Particle-based Monte Carlo simulations were employed to examine the molecular-level effects of bonding density on the retention of alkane and alcohol solutes in reversed-phase liquid chromatography. The simulations utilized octadecylsilane stationary phases with various bonding densities (1.6, 2.3, 2.9, 3.5, and 4.2 μmol/m²) in contact with a water/methanol mobile phase. In agreement with experiment, the distribution coefficient for solute transfer from mobile to stationary phase initially increases then reaches a maximum with increasing bonding density. A molecular-level analysis of the solute positional and orientational distributions shows that the stationary phase contains heterogeneous regions and the heterogeneity increases with increasing bonding density.