Energy transfer pathways in the collisional activation of peptides

Classical trajectory simulations were carried out to study details of the energy transfer mechanism for activation of polyglycine (gly)(n) and polyalanine (ala)(n) peptide ions via collisions with Ar atoms. The Amber valence force field was used to represent the peptide intramolecular potential and the argon-peptide interaction was modeled using parameters previously determined from high level ab initio calculations. Energy transfer was studied versus collision impact parameter b, the collision energy, and peptide temperature and structure. Energy transfer to rotation becomes important for extended peptides at large b, but with averaging over impact parameter is smaller than transfer to vibration. Specific pathways for vibrational energy transfer were distinguished by determining the efficiency of energy transfer with various combinations of low and high frequency modes constrained. With all stretching and bending modes constrained the efficiency of energy transfer is more than 80% of that without constraints, which illustrates the efficient excitation of the torsional modes. Varying the peptide structure has a significant effect on the energy transfer efficiency, with larger energy transfer for the folded structures. The efficiency of energy transfer increases with increase in collisional energy. (C) 2000 Elsevier Science B.V.