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

ToF-SIMS analysis of ultrathin films and their fragmentation patterns

Organic thin films are of great interest due to their intriguing interfacial and functional properties, especially for device applications such as thin-film transistors and sensors. As their thickness approaches single nanometer thickness, characterization and interpretation of the extracted data become increasingly complex. In this study, plasma polymerization is used to construct ultrathin films that range in thickness from 1 to 20 nm, and time-of-flight secondary ion mass spectrometry coupled with principal component analysis is used to investigate the effects of film thickness on the resulting spectra. We demonstrate that for these cross-linked plasma polymers, at these thicknesses, the observed trends are different from those obtained from thicker films with lower degrees of cross-linking: contributions from ambient carbon contamination start to dominate the mass spectrum; cluster-induced nonlinear enhancement in secondary ion yield is no longer observed; extent of fragmentation is higher due to confinement of the primary ion energy; and the size of the primary ion source also affects fragmentation (e.g., Bi1 versus Bi5). These differences illustrate that care must be taken in choosing the correct primary ion source as well as in interpreting the data.

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.

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.

A Tilted Surface and Ion Carpet Array for SID

The development of native mass spectrometry (MS) has provided structural biologists an additional tool to probe the structures of large macromolecular systems. Surface-induced dissociation (SID) is one activation method used within tandem MS experiments that has proven useful in interrogating the connectivity and topology of biologically-relevant protein complexes. We present here the use of a tilted surface and ion carpet array within a new SID device design, enabling decreased dimensions along the ion path and fewer lenses to tune. This device works well in fragmenting ions of both low (peptides) and high (protein complexes) m/z. Results show that the ion carpet array, while enabling simplification of the back-end of the device, has deficiencies in product collection and subsequently signal at higher SID energies when fragmenting protein complexes. However, the use of the tilted surface is advantageous as an effective way to shorten the device and reduce the number of independent voltages.

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

Molecular dynamics (MD) computer simulations are used to model ejection of particles from β-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.

Effect of energy per atom (E/n) on the Ar gas cluster ion beam (Ar-GCIB) and O2+ cosputter process

Gas cluster ion beam (GCIB) is a promising technique for preserving molecular structures during ion sputtering and successfully profiling biological and soft materials. However, although GCIB yields lower damage accumulation compared with C60+ and monoatomic ion beams, the inevitable alteration of the chemical structure can introduce artifacts into the resulting depth profile. To enhance the ionization yield and further mask damage, a low-energy O2+ (200-500 V) cosputter can be applied. While the energy per atom (E/n) of GCIB is known to be an important factor influencing the sputter process, the manner through which E/n affects the GCIB-O2+ cosputter process remains unclear. In this study, poly(ethylene terephthalate) (PET) was used as a model material to investigate the sputter process of 10-20 kV Ar1000-4000+ (E/n = 2.5-20 eV per atom) with and without O2+ cosputter at different energies and currents. Time-of-flight secondary ion mass spectrometry (ToF-SIMS) with Bi32+ as the primary ion was used to examine surfaces sputtered at different fluences. The sputter craters were also measured by alpha-step and atomic force microscopy in quantitative imaging mode. The SIMS results showed that the steady-state cannot be obtained with E/n values of less than 5 eV per atom due to damage accumulation using single GCIB sputtering. With a moderate E/n value of 5-15 eV per atom, the steady-state can be obtained, but the ∼50% decay in intensity indicated that damage cannot be masked completely despite the higher sputter yield. Furthermore, the surface Young's modulus decreased with increasing E/n, suggesting that depolymerization occurred. At an E/n value of 20 eV per atom, a failed profile was obtained with rapidly decreased sputter rate and secondary ion intensity due to the ion-induced crosslink. With O2+ cosputtering and a moderate E/n value, the oxidized species generated by O2+ enhanced the ionization yield, which led to a higher ion intensity at steady-state in general. Because higher kinetic energy or current density of O2+ led to a larger interaction volume and more structural damage that suppressed molecular ion intensity, the enhancement from O2+ was most apparent with low-energy-high-current (200 V, 80 μA cm-2) or high-energy-low-current (500 V, 5 μA cm-2) O2+ cosputtering with 0.5 μA cm-2 GCIBs. In these cases, little or no intensity drop was observed at the steady-state.

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.

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.

"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^-.

Visualizing molecular distributions for biomaterials applications with mass spectrometry imaging: a review

Mass spectrometry imaging (MSI) is a rapidly emerging field that is continually finding applications in new and exciting areas. The ability of MSI to measure the spatial distribution of molecules at or near the surface of complex substrates makes it an ideal candidate for many applications, including those in the sphere of materials chemistry. Continual development and optimization of both ionization sources and analyzer technologies have resulted in a wide array of MSI tools available, both commercially available and custom-built, with each configuration possessing inherent strengths and limitations. Despite the unique potential of MSI over other chemical imaging methods, their potential and application to (bio)materials science remains in our view a largely underexplored avenue. This review will discuss these techniques enabling high parallel molecular detection, focusing on those with reported uses in (bio)materials chemistry applications and highlighted with select applications. Different technologies are presented in three main sections; secondary ion mass spectrometry (SIMS) imaging, matrix-assisted laser desorption ionization (MALDI) MSI, and emerging MSI technologies with potential for biomaterial analysis. The first two sections (SIMS and MALDI) discuss well-established methods that are continually evolving both in technological advancements and in experimental versatility. In the third section, relatively new and versatile technologies capable of performing measurements under ambient conditions will be introduced, with reported applications in materials chemistry or potential applications discussed. The aim of this review is to provide a concise resource for those interested in utilizing MSI for applications such as biomimetic materials, biological/synthetic material interfaces, polymer formulation and bulk property characterization, as well as the spatial and chemical distributions of nanoparticles, or any other molecular imaging application requiring broad chemical speciation.

Low Temperature Plasma for the Preparation of Crater Walls for Compositional Depth Profiling of Thin Inorganic Multilayers

An indirect, compositional depth profiling of an inorganic multilayer system using a helium low temperature plasma (LTP) containing 0.2% (v/v) SF₆ was evaluated. A model multilayer system consisting of four 10 nm layers of silicon separated by four 50 nm layers of tungsten was plasma-etched for (10, 20, and 30) s at substrate temperatures of (50, 75, and 100) °C to obtain crater walls with exposed silicon layers that were then visualized using time-of-flight secondary ion mass spectrometry (ToF-SIMS) to determine plasma-etching conditions that produced optimum depth resolutions. At a substrate temperature of 100 °C and an etch time of 10 s, the FWHM of the 2nd, 3rd, and 4th Si layers were (6.4, 10.9, and 12.5) nm, respectively, while the 1/e decay lengths were (2.5, 3.7, and 3.9) nm, matching those obtained from a SIMS depth profile. Though artifacts remain that contribute to degraded depth resolutions, a few experimental parameters have been identified that could be used to reduce their contributions. Further studies are needed, but as long as the artifacts can be controlled, plasma etching was found to be an effective method for preparing samples for compositional depth profiling of both organic and inorganic films, which could pave the way for an indirect depth profile analysis of inorganic-organic hybrid structures that have recently evolved into innovative next-generation materials.

On the SIMS Ionization Probability of Organic Molecules

The prospect of improved secondary ion yields for secondary ion mass spectrometry (SIMS) experiments drives innovation of new primary ion sources, instrumentation, and post-ionization techniques. The largest factor affecting secondary ion efficiency is believed to be the poor ionization probability (α⁺) of sputtered material, a value rarely measured directly, but estimated to be in some cases as low as 10^-5. Our lab has developed a method for the direct determination of α⁺ in a SIMS experiment using laser post-ionization (LPI) to detect neutral molecular species in the sputtered plume for an organic compound. Here, we apply this method to coronene (C₂₄H₁₂), a polyaromatic hydrocarbon that exhibits strong molecular signal during gas-phase photoionization. A two-dimensional spatial distribution of sputtered neutral molecules is measured and presented. It is shown that the ionization probability of molecular coronene desorbed from a clean film under bombardment with 40 keV C₆₀ cluster projectiles is of the order of 10^-3, with some remaining uncertainty arising from laser-induced fragmentation and possible differences in the emission velocity distributions of neutral and ionized molecules. In general, this work establishes a method to estimate the ionization efficiency of molecular species sputtered during a single bombardment event. Graphical Abstract <!-- [INSERT GRAPHICAL ABSTRACT TEXT HERE] -->.

Ejection-ionization of molecules from free standing graphene

We present the first data on emission of C60- stimulated by single impacts of 50 keV C602+ on the self-assembled molecular layer of C₆₀ deposited on free standing 2 layer graphene. The yield, Y, of C60- emitted in the transmission direction is 1.7%. To characterize the ejection and ionization of molecules, we have measured the emission of C60- from the surface of bulk C₆₀ (Y = 3.7%) and from a single layer of C₆₀ deposited on bulk pyrolytic graphite (Y = 3.3%). To gain insight into the mechanism(s) of ejection, molecular dynamic simulations were performed. 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. In the case of 50 keV C602+ impacts on graphene plus C₆₀, the C atoms of the projectile collide with those of the target. The knocked-on atoms take on a part of the kinetic energy of the projectile atoms. Another part of the kinetic energy is deposited into the rim around the impact site. The ejection of molecules from the rim is a result of collective movement of the molecules and graphene membrane, where the membrane movement provides the impulse for ejection. The efficient emission of the intact molecular ions implies an effective ionization probability of intact C₆₀. The proposed mechanism of ionization involves the tunneling of electrons from the vibrationally exited area around the hole to the ejecta.

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.

Effect of graphitic layers encapsulating single-crystal apatite nanowire on the osteogenesis of human mesenchymal stem cells

An ideally designed scaffold for tissue engineering must be able to provide an environment that recapitulates the physiological conditions to control stem cell function. Here, we compared vertically aligned single-crystal apatite nanowires sheathed in graphitic layers (SANGs) with single-crystal apatite nanowires (SANs), which had the same geometric properties as--but differing nanotopographic surface chemistry than--SANGs, in order to evaluate the effect of the graphitic layer on the behavior of human mesenchymal stem cells (hMSCs). The difference in nanotopographic surface chemistry did not affect hMSC adhesion, growth, or morphology. However, hMSCs were more effectively differentiated into bone cells on SANGs through interaction with graphitic layers, which later degraded and thereby allowed the cells to continue differentiation on the bare apatite nanowires. Thus, SANGs provide an excellent microenvironment for the osteogenic differentiation of hMCS.

Low-temperature plasma for compositional depth profiling of crosslinking organic multilayers: comparison with C60 and giant argon gas cluster sources

RATIONALE

For organic electronics, device performance can be affected by interlayer diffusion across interfaces. Time-of-flight secondary ion mass spectrometry (TOF-SIMS) can resolve buried structures with nanometer resolution, but instrument artifacts make this difficult. Low-temperature plasma (LTP) is suggested as a way to prepare artifact-free surfaces for accurate determination of chemical diffusion.

METHODS

A model organic layer system consisting of three 1 nm delta layers of 2,9-dimethyl-4,7-diphenyl-1,10-phenanthroline (BCP) separated by three 30 nm layers of tris(8-hydroxyquinolinato)aluminum (Alq3) was used to evaluate the effectiveness of LTP etching for the preparation of crater edge surfaces for subsequent compositional depth profile analysis. This was compared with depth profiles obtained using an instrument equipped with an argon cluster sputter source.

RESULTS

The quality of the depth profiles was determined by comparing the depth resolutions of the BCP delta layers. The full width at half maximum gave depth resolutions of 6.9 nm and 6.0 nm using LTP, and 6.2 nm and 5.8 nm using argon clusters. In comparison, the 1/e decay length of the trailing edge gave depth resolutions of 2.0 nm and 1.8 nm using LTP, and 3.5 nm and 3.4 nm using argon clusters.

CONCLUSIONS

The comparison of the 1/e decay lengths showed that LTP can determine the thickness and composition of the buried structures without instrument artifacts. Although it does suffer from contaminant deposition, LTP was shown to be a viable option for preparing crater edges for a more accurate determination of buried structures.

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).

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

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

Surface analysis of lipids by mass spectrometry: more than just imaging

Mass spectrometry is now an indispensable tool for lipid analysis and is arguably the driving force in the renaissance of lipid research. In its various forms, mass spectrometry is uniquely capable of resolving the extensive compositional and structural diversity of lipids in biological systems. Furthermore, it provides the ability to accurately quantify molecular-level changes in lipid populations associated with changes in metabolism and environment; bringing lipid science to the "omics" age. The recent explosion of mass spectrometry-based surface analysis techniques is fuelling further expansion of the lipidomics field. This is evidenced by the numerous papers published on the subject of mass spectrometric imaging of lipids in recent years. While imaging mass spectrometry provides new and exciting possibilities, it is but one of the many opportunities direct surface analysis offers the lipid researcher. In this review we describe the current state-of-the-art in the direct surface analysis of lipids with a focus on tissue sections, intact cells and thin-layer chromatography substrates. The suitability of these different approaches towards analysis of the major lipid classes along with their current and potential applications in the field of lipid analysis are evaluated.

Exploring the surface sensitivity of TOF-secondary ion mass spectrometry by measuring the implantation and sampling depths of Bi(n) and C60 ions in organic films

The surface sensitivity of Bi(n)(q+) (n = 1, 3, 5, q = 1, 2) and C(60)(q+) (q = 1, 2) primary ions in static time-of-flight secondary ion mass spectrometry (TOF-SIMS) experiments were investigated for molecular trehalose and polymeric tetraglyme organic films. Parameters related to surface sensitivity (impact crater depth, implantation depth, and molecular escape depths) were measured. Under static TOF-SIMS conditions (primary ion doses of 1 × 10(12) ions/cm(2)), the 25 keV Bi(1)(+) primary ions were the most surface sensitive with a molecular escape depth of 1.8 nm for protein films with tetraglyme overlayers, but they had the deepest implantation depth (~18 and 26 nm in trehalose and tetraglyme films, respectively). The 20 keV C(60)(+2) primary ions were the second most surface sensitive with a slightly larger molecular escape depth of 2.3 nm. The most important factor that determined the surface sensitivity of the primary ion was its impact crater depth or the amount of surface erosion. The most surface sensitive primary ions, Bi(1)(+) and C(60)(+2), created impact craters with depths of 0.3 and 1.0 nm, respectively, in tetraglyme films. In contrast, Bi(5)(+2) primary ions created impact craters with a depth of 1.8 nm in tetraglyme films and were the least surface sensitive with a molecular escape depth of 4.7 nm.

ToF-SIMS Analysis of Adsorbed Proteins: Principal Component Analysis of the Primary Ion Species Effect on the Protein Fragmentation Patterns

In time-of-flight secondary ion mass spectrometry (ToF-SIMS), the choice of primary ion used for analysis can influence the resulting mass spectrum. This is because different primary ion types can produce different fragmentation pathways. In this study, analysis of single-component protein monolayers were performed using monatomic, tri-atomic, and polyatomic primary ion sources. Eight primary ions (Cs(+), Au(+), Au(3) (+), Bi(+), Bi(3) (+), Bi(3) (++), C(60) (+)) were used to examine to the low mass (m/z < 200) fragmentation patterns from five different proteins (bovine serum albumin, bovine serum fibrinogen, bovine immunoglobulin G and chicken egg white lysozyme) adsorbed onto mica surfaces. Principal component analysis (PCA) processing of the ToF-SIMS data showed that variation in peak intensity caused by the primary ions was greater than differences in protein composition. The spectra generated by Cs(+), Au(+) and Bi(+) primary ions were similar, but the spectra generated by monatomic, tri-atomic and polyatomic primary ion ions varied significantly. C(60) primary ions increased fragmentation of the adsorbed proteins in the m/z < 200 region, resulting in more intense low m/z peaks. Thus, comparison of data obtained by one primary ion species with that obtained by another primary ion species should be done with caution. However, for the spectra generated using a given primary ion beam, discrimination between the spectra of different proteins followed similar trends. Therefore, a PCA model of proteins created with a given ion source should only be applied to datasets obtained using the same ion source. The type of information obtained from PCA depended on the peak set used. When only amino acid peaks were used, PCA was able to identify the relationship between proteins by their amino acid composition. When all peaks from m/z 12-200 were used, PCA separated proteins based on a ratio of C(4)H(8)N(+) to K(+) peak intensities. This ratio correlated with the thickness of the protein films and Bi(1) (+) primary ions produced the most surface sensitive spectra.

Non-monotonic material contrast in scanning ion and scanning electron images

30keV Ga(+) focused ion beam induced secondary electron (iSE) imaging was used to determine the relative contrast between several materials. The iSE signal compared from C, Si, Al, Ti, Cr, Ni, Cu, Mo, Ag, and W metal layers does not decrease with an increase in target atomic number Z(2), and shows a non-monotonic relationship between contrast and Z(2). The non-monotonic relationship is attributed to periodic fluctuations of the stopping power and sputter yield inherent to the ion-solid interactions. In addition, material contrast from electron-induced secondary electron (eSE) and backscattered electron (BSE) images using scanning electron microscopy (SEM) also shows non-monotonic contrast as a function of Z(2), following the periodic behavior of the stopping power for electron-solid interactions. A comparison of the iSE and eSE results shows similar relative contrast between the metal layers, and not complementary contrast as conventionally understood. These similarities in the contrast behavior can be attributed to similarities in the periodic and non-monotonic function defined by incident particle-solid interaction theory.

Three-dimensional mass spectral imaging of HeLa-M cells--sample preparation, data interpretation and visualisation

Time-of-flight secondary ion mass spectrometry (ToFSIMS) is being applied increasingly to the study of biological systems where the chemical specificity of mass spectrometry and the high lateral resolution imaging capabilities can be exploited. Here we report a comparison of two cell sample preparation methods and demonstrate how they influence the outcome of the ToFSIMS analysis for three-dimensional (3D) imaging of biological cells using our novel buncher-ToF instrument (J105 3D Chemical Imager) equipped with a C(60) primary ion beam. Cells were analysed fixed and freeze-dried and non-fixed, frozen-hydrated. It is concluded that maintaining the cells in a non-fixed frozen-hydrated state during the analysis helps reduce chemical redistribution, producing cleaner spectra and improved chemical contrast in both 2D and 3D imaging. Insights into data interpretation are included and we present methods for 3D reconstruction of the data using multivariate analysis techniques.

ToF-SIMS Depth Profiling of Trehalose: The Effect of Analysis Beam Dose on the Quality of Depth Profiles

In static secondary ion mass spectrometry (SIMS) experiments, an analysis dose of 10(12) ions/cm(2) typically produces optimum results. However, the same dose used in dual beam depth profiling can significantly degrade the signal. This is because during each analysis cycle a high-energy beam is rastered across the same x-y location on the sample. If a sufficient amount of sample is not removed during each sputter cycle, the subsequent analysis cycle will sample a volume degraded by the previous analysis cycles. The dimensionless parameter R' is used to relate the amount of damage accumulated in the sample to the amount of analysis beam dose used relative to the etching beam. Depth profiles from trehalose films spin-cast onto silicon wafers acquired using Bi(1) (+) and Bi(3) (+) analysis beams were compared. As R' increased, the depth profile and the depth resolution (interface width) both degraded. At R' values below 0.04 for both Bi(1) (+) and Bi(3) (+), the shape of the profile as well as the depth resolution (9 nm) indicated that dual beam analysis can be superior to C(60) single beam depth profiling.

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.

Strong-field Photoionization of Sputtered Neutral Molecules for Molecular Depth Profiling

Molecular depth profiles of an organic thin film of guanine vapor deposited onto a Ag substrate are obtained using a 40 keV C(60) cluster ion beam in conjunction with time-of-flight secondary ion mass spectrometric (ToF-SIMS) detection. Strong-field, femtosecond photoionization of intact guanine molecules is used to probe the neutral component of the profile for direct comparison with the secondary ion component. The ability to simultaneously acquire secondary ions and photoionized neutral molecules reveals new fundamental information about the factors that influence the properties of the depth profile. Results show that there is an increased ionization probability for protonated molecular ions within the first 10 nm due to the generation of free protons within the sample. Moreover, there is a 50% increase in fragment ion signal relative to steady state values 25 nm before reaching the guanine/Ag interface as a result of interfacial chemical damage accumulation. An altered layer thickness of 20 nm is observed as a consequence of ion beam induced chemical mixing. In general, we show that the neutral component of a molecular depth profile using the strong-field photoionization technique can be used to elucidate the effects of variations in ionization probability on the yield of molecular ions as well as to aid in obtaining accurate information about depth dependent chemical composition that cannot be extracted from TOF-SIMS data alone.

Cluster secondary ion mass spectrometry of polymers and related materials

Cluster secondary ion mass spectrometry (cluster SIMS) has played a critical role in the characterization of polymeric materials over the last decade, allowing for the ability to obtain spatially resolved surface and in-depth molecular information from many polymer systems. With the advent of new molecular sources such as C(60)(+), Au(3)(+), SF(5)(+), and Bi(3)(+), there are considerable increases in secondary ion signal as compared to more conventional atomic beams (Ar(+), Cs(+), or Ga(+)). In addition, compositional depth profiling in organic and polymeric systems is now feasible, without the rapid signal decay that is typically observed under atomic bombardment. The premise behind the success of cluster SIMS is that compared to atomic beams, polyatomic beams tend to cause surface-localized damage with rapid sputter removal rates, resulting in a system at equilibrium, where the damage created is rapidly removed before it can accumulate. Though this may be partly true, there are actually much more complex chemistries occurring under polyatomic bombardment of organic and polymeric materials, which need to be considered and discussed to better understand and define the important parameters for successful depth profiling. The following presents a review of the current literature on polymer analysis using cluster beams. This review will focus on the surface and in-depth characterization of polymer samples with cluster sources, but will also discuss the characterization of other relevant organic materials, and basic polymer radiation chemistry.

ToF-SIMS Depth Profiling of Organic Films: A Comparison between Single Beam and Dual-beam Analysis

In dual-beam depth profiling, a high energy analysis beam and a lower energy etching beam are operated in series. Although the fluence of the analysis beam is usually kept well below the static SIMS limit, complete removal of the damage induced by the high energy analysis beam while maintaining a good depth resolution is difficult. In this study a plasma polymerized tetraglyme film is used as the model organic system and the dimensionless parameter R, (analysis beam fluence)/(total ion fluence), is introduced to quantify the degree of sample damage induced as a function of the analysis beam fluence. It was observed for a constant C(60) (+) etching beam fluence, increasing the analysis fluence (and consequently increasing the R parameter) increased in the amount of damage accumulated in the sample. For Bi(n) (+) (n = 1 and 3) and C(60) (+) depth profiling, minimal damage accumulation was observed up to R = 0.03, with a best depth resolution of 8 nm. In general, an increase in the Bi(n) (+) analysis fluence above this value resulted in a decrease in the molecular signals of the steady state region of the depth profile and a degradation of the depth resolution at the polymer/substrate interface.

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. a more isotropic solid are discussed.The results indicate that the trajectories of projectile fragments and, consequently, the primary energy can be channeled by the geometrical structure of the overlayer. Although, a similar process is known from sputtering of single crystals by atomic projectiles, it has not been anticipated to occur during C(60) bombardment due to the large size of the projectile. An open and ordered molecular structure of LB films is responsible for such behavior. Both the extent of damage and the efficiency of sputtering depend on the kinetic energy, the impact angle, and the layer thickness. The results indicate that the best depth profiling conditions can be achieved with low-energy cluster projectiles irradiating the organic overlayer at large off-normal angles.

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.

Fundamental studies of molecular depth profiling and 3D imaging using Langmuir-Blodgett films as a model

Molecular depth profiling and three-dimensional imaging using cluster projectiles and SIMS have become a prominent tool for organic and biological materials characterization. To further explore the fundamental features of cluster bombardment of organic materials, especially depth resolution and differential sputtering, we have developed a reproducible and robust model system consisting of Langmuir-Blodgett (LB) multilayer films. Molecular depth profiles were acquired, using a 40-keV C(60) (+) probe, with LB films chemically alternating between barium arachidate and barium dimyristoyl phosphatidate. The chemical structures were successfully resolved as a function of depth. The molecular ion signals were better preserved when the experiment was performed under cryogenic conditions than at room temperature. A novel method was used to convert the scale of fluence into depth which facilitated quantitative measurement of the interface width. Furthermore, the LB films were imaged as a function of depth. The reconstruction of the SIMS images correctly represented the original chemical structure of the film. It also provided useful information about interface mixing and edge effects during sputtering.