Cyclodextrins are useful models in the study of hydrogen bonded water clusters. In alpha-cyclodextrin hexahydrate (alpha-CD center dot 6H(2)O), water molecules are ordered and occupy well-defined positions whereas in the larger beta-cyclodextrin dodecahydrate (beta-CD center dot 12H(2)O), there is considerable disorder with water molecules freely arranged over several possible sites. Here it is shown that beta-CD exhibits substantial structural flexibility and proton mobility compared with alpha-CD which is relatively very rigid and exhibits negligible short-range protonic conduction. These properties are directly controlled by the effective dielectric constant of the molecule, which is determined by the rotational freedom of water molecules in the hydrogen bond network. This model may be relevant to proteins where water clusters of this kind are found on the protein surface and occasionally in the protein interior. The case of thrombin, an allosteric enzyme incorporating a network of 20 internal hydrogen bonded water molecules, is discussed.