Molecule liftoff from surfaces

Ar cluster bombardment of phenylalanine deposited on graphene-Effect of kinetic energy and projectile size

This study investigates the effects of kinetic energy and projectile size on particle emission from a phenylalanine overlayer adsorbed on a graphene bilayer during argon projectile bombardment. Projectiles of various sizes (1-1000 atoms) and kinetic energies (0.5-40 keV) are used to study their impact on the ejection efficiency, mass distribution, and kinetic and angular spectra of the emitted substances. Particle ejection mechanisms are discussed in scenarios with and without sample perforation. Additionally, this study investigated the potential use of graphene in secondary ion mass spectrometry or neutral secondary mass spectrometry analyses.

Unraveling the Molecular Dynamics of Glucose Oxidase Desorption Induced by Argon Cluster Collision

The bombardment of a protein multilayer target by an energetic argon cluster ion beam enables protein transfer onto a collector in the vacuum while preserving their bioactivity (iBEAM method). In parallel to this new soft-landing variant, protein transfer in the gas phase is a prerequisite for their characterization by mass spectrometry. The successful transfer of bioactive lysozymes (14 kDa) by cluster-induced soft landing and its mechanistic explanation by molecular dynamics (MD) simulations have sparked an important inquiry: Can heavier biomolecules be desorbed while maintaining their tridimensional structure and hence their bioactivity? To address this question, we employed MD simulations using a reactive force field (ReaxFF). Specifically, the Ar cluster-induced desorption of glucose oxidase from either a gold substrate or a lysozyme underlayer was modeled using the LAMMPS code. First, the force field parameters were trained by computing the dissociation energetics of a series of organic molecules with ReaxFF and DFT, in order to realistically describe N-S and O-S interactions in the bombarded glucose oxidase molecule. Second, bombardment simulations investigated the effects of cluster size (ranging from 1000 to 10000 Ar atoms) and kinetic energy (1.5 and 3.0 eV/atom) on the structural features and energetics of the desorbing glucose oxidase. Our results show that large argon clusters (≥7000) are needed to desorb glucose oxidase from a gold surface, yet protein fragmentation and/or pronounced denaturation occur. However, the transfer of structurally preserved glucose oxidase in the gas phase is predicted by the simulations when an organic layer is used as a substrate.

The Use of Computational Methods for the Development of Molecularly Imprinted Polymers

Recent years have witnessed a dramatic increase in the use of theoretical and computational approaches in the study and development of molecular imprinting systems. These tools are being used to either improve understanding of the mechanisms underlying the function of molecular imprinting systems or for the design of new systems. Here, we present an overview of the literature describing the application of theoretical and computational techniques to the different stages of the molecular imprinting process (pre-polymerization mixture, polymerization process and ligand-molecularly imprinted polymer rebinding), along with an analysis of trends within and the current status of this aspect of the molecular imprinting field.

Mass spectrometry as a tool to advance polymer science

In contrast to natural polymers, which have existed for billions of years, the first well-understood synthetic polymers date back to just over one century ago. Nevertheless, this relatively short period has seen vast progress in synthetic polymer chemistry, which can now afford diverse macromolecules with varying structural complexities. To keep pace with this synthetic progress, there have been commensurate developments in analytical chemistry, where mass spectrometry has emerged as the pre-eminent technique for polymer analysis. This Perspective describes present challenges associated with the mass-spectrometric analysis of synthetic polymers, in particular the desorption, ionization and structural interrogation of high-molar-mass macromolecules, as well as strategies to lower spectral complexity. We critically evaluate recent advances in technology in the context of these challenges and suggest how to push the field beyond its current limitations. In this context, the increasingly important role of high-resolution mass spectrometry is emphasized because of its unrivalled ability to describe unique species within polymer ensembles, rather than to report the average properties of the ensemble.

Hypervelocity cluster ion impacts on free standing graphene: Experiment, theory, and applications

We present results from experiments and molecular dynamics (MD) simulations obtained with C₆₀ and Au₄₀₀ impacting on free-standing graphene, graphene oxide (GO), and graphene-supported molecular layers. The experiments were run on custom-built ToF reflectron mass spectrometers with C₆₀ and Au-LMIS sources with acceleration potentials generating 50 keV C₆₀ ²⁺ and 440-540 keV Au₄₀₀ ⁴⁺. Bombardment-detection was in the same mode as MD simulation, i.e., a sequence of individual projectile impacts with separate collection/identification of the ejecta from each impact in either the forward (transmission) or backward (reflection) direction. For C₆₀ impacts on single layer graphene, the secondary ion (SI) yields for C₂ and C₄ emitted in transmission are ∼0.1 (10%). Similar yields were observed for analyte-specific ions from submonolayer deposits of phenylalanine. MD simulations show that graphene acts as a trampoline, i.e., they can be ejected without destruction. Another topic investigated dealt with the chemical composition of free-standing GO. The elemental composition was found to be approximately COH₂. We have also studied the impact of Au₄₀₀ clusters on graphene. Again SI yields were high (e.g., 1.25 C^-/impact). 90-100 Au atoms evaporate off the exiting projectile which experiences an energy loss of ∼72 keV. The latter is a summation of energy spent on rupturing the graphene, ejecting carbon atoms and clusters and a dipole projectile/hole interaction. The charge distribution of the exiting projectiles is ∼50% neutrals and ∼25% either negatively or positively charged. We infer that free-standing graphene enables detection of attomole to zeptomole deposits of analyte via cluster-SI mass spectrometry.

Mechanisms of silicon sputtering and cluster formation explained by atomic level simulations

In low-energy secondary ion MS, collision cascades result in rare sputter events or unfavourably low sputter yields. To better identify the origin of emission products generated by low-energy ion impacts, we carried out molecular dynamics simulations of the underlying collision cascades, using a reactive force field that accounts for the dynamic breaking and forming of bonds. A detailed explanation of the cluster formation and ejection processes for atomic oxygen and also atomic silicon bombardment of Si (100) is given for comparison.

Computer simulations of cluster impacts: effects of the atomic masses of the projectile and target

Cluster secondary ion mass spectrometry is now widely used for the characterization of nanostructures. In order to gain a better understanding of the physics of keV cluster bombardment of surfaces and nanoparticles (NPs), the effects of the atomic masses of the projectile and of the target on the energy deposition and induced sputtering have been studied by means of molecular dynamics simulations. 10 keV C60 was used as a model projectile and impacts on both a flat polymer surface and a metal NP were analyzed. In the first case, the mass of the impinging carbon atoms was artificially varied and, in the second case, the mass of the NP atoms was varied. The results can be rationalized on the basis of the different atomic mass ratios of the projectile and target. In general, the emission is at its maximum, when the projectile and target have the same atomic masses. In the case of the supported NP, the emission of the underlying organic material increases as the atomic mass of the NP decreases. However, it is always less than that calculated for the bare organic surface, irrespective of the mass ratio. The results obtained with C60 impacts on the flat polymer are also compared to simulations of C60 and monoatomic Ga impacts on the NP.

Theoretical and computational strategies for rational molecularly imprinted polymer design

The further evolution of molecularly imprinted polymer science and technology necessitates the development of robust predictive tools capable of handling the complexity of molecular imprinting systems. A combination of the rapid growth in computer power over the past decade and significant software developments have opened new possibilities for simulating aspects of the complex molecular imprinting process. We present here a survey of the current status of the use of in silico-based approaches to aspects of molecular imprinting. Finally, we highlight areas where ongoing and future efforts should yield information critical to our understanding of the underlying mechanisms sufficient to permit the rational design of molecularly imprinted polymers.

Computational view of surface based organic mass spectrometry

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.

Understanding Gold−Thiolate Cluster Emission from Self-assembled Monolayers upon Kiloelectronvolt Ion Bombardment

This article focuses on the emission of organometallic clusters upon kiloelectronvolt ion bombardment of self-assembled monolayers. It is particularly relevant for the elucidation of the physical processes underlying secondary ion mass spectrometry (SIMS). The experimental system, an overlayer of octanethiols on gold, was modeled by classical molecular dynamics, using a hydrocarbon potential involving bonding and nonbonding interactions (AIREBO). To validate the model, the calculated mass and energy distributions of sputtered atoms and molecules were compared to experimental data. Our key finding concerns the emission mechanism of large clusters of the form MxAuy up to M6Au5 (where M is the thiolate molecule), which were not observed under sub-kiloelectronvolt projectile bombardment. Statistically, they are predominantly formed in high-yield events, where many atoms, fragments, and (supra)molecular species are desorbed from the surface. From the microscopic viewpoint, these high-yield events mostly stem from the confinement of the projectile and recoil atom energies in a finite microvolume of the sample surface. As a result of the high local energy density, molecular aggregates desorb from an overheated liquidlike region surrounding the impact point of the projectile.

Microscopic Insights into the Sputtering of Thin Organic Films on Ag{111} Induced by C60 and Ga Bombardment

Molecular dynamics computer simulations have been employed to model the bombardment of Ag{111} covered with three layers of C6H6 by 15 keV Ga and C60 projectiles. The study is aimed toward examining the mechanism by which molecules are desorbed from surfaces by energetic cluster ion beams and toward elucidating the differences between cluster bombardment and atom bombardment. The results show that the impact of the cluster on the benzene-covered surface leads to molecular desorption during the formation of a mesoscopic scale impact crater via a catapulting mechanism. Because of the high yield of C6H6 with both Ga and C60, the yield enhancement is observed to be consistent with related experimental observations. Specific energy and angle distributions are shown to be associated with the catapult mechanism.

An investigation of enhanced secondary ion emission under Au(n)+ (n = 1-7) bombardment

We investigate the mechanism of the nonlinear secondary ion yield enhancement using Au(n)+ (n = 1, 2, 3, 5, 7) primary ions bombarding thin films of Irganox 1010, DL-phenylalanine and polystyrene on Si, Al, and Ag substrates. The largest differences in secondary ion yields are found using Au+, Au2+, and Au3+ primary ion beams. A smaller increase in secondary ion yield is observed using Au5+ and Au7+ primary ions. The yield enhancement is found to be larger on Si than on Al, while the ion yield is smaller using an Au+ beam on Si than on Al. Using Au(n)+ ion structures obtained from Density Functional Theory, we demonstrate that the secondary yield enhancement is not simply due to an increase in energy per area deposited into the surface (energy deposition density). Instead, based on simple mechanical arguments and molecular dynamics results from Medvedeva et al, we suggest a mechanism for nonlinear secondary ion yield enhancement wherein the action of multiple concerted Au impacts leads to efficient energy transfer to substrate atoms in the near surface region and an increase in the number of secondary ions ejected from the surface. Such concerted impacts involve one, two, or three Au atoms, which explains well the large nonlinear yield enhancements observed going from Au+ to Au2+ to Au3+ primary ions. This model is also able to explain the observed substrate effect. For an Au+ ion passing through the more open Si surface, it contacts fewer substrate atoms than in the more dense Al surface. Less energy is deposited in the Si surface region by the Au+ primary ion and the secondary ion yield will be lower for adsorbates on Si than on Al. In the case of Au(n)+ the greater density of Al leads to earlier break-up of the primary ion and a consequent reduction in energy transfer to the near-surface region when compared with Si. This results in higher secondary ion yields and yield enhancements on silicon than aluminum substrates.

Organic surfaces excited by low-energy ions: atomic collisions, molecular desorption and buckminsterfullerenes

This article reviews the recent progress in the understanding of kiloelectronvolt particle interactions with organic solids, including atomic displacements in a light organic medium, vibrational excitation and desorption of fragments and entire molecules. This new insight is the result of a combination of theoretical and experimental approaches, essentially molecular dynamics (MD) simulations and secondary ion mass spectrometry (SIMS). Classical MD simulations provide us with a detailed microscopic view of the processes occurring in the bombarded target, from the collision cascade specifics to the scenarios of molecular emission. Time-of-flight SIMS measures the mass and energy distributions of sputtered ionized fragments and molecular species, a precious source of information concerning their formation, desorption, ionization and delayed unimolecular dissociation in the gas phase. The mechanisms of energy transfer and sputtering are compared for bulk molecular solids, organic overlayers on metal and large molecules embedded in a low-molecular weight matrix. These comparisons help understand some of the beneficial effects of metal substrates and matrices for the analysis of molecules by SIMS. In parallel, I briefly describe the distinct ionization channels of molecules sputtered from organic solids and overlayers. The specific processes induced by polyatomic projectile bombardment, especially fullerenes, are discussed on the basis of new measurements and calculations. Finally, the perspective addresses the state-of-the-art and potential developments in the fields of surface modification and analysis of organic materials by kiloelectronvolt ion beams.

Enhancement of Sputtering Yields Due to C60versus Ga Bombardment of Ag{111} As Explored by Molecular Dynamics Simulations

The mechanism of enhanced desorption initiated by 15-keV C60 cluster ion bombardment of a Ag single crystal surface is examined using molecular dynamics computer simulations. The size of the model microcrystallite of 165,000 atoms and the sophistication of the interaction potential function yields data that should be directly comparable with experiment. The C60 model was chosen since this source is now being used in secondary ion mass spectrometry experiments in many laboratories. The results show that a crater is formed on the Ag surface that is approximately 10 nm in diameter, a result very similar to that found for Au3 bombardment of Au. The yield of Ag atoms is approximately 16 times larger than for corresponding atomic bombardment with 15-keV Ga atoms, and the yield of Ag3 is enhanced by a factor of 35. The essential mechanistic reasons for these differences is that the C60 kinetic energy is deposited closer to the surface, with the deeply penetrating energy propagation occurring via a nondestructive pressure wave. The numbers predicted by the model are testable by experiment, and the approach is extendable to include the study of organic overlayers on metals, a situation of growing importance to the SIMS community.

Secondary ion formation of low molecular weight organic dyes in time-of-flight static secondary ion mass spectrometry

Time-of-flight static secondary ion mass spectrometry (TOF-S-SIMS) was used to characterize thin layers of oxy- and thiocarbocyanine dyes on Ag and Si. Apart from adduct ions a variety of structural fragment ions were detected for which a fragmentation pattern is proposed. Peak assignments were confirmed by comparing spectra of dyes with very similar structures. All secondary ions were assigned with a mass accuracy better than 50 ppm. The intensity of molecular ions as well as fragment ions has been studied as a function of the type of organic dye, the substrate, the layer thickness and the type of primary ion. A large yield difference of two orders of magnitude was observed between the precursor ions of cationic carbocyanine dyes and the protonated molecules of the anionic dyes. Fragment ions, on the other hand, yielded similar intensities for both types of dye. As the dye layers deposited on an Ag substrate yielded higher secondary ion intensities than those deposited on a Si substrate, the Ag metal clearly acts as a promoting agent for secondary ion formation. The effect was more pronounced for precursor signals than for fragment ions. The promoting effect decreased as the deposited layer thickness of the organic dye layer was increased.