Collision-induced dissociation mechanisms of protonated penta- and octa-glycine as revealed by chemical dynamics simulations

In this work, we have studied the collision-induced dissociation (CID) of protonated penta- and octa-glycine (both with -COOH and -CONH2, C-terminal groups) by means of chemical dynamics simulations using a QM + MM approach. For the QM potential, a semi-empirical Hamiltonian (PM3) was employed. Simulations have shown that the full a(n)(+) and b(n)(+) series of fragments can be obtained. A detailed analysis of trajectories permitted to elucidate the mechanisms connecting reactants and products. In particular, both direct bond breaking and proton transfer initiated fragmentation pathways were observed. The two mechanisms are correlated with the way energy flows (or does not) through the modes after collision and before fragmentation. This study points out the importance of considering both mechanisms when modeling and studying fragmentation pathways of complex molecular systems. (C) 2015 Elsevier B.V. All rights reserved.