A MOLECULAR-DYNAMICS STUDY OF THE CONFORMATION OF THE ALANINE DIPEPTIDE IN AQUEOUS-SOLUTION USING A QUANTUM-MECHANICAL POTENTIAL

Molecular dynamics simulations of the aqueous solution of alanine dipe ptide have been carried out for seven configurations characteristic of important regions of the Ramachandran plot. A hybrid quantum mechanic al-molecular mechanical potential was used that describes the solute u sing the AM1 Hamiltonian and the solvent using the TIP3P model. The im portance of differential solute polarization and the preferential stab ilization of the extended structures alpha(L), alpha(R) and beta have been identified. The results are compared with experiment and with the predictions of the ab initio polarizable continuum model of solvation .