Glycosyl hydrolases catalyse the acid hydrolysis of the glycosidic bond of glycans. The structure of barley beta-D-glucan glucohydrolase in complex with a thiol substrate analogue presents very short contacts between the carboxyl oxygen atoms of the catalytic acid and the sulphur atom of the inhibitor. The geometries of acetic acid and dimethylsulfide in various ionisation states from ab initio molecular orbital calculations predict similar short contacts when an acetate anion forms a complex with a sulphonium cation. The energy of this complex is, however, significantly greater than the energy of the complex where both acetic acid and dimethylsulfide are neutral. Calculations on an active site model of barley beta-D-glucan glucohydrolase indicate that the protein environment is able to significantly reduce this energy. The energy required for mechanical constraint of the short S...O separations, however, is identical to that required for the transfer of the proton from the acid to the sulphur. The identity of the species participating in the short contacts remains unanswered.