Computer simulations of sputtering and fragment formation during keV C60 bombardment of octane and β -carotene

Atomistic simulations for investigation of substrate effects on lipid in-source fragmentation in secondary ion mass spectrometry

In beam-based ionization methods, the substrate plays an important role on the desorption mechanism of molecules from surfaces. Both the specific orientation that a molecule adopts at a surface and the strength of the molecule-surface interaction can greatly influence desorption processes, which in turn will affect the ion yield and the degree of in-source fragmentation of a molecule. In the beam-based method of secondary ion mass spectrometry (SIMS), in-source fragmentation can be significant and molecule specific due to the hard ionization method of using a primary ion beam for molecule desorption. To investigate the role of the substrate on orientation and in-source fragmentation, we have used atomistic simulations-molecular dynamics in combination with density functional theory calculations-to explore the desorption of a sphingolipid (palmitoylsphingomyelin) from a model surface (gold). We then compare SIMS data from this model system to our modeling findings. Using this approach, we found that the combined adsorption and binding energy of certain bonds associated with the headgroup fragments (C₃H₈N⁺, C₅H₁₂N⁺, C₅H₁₄NO⁺, and C₅H₁₅PNO₄ ⁺) was a good predictor for fragment intensities (as indicated by relative ion yields). This is the first example where atomistic simulations have been applied in beam-based ionization of lipids, and it presents a new approach to study biointerfacial lipid ordering effects on SIMS imaging.

Cluster-induced desorption investigated by means of molecular dynamics simulations-Microsolvation in clusters of polar and non-polar constituents

The desorption of surface-adsorbed molecules induced by cluster-surface collisions of neutral molecular clusters, in particular, SO₂ clusters, was investigated by means of molecular dynamics simulations. The desorption efficiency was found to be in general much higher for clusters of polar molecules when compared to nonpolar cluster constituents, for both nonpolar and polar adsorbates. In all cases, desorption is shown to proceed via dissolvation of the analyte in the cluster. In systems with nonpolar cluster constituents, the process is mainly driven by the increase in the entropy of the dissolved analyte in a larger cluster fragment. The latter process is enhanced by polar cluster constituents since the respective clusters show lower fragmentation at comparable kinetic energy and thus provide in average larger cluster fragments for the analytes to be dissolved in. In systems with clusters of polar constituents and polar adsorbates, the process is most efficient due to the additional energetic stabilization of the desorbed molecule in the solvation shell formed in the cluster fragment.

Seduction of Finding Universality in Sputtering Yields Due to Cluster Bombardment of Solids

Universal descriptions are appealing because they simplify the description of different (but similar) physical systems, allow the determination of general properties, and have practical applications. Recently, the concept of universality has been applied to the dependence of the sputtering (ejection) yield due to energetic cluster bombardment versus the energy of the incident cluster. It was observed that the spread in data points can be reduced if the yield Y and initial projectile cluster kinetic energy E are expressed in quantities scaled by the number of cluster atoms n, that is, Y/n versus E/n. The convergence of the data points is, however, not perfect, especially when the results for molecular and atomic solids are compared. In addition, the physics underlying the apparent universal dependence in not fully understood. For the study presented in this Account, we performed molecular dynamics simulations of Arn cluster bombardment of molecular (benzene, octane, and β-carotene) and atomic (Ag) solids in order to address the physical basis of the apparent universal dependence. We have demonstrated that the convergence of the data points between molecular and atomic solids can be improved if the binding energy of the solid U0 is included and the dependence is presented as Y/(E/U0) versus (E/U0)/n. As a material property, the quantity U0 is defined per the basic unit of material, which is an atom for atomic solids and a molecule for molecular solids. Analogously, the quantity Y is given in atoms and molecules, respectively. The simulations show that, for almost 3 orders of magnitude variation of (E/U0)/n, there are obvious similarities in the ejection mechanisms between the molecular and atomic solids, thus supporting the concept of universality. For large (E/U0)/n values, the mechanism of ejection is the fluid flow from a cone-shaped volume. This regime of (E/U0)/n is generally accessed experimentally by clusters with hundreds of atoms and results in the largest yields. For molecular systems, a large fraction of the total energy E is consumed by internal excitation and molecular fragmentation, which are energy loss channels not present in atomic solids. For small (E/U0)/n values, the cluster deforms the surface and the ejection occurs from a ring-shaped ridge of the forming crater rim. This regime of (E/U0)/n is generally accessed experimentally by clusters with thousands of atoms and results in the smallest yields. For the molecular systems, there is little or no molecular fragmentation. The simulations indicate, however, that the representation which includes U0 as the only material property cannot be completely universal, because there are other material properties which influence the sputtering efficiency. Furthermore, neither the Y/n nor Y/(E/U0) representation includes the energy loss physics associated with molecular fragmentation in the high (E/U0)/n regime. The analysis of the universal concept implies for practical applications that if the objective of the experiment is large material removal, then the high energy per cluster atom regime is applicable. If the objective is little or no molecular fragmentation in organic materials, then the low energy per atom regime is appropriate.