Unimolecular dissociation of peptides: statistical vs. non-statistical fragmentation mechanisms and time scales

Abstract

In the present work we have investigated mechanisms of gas phase unimolecular dissociation of a relatively simple dipeptide, the di-proline anion, by means of chemical dynamics simulations, using the PM3 semi-empirical Hamiltonian. In particular, we have considered two activation processes that are representative limits of what occurs in collision induced dissociation experiments: (i) thermal activation, corresponding to several low energy collisions, in which the system is prepared with a microcanonical distribution of energy; (ii) collisional activation where a single shock of hundreds of kcal mol (300 kcal mol in the present case) can transfer sufficient energy to allow dissociation. From these two activation processes we obtained different product abundances, and for one particular fragmentation pathway a clear mechanistic difference for the two activation processes. This mechanism corresponds to the leaving of an OH group and subsequent formation of water by taking a proton from the remaining molecule. This last reaction is always observed in thermal activation while in collisional activation it is less favoured and the formation of OH as a final product is observed. More importantly, we show that while in thermal activation unimolecular dissociation follows exponential decay, in collision activation the initial population decays with non-exponential behaviour. Finally, from the thermal activation simulations it was possible to obtain rate constants as a function of temperature that show Arrhenius behaviour. Thus activation energies have also been extracted from these simulations.

Characterization of Protonated Model Disaccharides from Tandem Mass Spectrometry and Chemical Dynamics Simulations

“…As already mentioned, direct collisional simulations providet he amount of [24] are more prone to provide proton transfers. Surely,t his possibility can be considered in the study of sugar fragmentation.…”

“…[13] Even if new semiempirical methods are now available, our work on sugars and, more recently,o npeptides, [24] have shown that PM3 is able to describe different systems correctly in both positive and negative modes. As tudy of the impact of the method on the fragmentation products will be an interesting topic but is, however, beyond the aim of the present work.…”

“…the path that connects minima and transition states (TSs)].H owever,amobilep rotonm odel mechanism is certainly ap ossible alternative to generate the fragment ions. We have shown recently forp eptide fragmentation that internal energy activation simulations [24] are more prone to provide proton transfers. Surely,t his possibility can be considered in the study of sugar fragmentation.…”

On the Use of Quantum Thermal Bath in Unimolecular Fragmentation Simulation

“…[8][9][10][11] At this aim, chemical dynamics simulations were used with different ways of energizing the fragmenting molecule: 12 (i) giving an excess of internal energy, (ii) by explicit collision with an inert gas. For example, it was possible to understand products structures and reaction mechanisms in collision induced dissociation (CID) of several systems, from small organic molecules, [13][14][15] to biological molecules like peptides [16][17][18][19][20] or sugars. 21,22 In addition to information on fragmentation products and mechanisms, chemical dynamics can be used to obtain kinetic informations on unimolecular dissociation.…”

Reactive molecular dynamics simulations of organometallic compound W(CO)6 fragmentation,

“…To date, a popular class of precursors for FEBID is metal carbonyls Me n (CO) m [12,13], which are composed of one or several metal atoms (Me) bound to a number of carbon monoxide ligands. Although such precursor molecules (for instance, W(CO) 6 , Fe(CO) 5 or Co 2 (CO) 8 ) were commonly adopted from the chemical vapor deposition method and thus were not specifically designed to be efficiently and completely dissociated under electron irra-diation, recent developments in optimization of the precursor deposition processes as well as the design of novel precursors for FEBID (e.g., HFeCo 3 (CO) 12 [14]) have made it possible to fabricate fully metallic structures made of Au, Pt, Fe, Co, Pb, and Co 3 Fe alloy [10].…”