Substituent Effect on the Intermolecular Arrangements of One

Dec 10, 2012 - The effect of methyl substitution in styrene molecules on the spatial arrangement of molecules in a one-dimensional (1-D) molecular ass...
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Substituent Effect on the Intermolecular Arrangements of OneDimensional Molecular Assembly on the Si(100)-(2×1)‑H Surface Md. Zakir Hossain,*,†,‡ R. S. Dasanayake-Aluthge,§ Taketoshi Minato,‡,⊥ Hiroyuki S. Kato,∥ and Maki Kawai*,‡,§ †

Advanced Scientific Research Leaders Development Unit, Advanced Engineering Research Team, Gunma University, Kiryu 376-8515, Japan ‡ Advanced Science Institute (ASI), RIKEN (The Institute of Physical Chemical Research), Wako, Saitama 351-0198, Japan § Department of Advanced Materials Science, The University of Tokyo, Kashiwa, Chiba 277-8501, Japan ∥ Department of Chemistry, Osaka University, Osaka 560-0043, Japan S Supporting Information *

ABSTRACT: The effect of methyl substitution in styrene molecules on the spatial arrangement of molecules in a onedimensional (1-D) molecular assembly on the Si(100)-(2×1)H surface has been studied using a scanning tunneling microscope (STM) at 300 K. Styrene molecules form welldefined 1-D molecular assemblies through a chain reaction mechanism along the dimer row direction, where the phenyl rings are separated by distances equal to that of the interdimer distance in a row and aligned parallel to each other. We observed that the substitution in a phenyl ring has no observable effect on the adsorption sites, configurations, and stacking of phenyl rings along the dimer row. In contrast, the methyl substitution at α site (α-methylstyrene) results in a 1-D assembly where the adsorption sites are similar to that of styrene but the adsorbed molecules are arranged in alternate geometrical configurations along the dimer row. In the case of β-methylstyrene, the adsorption sites (diagonal silicon atoms in a dimer row) and the geometrical configurations of adsorbed molecules along the dimer row are different from that of styrene. These results suggest that the selective arrangement of the molecules in a 1-D assembly can be achieved by inducing a steric hindrance through substitution at specific sites of the reacting molecule.



INTRODUCTION Predesigned alignment of atoms or molecules on the surface of metal and semiconductor has drawn much attention because of its interesting electronic phenomenon that can be utilized in the future miniature devices.1−5 Among various techniques, the radical chain reaction has emerged as one of the most promising approaches to fabricate one-dimensional (1-D) molecular assembly on the semiconductor surface.6−11 The unit cell of the (2×1) reconstructed Si(100) surface makes it an ideal template for making 1-D molecular assembly, where a significant intermolecular interaction exits.12,13 The parallel alignment of the phenyl rings (π−π stacking) of the adsorbed styrene was expected to show the charge transport phenomena.12,14 To tailor such molecular assembly into practical use, the π−π stacking system should possess tunable electrical properties, and the π states of the molecules should be decoupled from the substrate electronic states. Indeed, these could be achieved through a functional group attached to the molecules constituting the assembly.14 However, a functional group attached to the molecule may affect the ideal π-stacking pattern of the adsorbed molecules, which is not known in spite of a number of studies on the selective growth of molecular line on the Si(100)-(2×1)-H surface. © 2012 American Chemical Society

To date, a variety of molecules have been studied for the growth of molecular line on the H-terminated Si(100)-(2×1) surface.6,15−20 Most of the molecules that contain a phenyl πelectron system such as styrene,6,16 2,4-dimethylstyrene,17 4methylstyrene,18 4-bromostyrene,19 benzaldehyde,20 and benzophenone15 form molecular lines parallel to the dimer row direction, and the resulting π stacking patterns are similar; i.e., the adsorbed states of all molecules in a line are identical. Recently, we observed that acetophenone forms molecular lines both parallel and perpendicular to the dimer row directions with two different types of π stacking arrangements along the row.15 In addition to those ordered 1-D molecular assemblies, disorderly arrangement of adsorbed molecules along the growth direction was also observed for vinylferrocene molecules.21 Motivated by these variations in molecular arrangements in a molecular line, and the essential needs for the functional molecular assembly, we performed a systematic study on the substitutional effect on the arrangement of molecules in a molecular line. Received: September 4, 2012 Revised: December 4, 2012 Published: December 10, 2012 270

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molecular arrangement in a line. The calculations were performed using the commercially available DMol3 software package. Structure optimization of the adsorbed molecules was performed on a periodic (4 × 2) unit cell with five atomic layers depth. All the atoms except bottom two layers with hydrogen termination were allowed to relax. The optimized Si(100)(2×1)-H surface is used to obtain the molecular arrangements of each molecule, separately.

Taking styrene as a standard molecule, we studied the effect of a methyl substituent at the α and β positions of the >CC< group as well as at the phenyl ring (ortho and para), as shown in Scheme 1. Scanning tunneling microscope (STM) Scheme 1. Molecules Studied in the Present Studya



RESULTS AND DISCUSSION Figure 1 shows the high-resolution STM images of molecular lines formed by various molecules on the Si(100)-(2×1)-H

The substitution sites, ortho (o), meta (m), para (p), α and β, are named in styrene molecules. a

investigations on the molecular lines formed by those molecules suggest that the substitution in the phenyl ring has no observable effect on the arrangement of molecules in an assembly. For example, styrene and 2,4-dimethylstyrene form 1D assemblies, where the adsorbed states of all molecules in a line are identical; i.e., the adsorption sites and geometrical orientations of the adsorbed molecules are similar in an assembly. In contrast, the α- or β-substituted methylstyrene results in a 1-D molecular assembly that is different from that of styrene. Although the adsorption sites of α-methylstyrene are similar to that of styrene, the adsorption sites of the β-methyl styrene are different from the others. Variation in the molecular arrangements in an assembly seems to be driven by the steric hindrance between two adjacent molecules in a line.

Figure 1. Selected area STM images showing the molecular lines formed by exposure to (a) ∼2 L of styrene, (b) ∼2 L of 2,4dimethylstyrene, (c) ∼20 L of α-methylstyrene and (d) ∼50 L of βmethylstyrene on the Si(100)-(2×1)-H surface at 300 K. Vsample = −2.5 V; I = 0.2 nA.



surface through the chain reaction at 300 K. The H-terminated silicon dimer rows are seen as the parallel stripes running diagonally in each STM image. The bright barlike structures along the underlying dimer row in Figure 1a,b are the molecular lines formed by styrene and 2,4-dimethylstyrene, respectively.6,17 The typical single and double styrene lines are indicated in Figure 1a. Note that molecular structures of adsorbed styrene in both single and double lines have been theoretically investigated by several groups.20,21 The proposed parallel alignments of phenyl rings along the underlying dimer rows agree well with the high resolution STM images.24 In the case of a single line, the silicon atoms located at one side of the dimer row are occupied, whereas both of the silicon dimer atoms in a row are occupied by the adsorbed molecules in the case of the double line. The appearances of styrene and 2,4-dimethylstyrene lines in Figure 1a,b, respectively, seem similar; i.e., both lines appeared as a uniform bar-like structure. The uniformity of the lines suggests that the adsorbed states of all molecules in a line are identical in both cases. These observations are in agreement with the previous reports that 4-bromostyrene and 4methylstyrene molecules form molecular lines similar to that of styrene.18,19 Thus one can conclude that the substitution in the phenyl ring has no significant effect in the geometrical arrangements of adsorbed molecules in a line compared to that of styrene. Parts c and d of Figure 1 show the molecular lines formed by α-methylstyrene and β-methylstyrene, respectively. The large

EXPERIMENTAL SECTION The experiments were performed in an ultrahigh vacuum (UHV) chamber with a base pressure better than 5 × 10−11 mbar in RIKEN, Japan. A variable temperature scanning tunneling microscope (Omicron VT-STM) was used. The boron-doped silicon sample (0.01 Ω cm) was cleaned by prolonged annealing at ∼850 K (∼8 h) followed by repeated flashing up to 1400 K. The H-terminated surface was prepared by exposure to atomic H, generated by a hot W-filament (∼2100 K), at the surface temperature of ∼625 K. The freshly prepared H-terminated surface normally contains a dilute concentration of unpaired dangling bond (DB) sites resulting from the incomplete H-termination;22 otherwise, the DB at a predefined position is generated using the STM tip.23 The chemicals (styrene, 2,4-dimethylstyrene, α-methylstyrene, and β-methylstyrene) purchased from Tokyo Chemicals Industries Co., Ltd. (TCI) were purified by pumping out the vapor above the liquid or solid phases. The molecules were dosed onto the silicon surface through electronically controlled pulse-valve doser at room temperature. The amounts of molecule dosed are expressed in Langmuirs (1 L = 1 × 10−6 Torr·s), which is estimated from the background pressure reading by B. A. (Bayard-Alpert) gauge during the exposure.



THEORETICAL METHODS Density functional theory (DFT) with generalized-gradient approximation (GGA) was employed to understand the 271

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area STM images of molecular lines formed by these molecules are given in Supporting Information. Unlike styrene or 2,4dimethylstyrene lines, the molecular lines are resolved into many small protrusions, which are apparently arranged in zigzag fashion in the direction of the dimer row in both cases. The distance between two neighboring protrusions located at the same side of the dimer rows is estimated to be 7.6 Å (twice of the interdimer distance in a row), as indicated in Figure 1c,d. These results clearly suggest that the internal arrangements of α- and β-methylstyrene molecules in a line are different from that of styrene. Although the apparent arrangements of those small protrusions in both cases look similar, the appearance and registries of the individual protrusions with respect to the underlying dimer row are different. In the case of αmethylstyrene, all protrusions are aligned toward the left side of the line drawn through the centers of the dimers in a row (black line in Figure 1c) but the contrasts are not identical. In the case of β-methylstyrene, in contrast, the observed small protrusions are identical and apparently arranged on either side of the line drawn through the centers of the dimers in a row (black line in Figure 1d). Though the small oval-shaped protrusions are arranged interpenetratively with respect to the center line in β-methylstyrene assembly, we estimate the mean distance between the protrusions lying left and right side of the dimer-row is ∼3.8 Å (Figure 1d). The differences in the location of small protrusions with respect to the underlying dimer row in Figure 1c,d suggest that the arrangements of those adsorbed molecules along the dimer row are different. The α-methylstyrene molecules are bonded to the silicon atoms that lie at the same side of the dimer row; i.e., the adsorption sites of α-methylstyrene molecules are similar to that of styrene molecules forming a single line. However, the orientations of phenyl ring seem not identical for all molecules. We suggest that the zigzag arrangement of small protrusions is caused by two different geometrical orientations of the adsorbed molecules. The molecular arrangement formed by α-methylstyrene is similar to that observed for acetophenone molecules, which is quite reasonable as two molecules possess the similar molecular structure.15 As described above, the methyl substitution at vinyl group of styrene obviously affects the molecular arrangement in a line rather than that at phenyl ring. In the case of 2,4dimethylstyrene, the methyl group is attached to sp2 carbon atom of the phenyl ring and lies at the same plane of phenyl ring. Considering the van deer Waal’s redii of methyl group (∼1.7 Å), we can expect that the phenyl ring attached to methyl groups can align parallel to each other along the dimer row (the intermolecular distance is 3.8 Å) without suffering a significant steric hindrance. However, in the case of α- and βmethylstyrene, the methyl group is attached to the sp3 C atom because the sp2 carbon of vinyl groups becomes sp3 after chemisorption. Hence the methyl substituent and the phenyl− C−C− skeleton cannot maintain a single molecular plane anymore. Therefore, the spatial distribution of the overhang methyl group becomes important for the alignment of the adsorbed molecules as a molecular line. The optimized structures and the arrangements of adsorbed α-methylstyrene molecules in a line were calculated using DMol3 software package. Based on the total energy calculations, the two most probable minimum energy arrangements are shown in Figure 2. The molecular arrangement shown in Figure 2a can be regarded as styrene-type assembly, where the phenyl rings of the adsorbed molecules lie at the same side of the

Figure 2. Optimized structures of the assembly of α-methylstyrene along the dimer row on Si(100)-(2×1)-H. (a) Adsorption sites and geometrical configurations of all molecules are identical. (b) Two different geometrical configurations of adsorbed molecules are arranged alternately along one side of the dimer row.

dimer row and parallel to each other; i.e., the geometrical configurations of all molecules in a line are identical. In contrast, the molecules in Figure 2b are arranged with alternate geometrical configurations along the dimer rows. Indeed, this arrangement (Figure 2b) agrees with the observed STM image (Figure 1c) of α-methylstyrene line. In terms of adsorption energy, the configuration shown in Figure 2b is calculated to be more stable than the styrene-type configuration shown in Figure 2a by 0.04 eV. Hence we suggest that steric hindrance induced by the methyl substituent plays an important role in molecular line growth involving its final stability. One can see in Figure 2b that the phenyl rings are arranged in T-shaped configuration. Note that the recent DFT calculation on the styrene molecular assembly has also reported the T-shaped arrangement of phenyl rings as the lowest energy configuration.25,26 The registry of the small individual protrusions with respect to the underlying silicon dimers (Figure 1d) indicates that the β-methylstyrene are alternately bonded to the left and right atoms of the Si−Si dimers in a row, which is different from that of styrene and α-methylstyrene. From the total energy calculations, we extracted the three most possible minimum energy configurations of the adsorbed β-methylstyrene, as shown in Figure 3. The structures shown in Figure 3a,b are similar to the respective structures of α-methylstyrene (Figure 2a and 2b), but Figure 3c shows a new type of arrangement, where molecules are linked to the left and right atoms of the alternate silicon dimers in a row. The present calculations suggest that the arrangement shown in Figure 3b is less stable than that in Figure 3a by ∼0.4 eV; i.e., the β-methylstyrene cannot attain the arrangement similar to that of αmethylstyrene. However, the arrangement shown in Figure 272

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The occupation of the alternate silicon dimer atoms along the row suggests that the propagation of chain reaction by the β-methylstyrene molecule is different from that of the αmethylstyrene molecule. The α-methylstyrene molecule undergoes a chain reaction that propagates similarly to that of styrene, i.e., the intermediate C-centered radical, formed by the initial reaction between >CC< and DB site of the substrate, abstracting a neighboring H located on the same side of the dimer row. In contrast, the chain reaction of β-methylstyrene propagates diagonally along the dimer row direction. From the present data, it is not clearly understood how the reaction propagates in this unusual arrangement. There are two possible ways that a new DB site can be created at the diagonal silicon atom with respect to the adsorbed molecule, as shown in Figure 4. In one way, the C-centered radical of β-methylstyrene

Figure 3. Optimized structures of the adsorbed β-methylstyrene molecules in a line. (a) All molecules are linked to the silicon atoms that lie at the same side of the dimer row, and the geometrical configurations of the molecules are identical. (b) Molecules are linked to the same side of the dimer row with alternate geometrical configurations. (c) Molecules are linked to the silicon atoms that lie diagonally along the dimer row.

3c, where the molecules are linked to the right and left dimer atoms alternately, is found to be more stable than that of styrene-type arrangement by ∼0.1 eV. Hence, we ascribed the protrusions arranged in zigzag pattern in the STM image (Figure 1d) to the molecular configurations shown in Figure 3c. Though the overlapping of the phenyl rings (side view of figure 3c) is in agreement with the observed protrusions (Figure 1d), the distance between the centers of two phenyl rings in the side view is smaller than the estimated overall distance (∼3.8 Å) shown in Figure 1d. We think that the oval shape of the individual protrusion (Figure 1d) is due to the combination of phenyl and methyl groups of the adsorbed molecules. Note that both phenyl and methyl group appear as a bright protrusion in the STM image at the sample bias of ∼2.5 V.15 The difference between α- and β-methylstyrene may arise from the different distances of methyl group from the substrate silicon atom. In the case of β-methylstyrene, the C atom attached to the methyl group is directly linked to the silicon atom and closer to the substrate than that of α-methylstyrene. Hence, the methyl group in adsorbed β-methylstyrene should have less freedom, compared to that in α-methylstyrene, to keep away from the adjacent molecule to minimize the steric hindrance if they linked to the same side of the silicon dimer row.

Figure 4. Proposed reaction mechanism for β-methylstyrene molecules on the Si(100)-(2×1)-H surface.

(Figure 4b), formed by interaction with the dangling bond (Figure 4a), directly abstracts the H from the diagonal silicon atom and creates a new dangling bond site there (red arrow in Figure 4). In another way, the C-centered radical (Figure 4b) abstracts the H similarly as styrene or α-methylstyrene followed by the intradimer H transfer process resulting into a new dangling bond site at the diagonal position (green arrow in Figure 4). However, the distance from the C radical to the H atom at diagonal site is so long that it is unlikely that the radical can abstract the H at the diagonal site directly. Hence, the later path (green arrow in Figure 4) seems to be more likely. Note that the intradimer H transfer (Figure 4c) is a high energy barrier process, which is estimated to be ∼17.02 kcal/mol by Ferguson et al. using hybrid density functional theory.27 The calculated activation energy barrier (Ea) of 17.02 kcal/mol results the rate of intradimer H transfer process 3.36 s−1 at 298 K according to the rate equation of 1013 exp(−Ea/kT), where k is the Boltzmann constant and T is the temperature. The experimental observation of short β-methylstyrene line by relatively larger doses (∼50 L) of molecules onto the surface 273

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may relate to this slow rate of H-transfer process. In addition, some substrate mediated complex energy transfer processes during the chemisorption and abstraction events perhaps facilitate the intradimer H transfer process. The present study clearly indicates that the methyl substitution in the phenyl ring has very little or no effect on the arrangement of molecules in a line. On the other hand, the substitutions in the vinyl group, both in α and β positions, have significant effects on the adsorption sites as well as the geometrical configuration of the neighboring molecules. Methyl substitution in the α position can allow the molecules to be adsorbed on the silicon atoms similarly to that of styrene molecules but with alternate geometrical configurations. The alternate geometrical configurations of the adsorbed molecules seem to be driven by the steric hindrance between adjacent molecules in the line. This adsorbed structure of αmethylstyrene molecules are similar to that of acetophenone molecules, which also show predominantly the alternate geometrical configurations of the adsorbed molecules.15 When the methyl group is located at β position of styrene molecule, the steric hindrance seems stronger. This strong steric hindrance even did not allow attaining the adsorption structure similar to that of α-methylstyrene. To minimize the steric hindrance, the β-methylstyrene molecules prefer to adsorb at silicon atoms, which are diagonal in two adjacent dimers. Thus the present study suggests that the functionalization as well as the variation in the arrangement of 1-D molecular assemblies can be achieved through deliberate substitution at specific sites of the reacting molecules.

AUTHOR INFORMATION

Corresponding Author

*E-mail: M.K., [email protected]; M.Z.H., zakir@gunma-u. ac.jp. Present Address ⊥

Office of Society-Academia Collaboration for Innovation Kyoto University Gokasho, Uji, Kyoto 611-0011, Japan.

Notes

The authors declare no competing financial interest.



ACKNOWLEDGMENTS This work is supported by the Grant-in Aid for Nanoscience and Technology Program in RIKEN. M.Z.H. acknowledges partial support by the Program to Disseminate Tenure-Track System of the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) and Element Innovation (EI) project granted to Gunma University.



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CONCLUSIONS The effect of substitutions on the molecular line growth on the H-terminated Si(100)-(2×1) surface has been studied using a scanning tunneling microscope (STM) at 300 K. Taking styrene as a standard molecule, the effect of substituents at α (α-methylstyrene) and β (β-methylstyrene) positions of >C C< group as well as at the phenyl ring (2,4-dimethylstyrene) were studied. The STM investigations of the molecular lines formed by those molecules suggest that the methyl substitution in the phenyl ring has no observable effect on the arrangement of molecules in a assembly; i.e., styrene and 2,4-dimethylstyrene form the lines with similar molecular arrangements. In these cases, the adsorbed states of all molecules in a line are identical; i.e., the adsorption sites and geometrical orientations of adsorbed molecules are similar in both cases. In contrast, the α- or β-substituted methylstyrene gives molecular arrangements different from that of the standard styrene line. Although the adsorption sites of α-methylstyrene are similar to that of styrene, the geometrical orientations of two adjacent molecules are different. Moreover, the adsorption sites and geometrical configurations of β-methylstyrene are different from the others. This variation in the intermolecular arrangement in 1-D assemblies is believed to be driven by the steric hindrance suffered by the molecules when they adsorbed on two adjacent silicon dimers in a row.



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ASSOCIATED CONTENT

* Supporting Information S

Large area STM image. This material is available free of charge via the Internet at http://pubs.acs.org. 274

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