Specific interactions between silica and organic molecules play an important role in molecular imprinting, molecular recognition, and enzyme activity. To understand the specific interactions, six pairs of organic compounds were chosen and investigated for their molecular imprinting capabilities on silica. Silica adsorbents imprinted by methyl red or ρ-methyl red, methyl orange or ethyl orange, and histidine-alanine or histidine-leucine can recognize their imprinting molecules. Silica samples “imprinted” with methyl red or ethyl red, 4,9-diaminoflourenone or 3,3'-diaminodiphenylmethane, and l-histidine or d,l-histidine do not recognize their “imprinting” molecules. The molecular recognition is related to the structure of the imprinting molecules. The following lessons were learnt: 1) Three or more strong interaction sites on the imprinting molecules are necessary to endow silica with recognition capability; 2) Position of functional groups is more important than their size to achieve the molecular recognition; 3) Chiral recognition needs stronger interaction and/or more interaction sites