Silica nanostructures are biologically available and find wide applications for drug delivery, catalysts, separation processes, and composites. However, specific recognition of biomolecules on silica surfaces and control in biomimetic synthesis remain largely unpredictable. A silica force field is introduced that resolves numerous shortcomings of prior silica force fields over the last 30 years and reduces uncertainties in computed interfacial properties relative to experiment from several 100% to less than 5%. In addition, a silica surface model database is introduced for the full range of variable surface chemistry and pH (Q2, Q3, Q4 environments with adjustable degree of ionization) that have shown to determine selective molecular recognition. The force field enables accurate computational predictions of aqueous interfacial properties of all types of silica, which is substantiated by extensive comparisons to experimental measurements. The parameters are integrated into multiple force fields for broad applicability to biomolecules, polymers, and inorganic materials (AMBER, CHARMM, COMPASS, CVFF, PCFF, INTERFACE force fields). We also explain mechanistic details of molecular adsorption of water vapor, as well as significant variations in the amount and dissociation depth of superficial cations at silica−water interfaces that correlate with ζ-potential measurements and create a wide range of aqueous environments for adsorption and self-assembly of complex molecules. The systematic analysis of adsorption free energies and binding conformations of distinct peptides to silica surfaces as a function of pH and particle size will be specifically reported as a prime example for validation and specific predictions. Example peptides were positively charged, neutral, and negatively charged, and a variety of silica surfaces were employed. The computed binding affinities agree remarkably with adsorption isotherms and zeta potential measurements for the same systems, and underline the significance of the surface chemistry, pH, and topography for specific binding outcomes. Adsorption free energies and binding residues were quantitatively analyzed, and tunable contributions to binding identified, including ion pairing, hydrogen bonds, hydrophobic interactions, and conformation effects. The resulst show that molecular dynamics simulation with the CHARMM-INTERFACE force field and synthesis can be employed to optimize interactions of all types of silica surfaces with organic and biological molecules under realistic solution conditions at the scale of 1 to 100 nm. Applications include the controlled binding and release of drugs, cell receptors, polymers, surfactants, and gases.