The non-bridging oxygen atoms on the pore surfaces were protonated so that the net charge on the silica was zero. Molecular dynamics software will generally include a procedure for adding hydrogens to a system.

Dear Prof. Rudy

Thanks for your answers. I have one more questions, usually the silica is electro-neutral, why we still need to have the procedure of protonation?

Regards

My impression of the paper is that there were unsatisfied valences in the silica pores -- oxygen atoms that were not bridges between silicon atoms. Therefore, the investigators added protons to these non-bridging oxygen atoms.