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.

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.

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.

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.

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

Molecular dynamics (MD) computer simulations are used to model ejection of particles from β-carotene samples bombarded by 15 keV Ar. 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.

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

We present results from experiments and molecular dynamics (MD) simulations obtained with C and Au 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 C and Au-LMIS sources with acceleration potentials generating 50 keV C and 440-540 keV Au . Bombardment-detection was in the same mode as MD simulation, i.

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

A gas cluster ion beam (GCIB) source, consisting of CO 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 CO 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 CO clusters as they impact a surface under a variety of conditions.

"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 C 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.

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.

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.

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.

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.

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.

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.

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.

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 C cluster bombardment onto molecular solids.

Recent experimental measurements and calculations performed by molecular dynamics computer simulations indicate, for highly energetic C 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 C projectiles bombarding a coarse-grained benzene system resulted in calculations of nearly identical polar angle distributions.

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.

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.

Temperature effects in the sputtering of a molecular solid by energetic atomic and cluster projectiles.

Temperature effects in the sputtering of an organic molecule were investigated by subjecting a well defined film of coronene to Au and C primary ions at 100 and 300 K. Strong field photoionization of the sputtered neutral flux was employed to monitor the change in flight time and kinetic energy distributions of intact and fragmented species.

Molecular dynamics simulations of sputtering of Langmuir-Blodgett multilayers by keV C(60) projectiles.

Coarse-grained molecular dynamics computer simulations are applied to investigate fundamental processes induced by an impact of keV C(60) projectile at an organic overlayer composed of long, well-organized linear molecules. The energy transfer pathways, sputtering yields, and the damage induced in the irradiated system, represented by a Langmuir-Blodgett (LB) multilayers composed from molecules of bariated arachidic acid, are investigated as a function of the kinetic energy and impact angle of the projectile and the thickness of the organic system. In particular, the unique challenges of depth profiling through a LB film vs.

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.

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.