Large Argon Clusters Research Articles

Molecular Dynamics Simulations of Soft and Reactive Landing of Proteins Desorbed by Argon Cluster Bombardment.

Reactive molecular dynamics (MD) simulations were conducted to investigate the soft and reactive landing of hyperthermal velocity proteins transferred to a vacuum using large argon clusters. Experimentally, the interaction of argon cluster ion beams (Ar1000-5000+) with a target biofilm was previously used in such a manner to transfer lysozymes onto a collector with the retention of their bioactivity, paving the way to a new solvent-free method for complex biosurface nanofabrication. However, the experiments did not give access to a microscopic view of the interactions needed for their full understanding, which can be provided by the MD model. Our reactive force field simulations clarify the landing mechanisms of the lysozymes and their fragments on collectors with different natures (gold- and hydrogen-terminated graphite). The results highlight the conditions of soft and reactive landing on rigid surfaces, the effects of the protein structure, energy, and incidence angle before landing, and the adhesion forces with the collector substrate. Many of the obtained results can be generalized to other soft and reactive landing approaches used for biomolecules such as electrospray ionization and matrix-assisted laser desorption ionization.

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.

Enhancing Ion Signals and Improving Matrix Selection in Time-of-Flight Secondary Ion Mass Spectrometry with Microvolume Expansion Using Large Argon Clusters.

The molecular environment has an important impact on the ionization mechanism in time-of-flight secondary ion mass spectrometry (ToF-SIMS). In complex samples, desorption/ionization, and thus the detection of a molecular signal, can be hampered by molecular entanglement, ionization-suppressive neighbors, or even an unfavorable sample substrate. Here, a method called microvolume expansion is developed to overcome these negative effects. Large argon clusters are able to transfer biomolecules from a target to a collector in vacuum. In this study, argon gas cluster ion beams (Arn+-GCIB with n centered around 3000 or 5000) are used to expand a microvolume from the sample to a collector, which is a material ideally enhancing the ionization yield. The collector is then analyzed using a liquid metal ion gun. The signal amplification factor corresponding to the expansion of phosphatidylcholine (PC) lipid on collectors partially covered with acidic matrices was evaluated as an initial proof of concept. In one experiment, the PC expansion on a pattern of four drop-casted matrix-assisted laser desorption/ionization matrices led to the selection of α-cyano-4-hydroxycinnamic (CHCA) as the optimal candidate for cationic PC detection. The ion signal is increased by at least three orders of magnitude when PC was expanded using 10 keV Ar3000+ and Ar5000+ on a sublimated layer of CHCA. Finally, the expansion of the gray matter of a mouse on different materials (Si, Au-coated Si, CHCA, and polyethylene) was achieved with varying degrees of success, demonstrating the potential of the method to further analyze complex and fragile biological assemblies.

Deposition of Intact and Active Proteins In Vacuo Using Large Argon Cluster Ion Beams.

Providing inert materials with a biochemical function, for example using proteins, is a cornerstone technology underlying many applications. However, the controlled construction of protein thin films remains a major challenge. Here, an innovative solvent-free approach for protein deposition is reported, using lysozyme as a model. By diverting a time-of-flight secondary ion mass spectrometer (ToF-SIMS) from its standard analytical function, large argon clusters were used to achieve protein transfer. A target consisting of a pool of proteins was bombarded with 10 keV Ar5000+ ions, and the ejected proteins were collected on a silicon wafer. The ellipsoidal deposition pattern was evidenced by ToF-SIMS analysis, while SDS-PAGE electrophoresis confirmed the presence of intact lysozyme on the collector. Finally, enzymatic activity assays demonstrated the preservation of the three-dimensional structure of the transferred proteins. These results pave the way to well-controlled protein deposition using ion beams and to the investigation of more complex multilayer architectures.

Ion yield enhancement at the organic/inorganic interface in SIMS analysis using Ar-GCIB

Argon gas cluster ion beams (Ar-GCIBs) provide new opportunities for molecular depth profiling and imaging of organic materials and biological samples, thanks to recent technological developments that have led to the construction of new SIMS spectrometers where the traditional issues related to their low lateral resolution along with poor mass resolution and mass accuracy are overcome. The present fundamental contribution on SIMS molecular depth profiling investigates the variations of the secondary ion signals observed at the organic–inorganic hybrid interface when using Ar-GCIB as the analytical beam. With this in mind, depth profiling experiments were performed with a ToF-SIMS spectrometer using different analysis beams: 30-keV Bi5+ versus 10-keV Arn+ with a cluster size (n) of 800, 1500, 3000 and 5000 atoms, respectively. A 10-keV Ar3000+ beam was used for sputtering in all the experiments. Irganox 1010 and model polymers such as polystyrene (PS) and poly (methyl methacrylate) (PMMA) oligomers were chosen. Silicon wafer and a polymer-based substrates were employed to test materials with different stiffness, which is directly related to their Young’s moduli, an important parameter in this study. Ar-GCIB depth profiles systematically show ion signal enhancement of the characteristic fragments of PS and Irganox 1010 when approaching the interface with the silicon substrate, that can reach up to 60% for [M1010-H]− in Irganox films deposited onto silicon wafers. This enhancement increases with increasing n in both ion polarities. These results point out some ionization effects on the observed signal enhancement at the interface. The experimental observations will be explained on the basis of the physics of the impact of large argon clusters on different target materials and the energy confinement of the ion projectile in the organic overlayers. Finally, the thickness of organic films on rigid substrates in the nanoscale appears to be a crucial parameter to dramatically improve the sensitivity to molecular fragments when using large Ar cluster ions as analysis beams.

A quantitative determination of the polymerization of benzoxazine thin coatings by time‐of‐flight secondary ion mass spectrometry

Phenol‐paraphenylenediamine (P‐pPDA) benzoxazines exhibit excellent barrier properties, adequate to protect aluminum alloys from corrosion, and constitute interesting candidates to replace chromate‐containing coatings in the aeronautical industry. For the successful application of P‐pPDA coatings, it is necessary to decrease the curing temperature to avoid the delamination of the coating while preserving the mechanical properties of the alloy, as well as the barrier properties of the coating. However, decreasing the curing temperature leads to less polymerized films, the extent of which requires a quantitative assessment.While the conversion rate of the polymerization reaction is commonly evaluated for bulk samples using differential scanning calorimetry (DSC), a tool for its evaluation in thin films is missing. Therefore, a new approach was developed for that matter using time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS). The relation between the SIMS data integrated from inside thin films and the DSC results obtained on bulk samples with the same curing cycle allowed to calibrate the SIMS data. With this preliminary calibration of the technique, the polymerization of P‐pPDA coatings can be locally determined, at the surface and along the depth of the coating, using dual‐beam depth profiling with large argon cluster beam sputtering.

Hybrid Perovskites Depth Profiling with Variable-Size Argon Clusters and Monatomic Ions Beams.

Ion beam depth profiling is increasingly used to investigate layers and interfaces in complex multilayered devices, including solar cells. This approach is particularly challenging on hybrid perovskite layers and perovskite solar cells because of the presence of organic/inorganic interfaces requiring the fine optimization of the sputtering beam conditions. The ion beam sputtering must ensure a viable sputtering rate on hard inorganic materials while limiting the chemical (fragmentation), compositional (preferential sputtering) or topographical (roughening and intermixing) modifications on soft organic layers. In this work, model (Csx(MA0.17FA0.83)100−xPb(I0.83Br0.17)3/cTiO2/Glass) samples and full mesoscopic perovskite solar cells are profiled using low-energy (500 and 1000 eV) monatomic beams (Ar+ and Cs+) and variable-size argon clusters (Arn+, 75 < n < 4000) with energy up to 20 keV. The ion beam conditions are optimized by systematically comparing the sputtering rates and the surface modifications associated with each sputtering beam. X-ray photoelectron spectroscopy, time-of-flight secondary ion mass spectrometry, and in-situ scanning probe microscopy are combined to characterize the interfaces and evidence sputtering-related artifacts. Within monatomic beams, 500 eV Cs+ results in the most intense and stable ToF-SIMS molecular profiles, almost material-independent sputtering rates and sharp interfaces. Large argon clusters (n > 500) with insufficient energy (E < 10 keV) result in the preferential sputtering of organic molecules and are highly ineffective to sputter small metal clusters (Pb and Au), which tend to artificially accumulate during the depth profile. This is not the case for the optimized cluster ions having a few hundred argon atoms (300 < n < 500) and an energy-per-atom value of at least 20 eV. In these conditions, we obtain (i) the low fragmentation of organic molecules, (ii) convenient erosion rates on soft and hard layers (but still different), and (iii) constant molecular profiles in the perovskite layer, i.e., no accumulation of damages.

Internal Energy Distribution of Secondary Ions Under Argon and Bismuth Cluster Bombardments: "Soft" Versus "Hard" Desorption-Ionization Process.

The emission/ionization process under massive argon cluster bombardment was investigated by measuring the internal energy distributions of a series of benzylpyridinium ions. Argon clusters with kinetic energies between 10 and 20keV and cluster sizes ranging from 500 to 10,000 were used to establish the influence of their size, energy, and velocity on the internal energy distribution of the secondary ions. It is shown that the internal energy distribution of secondary ions principally depends on the energy per atom or the velocity of the cluster ion beam (E/n ∝ v2). Under low energy per atom (E/n˂10eV), the mean internal energy and fragmentation yield increase rapidly with the incident energy of individual constituents. Beyond 10eV/atom impact (up to 40eV/atom), the internal energy reaches a plateau and remains constant. Results were compared with those generated from bismuth cluster impacts for which the mean internal energies correspond well to the plateau values for argon clusters. However, a significant difference was found between argon and bismuth clusters concerning the damage or disappearance cross section. A 20 times smaller disappearance cross section was measured under 20keV Ar2000+ impact compared to 25keV Bi5+ bombardment, thus quantitatively showing the low damage effect of large argon clusters for almost the same molecular ion yield. Graphical Abstract ᅟ.

Effect of nanoconfinement on the sputter yield in ultrathin polymeric films: Experiments and model

This fundamental contribution on secondary ion mass spectrometry (SIMS) polymer depth-profiling by large argon clusters investigates the dependence of the sputter yield volume (Y) on the thickness (d) of ultrathin films as a function of the substrate nature, i.e. hard vs soft. For this purpose, thin films of polystyrene (PS) oligomers (∼4,000 amu) are spin-coated, respectively, onto silicon and poly (methyl methacrylate) supports and, then, bombarded by 10 keV Ar3000+ ions. The investigated thickness ranges from 15 to 230 nm. Additionally, the influence of the polymer molecular weight on Y(d) for PS thin films on Si is explored. The sputtering efficiency is found to be strongly dependent on the overlayer thickness, only in the case of the silicon substrate. A simple phenomenological model is proposed for the description of the thickness influence on the sputtering yield. Molecular dynamics (MD) simulations conducted on amorphous films of polyethylene-like oligomers of increasing thickness (from 2 to 20 nm), under comparable cluster bombardment conditions, predict a significant increase of the sputtering yield for ultrathin layers on hard substrates, induced by energy confinement in the polymer, and support our phenomenological model.

Molecular dynamics simulations study of nano particle migration by cluster impact

Molecular dynamics (MD) simulations are performed in order to investigate the radiation effects of a huge and slow gas cluster for the surface cleaning process. When a large argon cluster with the size ranging from 20,000 to 300,000 is accelerated with a total of 30 keV, each constituent atom carries very low energy ranging from 1.5 eV/atom to 0.1 eV/atom. In many cases, the cluster does not penetrate the solid target surface but is deflected in a lateral direction. This collisional process results in a high density particle flow spreading along the surface plane due to cohesion of the cluster, which suggests the capability to modify the irregular surface structure, without damage in the target. The MD simulations demonstrate that such a huge cluster sweeps a nano particle (NP, 3 nm in radius) attached on a planar silicon target's surface. From the investigation of various conditions of cluster impact, it is found that the migration distance is correlated with the kinetic energy applied on the NP by the impact of cluster atoms. Additionally, the MD results suggest the existence of optimized parameters for the maximum migration distance for the offset distance between the cluster and the NP, and the cluster size for constant total energy (equivalent to energy per atom or kinetic energy density). The optimized offset distance was estimated as the summation of radii of the incident cluster and the NP. The optimized energy per atom was suggested around 0.6 eV/atom, where the cluster efficiently spreads in lateral direction keeping higher kinetic energy density of particle flow.

Dual beam depth profiling of organic materials: assessment of capabilities and limitations

With the advent of large argon cluster beams, organic materials can be sputtered without the accumulation of radiation damage. The dual beam mode with a Bi cluster analysis beam is successfully applied to depth profiling and 3D analysis of organic materials providing both high‐depth resolution and high‐lateral resolution. For the analysis of very small sample volumes, it is desirable that a rather large fraction of the material is consumed by the analysis beam and contributes to the analytical signal. However, at higher analysis beam sputter rates, the radiation damage by the Bi clusters can become quite severe leading to a molecular ion signal decay with depth. In this paper, we investigate the conditions for the optimum use of the sample material in the dual beam mode using the Irganox delta layer structure introduced by NPL (National Physical Laboratory (UK)). A model that describes the dual beam mode and allows calculating the intact area fraction in the steady state is presented. Yield volumes and damage volumes are determined for Bi3+ and Bi5++ as well as the useful sample fraction that contributes to the molecular ion signal. We will compare the results to the depth profiling with C60 and Ar clusters in a single DC beam mode. Copyright © 2014 John Wiley &amp; Sons, Ltd.

Clustering and Photochemistry of Freon CF2Cl2 on Argon and Ice Nanoparticles

The photochemistry of CF2Cl2 molecules deposited on argon and ice nanoparticles was investigated. The clusters were characterized via electron ionization mass spectrometry, and the photochemistry was revealed by the Cl fragment velocity map imaging after the CF2Cl2 photodissociation at 193 nm. The complex molecular beam experiment was complemented by ab initio calculations. The (CF2Cl2)n clusters were generated in a coexpansion with Ar buffer gas. The photodissociation of molecules in the (CF2Cl2)n clusters yields predominantly Cl fragments with zero kinetic energy: caging. The CF2Cl2 molecules deposited on large argon clusters in a pickup experiment are highly mobile and coagulate to form the (CF2Cl2)n clusters on ArN. The photodissociation of the CF2Cl2 molecules and clusters on ArN leads to the caging of the Cl fragment. On the other hand, the CF2Cl2 molecules adsorbed on the (H2O)N ice nanoparticles do not form clusters, and no Cl fragments are observed from their photodissociation. Since the CF2Cl2 molecule was clearly adsorbed on (H2O)N, the missing Cl signal is interpreted in terms of surface orientation, possibly via the so-called halogen bond and/or embedding of the CF2Cl2 molecule on the disordered surface of the ice nanoparticles.

Time resolved observation of the solvation dynamics of a Rydberg excited molecule deposited on an argon cluster-I: DABCO☆at short times

This paper is a joint experimental and theoretical approach concerning a molecule deposited on a large argon cluster. The spectroscopy and the dynamics of the deposited molecule are measured using the photoelectron spectroscopy. The absorption spectrum of the deposited molecule shows two solvation sites populated in the ground state. The combined dynamics reveals that the population ratio of the two sites is reversed when the molecule is electronically excited. This work provides the timescale of the corresponding solvation dynamics. Theoretical calculation supports the interpretation. More generally, close examination of the short time dynamics (0-6 ps) of DABCO···Ar(n) gives insights into the ultrafast relaxation dynamics of molecules deposited at interfaces and provides hence the time scale for deposited molecules to adapt to their neighborhoods.

Comparison of fullerene and large argon clusters for the molecular depth profiling of amino acid multilayers

A major challenge regarding the characterization of multilayer films is to perform high-resolution molecular depth profiling of, in particular, organic materials. This experimental work compares the performance of C60(+) and Ar1700(+) for the depth profiling of model multilayer organic films. In particular, the conditions under which the original interface widths (depth resolution) were preserved were investigated as a function of the sputtering energy. The multilayer samples consisted of three thin δ-layers (~8 nm) of the amino acid tyrosine embedded between four thicker layers (~93 nm) of the amino acid phenylalanine, all evaporated on to a silicon substrate under high vacuum. When C60(+) was used for sputtering, the interface quality degraded with depth through an increase of the apparent width and a decay of the signal intensity. Due to the continuous sputtering yield decline with increasing the C60(+) dose, the second and third δ-layers were shifted with respect to the first one; this deterioration was more pronounced at 10 keV, when the third δ-layer, and a fortiori the silicon substrate, could not be reached even after prolonged sputtering. When large argon clusters, Ar1700(+), were used for sputtering, a stable molecular signal and constant sputtering yield were achieved throughout the erosion process. The depth resolution parameters calculated for all δ-layers were very similar irrespective of the impact energy. The experimental interface widths of approximately 10 nm were barely larger than the theoretical thickness of 8 nm for the evaporated δ-layers.

Molecular dynamics simulations of cluster impacts on solid targets: implantation, surface modification, and sputtering

The collisions of cluster projectiles on solid targets were studied using molecular dynamics (MD) simulations. The penetration range and damage induced by small boron and carbon cluster implantations are compared with those induced by monomers with the same energy per atom. The simulations indicated enhanced penetration depth and the formation of dense track damage at the surface region. In addition, large argon and fluorine clusters (up to 1 million atoms) have shown effects such as crater formation and low-damage surface etching of silicon. The MD simulations revealed that cluster penetration and crater formation depends not on the total incident energy, but on the incident energy per atom, and that the damage threshold for the argon cluster is several eV/atom. In the impact of a very large and slow fluorine cluster on silicon, an enhancement of chemical reactivity at the near surface region was observed because of the high density of fluorine molecules depositing kinetic energy.

Peptide dissociation patterns in secondary ion mass spectrometry under large argon cluster ion bombardment

The analysis of organic and biological substances by secondary ion mass spectrometry (SIMS) has greatly benefited from the use of cluster ions as primary bombarding species. Thereby, depth profiling and three-dimensional (3D) imaging of such systems became feasible. Large Ar(n)(+) cluster ions may constitute a further improvement in this direction. To explore this option, large Ar(n)(+) cluster ions (with n ~1500 Ar atoms per cluster) were used to investigate the emission of positive secondary ions from two peptide specimens (angiotensin I and bradykinin) by orthogonal time-of-flight SIMS using bombarding energies 6, 10 and 14 keV. For both peptides, the protonated molecular ion is observed in the mass spectra. In addition, distinct fragmentation patterns were observed; these indicate that fragment ions under Ar cluster irradiation form primarily via cleavage of bonds along the peptide backbone whereas the rapture of side chains occurs much less frequently. These features appear to be similar to low-energy collision-induced dissociation pathways. Tentatively, these findings can then be ascribed to the concerted action of the large number of Ar atoms in the impact zone of cluster at the surface: these low-energy Ar species (with an average energy of few eV) may effect the cleavage of the peptide bonds and lead, eventually, to the emission of the fragment ions.

Spectroscopy of 3, 4, 9, 10-perylenetetracarboxylic dianhydride (PTCDA) attached to rare gas samples: Clusters vs. bulk matrices. II. Fluorescence emission spectroscopy

The interaction between 3, 4, 9, 10-perylenetetracarboxylic dianhydride (PTCDA) molecules and solid rare gas samples is studied by means of fluorescence emission spectroscopy. Laser-excited PTCDA-doped large argon, neon, and para-hydrogen clusters along with PTCDA embedded in helium nanodroplets are spectroscopically characterized with respect to line broadening and shifting. A fast non-radiative relaxation is observed before a radiative decay in the electronic ground state takes place. In comparison, fluorescence emission studies of PTCDA embedded in bulk neon and argon matrices result in much more complex spectral signatures characterized by a splitting of the different emission lines. These can be assigned to the appearance of site isomers of the surrounding matrix lattice structure.

Surface spectrometry using large argon clusters

Large argon cluster ions can very successfully be applied as primary ion projectiles in SIMS, but until recently, these sources could not be used in combination with conventional TOF‐SIMS systems. The large cluster size distribution limited the possibility to pulse the primary ion beam, which is a prerequisite for high mass resolution surface spectrometry. We developed a unique 90° pulsing system which enables the generation of short primary ion pulses for high mass resolution surface spectrometry. The pulsing system allows the variation of the applied cluster size from 250 to 10000 atoms/cluster. In this contribution, we present and compare data about the influence of the cluster size on the spectra appearance, the fragmentation and the secondary ion yield on different organic sample systems. Copyright © 2012 John Wiley &amp; Sons, Ltd.

Enhanced K_α output of Ar and Kr using size optimized cluster target irradiated by high-contrast laser pulses

We observed that increasing the clusters size and laser pulse contrast can enhance the X-ray flux emitted by femtosecond-laser-driven-cluster plasma. By focusing a high contrast laser (10(-10)) on large argon clusters, high flux Kα-like X-rays (around 2.96 keV) is generated with a total flux of 2.5 × 10(11) photons/J in 4π and a conversion efficiency of 1.2 × 10-4. In the case of large Kr clusters, the best total flux for L-shell X-rays is 5.3 × 1011 photons/J with a conversion efficiency of 1.3 × 10-4 and, for the Kα X-ray (12.7 keV), it is 8 × 10(8) photons/J with a conversion efficiency of 1.6 × 10-6. Using this X-ray source, a single-shot high-performance X-ray imaging is demonstrated.

TOF-SIMS with Argon Gas Cluster Ion Beams: A Comparison with C60+

Time-of-flight secondary ion mass spectrometry (TOF-SIMS) is an established technique for the characterization of solid sample surfaces. The introduction of polyatomic ion beams, such as C(60), has provided the associated ability to perform molecular depth-profiling and 3D molecular imaging. However, not all samples perform equally under C(60) bombardment, and it is probably naïve to think that there will be an ion beam that will be applicable in all situations. It is therefore important to explore the potential of other candidates. A systematic study of the suitability of argon gas cluster ion beams (Ar-GCIBs) of general composition Ar(n)(+), where n = 60-3000, as primary particles in TOF-SIMS analysis has been performed. We have assessed the potential of the Ar-GCIBs for molecular depth-profiling in terms of damage accumulation and sputter rate and also as analysis beams where spectral quality and secondary ion yields are considered. We present results with direct comparison with C(60) ions on the same sample in the same instrument on polymer, polymer additive, and biomolecular samples, including lipids and small peptides. Large argon clusters show reduced damage accumulation compared with C(60) with an approximately constant sputter rate as a function of Ar cluster size. Further, on some samples, large argon clusters produce changes in the mass spectra indicative of a more gentle ejection mechanism. However, there also appears to be a reduction in the ionization of secondary species as the size of the Ar cluster increases.