Ab initio derived force‐field parameters for molecular dynamics simulations of deprotonated amorphous‐SiO₂/water interfaces

Abstract

We present a set of Coulomb point charges and van der Waals parameters for molecular dynamics simulations of interfaces between natively deprotonated amorphous SiO2 surfaces and liquid water, to be used in combination with standard biomolecular force fields. We pay particular attention to the extent of negative charge delocalisation in the solid that follows the deprotonation of terminal silanol groups, as revealed by extensive Bader analysis of electronic densities computed by density functional theory (DFT). The absolute charge values in our force field are determined from best‐fitting to the electrostatic potential computed ab initio (ESP charges). Our proposed parameter set is found to reproduce the energy landscape of single water molecules over neutral and deprotonated amorphous SiO2 surfaces and, after a minor adjustment, over thin oxide films on Si. Our analysis reveals a certain degree of arbitrariness in the choice of the DFT scheme used as the reference for the force‐field optimisation procedure, highlighting its intrinsic limits. Interaction between a water molecule and an oxidised Si surface calculated with several DFT and force‐field schemes, and delocalisation of the negative charge upon deprotonation of an amorphous SiO2 surface.

Prediction of Specific Biomolecule Adsorption on Silica Surfaces as a Function of pH and Particle Size

“…Prior force fields often required fixed atoms to avoid collapse of the models in the simulation, neglected the pH dependence of the surface chemistry, and involved other drastic approximations so that even approximate predictions of specific binding of biomolecules were essentially impossible. [43][44][45][46][47][48][49][50][51][52][53][54][55][56] The new, thermodynamically consistent silica parameters are compatible with comprehensive harmonic force fields for biopolymers, organic molecules, and inorganic compounds such as 7 CHARMM, AMBER, PCFF, COMPASS, CVFF, and INTERFACE. 26,37 The compatibility enables insight into a limitless number of silica hybrid materials by the possible combination of thousands of distinct silica surface structures with billions of distinct biopolymers, surfactants, and receptor molecules across a wide range of concentrations and solution conditions.…”

Understanding small biomolecule‐biomaterial interactions: A review of fundamental theoretical and experimental approaches for biomolecule interactions with inorganic surfaces

“…In recent years, forcefield based simulation techniques have been developed and applied in order to model the oxide/water interface,123–149 especially the TiO 2 ‐water interface 96, 150–155. The interaction of transition metal oxide surfaces with water, including dissolution and inorganic/organic species adsorption, is now being described.…”

Perspectives on the simulation of protein–surface interactions using empirical force field methods

“…Experimental approaches have the advantage of providing data on the actual behavior of the adsorption event while being limited by the ability to obtain suitable model amino acid–surface systems and generate values that can be closely matched to parameters obtained by molecular simulation. In comparison, ab initio QM methods provide a more direct approach to create molecular models that closely match those used in an empirical force field simulation, and this approach has been used by several groups to parameterize interfacial interactions [33,38,39,45,47,55–58]. While very useful for probing the interactions for small molecular systems for interfacial force field development, highly accurate QM methods are still too limited in terms of the number of atoms that can be represented in the simulation to enable bulk water over a surface to be explicitly represented in the simulation.…”