Chemisorption of 3-Aminopropyltrimethoxysilane on Si(001)-(2 × 2)

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J. Phys. Chem. C 2007, 111, 15020-15025

Chemisorption of 3-Aminopropyltrimethoxysilane on Si(001)-(2 × 2) G. Demirel,*,† M. C¸ akmak,‡ T. C¸ aykara,† and S¸ . Ellialtıogˇ lu§ Department of Chemistry and Department of Physics, Gazi UniVersity, Teknikokullar, 06500 Ankara, Turkey, and Department of Physics, Middle East Technical UniVersity, 06531 Ankara, Turkey ReceiVed: May 22, 2007; In Final Form: August 10, 2007

The results of an ab initio calculation, based on pseudopotentials and the density functional theory, for the atomic and electronic structures of the chemisorption of 3-aminopropyltrimethoxysilane (APTS) on the Si(001)-(2 × 2) surface are presented. Two possible models for the chemisorption location of the APTS molecule are considered on the hydroxylated Si(001)-(2 × 2) surface: (i) an above-pedestal position (intra-row) between adjacent Si dimers and (ii) an above-hollow position. The first case is found to be energetically more favorable than the latter by 1.04 eV. The electronic band structure of this site has been compared with that of the bare Si(001)-(2 × 2) surface. It is observed that the chemisorption of APTS has considerably changed the electronic structure of the Si(001)-(2 × 2) surface.

I. Introduction The adsorption or chemisorption of molecules on silicon surfaces is one of the most important subjects of current research, theoretically and experimentally. This interest might be attributed to both the fundamental nature of this problem, involving the interaction between finite units and periodic substrates, and its relevance to variety of recent technology, such as molecular electronics, nanolithography, and sensors.1-11 Self-assembled monolayers (SAMs) are a class of molecular assemblies that are prepared by spontaneous adsorption of molecules from solution onto a solid substrate. Recently, many self-assembly systems have been developed experimentally using various solid substrates by the researchers.12-17 Intensive ongoing research effort is devoted to the development of various experimental functionalizing procedures, the goal being to grow homogeneous organic films onto microelectronics substrates, like silica surfaces, in order to further address the nanobiotechnology applications. Amino-terminated SAMs form a hydrophilic surface that can strongly bond other materials. Potential uses of these patterned surfaces include to modulate nucleation and growth of minerals,18 to promote the attaching and spreading of neurons,19 to fix antigen-antibody,20 to attach peptides, to promote cell adhesion,21 to tether the DNA oligonucleotides,22 to immobilize heparin and hyaluronan, to enhance biocompatibility,23 and to maintain the bioactivity of enzymes on alloy surfaces.24 3-Aminopropyltrimethoxysilane (APTS) is one of the most useful molecules for the preparation of amino-terminated SAMs on Si surfaces because it possesses the methoxy groups.25-28 Two different assembly mechanisms have been assumed for the APTS molecule chemisorbed on the Si surfaces. In the first estimated mechanism, the reactive silane groups initially undergo a fast hydrolysis to form silanols, followed by a slow condensation to oligomers, which then hydrogen bonds to the surface hydroxyl groups and leads to the formation of covalent bonds during the final curing process.29 In this mechanism, water * Corresponding author. E-mail: [email protected]. † Department of Chemistry. ‡ Department of Physics. § Middle East Technical University.

molecules seem to be necessary for the surface formation. In the second estimated mechanism, the methoxy groups of APTS react with the native hydroxyl groups adorning the Si surface, and at the end, methanol molecules are produced as byproducts.30 The formation of this structure does not require any water molecule. However, formation mechanisms of these systems are not known for certain. As far as we are aware, despite several experimental investigations dedicated to the grafting of chain organosilane compounds to the silica, there are only few theoretical descriptions of such grafting and even fewer attempts to understand the self-assembly mechanisms. However, there are several theoretical calculations on the SAMs: simulations of hydrated multilamellar bilayer31,32 and molecular dynamics simulations of supported phospholipid-alkenethiol bilayers on a Au(111) surface.33 Dkhissi and co-workers theoretically investigated the preorganization of organosilanes onto silica,34 where they have assumed the polysiloxane interaction with the silane surface. In this work, using first principles calculations, we have studied the chemisorption of the APTS molecule onto a hydroxylated Si(001)-(2 × 2) surface, with the aim of understanding the structural and electronic modifications mutually induced at the surface upon chemisorption. For this purpose, we report ab initio theoretical investigations of the atomic geometry, electronic structures, chemical bonding, and energetics of APTS on the Si(001) surface. In addition, a comparison of the band structures for the clean Si(001)-(2 × 2), the hydroxylated Si(001)-(2 × 2), and the APTS/Si(001)-(2 × 2) systems have been made in order to understand the effect of APTS on the electronic behavior of Si surface. II. Method We carried out ab initio calculations using the Vienna ab initio simulation package (VASP)35-37 which is a DFT code, operating in a plane wave basis set. The electron-ion interaction was considered in the form of the projector-augmented-wave (PAW) method38,39 with plane wave up to an energy of 25 Ry. This cutoff was found to be adequate for the structural studies as well as for the electronic structure. We did not find any significant changes in the structural parameters when the energy

10.1021/jp073954l CCC: $37.00 © 2007 American Chemical Society Published on Web 09/22/2007

3-Aminopropyltrimethoxysilane on Si(001)-(2 × 2)

J. Phys. Chem. C, Vol. 111, No. 41, 2007 15021 TABLE 1: Calculated Lengths (in Angstroms) for the N-H, C-H, C-C, and C-O Bonds in the APTS Molecule this work r1-2a others b

Figure 1. Schematic view for APTS.

cutoff is increased from 25 to 30 Ry. For exchange and correlation, the functional proposed by Perdew and Zunger40 is used, with the addition of (nonlocal) generalized gradient corrections (GGA).41 Self-consistent solutions were obtained by employing a set (6 × 6 × 1) Monkhorst-Pack42 grid of k-points in the integration over the surface Brillouin zone for the (2 × 2) reconstructed unit cell. In our calculations, Si(001) surfaces were modeled by a slab, which is periodically repeated in [001] direction, with a (2 × 2) surface unit cell. The supercell included an atomic slab with seven layers of Si substrate plus a vacuum region equivalent to about 23 Å in thickness. This relatively large vacuum region was found to be necessary since the APTS possesses a long molecule (about 9 Å) and a rather extended electrostatic potential. The two back substrate layers were frozen into their bulk positions, and each Si atom at the back surface was saturated with two hydrogen atoms. All of the remaining substrate atoms, the adsorbate atoms, and the saturating H atoms were allowed to relax into their minimum energy positions. We used our theoretical equilibrium lattice constant for bulk Si (5.47 Å) in the surface calculations. III. Results and Discussions A. APTS Molecule. Before studying the chemisorption of APTS on Si(001), we have examined the chemical properties of the molecule itself. The APTS molecule consists of the following three main parts: an amino group, a bridging alkyl chain, and three methoxy groups bonded to Si via oxygens, as shown in Figure 1. The methoxy groups of APTS play an important role in binding to the sample surface.29 Moreover, with the help of the amino groups, other active molecules (e.g., protein, tissue, etc.) may easily be bonded to the APTS structure.26 In general, organic molecules may assume several conformations characterized by small energy differences. In case of the APTS molecule, this possibility is mainly related to the rotational freedom of the alkyl chain and the methoxy groups. We have first considered the APTS molecule inside a repeated cubic box of size 20 Å. The structures were relaxed toward their minimum energy configurations by using one special k-point. The calculated lengths for the N-H, C-H, C-C, and C-O bonds in the relaxed system are found to be 1.01, 1.10, 1.53, and 1.41 Å, respectively, as shown in Table 1. These values are in excellent agreement with the sum of their covalent radii43 and with other theoretically calculated values44-46 as seen in Table 1. For the isolated APTS molecule, we have found the highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gap to be 4.41 eV. This value is comparable with the calculated results of Gaussian03.47 B. Hydroxylated Si(001)-(2 × 2) Surface. It is very wellknown that the clean Si(001) surface reconstructs in a c(4 × 2)

rN-H

rC-H

rC-C

rC-O

1.01 1.00 1.02b

1.10 1.07 1.11c

1.53 1.54 1.50d

1.41 1.43 1.39c

a Sum of the covalent radii of the two atoms forming each bond.43 From ref 44. c From ref 45. d From ref 46.

phase which consists of alternating asymmetric dimers at low temperature, while at room temperature the reconstruction becomes (2 × 1). An earlier calculation revealed that the alternating dimer (2 × 2) reconstruction is more favorable than the (2 × 1) phase by approximately 0.24 eV/dimer.48 It is also known that the calculated dimer lengths obtained for the asymmetric (2 × 2) and the asymmetric c(4 × 2) reconstructions come closer to the experimentally determined value than those obtained from the (2 × 1) reconstructions.49 First of all, for the surface works, we have studied the bare Si(001)-(2 × 2) with alternating dimer reconstructions shown in Figure 2. On the clean surface, the Si-Si dimer bond length is found to be 2.35 Å, and the tilt angle is 19°; the alternating dimer is in the antiphase with about the same tilt angle. These results are in excellent agreement with other LDA calculations.48,50 Fritsch and Pavone, on the other hand, obtained a slightly shorter dimer bond length, being equal to 2.33 Å.50 Surface hydroxyl groups seem to be necessary for the formation of the alkoxysilane molecules (e.g., APTS molecule) on the silicon surfaces. In this study, there are four dimer components within the (2 × 2) unit cell. We have placed four -OH groups in close proximity of Si dimer components but have considered four different orientations for H atoms in the -OH groups (cf., Figure 3). Upon their relaxations, we have reached a symmetric dimer formation starting from the initially asymmetric Si dimers. The relative energies for the models in a-d cases are 0.0, 0.01, 0.2, and 0.6 eV, respectively. Model a is slightly lower in energy as compared with the antisymmetric arrangement (Model b) of the adjacent H-atom locations. The positions of the H atoms in this case are similar to those used in the calculations made by Sque et al.2 and also by Kanai and co-workers.44 The -OH groups saturate the Si dangling bonds, making all silicon atoms fourfold coordinated. In the relaxed geometry, the Si-Si dimers become symmetrical, and the Si dimer bond lengths are increased to 2.36 Å. This value is nearly the same with the calculated value of 2.37 Å.44 Our calculated Si-O bond length is 1.68 Å which is in excellent agreement with the results of other theoretical works.51,52 Another important key parameter is the O-H bond length, which is found in our calculation to be 0.97 Å. Sque et al.2 obtained this bond as 1.01

Figure 2. Schematic (a) top view and (b) side view for the Si(001)-(2 × 2) surface. The dashed lines show the surface (2 × 2) unit cell.

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Figure 4. Models for the binding of APTS molecules to hydroxylated silicon substrate. (a) The silicon atom in APTS forms one or two bonds to surface hydroxyl groups. The remainder of the Si-OCH3 bonds are hydrolyzed, resulting in the formation of silanols (Si-OH) and SiO-Si linkages between adjacent ORS. The Si-O-Si links can also bind within the monolayer ORSs whose silicon atom has not formed any bonds to the surface. (b) The silicon atom in the APTS forms three bonds to hydroxy groups at the surface. The formation of this structure does not require any water molecule.

Figure 3. Schematic top and side view for the hydroxy on the Si(001)-(2 × 2) surface, models a-d. The gray, dark, and white filled circles represent the Si, O, and H atoms, respectively.

Å on a diamond surface. Our calculations did not yield any surface states near the fundamental band gap region. Upon the adsorption of hydroxyl groups, the surface states of the bare Si(001)-(2 × 2) surface become fully occupied, and their energies are pushed down into the bulk valence band region. Similar results for the electronic band structure of hydroxylated surface have been reported by Sque and co-workers.2 C. APTS on the Si(001)-(2 × 2) Surface. There is no theoretically proposed geometry for the APTS molecule on the silicon surface. The chemisorption of the APTS molecule on the hydroxylated surface can be written as the following schematic reaction:

(Si-OH)surface + [APTS′-(OCH3)3] f (APTS′-Si)surface + 3CH3OH This means, chemically, the most straightforward procedure to attach APTS to the surface is expected to be an organic reaction via methoxy groups of the molecule. In such an organic reaction, the -OH groups of the surface react with the methoxy groups of APTS molecule (-O-CH3), and methanol molecules are produced as byproducts.

Experimentally, there are two different preorganization mechanisms for organosilane (ORS) molecules (e.g., APTS molecule). In the first mechanism, ORS molecules react rapidly with water to form ORS oligomers in the solution. In these oligomers, the alkyl chains are closely packed in order to minimize their energy via van der Waals interactions. However, complete polymerization in two dimensions is not possible because of the space constraints imposed by the chain. Thus, there will be residual silanol (Si-OH) groups dangling from the two-dimensional network. When the oligomers diffuse to the substrate, they may physisorb to the surface prior to chemisorption. The driving force for this step is lateral interaction between oligomers (two-dimensional condensation). The last and slow step in monolayer formation supposedly is the chemisorption to the surface, that is, elimination of water and formation of Si-O-Si bonds to the substrate (Figure 4a). In the second assumed mechanism, instead of oligomers, mainly monomers react with the surface. As the monomers on the surface are less mobile than they would be in solution, the twodimensional polymerization is sterically hindered compared with the situation in the oligomers described above.53 As a result of these, ORS molecules form three bonds to hydroxyl groups at the surface of the substrate (Figure 4b). In this formation mechanism, water molecules are not necessary for the preorganization of ORS. Dkhissi and co-workers theoretically investigated the preorganization of ORS onto the silica surface,34 where they have shown that a single ORS molecule interacting with the surface lies flat to it, inhibiting further homogeneous film growth. This adsorption exhibits two molecule surface interactions: a covalent bond on the side of the molecule and a hydrogen bond on the other side. In the same work, they have also investigated that the possible preorganization of the molecules before grafting due to the presence of water molecules either in the gas/liquid phase or near the surface. This gives rise to the formation of dimerized chains. They then demonstrate that this preorganization process prevents the subsequent lying flat of the molecules to the substrate after grafting. In this study, considering the second mechanism, for the chemisorption of APTS on the hydroxylated surface based on the bridge bonding model, two possible models were assumed: (i) an above-pedestal position (intra-row) between adjacent Si dimers as seen in Figure 5 (model I), and (ii) an above-hollow position (inter-row) as seen in Figure 6 (model II). Starting from an asymmetric dimer geometry with a tilt angle of 19°, we placed the APTS molecule onto the surface, consistent with the above models, in which the Si dimer components have become fourfold coordinated. No symmetry was imposed in the calcula-

3-Aminopropyltrimethoxysilane on Si(001)-(2 × 2)

J. Phys. Chem. C, Vol. 111, No. 41, 2007 15023

Figure 5. Schematics of the top (a) and the side views (b,c) for APTS chemisorbed on an above-pedestal (intra-row) position of Si(001)-(2 × 2) surface (model I). The 3-aminopropyl group is omitted for clarity in the top view.

Figure 6. Schematics of the top (a) and the side views (b,c) for APTS chemisorbed on an above-hollow (inter-row) position of Si(001)-(2 × 2) surface (model II). The 3-aminopropyl group is omitted for clarity in the top view.

tions within the (2 × 2) unit cell, in order to allow the APTS to behave independently. Upon relaxation of both models, model I was found to be energetically more favorable than model II by 1.04 eV per APTS. Our calculations for model I showed that the Si-Si dimer bond has become symmetric and stretched to 2.40 Å. The 2% increase in the dimer length means that its strength has been weakened only slightly. Moreover, having three bonds, the APTS molecule is not chemisorbed symmetrically in the fourcornered dimer environment. We have also calculated the average vertical distance between the APTS molecule and the Si-dimers which is found to be about 1.60 Å. The bond length between Si atoms in a dimer and the O atoms vary from 1.54 to 1.66 Å. On the other hand, the bond length between the Si atom in the APTS molecule and the O atom is about 1.68 Å. Our calculated Si-O bond length is in excellent agreement with the other theoretically calculated values of 1.66,51 1.68,52 and 1.64 Å.54 These values are quite shorter than the sum of the covalent radii (rSi-O ) 1.83 Å).43 Furthermore, the change in the alkyl chain length of the APTS is negligible upon chemisorption (a decrease less than 0.1 Å). We also found that, after an organic reaction occurs, the fully relaxed APTS extends vertically from the surface, to still be accessible for the other molecules to bind. In our previous study, we have experimentally observed that 3-aminopropyltrimethoxysilane (APTS) molecules were chemically bonded on the Si(001) surface.55 These prepared surfaces were characterized by using X-ray photoelectron spectroscopy (XPS), atomic force microscopy

(AFM), ellipsometry, and contact angle goniometers. According to our results obtained, APTS molecules were bonded to silicon surface by means of the methoxy end groups, leaving the amino head group free. On the other hand, further experimental results are still needed for the details of atomic structure describing the bridge binding on the Si(001)-(2 × 2) surface. In our previous studies, we have calculated fundamental band gap for bare Si(001)-(2 × 2).56 We have observed a total of four surface states in the vicinity of the fundamental band. In addition to this, we have also calculated band gap after the bonding of APTS molecule on the bare silicon surface. We have observed that the system is found to be semiconducting in nature, with two occupied surface states lying outside the fundamental band gap, except in a small region above the bulk valence continuum around M h , as seen in Figure 7. In Figure 8, we display the orbital nature of the total electronic charge density and that of the individual electronic states. Figure 8a, plotted on the plane cutting vertically through the O atom and the first topmost Si layer, reveals that the Si-O bonds in O-Si-SiO-H chain (plane 1) are polar covalent: having a large degree of covalency with some ionic character, giving rise to a shift in the charge density peak toward the more electronegative oxygen species. The total charge density picture shown in Figure 8b is plotted on the plane cutting through the system vertically, including the O-Si-Si-O chain (plane 2). We also depicted the total charge density of the plane containing the APTS molecule seen in 8c. In order to understand the surface states S1 and S2 we first recall that on the clean Si(001)-(2 × 2) surface

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Figure 7. Electronic band structure for (a) bare Si(001)-(2 × 2) and (b) the APTS molecule on Si(001)-(2 × 2) surface, according to model I. The thick dashed lines represent the surface bands in the gap. The region with thin lines is the bulk (2 × 2) projected band structures for Si.

IV. Summary From ab initio pseudopotential calculations, we have presented a detailed investigation of the atomic and electronic structure of the APTS on hydroxylated Si(001)-(2 × 2). Results can be summarized as follows: (a) Stability. Two possible models for the chemisorption of APTS molecule on the hydroxylated Si(001)-(2 × 2) surface are considered: (model I) an above-pedestal position (intrarow) between adjacent Si dimers, and (model II) an abovehollow position. Model I is found to be energetically more favorable than model II by 1.04 eV per APTS. Our theoretically estimated preorganization mechanism of the alkoxysilane molecules on the hydroxylated silicon surface may be useful for the nanobiotechnological application because of the more robust systems. (b) Geometry. Chemisorption of APTS on Si(001) surface leads to the Si-Si dimer length to be elongated by approximately 2% compared with its value for the clean surface. The bond lengths between dimer Si atoms to O atoms in the APTS molecule range from 1.54 to 1.66 Å. (c) Electronic Structure. Band structure results for Model I are compared with those of the bare Si(001)-(2 × 2) surface, and the chemisorption of APTS molecule is observed to affect the electronic structure of the Si(001)-(2 × 2) surface considerably. Figure 8. Top row: Electronic total charge density plots of (a) a plane cutting through vertically including the O-Si-Si-O-H (plane 1), (b) a plane cutting through vertically including the O-Si-Si-O (plane 2), and (c) a plane cutting through vertically including the APTS molecule (plane 3). Bottom row: The electronic charge density plots of the individual states, (d) S1 for plane 1, (e) S2 for plane 2, and (f) S3 for plane 1 at the M h point of the surface Brillouin zone.

Acknowledgment. This work was supported by Turkish State Planning Organization (Project Nos. 2001K120590 and 2003K120470-31). M.C¸ . and S¸ .E. gratefully acknowledge the METU President’s Office for the financial support under YUUP projects. References and Notes

with a symmetric dimer there are two pair overlapping π-derived dangling bond states49: these can be labeled as π* and π according to their orbital symmetries. The states S1 and S2, seen in Figure 8d,e, having the orbital character Opz-Siπ, now lie just above the silicon valence band edge at around M h . The unoccupied state S3 has a complex bonding picture because of the mainly surface dimer atoms and some contribution from the bulk (cf., Figure 8f).

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