Log Po/w based models are often used for the retention time prediction of reversed phase liquid chromatography. Here, we present the investigation of the applicability of log Po/w based retention time predictions for the separation in capillary electro-chromatography (CEC). A test set of five polycyclic aromatic hydrocarbons was separated using two different stationary phases with three different mobile phases each. The resulting retention times were correlated with the experimental log Po/w values as well as with calculated log Po/w values. The used methods include quantitative structure property relationship (QSPR) models as well as molecular dynamic methods such as the linear interaction energy (LIE) or the Bennett acceptance ratio (BAR). The results indicate that rigorous simulation models are capable of accurately reproducing experimental results and that the electrophoretic mobility of analytes in CEC separations leads to significant deviations in the retention time prediction.