Abstract: The quantitative analysis of the chromatographic behavior of basic compounds was performed in silico. The liquid chromatography (LC) data measured with pentyl-, hexenyl-, and octyl-bonded silica gels were analyzed in silico employing model phases. The main retention force was the van der Waals (VW) interaction, and the main desorption force was an electrostatic (ES) interaction. The contribution of hydrogen bonding (HB) was weak compared to that for acidic compounds. The quantitative explanation was achieved utilizing the calculated VW, HB, and ES energy values obtained from a molecular mechanics program. The electron localization was observed at the molecular interaction-site calculated MOPAC program. This fundamental approach was like that of explaining chemical reactions. The difference was electron localization in chromatography or electron transfer in a chemical reaction.