Thermodynamics and Mechanisms of Protonated Diglycine Decomposition: A Computational Study

pre-printWe present a full computational description of the fragmentation reactions of protonated diglycine (H+GG). Relaxed potential energy surface scans performed at B3LYP/6-31G(d) or B3LYP/6-311+G(d,p) levels are used to map the reaction coordinate surfaces and identify the transition states (TSs) and intermediate reaction species for seven reactions observed experimentally in the succeeding companion paper. All structures are optimized at the B3LYP/6-311+G(d,p) level, with single point energies of the key optimized structures calculated at B3LYP and MP2(full) levels using a 6-311+G(2d,2p) basis set. These theoretical structures and energies are compared to extensive calculations in the literature. Although the pathways elucidated here are generally in agreement with those previously outlined, new details and, for some reactions, lower energy transition states are located. Further, the mechanism for the combined loss of carbon monoxide and ammonia is explored for the first time

Thermodynamics and Mechanism of Protonated Cysteine Decomposition: A Guided Ion Beam and Computational Study

pre-printA quantitative molecular description of the decomposition of protonated cysteine, H+Cys, is provided by studying the kinetic energy dependence of threshold collision-induced dissociation (CID) with Xe using a guided ion beam tandem mass spectrometer (GIBMS). Primary dissociation channels are deamidation (yielding both NH3 loss and NH4 + formation) and (H2O + CO) loss reactions, followed by an additional six subsequent decompositions. Analysis of the kinetic energy-dependent CID cross sections provides the 0 K barriers for six different reactions after accounting for unimolecular decay rates, internal energy of reactant ions, multiple ion-molecule collisions, and competition among the decay channels. To identify the mechanisms associated with these reactions, quantum chemical calculations performed at the B3LYP/6-311+G(d,p) level were used to locate the transition states (TSs) and intermediates for these processes. Single point energies of the reactants, products, and key optimized TSs and intermediates are calculated at B3LYP, B3P86, and MP2(full) levels using a 6-311+G(2d,2p) basis set. The computational characterization of the elementary steps of these reactions including the structures of the final products is validated by quantitative agreement with the experimental energetics. In agreement with previous work, deamidation is facilitated by anchimeric assistance of the thio group, which also leads to an interesting rearrangement of the intact amino acid identified computationally