Dynamics of l-Phenylalanine Sputtering by Argon ... - ACS Publications

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Dynamics of L‑Phenylalanine Sputtering by Argon Cluster Bombardment Christian Mücksch, Christian Anders, Hubert Gnaser, and Herbert M. Urbassek* Fachbereich Physik und Forschungszentrum OPTIMAS, Universität Kaiserslautern, Erwin-Schrödinger-Straße, D-67663 Kaiserslautern, Germany S Supporting Information *

ABSTRACT: We simulate the impact of an Ar1000 cluster (energy 10 keV, impact angle 55°) into an amorphous L-phenylalanine target. By use of a ReaxFF potential, it is possible to model not only the emission dynamics of intact Phe molecules but also the fragmentation and reaction pathways taken. The simulated sputter yield is in close agreement with experiment. The simulated emission mass spectrum features both emission of large Phen clusters and entrainment of reaction products in the ejected flow, again in agreement with experimental observation. While H abstraction is a common fragmentation channel, the H radicals quickly combine with Phe in the amino group; no isolated H atom is ejected.

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INTRODUCTION Characterization of organic surfaces is one of the key disciplines in nanotechnology. Recently the method of secondary ion mass spectrometry (SIMS) has shown considerable potential to analyze the composition of organic and biological surfaces.1 If cluster ions rather than monoatomics are used as projectiles, it has been shown experimentally that even depth profiling of organic samples becomes possible.2,3 Molecular-dynamics simulation can be used to aid the understanding of underlying physical processes occurring after cluster impact in organic samples.4,5 Such simulations are limited by the available interatomic potentials (or “force fields”) that describe the interactions between atoms constituting the target molecules. Available simulations mostly used the AIREBO potential6 that allows the study of hydrocarbons, including their fragmentation and reactions; relevant studies of cluster-induced processes have been performed, for example, for benzene and polystyrene targets.1,7−10 Recently the so-called ReaxFF potentials have become available that permit performance of reactive molecular dynamics simulations for a larger class of organic molecules containing in addition to C and H also N, O, and other relevant atom species.11−14 Due to their large computational complexity, these potentials have up to now only rarely been employed for the study of irradiation-induced processes.15 We use these potentials to study cluster-impact-induced processes in an organic target, a condensed L-phenylalanine sample. Such a target provides a realistic example of an organic sample beyond the hydrocarbons studied hitherto. In addition, for this material dedicated experimental data are available16−19 that can be used for comparison. Our study concentrates on the sputter yield obtained and the composition of the sputtered flux © 2014 American Chemical Society

as well as reaction products remaining in the target. We use the specific example of Ar1000 cluster impact at an impact energy of 10 eV/atom. As did previous potentials, the ReaxFF potentials describe nonionized molecules; they cannot be used to predict charge states of the emitted particles. While ReaxFF uses atomic partial charges that are equilibrated dynamically for each atom, and thus charge transfer occurring in reactions can be modeled, the overall molecule charge is kept at zero. This means that the calculated spectra pertain to neutral ejecta, while experiment records ions. In addition, experimental data are taken several microseconds after emission, while our simulated data pertain to the emission state 20 ps after impact. These differences have to be kept in mind when simulated and experimental spectra are compared. In order to avoid confusion, we shall term the simulated mass distribution “simulated mass spectrum” in order to differentiate it clearly from the experimentally measured “experimental mass spectrum”.

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METHODS Target Preparation. All simulations were performed with LAMMPS.20 We use a target made of L-phenylalanine (Phe) molecules, C9H11NO2 (see Figure 1). A Phe molecule is composed of 23 atoms and has a total mass of 165 amu. The molecules are initially set up in their zwitterionic form; this is the preferred state under physiological conditions. In addition, biological force fields like CHARMM typically model this state, and also density functional theory (DFT) studies of Phe Received: December 17, 2013 Revised: March 19, 2014 Published: March 19, 2014 7962

dx.doi.org/10.1021/jp412348t | J. Phys. Chem. C 2014, 118, 7962−7970

The Journal of Physical Chemistry C

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Figure 1. L-Phenylalanine in (a) neutral and (b) zwitterionic forms.

crystals use this form.21 To obtain a starting structure, 29 400 Phe molecules were placed in a rectangular box by use of Packmol.22 In order to obtain an amorphous structure, the system was heated within 1 ns from 200 to 2000 K, under reflecting boundary conditions. The heating was then followed by a cooling phase from 2000 to 300 K in 2 ns. This annealing scheme was performed by use of the CHARMM force field23 with a time step of 1 fs; note that such long simulations are not yet possible with the computation-time-expensive ReaxFF potential. Annealing resulted in an average density of 0.788 g· cm−3. This is well below the density of crystalline Lphenylalanine, 1.332 g·cm−3,21 but compares well with the density of crystalline powder, 0.754 g·cm−3.24 After annealing with CHARMM, the system was briefly relaxed at 300 K for 10 ps by use of the ReaxFF potential for amino acids provided by Monti et al.14 Since the impact simulations require a realistic potential for close collisions, we combine the ReaxFF potentials with the Ziegler−Biersack− Littmark (ZBL) potential25 at small atom distances as in ref 15. Here a sinusoidal switching function limits the ZBL potential to small distances, which are adapted for each element (0.9 Å for C, O, and Ar; 0.3 Å for H; and 0.56 Å for N) so that the covalent part of the ReaxFF is not affected. We checked that the insertion of ZBL potential resulted in continuous potentialenergy functions. The distances at which we smoothly switch to the ZBL potential have been optimized for maximum smoothness of the potential and its derivative. The ReaxFF parameters for the Ar interaction with all other species were obtained from a noble-gas parameter set provided by van Duin26 and are presented in the Supporting Information. They describe the van der Waals interaction of Ar atoms. The target postrelaxation with ReaxFF resulted in an increase of the average density to 0.976 g·cm−3. It is known that ReaxFF tends to overestimate densities of molecular solids since the intermolecular van der Waals attraction is not sufficiently taken into account;27 the so-called lg-correction responsible for the improvement of the van der Waals forces is not available for Phe, since this ReaxFF parameter set has been optimized for protein adsorption simulations.14 The final size of the target amounts to 210 Å in depth and 250 Å laterally. We note that after the target preparation only 2.8% of the Phe molecules have remained in zwitterionic form. The annealing process resulted in a rugged organic surface containing cavities inside the bulk (see Figure 2). This appears realistic since in experiment the surface was produced by thermal evaporation; it can hence be assumed that it was neither crystalline nor smooth. Relaxation simulations were performed in an NVT ensemble with a Nosé−Hoover thermostat. Time steps were 1 fs for CHARMM and 0.1 fs for ReaxFF. Impact Simulation. For the impact simulation, bottom and lateral boundaries of the target are subjected to a viscous damping force in a 30 Å thick boundary; the viscous damping constant was set to 37 eV·fs/Å2, similar to our previous study on organic ices.15 The target surface is free. A spherical Ar1000

Figure 2. Perspective view of Ar1000 cluster impacting the amorphous Phe target.

cluster with radius 2.1 nm impacts the L-phenylalanine surface with a total energy of 10 keV at an impact angle of 55°. The impact simulation was performed in an NVE ensemble. The time step was dynamically adapted between 0.001 and 0.1 fs and stayed at the latter value for the major part of the simulation. Time t = 0 denotes the moment when the cluster impinges on the surface. Due to the high computational cost of the ReaxFF potential for our system size of 677 200 atoms and time step of 0.1 fs, we limited the total simulation time to 20.6 ps; this required 174 194 CPU hours of simulation. Figure 3 below confirms that within this time the sputter process is rather complete. Detection Methods. We analyze sputtering and the composition of the sputtered flux with the help of a modified cluster detector.28 Molecules were considered sputtered when they left the interaction zone of the target. The size of the interaction zone (rcut = 8.51 Å), was chosen in agreement with our previous simulation.15 The set of sputtered atoms is decomposed into disjoint sets (“clusters”); the atoms in any such set have zero interaction energy with atoms of other sets but nonzero interaction with at least one other atom of the same set. This detector, but with a smaller cutoff distance, also allows us to identify atoms that belong to the same molecule. Thus C, O, and N atoms are assigned to the same molecule if they are closer than 1.7 Å to another atom; the large value also includes vibrationally excited molecules. For H atoms the cutoff chosen is smaller, 1.3 Å. Local temperatures around an atom are calculated from the kinetic energy in the center-of-mass frame of all atoms within a sphere of radius rcut = 8.51 Å around this atom.29,30 In detail: Around each atom i we define a “local sphere” of radius rcut and volume Vc; it contains Ni atoms. The sphere moves with a center-of-mass velocity Vi. The local temperature Ti is connected via the Boltzmann constant k to the average kinetic energy of motion in the center-of-mass system via 7963



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Figure 3. Time evolution of ejection. (a) Total emission, differentiated with respect to Ar atom re-emission and true sputtering. Data are given both in units of atoms and in Phe-molecule equivalents (see text). (b) Sputtered Phe molecules, including molecules with an added or abstracted H atom. (c) Sputtered reaction products.

3 NkT i i = 2

Ni

∑ j=1

mj 2

amounts to 45.2 nm3, based on the Phe volume of 0.282 nm3 corresponding to our relaxed target density. Intact Phe molecules constitute the majority of the sputtered flux; in the course of emission, they may gain or lose an H atom. Figure 3b quantifies the evolution of these majority species. Note that the large cluster emitted at 10.3 ps is mainly composed of complete Phe. Figure 3c shows the evolution of a number of major reaction products; the full list of products available at the end of the simulation is assembled in Table 1. NH3, NH2, and H2O are the major components. These products are entrained in the emitted flow and are mostly emitted early after impact. In particular they appear to be less enriched in the late emission of large clusters. Figure 4 shows a cross-sectional snapshot through the target at the time of 5.6 ps, when emission has just started. Molecules are colored according to their local temperature. We note for reference that the boiling point of phenylalanine amounts to

(υj − Vi )2 (1)

where j enumerates the atoms in the local sphere, mj is the mass of atom j, and υj is its velocity. In this study, we perform classical simulations. This has the drawback that, besides reactions, vibrations are also treated classically. Collisional energy transfer into vibrations is influenced by the quantization of vibration,31 in particular if the vibrational quantum is large, such as in stiff stretch-bond vibrations. In consequence, our treatment overestimates vibrational excitation, and bond dissociation as its extreme case; however, it appears difficult to quantify this. For single collisions between diatomic molecules, the effects of quantum mechanics on vibrational excitation can be included approximately into a classical calculation;32,33 the resulting effects on vibrational excitation after ion irradiation of a diatomic molecular solid have been discussed in ref 34. We therefore use the local temperature distribution only for qualitative purposes; it informs us where the energy has been deposited in the target and how fast it spreads, and on the internal excitation of ejecta. Snapshots were rendered by use of VMD35 and Tachyon.36

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RESULTS AND DISCUSSION In total we observe that the equivalent of 160 Phe molecules has been sputtered. This total yield is in good agreement with the experimental result of 200 Phe at an impact energy of 11 keV obtained for a broad distribution of projectile cluster sizes centered around 2000.19 In the following we analyze the time dependence of the emission process and the composition of the sputtered flux. Time Evolution of Sputtering. Figure 3a shows the temporal evolution of all atoms and molecules emitted from the target. This figure confirms that sputtering reaches saturation at 20 ps after impact. Ar atoms are emitted continuously from the target throughout the sputtering process. The true sputter yield shows several jumps; these originate from the emission of large clusters from the target surface. Here emission of a large cluster at around 10.3 ps is most prominent. The total target sputter yield, excluding reflected Ar, amounts to 3686 atoms. Since Phe contains 23 atoms, this number can be expressed as Phemolecule equivalents by dividing by 23; thus the sputter yield amounts to 160 Phe equivalents. The sputtered volume thus

Figure 4. Temperature distribution in the target and ejected flux at 5.6 ps. 7964



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Figure 5. Final target surface (shown in silver) overlaid with emitted molecules/atoms that have been projected to their original position. The fate of emitted particles after impact is shown by a color code as explained in the figure. The darker region in the center indicates the crater that has formed; its lighter-shaded environment is the crater rim.

Figure 6. Fragmentation and reaction products at the end of the simulated sputtering process in (a) sputtered flux and (b) target. A detailed list of products is provided in Table 1 7965



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586 K.24 Ejected single atoms are colored blue, as it is not possible to assign them a temperature. Emitted molecules and clusters are colored according to their internal energy. The figure shows that the impinging cluster digs a deep crater of almost hemispherical form into the target, from which material is abundantly ejected. Crater walls and ejecta are strongly energized. We note that the maximum temperatures in the crater walls reach up to 2900 K at this moment. The temporary crater formed is typical of sputtering induced by cluster impact and points at a “gas-flow”37 mechanism of sputtering.38 It is known that reactions occur early after impact while reaction products are continuously swept out of the target with the flow.39 Large clusters originate late and preferably from the crater rim.40 Figure 5 visualizes the place of origin of the emitted molecules/atoms; note how intact Phe are swept away in the forward direction by the obliquely incident cluster projectile. We find that fragmented Phe molecules originated from target zones that were in direct contact with the impacting argon atoms, identified by the crater that evolved underneath. On the other hand, intact Phe emissions originated from the crater rim. These findings are in agreement with previous simulations of cluster-induced fragmentation and sputtering of organic films and overlayers.10,41 In particular, our results parallel those observed for energetic C60 impact into a octane or octatetraene crystal, where the analogous positions of origin of intact species and fragments have been found.42 Similar findings were obtained for a benzene target.43 Molecule Fragmentation and Reactions. Since the ReaxFF potential allows molecules to fragment and react, we investigate the reaction products formed. Some of the product molecules are displayed in Supporting Information. Figure 6 gives an overview of the molecules found in the sputtered flux or remaining in the target after impact. Ar atoms are not included here. The spectrum of the ejecta resembles closely that of the bombarded target. Among the sputtered species, we see some small fragments like NH2 and H2O. At 165 amu, the 82 intact sputtered Phe molecules are displayed; nearby we find the Phe molecules that have lost or gained one or two H atoms. At 294 amu, the reaction product C18H16NO3 of two Phe molecule fragments is seen, in which one NH2 group was lost. A detailed list of products, including those emitted as well as those remaining in the target, is given in Table 1. Intact Phe molecules constitute the largest part of the target, while the produced fragments are partly emitted. The most prominent mass peak in Figure 6 is around the mass of Phe; it is constituted of Phe molecules, possibly after loss or gain of an H atom. A further strong peak shows up at the small product molecule NH3 and, to a lesser amount, at H2O. Among the larger fragments, we find C9H7−10O1−2 (related to phenylpropionate), C7H7 (toluene missing an H atom), and C8H8 (styrene). All these products kept the phenyl ring intact. Note that there are also counts of ±1H variations around these peaks. A common fragmentation pathway is dissociation of an H atom from Phe. These H radicals are quick to react in the target; many combine with a Phe to form Phe + H (see Table 1). We find that these associate with the amino group, modifying NH2 to NH3. This explains why no H radicals have been ejected. This finding is in contrast to previous simulations on hydrocarbons performed with the AIREBO potential. In their

Table 1. List of Reacted Product Molecules in Sputtered Flux and in Target m (amu)

N (sputtered)

1 16 17 17 18 18 40 44 45 57 71 73 74 77 91 92 104 120 131 132 146 147 148 149 150 163 164 165 166 167 294 329 330 331 332

0 11 30 1 6 1 779 1 1 1

2 3 1 1 1 8 3 6 18 1 1 24 82 9

N (target) 289 45 125 1 26 221 2

1 2 13 1 14 1 2 7 16 1 1 20 106 21 2 4701 19975 4250 10

1 6 40 9 1

formula H• NH2 NH3 • OH H2O NH4 Ar CO2 CO2H C2H3NO C3H3O2 C2H3NO2 C2H4NO2 • C6H5 C7H7 C7H8 C8H8 C8H10N C9H7O C9H8O C9H6O2 C9H7O2 C9H8O2 C9H9O2 C9H10O2 Phe − 2H Phe − H Phe, intact Phe + H Phe + 2H C18H16NO3 Phe2 − H Phe2 Phe2 + H Phe2 + 2H

study of C60 impact on octane and octatetraene crystals, Garrison et al.42 found substantial H atom ejection. The different behavior may be traced back to the polarity of our sample, in which H radicals find easy places for attachment, while the hydrocarbons are unpolar. The fate of the H radicals is not irrelevant for SIMS experiments, since it has been proposed that H radicals may help in the ionization process in subsequent impacts.44 We also analyzed the ejected Phe − H molecules. In all cases, the H atom has been dissociated from the COOH carboxyl group. However, in the ejected Phe − 2H molecule, the carboxyl group was left intact and the two H atoms were abstracted from the phenylalanine backbone. We display these structures in Supporting Information. Among the 82 emitted Phe molecules, all but one were in the neutral form; only one was in zwitterionic form. The neutral form is typical for the gas phase, while the zwitterionic form is found in the solvated phase.45,46 Another important finding is that no peptide bonds were formed after impact. In Figure 7 we display the time evolution of the number of fragmented Phe molecules. Data include both ejected molecules and those remaining in the target. More specifically, we monitor the amino acids that lack the NHx (x = 2, 3) amino 7966



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Previous work analyzed reactions in water ice irradiated with 15 keV Au3 and C60 impact.47 These investigations focused on O−H bond breaks and found that bond breaks cease after 0.5− 1.0 ps. The spontaneous impact-induced reactions after Ar1000 impact in our case lasted longer, up to 2.4 ps. This finding demonstrates that large-cluster impact may induce fragmentations on a longer time scale than small-cluster impact. Mass Spectrum of Sputtered Flux. Figure 8 shows a comparison between simulated and experimental mass spectra. In the simulated spectrum (Figure 8a), we show the masses of all clusters. When comparing this quantity to experiment (Figure 8b),19 we must bear in mind that our simulated spectra are obtained only 20.6 ps after impact, where clusters are still quite hot (see Figure 4), while measured spectra are taken several microseconds after emission; in the meantime, some clusters may have broken up. In addition, the calculated spectra pertain to neutral ejecta, while experiment records ions. In Figure 8a, components containing Ar and pure organics are differentiated. A complete analysis of all ejected clusters is available in Supporting Information. There are some clusters containing a considerable amount of Ar. It may be expected that, due to the high internal temperature of the ejected clusters, these Ar atoms will boil out soon. We observe several similarities between experimental and simulated spectra. The regular sequence of Phen features in both spectra; a strong contribution of fragments and reaction products populates the spectrum between the Phen peaks. Certainly, the experimental spectrum is denser than the simulated spectrum; this is primarily due to the fact that we simulated only a single impact. Further impacts would give rise to different fragmentation and reaction patterns. In addition, in the simulation a large cluster with a mass equivalent of 38 Phe is ejected (outside the mass range displayed in Figure 8a). Its composition is 24 intact Phe, 6 Phe − H, 4 Phe + H, 2 NH2, 4 NH3, and 4 C9H9O2. We must expect that this large cluster will break up later during its flight. Its existence demonstrates, however, that (i) particle emission includes a “soft” component, in which large weakly bound clusters are formed late after the impact, and (ii) even these large clusters contain reaction products that result from early violent collision events. Clearly the existence of this cluster in

Figure 7. Time evolution of Phe molecules that lost their amino group, NHx fragments formed, and number of reactions NH2 + H → NH3.

group. This gives us an estimate of the time when fragmentation reactions occur in the target. Most fragmentations occur up to around 2.4 ps after the impact; these are obviously immediately caused by the high pressures and temperatures induced at the impact point. In detail: while the cluster projectile penetrates into the target (t < 0.9 ps), there are still only a few reactions; these set strongly in when the target material has been compressed and heated. The steep rise continues until t = 2.4 ps, during which time both the NH2 and NH3 fragment numbers correspondingly increase. After this time, Phe molecules fragment with an approximately constant rate. We assume this is due to the high temperatures remaining in the target after impact (see Figure 4). In that figure, taken at a time of 5.6 ps, a substantial part of the sample has temperatures above the boiling point and the maximum temperature observed is 2900 K. The number of NH3 fragments increases with the number of fragmented Phe, while the number of NH2 fragments stagnates. We found that this is due to a constant conversion of NH2 to NH3 via addition of free H atoms; the number of these reactions is also displayed in Figure 7.

Figure 8. (a) Simulated mass spectrum of ejected material. (b) Experimental mass spectrum19 from 10 keV impact with an average cluster size of 1500 Ar atoms. 7967



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The crater size of around 1100 Phe equivalents is considerably larger than the sputter yield of 160 Phe equivalents. Only a small part of the molecules missing in the crater have been sputtered; the remainder have been pushed down or laterally away inside the target. The highly porous structure of the amorphous Phe target (see Figure 4) as well as the large compressibility of this material allow for the large size of the temporary crater. Similarly to previous cratering studies in condensed noble-gas targets,49 it must be assumed that this crater will relax on still larger time scales than those available here. Previous studies49 of Ar1000 impacts into an Ar target showed that crater relaxation is a slow process, considerably slower than sputtering. In the case studied there, with 500 eV total impact energy, sputtering was over after around 20 ps, similar to the present case, while the crater needed more than 100 ps for relaxation. The reason for this slow behavior is that the crater walls are still hot after the impact and consist of highly mobile material. Only after the structure has sufficiently cooled down can the final crater structure settle.

the simulation features the processes giving rise to the emission of large Phen clusters such as those observed in experiment.19 Crater Analysis. The impact leaves a crater in the surface (Figure 9). Its size can be determined by counting the number

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CONCLUSIONS

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ASSOCIATED CONTENT

By use of up-to-date classical potentials of the ReaxFF type, it is possible to model the energetic cluster impact on organic solids and the fragmentation and reaction pathways taken. For the particular case simulated here, 10 keV Ar1000 impact on an amorphous Phe sample, we obtain a sputter yield in close agreement with experiment. Among the sputtered particles, 50% are constituted of intact Phe and another 25% are Phe molecules with an H atom added or abstracted, while only 25% consist of fragments and reaction products. The dominant reaction is H abstraction from Phe, often from the carboxyl group. The resulting free H radicals quickly react with Phe at the amino group. This demonstrates that the soft (10 eV/ atom) noble-gas cluster impact leads to strong reactions in the hot and compressed zone under the impacting cluster. A comparison of the simulated mass spectrum with the experimental spectrum is possible qualitatively and features both emission of large Phen clusters and entrainment of reaction products in the ejected flow.

Figure 9. Crater produced in L-phenylalanine surface by Ar cluster impact at the end of the simulation. Ar atoms are shown in green.

S Supporting Information *

Two tables, with complete analysis of all ejected clusters and potential parameters for the Ar interaction, and two figures of intact and reacted Phe molecules. This material is available free of charge via the Internet at http://pubs.acs.org.

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AUTHOR INFORMATION

Corresponding Author

*E-mail [email protected]; phone +49-0-6312053022.

Figure 10. Time evolution of crater volume, measured in Phe molecule equivalents.

Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS We thank Adri von Duin for providing the ReaxFF parameters for proteins and noble gases, and we appreciate the computational resources provided by the computer cluster “Elwetritsch” of the University of Kaiserslautern.

of particle positions that are left empty after impact.48 Figure 10 shows that the time evolution of the crater volume is similar to that of sputtering (Figure 3); after around 10 ps, the crater has found its maximum volume of around 1200 Phe equivalents. At later times the crater volume slightly relaxes. 7968



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