Gas phase unimolecular fragmentation kinetics of cyclic peptides from chemical dynamics simulations

Ariel Francis Pérez Mellor
Laboratoire de Chimie Théorique, Sorbonne Université & CNRS, Paris, France Mercredi 12 Décembre 2018, 11h00
bibliothèque LCT, tour 12 - 13, 4^ème étage

After a brief introduction to my scientific interests, I will be discussing my last year post-doctoral research activity. My work lies in the development of a theoretical framework that allows the computation of rate constants from an ensemble of Born-Oppenheimer Molecular Dynamics (BOMD) simulations. In particular, we focus on the primary fragmentation process in the gas phase that takes place during Collision-Induced Dissociation experiments. The latest is an experimental technique widely used in the characterization of charged molecules in the gas phase according to their fragmentation pattern.
The BOMD is carried out on the smallest diketopiperazine protonated peptide cyclo Gly-GlyH⁺ by internal energy activation through a micro-canonical ensemble. The RM1-D semi-empirical Hamiltonian has been used for this purpose which shows a good balance between accuracy and computational time. All the simulations were carried out using a coupling between VENUS (for dynamics) and MOPAC (for electronic structure calculation) packages.

[Picture]

Figure 1

The theoretical framework proposes the primary fragmentation, that is a multiple state process, can be divided only into three different states: the starting point (SP), the 'effective' intermediate (INT), and the primary fragmentation (PF) itself (see Figure 1 left panel). Once the three states are well defined, a given kinetic model (KM) is built and solved (see Figure 1 central panel). Finally, by monitoring the population of the states along the time through the analysis of the BOMD trajectories one can fit it with the analytical solution from the proposed KM, and the rates constants for the given process are obtained (see Figure 1 right panel).
All the details according to the definition of the states as well as the multi-fit analysis will be discussed.