardous or biocompatible depending on parameters such as particle size, shape or surface properties. Effective simulation at the quantum level of large silica-based bio-composites is necessary to gain a deeper insight into the properties of such materials. How to bridge between structural extraction from large scale classical simulation to predictions by quantum chemistry for silica based structures is the focus of our contribution. In this presentation we present MD and DFT simulation data, complemented by experimentally derived vibrational and optical spectroscopic data for the study of (a) 2nm silica nanoparticles, (b) the possible effects of local fields next to such nanoparticles and (c) the interaction of silica with 7-mer peptides.