Thermodynamics and Mechanisms of Protonated Diglycine Decomposition: A Computational Study

Abstract

We present a full computational description of the fragmentation reactions of protonated diglycine (H + GG). Relaxed potential energy surface scans performed at B3LYP/6-31 G(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(2 d,2p) basis set. These theoretical structures and energies are compared with 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.

Relative Stability of Peptide Sequence Ions Generated by Tandem Mass Spectrometry

“…That P-containing peptide has a wellestablished low barrier residue specific bond cleavage (for comparison [AAAAA + H] + is 135.6 kJ mol -1 [71]) unlike YGGFL, but the barrier is still higher than that from BIRD. In contrast, recent guided ion beam studies are in good agreement with DFT theory [78,79] but, again, for comparatively small systems. Bottom line: this issue is too complex to be resolved (or even discussed at length) in the present paper.…”

Thermodynamics and Mechanisms of Protonated Diglycine Decomposition: A Guided Ion Beam Study

“…For instance, we can unambiguously assign the structure of the b 2 ion formed by dehydration in reaction 4 as At threshold, the C 3 H 7 N 2 O + (a 2 ) product is likely to have the acyclic form (see Scheme 1), rather than the more stable cyclic form, a species that requires passing over a tight TS lying another 8-12 kJ/mol higher in energy according to theory [11]. In this regard, such structural identifications are comparable to those conducted by infrared multiple photon dissociation (IRMPD) experiments, in which comparison of the experimental spectra with theoretically calculated one-photon spectra often allow assignment of the structure.…”

“…We measure absolute experimental energetics for the observed reactions utilizing calculations from the preceding paper (paper I) [11] to provide structures, vibrational frequencies, and rotational constants needed for accurate analysis. Experimental threshold energies are compared with theoretical single point energy calculations at both B3LYP and MP2 levels from paper I in order to fully characterize the key steps of H + GG decomposition.…”

Re-print of “Theoretical Investigation and Reinterpretation of the Decomposition of Lithiated Proline and N-Methyl Proline”

“…Final geometry optimization calculations and frequency analysis of all reactants, intermediates, and transition states were done at the B3LYP/6-311+G(d,p) level. The B3LYP/6-311+G(d,p) level has been shown to give accurate descriptions of comparable metal-ligand systems [31][32][33][34][35]. Single point energy calculations for all key structures were carried out at three different levels of theory, B3LYP, B3P86, and MP2(full) using the 6-311+G(2d, 2p) basis set.…”