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.

Intuitive Model of Surface Modification Induced by Cluster Ion Beams.

Topography development is one of the main factors limiting the quality of depth profiles during depth profiling experiments. One possible source of topography development is the formation of self-organized patterns due to cluster ion beam irradiation. In this work, we propose a simple model that can intuitively explain this phenomenon in terms of impact-induced mass transfer. By coupling our model with molecular dynamics simulations, we can predict the critical incidence angle, which separates the smoothening and roughening regimes. The results are in quantitative agreement with experiments. It is observed that the problems arising from topography development during depth profiling with cluster projectiles can be mitigated by reducing the beam incidence angle with respect to the surface normal or increasing its kinetic energy.

Three-Dimensional Mass Spectrometric Imaging of Biological Structures Using a Vacuum-Compatible Microfluidic Device.

Three-dimensional (3D) molecular imaging of biological structures is important for a wide range of research. In recent decades, secondary-ion mass spectrometry (SIMS) has been recognized as a powerful technique for both two-dimensional and 3D molecular imaging. Sample fixations (e.g., chemical fixation and cryogenic fixation methods) are necessary to adapt biological samples to the vacuum condition in the SIMS chamber, which has been demonstrated to be nontrivial and less controllable, thus limiting the wider application of SIMS on 3D molecular analysis of biological samples. Our group recently developed in situ liquid SIMS that offers great opportunities for the molecular study of various liquids and liquid interfaces. In this work, we demonstrate that a further development of the vacuum-compatible microfluidic device used in in situ liquid SIMS provides a convenient freeze-fixation of biological samples and leads to more controllable and convenient 3D molecular imaging. The special design of this new vacuum-compatible liquid chamber allows an easy determination of sputter rates of ice, which is critical for calibrating the depth scale of frozen biological samples. Sputter yield of a 20 keV Ar1800+ ion on ice has been determined as 1500 (±8%) water molecules per Ar1800+ ion, consistent with our results from molecular dynamics simulations. Moreover, using the information of ice sputter yield, we successfully conduct 3D molecular imaging of frozen homogenized milk and observe network structures of interesting organic and inorganic species. Taken together, our results will significantly benefit various research fields relying on 3D molecular imaging of biological structures.

Effect of the Impact Angle on the Kinetic Energy and Angular Distributions of ß-Carotene Sputtered by 15 keV Ar2000 Projectiles.

Molecular dynamics (MD) computer simulations are used to model ejection of particles from ß-carotene samples bombarded by 15 keV Ar2000. The effect of the incidence angle on the angular and kinetic energy distributions is investigated. It has been found that both of these distributions are sensitive to the variation of the incidence angle, particularly near the normal incidence. For impacts along the surface normal, material ejection is azimuthally symmetric, and a significant emission occurs along the surface normal. The kinetic energy distribution of intact molecules has a maximum near 1 eV and terminates below approximately 2 eV. An increase of the incidence angle breaks the azimuthal symmetry. Most of the intact molecules become ejected in the forward direction. The maximum in the polar angle distribution shifts toward large off-normal angles. In addition, the most probable kinetic energy of ejected molecules is significantly increased. The mechanisms of molecular emission responsible for the observed changes are delineated. The implications of the observed ejection characteristics for the utilization of large gas cluster projectiles in secondary neutral mass spectrometry are discussed.

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.

"Trampoline" ejection of organic molecules from graphene and graphite via keV cluster ions impacts.

We present the data on ejection of molecules and emission of molecular ions caused by single impacts of 50 keV C602+ on a molecular layer of deuterated phenylalanine (D8Phe) deposited on free standing, 2-layer graphene. The projectile impacts on the graphene side stimulate the abundant ejection of intact molecules and the emission of molecular ions in the transmission direction. To gain insight into the mechanism of ejection, Molecular Dynamic simulations were performed. It was found that the projectile penetrates the thin layer of graphene, partially depositing the projectile's kinetic energy, and molecules are ejected from the hot area around the hole that is made by the projectile. The yield, Y, of negative ions of deprotonated phenylalanine, (D8Phe-H)-, emitted in the transmission direction is 0.1 ions per projectile impact. To characterize the ejection and ionization of molecules, we have performed the experiments on emission of (D8Phe-H)- from the surface of bulk D8Phe (Y = 0.13) and from the single molecular layer of D8Phe deposited on bulk pyrolytic graphite (Y = 0.15). We show that, despite the similar yields of molecular ions, the scenario of the energy deposition and ejection of molecules is different for the case of graphene due to the confined volume of projectile-analyte interaction. The projectile impact on the graphene-D8Phe sample stimulates the collective radial movement of analyte atoms, which compresses the D8Phe layer radially from the hole. At the same time, this compression bends and stretches the graphene membrane around the hole thus accumulating potential energy. The accumulated potential energy is transformed into the kinetic energy of correlated movement upward for membrane atoms, thus the membrane acts as a trampoline for the molecules. The ejected molecules are effectively ionized; the ionization probability is ∼30× higher compared to that obtained for the bulk D8Phe target. The proposed mechanism of ionization involves tunneling of electrons from the vibrationally excited area around the hole to the molecules. Another proposed mechanism is a direct proton transfer exchange, which is suitable for a bulk target: ions of molecular fragments (i.e., CN-) generated in the impact area interact with intact molecules from the rim of this area. There is a direct proton exchange process for the system D8Phe molecule + CN-.

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 ß-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.

Oscillations in the stability of consecutive chemical bonds revealed by ion-induced desorption.

While it is a common concept in chemistry that strengthening of one bond results in weakening of the adjacent ones, no results have been published on if and how this effect protrudes further into the molecular backbone. By binding molecules to a surface in the form of a self-assembled monolayer, the strength of a primary bond can be selectively altered. Herein, we report that by using secondary-ion mass spectrometry, we are able to detect for the first time positional oscillations in the stability of consecutive bonds along the adsorbed molecule, with the amplitudes diminishing with increasing distance from the molecule-metal interface. To explain these observations, we have performed molecular dynamics simulations and DFT calculations. These show that the oscillation effects in chemical-bond stability have a very general nature and break the translational symmetry in molecules.

Computed molecular depth profile for C60 bombardment of a molecular solid.

Molecular dynamics (MD) simulations have been performed for 10 keV C60 bombardment of an octane molecular solid at normal incidence. The results are analyzed using the steady-state statistical sputtering model (SS-SSM) to understand the nature of molecular motions and to predict a depth profile of a δ-layer. The octane system has sputtering yield of ~150 nm(3) of which 85% is in intact molecules and 15% is fragmented species. The main displacement mechanism is along the crater edge. Displacements between layers beneath the impact point are difficult because the nonspherically shaped octane molecule needs a relatively large volume to move into and the molecule needs to be aligned properly for the displacement. Since interlayer mixing is difficult, the predicted depth profile is dominated by the rms roughness and the large information depth because of the large sputtering yield.

Dynamics displayed by energetic C60 bombardment of metal overlayers on an organic substrate.

Cluster bombardments of 15 keV C(60) on metal-organic interfaces composed of silver atoms and octatetraene molecules were modeled using molecular dynamics computer simulations. Dynamics revealed by the simulations include the formation of holes in the metal overlayers from which underlying organic molecules are sputtered predominantly by a rapid jetlike motion and the implantation of metal atoms and clusters in the underlying organic solid. Both of these processes negatively affect the information depth for cluster bombardment of metal-organic interfaces; therefore, the simulations presented here give a clear picture of the issues associated with depth profiling through metal-organic interfaces.

Partnering analytic models and dynamic secondary ion mass spectrometry simulations to interpret depth profiles due to kiloelectronvolt cluster bombardment.

The analytical steady-state statistical sputtering model (SS-SSM) is utilized to interpret molecular dynamics (MD) simulations of depth profiling of Ag solids with keV cluster beams of C(60) and Au(3) under different incident energy and angle conditions. Specifically, the results of the MD simulations provide the input to the SS-SSM and the result is a depth profile of a delta layer. It has been found that the rms roughness of each system correlates with the total displacement yield, a new quantity introduced in this study that follows naturally from the SS-SSM. The results indicate that the best depth profiles occur when the displacement yield is low and the sputtering yield is high. Moreover, it is determined that the expected value of the delta layer position as calculated from a depth profile rather than the peak position in the depth profile is the best indicator of the actual delta layer position.

Development of a Charge-Implicit ReaxFF for C/H/O Systems.

Modeling chemical reactions in condensed phases is difficult. Interaction potentials (or force fields) like ReaxFF can perform this modeling with a high overall accuracy, but the disadvantage of ReaxFF is a low simulation speed arising from costly algorithms, in particular charge equilibration. Therefore, we reparametrized ReaxFF to incorporate Coulomb forces into other terms of the force field. Because of this change, our charge-implicit ReaxFF-CHO is >2 times faster than the original parametrization. Despite the lack of explicit electrostatic interactions, our potential can correctly model the reactions and densities of systems containing carbon, hydrogen, and oxygen atoms. We have used the new potential to simulate bombardment of trehalose by water clusters. It has been observed experimentally that these water projectiles can increase the sensitivity of secondary ion mass spectrometry by more than an order of magnitude, but no explanation for this phenomenon was given. Our simulations show that the increase in the intensity of the recorded signal coincides with the emission of trehalose-water complexes.

Internal energy of molecules ejected due to energetic C60 bombardment.

The early stages of C(60) bombardment of octane and octatetraene crystals are modeled using molecular dynamics simulations with incident energies of 5-20 keV. Using the AIREBO potential, which allows for chemical reactions in hydrocarbon molecules, we are able to investigate how the projectile energy is partitioned into changes in potential and kinetic energy as well as how much energy flows into reacted molecules and internal energy. Several animations have been included to illustrate the bombardment process. The results show that the material near the edge of the crater can be ejected with low internal energies and that ejected molecules maintain their internal energies in the plume, in contrast to a collisional cooling mechanism previously proposed. In addition, a single C(60) bombardment was able to create many free and reacted H atoms which may aid in the ionization of molecules upon subsequent bombardment events.

C-O Bond Dissociation and Induced Chemical Ionization Using High Energy (CO2)n+ Gas Cluster Ion Beam.

A gas cluster ion beam (GCIB) source, consisting of CO2 clusters and operating with kinetic energies of up to 60 keV, has been developed for the high resolution and high sensitivity imaging of intact biomolecules. The CO2 molecule is an excellent molecule to employ in a GCIB source due to its relative stability and improved focusing capabilities, especially when compared to the conventionally employed Ar cluster source. Here we report on experiments aimed to examine the behavior of CO2 clusters as they impact a surface under a variety of conditions. Clusters of (CO2)n+ (n = 2000~10,000) with varying sizes and kinetic energies were employed to interrogate both an organic and inorganic surface. The results show that C-O bond dissociation did not occur when the energy per molecule is less than 5 eV/n, but that oxygen adducts were seen in increasing intensity as the energy is above 5 eV/n, particularly, drastic enhancement up to 100 times of oxygen adducts was observed on Au surface. For Irganox 1010, an organic surface, oxygen containing adducts were observed with moderate signal enhancement. Molecular dynamics computer simulations were employed to test the hypothesis that the C-O bond is broken at high values of eV/n. These calculations show that C-O bond dissociation occurs at eV/n values less than the C-O bond energy (8.3 eV) by interaction with surface topological features. In general, the experiments suggest that the projectiles containing oxygen can enhance the ionization efficiency of surface molecules via chemically induced processes, and that CO2 can be an effective cluster ion source for SIMS experiments. Graphical Abstract.

Development of a Charge-Implicit ReaxFF Potential for Hydrocarbon Systems.

Molecular dynamics (MD) simulations continue to make important contributions to understanding chemical and physical processes. Concomitant with the growth of MD simulations is the need to have interaction potentials that both represent the chemistry of the system and are computationally efficient. We propose a modification to the ReaxFF potential for carbon and hydrogen that eliminates the time-consuming charge equilibration, eliminates the acknowledged flaws of the electronegativity equalization method, includes an expanded training set for condensed phases, has a repulsive wall for simulations of energetic particle bombardment, and is compatible with the LAMMPS code. This charge-implicit ReaxFF potential is five times faster than the conventional ReaxFF potential for a simulation of keV particle bombardment with a sample size of over 800 000 atoms.

Effect of Oxygen Chemistry in Sputtering of Polymers.

Molecular dynamics computer simulations are used to model kiloelectronvolt cluster bombardment of pure hydrocarbon [polyethylene (PE) and polystyrene (PS)] and oxygen-containing [paraformaldehyde (PFA) and polylactic acid (PLA)] polymers by 20 keV C60 projectiles at a 45° impact angle to investigate the chemical effect of oxygen in the substrate material on the sputtering process. The simulations demonstrate that the presence of oxygen enhances the formation of small molecules such as carbon monoxide, carbon dioxide, water, and various molecules containing C═O double bonds. The explanation for the enhanced small molecule formation is the stability of carbon and oxygen multiple bonds relative to multiple bonds with only carbon atoms. This chemistry is reflected in the fraction of the ejected material that has a mass not higher than 104 amu. For PFA and PLA, the fraction is approximately 90% of the total mass, whereas for PE and PS, it is less than half.

CO2 Cluster Ion Beam, an Alternative Projectile for Secondary Ion Mass Spectrometry.

The emergence of argon-based gas cluster ion beams for SIMS experiments opens new possibilities for molecular depth profiling and 3D chemical imaging. These beams generally leave less surface chemical damage and yield mass spectra with reduced fragmentation compared with smaller cluster projectiles. For nanoscale bioimaging applications, however, limited sensitivity due to low ionization probability and technical challenges of beam focusing remain problematic. The use of gas cluster ion beams based upon systems other than argon offer an opportunity to resolve these difficulties. Here we report on the prospects of employing CO2 as a simple alternative to argon. Ionization efficiency, chemical damage, sputter rate, and beam focus are investigated on model compounds using a series of CO2 and Ar cluster projectiles (cluster size 1000-5000) with the same mass. The results show that the two projectiles are very similar in each of these aspects. Computer simulations comparing the impact of Ar2000 and (CO2)2000 on an organic target also confirm that the CO2 molecules in the cluster projectile remain intact, acting as a single particle of m/z 44. The imaging resolution employing CO2 cluster projectiles is improved by more than a factor of two. The advantage of CO2 versus Ar is also related to the increased stability which, in addition, facilitates the operation of the gas cluster ion beams (GCIB) system at lower backing pressure. Graphical Abstract ᅟ.

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.

On Universality in Sputtering Yields Due to Cluster Bombardment.

Molecular dynamics simulations, in which atomic and molecular solids are bombarded by Arn (n = 60-2953) clusters, are used to explain the physics that underlie the "universal relation" of the sputtering yield Y per cluster atom versus incident energy E per cluster atom (Y/n vs E/n). We show that a better representation to unify the results is Y/(E/U0) versus (E/U0)/n, where U0 is the sample cohesive energy per atom or molecular equivalent, and the yield Y is given in the units of atoms or molecular equivalents for atomistic and molecular solids, respectively. In addition, we identified a synergistic cluster effect. Specifically, for a given (E/U0)/n value, larger clusters produce larger yields than the yields that are only proportional to the cluster size n or equivalently to the scaled energy E/U0. This synergistic effect can be described in the high (E/U0)/n regime as scaling of Y with (E/U0)(α), where α > 1.