The molecular dynamics (MD) simulation technique has been applied to investigate fundamental aspects of matrix-assisted laser desorption. In this paper, we focus on direct comparisons of the results from the simulations with experimental data and on establishing links between the measured or calculated parameters and the basic mechanisms of molecular ejection. The results on the fluence dependence of the ablation/desorption yields and composition of the ejected plume are compared with mass spectrometry and trapping plate experiments. Implications of the prediction of a fluence threshold for ablation are discussed. The strongly forward-peaked velocity and angular distributions of matrix and analyte molecules, predicted in the simulations, are related to the experimental distributions. The shapes and amplitudes of the acoustic waves transmitted from the absorption region through the irradiated sample are compared to recent photoacoustic measurements and related to the ejection mechanisms. The conformational changes during plume evolution and the ejection velocities of analyte molecules are studied and the directions for future investigations are discussed. Finally, we demonstrate that the MD simulation technique can be used to model other processes relevant to mass spectrometry applications, such as laser disintegration of aerosol particles and laser ablation in the presence of photochemical reactions.

A series of molecular dynamics (MD) simulations are performed in order to provide qualitative information on the mechanisms of disintegration of aerosol particles as used in aerosol mass spectrometry. Three generic types of aerosol particles are considered: strongly absorbing particles with homogeneous composition, transparent particles with absorbing inclusion, and absorbing particles with transparent inclusion. To study the effect of the mechanical properties of the aerosol material on the disintegration process, the results for crystalline (brittle) and amorphous (ductile) particles are compared. For large laser fluences, nearly complete dissociation of the absorbing material is observed, whereas the nonabsorbing portions remain fairly intact. Because large fluences can cause photofragmentation of constituent molecules, multiple pulses at low laser fluence and/or lasers with different wavelengths are recommended for the best representative sampling of multicomponent aerosol particles in laser desorption/ionization (LDI) mass spectrometry.

The mechanisms of disintegration of submicrometer particles irradiated by short laser pulses are studied by a molecular dynamics simulation technique. Simulations at different laser fluences are performed for particles with homogeneous composition and particles with transparent inclusions. Spatially nonuniform deposition of laser energy is found to play a major role in defining the character and the extent of disintegration. The processes that contribute to the disintegration include overheating and explosive decomposition of the illuminated side of the particle, spallation of the backside of large particles, and disruption of the transparent inclusion caused by the relaxation of the laser-induced pressure. The observed mechanisms are related to the nature of the disintegration products and implications of the simulation results for aerosol time-of-flight mass spectrometry are discussed. Application of multiple laser pulses is predicted to be advantageous for efficient mass spectrometry sampling of aerosols with a large size to laser penetration depth ratio.

Fluorination of a dimerized Si(001)-2×1 surface near single-layer high step edges has been studied with molecular statics and dynamics simulations using the Stillinger–Weber potential for Si–Si, Si–F, and F–F interactions. Binding energies for up to three F atoms on Si atoms at the step edges have been investigated for fully relaxed systems. We find that F-bonded Si atoms relax away from the surface with increasing fluorination which lowers the desorption/etching energies of SiFx(x=1,3) species. Room temperature molecular dynamics simulations then show direct etching of SiF3 from Si atoms bonded to step edges. The calculations predict an anisotropy in the step edge induced etching of the Si(001)-2×1 surface. This is in qualitative agreement with an experimental observation on the same surface though using Cl instead of F atoms.

Molecular dynamics simulations of the reactions between gaseous fluorine atoms and (SiFx)(n) adsorbates on the Si(100)-(2 x 1) surface are performed using the SW potential with the WWC reparameterization. The objective of the simulations is to determine how the chemical composition and energy distribution of the etched gas-phase products depend on the identity of the reacting adsorbate. Reactions of normal incident fluorine atoms with SiF3, SiF2-SiF3, and SiF2-SiF2-SiF3 adsorbates are simulated at incident kinetic energies from 3.0 to 9.0 eV. SiF4 is the major product in nearly all cases. An S(N)2-like mechanism is responsible for the formation of SiF4, Si2F6, and Si3F8. In addition, at 7.0 and 9.0 eV, the simulations have discovered a previously unknown mechanism for the formation of SiF4, which involves an insertion between a silicon-silicon bond. The simulations predict that radical species are formed predominantly from fragmentation of the higher mass etched products with only a few being formed directly from the reaction between the incoming fluorine atom and the adsorbate. Comparisons are made to experimental data on silicon-fluorine etching with both thermal and hyperthermal fluorine atoms.

Molecular dynamics simulations of the reactions between gaseous fluorine atoms and (SiFx)n adsorbates on the Si{100} — (2 × 1) surface are performed using the SW potential and compared to simulations with the WWC reparameterization of the SW potential. Theoretical and experimental work has demonstrated that the reactive fluorosilyl layer during siliconfluorine etching is composed of tower-like adspecies of SiF, SiF2, and SiF3 groups. The objective of the simulations is to determine how the chemical composition, mechanism of formation, and energy distribution of the etched gas-phase products depend on the identity of the reacting adsorbate, the incident kinetic energy, and the parameterization of the potential energy function. Three reactions are simulated: F(g) + SiF3(a), F(g) + SiF2SiF3(a), and F(g) + SiF2SiF2SiF3(a). SiF4 is the major product and Si2F6 and Si3F8 are minor products. In Si2F6 and Si3F8, the silicon-fluorine bond that is formed is stronger than the silicon-silicon bond in the molecule and, therefore, the majority of these products have enough energy to dissociate and will fragment before reaching the detector. An SN2-like mechanism is the primary mechanism responsible for the formation of SiF4, Si2F6, and Si3F8. In addition, at higher energies, the simulations have discovered a previously unknown mechanism for the formation of SiF4, which involves an insertion between a silicon-silicon bond. The results of the simulations with the two potentials differ quite substantially in their prediction of the reactivity of the adsorbates. The SW potential predicts a 2- to 3-eV lower energy threshold for reaction and a much higher reaction cross-section, especially for the SiF4 product. These results are explained in terms of the differences in the potential energy functions used to describe the silicon-fluorine interactions. In addition, the results are compared to experimental data on silicon-fluorine etching.

Molecular dynamics simulations are performed to examine the adsorption of fluorine molecules, having incident translational kinetic energies between 0.0195 and 1.67 eV, on a clean Si{100}(2×1) surface at 1000 K. Results using the Stillinger and Weber potential energy function and the Weakliem, Wu, and Carter parameterization of this potential energy function are compared to each other and to experimental results. The initial sticking probability increases as the incident kinetic energy increases. As the incident kinetic energy increases, more difluorination and less monofluorination is observed as barriers to adsorption are overcome. For difluorination, a time delay between the two atom adsorption events is quantified.

Etching of the dimer reconstructed silicon surface with an initial coverage of a monolayer of fluorine by 3.0-eV fluorine atoms at normal incidence has been examined with molecular dynamics. In the simulation, fluorine adsorption and product etching occur at the top of two atomic layers of silicon, which are exposed to the vacuum. We have identified mechanisms responsible for the gas-phase products SiF4 and Si2F(x), where x = 5 and 6. In addition, we have simulated a near-steady-state etched surface where the majority of the adspecies are monofluorinated species with a significant amount of difluorinated and trifluorinated species. Observed fluorosilyl towerlike structures are found to be important to the etching of the Si2F(x) species, and they also provide insight as to the possible structure of the adlayer formed on silicon samples after long time exposure to XeF2.

We have calculated the initial sticking probability S0 for near thermal atomic fluorine on the clean dimer reconstructed Si{100}(2×1) surface to be near unity using molecular dynamics simulations. The dependence of the sticking probability on coverage decreases to approximately zero for the fully fluorinated surface. The sticking probability of an F atom on a fully fluorinated silicon surface increases when the kinetic energy of the fluorine atom is above 0.50 eV.