Computational view of surface based organic mass spectrometry

Abstract

Surface based mass spectrometric approaches fill an important niche in the mass analysis portfolio of tools. The particular niche depends on both the underlying physics and chemistry of molecule ejection as well as experimental characteristics. In this article, we use molecular dynamics computer simulations to elucidate the fundamental processes giving rise to ejection of organic molecules in atomic and cluster secondary ion mass spectrometry (SIMS), massive cluster impact (MCI) mass spectrometry, and matrix‐assisted laser desorption ionization (MALDI) mass spectrometry. This review is aimed at graduate students and experimental researchers. © 2008 Wiley Periodicals, Inc., Mass Spec Rev 27: 289–315, 2008

Sputtering of Benzene Sample by Large Ne, Ar and Kr Clusters - Molecular Dynamics Computer Simulations

“…Details of the MD computer simulations used to model cluster bombardment are described elsewhere [6]. The model approximating the benzene crystal consists of 307366 molecules arranged in a hemispherical sample of * corresponding author; e-mail: lrzeznik@wsiz.rzeszow.pl the radius 26 nm.…”

Development of a Primary Ion Column for Mass Spectrometry-Based Surface Analysis

“…Programs commonly utilized to model these processes are Stopping Range of Ions in Matter, and Marlowe 51 , 52 . The former is far more prevalent, and has been found to be able to model some cluster systems, however it has difficulties simulating the full life-span of the projectile and surface following PI impact 53 . Fully elucidating a cluster impact however still remains challenging due collective effects from many-body interactions and concerted motions of atoms characteristic to a thermal spike mechanism 53 .…”

“…The former is far more prevalent, and has been found to be able to model some cluster systems, however it has difficulties simulating the full life-span of the projectile and surface following PI impact 53 . Fully elucidating a cluster impact however still remains challenging due collective effects from many-body interactions and concerted motions of atoms characteristic to a thermal spike mechanism 53 . In molecular dynamic calculations the forces between different constituents of the system are computed based on positions and interaction potentials 50,53 .…”

“…Fully elucidating a cluster impact however still remains challenging due collective effects from many-body interactions and concerted motions of atoms characteristic to a thermal spike mechanism 53 . In molecular dynamic calculations the forces between different constituents of the system are computed based on positions and interaction potentials 50,53 . Hamiltonian equations of motion are integrated to produce information regarding the velocity and direction of the particle per time step 48,53 .…”

“…In molecular dynamic calculations the forces between different constituents of the system are computed based on positions and interaction potentials 50,53 . Hamiltonian equations of motion are integrated to produce information regarding the velocity and direction of the particle per time step 48,53 . MD models also provide behavior information for a range of energies, bond breakage/formation processes, and the morphology of the interaction 50 .…”