  We have investigated the potential energy surface for neutral and charged
alanine and glycine chains consisting of up to 6 amino acids. For these
molecules we have calculated potential energy surfaces as a function of the
Ramachandran angles phi and psi. Our calculations are performed within it ab
initio theoretical framework based on the density functional theory and also
within semi-empirical model approaches. We have demonstrated that the excessive
positive charge of the system influences strongly its geometrical and
conformational properties. With increasing of the excessive charge amino acid
chains become unstable and decay into two or more fragments. We have analysed
how the secondary structure of polypeptide chains influences the formation of
the potential energy landscapes. We have calculated the energy barriers for
transitions between different molecular conformations and determined the ones
being energetically the most favourable.
