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.

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.

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.

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.

Investigation of carbon buildup in simulations of multi-impact bombardment of Si with 20 keV C60 projectiles.

Beams of single C(+) ions are used for the incorporation of Si in the synthesis of thin films of SiC, which have a wide range of technological applications. We present a theoretical investigation of the use of C60 cluster beams to produce thin films of SiC on a Si substrate, which demonstrates that there are potential advantages to using C60(+) cluster ion beams over C(+) single ion beams. Molecular dynamics simulations of the multi-impact bombardment of Si with 20 keV normal incident C60 projectiles are performed to study the buildup of carbon and the formation of a region of Si-C mixing up to a fluence of 1.6 impacts/nm(2) (900 impacts). The active region of the Si solid is defined as the portion of target that contains almost all of the C atoms and the height ranges from 3 nm to more than 7 nm below the average surface height. The C fraction in the active region is calculated as a function of fluence, and a simple model is developed to describe the dependence of the C fraction on fluence. An analytic function from this model is fit to the data from the molecular dynamics simulations and extrapolated to predict the fluence necessary to achieve equilibrium conditions in which the C fraction is constant with fluence. The fraction of C atoms at equilibrium is predicted to be 0.19, and the fluence necessary to achieve 90% of this asymptotic maximum value is equal to 4.0 impacts/nm(2).

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.

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.

Depth profiling of metal overlayers on organic substrates with cluster SIMS.

Molecular depth profiling of organic thin films by erosion with energetic cluster ion beams is a unique aspect of secondary ion mass spectrometry (SIMS) experiments. Although depth profiles of complex multilayer organic structures can be acquired with little damage accumulation and with depth resolution of <10 nm using either C60(+) or Arx(+) with x = 500-5000, hybrid materials consisting of both organic and inorganic layers often yield poor results. To unravel the factors that lead to this difficulty, we developed a model system composed of a thin gold layer of 1.4 to 3.5 nm deposited either on top of or sandwiched within a cholesterol thin film matrix which is several hundred nanometers thick. For these systems, the results show that by erosion with a 40 keV C60(+) beam, reliable depth profiles can always be acquired as indicated by the presence of a steady state molecular ion signal. During the erosion process, however, gold atoms from the gold overlayer are implanted into the cholesterol matrix beneath it, resulting in a reduced sputter yield, an increase in the amount of cholesterol fragmentation and an increase in the thickness of the cluster ion-induced altered layer. The results also show that the effects of the metal film on the organic substrate are independent of the gold film thickness once the film thickness exceeds 1.4 nm. In general, this model study provides mechanistic insight into the depth profiling of heterogeneous thin film structures and offers a possible path for improving the quality of the depth profiles by employing low energy atomic ion sputtering in the region of the metal layer.

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.

An experimental and theoretical view of energetic C60 cluster bombardment onto molecular solids.

Recent experimental measurements and calculations performed by molecular dynamics computer simulations indicate, for highly energetic C60 primary ions bombarding molecular solids, the emission of intact molecules is unique. An energy- and angle-resolved neutral mass spectrometer coupled with laser photoionization techniques was used to measure the polar angle distribution of neutral benzo[a]pyrene molecules desorbed by 20-keV [Formula: see text] primary ions and observed to peak at off-normal angles integrated over all possible emission energies. Similarly, computer simulations of 20-keV C60 projectiles bombarding a coarse-grained benzene system resulted in calculations of nearly identical polar angle distributions. Upon resolving the measured and calculated polar angle distributions, sputtered molecules with high kinetic energies are the primary contributors to the off-normal peak. Molecules with low kinetic energies were measured and calculated to desorb broadly peaked about the surface normal. The computer simulations suggest the fast deposition of energy from the C60 impact promotes the molecular emission by fluid-flow and effusive-type motions. The signature of off-normal emission angles is unique for molecules because fragmentation processes remove molecules that would otherwise eject near normal to the surface. Experimental measurements from a Ni {001} single crystal bombarded by 20-keV [Formula: see text] demonstrate the absence of this unique signature.

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.

Fluid Flow and Effusive Desorption: Dominant Mechanisms of Energy Dissipation after Energetic Cluster Bombardment of Molecular Solids.

The angular distribution of intact organic molecules desorbed by energetic C(60) primary ions was probed both experimentally and with molecular dynamics computer simulations. For benzo[a]pyrene, the angular distribution of intact molecules is observed to peak at off-normal angles. Molecular dynamics computer simulations on a similar system show the mechanism of desorption involves fast deposition of energy followed by fluid-flow and effusive-type emission of intact molecules. The off-normal peak in the angular distribution is shown to arise from emission of intact molecules from the rim of a crater formed during the cluster impact. This signature is unique for molecules because fragmentation processes remove molecules that would otherwise eject at directions near-normal to the surface.

Biological cluster mass spectrometry.

This article reviews the new physics and new applications of secondary ion mass spectrometry using cluster ion probes. These probes, particularly C(60), exhibit enhanced molecular desorption with improved sensitivity owing to the unique nature of the energy-deposition process. In addition, these projectiles are capable of eroding molecular solids while retaining the molecular specificity of mass spectrometry. When the beams are microfocused to a spot on the sample, bioimaging experiments in two and three dimensions are feasible. We describe emerging theoretical models that allow the energy-deposition process to be understood on an atomic and molecular basis. Moreover, experiments on model systems are described that allow protocols for imaging on biological materials to be implemented. Finally, we present recent applications of imaging to biological tissue and single cells to illustrate the future directions of this methodology.

Advanced Monte Carlo approach to study evolution of quartz surface during the dissolution process.

A newly developed Monte Carlo (MC) algorithm designed to study the complex interplay of dissolution and precipitation reactions on mineral surface is presented. This algorithm utilizes existing advanced reactive and configurational-biased MC techniques with new protocols specific for mineral-water interfaces. This time-independent methodology is especially advantageous for studying the kinetically slow quartz-water dissolution process. The aim is to use this method to understand the role of the local arrangement of reactive sites and surface topography in the surface evolution during dissolution. The simulations were performed in neutral pH medium, and two possible dissolution mechanisms were tested. The results indicate that out of the direct and stepwise mechanisms, the direct mechanism leads to complete dissolution that is not experimentally observed in the natural environment. On the other hand, the stepwise dissolution is more realistic, as it resembles the experimentally observed steady-state dissolution of the quartz-water system. These simulations identify the least coordinated surface sites (Q(1)) as the primary reactive site for hydrolysis and precipitation. Other surface sites (Q(2) and Q(3)) also undergo hydrolysis, but they are sterically hindered and are turned passive by precipitating Q(1) groups. The conclusions from the simulations are dominated by the surface topology of quartz; thus, we believe that the results are applicable for other polymorphs of silica and other protonation conditions.

Kinetic nucleation model for free expanding water condensation plume simulations.

Recent direct simulation Monte Carlo (DSMC) simulations of homogeneous condensation in free expansion water plumes [Z. Li, J. Zhong, D. A. Levin, and B. Garrison, AIAA J. 47, 1241 (2009)] show that the nucleation rate is a key factor for accurately modeling condensation phenomenon. In this work, we use molecular dynamics (MD) simulations of a free expansion to explore the microscopic mechanisms of water dimer formation and develop collision models required by DSMC. Bimolecular and termolecular dimer cluster formation mechanisms are considered and the former is found to be the main mechanism in expanding flows to vacuum. MD simulations between two water molecules using the simple point charge intermolecular potential were performed to predict the bimolecular dimer formation probability and the probability was found to decrease with collision energy. The formation probabilities and postcollisional velocity and energy distributions were then integrated into DSMC simulations of a free expansion of an orifice condensation plume with different chamber stagnation temperatures and pressures. The dimer mole fraction was found to increase with distance from the orifice and become constant after a distance of about two orifice diameters. Similar to experiment, the terminal dimer mole fraction was found to decrease with chamber stagnation temperatures and increase linearly with chamber stagnation pressures which is consistent with a bimolecular nucleation mechanism.

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.

Ab initio investigation of dissolution mechanisms in aluminosilicate minerals.

The reactions of aluminosilicate clusters with water are investigated using ab initio calculations. There are several reaction sites on a mineral surface, and, in the case of aluminosilicates, the dissolution chemistry is dictated by chemically distinct surface termination sites: Al and Si. Environmental factors such as pH determine the protonation state and configuration around these terminal sites. The dissolution mechanisms for Al- and Si-terminated sites in protonated, neutral, and deprotonated states are determined using density functional theory calculations. In all protonation states, Si are tetra-coordinated; however, the ability of Al to exist in tetra-, penta-, and hexa-coordination states makes the dissolution mechanisms for the two types of terminal sites fundamentally different. The calculated barrier heights for Al-terminated sites are predicted to be lower than those for Si-terminated sites, a trend that has been observed in experimental studies. The sensitivity of the calculations on the choice of density functionals and basis sets is tested using three functionals: B3LYP, PBE1PBE, and M05-2X, in combination with the 6-311+G(d,p) and MG3S basis sets. For all these calculations, the geometries of the stationary points along the reaction path and the barrier heights are presented.

A molecular dynamics study of the effects of the inclusion of dopants on ablation in polymethyl methacrylate.

Molecular dynamics simulations are used to elucidate mechanisms of ablation in dopant-polymer systems. In one set of simulations, a uniform distribution of thermal absorbers are added to a polymethyl methacrylate substrate and are excited. Chemical decomposition occurs in the regions near the absorbers. Ejection of large pieces of substrate then follows the thermo-chemical breakdown of material. In another set of simulations, an absorbing cluster is embedded in the polymethyl methacrylate substrate at a depth of 50 or 250 A. Only the particles comprising the cluster are excited during the laser pulse. Ejection of material is initiated upon the fracture of the cluster and the cleavage of the surrounding polymer bonds with little chemical damage during the process. These two mechanisms of ejection suggest different pathways of ablation in doped polymer materials.