Sticky-MARTINI as a reactive coarse-grained model for molecular dynamics simulations of silica polymerization

Tools

Carvalho, André and Santos, Sérgio M. and Pérez-Sánchez, Germán and Gouveia, Daniel and Gomes, José R. B. and Jorge, Miguel (2022) Sticky-MARTINI as a reactive coarse-grained model for molecular dynamics simulations of silica polymerization. npj Computational Materials, 8 (1). 49. ISSN 2057-3960 (https://doi.org/10.1038/s41524-022-00722-w)

[thumbnail of Carvalho-etal-npjCM-2022-Sticky-MARTINI-as-a-reactive-coarse-grained-model-for-molecular-dynamics-simulations]
Preview
 Text. Filename: Carvalho_etal_npjCM_2022_Sticky_MARTINI_as_a_reactive_coarse_grained_model_for_molecular_dynamics_simulations.pdf
Final Published Version
License: Creative Commons Attribution 4.0 logo
Download (3MB)| Preview

Abstract

We report a molecular modeling paradigm to describe silica polymerization reactions in aqueous solutions at conditions that are representative of realistic experimental processes like biosilicification or porous silica synthesis – i.e. at close to ambient temperatures and over a wide range of pH. The key point is to describe the Si-O-Si chemical bond formation and breakage processes through a continuous potential with a balance between attractive and repulsive interactions between suitably placed virtual sites and sticky particles. The simplicity of the model, its applicability in standard parallelized molecular dynamics codes, and its compatibility with the widely used MARTINI coarse-grained force-field allows for the study of systems containing millions of atoms over microsecond time scales. The model is calibrated to match experimental results for the temporal evolution of silica polymerization in aqueous solution close to the isoelectric point, and can describe silica polymerization and self-assembly processes during encapsulation of a surfactant micelle.

ORCID iDs

Carvalho, André, Santos, Sérgio M., Pérez-Sánchez, Germán, Gouveia, Daniel, Gomes, José R. B. and Jorge, Miguel ORCID logoORCID: https://orcid.org/0000-0003-3009-4725;
CORE (COnnecting REpositories)