Atomic and Electronic Structure of Pyrrole on Ge(100) - The Journal of

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J. Phys. Chem. C 2008, 112, 7412-7419

Atomic and Electronic Structure of Pyrrole on Ge(100) Do Hwan Kim,†,‡,§ Dae Sik Choi,† Suklyun Hong,*,‡ and Sehun Kim*,† Department of Chemistry and School of Molecular Science (BK 21), Korea AdVanced Institute of Science and Technology, Daejeon 305-701, Republic of Korea, Department of Physics and Institute of Fundamental Physics, Sejong UniVersity, Seoul 143-747, Republic of Korea, and DiVision of Science Education, Daegu UniVersity, Gyeongbuk 712-714, Republic of Korea ReceiVed: October 5, 2007; In Final Form: January 10, 2008

We have performed ab initio pseudopotential density-functional calculations for pyrrole adsorbed on the Ge(100) surface in order to investigate its atomic and electronic structure. A large number of the pyrrole/Ge(100) adsorption configurations that could result from cycloadditions and Lewis acid-base reactions were examined. The configuration with both Ge-N and Ge-C linkages was found to be the most stable. The Ge-N linkage is formed by dative bonding after N-H dissociation, and the Ge-C linkage is a weak chemical interaction leading to the loss of aromaticity from the pyrrole ring. The pyrrole molecule bridges two downGe atoms in adjacent Ge dimer rows. This configuration was used to explain the experimental scanning tunneling microscopy (STM) images.

Introduction The production of well-defined organic layers on semiconductor surfaces is important to the development of biological and chemical sensors, optical devices, and thin film displays.1-3 Understanding the reactions between organic molecules and semiconductor surfaces makes it possible to design new types of organic compounds and to predict the nature of the reactions between large biomolecules and semiconductor surfaces. As a result of the intensive research in this area, many different types of reactions have been found that are analogues to those found in solution chemistry. The adsorption of N-containing aromatic compounds is interesting because of the possible reactions involving the lone pair of electrons and π electrons.4-7 Pyrrole, a five-membered N-containing aromatic molecule, could be interesting for molecular electronics applications because polypyrrole has been shown to be a good organic conductor.8 The silicon surface covered with polypyrrole is also used for “gene tip” technologies, where biological information is gained by use of polypyrrole DNA chips.9 In our previous paper,10 we concluded that a β-C-Ge interaction enables pyrrole, a five-membered heterocyclic compound, to bridge adjacent Ge dimer rows, and presented only the key theoretical results necessary for the interpretation of our scanning tunneling microscopy (STM) results. In this paper, we present our results for the atomic and electronic structures of pyrrole molecules on Ge(100) in detail. There are many types of reactions that are possible as a result of the interaction between pyrrole molecules and Ge(100) and Si(100) surfaces, due to its various functional groups, as shown in Figure 1. The most thermodynamically favorable adsorption geometry is the configuration with the highest adsorption energy. The chemical and physical interactions between Ge atoms and the atoms of the pyrrole ring determine the adsorption energy. The interaction can be confined to a dimer row, but the pyrrole * Corresponding authors: e-mail [email protected] (S.H.) or [email protected] (S.K.). † Korea Advanced Institute of Science and Technology. ‡ Sejong University. § Daegu University.

Figure 1. Possible pathways of reaction of pyrrole with the Ge(100) surface.

ring can also interact with two adjacent dimer rows as in pyrimidine on Ge.7 Further, the fate of the dissociated hydrogen atom in the N-H dissociation pathway should also be considered. The aromaticity of the pyrrole molecule, which contains a conjugated double bond and a lone pair of electrons on the nitrogen atom, affects the reaction site and the relative stability of the final products. Of the many possible adsorption configurations for pyrrole/ Ge(100), N-H dissociative adsorption was found to be the most stable. The fate of the dissociated H was also studied. The reaction pathway for H-diffusion was found to explain the favorable position of H near the pyrrole molecule/Ge surface

10.1021/jp709740n CCC: $40.75 © 2008 American Chemical Society Published on Web 04/18/2008

Atomic and Electronic Structure of Pyrrole on Ge(100)

J. Phys. Chem. C, Vol. 112, No. 19, 2008 7413

Figure 2. Optimized configurations for the c(4 × 2) unit cell at a pyrrole coverage of 0.25 ML for dative-bonding reactions between a pyrrole molecule and the down-Ge atom of a Ge dimer: (a, b) N-dative bonding; (c, e) R-C dative bonding; (d, f) β-C dative bonding. Parallel configurations are in panels b, c, and f; tilted configurations are in panels a, d, and e. White, black, and gray balls represent C, N, and Ge atoms, respectively; hydrogen atoms are represented by small white balls.

TABLE 1: Relative Energies of Dative Bonding Configurations of Pyrrole on Ge(100) within the c(4 × 2) Unit Cella configuration

DN1

DN2

DC1

DC2

DC3

DC4

∆E (eV/molecule)

0.73

0.79

0.34

0.37

0.45

0.46

a

Energy ∆E is referred to the total energy of DA3 shown in Figure 6.

bond. Theoretical STM images for the favorable geometries were compared with the experimental images. Our calculation methods are described in the next section, and the results and discussion follow. Calculations To investigate the configuration of pyrrole on the Ge(100) surface, we performed ab initio calculations within the local density approximation (LDA) using the Vienna ab initio simulation package (VASP).11 Plane waves with energy up to 224.5 eV were included to expand the wave functions, and the atoms were represented by ultrasoft pseudopotentials, as provided by VASP.12 In the surface calculations, the theoretical lattice constant of germanium was determined (5.634 Å), which is in good agreement with the experimental value (5.658 Å). In contrast, the calculations with gradient-corrected density functional theory (DFT-GGA) resulted in an overestimate of the lattice constant (5.768 Å). The pyrrole-adsorbed Ge(100) surface was modeled as a slab composed of six Ge atomic layers and adsorbed pyrrole

molecules. The Ge bottom layer was passivated with two H atoms per Ge atom. The four topmost layers of the slab and the adsorbed molecules were allowed to relax with respect to the calculated Hellmann-Feynman forces, and the two remaining Ge layers were kept frozen during the structure optimization. Our calculations employed the residual minimization methoddirect inversion in the iterative subspace (RMM-DIIS) algorithm to minimize the total energy of the system. The surface structure was relaxed until the Hellmann-Feynman forces were smaller than 20 meV/Å. For the Brillouin-zone integration we used a 4 × 4 × 1 grid in the Monkhorst-Pack special point scheme. A Gaussian broadening with a width of 0.02 eV was used to accelerate the convergence in the k-point sum. By use of self-consistent Kohn-Sham eigenvalues and wavefunctions, the constant-current STM images were simulated within the Tersoff-Hamann scheme.13 The tunneling current I(r, (V) is proportional to the energy-integrated local density of states:

I(r, (V) ∝

∫E ∑ nk

EF(V F

|ψnk(r)|2 δ(E - Enk) dE

where +V and -V are the sample bias voltages for the emptystate and filled-state measurements respectively. The transition states for adsorption were investigated by the nudged elastic band (NEB) method.14 Results and Discussion We performed geometry optimization for almost all conceivable configurations. We first optimized the atomic structures with one pyrrole molecule per c(4 × 2) surface unit cell. We subsequently studied the effects of intermolecular interactions by extending the unit cell to p(4 × 2) or p(4 × 4) without increasing the number of adsorbed pyrrole molecules. First, we consider the dative bonding configurations resulting from Lewis acid-base reactions. The electron-deficient downGe atom plays the role of a Lewis acid and reacts with adsorbed pyrrole (the Lewis base) to form a dative bond. There are three possible Lewis base positions in a pyrrole molecule, the R- and β-carbons and the nitrogen atom. For each position, two configurations are possible, depending on the orientation of the aromatic ring relative to the Ge surface, which can be parallel or tilted. The optimized structures and the calculated bond lengths are shown in Figures 2 and 3. The relative energies ∆E (in units of electronvolts per molecule) of the dative reactions are given in Table 1 with respect to the total energy of the most stable configuration (see Figure 6c) found in this study. Note that all the energies shown in the tables in this paper are relative to the energy of this configuration. From Table 1, dative bonding through R-C (Figure 2c) is the most stable of all the dativebonding configurations. Wang et al.15 predicted that the main

Figure 3. Bond lengths of the pyrrole ring upon adsorption on Ge(100) through relatively stable C-end-on dative bonding: (a) pyrrole, (b) R-C dative bonding with the pyrrole ring parallel to the Ge surface (Figure 2c), and (c) β-C dative bonding with the pyrrole ring tilted relative to the Ge surface (Figure 2d).

7414 J. Phys. Chem. C, Vol. 112, No. 19, 2008

Figure 4. Configurations for the c(4 × 2) unit cell at a pyrrole coverage of 0.25 ML for the electrophilic aromatic substitution reactions between a pyrrole molecule and a down-Ge atom of a Ge dimer: (a-f) reactions at the R-carbon atom; (g-l) reactions at the β-carbon atom. The notation for configuration EA10 is different from that used in our previous paper (EA2).10

reaction pathway in this system arises through the initial attachment of the pyrrole molecule at the R-carbon position. The delocalization of π electrons makes dative bonding through the carbon atom energetically favorable. In our calculations, dative bonding through the R-carbon atom is 0.03 eV/molecule more stable than that for the β-carbon. This result is consistent with that of previous DFT calculations15 and is expected from the number of possible resonance structures stabilizing the developed positive charge. The distance between the R-carbon and the down-Ge atom (2.30 Å) is longer than found in Ge-N dative bonding with pyridine (2.04 Å).5 The Ge-C interaction is thought to consist mainly of weak π electron donation from the R-carbon atom to the down-Ge atom. The bond length between the R- and β-carbon atoms is slightly elongated from 1.39 to 1.43 Å. Similarly, in the case of dative bonding through the β-carbon, the bond length between the two β-carbon atoms changes from 1.43 to 1.45 Å. The R-C-end-on dative-bonded configuration (Figure 2c) retains a planar , but the aromaticity

Kim et al. of the pyrrole ring is weakened slightly by the weak π electron donation to the down-Ge atom. The C-C distance in the pyrrole molecule is slightly elongated (Figure 3b) but is still closer to the resonant bond length of aromatic compounds (1.39 Å) than to that of a C-C single bond (1.54 Å) or of a CdC double bond (1.34 Å). Dative bonding through nitrogen atoms has been observed in the adsorption of aliphatic amines on Ge(100).15 In the case of N-end-on dative bonding for pyrrole on Ge(100), the distance between the nitrogen and down-Ge atoms is 2.30 Å (tilted, Figure 2a) or 2.39 Å (parallel, Figure 2b) depending upon the orientation of the pyrrole ring to the Ge surface. The N-end-on dative bonding structure (DN1) is less stable than the C-endon bonding structure (DC1) by 0.39 eV, so the N-end-on dativebonding structure is thermodynamically unfavorable. Further H-removal from the carbon atom of the C-end-on dative-bonding configuration is analogous to electrophilic aromatic substitution in organic molecular reactions. The released hydrogen atom can bind to the electron-rich up-Ge atom in the same Ge dimer, or might diffuse to the next dimer. The optimized structures for this reaction type are shown in Figure 4. The Ge-C bond length is 1.96 Å, which is shorter than the bond length of 2.30 Å found in C-end-on dative-bonded configurations. The orientation of the pyrrole ring is either tilted or perpendicular to the Ge surface. In perpendicular configurations, both the R- and β-C-end-on products have aromatic pyrrole rings with nearly the same bond distances as free pyrrole molecules (EA4 and EA10 in Figure 5). If the pyrrole ring is tilted with respect to the Ge surface, each of these configurations becomes more stable. Of all the tested geometries resulting from electrophilic aromatic substitution, the R-C-end-on tilted configuration (EA1) shown in Figure 4 is the most stable and is higher in energy by just 0.16 eV/molecule than configuration DA3 shown in Figure 6, as listed in Table 2. However, the pyrrole ring in the tilted geometry has a slightly different bond length than that in the free pyrrole molecule, which means that it has weaker aromaticity. The greater stability of the tilted configurations is due to the additional interaction between the carbon atom of the pyrrole ring and the down-Ge atom in the adjacent dimer row. The distance between the β-C and the down-Ge atom in the adjacent dimer row is 2.48 Å, which is comparable to the β-C dative bonding distance (2.29 Å in Figure 2d). The details of this interaction are discussed in the following section. Configurations in which dissociated H is bonded to a diagonal Ge atom are all unstable. This is due to (1) the buckling behavior of the Ge surface, in which every Ge dimer has the same buckling symmetry, and (2) the repulsive interaction between the pyrrole ring and the H atom, which exist according to the repeating c(4 × 2)unit cells. The instability of these configurations is discussed again when the N-H dissociative adsorption products are considered.

Figure 5. Bond lengths of the pyrrole ring upon adsorption on Ge(100) through electrophilic aromatic substitution: (a) pyrrole, (b) EA1, (c) EA4, (d) EA7, and (e) EA10. These configurations are as defined in Figure 4.



Figure 6. Configurations for the c(4 × 2) unit cell at a pyrrole coverage of 0.25 ML for the dissociative adsorption reactions between a pyrrole molecule and a Ge atom: in panels a, c, and e, the plane of the pyrrole ring is tilted, while in panels b, d, and f it is perpendicular to the Ge(100) surface. Additional H are present in the adjacent dimer row because of the repetition of the c(4 × 2) unit cell.

Dissociative adsorption after N-H bond dissociation results in the most stable configuration. The nitrogen atom in the pyrrole ring is bound to the electron-deficient down-Ge atom of a Ge dimer, and the dissociated hydrogen atom migrates to an electron-rich up-Ge atom. The relevant structures are presented in Figure 6. N-H dissociative adsorption results in very stable configurations. The nitrogen atom of the pyrrole ring is bound to an electron-deficient down-Ge atom of a Ge dimer, and the dissociated hydrogen atom migrates to an electron-rich up-Ge atom. The N-end-on tilted structures are more stable than the perpendicular structures. The N-H dissociative adsorption products shown in Figure 6a,c are the most stable of the tested geometries, as listed in Table 3. With regard to aromaticity and the additional C-Ge interaction, the trend is very similar to

that for the electrophilic aromatic substitution products discussed above. The calculated bond distance in the pyrrole ring (Figure 7) indicates that the aromaticity of the pyrrole ring is slightly diminished for the tilted configuration. For DA3 (Figure 7c), the bond length between the R- and β-carbon atoms is 1.43 Å and the distance between the β- and γ-carbon atoms is 1.45 Å. The Ge-N distance changes from 1.85 Å in the perpendicular geometry to 1.99 Å in the tilted structure, and the distance between the β-carbon and the Ge atom in the adjacent dimer row decreases from 4.94 to 2.27 Å. This distance is nearly the same as that of C-end-on dative-bonded configurations (2.29 Å) and means that there is a weak chemical interaction between Ge and this carbon atom. It is clear that this additional C-Ge interaction affects the aromaticity of the pyrrole ring and contributes to the stability of tilted structures, as pointed out in our previous paper.10 This interaction results in the buckling of the Ge dimers in adjacent dimer rows, leading to a c(4 × 2) structure on the surface. As a result, the pyrrole ring bridges two Ge dimer rows. A bridged configuration has also been found for pyrimidine on Ge(100), where the interaction is double dative bonding through the nitrogen lone pair that does not affect the aromaticity of the pyrimidine ring.7 In the case of the Hdissociated N-end-on perpendicular geometry when there is no interaction with the adjacent dimer row, the pyrrole ring fragment retains a planar geometry and its aromaticity, but this configuration is energetically less favorable than tilted structures. Therefore, the additional C-Ge interaction is a more important factor than aromaticity in determining the reaction product of pyrrole on Ge(100). This interaction compensates for the weakening of the resonance, as suggested in our previous paper.10 Previous theoretical studies of the adsorption of pyrrole on Si(100) found that the N-end-on perpendicular structure is more stable than the N-end-on tilted geometry.16,17 The different trend obtained here might be due to the difference in the feasibility of forming a bridged configuration between two dimer rows. The equilibrium lattice constant is 5.43 Å for Si but 5.658 Å for Ge.18 Thus the interdimer distance is longer for the Ge surface, so the Ge(100) surface can accommodate adsorbed molecules in bridge sites. Our study of the coverage dependence clearly shows the effects of this β-C-Ge interaction. For a pyrrole coverage of 0.25 ML, the migration of dissociated hydrogen to the diagonal

Figure 7. Bond lengths of the pyrrole ring upon adsorption on Ge(100) via N-H dissociative adsorption: (a) pyrrole, (b) DA2, and (c) DA3. These configurations are as defined in Figure 6.

TABLE 2: Relative Energies of the Electrophilic Aromatic Substitution Product of Pyrrole on Ge(100)a R-C-end-on tilted

β-C-end-on perpendicular

tilted

perpendicular

configuration

EA1

EA2

EA3

EA4

EA5

EA6

EA7

EA8

EA9

EA10

EA11

EA12

∆E (eV/molecule)

0.16

0.17

0.48

0.27

0.50

0.56

0.32

0.22

0.56

0.39

0.53

0.57

a

Energy references are the same as in Table 1.


Kim et al.

Figure 8. Configurations for N-H dissociative adsorption reactions with the dissociated hydrogen on a diagonal Ge atom: (a, b) for the c(4 × 2) unit cell at a coverage of 0.25 ML; (c, d) for the p(4 × 2) unit cell at a coverage of 0.125 ML. Side views of the optimized geometries are shown in panels a and c, whereas top views are shown in panels b and d.

TABLE 3: Relative Energies of the N-H Dissociative Adsorption Product of Pyrrole on Ge(100)a tilted

perpendicular

configuration

DA1

DA3

DA5

DA2

DA4

DA6

∆E (eV/molecule)

0.05

0.00

0.45

0.32

0.37

0.43

a


Figure 10. Configurations for the c(4 × 2) unit cell at a coverage of 0.25 ML for the cycloaddition reactions: (a-c) [2 + 2] cycloaddition; (d-f) [4 + 2] cycloaddition; (g, h) tight bridge. C2-1, C4-1, and TB1 appear as C2, C4, and TB, respectively, in our previous paper.10

TABLE 4: Relative Energies of the C- and N-end-on Adsorption Product of Pyrrole on Ge(100)a

a

Figure 9. Configurations for the c(4 × 2) unit cell at a coverage of 0.25 ML for the C- and N-end-on configurations. The on-top bridgetype configuration is shown in panel b.

position of the next Ge dimer (DA5 in Figure 6) in the same dimer row is about 0.45 eV less favorable than for the DA3 configuration. The hydrogen atom in the adjacent dimer row repels the pyrrole ring, and the C-Ge distance is 3.98 Å, which means that there is no C-Ge interaction. However, for the p(4 × 2) unit cell with a pyrrole coverage of 0.125 ML, the β-CGe distance is 2.31 Å, indicating the influence of the Ge-C interaction and configurational change. This configuration is only 0.20 eV/molecule less stable than the most stable configuration (DA3). The optimized structures for various coverages are shown in Figure 8. An adsorption structure containing both C-Ge and N-Ge bonding was suggested by Cao et al.3 for the adsorption of pyrrole on Si on the basis of FT-IR measurements. Seino et al.16 confirmed that this configuration is the most stable configuration for pyrrole on Si(100) up to a coverage of 0.5 ML. The optimized geometries are shown in Figure 9. In our calculations, this type of reaction results in stable products. H-migrated structures (CN1 and CN2) are relatively stable, that is, only 0.16∼0.22 eV less stable than DA3 in spite of the loss of the aromaticity of the pyrrole ring. The end-bridge geometry

configuration

CN1

CN2

CN3

∆E (eV/molecule)

0.22

0.16

0.92


(CN2) is more stable than on-top (CN1) by 0.06 eV, as shown in Table 4. Both CN1 and CN2 have symmetric (2 × 1) structures. As a conjugated diene compound, pyrrole might react via a cycloaddition pathway. The optimized cycloaddition products are shown in Figure 10. For the symmetry-forbidden [2 + 2] cycloaddition, there are two stereochemically isomeric on-top configurations and one end-bridge configuration. The two ontop isomers have different positions of their hydrogen atoms and thus different directions of the plane of the aromatic ring relative to the Ge surface. We found that the [2 + 2] cycloaddition configuration with a parallel pyrrole ring (Figure 10a) is more stable than the configuration with a perpendicular ring (Figure 10b). For the symmetry-allowed [4 + 2] cycloaddition, the configuration in which the N-H bond points downward (Figure 10d) relative to the Ge surface is more stable than the case in which it points upward (Figure 10e). Pyrrole can react with two Ge atoms in adjacent dimers, forming endbridge products (Figure 10c,f). As expected, the on-top adducts are symmetric surface dimers, whereas the end-bridge products remain buckled. The end-bridge product is less stable than the most stable on-top products for both [2 + 2] and [4 + 2] cycloadditions. The most stable [4 + 2] Diels-Alder reaction product (Figure 10d) is 0.3 eV more stable than the [2 + 2] analogue (Figure 10a). This trend is consistent with previous theoretical calculations based on (1) the DFT cluster model for pyrrole on Ge(100) (∆E ) 0.33 eV)15 and (2) the slab model for pyrrole on Si(100) (∆E )0.48 eV).16



Figure 11. STM images of the pyrrole-adsorbed Ge(100) surface at room temperature : (a) bright protrusion, Vs ) -1.966 V; (b) flowerlike feature, Vs ) -1.700 V; (c) flowerlike feature with dark region, Vs ) -1.800 V. The assigned features can be clearly seen in the square box. Detailed experimental conditions are described in our previous paper.10

TABLE 5: Relative Energies of Cycloaddition-type Configurations of Pyrrole on Ge(100)a

a

configuration

C2-1

C2-2

C2-3

C4-1

C4-2

C4-3

TB1

TB2

∆E (eV/molecule)

0.79

1.61

1.01

0.49

0.64

0.64

0.64

0.58


TABLE 6: Relative Energies of Relatively Stable Configurations of Pyrrole on Ge(100) for Various Coveragesa ∆E (eV/molecule) coverage

DA1

DA2

DA3

DA5

EA1

EA2

CN1

CN2

0.125 ML 0.250 ML

0.00 0.05

0.34 0.32

0.03 0.00

0.23 0.45

0.06 0.16

0.17 0.17

0.22 0.22

0.16 0.16

a c(4 × 2) unit cells are chosen for 0.25 ML and p(4 × 2) for 0.125 ML, respectively. Energy references for 0.25 ML are the same as in Table 1, and those for 0.125 ML are referred to the total energy of DA1 shown in Figure 6.

Figure 12. Theoretical filled-state (-1.8 V) STM images for (a) DC1 in Figure 2 within the p(4 × 2) unit cell, (b) N-H dissociative adsorption product within the p(4 × 4) unit cell when H has diffused out of the region of interest, and (c) DC2 in Figure 2 within the p(4 × 2) unit cell. The image of the experimentally observed flowerlike STM feature is shown in panel d.

Two tight bridged products (Figure 10g,h) are similar to those found in pyridine adsorbed on Si(100)19 and may form via [2 + 2] cycloaddition following [4 + 2] cycloaddition, depending upon the outcome of the initial [4 + 2] reaction. The cycloaddition products are all energetically less favorable than the N-H dissociative adsorption products. The relative energies for all the cycloaddition products are listed in Table 5. The relatively stable interface geometries discussed above were also investigated at pyrrole coverages of 0.25 and 0.125 ML, and the adsorption energies are summarized in Table 6. Here 1 ML is defined as one molecule adsorbed per surface Ge

atom. In the experimental STM observations, the adsorption features were not clearly identifiable above 0.2 ML. So the coverage dependence was investigated up to 0.25 ML. The reference adsorption energies for each coverage are 1.50 eV/ molecule for 0.25 ML (DA3 in Figure 6) and 1.51 eV/molecule for 0.125 ML (DA1 in Figure 6). Table 6 shows that the ordering of the adsorption energies at different coverages is nearly the same, with decreasing adsorption energies at higher pyrrole coverages, indicating that there is a repulsive interaction between the adsorbed molecules. This repulsion is particularly obvious for the DA5 configuration. Finally, to interpret the experimental filled-state STM images we simulated the constant-current STM images. The experimental STM image after adsorption of 0.18 ML of pyrrole at room temperature contains three different types of adsorption features. The bright protrusions (Figure 11a) are very similar to those for pyrrole on Si(100)20 and are thus likely to be due to the random distribution over the Ge surface of H-dissociated pyrrole molecules in N-end-on or C-end-on configurations. These features are located on either side of single dimer units. The flowerlike features (Figure 11b) are very similar to those found for pyridine on Ge(100),6 in which pyridine molecules bond datively to the down-Ge atom of one dimer row and are located between two dimers. Flowerlike features with dark regions (Figure 11c) are also observed. The dark region is located either in the diagonal or the orthogonal position inside the hexagonal flowerlike feature with respect to the dimer row direction. We simulated the theoretical STM images for several bonding configurations with lower energies (not all reported here). The simulated filled-state STM images for the C-end-on dativebonded configuration DC1 (Figure 12a) and the H-removed NH-


Kim et al.

Figure 13. Theoretical filled-state (-1.8 V) STM images for (a) DA1 in Figure 6, (b) EA1 in Figure 4, (d) DA3 in Figure 6, and (e) EA2 in Figure 4. Panels a and b are within the p(4 × 2) unit cell, whereas panels d and e are within the p(4 × 4) unit cell. Experimentally observed STM images of flowerlike features with dark regions are shown in panels c and f.

dissociative adsorption configuration (Figure 12b) are in good agreement with the experimentally observed flowerlike feature (Figure 12d), and the simulated image for DC2 (Figure 12c) shows that the bright protrusion inside the hexagon is shifted toward one dimer row. Considering that the acidity of pyrrole molecules is not high (pKa ) 23.0 in dimethyl sulfoxide, DMSO21), pyrrole molecules could interact with surface Ge atoms without further N-H or C-H dissociation. However, the dative bonded configuration is energetically less favorable than the N-H dissociative adsorption product. The energetics indicate that the flowerlike feature corresponds to the H-removed N-H dissociative adsorption product. To investigate the Hdiffusion related to the feature in Figure 11b, we considered the activation barrier to the H-diffusion process. Note that Russell and Ekerdt22 estimated the H-diffusion barrier on Gecovered Si surfaces to be 1.0 eV/molecule from thermal desorption data. Previously, using the NEB method we calculated the H-diffusion barrier for acetic acid on Ge(100) to be 1.1 eV/molecule.23 Our NEB calculations for H-diffusion in pyrrole/Ge(100) indicate a barrier of 1.02 eV/molecule, which is nearly the same as the values obtained in previous studies. This barrier is very high at room temperature, so the feature in Figure 11b appears less frequently at room temperature. The theoretical STM images in Figure 13a,d for the most stable NH-dissociative N-end-on tilted structures contain flowerlike features with dark regions within p(4 × 2) and p(4 × 4) unit cells, respectively. The position of the dark region depends on the adsorption site of the dissociated H atom. Meanwhile, the simulated STM images for the electrophilic aromatic substitution products (EA1 and EA2 in Figure 4) resulting from C-H dissociation are similar to those for DA1 and DA3 and are 0.16-0.17 eV/molecule higher in energy than DA3 for 0.25 ML. Thus these products will also make minor contributions to the feature in Figure 11c.

The theoretical images for the NH dissociated N-end-on perpendicular structures (DA2 and DA4 in Figure 14b,c), for which the aromaticity of the pyrrole ring is totally conserved, did not correspond to the above observed features but are somewhat similar to the bright protrusions in Figure 11a. The theoretical STM image for CN2 (Figure 14a) also contains bright protrusions, implying that CN2 could be responsible for the bright protrusions. Considering the relative stability of these configurations, it is more likely that the bright protrusions are due to CN2. The arrangement and size of the bright protrusions vary depending upon the bonding of the adsorbed pyrrole molecule. In these configurations (CN2, DA2, and DA4), the pyrrole molecules are bound to one dimer row and will experience less steric hindrance at higher coverages of pyrrole molecules than in DA1 or DA3. This might be why the bright protrusions appear more randomly over the Ge(100) surface and why the population of bright protrusions increases at higher coverages. Conclusion We have investigated the adsorption of pyrrole molecules on the Ge(100) surface using ab initio calculations. We calculated the total energies of many possible configurations resulting from various types of chemical reactions between adsorbed pyrrole molecules and Ge(100) surface atoms. The most stable configuration arises when a pyrrole molecule adsorbs on Ge dimers via Ge-N bonding and an additional Ge-C interaction, forming a bridged structure between adjacent Ge dimer rows. The aromaticity of the pyrrole ring is affected because of the interaction between the β-carbon atom and the Ge atom in the adjacent row. The simulated image for this optimized geometry contains a flowerlike feature with a dark region, which is consistent with the most dominant feature in the observed STM


J. Phys. Chem. C, Vol. 112, No. 19, 2008 7419 Acknowledgment. This research was supported by the Brain Korea 21 Project, the SRC program (Center for Nanotubes and Nanostructured Composites) of MOST/KOSEF, and Korea Research Foundation Grant KRF-2005-070-C00063. The calculations were supported by the KISTI through the eighth Strategic Supercomputing Support Program. References and Notes

Figure 14. Theoretical filled-state (-1.8 V) STM images for (a) CN2 in Figure 9 within the p(4 × 2) unit cell and (b) DA2 in Figure 6 and (c) DA4 in Figure 6 within the c(4 × 2) unit cell. The experimentally observed STM images of bright protrusion features are shown in panel d.

images. Further, a similar configuration but with a dissociated H that has diffused out of the region of interest can also explain the experimental images with a flowerlike feature without a dark region. Finally, the C- and N-end-on configurations, in which a pyrrole molecule is located on one dimer row, appear as bright protrusions in the STM images.

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Atomic and Electronic Structure of Pyrrole on Ge(100) - The Journal of

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