Molecular Dynamics Model for Laser Ablation and Desorption of Organic Solids

Desorption and ablation regimes in UV-MALDI: the critical fluence

Although MALDI is a widely used technique, there is so far no theoretical description able to reproduce some critical aspects of the experimental results. For example, there is experimental as well as theoretical controversy regarding the minimum laser fluence, i.e., the so-called fluence threshold (F T), required to evaporate a sample. Furthermore, although the different processes involved in ion production have been the focus of many investigations, the fact is that the primary process for ion formation in MALDI is not desorption but ablation. In this work, we present a new phenomenological approach for understanding MALDI results based on a simple, but physically intuitive, idea consisting of limiting the laser-matter interaction process to three layers. This description allows us to consider the different processes that dominate ion formation, i.e., heat dissipation, as well as the different existing regimes. Concretely, we present the results for three different matrices, i.e., DHB, ferulic acid (FA) and α-cyano-4-hydroxycinnamic acid (CHCA), in the limit of low fluence. The simulations we carried out show great qualitative and pseudo-quantitative agreement with the experimental results. Also, based on the simulation results, it is possible to distinguish clearly between the two dominant regimes, i.e., desorption and ablation, and it is possible, therefore, to estimate the critical fluence (F C) that defines the transition from one regime to another.

Generation and Propagation of MALDI Ion Packets Probed by Sheet-Like Nanosecond UV Laser Light

A sheet-like ultraviolet (UV) probe laser is used to investigate the ejection and propagation of ion packets of matrix CHCA, which are produced by matrix-assisted laser desorption and ionization (MALDI). Laser irradiation of the expanding MALDI plume induced photodissociation of the CHCA-related ions, which existed in a sheet-like volume, leading to their absence in their MALDI signal profiles. The MALDI spectra were measured under varying conditions: the temporal delay of the lasers and the distance of the sheet-like probe laser from the MALDI sample surface. It was found that the center of the (CHCA)H⁺ packets were ejected at 46±11 ns after MALDI laser irradiation, while the (CHCA)₂H⁺ packets were ejected at 64±12 ns, regardless of the magnitude of acceleration static high-voltage in 3.5–5.5 kV. This suggests that (CHCA)₂H⁺ is formed by a proton transfer reaction from (CHCA)H⁺ to (CHCA)₂ in the heated condensed phase and/or near the surface. This study represents the first experimental determination of ion ejection time in the MALDI process, which is also applicable to other species in the MALDI plume.

Biomolecular Clusters Distribution up to Mega Dalton Region Using MALDI-Quadrupole Ion Trap Mass Spectrometer

We present the first report on complete cluster distributions of cytochrome c (molecular weight of 12.4 kDa) and bovine serum albumin ((BSA), molecular weight of 66.4 kDa) with mass-to-charge ratio (m/z) reaching 350,000 and 1,400,000, respectively, by matrix-assisted laser desorption/ionization (MALDI). Large cluster distributions of the analytes were measured by our homemade frequency-scanned quadrupole ion trap (QIT) mass spectrometer with a charge detector. To our knowledge, we report the highest m/z clusters of these two biomolecules. The quantitative results indicate that large clusters ions of cytochrome c and BSA follow the power law (r² > 0.99) with cluster size distribution, which provides experimental evidence for the laser ablation studies of MALDI.

Two mechanisms of nanoparticle generation in picosecond laser ablation in liquids: the origin of the bimodal size distribution

The synthesis of chemically clean and environmentally friendly nanoparticles through pulsed laser ablation in liquids has shown a number of advantages over conventional chemical synthesis methods and has evolved into a thriving research field attracting laboratory and industrial applications. The fundamental understanding of processes leading to the nanoparticle generation, however, still remains elusive. In particular, the origin of bimodal nanoparticle size distributions in femto- and picosecond laser ablation in liquids, where small nanoparticles (several nanometers) with narrow size distribution are commonly observed to coexist with larger (tens to hundreds of nanometers) ones, has not been explained so far. In this paper, joint computational and experimental efforts are applied to understand the mechanisms of nanoparticle formation in picosecond laser ablation in liquids and to explain the bimodal nanoparticle size distributions. The results of a large-scale atomistic simulation reveal the critical role of the dynamic interaction between the ablation plume and the liquid environment, leading to the generation of large nanoparticles through a sequence of hydrodynamic instabilities at the plume-liquid interface and a concurrent nucleation and growth of small nanoparticles in an expanding metal-liquid mixing region. The computational predictions are supported by a series of stroboscopic videography experiments showing the emergence of small satellite bubbles surrounding the main cavitation bubble generated in single pulse experiments. Carefully timed double pulse irradiation triggers expansion of secondary cavitation bubbles indicating, in accord with the simulation results, the presence of localized sites of laser energy deposition (possibly large nanoparticles) injected into the liquid at the early stage of the bubble formation.

Generation of Subsurface Voids, Incubation Effect, and Formation of Nanoparticles in Short Pulse Laser Interactions with Bulk Metal Targets in Liquid: Molecular Dynamics Study

The ability of short pulse laser ablation in liquids to produce clean colloidal nanoparticles and unusual surface morphology has been employed in a broad range of practical applications. In this paper, we report the results of large-scale molecular dynamics simulations aimed at revealing the key processes that control the surface morphology and nanoparticle size distributions by pulsed laser ablation in liquids. The simulations of bulk Ag targets irradiated in water are performed with an advanced computational model combining a coarse-grained representation of liquid environment and an atomistic description of laser interaction with metal targets. For the irradiation conditions that correspond to the spallation regime in vacuum, the simulations predict that the water environment can prevent the complete separation of the spalled layer from the target, leading to the formation of large subsurface voids stabilized by rapid cooling and solidification. The subsequent irradiation of the laser-modified surface is found to result in a more efficient ablation and nanoparticle generation, thus suggesting the possibility of the incubation effect in multipulse laser ablation in liquids. The simulations performed at higher laser fluences that correspond to the phase explosion regime in vacuum reveal the accumulation of the ablation plume at the interface with the water environment and the formation of a hot metal layer. The water in contact with the metal layer is brought to the supercritical state and provides an environment suitable for nucleation and growth of small metal nanoparticles from metal atoms emitted from the hot metal layer. The metal layer itself has limited stability and can readily disintegrate into large (tens of nanometers) nanoparticles. The layer disintegration is facilitated by the Rayleigh-Taylor instability of the interface between the higher density metal layer decelerated by the pressure from the lighter supercritical water. The nanoparticles emerging from the layer disintegration are rapidly cooled and solidified due to the interaction with water environment, with a cooling rate of ∼2 × 10¹² K/s observed in the simulations. The computational prediction of two distinct mechanisms of nanoparticle formation yielding nanoparticles with different characteristic sizes provides a plausible explanation for the experimental observations of bimodal nanoparticle size distributions in laser ablation in liquids. The ultrahigh cooling and solidification rates suggest the possibility for generation of nanoparticles featuring metastable phases and highly nonequilibrium structures.

Molecular dynamics investigation of desorption and ion separation following picosecond infrared laser (PIRL) ablation of an ionic aqueous protein solution

Molecular dynamics simulations were performed to characterize the ablation process induced by a picosecond infrared laser (PIRL) operating in the regime of desorption by impulsive vibrational excitation (DIVE) of a model peptide (lysozyme)/counter-ion system in aqueous solution. The simulations were performed for ablation under typical experimental conditions found within a time-of-flight mass spectrometer (TOF-MS), that is in vacuum with an applied electric field (E = ± 10⁷ V/m), for up to 2 ns post-ablation and compared to the standard PIRL-DIVE ablation condition (E = 0 V/m). Further, a simulation of ablation under an extreme field condition (E = 10¹⁰ V/m) was performed for comparison to extend the effective dynamic range of the effect of the field on charge separation. The results show that the plume dynamics were retained under a typical TOF-MS condition within the first 1 ns of ablation. Efficient desorption was observed with more than 90% of water molecules interacting with lysozyme stripped off within 1 ns post-ablation. The processes of ablation and desolvation of analytes were shown to be independent of the applied electric field and thus decoupled from the ion separation process. Unlike under the extreme field conditions, the electric field inside a typical TOF-MS was shown to modify the ions' motion over a longer time and in a soft manner with no enhancement to fragmentation observed as compared to the standard PIRL-DIVE. The study indicates that the PIRL-DIVE ablation mechanism could be used as a new, intrinsically versatile, and highly sensitive ion source for quantitative mass spectrometry.

Laser-induced phase separation of silicon carbide

Understanding the phase separation mechanism of solid-state binary compounds induced by laser-material interaction is a challenge because of the complexity of the compound materials and short processing times. Here we present xenon chloride excimer laser-induced melt-mediated phase separation and surface reconstruction of single-crystal silicon carbide and study this process by high-resolution transmission electron microscopy and a time-resolved reflectance method. A single-pulse laser irradiation triggers melting of the silicon carbide surface, resulting in a phase separation into a disordered carbon layer with partially graphitic domains (∼2.5 nm) and polycrystalline silicon (∼5 nm). Additional pulse irradiations cause sublimation of only the separated silicon element and subsequent transformation of the disordered carbon layer into multilayer graphene. The results demonstrate viability of synthesizing ultra-thin nanomaterials by the decomposition of a binary system.

The Coupled Chemical and Physical Dynamics Model of MALDI

The coupled physical and chemical dynamics model of ultraviolet matrix-assisted laser desorption/ionization (MALDI) has reproduced and explained a wide variety of MALDI phenomena. The rationale behind and elements of the model are reviewed, including the photophysics, kinetics, and thermodynamics of primary and secondary reaction steps. Experimental results are compared with model predictions to illustrate the foundations of the model, coupling of ablation and ionization, differences between and commonalities of matrices, secondary charge transfer reactions, ionization in both polarities, fluence and concentration dependencies, and suppression and enhancement effects.

Simulation of emission spectra from nonuniform reactive laser-induced plasmas

We demonstrate that chemical reactions leading to the formation of AlO radicals in plasmas produced by ablation of aluminum or Ti-sapphire with ultraviolet nanosecond laser pulses can be predicted by the model of local thermodynamic equilibrium. Therefore, emission spectra recorded with an echelle spectrometer and a gated detector were compared to the spectral radiance computed for uniform and nonuniform equilibrium plasmas. The calculations are based on analytical solutions of the radiation transfer equation. The simulations show that the plasmas produced in argon background gas are almost uniform, whereas temperature and density gradients are evidenced in air. Furthermore, chemical reactions exclusively occur in the cold plume periphery for ablation in air. The formation of AlO is negligible in argon as the plasma temperature is too large in the time interval of interest up to several microseconds. Finally, the validity of local thermodynamic equilibrium is shown to depend on time, space, and on the elemental composition. The presented conclusions are of interest for material analysis via laser-induced breakdown spectroscopy and for laser materials processing.

Ghost peaks observed after atmospheric pressure matrix-assisted laser desorption/ionization experiments may disclose new ionization mechanism of matrix-assisted hypersonic velocity impact ionization

RATIONALE

Understanding the mechanisms of matrix-assisted laser desorption/ionization (MALDI) promises improvements in the sensitivity and specificity of many established applications in the field of mass spectrometry. This paper reports a serendipitous observation of a significant ion yield in a post-ionization experiment conducted after the sample had been removed from a standard atmospheric pressure (AP)-MALDI source. This post-ionization is interpreted in terms of collisions of microparticles moving with a hypersonic velocity into a solid surface. Calculations show that the thermal energy released during such collisions is close to that absorbed by the top matrix layer in traditional MALDI. The microparticles, containing both the matrix and analytes, could be detached from a film produced inside the inlet capillary during the sample ablation and accelerated by the flow rushing through the capillary. These observations contribute some new perspective to ion formation in both laser and laser-less matrix-assisted ionization.

METHODS

An AP-MALDI ion source hyphenated with a three-stage high-pressure ion funnel system was utilized for peptide mass analysis. After the laser had been turned off and the MALDI sample removed, ions were detected during a gradual reduction of the background pressure in the first funnel. The constant-rate pressure reduction led to the reproducible appearance of different singly and doubly charged peptide peaks in mass spectra taken a few seconds after the end of the MALDI analysis of a dried-droplet spot.

RESULTS

The ion yield as well as the mass range of ions observed with a significant delay after a completion of the primary MALDI analysis depended primarily on the background pressure inside the first funnel. The production of ions in this post-ionization step was exclusively observed during the pressure drop. A lower matrix background and significant increase in relative yield of double-protonated ions are reported.

CONCLUSIONS

The observations were partially consistent with a model of the supersonic jet from the inlet capillary accelerating detached particles to kinetic energies suitable for matrix-assisted hypersonic-velocity impact ionization.

MALDI and Related Methods: A Solved Problem or Still a Mystery?

MALDI ionization mechanisms remain a topic of controversy. Some of the major modern models are compared, with emphasis on those of the author. Primary formation, secondary reaction, and loss mechanisms are considered.

Multiscale Aspects of Modeling Gas-Phase Nanoparticle Synthesis

Aerosol reactors are utilized to manufacture nanoparticles in industrially relevant quantities. The development, understanding and scale-up of aerosol reactors can be facilitated with models and computer simulations. This review aims to provide an overview of recent developments of models and simulations and discuss their interconnection in a multiscale approach. A short introduction of the various aerosol reactor types and gas-phase particle dynamics is presented as a background for the later discussion of the models and simulations. Models are presented with decreasing time and length scales in sections on continuum, mesoscale, molecular dynamics and quantum mechanics models.

Plume characteristics and dynamics of UV and IR laser-desorbed oligonucleotides

Laser desorption of dye-tagged oligonucleotides was studied using laser-induced fluorescence imaging. Desorption with ultra violet (UV) and infra-red (IR) lasers resulted in forward directed plumes of molecules. In the case of UV desorption, the initial shot desorbed approximately seven-fold more material than subsequent shots. In contrast, the initial shot in IR desorption resulted in the ejection of less material compared to subsequent shots and these plumes had a component directed along the path of the laser. Thermal equilibrium of the molecules in the plume was achieved after approximately 25 μs with a spread in molecular temperature which was described by a modified Maxwell-Boltzmann equation.

What determines MALDI ion yields? A molecular dynamics study of ion loss mechanisms

Ion recombination in matrix-assisted laser desorption/ionization (MALDI) is as important as any ion formation process in determining the quantity of ions observed but has received comparatively little attention. Molecular dynamics simulations are used here to investigate some models for recombination, including a Langevin-type model, a soft threshold model and a tunneling model. The latter was found to be superior due to its foundations in a widespread physical phenomenon, and its lack of excessive sensitivity to parameter choice. Tunneling recombination in the Marcus inverted region may be a major reason why MALDI is a viable analytical method, by allowing ion formation to exceed ion loss on the time scale of the plume expansion. Ion velocities, photoacoustic transients and pump-probe measurements might be used to investigate the role of recombination in different MALDI matrices, and to select new matrices.

Computational model for multiscale simulation of laser ablation

Multiscale computational approach that combines different methods to study laser ablation phenomenon is presented. The methods include the molecular dynamics (MD) breathing sphere model for simulation of the initial stage of laser ablation, a combined MD - finite element method (FEM) approach for simulation of propagation of the laser-induced pressure waves out from the MD computational cell, and the direct simulation Monte Carlo (DSMC) method for simulation of the ablation plume expansion. The multiscale approach addresses different processes involved in laser ablation with appropriate resolutions and, at the same time, accounts for the interrelations between the processes. A description of the ablation plume appropriate for making a connection between the MD simulation of laser ablation and the DSMC simulation of the ablation plume expansion is discussed.

Pressure Waves in Microscopic Simulations of Laser Ablation Leonid

Laser ablation of organic solids is a complex collective phenomenon that includes processes occurring at different length and time scales. A mesoscopic breathing sphere model developed recently for molecular dynamics simulation of laser ablation and damage of organic solids has significantly expanded the length-scale (up to hundreds of nanometers) and the time-scale (up to nanoseconds) of the simulations. The laser induced buildup of a high pressure within the absorbing volume and generation of the pressure waves propagating from the absorption region poses an additional challenge for molecular-level simulation. A new dynamic boundary condition is developed to minimize the effects of the reflection of the wave from the boundary of the computational cell. The boundary condition accounts for the laser induced pressure wave propagation as well as the direct laser energy deposition in the boundary region.

Molecular dynamics simulations of MALDI: laser fluence and pulse width dependence of plume characteristics and consequences for matrix and analyte ionization

Molecular dynamics simulations of matrix-assisted laser desorption/ionization were carried out to investigate laser pulse width and fluence effects on primary and secondary ionization process. At the same fluence, short (35 or 350 ps) pulses lead to much higher initial pressures and ion concentrations than longer ones (3 ns), but these differences do not persist because the system relaxes toward local thermal equilibrium on a nanosecond timescale. Higher fluences accentuate the initial disparities, but downstream differences are not substantial. Axial velocities of ions and neutrals are found to span a wide range, and be fluence dependent. Total ion yield is only weakly dependent on pulse width, and consistent with experimental estimates. Secondary reactions of matrix cations with analyte neutrals are efficient even though analyte ions are ablated in clusters of matrix.

Matrix suppression and analyte suppression effects of quaternary ammonium salts in matrix-assisted laser desorption/ionization time-of-flight mass spectrometry: an investigation of suppression mechanism

In the matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS) analysis of some quaternary ammonium salts (QASs), very clean spectra of the quaternary ammonium ions were recorded with a strong matrix suppression effect (MSE). The QASs also showed a considerable analyte suppression effect (ASE). It was demonstrated that the MSE and ASE of the QASs can be explained well by the cluster ionization model. According to this model, MALDI ions are formed from charged matrix/analyte clusters. Various analyte ions and matrix ions might coexist in the cluster, and they will compete for the limited number of net charges available. If enough quaternary ammonium ions are present in the cluster, they will take away the net charges, thus resulting in the MSE and ASE. Our results also suggest that 'the cluster ionization model' is not in conflict with 'the theory of ionization via secondary gas-phase reactions'. The initial MALDI ions produced from charged matrix/analyte clusters will collide with other molecules or ions in the MALDI plume. Depending on the properties of the initial ions and the composition of the MALDI plume, secondary gas-phase reactions might result from these collisions. The final ions observed are the combined results of 'cluster ionization' and 'ionization via secondary gas-phase reactions'.

Comparison between vacuum sublimed matrices and conventional dried droplet preparation in MALDI-TOF mass spectrometry

The properties of several cinnamic acid compounds used as matrices for matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) were investigated as standard dried droplet (DD) and vacuum sublimed preparations. The differences between both preparation methods were analyzed with regard to matrix grain size, internal ion energy, initial velocity, analyte intensity, and analyte incorporation depth. Some of the used cinnamic acid derivatives exhibit clearly reduced grain sizes as sublimed preparations compared with standard DD approaches. In these cases higher effective temperatures could be measured accompanied by increased analyte intensities, which can be explained by stronger volatilization processes caused by a hindered heat dissipation resulting in a raised analyte transfer into the gas phase. For all sublimed compounds, a strong increase of the initial ion velocity compared with DD preparations could be measured. Higher initial ion velocities correlate with a decrease in internal ion energy which might be attributed to the very uniform crystal morphology exhibited by sublimed compounds. For sublimed matrices without reduced grain size, at least slightly higher analyte intensities could be detected at raised laser fluences. Analyte accumulation in the uppermost matrix layers or the detected higher ion stability can be explanations for these results.

Dependence of the ejection velocities of laser-ablated ions on the laser wavelength and fluence

Drift measurements of initial ejection velocities of matrix-assisted laser desorption/ionization matrix compounds have been made as a function of ablating laser wavelength and laser fluence. For pulsed laser irradiation just above the matrix ion appearance threshold, initial ejection velocities of protonated molecular ions of an anthranilic acid target increase from ~ 1350 m/s to ~ 1640 m/s (kinetic energies of 1.3 eV and 1.9 eV, respectively) when the ablation laser wavelength is changed from 355 nm to 266 nm. Increasing the laser fluence per pulse by up to a factor of 10 above threshold results in the appearance of a slower component of the ejected ion flux. The results are interpreted by a photomechanical ejection model in which a photoexcited surface molecule instantaneously becomes larger and recoils away from the surface.

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.

Using fluorescence dyes as a tool for analyzing the MALDI process

In a recent paper (Setz, P. D.; Knochenmuss, R. Phys. Chem. A2005, 109, 4030-4037) energy-transfer from excited matrix molecules to fluorescent traps was used to study the role of pooling reactions for the ionization processes in matrix-assisted laser desorption ionization (MALDI) using 2,5-dihydroxybenzoic acid as matrix. Exciton trapping was shown to interfere with matrix ionization. These investigations were extended to analyze the influence of fluorescent traps on both matrix and analyte ions for alpha-cyano-4-hydroxycinnamic acid and further matrices. A strong influence of the fluorescent traps on both matrix and analyte ionization was revealed, depending on the matrix:trap ratio, and manifested itself differently for low and high mass analytes. The observations are rationalized by the intermediate formation of a "hot spot" due to an efficient conversion of electronic excitation energy to vibronic energy within the fluorescent traps. This process favors the desorption and ionization of small vaporizable analytes and compromises the cluster ablation process needed for larger analyte ions.

Elucidating the thermal, chemical, and mechanical mechanisms of ultraviolet ablation in poly(methyl methacrylate) via molecular dynamics simulations

[Figure: see text]. Laser ablation harnesses photon energy to remove material from a surface. Although applications such as laser-assisted in situ keratomileusis (LASIK) surgery, lithography, and nanoscale device fabrication take advantage of this process, a better understanding the underlying mechanism of ablation in polymeric materials remains much sought after. Molecular simulation is a particularly attractive technique to study the basic aspects of ablation because it allows control over specific process parameters and enables observation of microscopic mechanistic details. This Account describes a hybrid molecular dynamics-Monte Carlo technique to simulate laser ablation in poly(methyl methacrylate) (PMMA). It also discusses the impact of thermal and chemical excitation on the ensuing ejection processes. We used molecular dynamics simulation to study the molecular interactions in a coarse-grained PMMA substrate following photon absorption. To ascertain the role of chemistry in initiating ablation, we embedded a Monte Carlo protocol within the simulation framework. These calculations permit chemical reactions to occur probabilistically during the molecular dynamics calculation using predetermined reaction pathways and Arrhenius rates. With this hybrid scheme, we can examine thermal and chemical pathways of decomposition separately. In the simulations, we observed distinct mechanisms of ablation for each type of photoexcitation pathway. Ablation via thermal processes is governed by a critical number of bond breaks following the deposition of energy. For the case in which an absorbed photon directly causes a bond scission, ablation occurs following the rapid chemical decomposition of material. A detailed analysis of the processes shows that a critical energy for ablation can describe this complex series of events. The simulations show a decrease in the critical energy with a greater amount of photochemistry. Additionally, the simulations demonstrate the effects of the energy deposition rate on the ejection mechanism. When the energy is deposited rapidly, not allowing for mechanical relaxation of the sample, the formation of a pressure wave and subsequent tensile wave dominates the ejection process. This study provides insight into the influence of thermal, chemical, and mechanical processes in PMMA and facilitates greater understanding of the complex nature of polymer ablation. These simulations complement experiments that have used chemical design to harness the photochemical properties of materials to enhance laser ablation. We successfully fit the results of the simulations to established analytical models of both photothermal and photochemical ablation and demonstrate their relevance. Although the simulations are for PMMA, the mechanistic concepts are applicable to a large range of systems and provide a conceptual foundation for interpretation of experimental data.

UV-MALDI mass spectrometry analysis of NBD-glycosphingolipids without an external matrix

Each day, advances in the instrumentation and operating protocols bring new applications and insights into the molecular processes of ultra violet-matrix assisted laser desorption/ionization-mass spectrometry (UV-MALDI MS), increasing its potential use. We report here an approach in which mass spectrometry analysis of sphingolipids has been performed using a fluorescent tag (nitrobenz-2-oxa-1, 3-diazole, NBD) covalently linked to the sphingoid base as matrix. Thus, different labeled-sphingolipids were analyzed: ceramide, dihydroceramide, acetylceramide, glucosylceramide, galactosylceramide, galactosyldihydroceramide. In addition an extract of glycosphingolipids obtained from epimastigote forms of Trypanosoma cruzi metabolically labeled with NBD-ceramide was analyzed. The goal of this work is to show that no matrix needs to be added for the mass spectrometry analysis as the same tag used to label the lipids may generate efficiently analyte ions to obtain high quality signals.

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. This review is aimed at graduate students and experimental researchers.

Coupled molecular dynamics-Monte Carlo model to study the role of chemical processes during laser ablation of polymeric materials

The coarse grained chemical reaction model is enhanced to build a molecular dynamics (MD) simulation framework with an embedded Monte Carlo (MC) based reaction scheme. The MC scheme utilizes predetermined reaction chemistry, energetics, and rate kinetics of materials to incorporate chemical reactions occurring in a substrate into the MD simulation. The kinetics information is utilized to set the probabilities for the types of reactions to perform based on radical survival times and reaction rates. Implementing a reaction involves changing the reactants species types which alters their interaction potentials and thus produces the required energy change. We discuss the application of this method to study the initiation of ultraviolet laser ablation in poly(methyl methacrylate). The use of this scheme enables the modeling of all possible photoexcitation pathways in the polymer. It also permits a direct study of the role of thermal, mechanical, and chemical processes that can set off ablation. We demonstrate that the role of laser induced heating, thermomechanical stresses, pressure wave formation and relaxation, and thermochemical decomposition of the polymer substrate can be investigated directly by suitably choosing the potential energy and chemical reaction energy landscape. The results highlight the usefulness of such a modeling approach by showing that various processes in polymer ablation are intricately linked leading to the transformation of the substrate and its ejection. The method, in principle, can be utilized to study systems where chemical reactions are expected to play a dominant role or interact strongly with other physical processes.

Fragmentation of leucine enkephalin as a function of laser fluence in a MALDI TOF-TOF

The effects of laser fluence on ion formation in MALDI were studied using a tandem TOF mass spectrometer with a Nd-YAG laser and alpha-cyano hydrocinnamic acid matrix. Leucine enkephalin ionization and fragmentation were followed as a function of laser fluence ranging from the threshold of ion formation to the maximum available, that is, about 280-930 mJ/mm2. The most notable finding was the appearance of immonium ions at fluence values close to threshold, increasing rapidly and then tapering in intensity with the appearance of typical backbone fragment ions. The data suggest the presence of two distinct environments for ion formation. One is associated with molecular desorption at low values of laser fluence that leads to extensive immonium ion formation. The second becomes dominant at higher fluences, is associated initially with backbone type fragments, but, at the highest values of fluence, progresses to immonium fragments. This second environment is suggestive of ion desorption from large pieces of material ablated from the surface. Arrhenius rate law considerations were used to estimate temperatures associated with the onset of these two processes.

Analysis of arsenic and calcium in soil samples by laser ablation mass spectrometry

We present an analytical procedure based on laser ablation mass spectrometry (LAMS) in order to detect and quantify arsenic and calcium in soil samples and we analyze the diverse factors that influence the precision of LAMS, such as laser fluence and matrix effect. The results indicate that a Zn matrix is a good choice for the analysis of those metals in soil samples. This work also provides a method for the direct determination of As in soil samples whose concentrations are lower than 100 ppm with a 70 ppm minimum detection limits (MDL).

Molecular dynamics simulation of laser desorption of a fragment of protein kinase A from two MALDI matrices

We have carried out molecular dynamics simulations to study the desorption of a dephosphorylated fragment of protein kinase A from two matrices, sinapic acid (SA) and 2,5-dihydroxybenzoic acid (DHB), after laser excitation. We have examined the results as a function of the laser fluence and of the burial depth of the guest peptide in the matrices. In most cases, we found that the energy transferred from the matrix to the guest peptide was not sufficiently large to fragment the peptide. Exceptions occurred when the peptide was more buried. This finding suggested that protein analytes might be less likely to break into smaller fragments if they were placed closer to the surface of the matrix. We have also examined how likely the guest peptide could form small clusters with the matrix molecules and found that the results depended on the degree of burial of the peptide, on the laser fluence, and on which matrix was used. Generally, stable clusters were more likely to be formed for guest peptides that were more buried, at a lower laser fluence, and in the SA rather than the DHB matrix. In addition, we found that the DHB matrix was broken down more easily by the laser than the SA matrix.

Ion formation mechanisms in UV-MALDI

Matrix Assisted Laser Desorption/Ionization (MALDI) is a very widely used analytical method, but has been developed in a highly empirical manner. Deeper understanding of ionization mechanisms could help to design better methods and improve interpretation of mass spectra. This review summarizes current mechanistic thinking, with emphasis on the most common MALDI variant using ultraviolet laser excitation. A two-step framework is gaining acceptance as a useful model for many MALDI experiments. The steps are primary ionization during or shortly after the laser pulse, followed by secondary reactions in the expanding plume of desorbed material. Primary ionization in UV-MALDI remains somewhat controversial, the two main approaches are the cluster and pooling/photoionization models. Secondary events are less contentious, ion-molecule reaction thermodynamics and kinetics are often invoked, but details differ. To the extent that local thermal equilibrium is approached in the plume, the mass spectra may be straightforwardly interpreted in terms of charge transfer thermodynamics.

Coarse-Grained Model of the Interaction of Light with Polymeric Material: Onset of Ablation

A coarse-grained model has been developed for molecular dynamics simulations of the interaction of light with polymeric materials. The photon energy can result in a vibrational excitation (photothermal process) or disruption of a chemical bond (photochemical process) in a polymer. In the latter case, the formation of active radial sites and the occurrence of chemical reactions have to be taken into consideration. The novel feature of this model is the incorporation of chemical reactions into the united atom approximate representation of the polymer structure, which permits the study of laser ablation, degradation, or the effect of various chemical reactions on large time and length scales. The chemical reactions are included in the model in a probabilistic manner as in the kinetic Monte Carlo method. This model adopts physically and experimentally known quantities such as enthalpies and probabilities of reactions. Properties such as laser irradiation time, laser fluence, and wavelength are explicitly included. Moreover, no chemically correct interaction potential is required to incorporate the effects of chemical reactions on the dynamics of the system after energy deposition. We find that the model provides a plausible description of the essential processes. The laser-induced pressure relaxation is the main mechanism responsible for the onset of polymer ablation. Since the pressure relaxation processes are slow, there is a delay in the onset of ablation after the end of the laser pulse as is observed experimentally. The vaporization processes are not efficient for material removal, and the effect is minimal for both photochemical and photothermal processes. A lower fluence is needed for the onset of ablation with photochemical processes than photothermal processes.