Atomistic simulations are used to characterize the molecular dynamics (MD) of alkyl chains with different functionalizations in different water/acetonitrile mixtures (80/20 and 50/50). Starting from fully equilibrated solvent systems (flat density profile for both components), microheterogeneous structuring of the solvent in the chromatographic system is found for both mixtures. Depending on the functionalization of the alkyl chain (nitrile, amide, nitro, phenyl), differences in the density profiles of the two solvents (water/acetonitrile), the effective width of the stationary phase and the solvent gradients in the overlap region are observed. The solvent mixture (mobile phase) in RPLC is a liquid which is directly involved in the physical process and must be included explicitly. Far from the surface, the solvent displays bulk properties; closer to it the mixed solvent partitions due to the presence of the stationary phase. This creates a gradient in solvent strength perpendicular to the surface which influences the motions of the analyte. The surface is found to define the amount of water that can bind to it and defines its hydrophilic character. Proposals from the literature, such as the existence of persistent water filaments extending from the functionalized silica layer towards the bulk solvent, are discussed. Simulations of acridine orange near a –NH₂- and –phenol-functionalized surface highlight the different dynamical behaviour (insertionvs. adsorption) of an analyte depending on the functionalization of the surface.