In order to achieve a simple description of aggregates of deformable water molecules, a new model has been constructed which treats H+ and ()2-particles as the basic dynamical and structural elements. The H+ units are bare protons, while the ()2-units possess a form of noniocaJ poIarizability consistent with their electronic structure. The model yields water molecules which have the correct geometry and dipole moment, and which engage in hydrogen bonding to one another. Minimum-energy structures have been detennined for the water dimer and trimer and for small hydrate clusters of H+ and OH-; comparison with relevant experiments and quantum-mechanical calculations is satisfactory.

A geometry search was carried out to locate the global energy minimum for (H2O)8, in its full 66 dimensional space of relative configurations. The ’’polarization model’’ was used to represent interactions. The optimal structure uncovered has nine nearly linear hydrogen bonds, and amounts to an aqueous analog of the saturated hydrocarbon bicyclo[2.2.2] octane. This structure is recognizable as a fragment of the hexagonal ice crystal, and thus may be important as a prenucleation cluster for that phase. The zwitterionic form of the octamer was found to have no region of local stability.

The energy of formation of salt linkages between Arg or Lys with Asp or Glu in a polypeptide chain having the collagen fold have been estimated using the fully empirical energy minimization scheme AMBER. The polypeptide was considered both in an isolated and a hydrated triple helical state. The collagen fold associated with a one-bonded triple helical conformation allows intrachain salt linkages having stabilization energies of 60-100 kcal when the reacting residues are separated by no more than two intervening residues. The amino end of one side chain always approaches the carboxyl end of the other side chain, and simultaneously approaches the carbonyl oxygen of the intervening backbone residue. The salt linkage conformation and the backbone conformation of the isolated collagen fold in vacuo are maintained when the molecules are in a hydrated triple helix. These results are compatible with a fold-forming role for salt linkages, especially in proline poor regions, during collagen polypeptide synthesis, and with the persistence of intrachain salt linkages throughout molecular and fibril assembly.

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Voronoi polyhedra are employed to generate a coherent description of the immediate solvent sheath of complex solutes in water solution.