Cluster molecules intermolecular interactions

After generating optimized clusters, the intermolecular interaction energies between pair molecules a and / ( ) in the cluster were calculated using the supermolecular approach ... 

Supramolecular aggregations are commonly referred to by a variety of terms, including adduct, complex, and van der Waals molecule. In this chapter we shall primarily employ the more neutral term cluster, which may, if desired, be qualified with the type of intermolecular interaction leading to clustering (e.g., H-bonded cluster ). General and specific types of intermolecular forces are discussed in the following sections. 

This packing of the tropocollagen molecules with a displacement of 67 nm is caused by repeating clusters of charged and uncharged residues along the polypeptide chains with a periodicity of 67 nm. Hence the maximum number of intermolecular interactions (electrostatic and hydrophobic) is formed when the tropocollagen molecules are displaced by multiples of 67 nm. 

With the success of these calculations for isolated molecules, we began a systematic series of supermolecule calculations. As discussed previously, these are ab initio molecular orbital calculations over a cluster of nuclear centers representing two or more molecules. Self-consistent field calculations include all the electrostatic, penetration, exchange, and induction portions of the intermolecular interaction energy, but do not treat the dispersion effects which can be treated by the post Hartree-Fock techniques for electron correlation [91]. The major problems of basis set superposition errors (BSSE) [82] are primarily associated with the calculation of the energy. 

When attempting to treat ensembles of molecules it is essential to be able to represent the intermolecular interactions, at least beyond some cut-off distance, by pre-determined functions of distance so that high level quantum mechanical calculations do not have to be extended to larger and larger clusters. Masia et a/.88 have addressed the question of how the interaction of a water or carbon tetrachloride molecule interacting with a point charge can be represented. They monitor the molecular dipole as a function of the charge-molecule distance for various orientations of the molecule as calculated by ab initio methods. They find that the most satisfactory method is to represent the molecule by a small number of induced point dipoles with different orientations. In the case of water the ab initio induced dipoles are reproduced at all distances. 

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