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Dissociative adsorption of guanine on Ge(100)† Cite this: DOI: 10.1039/c5cc03532e
Young-Sang Youn,*ab Do Hwan Kim,*c Hye Jin Leed and Sehun Kima
Received 28th April 2015, Accepted 5th July 2015 DOI: 10.1039/c5cc03532e www.rsc.org/chemcomm
Adsorption of guanine on Ge(100) was investigated using scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. Guanine appears dark in STM images, indicating that its adsorption occurs through N–H dissociation. DFT calculations revealed that ‘‘N(1)–H dissociation through an O dative bonded structure’’ is the most favorable configuration.
Interactions between biomolecules and semiconductor surfaces have been extensively studied, as they can be exploited for industrial applications and for biodevices such as biosensors, biochips, and medical implants.1–3 Biosensing silicon-based devices include an integrated sensing device for genome sequencing4 and a nanowire field effect transistor for DNA sensing,5 both of which were manufactured using the complementary metal-oxide semiconductor (CMOS) process. Recently, a germanium nanowire grating fabricated on a graphene layer coated on a gold film, which is a surface plasmon resonance platform, has been demonstrated for immunoassay measurements.6 Considering that the spatial resolutions of the latest biosensing devices are decreasing from the micron to the nanoscale, investigations on elucidating interactions between biomolecules and surfaces at an atomic level become even more important. Furthermore, understanding possible reaction mechanisms alongside structural changes upon the adsorption of biomolecules on semiconductors could greatly help with functionalizing the surfaces
of semiconductor based sensors for improved sensing performance.4–6 For instance, the adsorption of DNA nucleobases on either semiconductor or metal surfaces has been reported.6–8 Additionally, the adsorption of guanine, a derivative of purine consisting of a pyrimidine ring with an imidazole ring (Fig. 1), has been reported on metal surfaces.9–12 However, the structural properties of guanine adsorbed on any semiconductor surface are yet to be investigated. In this work, we report the first observation on the adsorptive behavior of guanine on a Ge(100) surface using STM measurements and DFT calculations. This is important because the differences in guanine adsorption behavior between semiconductor and metal surfaces cannot be inferred as the surface properties of semiconductors are different from those of metals. In other words, when dealing with molecular adsorption on any surfaces, the characteristics of surface atoms should be considered. In the case of the (100) surfaces of group IV semiconductors, the surface atoms are reconstructed as surface dimers. As a result, they exhibit weak p-bonding and electrophilic– nucleophilic characteristics.13,14 Therefore, these surface dimers can react with molecules through cycloaddition and/or Lewis acid–base reactions.13,15,16 The adsorption process of various molecules (incl. methylamine, aluminum trichloride, glycine, etc.) on the Ge(100) surface through cycloaddition and/or Lewis acid–base reactions have been previously reported.17–22
a
Molecular-Level Interface Research Center, Department of Chemistry, KAIST, 291, Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea b Nuclear Chemistry Research Division, Korea Atomic Energy Research Institute, 111, Deadeok-daero 989beon-gil, Yuseong-gu, Daejeon 34057, Republic of Korea. E-mail: [email protected] c Division of Science Education, Daegu University, 201, Daegudae-ro, Gyeongsan-si, Gyeongbuk-do 38453, Republic of Korea. E-mail: [email protected] d Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, 80 Daehakro, Buk-gu, Daegu 702-701, Republic of Korea † Electronic supplementary information (ESI) available: Experimental and computational methods, theoretically simulated STM image, schematic illustrations of the possible adsorption structures attributable to N–H dissociation and a dative bonding, and the results of DFT calculations of the dative bonded adducts. See DOI: 10.1039/c5cc03532e
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Fig. 1 Schematic diagram of a guanine molecule. The numbers denote the atoms in the molecule, while the gray, blue, red, and white balls indicate carbon, nitrogen, oxygen, and hydrogen atoms, respectively.
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Fig. 2 (a) Filled-state STM image (13.5 13.5 nm2, Vs = 2.0 V, It = 0.1 nA) of a 0.05 ML of guanine adsorbed on Ge(100) at room temperature. (b) Magnified STM image (5.0 5.0 nm2), corresponds to the yellow dashed box in (a), in which three adsorption features are seen (each is represented by a white solid box). The yellow arrows indicate the dimers adjacent to the absorbed guanine molecules. (c) Schematic model of the adsorption features (represented by the dashed circles) on Ge(100) shown in (b). The bright protrusions of the Ge atoms (indicated by the yellow spots) are shown as red lines; these exhibit symmetric 2 1 dimers. The dashed lines depict the boundaries of the Ge dimer rows.
From the filled-state STM images featuring a Ge(100) surface after exposure to a 0.05 monolayer (ML) of guanine at room temperature, the adsorbed guanine appears as a dark feature without a bright protrusion (see Fig. 2a and b). This is the signature of the adsorption configurations on Ge(100) and Si(100) surfaces, which involves O–H or N–H dissociation reactions.23–25 Since guanine contains three N–H groups without any O–H moieties, it can be concluded that the adsorption process on Ge(100) could occur via N–H dissociation. In addition, the guanine molecules could potentially react with Ge dimers via different reaction sites leading to different reaction pathways. However, the observation of bean-shaped protrusions (represented by the yellow arrows in Fig. 2b) assigned to Ge dimers adjacent to the absorbed guanine molecule, which are the characteristics of symmetric 2 1 structure, indicates that the adsorption of guanine on Ge(100) occurs on a single Ge dimer without any interaction with the adjacent dimers. If the guanine molecule adsorbed on a single Ge dimer additionally interacts with the neighboring dimers through dative bonding, the dimers are always converted into asymmetric c(4 2) or p(2 2) structures because the additional reaction will prevent the flip-flop of the dimer leading to the symmetric 2 1 structure.13,19 This confirms that the adsorption of guanine takes place on a single Ge dimer through only one N–H dissociation. The possible reaction pathways via N–H dissociation for the adsorption of guanine on Ge(100) are proposed in Fig. S1 (see the ESI†). DFT calculations were further performed to verify the stabilities of these adsorption structures. As shown in Fig. 3, among all possible adsorption structures, ‘‘N(1)–H dissociation through an O dative bonded structure’’ (with an Eads of 42.5 kcal mol 1) is the most stable. In addition, it is difficult for the reaction to occur through the dative bonding of
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Fig. 3 Optimized adsorption configurations and adsorption energies (Eads) for (a) N(1)–H dissociation through an O dative bonded structure, (b) N(9)–H dissociation through a N(7) dative bonded structure, (c) N(10)–H dissociation through a N(3) dative bonded structure, (d) N(1)–H dissociation through a N(3) dative bonded structure, (e) N(1)–H dissociation structure, (f) N(10)–H dissociation structure, and (g) N(9)–H dissociation structure. The gray, blue, red, white, and teal balls represent carbon, nitrogen, oxygen, hydrogen, and germanium atoms, respectively.
N(1), N(9), and N(10) atoms in guanine because their lone electron pairs are involved in the aromatic system. Thus, we once more speculate that the ‘‘N(1)–H dissociation through an O dative bonded structure’’ is the most favorable. This can also be supported by the fact that the N–H dissociation of amine molecules is suppressed on Ge(100) at room temperature, but the presence of the CQO functional group could facilitate the N–H dissociative adsorption of primary and secondary amine molecules on Ge(100).17,26 The adsorption feature of guanine on Ge(100) rarely changes; if it does, it is reinstated, as shown in Fig. 4. After the formation of ‘‘N(1)–H dissociation through an O dative bonded structure’’, additional dative bonding could take place through the N(3), N(7), N(9), N(10), O atoms in the adsorbed guanine on Ge(100),
Fig. 4 Sequential filled-state STM images (4.0 4.0 nm2, Vs = 2.0 V, It = 0.1 nA) of the same region of the Ge(100) surface after exposure to 0.05 ML guanine. The STM images were obtained at an interval of 3 min. The white dashed circles demarcate the adsorption feature of guanine on Ge(100), while the white arrows highlight the bright protrusion of the adsorption feature. The numbers denote the sequence of the STM images.
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Fig. 5 Series of filled-state STM images (Vs = 2.0 V, It = 0.1 nA) of the same region of a Ge(100) surface. The white and yellow dashed circles demarcate the major and minor adsorption features of guanine on Ge(100), respectively. The major adsorption feature remains unchanged, whereas the minor one migrates along the dimer row or perpendicular to the dimer row. The numbers denote the sequence of the STM images. The yellow stars indicate identical areas in the images.
which could in turn cause the bright protrusion in the second and third STM images in Fig. 4. The difference in positions of the bright protrusion in these STM images indicates that the additional reaction atom of the adsorbed guanine molecule is displaced. After the recovery of the ‘‘N(1)–H dissociation through an O dative bonded structure’’ (see the fourth STM image in Fig. 4), it remains unchanged during subsequent STM imaging. We infer that this phenomenon is attributable to the instability of the new adsorption configuration created by the additional reaction. Therefore, it was confirmed that ‘‘N(1)–H dissociation through an O dative bonded structure’’ is the stable adsorption configuration. We observed the adsorption structure of guanine on Ge(100) as a dark feature without any bright protrusions. This is comparative to the pyridine and pyrimidine adsorbed on Ge(100) where the adsorbed molecules appeared as bright protrusions in STM images at higher bias voltage, but the protrusions disappeared at a lower bias voltage for the same tunneling current.27,28 The STM image was also compared with a simulated image at low bias voltage to investigate the ‘‘N(1)–H dissociation through an O-dative bonded structure’’. The simulated image is shown in Fig. S2 (ESI†) and was calculated using the optimized geometry shown in Fig. 3a with the Tersoff–Hamann scheme.29,30 A dark region around the adsorbed guanine molecule in the simulated image, similar to the experimental feature (Fig. 2a and b), indicates that the dissociative adsorption of guanine molecule reduces the electron density around the Ge atoms. Further studies on changes in electron charge density after the adsorption of the guanine molecule are in progress to more accurately understand this phenomenon. In addition to ‘‘N(1)–H dissociation through an O dative bonded structure’’, we observed a minor adsorption structure from the series of STM images in Fig. 5; the minor feature
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(indicated by the yellow dashed circle) migrates on the Ge(100) surface, whereas the major one (marked as white dashed circle) does not. The minor structure appears as a bright protrusion without a dark site indicating that guanine reacts with Ge(100) via dative bonding.22 The possible adsorption configurations of guanine through dative bonding on Ge(100) are shown in Fig. S3 (ESI†). As mentioned above, the reaction through dative bonding of N(1), N(9), and N(10) atoms of guanine does not readily occur because the aromaticity must be broken when the dative bonds form. Therefore, we concluded that minor features shown in Fig. 5 are more likely to reflect the adsorption structures in Fig. S3a–c (ESI†) than those in Fig. S3d–f (ESI†). DFT calculations were further performed to determine possible dative bonded configurations of guanine on Ge(100) along with their respective adsorption energies. We obtained four optimized structures; a ‘‘N(7) dative bonded,’’ a ‘‘N(3) dative bonded,’’ and an ‘‘O dative bonded’’ were more stable than a ‘‘N(10) dative bonded structure’’ (see Fig. S4, ESI†). However, the possible adsorption structures in Fig. S3e and f (ESI†) could not be determined since they were unstable due to the loss of the aromaticity. Furthermore, the minor feature in Fig. 5 moves along or perpendicular to the dimer row. Hence, we propose that the migration of the minor feature is caused by competitive reactions between the atoms in the guanine molecule with Ge(100) via dative bonding, considering that the difference in the adsorption energies is relatively small (Fig. S4, ESI†). In conclusion, we elucidated the adsorption structure of guanine on Ge(100) at room temperature using an STM approach and DFT calculations. STM analysis revealed that the adsorption of guanine on Ge(100) occurs via N–H dissociation while the DFT calculations provide the optimized adsorption configurations with the corresponding adsorption energies. The most favorable configuration when guanine is adsorbed on Ge(100) was found to be ‘‘N(1)–H dissociation through an O dative bonded structure’’. This research was supported by the National Research Foundation of Korea (NRF) grant funded by the Korean government (MSIP) (Grant No. 20090083525, 2012M2A8A5025925, and 2010-0023313). Calculations were performed by using the supercomputing resources of KISTI.
Notes and references 1 S. R. Whaley, D. S. English, E. L. Hu, P. F. Barbara and A. M. Belcher, Nature, 2000, 405, 665–668. 2 B. Kasemo, Surf. Sci., 2002, 500, 656–677. 3 K. Goede, P. Busch and M. Grundmann, Nano Lett., 2004, 4, 2115–2120. 4 J. M. Rothberg, W. Hinz, T. M. Rearick, J. Schultz, W. Mileski, M. Davey, J. H. Leamon, K. Johnson, M. J. Milgrew, M. Edwards, J. Hoon, J. F. Simons, D. Marran, J. W. Myers, J. F. Davidson, A. Branting, J. R. Nobile, B. P. Puc, D. Light, T. A. Clark, M. Huber, J. T. Branciforte, I. B. Stoner, S. E. Cawley, M. Lyons, Y. Fu, N. Homer, M. Sedova, X. Miao, B. Reed, J. Sabina, E. Feierstein, M. Schorn, M. Alanjary, E. Dimalanta, D. Dressman, R. Kasinskas, T. Sokolsky, J. A. Fidanza, E. Namsaraev, K. J. McKernan, A. Williams, G. T. Roth and J. Bustillo, Nature, 2011, 475, 348–352. 5 A. Gao, N. Lu, Y. Wang, P. Dai, T. Li, X. Gao, Y. Wang and C. Fan, Nano Lett., 2012, 12, 5262–5268. 6 P. Jahanshahi and F. R. M. Adikan, J. Med. Bioeng., 2015, 4, 145–149. 7 M. Kasaya, H. Tabata and T. Kawai, Surf. Sci., 1998, 406, 302–311. 8 A. Lopez, O. Chen and N. V. Richardson, Surf. Interface Anal., 2002, 33, 441–446.
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Communication ¨ck, L. M. Molina, E. Lægsgaard, I. Stensgaard, 9 R. Otero, M. Scho B. Hammer and F. Besenbacher, Angew. Chem., Int. Ed., 2005, 44, 2270–2275. 10 M. Furukawa, T. Yamada, S. Katano, M. Kawai, H. Ogasawara and A. Nilsson, Surf. Sci., 2007, 601, 5433–5440. 11 W. Xu, R. E. A. Kelly, H. Gersen, E. Lægsgaard, I. Stensgaard, L. N. Kantorovich and F. Besenbacher, Small, 2009, 5, 1952–1956. ´b, V. Matolı´n and K. C. Prince, 12 V. Feyer, O. Plekan, F. ˇ Sutara, V. Cha Surf. Sci., 2011, 605, 361–365. 13 J. A. Kubby and J. J. Boland, Surf. Sci. Rep., 1996, 26, 61–204. 14 H. J. W. Zandvliet, Phys. Rep., 2003, 388, 1–40. 15 H. N. Waltenburg and J. T. Yates, Chem. Rev., 1995, 95, 1589–1673. 16 M. A. Filler and S. F. Bent, Prog. Surf. Sci., 2003, 73, 1–56. 17 C. Mui, J. H. Han, G. T. Wang, C. B. Musgrave and S. F. Bent, J. Am. Chem. Soc., 2002, 124, 4027–4038. 18 S. J. Jung, Y.-S. Youn, H. Lee, K.-J. Kim, B. S. Kim and S. Kim, J. Am. Chem. Soc., 2008, 130, 3288–3289. 19 Y.-S. Youn, S. J. Jung, H. Lee and S. Kim, Langmuir, 2009, 25, 7438–7442. 20 S.-S. Bae, S. Kim and J. W. Kim, Langmuir, 2009, 25, 275–279.
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ChemComm 21 Y.-S. Youn, H. Lee and S. Kim, ChemPhysChem, 2010, 11, 354–356. 22 Y.-S. Youn, K.-j. Kim, B. Kim, D. H. Kim, H. Lee and S. Kim, J. Phys. Chem. C, 2011, 115, 710–713. 23 S. J. Jung, J. Y. Lee, S. Hong and S. Kim, J. Phys. Chem. B, 2005, 109, 24445–24449. 24 O. N. Chung, H. Kim, S. Chung and J.-Y. Koo, Phys. Rev. B: Condens. Matter Mater. Phys., 2006, 73, 033303. 25 S.-S. Bae, D. H. Kim, A. Kim, S. J. Jung, S. Hong and S. Kim, J. Phys. Chem. C, 2007, 111, 15013–15019. 26 A. J. Keung, M. A. Filler and S. F. Bent, J. Phys. Chem. C, 2007, 111, 411–419. 27 Y. E. Cho, J. Y. Maeng and S. Kim, J. Am. Chem. Soc., 2003, 125, 7514–7515. 28 J. Y. Lee, S. J. Jung, S. Hong and S. Kim, J. Phys. Chem. B, 2005, 109, 348–351. 29 J. Tersoff and D. R. Hamann, Phys. Rev. Lett., 1983, 50, 1998–2001. 30 J. Tersoff and D. R. Hamann, Phys. Rev. B: Condens. Matter Mater. Phys., 1985, 31, 805–813.
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Dissociative adsorption of guanine on Ge(100)† Cite this: DOI: 10.1039/c5cc03532e
Young-Sang Youn,*ab Do Hwan Kim,*c Hye Jin Leed and Sehun Kima
Received 28th April 2015, Accepted 5th July 2015 DOI: 10.1039/c5cc03532e www.rsc.org/chemcomm
Adsorption of guanine on Ge(100) was investigated using scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. Guanine appears dark in STM images, indicating that its adsorption occurs through N–H dissociation. DFT calculations revealed that ‘‘N(1)–H dissociation through an O dative bonded structure’’ is the most favorable configuration.
Interactions between biomolecules and semiconductor surfaces have been extensively studied, as they can be exploited for industrial applications and for biodevices such as biosensors, biochips, and medical implants.1–3 Biosensing silicon-based devices include an integrated sensing device for genome sequencing4 and a nanowire field effect transistor for DNA sensing,5 both of which were manufactured using the complementary metal-oxide semiconductor (CMOS) process. Recently, a germanium nanowire grating fabricated on a graphene layer coated on a gold film, which is a surface plasmon resonance platform, has been demonstrated for immunoassay measurements.6 Considering that the spatial resolutions of the latest biosensing devices are decreasing from the micron to the nanoscale, investigations on elucidating interactions between biomolecules and surfaces at an atomic level become even more important. Furthermore, understanding possible reaction mechanisms alongside structural changes upon the adsorption of biomolecules on semiconductors could greatly help with functionalizing the surfaces
of semiconductor based sensors for improved sensing performance.4–6 For instance, the adsorption of DNA nucleobases on either semiconductor or metal surfaces has been reported.6–8 Additionally, the adsorption of guanine, a derivative of purine consisting of a pyrimidine ring with an imidazole ring (Fig. 1), has been reported on metal surfaces.9–12 However, the structural properties of guanine adsorbed on any semiconductor surface are yet to be investigated. In this work, we report the first observation on the adsorptive behavior of guanine on a Ge(100) surface using STM measurements and DFT calculations. This is important because the differences in guanine adsorption behavior between semiconductor and metal surfaces cannot be inferred as the surface properties of semiconductors are different from those of metals. In other words, when dealing with molecular adsorption on any surfaces, the characteristics of surface atoms should be considered. In the case of the (100) surfaces of group IV semiconductors, the surface atoms are reconstructed as surface dimers. As a result, they exhibit weak p-bonding and electrophilic– nucleophilic characteristics.13,14 Therefore, these surface dimers can react with molecules through cycloaddition and/or Lewis acid–base reactions.13,15,16 The adsorption process of various molecules (incl. methylamine, aluminum trichloride, glycine, etc.) on the Ge(100) surface through cycloaddition and/or Lewis acid–base reactions have been previously reported.17–22
a
Molecular-Level Interface Research Center, Department of Chemistry, KAIST, 291, Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea b Nuclear Chemistry Research Division, Korea Atomic Energy Research Institute, 111, Deadeok-daero 989beon-gil, Yuseong-gu, Daejeon 34057, Republic of Korea. E-mail: [email protected] c Division of Science Education, Daegu University, 201, Daegudae-ro, Gyeongsan-si, Gyeongbuk-do 38453, Republic of Korea. E-mail: [email protected] d Department of Chemistry and Green-Nano Materials Research Center, Kyungpook National University, 80 Daehakro, Buk-gu, Daegu 702-701, Republic of Korea † Electronic supplementary information (ESI) available: Experimental and computational methods, theoretically simulated STM image, schematic illustrations of the possible adsorption structures attributable to N–H dissociation and a dative bonding, and the results of DFT calculations of the dative bonded adducts. See DOI: 10.1039/c5cc03532e
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Fig. 1 Schematic diagram of a guanine molecule. The numbers denote the atoms in the molecule, while the gray, blue, red, and white balls indicate carbon, nitrogen, oxygen, and hydrogen atoms, respectively.
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Fig. 2 (a) Filled-state STM image (13.5 13.5 nm2, Vs = 2.0 V, It = 0.1 nA) of a 0.05 ML of guanine adsorbed on Ge(100) at room temperature. (b) Magnified STM image (5.0 5.0 nm2), corresponds to the yellow dashed box in (a), in which three adsorption features are seen (each is represented by a white solid box). The yellow arrows indicate the dimers adjacent to the absorbed guanine molecules. (c) Schematic model of the adsorption features (represented by the dashed circles) on Ge(100) shown in (b). The bright protrusions of the Ge atoms (indicated by the yellow spots) are shown as red lines; these exhibit symmetric 2 1 dimers. The dashed lines depict the boundaries of the Ge dimer rows.
From the filled-state STM images featuring a Ge(100) surface after exposure to a 0.05 monolayer (ML) of guanine at room temperature, the adsorbed guanine appears as a dark feature without a bright protrusion (see Fig. 2a and b). This is the signature of the adsorption configurations on Ge(100) and Si(100) surfaces, which involves O–H or N–H dissociation reactions.23–25 Since guanine contains three N–H groups without any O–H moieties, it can be concluded that the adsorption process on Ge(100) could occur via N–H dissociation. In addition, the guanine molecules could potentially react with Ge dimers via different reaction sites leading to different reaction pathways. However, the observation of bean-shaped protrusions (represented by the yellow arrows in Fig. 2b) assigned to Ge dimers adjacent to the absorbed guanine molecule, which are the characteristics of symmetric 2 1 structure, indicates that the adsorption of guanine on Ge(100) occurs on a single Ge dimer without any interaction with the adjacent dimers. If the guanine molecule adsorbed on a single Ge dimer additionally interacts with the neighboring dimers through dative bonding, the dimers are always converted into asymmetric c(4 2) or p(2 2) structures because the additional reaction will prevent the flip-flop of the dimer leading to the symmetric 2 1 structure.13,19 This confirms that the adsorption of guanine takes place on a single Ge dimer through only one N–H dissociation. The possible reaction pathways via N–H dissociation for the adsorption of guanine on Ge(100) are proposed in Fig. S1 (see the ESI†). DFT calculations were further performed to verify the stabilities of these adsorption structures. As shown in Fig. 3, among all possible adsorption structures, ‘‘N(1)–H dissociation through an O dative bonded structure’’ (with an Eads of 42.5 kcal mol 1) is the most stable. In addition, it is difficult for the reaction to occur through the dative bonding of
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Fig. 3 Optimized adsorption configurations and adsorption energies (Eads) for (a) N(1)–H dissociation through an O dative bonded structure, (b) N(9)–H dissociation through a N(7) dative bonded structure, (c) N(10)–H dissociation through a N(3) dative bonded structure, (d) N(1)–H dissociation through a N(3) dative bonded structure, (e) N(1)–H dissociation structure, (f) N(10)–H dissociation structure, and (g) N(9)–H dissociation structure. The gray, blue, red, white, and teal balls represent carbon, nitrogen, oxygen, hydrogen, and germanium atoms, respectively.
N(1), N(9), and N(10) atoms in guanine because their lone electron pairs are involved in the aromatic system. Thus, we once more speculate that the ‘‘N(1)–H dissociation through an O dative bonded structure’’ is the most favorable. This can also be supported by the fact that the N–H dissociation of amine molecules is suppressed on Ge(100) at room temperature, but the presence of the CQO functional group could facilitate the N–H dissociative adsorption of primary and secondary amine molecules on Ge(100).17,26 The adsorption feature of guanine on Ge(100) rarely changes; if it does, it is reinstated, as shown in Fig. 4. After the formation of ‘‘N(1)–H dissociation through an O dative bonded structure’’, additional dative bonding could take place through the N(3), N(7), N(9), N(10), O atoms in the adsorbed guanine on Ge(100),
Fig. 4 Sequential filled-state STM images (4.0 4.0 nm2, Vs = 2.0 V, It = 0.1 nA) of the same region of the Ge(100) surface after exposure to 0.05 ML guanine. The STM images were obtained at an interval of 3 min. The white dashed circles demarcate the adsorption feature of guanine on Ge(100), while the white arrows highlight the bright protrusion of the adsorption feature. The numbers denote the sequence of the STM images.
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Fig. 5 Series of filled-state STM images (Vs = 2.0 V, It = 0.1 nA) of the same region of a Ge(100) surface. The white and yellow dashed circles demarcate the major and minor adsorption features of guanine on Ge(100), respectively. The major adsorption feature remains unchanged, whereas the minor one migrates along the dimer row or perpendicular to the dimer row. The numbers denote the sequence of the STM images. The yellow stars indicate identical areas in the images.
which could in turn cause the bright protrusion in the second and third STM images in Fig. 4. The difference in positions of the bright protrusion in these STM images indicates that the additional reaction atom of the adsorbed guanine molecule is displaced. After the recovery of the ‘‘N(1)–H dissociation through an O dative bonded structure’’ (see the fourth STM image in Fig. 4), it remains unchanged during subsequent STM imaging. We infer that this phenomenon is attributable to the instability of the new adsorption configuration created by the additional reaction. Therefore, it was confirmed that ‘‘N(1)–H dissociation through an O dative bonded structure’’ is the stable adsorption configuration. We observed the adsorption structure of guanine on Ge(100) as a dark feature without any bright protrusions. This is comparative to the pyridine and pyrimidine adsorbed on Ge(100) where the adsorbed molecules appeared as bright protrusions in STM images at higher bias voltage, but the protrusions disappeared at a lower bias voltage for the same tunneling current.27,28 The STM image was also compared with a simulated image at low bias voltage to investigate the ‘‘N(1)–H dissociation through an O-dative bonded structure’’. The simulated image is shown in Fig. S2 (ESI†) and was calculated using the optimized geometry shown in Fig. 3a with the Tersoff–Hamann scheme.29,30 A dark region around the adsorbed guanine molecule in the simulated image, similar to the experimental feature (Fig. 2a and b), indicates that the dissociative adsorption of guanine molecule reduces the electron density around the Ge atoms. Further studies on changes in electron charge density after the adsorption of the guanine molecule are in progress to more accurately understand this phenomenon. In addition to ‘‘N(1)–H dissociation through an O dative bonded structure’’, we observed a minor adsorption structure from the series of STM images in Fig. 5; the minor feature
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(indicated by the yellow dashed circle) migrates on the Ge(100) surface, whereas the major one (marked as white dashed circle) does not. The minor structure appears as a bright protrusion without a dark site indicating that guanine reacts with Ge(100) via dative bonding.22 The possible adsorption configurations of guanine through dative bonding on Ge(100) are shown in Fig. S3 (ESI†). As mentioned above, the reaction through dative bonding of N(1), N(9), and N(10) atoms of guanine does not readily occur because the aromaticity must be broken when the dative bonds form. Therefore, we concluded that minor features shown in Fig. 5 are more likely to reflect the adsorption structures in Fig. S3a–c (ESI†) than those in Fig. S3d–f (ESI†). DFT calculations were further performed to determine possible dative bonded configurations of guanine on Ge(100) along with their respective adsorption energies. We obtained four optimized structures; a ‘‘N(7) dative bonded,’’ a ‘‘N(3) dative bonded,’’ and an ‘‘O dative bonded’’ were more stable than a ‘‘N(10) dative bonded structure’’ (see Fig. S4, ESI†). However, the possible adsorption structures in Fig. S3e and f (ESI†) could not be determined since they were unstable due to the loss of the aromaticity. Furthermore, the minor feature in Fig. 5 moves along or perpendicular to the dimer row. Hence, we propose that the migration of the minor feature is caused by competitive reactions between the atoms in the guanine molecule with Ge(100) via dative bonding, considering that the difference in the adsorption energies is relatively small (Fig. S4, ESI†). In conclusion, we elucidated the adsorption structure of guanine on Ge(100) at room temperature using an STM approach and DFT calculations. STM analysis revealed that the adsorption of guanine on Ge(100) occurs via N–H dissociation while the DFT calculations provide the optimized adsorption configurations with the corresponding adsorption energies. The most favorable configuration when guanine is adsorbed on Ge(100) was found to be ‘‘N(1)–H dissociation through an O dative bonded structure’’. This research was supported by the National Research Foundation of Korea (NRF) grant funded by the Korean government (MSIP) (Grant No. 20090083525, 2012M2A8A5025925, and 2010-0023313). Calculations were performed by using the supercomputing resources of KISTI.
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