Notes on Silk (Poly-(Gly-Ala))

Although silk, poly-(Gly-Ala), is a natural product, it is possible to construct a model of the crystalline polymer.  In this model individual polymer chains are oriented in a β-sheet, that is, alternating chains run in opposite directions, this allowing optimum hydrogen-bonding between chains.  No X-ray structure was used in making the starting model, instead the models for the "PDB" reference geometry were the optimized PM6-D3H4 and PM7 geometries. This choice of starting structure meant that it and all the derived structures - a bias of 10 and 3 kcal mol-1 Å-1 and the unconstrained structure - were identical.

This was the only true protein polymer calculated.  For obvious reasons the COSMO implicit solvation method, keyword EPS=78.4, was not used.