Molecular dynamics simulations of mixed-mode chromatography: Generation and solvation of a silica-based, reversed-phase/anion-exchange stationary phase

• Molecular dynamics simulations applied to mixed-mode liquid chromatography. • Silica-based, reversed-phase/anion-exchange (RP/AEX) stationary phase constructed. • Bonded-phase islands interspersed with hydroxylated silica patches exposed to mobile phase. • Surface topology shields AEX function from contact with hydrophilic counterions. • Sorption of analytes with both hydrophobic and hydrophilic structural elements favored. As a first step towards predicting retention for mixed-mode liquid chromatography (MMLC) separations of small, hydrophilic, ionizable analytes, we created a slit-pore model of a silica-based, endcapped, reversed-phase/anion-exchange (RP/AEX) stationary phase and performed molecular dynamics simulations of its solvation by a water‒acetonitrile (W‒ACN) mobile phase under conditions where the AEX function is neutral or charged. In the latter case, sodium and chloride ions were added as co-ions and counterions, respectively, to the 60/40 (v/v) W/ACN mobile phase. The silica surface functionalization, which modeled existing column technology, yielded a unique surface topology, where bonded-phase islands formed by octadecylsilyl chains around a central tertiary alkylamine group are interspersed with hydroxylated silica patches that are exposed to the mobile phase. The two MMLC systems were analyzed regarding the solvent density, structure, and orientation with respect to the density distribution of hydrophobic and hydrophilic bonded-phase elements (alkyl groups and nitrogen atoms, respectively) at different distances from the silica surface. Effects originating from the surface functionalization were captured by comparison with a conventional RPLC stationary phase, whereas effects originating from the presence of charge were quantified by comparing the two simulated MMLC systems (neutral vs. charged surface). The analysis of ion density distributions and ion contact profiles, in particular, suggested that the surface topology of the MMLC stationary phase shields the AEX function from contact with hydrophilic counterions and favors the accumulation of analyte compounds with both hydrophobic and hydrophilic structural elements.