J. Phys. Chem. C 2008, 112, 11357–11362
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Preferential Sputtering of DNA Molecules on a Graphite Surface by Ar Cluster Ion Beam Kousuke Moritani,*,† Shingo Houzumi,† Keigo Takeshima,† Noriaki Toyoda,‡ and Kozo Mochiji† Department of Mechanical and System Engineering and Department of Electrical Engineering and Computer Sciences, Graduate School of Engineering, UniVersity of Hyogo, 2167 Shosha, Himeji, Hyogo 671-2201, Japan ReceiVed: February 7, 2008; ReVised Manuscript ReceiVed: April 30, 2008
The process of sputtering by bombardment with gas cluster ions was investigated from the perspective of the kinetic energy per constituent atom (Eatom) of an incident cluster ion, which determines the threshold for the formation of craterlike defects by irradiation of an argon gas cluster ion beam (Ar-GCIB) onto a graphite surface. Furthermore, DNA molecules adsorbed on a graphite surface were preferentially sputtered by adjusting Eatom of the Ar-GCIB down to this threshold, while the substrate graphite surface retained its carbon lattice structure without the formation of craterlike defects. These results indicate that a GCIB could be used as a primary ion beam for secondary ion mass spectrometry (SIMS), which would enable the preferential analysis of an adsorbed layer on a substrate without causing damage to the substrate. 1. Introduction Cluster ion beam technologies have been used in a wide range of applications.1 A cluster ion can transport and locally deposit a large amount of material. Energetic clusters can produce multiple collisions by constituent particles and deposit a high energy density on a solid surface. These characteristic features of cluster ions contribute to the nonlinear effects of sputtering,2 energy loss,3–5 damage,6–8 and secondary ion emission9 in collisions with solid surfaces. Among cluster ion beam technologies, gas cluster ion beams (GCIBs) are one of the most promising tools for nanometer-scale surface modification including surface smoothing,10,11 ion implantation,12 and growth of thin films.13–15 Gas cluster ion beams have also been suggested for use as projectiles for low damage secondary ion mass spectrometry (SIMS).16 SIMS is a powerful tool for the chemical characterization of surfaces, and thus, it is expected to be used for the analysis of organic and biomaterials surfaces,17 as well as for the characterization of DNA microarrays.18 However, the projectiles of an atomic ion beam and a small cluster ion beam damage the molecules and also the substrate, which causes mixing of the chemical species from the adsorbates and substrate in the SIMS spectra. Very recently, a theoretical study predicted that the sputtering yield, sputtered species, and damage to the substrate by sputtering from a thin organic layer can be controlled using large Ar cluster ions,19 which suggests that a GCIB could significantly improve the efficiency and performance of SIMS. However, controlling the sputtering process of a thin organic layer has not yet been achieved experimentally. A GCIB enables the sputtering of a target by extremely lowenergy particles. Because a gas cluster consists of multiple atoms that are bound by weak intermolecular forces, such as van der Waals attractions, the fragile gas cluster ions produce many constituent particles in a collision on a solid surface. The kinetic energy of a cluster ion is distributed among the constituent particles; therefore, the particles produced on the solid surface * Author to whom all correspondence should be addressed. E-mail:
[email protected] † Department of Mechanical and System Engineering. ‡ Department of Electrical Engineering and Computer Sciences.
have very low mean kinetic energies compared to monoatomic ions. The average kinetic energy of each constituent atom can be estimated by dividing the kinetic energy of a gas cluster ion by the number of constituent atoms (cluster size), so that, when a gas cluster ion, which typically consists of several thousands constituent atoms or molecules, is accelerated by an electric field of several kilovolts, each constituent particle has a mean kinetic energy of several electronvolts. An energy range of several electronvolts is comparable to the activation barrier for surface reactions, such as the dissociation of chemical bonds, the adsorption or desorption of molecular and/or atomic species, and also the diffusion of adatoms on a solid surface. Thus, such low-energy particles can induce these surface reactions.20–24 However, energies of several electronvolts are significantly lower than the energy required for sputtering,25,26 which indicates that, by controlling the cluster size and impact energy, the surface reaction can be controlled without damaging the substrate surface. Therefore, size-selected gas cluster ion beams (SS-GCIBs) are of great interest for practical applications in nanofabrication and also as cluster projectiles for SIMS. Recently, it was reported that the probability of forming craterlike damage on a graphite surface, induced by collision with a large gas cluster ion, depends on the kinetic energy per constituent atom (Eatom) of the incident cluster ion.27 This result suggests that bond breaking and desorption processes can be controlled without sputtering of the substrate surface by adjusting the energy per constituent atom of the cluster ion. In this study, the formation of craterlike defects by Ar-GCIB has been investigated. We found that the threshold for craterlike defect formation by an Ar cluster ion is given by Eatom. Moreover, we demonstrate the preferential sputtering of DNA adsorbed on a graphite surface using an Ar-GCIB with Eatom controlled to below the threshold energy of defect formation. To our knowledge, this is the first experimental report of the preferential sputtering of a thin organic layer using large Ar cluster ions. 2. Experimental Section Bombardment with GCIBs was performed using two different apparatuses: a compact-type cluster ion beam apparatus and a
10.1021/jp801121r CCC: $40.75 2008 American Chemical Society Published on Web 07/08/2008
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Figure 1. Typical size distribution of Ar cluster ions (Ei ) 10 keV) generated by a compact-type cluster ion beam apparatus. The cluster size was determined from the TOF spectrum.
size-selected cluster ion beam irradiation apparatus. The compacttype cluster ion beam apparatus was combined with an scanning tunneling microscope (remodeled UMS-1100s, Unisoku Ltd.). The compact-type cluster ion beam apparatus consisted of four differentially pumped chambers that were evacuated using turbomolecular pumps with pumping speeds of 360, 350, 350, and 180 L · s-1. The first chamber was the cluster source chamber, which generated neutral Ar clusters by adiabatic expansion from a Laval-shaped nozzle made of glass with a 0.1-mm-diameter aperture and a 30-mm expansion/cooling zone. The cluster beam was collimated by a conical skimmer with an opening of 0.1-mm diameter and then flowed into the ionization chamber, which contained an electron cathode for ionization, multiple electrodes for acceleration, an ion deflector to generate the pulsed ion beam, and a magnet with a magnetic field of 0.3 T to remove the monoatomic ions from the ion beam. The neutral cluster was ionized by electron impact and accelerated toward the sample by the acceleration voltage, which controlled the impact energy of the cluster ions (Ei). The pressure in the ionization chamber during operation was 6 × 10-4 Pa, which was sufficiently low to avoid any decrease in the kinetic energy of the cluster ion due to collision with residual gas.28,29 The third part of the apparatus was the surface-sputtering chamber, which contained a sample holder and a transfer rod. The base pressure of the sputtering chamber was 5 × 10-8 Pa. The size distribution of clusters generated by the compacttype cluster ion beam apparatus was determined using the timeof-flight (TOF) technique under each set of experimental conditions. The continuous flow of cluster ions generated at the ionizer was chopped by application of a pulsed electric field of 1.0 kV at an ion deflector installed at the ionizer. The pulsed ion beam was detected by a microchannel plate (MCP) 100 mm downstream from the sample. The signal was fed into a digital oscilloscope (Iwatsu-LeCroy LT322) to accumulate the TOF spectra after being amplified by a current amplifier (Stanford Research SR570). The flight length between the ion deflector and the MCP was 550 mm. Figure 1 shows a typical cluster size distribution determined by the TOF method at Ei ) 10 keV. The peak cluster size was 700 atoms/cluster under these conditions. The TOF spectra were broadened because of the cluster size distribution, and the estimated width of the cluster size distribution in terms of the full width at half-maximum (FWHM) was 1250 atoms/cluster. Under these conditions, the
Moritani et al. mean energy per atom was 14 eV/atom, but the distribution ranged from 6.7 to 40 eV/atom at FWHM because Eatom had a distribution related to the cluster size distribution. The highly oriented pyrolytic graphite (HOPG) samples were cleaved with adhesive tape in air. The plasmid DNA sample (pUC18, 26 867 base pairs) was supplied by Takara Bio Inc. The preparation of the DNA sample and the detailed conditions used for the scanning tunneling microscopy (STM) observations are described elsewhere.30 The DNA sample was irradiated by the continuous Ar cluster ion beam along the surface normal. After cluster ion beam irradiation, the sample was brought to the STM chamber under ultrahigh-vacuum (UHV) conditions, and STM images were obtained. In addition, an atomic force microscopy (AFM; Nanoscope IIIa-Dimension 3100, Veeco) image was obtained in air. The background pressure during ArGCIB irradiation was 6 × 10-4 Pa. The size-selected cluster ion beam irradiation apparatus was used for the bombardment of a bare graphite surface with a size-selected Ar cluster ion beam. In this apparatus, large Ar clusters generated during adiabatic expansion were ionized by electron impact. The cluster ion beam was bent with a magnetic field of 1.2 T and separated according to mass. Typical mass resolution (M/∆M) was 3.8 at an Ar cluster size of 3000 atoms/ cluster. Details of the experimental setup and mass resolution are provided elsewhere.31 A bare graphite surface was irradiated with the size-selected Ar-GCIB along the surface normal. After Ar-GCIB irradiation, the sample was taken out into the air atmosphere and then brought into the STM chamber for observation of the structural changes of the surface. In all experiments, the ion dose during beam irradiation was determined from the current density on the sample and the beam irradiation time. All experiments were performed at room temperature. 3. Results and Discussion 3.1. Structural Changes of a Graphite Surface upon GCIB Bombardment. Figure 2a,b shows STM images of a graphite surface after irradiation with a size-selected Ar cluster ion beam and the typical structure of a craterlike defect, respectively. The peak cluster size of the Ar cluster was 1000 atoms/cluster, and Ei was 10 keV, where the mass resolution (M/∆M) was 3.0. Each constituent atom in a cluster had a mean kinetic energy of 10 eV/atom. Eatom had a width from 8.6 to 12 eV/atom (FWHM) because of the M/∆M of the size-selected cluster beam. The cluster ion dose was 2 × 1011 ions · cm-2. The doughnut-shaped traces in this image proved to be craterlike defects induced on the graphite surface by collision with a single Ar cluster ion.7,27 The detailed features of the defects, such as cross-sectional height profile, are described elsewhere.27 Briefly, the bright area indicates a region that is higher than the graphite surface level, and the darker part surrounded by the brighter region indicates a region that is lower than the surface level of the nonirradiated graphite surface. The carbon atoms and their lattice structure can be observed outside the craterlike defect as shown in Figure 2b. Figure 3 shows the probability of the formation of craterlike defects by Ar-GCIB for various cluster sizes and impact energies, scaled by Eatom of the Ar cluster ion. The probability is defined as the number of craters observed divided by the ion dose of the Ar-GCIB. The Ar cluster size was varied from 250 to 8000 atoms/cluster. Here, we defined a craterlike defect as a doughnutlike defect structure. The minimum inner diameter of the doughnutlike trace was 1 nm. A few single-dot-like structures included in the STM images were excluded from the
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Figure 2. STM images of a graphite surface after Ar-GCIB irradiation. The cluster size, impact energy, and the ion dose were 1000 atoms/cluster, Ei)10 keV, and 2 × 1011 ions · cm-2, respectively. The mass resolution and distribution width of Eatom are described in the text. The scanned area was (a) 200 × 200 and (b) 10 × 10 nm2.
Figure 3. Dependence of the crater formation probability on the energy per atom. Ei ) 5, 6.5, 8, 10, and 20 keV. The crater formation probability was defined as the number of craters observed divided by the dose of the Ar cluster ion beam.
counts; such structures comprised 10 keV. Although the sputtering rate is rather low at Ei ) 2 keV, the networklike structure was reduced, and the DNA residues had a clumped shape as the ion dose was increased above 2.5 × 1012 ions · cm-2, similar to Figure 6b. A further increase in the dose above 1.0 × 1013 ions · cm-2 resulted in a reduction of the residue clump size, and an even further increase to 2.5 × 1013 ions · cm-2 completely diminished the DNA molecule residues. Figure 7 and the inset show a widely scanned AFM image and an atomic STM image, respectively, of the DNA-adsorbed graphite surface after irradiation with a cluster ion beam at Ei ) 2 keV and an increased dose of 2.5 × 1013 ions · cm-2. In the AFM image, no residues of the DNA molecules are observed. The histogram analysis of particle height by AFM also indicated that there were no residual DNA molecules (not shown). It should be noted that there were no craterlike defects and the carbon lattice structure of the graphite surface was retained even after irradiation with the cluster ion beam, as shown in the STM image of Figure 7. A series of AFM and STM images indicates that the DNA molecules can be preferentially sputtered without damage to the graphite surface by adjusting the energy per atom of the gas cluster ions. In the energy range below several electronvolts per atom, it is probable that the kinetic energy per constituent atom is sufficiently high to break the chemical bonds in DNA molecules, but not high enough to form craters in the graphite substrate. These results suggest that a very thin layer of organic molecule can be preferentially sputtered away without damaging the substrate by using large gas cluster ions, whereas such sputtering has never been realized by employing monoatomic ions. However, it should be noted that some hillocklike damage was observed that originated from monoatomic or small cluster ions that were included as impurities in the GCIB. This result motivated us to develop a size-selected gas cluster TOF-SIMS,34,35 which is aimed at high-resolution depth profiling or mass analysis of
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Figure 7. AFM image of a DNA-adsorbed graphite surface after irradiation with an Ar cluster ion beam at Ei ) 2 keV. The ion dose was 2.5 × 1013 ions · cm-2. The scanned area was 1.0 × 1.0 µm2. The inset shows an STM image of the same sample (scanned area was 5 × 5 nm2).
biological molecules without damage by the precise control of the energy per constituent atom. Moreover, it should be mentioned that the DNA molecules were perfectly sputtered from the surface at an ion dosage of 2.5 × 1013 ions · cm-2, which is much lower than the number of atoms on the surface. Such a low ion density is generally used under static SIMS measurements that employ monoatomic ions.17 However, the high sputtering rate of DNA by GCIB indicates that the static limit for GCIB-SIMS must be changed to lower ion doses. This is possibly due to the large collision cross section of the gas clusters and the high sputtering rate caused by the lateral sputtering effect.12 4. Conclusion The probability of crater formation on a graphite surface was studied using size-selected Ar-GCIB. It was found that there is a threshold of kinetic energy per atom for crater formation on a graphite surface. We successfully demonstrated that DNA molecules were preferentially sputtered without damage to the graphite substrate surface, by decreasing the kinetic energy of the constituent atoms of the GCIB below the threshold energy for crater formation. This is the first experimental evidence of material-specific sputtering using a large cluster ion, which was suggested only threoretically.19 These results suggest that gas cluster ions can sputter specific materials on a solid surface, which means that cluster-induced surface reactions can be controlled by control of the kinetic energy per atom of the clusters. Acknowledgment. This research was financially supported by the Japan Science and Technology Agency and the Hyogo Science and Technology Association. Figure 6. AFM images of a DNA-adsorbed graphite surface (a) before and (b,c) after irradiation with an Ar cluster ion beam at Ei ) (b) 10 and (c) 2 keV. The peak cluster size was (b) 700 and (c) 1500 atoms/ cluster. The ion dose was 2.5 × 1011 ions · cm-2. The scanned area was 1.0 × 1.0 µm2.
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