Direct Dynamics Simulations of the Thermal Fragmentation of a Protonated Peptide Containing Arginine

Arginine has significant effects on fragmentation patterns of the protonated peptide due to its high basicity guanidine tail. In this article, thermal dissociation of the singly protonated glycine-arginine dipeptide (GR-H⁺) was investigated by performing direct dynamics simulations at different vibrational temperatures of 2000-3500 K. Fourteen principal fragmentation mechanisms containing side-chain and backbone fragmentation were found and discussed in detail. The mechanism involving partial or complete loss of a guanidino group dominates side-chain fragmentation, while backbone fragmentation mainly involves the three cleavage sites of a1-x1⁺, a2⁺-x0, and b1-y1⁺. Fragmentation patterns for primary dissociation have been compared with experimental results, and the peak that was not identified by the experiment has been assigned by our simulation. Kinetic parameters for GR-H⁺ unimolecular dissociation may be determined by direct dynamics simulations, which are helpful in exploring the complex biomolecules.