Molecular dynamics simulation of amine groups formation during plasma processing of polystyrene surfaces

Plasma Sources Science and Technology PAPER • OPEN ACCESS Molecular dynamics simulation of amine groups formation during plasma processing of polystyrene surfaces To cite this article: Miroslav Michlíek et al 2020 Plasma Sources Sci. Technol. 29 105020 View the article online for updates and enhancements. Recent citations Modeling characterisation of a bipolar pulsed discharge Zoltán Donkó et al - This content was downloaded from IP address 147.229.117.44 on 20/04/2021 at 06:25 Plasma Sources Science and Technology Plasma Sources Sci. Technol. 29 (2020) 105020 (13pp) https://doi.org/10.1088/1361-6595/abb2e8 Molecular dynamics simulation of amine groups formation during plasma processing of polystyrene surfaces Miroslav Michl´ ıˇ cek1, Satoshi Hamaguchi2and Lenka Zaj´ ıˇ cková1,3,∗ 1CEITEC–Central European Institute of Technology & Dept. Phys. Electronics, Faculty of Science, Masaryk University, ˇ Zerot´ ınovo nám. 9, Brno 60177, Czech Republic 2Center for Atomic and Molecular Technologies, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan 3CEITEC–Central European Institute of Technology, Brno University of Technology, Purkynˇova 123, Brno 61200, Czech Republic E-mail: [email protected] and [email protected] Received 28 December 2019, revised 12 August 2020 Accepted for publication 26 August 2020 Published 30 October 2020 Abstract Plasma treatment and plasma polymerization processes aiming to form amine groups on polystyrene surfaces were studied in-silico with molecular dynamics simulations. The simulations were compared with two experiments, (i) plasma treatment in N2/H2bipolar pulsed discharge and (ii) plasma polymerization in cyclopropylamine/Ar radio frequency (RF) capacitively coupled discharge. To model favorable conditions for the incorporation of primary amine groups, we assumed the plasma treatment as the flux of NH2radicals and energetic NH3 ions, and the plasma polymerization as the flux of cyclopropylamine molecules and energetic argon ions. It is shown in both the simulation and the experiment that the polystyrene treatment by the bipolar pulsed N2/H2plasmas with an applied voltage of about ±1kVformed a nitrogen-rich layer of a thickness of only a few nm. The simulations also showed that, as the NH3incident energy increases, the ratio of primary amines to the total number of N atoms on the surface decreases. It is because the energetic ion bombardment brakes up N–H bonds of primary amines, which are mostly brought to the surface by NH2radical adsorption. Our previous experimental work on the CPA plasma polymerization showed that increased RF power invested in the plasma leads to the deposition of films with lower nitrogen content. The MD simulations showed an increase of the nitrogen content with the Ar energy and a limited impact of the energetic bombardment on the retention of primary amines. Thus, the results highlighted the importance of the gas-phase processes on the nitrogen incorporation and primary amines retention in the plasma polymers. However, the higher energy flux towards the growing film clearly decreases amount of hydrogen and increases the polymer cross-linking. Original content from this work may be used under the terms of the Creative Commons Attribution 4.0 licence. Any further distribution of this work must maintain attribution to the author(s) and the title of the work, journal citation and DOI. ∗Author to whom any correspondence should be addressed. Keywords: amine functionalization, plasma treatment, plasma polymerization, molecular dynamics SSupplementary material for this article is available online (Some figures may appear in colour only in the online journal) 0963-0252/20/105020+13$33.00 1 ©2020 The Author(s). Published by IOP Publishing Ltd Printed in the UK Plasma Sources Sci. Technol. 29 (2020) 105020 MMichl ´ ıˇ cek et al 1. Introduction Plasma modification of materials by amine groups is promising for applications in which cells interact with the surface as well as for immobilization of proteins and covalent bonding of drugs [1]. The simplest technique relies on introducing amine groups on the polymer surface by plasma treatment in nitrogen (N2), nitrogen and hydrogen (N2/H2) or ammonia (NH3) discharges [2,3]. An alternative way to create amine surfaces is plasma deposition, either the co-polymerization of hydrocarbon monomers CxHy(e.g., acetylene C2H2, ethylene C2H4) with NH3[4–6] or the plasma polymerizationof various monomers containing amine groups [7–13]. Different approaches have been developed to maximize the concentration of the introduced primary amine groups. Plasma treatment of polymers was intensively studied in many configurations, generally showing optimum for a certain power, mixture, pulsing settings and treatment time [14–16]. Plasmachemical mechanism of primary amine incorporation into hydrocarbonswas studied particularly for N2,N 2/H2and NH3, showing the importance of NH and NH2radicals [2,17]. In absence of hydrogen, the combined action of excited nitrogen N2(A) and ground state N radical was suggested as a plausible mechanism for the formation of labile nitrogen groups, which subsequentlyhydrolyzeto aprimaryamine in the openair [17]. A very high specificity of primary amine incorporationwas, however, reported only in processes without ion bombardment, such as NH3afterglow process ([NH2]/[N] >70%, at [N] ≈5at.%)[3]. Moreover, simple plasma treatment of polymers has only limited stability in time [18]. A possible way to prevent this effect of hydrophobic recovery is to deposit an amine-containing layer. In the case of plasma polymerization, the high retention of the original precursor is usually achieved by using low specific power which, however, has to be balanced with the film stability [1,19,20]. Other approaches have been also reported, recently e.g., method based on the deposition of protonated precursor ions via α–γtransition [21]. Despite these efforts, the amine concentration is usually limited to few atomic percent, especially in conditions with treated surface or growing layer subjected to ion bombardment [8,20,22–24]. It should be empathized, that reported primary amine concentrations based on TFBA derivatization should be considered as an upper estimate due to possible ambiguity of TFBA nucleophilic addition reactions [25]. In plasma processing, energetic ions incident upon the surface typically provide necessary energy to initiate surface chemical reactions, so that surface modification, film deposition, or surface etching can take place at low surface temperaturein non-thermodynamical-equilibriumconditions[26]. Molecular dynamics (MD) simulation for gas-phase ions and atoms interacting with atoms of a solid material can reveal some aspects of such non-equilibrium surface chemical reactions taking place during plasma treatment of polymers at the atomic level [27,28]. As a practical motivation for the paper, we performed induced pluripotent stem (iPS) cells cultivation on non-treated cultivation polystyrene Petri dish and dishes treated by N2/H2 inverter and plasma polymerized cyclopropylamine (CPA). In preliminary experiments, we observed that compared with the control case the inverter plasma-treated dishes and the CPA plasma polymerized dishes help iPS cells retain their multipotency. Although the details of underlying cell-surface interaction remain unclear, the critical part is the selective bindingof mediatingproteins(albumins)and proteinsof extracellular matrix to amine groups. The adsorbed proteins effectivelycreate coatingwith specific ligands requiredfor iPS cells attachment and proliferation [29,30]. Despite this is merely a qualitative observation, this result suggests that both surfaces modified by plasma processes result in surfaces with sufficient concentration of primary amine groups for cell attachment. MD simulations were carried out to assess a possible difference between the plasma treatment of polymers aiming to introduce amine groups at the surface and plasma polymerization in the mixture with high potential to produce amine-rich thin films. The simulation initial conditions were chosen to resemble some relevant experiments into which the simulation results could bring more understandingand to which they could be compared. The first case assumed that NH2radicals arriving at the surface of polystyrene with near thermal energy together with fast NH3molecule having the energy of 100 eV. These conditions can represent some of the best yet realistic situation for the introduction of NH2groups onto polystyrene and can be linked to the N2/H2inverter plasma experiment. A highly simplified view on the plasma polymerization with a precursor containing NH2groups was obtained by the MD simulations in which cyclopropylamine molecules arrived at the polystyrene surface with near thermal energy together with Ar atoms with low energyof 10 eV. Furthermore,the energyof fast particles in respective simulations was varied to study the effect of bombardment energy. Particularly for CPA/Ar mixtures, this can represent the plasma polymerization in radiofrequency (RF) capacitively coupled plasma (CCP) of various configurations and DC self-bias imposed at the substrate electrode. 2. Outline of molecular dynamics simulations A classical MD simulation approach based on the integration of Newton’s equations of motion was used to obtain some insight into the process of plasma-based amine ion implantation and amine plasma polymerization on a polystyrene substrate. Interactions among atoms were described by multibody potential functions are essentially the same as those described in reference [27], which extended Stillinger–Weber type interatomic potential functions [31–34] to double and triple bonds and was used for MD studies on various plasmapolymer interactions [27,35–39]. The details of the potential functions are provided in Supplementary Information (https://stacks.iop.org/PSST/29/105020/mmedia), section 1. A model of polystyrene, a rectangular box with the base dimensions2.32 nm by 2.08nm, was constructedas a substrate for plasma treatment and deposition. The exact lateral dimensions conveniently fit a prebuilt model of polystyrene, which consisted of horizontallyalignedspiral polystyrenechains (see figure S2 in supplementaryinformation).The base dimensions 2 Plasma Sources Sci. Technol. 29 (2020) 105020 MMichl ´ ıˇ cek et al Figure 1. Schemes of the NH2/NH3(left) and CPA/Ar (right) MD simulations. The model consists of the injection of a fast neutral, either NH3or Ar, followed by four cycles with the deposition of NH2radicals or CPA molecules having a near thermal velocity. of about 2 ×2 nm and the height of ≈11 nm were chosen as a compromise between computational time (number of particles and therefore computationaltime increases as the product of length and width), the fidelity of simulated polymer properties (which requires long chains) and the depth of energetic particle penetration that should not reach the bottom of the box. The periodic boundaries were imposed to simulate larger surfaces. Impinging particles were inserted into the simulation with the velocity vector in the direction normal to the surface. All particles were modeled as charge-neutral,assuming the Auger neutralization process for bombarding ions. Each cycle the MD simulation was performed for 2000 fs. For each impact, the simulation was performed in the microcanonical conditions for1000 fs. Then the system was broughtto thermalequilibrium at 300 K by the Langevin and subsequently Berendsen thermostatfor 900 and 100 fs, respectively, applied to all particles. Desorbed particles were removed from the system at the end of the microcanonicalsub-cycleand at the end of the cycle, so their rescaled velocities do not affect the subsequent simulation. With this artificial cooling and relaxation process, excess heat is removed from the system and makes the system ready for the subsequent energetic particle injection. The thermostat algorithm, however, cannot well reproduce long-term thermal relaxation processes of the surface that ensue for microseconds or even milliseconds after each impact of an energetic particle. The simulations of plasma treatment and deposition were performed by alternating the insertion of the energetic particle (i.e. NH3molecule and Ar atom, respectively) and slow neutral particles (i.e. NH2radicals and CPA molecules, respectively). Each simulation was performed with one selected energy of the energetic particle in order to represent the effect of ion bombardment. In the case of the plasma treatment, the cycle with NH3molecule injection with the selected energy from interval 50–200 eV was followed by 4 cycles each with the injection of 25 NH2radicals having near thermal energy of 0.5 eV. Similarly, for the CPA plasma deposition, the cycle with the injection of Ar with the selected energy from interval 10–110 eV was followedby 4 cycles each with the injection of 16 CPA molecules with the near thermal energy of 0.1 eV. The figure 1visually summarizes typical simulation procedures. All the simulations were run for a total of 2000 cycles. Additionally, simulations without energetic particles were run for both presented models. To achieve the same dose of neutrals, the number of cycles was reduced to 1600 with otherwise the same conditions. 3. Experimental details 3.1. N2/H2plasma treatment in bipolar pulsed DC glow discharge The polystyrene dishes (35 mm in diameter) were treated in bipolarpulsed dc glowdischarge ignited in N2/H2. The bottom molybdenum electrode, 190 mm in diameter, was connected to the inverter power supply whereas the top aluminum electrode (80 mm) was grounded (figure 2)[40,41]. The distance between the electrodes was 38 mm. The plasma chamber was pumped by a turbomolecular pump backed by a rotary pump. The pressure during the discharge operation was 250 Pa. The flow rates of N2and H2were 13.3 and 5 sccm, respectively. The applied positive and negative voltage pulses had the width of 1 μs and the applied voltages were 1.3 and −1.1 kV, respectively. The repetition frequency was 5 kHz. The samples were treated for 30 min. 3.2. CPA plasma polymerization in capacitively coupled plasma The CPA plasma polymers (CPA PPs) into the polystyrene dishes and on Si substrates (double-side polished) were prepared in a custom build stainless steel parallel plate reactor similarly as in the previous work of Manakhov et al.[42]. The bottom electrode, 420 mm in diameter, was connected via a matching box to an RF generator working at the frequency of 13.56MHz. The gases were supplied into the chamber through a grounded upper showerhead electrode, 380 mm in diameter. The distance between the electrodes was 55 mm. The bottom electrode with substrates was negatively DC self-biased due to the reactor geometric asymmetry. The reactor was pumped down to ≈10−4Pa by a turbomolecular pump backed by a rotary pump. The deposition was carried out with the rotary pump only. The leak rate including wall desorption was below 0.1 sccm. The CPA was polymerized in square pulsed CPA/Ar plasma at the nominal power of 100 W and the pressure of 50 Pa. The pulse duty cycle and repetition frequency were 33% and 500 Hz, respectively. The flow rate of Ar was set to 28 sccm and regulated by an electronic flow controller Hastings, whereas the flow rate of CPA vapors was set to 2 sccm by a needle valve. The substrates were sputter-cleaned by pulsed 3 Plasma Sources Sci. Technol. 29 (2020) 105020 MMichl ´ ıˇ cek et al Figure 2. Schemes of the bipolar pulsed DC discharge (left) and capacitively coupled plasma (right) reactors. Ar plasma for 10 min prior to the deposition. The deposition time was 60 min. The film thickness measured by ellipsometry in the UV-visible range was 249 nm. 3.3. Sample analysis Thequantitativeatomic composition(withouthydrogen)of the CPA PPs on Si substrate was obtained by monochromatized X-ray photoelectron spectroscopy (XPS) using the Axis Supra spectrometer (Kratos Analytical) at the pass energy of 20 eV. The maximum lateral dimension of the analyzed area was 0.7 mm. A sample differential charging was avoided by a chargeneutralizationin the overcompensatedmode. Thedepth profiling was performed with Ar cluster gun rastering over a square area with the side dimension of 1.9 mm. Argon clusters with an average size of 500 atoms were accelerated to the energy of 20 keV. The quantitative atomic compositions of the samples preparedbytheN 2/H2plasma treatment of the polystyrene were obtained by non-monochromatized XPS ESCA850M (Shimadzu Corporation) using pass energy of 75 eV. The spot diameter was 8 mm. The depth profiling was performed by Ar ion gun with the accelerating voltage of 1 kV. 4. Results and discussion 4.1. Simulation of NH2/NH3surface treatment The MD simulation performed with slow NH2radicals and NH3energetic molecules represents one of the best scenarios for the formation of primary amine groups at the polystyrene surface treated in plasma with support of energetic ions. The resulting structures are evaluated after 2000 simulation cycles, which is sufficient to reach a steady-state of presented observable quantities. As an example, we discuss the simulation with the NH3energy of 100 eV. Few snapshots of the atomic configurations during simulation can be found in the supplementary information, figure S3. Figure 3depicts the depth profiles of elements (a) and interatomic bonds in carbon and nitrogen environments (b and c, respectively). The simulation predicts overall slow etching of the original polystyrene surface. Approximately 0.2 carbon atom is removed per impact of energetic particle. A locally higher concentration of nitrogen than carbon can be noted near the surface in figure 3(a). We will first introduce a naive approach to the calculation of nitrogen content as it would appear by XPS analysis of simulated surfaces and refine it later. Since the nitrogen concentration is not constant, the lower edge of the modified layer was considered as the depth in which the nitrogen intensity reaches half of the maximum. The nitrogen content of the modified layer is calculated only from the volume above the edge of the modified layer. For the comparison with the experimental results, the ratio [N]/([N] + [C]) in the modified/deposited layers is used throughout the text because XPS is not able to detect the hydrogen and [N]/([N] +[C]) ratio is therefore analogous to atomic concentration. In the example given in figure 3, i.e., for the NH3 energy of 100 eV, the [N]/([N] +[C]) is 0.69 and the thickness of nitrogen-containing mixing layer is about 20 Å. The depth profiles of chemical bonds in figures 3(b) and (c) show that N–H and C–N bonds are dominant near the top surface, followed by the number density of cross-linking bonds C–C and N–N bonds. The C–H terminating bond of the original polymer is almost not present. The high concentration of C–N bonds reveals that incorporated NH2radicals are easily dehydrogenated by other incoming radicals and form new C–N bond with neighboring carbon atoms. The high concentration of relatively weak N–N bonds (hydrazinesor diazanes) can be explained by the simultaneous introduction of many NH2radicals. During the impact, NH2radicals readily form hydrazine (N2H4) which is incorporated into the surface. This is further supported by CPA/Ar simulations where N–N bonds are practically not present. The highly cross-linked nature of mixing surface layer is highlighted by low hydrogen content of 44%, significantly lower than the estimate for the CPA simulations even at the highestargonatom energy.Based on the nitrogen environment showninfigure3(c), two sublayers can be roughly distinguished in the nitrogen-rich layer: a highly cross-linked C–N rich sublayer close to the surface, and an N–H rich sublayer closer to the bulk polystyrene. Since the stopping distance of particles with the energy of 100 eV is just a few atomic layers [43], the majority of its energy is released in the topmost layer, causing surface mixing and cross-linking, while deeper layers are relatively unaffected. The evaluation of amine groups in the whole volume gives the content of primary amines of 30%, secondary 39% and tertiary 31%. If we focus only on the top C–N rich sublayer, the relative concentrations shift towards more cross-linked (primary amines is 23%, secondary 4 Plasma Sources Sci. Technol. 29 (2020) 105020 MMichl ´ ıˇ cek et al Figure 3. MD simulation results of polystyrene surface treated by NH2radicals and energetic NH3molecules (100 eV). Figures present (a) depth profiles of elements, (b) different carbon and (c) nitrogen bonds. The depth is given relative to the original polystyrene surface. 42% and tertiary 35%) showing that primary amine groups are preferentially buried deeper as suggested in the previous paragraph. Further analysis also shows the formation of some nitriles (triplebonded C ≡N),which are not presentin CPA/Ar simulations. The reflected and etched species are dominated by nonsticking NH2radicals and volatile products such as N2H4and NH3. Further, less abundant species produced by surface reactions are H2,N 2, CN and CNH. There is no prevalent channel of carbon removal from the original polystyrene surface. Various small molecules (e.g., C2H2, CN or CNH), and even some large ones (typically C5+N10+H15+) contribute to etching. 4.2. Simulation of CPA/Ar plasma deposition Unlike in high voltage N2/H2and NH3plasma treatment [2], the plasma polymerization is performed under much milder energetic conditions because the functional groups of the monomer should be retained as much as possible [20]. Therefore, the MD simulation of CPA/Ar with the Ar atom energy of 10 eV was chosen as a typical example for the discussion of the process in this section. Few snapshots of the atomic configurations during the simulation can be found in the supplementary information, figure S4. The film composition profiles (elements and chemical bonds)obtained from the MD simulation are shown in figure 4. Even at such low energy, the nitrogen concentration extends below the original substrate-level due to partial etching of polystyrene and the creation of the mixing layer. This effect is even more pronouncedfor higher energies as discussed below. It should be noted that, besides Ar kinetic energy, effectively also internal potential energy is introduced with each CPA molecule. Due to high internal bond stress, the CPA carbon ring is prone to relax by ring-opening and formation of a radical. Thus, each CPA molecule brings ≈6.5 eV of internal energy. It can be considered as plasma activation, which is in fact required as non-radical CPA neutrals would have very low sticking probability. The MD simulation predicts slow deposition of nitrogencontaining thin film, with relatively constant concentration profiles. Only about one carbon or nitrogen atom is on average deposited per CPA cycle, i.e., per 64 CPA molecules. The resulting thin film is significantly different from layer predicted in NH2/NH3simulation in both the elemental composition and chemistry. The simulated nitrogen concentration captured by the ratio [N]/([N] +[C]) of 0.18 is only about one third of the value for NH2/NH3. Compared to the NH2/NH3 simulation, the CPA film is also more hydrogenated ([H] > 0.53). As expected from elemental composition, the bond profiles show that dominant bonds are terminating C–H, followed by cross-linking C–C and C–N bond. In the nitrogen environment, the concentration of N–H bonds is significantly lower than cross-linking C–N bonds. It suggests that the majority of nitrogen forms secondary or tertiary amines. The species reflected and sputtered from the surface during the deposition are volatile and non-sticking products of surface reactions. Interestingly, the most prominent fragment is not CPA (C3NH7) reflected from the surface but C2NH5fragment, followed in abundance by NH2,C 3H5and then C3NH7. All these fragments smaller then CPA are products of single dissociation of linear C3NH7. Fragments larger than the original molecule are also present, however, with a lower relative 5 Plasma Sources Sci. Technol. 29 (2020) 105020 MMichl ´ ıˇ cek et al Figure 4. Depth profiles of simulated CPA plasma polymer layer for Ar energy of 10 eV. Figures present (a) depth profiles of elements, (b) different carbon and (c) nitrogen bonds. The depth is given relative to the original polystyrene surface. Figure 5. The composition profiles resulting from NH2/NH3 simulations with the NH3energy of 0, 50, 100 and 200 eV. The steady-state thickness of the nitrogen-rich layer and the nitrogen concentration is depicted for each simulation. The depth is given relative to the original polystyrene surface. abundance which is significantly decreasing with the fragment mass. 4.3. Effect of particle energy in MD simulations To study further the effect of ion bombardment on the plasma treatment and deposition we run series of simulations with varying energy of fast NH3molecule and Ar atom, respectively. 4.3.1. NH2/NH3surface treatment. As demonstrated by the elemental compositionprofiles in figure 5,a nitrogen-richmixing layer is formed for all the tested NH3energies, even if the energy is set to zero. The nitrogen-rich layer has the steadystate thickness of 20 Å being almost unaffected by the energy of NH3molecule. The profiles simulated with 50 eV NH3 are similar to the results with 0 eV. The polystyrene etching becomes noticeable for 100 eV and it is clearly pronounced for 200 eV. The nitrogen content [N]/([N] +[C]), also given in figure 5, is similar for all tested energies except 0 eV simulation, that resulted in a lower value of 0.61. The values of [N]/([N] +[C]) appear unrealistically high when compared to the surface analysis of experimentalsamples but the simulated values need some corrections as discussed in section 4.4. The density of the nitrogen-rich layer formed in the polystyrene (figure 6(a)) exhibits a maximum at 100 eV of NH3and then decreases for the highest energy of 200 eV. We assume that sputtering effects at 200 eV result in fast removal of material from the surface. Even though the energy and momentum are higher in the 200 eV case, the residence time in the surface volume is significantly shortened and overall physical densification by energetic bombardment is, therefore, lower than for the lower bombardment energy. At the same time, the chemical effects of energetic bombardment show simple trends even for the highest energy (figure 6). The content of hydrogen, the relative amount of terminating N–H bonds and weak N–N bonds are decreasing with the NH3 energy, while the relative amount of strong cross-linking C–N bonds in the nitrogen environment increases. Figure 7shows the effect of ion bombardment on the relative concentrations of different amine groups. The content of primary amines of 52% is obtained in the simulation without 6 Plasma Sources Sci. Technol. 29 (2020) 105020 MMichl ´ ıˇ cek et al Figure 6. Properties of simulated nitrogen-rich layers in polystyrene treated by NH3/NH2in dependence on NH3energy: (a) hydrogen concentration and density, and (b) nitrogen chemical environment. Figure 7. Relative concentrations of primary (NH2), secondary (NH1) and tertiary amines (NH0)inNH 2/NH3simulations. energetic bombardment. Although such simulation represents an almost ideal case for the functionalization of polystyrene by primary amine groups, the surface reactions initiated by the NH2radicals are sufficient to reduce the primary amine specificity to approximately a half. The content of primary amines is decreasing with the NH3energy down to ≈30%. Secondary amines exhibit quite stable concentration at ≈35%, slightly increasing to ≈40% for the higher energies. The concentration of highly cross-linked tertiary amines is increasing from 13% to 25% with the NH3bombardment energy. We show products of energetic bombardment by NH3in figure 8depicting number of selected species desorbed or sputtered from the surface during the total of 400 energetic NH3cycles. Populations of all the species are increasing with the energy of incident NH3molecule. The high number of NH2and N2H4even for the lowest energy of 50 eV suggest that these species remain weakly attached to the surface Figure 8. Number of selected species desorbed from the surface during energetic NH3cycles in the NH2/NH3simulations. from the previous cycles and are readily removed even by relatively low energy bombardment. The figure also highlights C2H2molecule as the main channel for carbon etching by high energy bombardment. 4.3.2. CPA/Ar plasma deposition. Figure 9shows that the deposition rate decreases with the energy of Ar atom in CPA/Ar simulation. It suggests that the internal energy of CPA is sufficient for radical formation and promotion of sticking probability even without a surface activation by energetic particles. Increasing energy of Ar atom causes a gradual decrease of the deposition rate which is becoming significantly steeper for the energy of 50 eV and higher. Unlike metals, polymers do not show a threshold energy for sputtering. A variety of physical and chemical effects is induced by particle bombardment, including both atomic and molecular motion regimes of collision cascade inside a polymer chain and collisional mixing [44]. In principle, any particle with kinetic energy higher than the dissociation energy is able to release fragments from the surface, although with a very low probability for small 7 Plasma Sources Sci. Technol. 29 (2020) 105020 MMichl ´ ıˇ cek et al Figure 9. The position of the CPA-film top and bottom surfaces with respect to the surface of the original polystyrene substrate in the dependence on the Ar atom energy as obtained from the MD simulations. The dependence of the resulting CPA-film deposition rate on the Ar atom energy is shown on the right y-axis. energies. The physical sputtering of polymers by very low energy argon ions (<100 eV) was not studied in detail to our knowledge. However, extrapolating from limited published data, sputtering of the polymer can become significant at this energy [45]. The simulated nitrogen content [N]/([N] +[C]) for higher energies of Ar atom is shown in figure 10. Surprisingly, we observe an increasing trend with argonenergy.The data points at higher energies have worse statistics as there is a slower deposition rate and, therefore, a lower number of film particles in the simulation. However, this effect cannot account for the increasing trend. In a highly cross-linked material subjected to energetic bombardment,nitrogen could be considered more volatile than carbon, as it has one bond less. Since the simulated films are still far from fully cross-linked (with about 50% of hydrogen), we conjecture that some geometrical effect of CPA dissociation might be responsible for preferential carbon removal. We further discussed the increasing trend of nitrogen concentration with energy in section 4.4. The increasing cross-linking of simulated CPA thin films with Ar energy is reflected in the concentration of hydrogen and thin film density shown in figure 11(a). Since hydrogen cannot participate in the chain propagation its concentration can be used as a rule of the thumb for polymer cross-linking [46]. The decrease in hydrogen content and densification by bombardmentis reflected also by the calculated density shown in the figure right axis. The simulated densities increase from 1.17 to 1.57g cm−3with increasingbombardmentenergy,consistently with both, the experiment and theory [47]. The trend in cross-linking is further supported by figure 11(b) showing an increasing ratio of C–N bonds in the nitrogen environment. Further analysis of different amine groups in figure 12 reveals that their relative concentrations are relatively stable, particularly for the lower energy of Ar atom. The relative content of primary amines is lower than in the case of NH2/NH3 simulations. Even without energetic bombardment (0 eV), it is limited to 21% and remains similar for low bombardment Figure 10. Nitrogen concentration in CPA plasma polymer as simulated by molecular dynamics. Linear fit is added as a guide to the eye. energy (<50 eV). Finally, for the energy of 50 eV and higher, the relative content of primary amines decreases to ≈16%. The relative content of secondary amines is ≈35%. The concentration of highly cross-linked tertiary amines is increasing with bombardment energy, from ≈40% to ≈50%. Since primary and secondary amines contain both C–N and N–H bonds, the effect of bombardment (figure 11(b)) almost cancels out, yielding a relativelystable concentration,while tertiary amines formed by C–N bonds increase with the Ar energy. Thus the analysis reveals that even though ion bombardment has a significant effect on thin film deposition rate, cross-linking and densification, the impact onto the chemistry is rather limited. We hypothesizethat once the surface is given sufficient energy the system tends to stabilize at a state with minimum energy, that is likely the chemistry with a lower content of primary amines. Moreover, in the experiment, the lower accessibility of primary amines due to increased cross-linking and densification can further contribute to a lower detected concentration of primary amines for higher power and bombardment energy conditions [48]. Comparing populations of species desorbed or sputtered during the energetic Ar cycles (total of 400) in figure 13 gives further hints on bombardment effects on the surface. The majority of species with a high abundance are products of CPA dissociation (C2NH5,C 3H5,NH 2,CH 3) and CPA itself (C3NH7). Populations of all these are largely unaffected by bombardmentand are removed even by Ar bombardment with the lowest energy of 10 eV, suggesting that they are only loosely bonded to the surface and might be eventually released even without bombardment. Contrary, some small molecules (H, H2,C 2H2and C2H2) exhibit clear increasing trend with Ar bombardment energy, implying that they are sputtered by the bombardment. Note that this sputtering is preferential to carbon, as the nitrogen-containing species do not display on average such strong dependence to Ar energy. We assume, the preferential sputtering is a geometrical effect is caused by dissociation and bonding pattern of CPA molecule. 8