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Ithas been shown that molecular dynamics (MD) simulations area powerful tool to generate knowledge about complex interactions inthe field of bioprocess technologies at the atomic level. In thisfield, one of the most important nonspecific interactions is the hydrophobicinteraction, which is still not fully understood after nearly 30 yearsof research. To date established hydrophobicity scales, which basemostly on proteins’ primary structure, are used to estimatethe overall hydrophobicity. The structural complexity and the influenceof the protein’s environment cannot be accommodated with thesescales. In this work, free solution molecular dynamics simulationswere used to investigate the hydrophobic character of low molecularweight peptides. Therefore, local densities of a small hydrophobictracer molecule and unprotonated triethylamin (TEA) in particularwere used to localize and quantify hydrophobic patches among the peptidesurface. Comparisons between local densities and the retention behaviorin reversed phase chromatography showed significant correlations.Moreover, neighbor effects caused by charges could be identified.We were able to show that the developed in silicomethod is applicable to characterize peptides in respect to hydrophobicityin agreement with experimental data. We are confident to apply thismethod to larger protein structures. [ABSTRACT FROM AUTHOR]