Energy transfer pathways in the collisional activation of peptides

Classical trajectory simulations were carried out to study details of the e nergy transfer mechanism for activation of polyglycine (gly)(n) and polyala nine (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 deter mined from high level ab initio calculations. Energy transfer was studied v ersus collision impact parameter b, the collision energy, and peptide tempe rature and structure. Energy transfer to rotation becomes important for ext ended peptides at large b, but with averaging over impact parameter is smal ler than transfer to vibration. Specific pathways for vibrational energy tr ansfer 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 tran sfer is more than 80% of that without constraints, which illustrates the ef ficient excitation of the torsional modes. Varying the peptide structure ha s a significant effect on the energy transfer efficiency, with larger energ y transfer for the folded structures. The efficiency of energy transfer inc reases with increase in collisional energy. (C) 2000 Elsevier Science B.V.