Supermolecules glycine

Figure 6. ORTEP drawing of fully optimized structures for c/ s- and frans-protonated glycine supermolecule with four waters of hydration (stereo view).

Specific solute-solvent interactions, which are not explicitly taken into account in continuum models, can play a significant role especially for charged species. A typical cluster formed by the glycine anion radical with four water molecules is shown in figure 16. The analogous supermolecule obtained for the neutral form is quite similar, except for the much weaker interaction energies involved in the neutral species. The number and the position of the solvent molecules are determined by molecular dynamics simulations performed by the AMBER force field [141]. 

Proteins are supermolecules that have been designed by nature to carry out certain specific tasks and to demonstrate distinctive properties. These molecules are built with a palette of 20 amino acids of which all but one, glycine, are chiral L-amino acids. The amino acids are strung together in a linear manner, like beads on a string, by way of peptide linkages, to form the backbone of the protein. The amino acid side chains stick out from this backbone. The architectural principles involved in constructing a supermolecule that can perform the required functions are described here. 

Quantum mechanical methods have also been applied to crystal structure prediction. A recent example involved the use of ab initio crystal field methods with the SM (supermolecule) model and the PC (point charge) model applied to the three known polymorphs of glycine [77]. Comparison of the optimised structures with published X-ray structures for these forms indicated that the quantum-mechanically based SM model employing a 15-molecule cluster produced results in better agreement with experiment than the PC model which describes the crystal environment purely electrostatically. 

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