The Mechanism for the Thermally Driven Self-Assembly of Pyrazine

Jul 9, 2013 - The chemisorption of pyrazine on Si(100) is a unique and experimentally demonstrated example for the growth of an ordered 1D line of org...
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The Mechanism for the Thermally Driven Self-Assembly of Pyrazine into Ordered Lines on Si(100) Wilson K. H. Ng,† S. T. Sun,† J. W. Liu,‡ and Z. F. Liu*,† †

Department of Chemistry and Centre for Scientific Modeling and Computation, The Chinese University of Hong Kong, Shatin, Hong Kong, People’s Republic of China ‡ National Supercomputing Center in Shenzhen, Shenzhen, People’s Republic of China ABSTRACT: The chemisorption of pyrazine on Si(100) is a unique and experimentally demonstrated example for the growth of an ordered 1D line of organic molecules on a very reactive silicon surface. Two key factors are identified, using first principles calculations, as being responsible for this remarkable process. First, van der Waals interaction between pyrazine and Si(100) varies considerably depending on the orientation of a pyrazine molecule, which opens up a significant gap in the activation barriers and makes the adsorption selective. Second, the presence of multiple reaction channels at elevated temperature could actually facilitate the self-assembly of adsorbed molecules into ordered structure, due to the presence of a cooperative effect. Consideration of these two factors should be useful in the search for other organic molecules to grow 1D lines on clean silicon surfaces.

1. INTRODUCTION The formation of one-dimensional (1D) nano lines has been an important goal for the study of chemisorption of organic molecules on silicon surfaces, which hold the potential for making functional nanodevices. Impressive progress has been made on Si(100) passivated by hydrogen. When a surface Si−H bond is broken to produce a dangling site, either by the application of a voltage through an STM tip or by photon irradiation, a chain reaction could be initiated.1 As an unsaturated organic molecule is chemisorbed on the dangling site, it turns into a radical which plucks away the H atom on an adjacent site to produce another dangling site. By carefully choosing the unsaturated organic molecules, it is possible to form 1D lines both along and perpendicular to the dimer row direction.2−6 By controlling the temperature, it is also possible to reverse the chemisorption process.7 In contrast, it is much harder to control the growth of ordered 1D structures on clean Si(100). The well-known surface dimers on reconstructed Si(100)−2 × 1 are highly reactive, and there are often multiple reaction pathways, and therefore multiple chemisorption configurations, producing adsorption sites scattered around the surface.8 Some progress has been made, notably by Polanyi and co-workers in two cases: the growth of line by dipole directed assembly of 1,5dichloropentane perpendicular to the dimer row (95%),9 and two modes of chain growth with a ratio of 80% to 20% in the dissociative chemisorption of CH3Cl.10 To date, the growth of 1D line on Si(100), along just one direction and with a single basic unit, has been achieved only in one case, the chemisorption of pyrazine. Pyrazine (C4H4N2) © 2013 American Chemical Society

belongs to the category of aromatic compounds, which, with their conjugate π bonds, are ideal building blocks for new functional materials.11 With three double bonds and two N atoms in a six-member ring, many possible adsorption geometries were expected, just within one dimer row.12,13 However, vibrational and core-level electron measurement indicated a simple structure, in which the two N atoms were bonded to the surface.12,14 By photoelectron diffraction and STM, it was identified as a cross-dimer-row structure, with a pyrazine laying flat as a bridge linking two surface dimer by a Si−N bond at each end.15 Even more surprising is the recent study at elevated temperature by Omiya and co-workers.16 With the substrate heated to 60−170 oC, the chemisorbed pyrazine molecules lined up to form well-ordered 1D lines, based exclusively on the cross-dimer-row configurations. Usually, heating silicon substrates during chemisorption would open up more reaction channels and produce a disordered mixture of various configurations. But in the case of pyrazine, it leads to wellordered 1D lines, which cannot be explained by previous calculation results on adsorption energies.13,15,17 While such observations are intriguing, they also hold an interesting prospect: well-ordered organic 1D lines can be formed even on the reactive Si(100) by simple heating, given the right choice of organic molecules. To guide such choices, it is essential to fully understand the mechanisms of surface Received: May 17, 2013 Revised: July 3, 2013 Published: July 9, 2013 15749

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reaction between pyrazine and Si(100), which is the subject of this report, based on first-principles calculations.

2. COMPUTATIONAL DETAILS Density Functional Theory (DFT) calculations were carried out using the Vienna Ab-initio Simulation Package (VASP),18−20 with the PBE exchange-correlation functional.21,22 The atomic cores were described by PAW pseudopotentials,23 and the valence bands were expanded in planewaves with a cutoff energy of 400 eV. Van der Waals corrections, when added, were calculated by the DFT-D2 method.24,25 For the adsorption of one pyrazine, a (4 × 4) supercell with a c(4 × 2) surface structure was employed, and the slab size was 15.46 × 15.46 × 18.00 Å3. For the calculation of the cooperative effect produced by multiple adsorptions, a larger (8 × 2) supercell was employed, with either p(2 × 2) or c(4 × 2) structure, and the slab size was 30.93 × 7.73 × 18.00 Å3. For both slab models, there were 5 silicon layers, and the number of irreducible K-points sampled was 5 and 8, for (4 × 4) and (8 × 2), respectively. The minimum energy reaction path was mapped out by the Nudged Elastic Band method developed by Jonsson and co-workers.26 Figure 1. Two most favorable chemisorption paths for pyrazine on Si(100), starting from the N-end-on I, without considering van der Waals correction. Above, cross-row addition; Below, [2 + 2] intradimer addition, followed by [4 + 2] addition, leading to a chair structure. See Table 1 for van der Waals corrected values.

3. RESULTS AND DISCUSSION 3.1. Surface Reaction Paths. We shall first take a look at the reaction paths obtained by PBE functional21 without van der Waals corrections. The first step of pyrazine adsorption on Si(100) is clear and simple. Like other molecules with an electron-negative atom,27 such as O and N, one of the N atoms in pyrazine shall form an N-end-on structure, with a dative bond between N and the down Si atom of a surface dimer. The process is barrierless and exothermic by 1.29 eV, in good agreement with previous slab results.17 There are several possibilities to consider for the next reaction step. The simplest one is the cross-dimer-row addition, observed exclusively in experiment,14,15 which is actually endothermic by 0.14 eV without vdW correction, as shown in Figure 1. The barrier for this reaction, reported here for the first time, is 0.48 eV. Next in importance is the intradimer [2 + 2] addition, also shown in Figure 1, which is endothermic by 0.31 eV and not considered in previous slab calculations. Its barrier, at 0.51 eV, is competitive with the cross-dimer-row addition. Furthermore, it can be followed by one more step of [4 + 2] addition to an adjacent Si dimer along the same row, which is more facile with a barrier of 0.27 eV. This chair structure, labeled III in Figure 1, is more stable than both the N-end-on I and the cross-dimerrow II. Obviously, these results cannot explain the experiments. In terms of adsorption energy, the chair III, rather than the crossdimer-row II, is the most stable. In terms of reaction barrier, intradimer [2 + 2] addition is competitive with cross-dimer-row addition, and the barrier difference of only 0.03 eV would translate to a kinetic ratio of 0.3:1 by Boltzmann distribution at 300 K. There are also other reaction channels, as shown in Figure 2. For intradimer reaction, the chemisorption could also be initiated by [4 + 2] (N...N) addition. For interdimer reaction, both [2 + 2] and [4 + 2] additions are possible. And all these initial steps could be followed by one further step, to put pyrazine on top of two adjacent dimers along the same row. However, the barriers for these channels are 0.9 eV or higher,

and they are not expected to make a significant contribution at room temperature. 3.2. van der Waals Corrections. What is missing in the above results is the van der Waals interaction, which has been shown to be important for the adsorption energy of aromatic molecules on Si(100),28 and specifically for pyrazine too.17 It cannot be addressed by the PBE functional. We use the DFTD2 method24,25 to calculate the energies and barriers with van der Waals corrections, which are listed in Table 1. The qualitative picture remains the same when only corrected adsorption energies are considered. While the values for both the chaired III and the cross-dimer-row II are lowered, the former is still more stable. It is the change in reaction barrier that makes the difference. For the intradimer [2 + 2] addition, the barrier remains at 0.51 eV (Table 1), barely affected by van der Waals correction, since the pyrazine ring is almost perpendicular to the surface. But for the cross-dimer-row addition, the activation barrier decreases from 0.48 to 0.23 eV, as the pyrazine molecule lies flat between two dimer rows, which is more favorable for its van der Waals interactions with the surface. Significantly, a gap of 0.28 eV in reaction barrier is now found between the cross-dimer-row and the intradimer [2 + 2] addition. At 300 K, 99.99% of the chemisorption would go through the cross-dimer-row channel based on a kinetic estimate, as indeed observed in experiment.14,15 Here is an example when van der Waals interaction dramatically alters the landscape of the potential surface and pushs reactions into one single channel, in this case, the crossdimer-row addition. The reaction barriers for other intradimer and interdimer channels are also revised down by van der Waals correction, especially for [4 + 2] additions, which also require a pyrazine ring to lie flat on the surface. But as listed in Table 1, with 15750

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Table 1. Activation Barrier (Ea), Reaction Energy (dE) and Adsorption Energy for the Adsorption of One Pyrazine on Si(100), both with (D2-Corrected) and without Considering van der Waals Interactionsa first step chemisorption

a

second step

chemisorption energy (label)

Ea

dE

N-end-on D2 corrected

0.0 0.0

−1.29 −1.69

1.29 1.69(I)

cross-dimer-row D2 corrected

0.48 0.23

0.14 −0.22

1.15 1.91(II)

intradimer[2 + 2] D2 corrected

0.51 0.51

0.31 0.29

0.27 0.12

−0.45 −0.63

1.43 2.03(III)

intradimer[4 + 2] D2 corrected

1.44 1.34

0.38 0.22

0.92 0.88

−0.11 −0.14

1.02 1.61(IV)

interdimer[2 + 2] D2 corrected

0.89 0.87

0.83 0.80

0.31 0.27

−0.69 −0.86

1.15 1.75(V)

interdimer[4 + 2] D2 corrected

1.14 0.98

0.27 0.07

0.21 0.20

−0.35 −0.35

1.37 1.97(VI)

Ea

dE

For I, II, and III, see Figure 1. For IV, V, and VI, see Figure 2.

In contrast, a cross-dimer-row configuration leaves two unsaturated Si, each on two cross-row adjacent dimers, which are destabilized. Indeed, this is probably the reason that the adsorption energy for the cross-dimer-row II is less than that for the chaired III. Jung and Kang observed in their calculations that when two pyrazines were lined up in the cross row direction to saturate the two dangling Si within a (4 × 2) unit cell, the adsorption energy for the second pyrazine became more favorable than the end-on structure I.17 But for the growth of 1D line, the question should be: as more pyrazine molecules are chemisorbed along the cross-dimer-row direction and the two dangling Si atoms are more separated, does the adsorption energy for each successive pyrazine become more favorable? Furthermore, such comparisons should be made against the chaired III, rather than the less stable N-end-on I. To model such effects, we employ an elongated (8 × 2) unit cell, containing four dimer rows, each with two silicon dimers, as shown in Figure 3. Cross dimer addition proceeds in four steps, forming a line perpendicular to the dimer rows. Within such a supercell, the dimers could either be tilted in one direction with a p(2 × 2) structure, or tilted in alternative directions with a c(4 × 2) structure. In the c(4 × 2) case, the adsorption energy (with van der Waals correction) increases only slightly to 1.99 eV by the second pyrazine, but more significantly to to 2.27 and 2.22 eV by the third and fourth pyrazine, which is more favorable than the value of 2.01 eV for III. In the p(2 × 2) case, the adsorption energy reaches 2.19 eV by the second pyrazine. In other words, there is an important cooperative effect in both cases: when more than two pyrazines are lined up, each new cross-dimer-row addition along the line produces the largest adsorption energy. Kinetically, the consecutive cross-dimer-row additions are also favorable. The formation of N-end-on structure is always barrierless, even when it is added to a neighboring upper Si. The calculated barrier for the cross-dimer-row addition step, between 0.2−0.3 eV, remains favorable.

Figure 2. Three more pyrazine reaction channels. They are unfavorable at room temperature, but are accessible at elevated temperature. They play an important role in the migration of pyrazine upon heating. Starting from N-end-on structure, top: intradimer [4 + 2], followed by [2 + 2]; middle: interdimer [2 + 2], followed by [4 + 2]; bottom: interdimer [4 + 2], followed by [2 + 2]. The energy values are not corrected by van der Waals interactions. Corrected values are listed in Table 1.

barriers still above 0.8 eV, these channels remain unfavorable at room temperature. 3.3. Multiple Adsorption and Cooperative Effects. When the temperature is raised to 60−170 oC in experiment, all of the channels discussed above shall become accessible. The equilibrium among various configurations is then determined by the adsorption energies listed in Table 1, and there should be a number of configurations, with the chaired III being the most abundant, again in contradiction to the experimental observation of ordered 1D line at elevated temperature with the cross dimer II as the only unit.16 To explain the formation of 1D line, we must go beyond the adsorption of a single pyrazine and consider the effects of multiple adsorption. When the adsorption of a pyrazine is within the same dimer row, the two step reaction always leads to the saturation of two adjacent silicon dimers, whether it is initiated by intradimer or interdimer addition. In other words, the first pyrazine would have little effect on the adsorption of the next pyrazine, except for steric repulsion on dimers immediately adjacent to the first site along the same row. 15751

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Figure 3. Cooperative effect for pyrazine molecules lined up perpendicular to dimer rows by cross-dimer-row structures. The stepwise adsorption energy is calculated with a (8 × 2) supercell and with van der Waals correction. Both c(4 × 2) and p(2 × 2) structures are considered.

3.4. Migration Paths for Adsorbed Pyrazine. For the formation of 1D line, it is unlikely that pyrazine molecules fall in line consecutively. Statistically, pyrazine molecules should be scattered around the surface, forming isolated configurations, and then migrating on the surface, to produce the energetically favorable 1D lines, as previously suggested.16 Upon heating, Nend-on I must have a larger presence, since it has more freedom in vibration and rotation and is favored by entropy. By going through [4 + 2] interdimer addition, a pyrazine could migrate along a dimer row, with a maximum barrier of 0.98 eV (Table 1). By a combination of cross-dimer-row addition and intradimer [4 + 2] addition, a pyrazine could migrate in a direction perpendicular to a dimer row, with a maximum barrier of 1.34 eV. In fact, at elevated temperature, the number of accessible configurations is larger than that listed in Table 1. In the top panel of Figure 4, a [2 + 2] intradimer addition is followed by another [2 + 2] intradimer addition on the next dimer, and the breaking of the first C−Si and N−Si bonds eventually leads to an N-end-on structure on the diagonal Si. In the bottom panel, the migration is again initiated by intradimer [2 + 2] addition, and followed by [2 + 4] addition, leading to the chaired III. After breaking the two bonds in the initial [2 + 2] addition, it could be followed by another [2 + 2] addition on the other side, and in two dissociation steps, an N-end-on structure is again formed, with the N−Si bond migrated by two dimers and to the other side. By a combination of these two paths, an Nend-on pyrazine could migrate to any Si atom along a dimer row with the highest barrier being only ∼0.7 eV, while jumping from one dimer row to the next row is even more facile by the cross-dimer-row addition. When more than two cross-dimer-row pyrazines are linked, it becomes energetically more favorable for other migrating pyrazine molecules to fall into the line, driven now by more favorable adsorption energy due to cooperative effects. At high coverage, the formation of many such lines, which are separated

Figure 4. Two migration paths, initiated by [2 + 2] intradimer addition and followed by further addition and dissociation steps. The barriers, calculated with van der Waals corrections, are below 0.8 eV. The top path moves the N-end-on structure diagonally to a neighboring dimer, and the bottom path moves it over two dimers and to the opposite side. Combinations of these two paths could move the N-end-on structure to any Si atoms along a dimer row.

from each other by one free dimer due to van der Waals repulsions, would lead to the 2D arrays with a (2 × 2) unit observed in experiment.16

4. CONCLUSIONS In summary, the adsorption of pyrazine on Si(100) provides an interesting model for the thermally driven growth of 1D lines on Si(100). The two factors responsible for such a process provide a general guidance toward finding other suitable organic molecules for the growth of ordered structures on clean Si(100). Van der Waals interaction could play a constructive role to differentiate competing surface reaction channels. In the case of pyrazine adsorption on Si(100), it opens up a significant gap in the activation barrier between the cross-dimer-row and the intradimer [2 + 2] additions. Similar gaps are expected for other aromatic and ring molecules, for which van der Waals interaction differs considerably depending on the orientation of the aromatic ring relative to the silicon surface. Although many surface reaction channels become accessible at elevated temperature, it does not necessarily mean that heating would produce a mixture of configurations. When there are cooperative effects for multiple adsorptions, as in the case of pyrazine on Si(100), the presence of many channels could actually facilitate the migration of the adsorbed molecules, until 15752

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they are aligned to take advantage of the cooperative effects. Provided that the adsorbed molecules are stable upon heating, these migrations could lead to the self-assembly of adsorbed molecules into low-dimensional structures.

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AUTHOR INFORMATION

Corresponding Author

*Fax: +852 2603 5057; e-mail: zfl[email protected]. Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS We are grateful for the generous allocation of computer time on the National Supercomputing Center in Shenzhen and on the clusters of PCs and AlphaStations at the Center for Scientific Modeling and Computation at the Chinese University of Hong Kong. This project is supported by a Direct Grant (2060401) from The Chinese University of Hong Kong. J.W.L. thanks Shenzhen Strategic Emerging Industry Special Fund Program of China (Grant No. GGJS20120619101655715) for financial support.

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