DFT Characterization of Metallole-Decorated Silicon (001) Surface

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C: Surfaces, Interfaces, Porous Materials, and Catalysis

DFT Characterization of Metallole-Decorated Silicon (001) Surface Cagil Kaderoglu, and Sinasi Ellialtioglu J. Phys. Chem. C, Just Accepted Manuscript • DOI: 10.1021/acs.jpcc.9b00623 • Publication Date (Web): 16 Apr 2019 Downloaded from http://pubs.acs.org on April 16, 2019

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The Journal of Physical Chemistry

DFT Characterization of Metallole-Decorated Silicon (001) Surface Çağıl KADEROĞLU1,*and Şinasi ELLİALTIOĞLU2 1 Department

of Physics Engineering, Ankara University, Ankara, Turkey

2 Basic

Sciences, TED University, Kolej, Ankara, Turkey

*Corresponding author: [email protected] Abstract Multifunctional molecules have been important for being building blocks of interesting molecular systems. Combining these multifunctional molecules with conventional semiconductor surfaces have been utilized in designing new materials for different electronic and optical applications. Metalloles, as a group of multifunctional molecules, have unique electronic and photophysical properties. In this study, Density Functional Theory (DFT) calculations were performed to examine the structural and electronical properties of metallole (MC4H6; M = Si, Ge, Sn)-decorated Si(001)(2×2) surfaces. After determining the structural parameters of single isolated metallole molecules, eight different adsorption configurations on silicon surface were proposed to find out the most stable binding models for each. The self-dissociation of H atom in stannole [4+2]-(II) model during these calculations led to three different dissociation models (including M–H and C–H dissociation) to be considered for all M atoms. As a result of total and adsorption energy calculations, Bridge-(I) model was found to be the most stable configuration for non-dissociated molecules, while M–H dissociation was the most stable for dissociated configurations. The reaction paths of structural transitions between proposed models were also plotted to compare the energy barriers. The highest barrier was seen for [2+2]-(II) to Bridge-(II) transition. Dimerization of these metallole molecules were also studied. The exo model dimer adsorption on Si(001)-(2×2) surface was found to be the most stable one. According to the electronic structure calculations, the energy band gap of the clean (2×2) silicon surface widens from ~ 0.05 eV to ~ 0.9 eV (direct) and ~ 0.6 eV (indirect) upon adsorption of metallole monomers and dimers, respectively.

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1. INTRODUCTION The silacyclopentadiene molecules (Figure 1), more commonly known as siloles, are unsaturated five-membered heterocyclic compounds, that is the structural analogue of cyclopentadienes in which the bridge-site carbon is replaced by silicon1. Such cyclopentadiene derivatives are also named as metalloles due to the metallic nature of the heteroatom in the molecule. The R sites allow the silole molecule to bind to six other atoms or molecules and thus make it the building block of many interesting molecular systems that can be categorised as substituted or fused siloles2,3. Silole containing molecules were first synthesized at the beginning of 1960s4–9. Since then, silole derivatives have been in the focus of many technological research due to the unique electronic and photophysical properties they reveal10,11. It also should be specified that substitution of 1–1, 2–5 or 3–4 positions of the parent molecule has a major tuning effect on these electronic and photophysical properties12,13. As a result of the interaction between the σ∗ and π∗ orbitals of the SiR2 moiety and butadiene moiety, siloles own a low-lying LUMO level aiming for the high electron acceptability and fast electron mobility14. This feature makes the silole derivatives ideal for electron transport applications such as in organic light emitting diodes (OLEDs)15–19. Furthermore, in 2001, it was discovered that non-luminescent silole molecules in solution form become emissive when aggregated in thin film form20,21. This so-called aggregation-induced emission (AIE) feature allows silole derivatives to be incorporated into a wide range of different technological applications ranging from bio-labelling to trinitrotoluene (TNT) censoring22–26.

Figure 1. Structural representation of the Silole/Germole/Stannole molecule


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Although silole derivatives have been extensively studied for their above-mentioned technological applications, studies on the parent silole (SiC4H6) itself have been very limited due to difficulties in synthesizing, thus making it one of the least studied member of the organosilicon group27–31. However, in a recent study32, the first gas-phase synthesis of parent silole was carried out under single-collision conditions. This study motivated us to perform some DFT simulations for a prediction about the atomic and electronic properties of the new surface structure formed by silole adsorption on silicon. Because, reformation of inorganic surfaces by adsorption of interesting molecules is a widely used method to create new materials whose electronic and optical characteristics can be tuned for different applications33–37. In addition, the main reason why silicon is chosen as the substrate is its widespread use in nano-electronic studies due to its electronic properties and suitable surface structure for the formation of atomic-scale hybrid surfaces38–40.

In order to take our work a step further, we have also considered two other metalloles, germole (GeC4H6) and stannole (SnC4H6), that are the germanium and tin congeners of the silole, as the adsorbate. The reason we include these two in this study is not only their technological use 41,42 but also to see if a heavier hetero–atom with different electronegativity in the adsorbate molecule affects the electronic properties of the overall surface structure.

2. METHODS As mentioned in the INTRODUCTION section, silicon was used as the substrate for the adsorption process, since it is one of the cornerstones of semiconductor technology. The (2×2) reconstructed (001) silicon surface was chosen because the dimerized surface structure provides a suitable medium for the various adsorption geometries of the cyclic MC4H6 (M = Si, Ge, Sn) molecules. Furthermore, in a previous work43, (2×2) reconstructed (001) silicon surface was shown to be more stable by 0.24 eV than (1×2) surface known as the room temperature configuration.


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The substrate was composed of 11 atomic layers and a ~20 Å vacuum in a supercell formation. In order to avoid the possible interactions between two consecutive substrate blocks in the supercell, the unsaturated broken bonds of each silicon atom at the bottom layer were passivated with two hydrogen atoms. All of these hydrogen atoms and top 6 layers of the silicon were allowed to relax into their energy minima, while bottom 5 Si layers were fixed into their bulk positions. Vienna Abinitio Simulation Package (VASP), which is a DFT implemented code based on plane wave basis set and pseudo-potential approach44–47 was used to perform the ab-initio total energy calculations for all structural models. Projector augmented wave (PAW) approach48,49 with a 520 eV cut-off energy, and Perdew–Burke–Ernzerhof (PBE) functionals with generalized gradient approximation (GGA) including the van der Waals corrections50-52 were used for electron–ion and electron– electron interactions, respectively. As the result of the k-points convergence test, (4×4×1) Monkhorst–Pack k-point scheme53 was found to be appropriate for the Brillouin zone integration of the (2×2) silicon substrate. Structures were optimized according to conjugate-gradient algorithm with an electronic minimization parameter of 10–5eV. The atomic structure and charge density visuals were created by using VESTA program54. The lattice parameter used to model this substrate was calculated as 5.46 Å, which is in the range of previous experimental55 and theoretical38,56–58 results. The lengths and the tilt angles of the relaxed asymmetric dimers on the clean silicon surface were measured as 2.357 Å and 18.3, respectively.

3. RESULTS and DISCUSSION In the first step of the study, silole, germole, and stannole monomers were optimized in order to find their geometric parameters. In these three monomers having a planar shape, C–M bond lengths increase and the C–M–C angles () decrease, as M with a larger atomic radius is considered. The calculated parameters given in Table 1 are in good agreement with that of theoretical and experimental results in Ref.59–60 and 61–62, respectively.


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Table 1. The calculated parameters of Silole/Germole/Stannole monomers. Bond lengths are in Å and angles are in degrees. (a, b, c, and d show the values taken from Ref. 59–62, respectively.)

M–C1  M–C2

C1 –C3  C2–C4

M = Si

M = Ge

1.870 a 1.879 (1.869, 1.877)b

1.965 a 1.959 (1.927, 1.938)b

1.868c 1.356 1.355a (1.354, 1.349)b

1.945d 1.351 1.352a (1.353, 1.347)b

M = Sn 2.154 2.165a 1.351 1.352a

1.358c 1.483 1.487a (1.482, 1.487)b

1.347d 1.483 1.486a (1.485, 1.479)b

1.511c 1.495 1.494a (1.488, 1.489)b 1.089 (1.090, 1.084)b 1.095 (1.085, 1.089)b 93 92.4a 107.9 108.3a

1.508d 1.551 1.543a (1.549, 1.534)b 1.089 (1.090, 1.083)b 1.095 (1.085, 1.089)b 89.5 89.4a 109.0 109.2a

83.8 83.4a 109.0 109.4 a

1  2

106.3

106.8

107.1

3  4

117.1 116.9a

118.4 118a

121.1 121a

C3–C4 M–H C1–H  C2–H C3–H  C4–H  

1.483 1.487a 1.726 1.735a 1.089 1.096

Secondly, silole, germole, and stannole adsorptions on clean Si(001)-(2×2) substrate were modelled. For this process, eight different possible adsorption models including [4+2] and [2+2] cycloadditions and bridge-type bondings were considered for each metallole molecule, as seen in Figure 2. Three different [2+2] cycloaddition models were proposed, in one of which the molecule is bound to a single silicon dimer (see Figure 2 (a)), and in the other two, it binds to two neighbouring silicon dimers (Figure 2 (b) and (c)) which can also be considered as a kind of a semibridge model. In Figure 2 (d), (e), and (f), [4+2] cycloaddition models are depicted for different adsorption sites on the surface. The last two models presented in Figure 2 (g) and (h) are two different bridge-type models among which the molecule in one is rotated 90 relative to the other.


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Figure 2. Top and side views of non-dissociated models considered ACS Paragon Plus Environment

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In order to determine the most stable adsorption model for each adsorbate, the adsorption energies were calculated according to 𝐸Ad = 𝐸Substrate + Molecule ― (𝐸Substrate + 𝐸Molecule) and tabulated in Table 2. Here, the negative values mean that the overall reactions are exothermic and surfaces are chemically stable. According to these data, the most stable adsorption geometries for nondissociated configurations are the Bridge-(I) models. It is already expected that the [4+2] and [2+2] cycloaddition models are more energetic than the bridge models, because two of the dimer components on these surfaces are not bonded with the adsorbate and remain electronically unsaturated. On the other hand, for all configurations, the saturated dimers became almost symmetric during the adsorption process. This situation was also confirmed by previous studies done with other 5- and 6-membered cyclic molecules38,63,64. Among all non-dissociated structures, the adsorption energy of Bridge-(I) stannole/Si(001)-(2×2) surface is the lowest.

Table 2. The calculated total and adsorption energies of the considered surfaces. EAd is the adsorption energy (in eV). EAd for silole

EAd for germole

EAd for stannole

I

–2.44

–2.48

–2.77

II

–2.19

–2.19

–2.23

III

–2.30

–2.32

–2.41

I

–2.96

–3.02

II

–3.19

–3.30

III

–3.06

–3.15

–3.15 dissociated Fig. 3 (a) –3.33

I

–3.55

–3.56

–3.63

II

–3.34

–3.37

–3.42

Models

[2+2]

[4+2]

Bridge

Unlike silole and germole, [4+2]-(II) model of stannole can not stay stable in this configuration, and eventually dissociates. Due to the larger atomic size of Sn, H atom gets much closer to the dimer-Si. Here, one of the two hydrogens bonded to Sn atom dissociates from the molecule and binds to one of the Si atoms on the neighbouring free dimer. As a result, another new bond appears between now-unsaturated Sn and the second Si atom of the neighbouring free dimer (see Figure 3 (a)). ACS Paragon Plus Environment

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Cyclic molecules generally do not tend to dissociate. However, this result for stannole has led us to examine the other dissociated models. Therefore, in addition to metal–H dissociation (Figure 3 (a)), we have also considered two other carbon–H dissociated models shown in Figure 3 (b) and (c).

Figure 3. Considered dissociated models The energy differences (E) of these dissociated structures given in the figure were normalized according to the most stable non-dissociated Bridge-(I) models. Here, it is obvious that M–H dissociated models are more stable than the bridge configurations, while the total energies of the remaining two models are much higher.

The exothermic nature of all adsorption models indicates that the system is more unstable when the molecule approaches the surface before the reaction begins, and after that when the molecule is attached to the surface, the system will shift to a more stable energy state. Therefore, reaction paths of non-dissociated models were plotted in Figure 4 (a)–(d) to see the energy profiles of the structural transitions between stable models. In addition, the whole reaction paths for the most stable M–H dissociated models were plotted in Figure 4 (e). In order to obtain these energy profiles, the Cl-NEB (Climbing Nudged Elastic Band) method65–68, which is based on optimizing a certain number of intermediate structures between given initial and final states, was used. To create these


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reaction paths, four equidistant intermediate structures were used in (a)–(d), while this number is eight in (e).

Figure 4. Reaction paths of different structural transitions (Color on-line) ACS Paragon Plus Environment

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The energy barriers (Ebar) for (a)–(d) are given in Figure 4. In Figure 4 (c), the energy barrier values are much higher when compared to the other transitions. This is due to the fact that the lower hydrogen of the metal in [2+2]-(I) configuration is also close to the silicon atom of the dimer. So, even if no dissociation occurs here by itself, there is still a small interaction between H and Si atoms. As seen from Figure 4 (e), there is no energy barrier for stannole, and this is why we can not reach a stable [4+2]-(II) configuration. In contrast, silole and germole appears to have local minima at the [4+2]-(II) configuration. The energy differences between local minima and the peak values in barriers of H-dissociation for silole and germole are 0.35 eV and 0.10 eV, respectively.

Table 3. Calculated atomic key parameters of Bridge-(I) and M–H dissociated metallole adsorptions on Si (001). (Bond lengths and angles are in Å and degrees, respectively. The indices (1) and (2) represent the right and left silicon dimers in Figure 2, respectively. Atom numbering is the same as in Table 1.)

Bond Lengths

Silole

Angles

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

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Germole

Stannole

Bridge- (I)

M–H Dissociated

Bridge- (I)

M–H Dissociated

Bridge- (I)

M–H Dissociated

Si–Si dimer (1)

2.40

2.40

2.40

2.40

2.41

2.41

Si–Si dimer (2)

2.35

2.38

2.35

2.38

2.35

2.38

Sidimer–C1 / Sidimer–C2

1.96

1.94 / 1.93

1.95

1.93 / 1.92

1.95

1.91 / 1.92

Sidimer–C3 / Sidimer–C4

2.02

-

2.02

-

2.03

-

M–C1 / M–C2

1.89

1.99 / 1.91

2.00

2.11 / 2.02

2.20

2.30 / 2.22

M–Sidimer

-

2.46

-

2.53

-

2.70

C1–C3 / C2–C4

1.57

1.51 / 1.50

1.56

1.50 / 1.49

1.56

1.50 / 1.49

C3–C4

1.60

1.35

1.60

1.35

1.61

1.35

M–H

1.50

1.50

1.56

1.57

1.74

1.75

C1–H / C2–H

1.10

1.10

1.10

1.10

1.10

1.10

C3–H / C4–H

1.10

1.09

1.10

1.09

1.10

1.10

Sidimer–H

-

1.51

-

1.51

-

1.51



92.0

91

87.5

87.4

81

82



109.0

-

110.6

-

110.9

-

1 / 2

99.3

102 / 105

99.7

102 / 105

100.0

102 / 104

3 / 4

110.8

119 / 118

111.9

121 / 120

113.7

123 / 122


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Table 3 shows the bond lengths and angles calculated for the most stable non-dissociated and dissociated surface structures. The length of the silicon dimers to which the C3 and C4 of Bridge-(I) are attached was slightly shortened than on the clean surface, while the other dimer on the heteroatom side was elongated.

For dissociated models, however, both dimer lengths were

elongated. Since these values are in the experimentally measured range (2.20 – 2.47 Å), it can be said that the metalloles did not break the Si bonds on the surface during adsorption. Comparison of Table 1 and Table 3 shows that all bond lengths in the monomers increased slightly after adsorption on silicon. In addition, both  and  angles in Bridge-(I) models decreased while  angles increased. In dissociated configurations, while 1 and 2 decreased, 3 and 4 increased slightly. This variation in bond lengths and angles can be explained by the change of the planar structures of the molecules and the electronic configuration of the surfaces after adsorption.

In this part of the work, the electronic band structures and their corresponding total and partial density of states (DOS) were plotted in Figure 5 in order to investigate the electronic properties of metallole adsorbed silicon surfaces. The energy bands and DOS patterns of these surfaces are very similar to each other, therefore the graphs in Figure 5 were plotted only for non-dissociated silole and dissociated stannole adsorption to show the general electronic behaviour of these structures. The grey area in the background of the energy band diagrams represents the projected bulk bands of non-dimerized Si(2×2) infinite surface, while dotted lines represent the energy bands of reconstructed surfaces. Figure 5 shows that the asymmetric dimerization on the top layer of clean silicon surface leads to four surface states in the fundamental gap of projected bulk bands with an almost vanishing band gap57. The origin of these surface states is the difference between upper and lower components of silicon dimers69. The lower Si atoms of dimers with empty dangling bonds give rise to the surface states close to the conduction band while upper Si atoms with fully occupied dangling bonds constitute the other two states close to valance band. It is clear from Figure 5 that the band gap of this clean surface widens when silole/germole/stannole molecule attaches to the


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silicon dimers. This means the charge transfer between surface and molecule rearranges the electronic states of dimer components. Therefore, these dimers become symmetric and surface states originated from them are pushed down and widen the band gap. Bridge-(I) configurations have direct band gaps of 0.923 eV, 0.915 eV, and 0.901 eV while M–H dissociated configurations have 0.917 eV, 0.913 eV and 0.912 eV at the  point of the Brillouin zone for silole, germole, and stannole, respectively.

Figure 5. Electronic band diagrams and DOS plots of Metallole/Si(001)-(2×2) surfaces (Bridge-(I) diagrams belong to non-dissociated silole adsorption, M–H dissociated diagrams belong to stannole adsorption)

This widening of the band gap region is also shown in the total DOS plots obtained by superimposing both clean and metallole adsorbed silicon surfaces. According to the partial contributions of orbitals over the entire DOS in Figure 5, the valance bands are mainly composed of p-orbitals with less mixture of s-orbitals between 0 eV and 4 eV. As one moves down in the


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valence bands away from the gap region, s-orbital mixing increases. The shoulder at +1 eV in the DOS plot of M–H dissociation corresponds to resonance bands partially fall in the gap around J and J. Decoration of semiconductor surfaces with some functional molecules is one of the popular methods to create micro/nano hybrid electronic devices70–72. Hence, utilization of our results may be helpful in the field of band gap engineering.

Figure 6. (a) Charge density difference isosurfaces of Metallole/Si(001)-(2×2). The isosurface value is  0.004 eÅ–3. Red (blue) color symbolizes the charge accumulation (depletion). (b) DDEC6 net charge and bond order analyses (Bond orders are given in parenthesis).


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To have a deeper insight in the electronic nature of these surfaces, charge density differences were calculated and presented in Figure 6 (a). Here, isosurfaces were plotted according to the formula ∆𝜌 = 𝜌Substrate + Molecule ―(𝜌Substrate + 𝜌Molecule) with an isosurface value of 0.004 eÅ–3. Red color symbolizes charge accumulation, while blue is used for charge depletion. According to Figure 6 (a), charge depletion areas (blue) on C and dimer-Si atoms, and charge accumulation areas (red) in between these atoms denote that each one of the C=C double bonds are broken and form new bonds of mostly -character with dimer-Si atoms to bind the molecule to the surface. This is also confirmed by a ~ 16% increase in the C–C bond lengths in Table 3 compared to those in Table 2. On the other hand, the net charges on the molecules and bond orders of each atom can be visualized in Figure 6 (b) obtained by employing Density Derived Electrostatic and Chemical charge analysis method (DDEC6)73–75. As can be seen from the figure, during the adsorption process of metalloles on silicon, charge transfer direction is from the surface to the molecule. Despite the fact that the total amounts of transferred charges are close to each other, their distributions on the molecules are different. The net charge on molecules for non-dissociated models are higher than that of dissociated ones.

Finally, dimerization energy of metallole molecules relative to the two isolated monomers were calculated. Based on the well-known models of dicyclopentadiene molecule76, six different dimer models were considered for this work. Two of them, named as endo and exo (Figure 7 (a), (b)) are known to be the most stable ones for dicyclopentadiene, while other four models (Figure 7 (c)(f)) are hypothetically possible. As seen from the energy values given in the figure inset, dimerization energy of endo and exo models of metalloles are very close to each other and lower than the rest.


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Figure 7. Dimer models of free metallole molecules

Inspired by a similar work done for dicyclopentadiene adsorption on Si(001)-(1×2) surface77, adsorption energy (EAd) calculations for endo and exo dimer on clean silicon surface were performed (Figure8). For all M atoms, exo models seems to be more stable. Also, as in monomer adsorption (see Table 2), the lowest energy of dimer adsorption is for exo-Sn.

Figure 8. Endo and exo dimer adsorption on Si(001)-(2×2) surface ACS Paragon Plus Environment

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Electronic band structure and partial charge densities of exo-dimer-adsorbed silicon surface are given in Figure 9. Since they are similar for all M atoms, the plots only for M = Si are given here. Exo configurations have an indirect energy band gap of 0.567 eV for silole, 0.562 eV for germole, and 0.555 eV for stannole. The indirect energy band gap values for endo configurations are 0.626 eV, 0.623 eV, and 0.663 eV for silole, germole, and stannole, respectively. Two surface states (S1 and S2) appear in the fundamental band gap are mainly due to p-orbitals of silicon dimer components that the molecule did not attach. This is clearly seen in band decomposed charge density plots in Figure 9. This also can be seen from the comparison of this band graph with that of clean surface in Figure 5.

Figure 9. Electronic band structure and DOS graphics of exo-dimers/Si(001)-(2×2) surfaces

4. CONCLUSION In this work, adsorption of Si-, Ge-, and Sn-containing metallole molecules on Si(001)-(2×2) surface was studied by using DFT methods, considering both non-dissociated and dissociated models. Among non-dissociated models, Bridge-(I) type binding (Figure 2) was found to be the most stable adsorption geometry for each of the three metallole molecules. The comparison of EAd ACS Paragon Plus Environment

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values in Table 2 shows the adsorption energy of Bridge-(I) stannole is 0.08 eV (0.07 eV) lower than the silole (germole). According to the energy profiles of these non-dissociated models, the lowest energy barrier is seen in transition from [2+2]-(II) model to Bridge-(I) model. Moreover, the energy band diagrams show that the band gap of metallole-adsorbed silicon surface is about 0.9 eV wide since the formation of new bonds, between molecule and dimer-Si atoms, removes the surface states from the gap.

Unlike silole and germole, [4+2]-(II) model of stannole dissociates by itself. Based on this difference, three possible dissociation models were taken into consideration. Among them, M–H dissociation was found to be more favourable than the C–H dissociations. The electronic band structures of dissociated models are not too different than those of non-dissociated ones.

In the last section, dimerization energy of these molecules were calculated for six different configurations. Endo and exo models were found to be more stable than the others. According to adsorption energies, metallole dimers prefer the exo model on the silicon surface. Electronic band gap of dimer adsorbed surface was found to be ~ 0.6 eV with two surface states originating from free Si dimer of the substrate.

Consequently, in most cases the three considered molecules followed a similar trend, except for Stannole [4+2]-(II) in which one of the two hydrogens dissociates from Sn by itself without energy barrier.

Acknowledgment The study is supported by the Ministry of Development of Turkey under Grant No: DPT2006K120470.


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DFT Characterization of Metallole-Decorated Silicon (001) Surface

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