Role of Chemical Dynamics Simulations in Mass Spectrometry Studies of Collision-Induced Dissociation and Collisions of Biological Ions with Organic Surfaces

Abstract

In this article, a perspective is given of chemical dynamics simulations of collisions of biological ions with surfaces and of collision-induced dissociation (CID) of ions. The simulations provide an atomic-level understanding of the collisions and, overall, are in quite good agreement with experiment. An integral component of ion/surface collisions is energy transfer to the internal degrees of freedom of both the ion and the surface. The simulations reveal how this energy transfer depends on the collision energy, incident angle, biological ion, and surface. With energy transfer to the ion's vibration fragmentation may occur, i.e. surface-induced dissociation (SID), and the simulations discovered a new fragmentation mechanism, called shattering, for which the ion fragments as it collides with the surface. The simulations also provide insight into the atomistic dynamics of soft-landing and reactive-landing of ions on surfaces. The CID simulations compared activation by multiple "soft" collisions, resulting in random excitation, versus high energy single collisions and non-random excitation. These two activation methods may result in different fragment ions. Simulations provide fragmentation products in agreement with experiments, and hence can provide additional information regarding the reaction mechanisms taking place in experiment. Such studies paved the way on using simulations as an independent and predictive tool in increasing fundamental understanding of CID and related processes.

Fast fragmentation during surface-induced dissociation: An examination of peptide size and structure

“…Our approach to performing direct dynamics simulations of collision systems relevant to mass spectrometry has recently been detailed in three review articles [32][33][34], and hence, we shall only provide an outline of the approach here. Several of the original works on the specific topic of protonated peptides colliding with organic self-assembled monolayers [11,[35][36][37] would also provide additional technical detail.…”

In Silico Tandem Mass Spectrometer: an Analytical and Fundamental Tool

“…[12,14c-e,20] For V ion/neutral it is possible to use analytical functions, parametrized on accurate quantum chemistry calculations, [14b,e,19,20b,21] while semi-empirical Hamiltonians are well performing for N 2 . [22] Andrea Initial conditions (positions and velocities) are obtained by semi-classical sampling: [23] the ion minimum energy geometry is determined (in principle it needs to be just a local minimum) and normal modes calculated. Then, the population of each mode is determined either by setting a temperature (normal mode Boltzmann sampling) or a total internal vibrational energy.…”

Shattering During Surface-Induced Dissociation: An Examination of Peptide Size and Structure

“…Our approach to performing direct dynamics simulations of collision systems relevant to mass spectrometry has recently been detailed in three review articles [29][30][31], and hence, we shall only provide an outline of the approach here. Several of the original works on the specific topic of protonated peptides colliding with organic self-assembled monolayers [9,[32][33][34] would also provide additional technical detail.…”