Liquid chromatography (LC) is one of the most powerful techniques for the separation of various nonvolatile organic compounds. Nevertheless, the separation mechanism in LC has not yet been completely clarified. It is well known that the retention in LC is generated by a dispersion of the analyte between the mobile phase and the stationary phase. Especially, the intermolecular interaction of the analyte and the stationary phase ligand molecule plays a very important role during the retention process in LC. Therefore, the characterization of the surface structure of the stationary phase at the molecular level is very important.Octadecylsilica (ODS) has been most widely used as a stationary phase in LC because of its high separation ability. A number of attempts to understand the surface structure of the ODS stationary phase have been reported, in which spectroscopic techniques were used, such as nuclear magnetic resonance (NMR) spectroscopy, 1-7 Fourier-transform infrared spectroscopy (FT-IR), 5,8 Raman spectroscopy, 9-16 contact-angle measurements, 17 thermal analysis 5,18 and actual chromatographic methods. 19 Also, the influence of the temperature and bonding chemistry on the alkyl ligand conformation have also been well described in these reports.It is also experimentally known that a slight difference of the mobile-phase composition dramatically changes the LC retention. However, most of these reports are described based on the structure of the alkyl bonded silica surface in air, or in a pure solvent, such as water, methanol or acetonitrile. Pemberton et al. have recently studied the ODS ligand conformation systematically using Raman spectroscopy, [13][14][15][16] in which the bonding density, temperature, some kinds of solvents were considered to be the contributing factors. Sander et al. investigated the relationship between the alkyl ligand conformation and the mobile-phase composition using FT-IR spectroscopy. 8 Molecular dynamics (MD) simulations represent a powerful method to estimate the time-series structural changes of a multimolecular system, and are widely used in biochemistry to characterize the higher structures of biomolecules. Although this technique is used by only a limited number of researchers, because it needs computational resources, the advances of computer technologies have made it possible to use this technique on personal computers, and also to easily handle calculations for a huge molecular system, such as the stationary phase in LC. Some articles or reviews have been reported to characterize the stationary-phase ligand conformation using this type MD simulation. [20][21][22][23][24][25][26][27][28] Klatte and Beck applied MD simulations to molecular models that consisted of tethered and randomly placed n-alkane monolayers, and investigated the influence of the temperature, alkyl chain length and density of alkane molecules on the physical properties, such as the alkyl chain conformation and phase transition. 20,21 Although these results interpreted the behavior of the surface struct...