Comparison and Contrast Analysis of Adsorption Geometries of

Nov 21, 2012 - Department of Chemistry, Sookmyung Women's University, Seoul 140-742, Republic of Korea. •S Supporting Information. ABSTRACT: The ...
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Comparison and Contrast Analysis of Adsorption Geometries of Phenylalanine versus Tyrosine on Ge(100): Effect of Nucleophilic Group on the Surface Sena Yang,† Heeseon Lim,† Eun Hee Park,† Yaewon Kim,‡ Young Hwan Min,† Hee-Seung Lee,*,† Sehun Kim,*,† and Hangil Lee*,‡ †

Molecular-Level Interface Research Center, Department of Chemistry, KAIST, Daejeon 305-701, Republic of Korea Department of Chemistry, Sookmyung Women’s University, Seoul 140-742, Republic of Korea

‡

S Supporting Information *

ABSTRACT: The discrepancy of geometric configuration between phenylalanine and tyrosine adsorbed on Ge(100) surfaces was investigated using scanning tunneling microscopy (STM) in conjunction with density functional theory (DFT) calculations and core-level photoemission spectroscopy (CLPES). The study focused on the role of nucleophilic group (hydroxyl group) on phenyl ring of tyrosine, and we elucidated the difference of the adsorption geometry between phenylalanine and tyrosine on Ge(100) surfaces. We first confirmed that the “O−H dissociated−N dative bonded structure” was the most favorable structure in both molecules at low coverage by results of CLPES and DFT calculations. Geometric differences for the adsorption configurations between phenylalanine and tyrosine were observed: the phenyl ring of phenylalanine was aligned axially with respect to the Ge(100) surface, whereas that of tyrosine was tilted, as determined by DFT calculations. In sequence, we found out the results of STM images to confirm DFT results. We determined the different geometric configurations are attributed to the nucleophilic hydroxyl group of tyrosine, which creates an uneven charge distribution.

1. INTRODUCTION As the industrial applications of semiconductors are extended, research into the chemical modifications and molecular adsorption structures adsorbed on semiconductor surfaces has become important in a variety of industrial and academic fields.1−3 Organic materials may be functionalized to tune their chemical properties via substitution or addition reactions, and the adsorption of such organic materials may be readily exploited in applications such as biosensors, biochips, and electronic devices.4−8 Recently, several studies have examined the adsorption of a variety of bioorganic molecules on surfaces.9−12 Specially, research into the adsorption of amino acids, which include carboxyl, amino, sulfur, or a variety of functional groups, onto semiconductor surfaces is expected to provide fundamental knowledge of semiconductor functionalization for various biorelated applications.13−16 Among various semiconductors, germanium (Ge) is a potential candidate for the new channel material because of its superior electronic properties.17 Specifically, Ge(100)-2×1 reconstructed surfaces feature tilted dimers with a strong σ bond and a weak π bond at room temperature. The tilted dimers create an uneven charge distribution over the dimer, resulting in an electron-rich (nucleophilic) “up” atom and an electron-deficient (electrophilic) “down” atom, and thus the up and down atoms of the © 2012 American Chemical Society

dimers show zwitterionic character and function as a Lewis base and acid, respectively, which makes Ge(100)-2×1 reconstructed surfaces an excellent substrate for various adsorption reactions with multifunctionalized molecule.4,18 We have examined the adsorption structures and behaviors of 10 natural amino acids on Ge(100)-2×1 surfaces.19−26 We have identified the general trend among the adsorption structures of amino acids that the “O−H dissociated−N dative bonded structure” is the most stable structure at low coverage. We also have investigated the effects of functional groups and steric hindrance on the adsorption geometries to explain the observed differences. In this study, we focused on the differences in geometric configurations between phenylalanine and tyrosine in spite of their structural similarities when they adsorb on Ge(100) surfaces. Phenylalanine and tyrosine are composed primarily of a central carbon atom bonded to a carboxyl group (−COOH), an amino group (−NH2), and either a phenyl or a phenol ring, respectively. Except for the presence of the hydroxyl group on the phenyl ring of tyrosine, the two amino acids have identical Received: August 30, 2012 Revised: November 15, 2012 Published: November 21, 2012 25840

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structures. We assume that the hydroxyl group of tyrosine differentiates the two amino acids adsorption configurations. The goal of this study is to clarify a discrepancy of geometric configurations between phenylalanine (Scheme 1a) and

DFT calculations were used to analyze the energetics of the potential pathways for the tyrosine and phenylalanine reactions on the Ge(100) surface. All DFT calculations of the adsorption energies were performed using the JAGUAR 9.1 software package, which applies a hybrid density functional method and includes Becke’s three-parameter nonlocal-exchange functional with the correlation functional of Lee−Yang−Parr (B3LYP).28 The calculations were performed using a six-dimer (Ge49H40) cluster model. The geometries of important local minima on the potential energy surface were determined at the B3LYP/ LACVP** level of theory. The LACVP** basis set is a mixed basis set that uses the LACVP basis set to describe the Ge atoms and the 6-31G basis set to describe the remaining atoms. The LACVP basis set is useful for describing atoms heavier than Ar in the periodic table and is based on the Los Alamos effective core potentials developed by Hay and Wadt.29 Optimization of each cluster was performed by fixing the bottom two layers of the Ge atoms in the ideal Ge crystal positions, permitting the top layer of Ge atoms (including the dimer atoms) and the atoms of the chemisorbed adsorbate to relax. The geometries of important local minima and transition states on each energy diagram were calculated. The local minima and transition states in the optimized structures were verified using the same set of basis sets.30 STM observations were performed in an ultrahigh vacuum (UHV) chamber equipped with an OMICRON VT-STM instrument at a base pressure below 1.0 × 10−10 Torr. All STM images were recorded with electrochemically etched W-tips at bias voltages of Vs = −2.0 V and a tunneling current of It = 0.1 nA to obtain the filled-state images.

Scheme 1. Models of the Chemical Structures of (a) Phenylalanine and (b) Tyrosinea

a

The gray, blue, red, and white balls indicate carbon (C), nitrogen (N), oxygen (O), and hydrogen (H), respectively.

tyrosine (Scheme 1b) adsorbed on the Ge(100) surface and to identify how the hydroxyl group (nucleophilic site) of tyrosine affects the geometric configurations in the adsorption process. Information about the adsorption structures and geometric configurations of phenylalanine and tyrosine on Ge(100) surfaces was obtained using core-level photoemission spectroscopy (CLPES) in conjunction with density functional theory (DFT) calculations and scanning tunneling microscopy (STM). We determined the effects of the −OH group of tyrosine on the adsorption geometry in terms of the interactions between the hydroxyl group (nucleophile) and adjacent down dimer (electrophile) of the Ge(100) surface. To our knowledge, this is the first experimental and theoretical characterization of the adsorption structures and geometrical configurations of phenylalanine and tyrosine on Ge(100) surfaces using CLPES, DFT calculations, and STM techniques.

3. RESULTS AND DISCUSSION We first acquired CLPES data for phenylalanine and tyrosine adsorbed on Ge(100) surfaces. Figure 1 shows the C 1s, N 1s, and O 1s core-level spectra being included in both molecules. The top and bottom panels indicate the three core-level spectra of the phenylalanine and tyrosine adsorbed on the Ge(100) surfaces at 300 K. Figure 1a shows the C 1s core-level spectrum obtained after 0.15 monolayer (ML) phenylalanine deposition on the Ge(100) surface (at low coverage: below half

2. EXPERIMENTAL AND COMPUTATIONAL SECTION Ge(100) surfaces (p-type, R = 0.10−0.39 Ω) were cleaned by several cycles of sputtering with 1 keV Ar+ ions at 700 K for 20 min, followed by annealing at 900 K for 10 min. The cleanliness of the Ge(100)-2×1 surfaces was checked using low energy electron diffraction (LEED) and STM. Phenylalanine (C9H11NO2, 99% purity) and tyrosine (C9H11NO3, 99% purity) were purchased from Aldrich and were further purified through several sublimation and pumping cycles to remove dissolved gases prior to exposure to the Ge(100) surface. We performed CLPES at the 10D beamline of the Pohang Accelerator Laboratory. The C 1s, N 1s, and O 1s core-level spectra were obtained with a PHOIBOS 150 electron energy analyzer equipped with a two-dimensional charge-coupled device (2D CCD) detector (Specs GmbH) using photon energies of 340, 460, and 588 eV to enhance the surface sensitivity. The binding energies of the core-level spectra were calibrated with respect to the clean Au 4f core-level spectrum (84.0 eV) collected at the same set of photon energies. The base pressure in the chamber was maintained below 9.5 × 10−11 Torr. All spectra were recorded in the normal emission mode. The core-level spectra were carefully analyzed using a standard nonlinear least-squares fitting procedure with Voigt functions.27

Figure 1. C 1s, N 1s, and O 1s core-level spectra (a)−(c) of phenylalanine and (d)−(f) of tyrosine obtained at a low coverage (0.15 ML) deposition on a Ge(100) surface. The dots indicate experimental values, and the solid lines represent the results of peak fitting. 25841

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Table 1. Changes in the Binding Energies of Three Core-Level Spectra for 0.15 ML Phenylalanine and Tyrosine Adsorbed on the Ge(100) Surface at 300 K coverage (0.15 ML)

C 1s (eV)

N 1s (eV)

O 1s (eV)

phenylalanine

C1/C2/C3/C4 284.7/284.0/285.8/288.6 C1′/C2′ /C3′/C4′ /C5′ 284.9/284.1/285.6/288.6/287.4

N1 401.1 N1′ 400.4

O1/O2 531.1/532.0 O1′/O2′ /O3′ 530.8/531.9/532.8

tyrosine

Figure 2. DFT calculation results for the O−H dissociated−N dative bonded structures of (a) phenylalanine and (b) tyrosine on the Ge(100) surface.

As in a previous study, the O1 and O2 peaks could be assigned to OGe (531.1 eV) and −CO (532.0 eV) in the carboxyl groups of phenylalanine molecules adsorbed on the Ge(100) surface. These results indicated the occurrence of typical OH dissociation, and only one oxygen atom in the carboxyl group participated in the adsorption reaction.19−26,33 The O 1s corelevel spectrum at 300 K was obtained after deposition of 0.15 ML tyrosine (Figure 1f). With consideration for the electronegativity and number of oxygen atoms in a tyrosine molecule, the spectral features were divided into three bonding states. As in the case of phenylalanine, O1′ and O2′ were assigned to OGe (530.8 eV) and −CO (531.9 eV). We observed a new peak as shown in Figure 1f: O3′ (532.8 eV). Considering the electronegativity of O3′, this peak was assigned to the hydroxyl group on the phenyl ring of tyrosine. Bonding of the hydroxyl group on the tyrosine phenyl ring to the Ge(100) surface would have resulted in the disappearance of the hydroxyl peak (−OH) typically located at 532.8 eV. The hydroxyl peak actually was observed at 532.8 eV, as shown in Figure 1f, suggesting that the oxygen of the hydroxyl group bonded to the phenyl ring did not participate in the adsorption on the Ge(100) surface, and only one oxygen atom in tyrosine participated in the adsorption reaction. As a result, our analysis of C 1s, N 1s, and O 1s data showed that the adsorption structures of phenylalanine and tyrosine on the Ge(100) surfaces predominantly formed “O−H dissociated−N dativebonded structures” at low coverage (0.15 ML). The binding energies are summarized in Table 1. Density functional theory (DFT) calculations were used to analyze the kinetic pathways relevant to the phenylalanine and tyrosine adsorption reactions on the Ge(100) surfaces. A total of six possible adsorption structures of each amino acid were examined, and the most stable structure was identified (see the Supporting Information). Figure 2 shows the “O−H dissociated−N dative bonded structure”, which was found to be the most favorable adsorption structure for both amino acids, along with the respective adsorption energies obtained from DFT calculations. O−H dissociated bond signified that O−H group adsorbed on Ge(100) as dissociation: O adsorbed on Ge down dimer and H(s) adsorbed on neighbor Ge up dimer. As

monolayer). Four chemically distinct types of carbon features were present on the Ge(100) surface. Remarkably, the strongest intensity component emerged at 284.7 eV, attributed to the phenyl ring of phenylalanine, labeled C1 (−C6H5). The Pauling electronegativities and peak intensities were used to assign the bonding features as CH2− (284.0 eV: C2), C−NH2 (285.8 eV: C3), and COO− (288.6 eV: C4). The peak assignments confirmed that phenylalanine was well-adsorbed on the Ge(100) surface without incurring bond breakage. Figure 1d shows the C 1s core-level spectrum acquired after 0.15 ML tyrosine deposition on the Ge(100) surface. This spectrum indicated the presence of five chemically distinct types of carbon on the Ge(100) surface. The strongest intensity component was observed at 284.9 eV, corresponding to the phenyl ring in tyrosine (labeled C1′ (−C5H4−)). Three other bonding features were assigned as CH2− (284.1 eV: C2′), C− NH2 (285.6 eV: C3′), and COO− (288.6 eV: C4′), similar to the case of phenylalanine. A new peak was observed in the adsorbed tyrosine spectrum at 287.4 eV, which was denoted C−OH− (287.4 eV: C5′). We expected that it arose from a hydroxyl group of tyrosine that distinguishes tyrosine from phenylalanine. Panels b and e of Figure 1 show the N 1s core-level spectrum obtained after deposition of 0.15 ML phenylalanine and tyrosine on the Ge(100) surface at 300 K. These spectra displayed a single N 1s peak with a binding energy of 401.1 eV (marked N1) and 400.4 eV (marked N1′). Previous studies of N dative bonding molecular adsorption structures on Ge(100) surfaces clearly indicated that the nitrogen atom in the amine group was adsorbed on Ge(100) surfaces in a dative bonding configuration at low initial coverage.31,32 According to the binding energies, we found that the amino nitrogen atoms of both phenylalanine and tyrosine were adsorbed on the Ge(100) surface in charged states that implied N dative bonded formation. The growth of O 1s peaks was observed during the adsorption of phenylalanine and tyrosine on the Ge(100) surface at 300 K. Figure 1c displays the O 1s core-level spectrum obtained after the deposition of 0.15 ML phenylalanine. The figure shows that the O 1s core-level peak could be fit to two components of chemically inequivalent oxygen atoms. 25842

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Figure 3. Reaction pathways for the O−H dissociated−N dative bonded structures of (a) phenylalanine and (b) tyrosine on the Ge(100) including the transition state.

shown in Figure 2a, the adsorption energy of the “O−H dissociated−N dative bonded structure” of phenylalanine adsorbed onto a Ge(100) surface was −54.7 kcal/mol. Comparison to the adsorption energies of the other model structures indicated that the “O−H dissociated−N dative bonded structure” was the most favorable structure. The N1 and O2 peaks obtained from CLPES at low coverage (Figure 1b,c) were consistent with the “O−H dissociated−N dative bonded structure” obtained from the DFT calculations shown in Figure 2a. Figure 2b shows the DFT calculation results for the adsorption structure of tyrosine on the Ge(100) surface. The adsorption energy of tyrosine was Eads = −52.5 kcal/mol, demonstrating that the “O−H dissociated−N dative bonded structure” was most stable among the six proposed structures. These results supported the conclusion that the CLPES and DFT calculations agreed well at low (initial) coverage. We obtained the reaction pathway models, including transition states, for the process by which the “O−H dissociated−N dative bonded structure” formed for possible experimental confirmation. The zero energy value (0.00 kcal/ mol) in Figure 3 corresponds to a system in which the free phenylalanine or tyrosine were separated from the clean Ge(100) surface. Figure 3a shows the theoretically calculated adsorption pathway of the “O−H dissociated−N dative bonded structure” derived from the “O−H dissociation bonded structure” of phenylalanine adsorbed on the Ge(100) surface. The transition-state energy of the “O−H dissociated−N dative bonded structure” was found to be −33.1 kcal/mol. This value indicated that the reaction was experimentally favorable (spontaneous, with a transition-state energy of less than 0.00 kcal/mol).34 Figure 3b shows the transition state of the tyrosine reaction from the “O−H dissociation bonded structure” to the “O−H dissociated−N dative bonded structure”. The transitionstate energy of tyrosine was −36.3 kcal/mol, also less than 0.00 kcal/mol. Considering these two energies of the transition state for the pathway (−33.1 and −36.3 kcal/mol), we can confirm that both are below the energy of the reactant (0.00 kcal/mol), and these barriers may be overcome at room temperature. Through DFT calculations, we found that the “O−H dissociated−N dative bonded structures” are predicted to be favorable for both phenylalanine and tyrosine, and the activation barriers could, therefore, be easily overcome at room temperature.28 The adsorption energies are summarized in Table 2.

Table 2. Adsorption Energies (Eads, kcal/mol) of the Two Most Probable Adsorption Structures of Phenylalanine and Tyrosine on the Ge(100)-2×1 Surface configuration

O−H dissociation bonded structure

transition state

O−H dissociated−N dative bonded structure

phenylalanine tyrosine

−40.7 −41.4

−33.1 −36.3

−54.7 −52.5

The “O−H dissociated−N dative bonded structures” of phenylalanine and tyrosine on the Ge(100) surfaces differed with respect to the phenyl ring geometries in phenylalanine and tyrosine. The adsorption geometry shown in Figure 2a was compared with that shown in Figure 2b. DFT calculations suggested that the phenyl ring of phenylalanine was located in the axial position to the Ge(100) surface whereas the phenyl ring being included in tyrosine was tilted with respect to the Ge(100) surface. The geometric differences between the adsorption structures were examined by performing STM imaging experiments to clarify DFT calculation results. Figure 4 displays the STM images obtained at low coverage, showing the adsorption structures and geometric configurations of both phenylalanine and tyrosine with high precision. The STM images were compared with the model structures

Figure 4. Filled-state STM images (7.0 × 7.0 nm2, Vs = −2.0 V, It = 0.1 nA) of (a) phenylalanine and (b) tyrosine adsorbed on the Ge(100) surface at 300 K after exposure to 0.05 ML (at low coverage), respectively. The magnified STM images (2.0 × 2.0 nm2) indicated the presence of a typical “O−H dissociated−N dative bonded structure” in each inset image. Phenylalanine revealed bright round protrusions, whereas tyrosine displayed bright oval protrusions on the Ge(100) surface. (Scale bar = 1.5 nm.) 25843

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Figure 5. Comparison of the STM images and DFT calculations of (a) and (c) phenylalanine and (b) and (d) tyrosine on the Ge(100). (e) Schematic model for the role of the nucleophilic −OH groups.

repulsion. The phenylalanine phenyl ring preferred an orientation along the axial position. The DFT calculation results shown in Figure 2 distinguished the important differences of the adsorption geometries of the phenyl rings between phenylalanine and tyrosine. The STM images in Figure 5 represent the different adsorption structures between phenylalanine (bright circle protrusion in Figure 5a) and tyrosine (bright oval protrusion in Figure 5b). The discrepancies could be explained in terms of the differences in the charge distribution. The phenyl ring of phenylalanine preferred an orientation along the axial direction with respect to the Ge(100) surface, although the adsorption structure of phenylalanine on Ge(100) included a charged nitrogen moiety (−NH2+). The positively charged nitrogen on phenylalanine was mostly counterbalanced by the charge distribution on the adjacent up dimer (δ−) of the Ge(100) surface with a negatively charged character. The total charge, then, was nearly neutral. Therefore, the charged nitrogen (−NH2+) did not affect the adsorption geometry, and the phenyl ring of phenylalanine did not interact with the down dimer of the Ge(100) surface (Figure 5e). In contrast with the case of phenylalanine, the oval protrusion indicated that the phenol ring on tyrosine was tilted with respect to the Ge(100) surface, as viewed from above the surface. As mentioned, we hypothesized that the −OH group on tyrosine contributed to this interesting difference in the adsorption structures. The “O−H dissociated−N dative bonded structure” observed for tyrosine on a Ge(100) surface at low coverage (see Figure 4b) included not only the charged nitrogen (NH2+) but also nucleophilic (electron rich) −OH groups of tyrosine, with a relatively negative charge. Tyrosine must, therefore, have been attracted to another electrophilic down dimer on the Ge(100) surface to neutralize the nucleophile and maintain a stable adsorption configuration (Figure 5e). Therefore, the “O−H

obtained from CLPES results. As mentioned above, CLPES results indicated that both phenylalanine and tyrosine structures featured adsorption on the Ge(100) surface through an “O−H dissociated−N dative bonded structure” at low coverage. The dark dimer resulted from the saturation of two dangling Ge bonds via O−H dissociated adsorption, and the bright protrusions arose from the N dative bonded regions. Figure 4a shows an STM image of phenylalanine adsorbed on a Ge(100) surface at 0.05 ML. Bright round protrusions on one side of a dimer row and dark adjacent dimers (indicated as a red dotted oval: labeled A) were observed. A bright protrusion and a dark adjacent dimer (marked as red-dotted oval shape) were observed in the tyrosine images, as shown in Figure 4b. Contrasting with the round protrusions of phenylalanine, bright oval protrusions from the tyrosine molecules bridged the dimer row diagonally. These differences were attributed to the presence of a hydroxyl group on the phenyl ring of the tyrosine, which was not present on the phenylalanine. Because the “O−H dissociated−N dative bonded structure” of tyrosine on the Ge(100) surface included a charged nitrogen moiety and a nucleophilic −OH group (0.082 eV of nucleophilicity) on the phenyl ring, the ring was attracted by the down dimer (electrophilic) on the Ge(100) surface, which stabilized the adsorption geometry.35 The tyrosine phenol ring in an “O−H dissociated−N dative bonded structure” lays down in a tilted configuration on the Ge(100) surface due to interactions between the −OH group on the phenyl ring and adjacent down dimer on the Ge(100) surface. On the other hand, the phenylalanine phenyl ring of the “O−H dissociated− N dative bonded structure” on the Ge(100) surface did not interact with the down dimer of the Ge(100) surface in the absence of a nucleophilic group. A tilting conformation toward the Ge dimer is expected to yield an unstable “O−H dissociated−N dative bonded structure” with a high degree of 25844

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dissociated−N dative bonded structure” of tyrosine adsorbed onto a Ge(100) surface resulted in the tilting of the phenol ring with respect to the Ge(100) surface due to interactions between the −OH groups of the phenol rings and the adjacent down dimer on the Ge(100) surface.

4. CONCLUSION We determined the discrepancies in the bonding configurations between phenylalanine and tyrosine adsorbed on Ge(100) surfaces using CLPES, DFT calculations, and STM results. The C 1s, N 1s, and O 1s core-level spectra revealed that the amine and carboxyl groups of phenylalanine and tyrosine participated in the adsorption process on the Ge(100) surface. DFT calculations supported the conclusion that the “O−H dissociated−N dative bonded structure” was the most stable structure assumed at low coverage. We confirmed that the phenyl ring of phenylalanine was oriented along the axial position with respect to the Ge(100) surface, whereas the phenyl ring of tyrosine was stabilized in a tilted structure with respect to the Ge(100) surface due to the effects of the nucleophilic −OH group, as shown in the STM results and DFT calculations.

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ASSOCIATED CONTENT

* Supporting Information S

Figure of six possible adsorption structures of phenylalanine on the Ge(100) surface and table of comparison of adsorption energies of phenylalanine and tyrosine. This material is available free of charge via the Internet at http://pubs.acs.org.

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AUTHOR INFORMATION

Corresponding Author

*H.-S.L.: tel, +82-42-350-2846; fax, +82-42-350-2810; e-mail, [email protected]. S.K.: tel, +82-42-350-2831; fax: +82-42-350-2810; e-mail, [email protected]. H.L.: tel, +82-2-710-9409; fax, +82-2-2077-7321; e-mail, easyscan@ sookmyung.ac.kr. Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (2012-000875). Additionally, it was also supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education, Science and Technology (2012-0000905).

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