The silanol activity and trace metal detection methods for chemically bonded silica gels were evaluated in silico. Test compounds with large molecular sizes may demonstrate negative results because of the possibility of indirect hydrogen bonding via short alkyl groups or siloxane of the silica gels. This hypothesis was based on the observation of weak hydrogen bonding energy values similar to those observed in the study of the alkyl group effect on the hydrogen bonding of alkanols. Consequently, smaller molecules may be a better choice for the analysis of bonded-phase quality.