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J. Phys. Chem. C 2008, 112, 6850-6859
Two-Dimensional Self-Assemblies of Thiophene-Fluorenone Conjugated Oligomers on Graphite: A Joint STM and Molecular Modeling Study Mathieu Linares,*,† Lorette Scifo,‡ Renaud Demadrille,‡ Patrick Brocorens,† David Beljonne,† Roberto Lazzaroni,† and Benjamin Grevin‡ Laboratory for Chemistry of NoVel Materials - UniVersity of Mons-Hainaut, Place du Parc 20, B-7000 Mons, Belgium, and UMR5819 (CEA-CNRS-UniVersite´ Grenoble I), CEA/INAC/SPrAM/LEMOH, CEA-Grenoble, 17 rue des Martyrs, 38054 Grenoble Cedex 9, France ReceiVed: NoVember 20, 2007; In Final Form: January 22, 2008
The formation of self-assembled monolayers of bithiophene-fluorenone conjugated oligomers, 2,7-bis-(4octyl-thien-2-yl)-fluoren-9-one (B4OTF) and 2,7-bis-(5-octyl-thien-2-yl)-fluoren-9-one (B5OTF), has been studied on highly oriented pyrolitic graphite (HOPG) by scanning tunneling microscopy (STM), with the aim of determining the influence of the molecular structure and conformation on the supramolecular organization. The experimental data are discussed in light of a modeling study of the molecular conformation and the adsorption on graphite using molecular mechanics and molecular dynamics simulations. It is shown that molecules with alkyl groups grafted in the C4 position (B4OTF) self-assemble into an anti-anti chiral lattice which is favored both by dipole-dipole and Van der Waals interactions. The short-range organization appears more complex for molecules with alkyl groups grafted in the C5 position (B5OTF). Due to a competition between dipole-dipole and Van der Waals interactions, the modeled assemblies based on syn-syn, synanti, and anti-anti B5OTF conformers are all stable and very close in energy, but do not explain the feature of a long-range periodicity evidenced from large-scale STM images. On the basis of the comparative analysis between the experimental data and the modeling, it is then suggested that the supramolecular self-assembly of B5OTF on HOPG implies the presence of several conformers in the monolayer.
Introduction The performance of organic electronic devices is dependent on the opto-electronic properties of π-conjugated (polymer or molecular) materials in thin films. It is now clearly established that, besides the “primary” chemical structure of the molecules, the supramolecular arrangement in the solid state has a very strong influence on those opto-electronic properties. For instance, the main characteristics of organic field effect transistors arise primarily from the organization of the very first monolayers of conjugated molecules deposited on top of the dielectric surface, as charge transport occurs mostly through a very thin conducting channel at the semiconductor-insulator interface. It is therefore of prime importance to understand and control the supramolecular assembly in thin layers of conjugated polymers or oligomers.1 In this work, we designed, synthesized, and investigated the self-assembly of new mixed conjugated oligomers, combining a fluorenone central unit and two alkylated thiophene rings, in monolayers adsorbed on highly oriented pyrolytic graphite (HOPG). The chemical structures of these compounds, namely, 2,7-bis-(4-octyl-thien-2-yl)-fluoren-9-one (abbreviated as B4OTF) and 2,7-bis-(5-octyl-thien-2-yl)-fluoren-9-one (abbreviated as B5OTF), are shown in Figure 1. The growing interest for fluorene-based and “mixed” fluorene-thiophene or fluorenone-thiophene-based materials relies on their efficient application as active components for OLEDs,2,3 photovoltaic cells,4,5 or field effect transistors6-8 (OFET). Our interest in this family of “mixed” π-conjugated materials arises † ‡
University of Mons-Hainaut. CEA-CNRS-Universite´ Grenoble I.
from the possibility to precisely tune, by the introduction of fluorenone units within the conjugated backbone of polymers or oligomers, their absorption and emission properties,9 their electronic properties (band gap, energy levels of the frontier orbitals), and their electrical transport properties.6 However, to the best of our knowledge, there has been no study reported in the literature dealing with the influence of the molecular structure of fluorenone-thiophene-based materials on their selforganization properties. Among the different features available to control the packing of molecular layers on surfaces, substitution of the main conjugated backbone with, e.g., alkyl chains turns out to be a powerful approach. For instance, in lamellar structures, the alkyl chains play the role of a spacer between the π-systems, thereby allowing controlled tuning of the interlamellae distance via the length of the alkyl chains.10 The length of the side chains has also been shown to drastically affect the organization of molecules on surfaces:11 on the HOPG surface, which is nonchiral, this parameter can govern the formation of chiral domains for achiral molecules.12,13 For some discotic liquid crystals,13 a chiral ordering of the self-assembled monolayer (SAM) has indeed been obtained by increasing the triangular aspect ratio of the molecules through the tuning of their alkoxy side chain length. Wei et al. have shown that the occurrence of chirality in monolayers of anthracene derivatives12 is governed by the number of non-hydrogen atoms of the side chains. Last, adsorption-induced asymmetric assembly has been recently reported in the case of octadecanol SAMs,14 due to the alkyl chain distortion upon adsorption on the surface. The main purpose of this study is to determine the influence of (i) the molecular structure (in particular the position of the
10.1021/jp711047x CCC: $40.75 © 2008 American Chemical Society Published on Web 04/08/2008
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Figure 1. Chemical structure of the 2,7-bis-(4-octyl-thien-2-yl)-fluoren-9-one (B4OTF) and 2,7-bis-(5-octyl-thien-2-yl)-fluoren-9-one (B5OTF) molecules.
alkyl chains grafted on the thiophene rings) and (ii) the molecular conformation (in particular the syn or anti conformation of the thiophene and fluorenone rings) on the structure of the self-assembled monolayers. The position of the alkyl (octyl) groups on either the C4 or C5 atoms of the thiophene rings and the relative orientation of the thiophene and fluorenone rings can affect the overall shape of the molecule and its capacity to generate the intermolecular interactions that govern the assembly into ordered monolayers on graphite. The structural organization of these layers is investigated here by scanning tunneling microscopy (STM) imaging. The STM data are interpreted with the assistance of molecular modeling based on force-field calculations. These molecular mechanics (MM) and molecular dynamics (MD) simulations not only allow identification of the most realistic molecular assemblies, whose structural parameters can subsequently be compared to the STM data, but also provide a deep insight into the nature of the intra- and intermolecular interactions ruling the supramolecular organization. Such information, in turn, proves useful when examining the potential of conjugated molecules as active components in a wide range of opto-electronic devices. The modeling is based on a twostage approach, involving first a conformational study of the isolated molecules at the density functional theory (DFT) level, followed by MM/MD simulations of the adsorption and selfassembly of the most stable conformers on graphite. Experimental Results Figures 2 and 3 represent STM images of B4OTF and B5OTF molecules assembled on graphite, respectively. In Figures 2a and 3a, three domains rotated by 120° with respect to each other can be clearly identified. It is well-known that alkyl chains tend to adsorb following the main graphite axes,15 which can drive the self-assembly of alkyl-substituted molecules with complex chemical structures.16-18 This is most probably also the case here, since the relative orientations of the three domains are consistent with the C3 symmetry of graphite. Figures 2b and 3b are close-ups on one monodomain, showing regular arrangements for both B4OTF and B5OTF (P1 plane group symmetry). On higher-resolution STM images (Figures 2c and 3c), one can distinguish elongated objects that are slightly curved. The length of those objects is around 1.4 nm for both molecules, which roughly corresponds to the length of the aromatic backbone of B4OTF and B5OTF. This suggests that the molecules are lying flat on the graphite surface owing to favorable π-π interactions with the substrate. The non-homogeneous contrast observed over the length of the objects may reflect different sections of the conjugated backbone: (i) the central part showing up with lower intensity could be associated with the central fluorenone unit; and (ii) the outer regions of the molecules that appear brighter on the STM images could be attributed to the thiophene rings. The overall morphologies of the B4OTF and B5OTF layers are similar; however, a detailed analysis reveals significant differences, as described hereafter. From the Fourier transform of the STM images on B4OTF, the elementary lattice parameters for the self-assembly of
B4OTF on HOPG are calculated to be as follows: a ) 3.88 ( 0.26 nm; b ) 1.19 ( 0.07 nm; and q (the angle between a and b axes) ) 93.5 ( 5.9° (Figure 2c and Table 1). In Figure 2d, we propose a simple model for the self-assembly, with two molecules of B4OTF in the elementary unit cell. B4OTF STM images on a large scale (Figure 2a,b) show brighter lines over a darker background. On a smaller scale (Figure 2c), it appears that these bright lines are actually formed from pairs of bright spots, which we tentatively attribute to the thiophene rings of adjacent molecules. The remaining thiophenes also form a network of paired rings, but appear on most of the images less contrasted, as they are located in the middle of the darker areas. To understand the origin of this difference in contrast, we measure the lattice formed by the thiophene rings in the brighter line (I) and in the darker line (II). We find a single set of parameters for the two lines, with the following values: c ) 1.19 ( 0.07 nm, d ) 0.64 ( 0.15 nm, u ) 73.4 ( 5.2° (Figure 2c and Table 1). This suggests that the difference in contrast originates more from a different adsorption position of the molecular groups on graphite than from a specific conformation of the molecules, as confirmed hereafter by the modeling and the analysis of the monolayer chirality. For B5OTF, if one assumes an elementary lattice with two molecules per unit cell, estimated mean values are as follows: a ) 3.90 ( 0.56 nm; b ) 1.21 ( 0.13 nm; q ) 89.0 ( 9.3° (Figure 3c and Table 2). These results are close to those obtained for B4OTF, but the B5OTF organization is, however, more complex. On a short scale, it appears indeed that B5OTF molecules self-assemble only into a “pseudo” lattice. In Figure 3c, an elementary cell has been tentatively represented for B5OTF in full lines. When applying a translation vector, one gets a clear mismatch with respect to the real location of the thiophene rings. In contrast to B4OTF (for which any translation will give a perfect matching; see Figure 2c), bright parallel lines are not observed (as highlighted by the red circles in Figure 3c), and at least two sets of parameters can be proposed for the location of the thiophene rings of adjacent molecules: (i) c1 ) 1.21 ( 0.08 nm, d1 ) 0.78 ( 0.09 nm, u1 ) 52.6 ( 7.0°; (ii) c2 ) 1.20 ( 0.08 nm, d2 ) 0.78 ( 0.09 nm, u2 ) 62.8 ( 5.8° (Figure 3c and Table 2). The difference in the angle for the two lattices suggests a nonsymmetric arrangement of the molecules in the layer. Remarkably, large-scale images display a perfectly regular long-range modulation (Figure 3b), with a periodicity in the b direction (determined from Fourier transform images, not shown) of 12 nm ) 10 × b. This feature is observed on B5OTF monolayers regardless of the experimental conditions, and systematic tests (such as increasing the scanning rate while keeping the same image size or checking the tunneling current noise) have been carried out to confirm the absence of any artifact. It becomes henceforth possible to define a superlattice (a, 10 × b, q), whose elementary unit cell includes 20 molecules (Figure 3b). At this stage, we turned to modeling in order to understand the details of the molecular assembly leading to the observed structures, in particular, in terms of the conformation and the
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Figure 2. STM images of B4OTF monolayers. (a) 147 × 147 nm2, 300 × 300 pixels, It ) 4 pA, Vg ) 0.7 V; three domains oriented according to the graphite axis rotated by 120° with respect to each other. (b) 47 × 63 nm2, 362 × 485 pixels, It ) 60 pA, Vg ) 0.9 V. (c) 15 × 15 nm2, 300 × 300 pixels, It ) 10 pA, Vg ) 1.0 V. Lattice parameters: a ) 3.88 ( 0.26 nm, b ) 1.19 ( 0.07 nm, q ) 93.5 ( 5.9°. Sulfur lattice parameters: c ) 1.19 ( 0.07 nm, d ) 0.64 ( 0.15 nm, u ) 73.4 ( 5.2°. Two elementary cells, shifted from each other by a 4b,a vector (dotted black arrow), are represented (in full and dotted black lines, respectively). (d) sketch of the organization of B4OTF molecules on the graphite surface.
supramolecular organization of the conjugated backbone and the alkyl chains. Conformational and Electronic Properties of Isolated Molecules We first studied the conformation of a single bis-thiophene fluorenone molecule (without alkyl chains) in a vacuum with a DFT hybrid method (B3LYP) and a Pople Gaussian Basis Set (6-31+G(d)). This part of the molecule is common for both B4OTF and B5OTF. Figure 4 shows the potential energy surface for the rotation of a thiophene ring with respect to the fluorenone core. The two possible minima on the path of rotation are very close in energy. They correspond to conformations in which the carbonyl group of the fluorenone and the sulfur atom of the thiophene ring are on the same side (syn; angle ≈ 150°) or on opposite sides (anti; angle ≈ 30°) of the molecule. The energy barrier to pass from one minimum to the other through 90° is rather low (2.8 kcal/mol) and can be overcome at room temperature in vacuum. The two minima correspond to slightly
tilted conformations, but planar conformations (0° and 180°) are very close in energy. The adsorption of the molecules on the surface most probably favors the planar conformations, to maximize the π-π stacking interactions between the aromatic rings and the graphite surface. For this reason, we can suppose that it will be difficult for molecules adsorbed on the surface to pass from one conformer to the other. On the basis of the results of Figure 4, one can generate three possible conformations for the bis-thiophene fluorenone: (i) the syn-syn conformation, where the oxygen atom of the fluorenone and the sulfur atoms of both thiophene rings are pointing in the same direction; (ii) the syn-anti conformation, where only one sulfur atom is pointing in the same direction that the oxygen atom of the fluorenone; (iii) the anti-anti conformation, where the sulfur atoms of both thiophene rings are pointing in the opposite direction of the fluorenone oxygen. These three conformers are very close in energy. The difference is lower than 0.3 kcal/mol (B3LYP/6-31+G(d)). Therefore, it is not possible to rule out one of these structures at this point of the
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Figure 3. STM images of B5OTF monolayers. (a) 220 × 220 nm2, 220 × 220 pixels, It ) 2.8 pA, Vg ) 1.0 V; three domains oriented according to the graphite axis rotated by 120° with respect to each other. (b) 47 × 63 nm2, 362 × 485 pixels, It ) 10 pA, Vg ) 1.2 V. The unit cell of the superlattice is highlighted. (c) 15 × 15 nm2, 300 × 300 pixels, It ) 15 pA, Vg ) 1.2 V. Lattice parameters: a ) 3.90 ( 0.56 nm, b ) 1.21 ( 0.13 nm, q ) 89.0 ( 9.3°. Sulfur lattice parameters: c1 ) 1.21 ( 0.08 nm, d1 ) 0.78 ( 0.09 nm, u1 ) 52.6 ( 7.0°; c2 ) 1.20 ( 0.08 nm, d2 ) 0.78 ( 0.09 nm, u2 ) 62.8 ( 5.8°. An elementary cell has been represented in full lines (black). When applying a 4b,a translation vector (dotted black arrow), one shifts to the location indicated by black dotted lines, evidencing a mismatch with respect to the real location of thiophene rings. Note also the difference of contrast between thiophenes on the top right corners of both cells, highlighted by red circles.
study. Moreover, we expect the adsorption energy on graphite of these three conformers to be quite similar. Since the energy of the three conformers and their adsorption energy on the surface are almost the same, the dipole moments (and dipole-dipole interactions between adjacent molecules) may play an important role in determining which assembly is the most stable. The dipole moments are calculated (B3LYP/ 6-31+G(d)) to be 4.26, 3.25, and 2.21 D for the syn-syn, synanti, and anti-anti flat conformers, respectively. The evolution of the dipole moment in the series can be explained taking into account three main components: the first one is the dipole coming from the CdO bond of fluorenone, and the other two come from each thiophene ring. The dipole of the isolated fluorenone is 3.62 D, and that of thiophene is 0.62 D. So in the syn-syn conformer, all three dipoles are in the same direction, and that conformation has the largest dipole moment. In the
anti-anti conformation, the dipoles of the thiophene rings point opposite to that of the fluorenone (and that conformation has the smallest dipole moment). The case of the syn-anti system is intermediate. We present in Figure 5 the shape of the HOMO and LUMO computed at the B3LYP/6-31+G(d) level for the three conformers of the molecule without alkyl chains (the alkyl groups play no role in the frontier orbitals). These two orbitals can play a crucial role in the tunneling process, so the shape of these orbitals may help in the interpretation of the STM images. For the three conformations, the HOMO and the LUMO are fully delocalized over the fluorenone and the two thiophene rings. Thus, all the bright zones on the STM images may be attributed to the fluorenone unit or the thiophene rings. Moreover, there is no significant difference in the overall shape of those orbitals among the three conformers, which indicates that the three
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TABLE 1a B4OTF syn-syn (MD) a b q c d u total energy van der Waals energy dipole-dipole energy adsorption energy
3.76 ( 0.05 1.28 ( 0.15 91.6 ( 20.0 1.25 ( 0.14 0.63 ( 0.09 64.2 ( 20.7 241.8 ( 8.7 -785.2 ( 5.2 8.9 ( 1.3 -1302.2 ( 4.6
syn-anti (MD)
anti-anti (MD)
Lattice Parameters 3.80 ( 0.05 1.20 ( 0.04 100.3 ( 3.8 Sulfur Lattice Parameters c1 ) 1.20 ( 0.05 c2 ) 1.20 ( 0.05 d1 ) 0.63 ( 0.07 d2 ) 0.52 ( 0.07 u1 ) 64.0 ( 5.7 u2 ) 77.8 ( 5.5 223.9 ( 6.6 -795.0 ( 4.8 0.8 ( 0.1 -1304.0 ( 4.0
STM
3.75 ( 0.04 1.20 ( 0.04 91.3 ( 3.4
3.88 ( 0.26 1.19 ( 0.07 93.5 ( 5.9
1.20 ( 0.05 0.53 ( 0.07 77.5 ( 5.5 204.7 ( 5.3 -803.5 ( 3.7 -4.5 ( 0.0 -1310.2 ( 2.5
1.19 ( 0.07 0.64 ( 0.15 73.4 ( 5.2
a The theoretical structural data (in nm) correspond to the average values and standard deviations over the 400 ps MD run, after equilibration. The energetic values (in kcal/mol) correspond to the average and standard deviation over the optimized points along the MD runs for the whole lattice containing 20 molecules.
TABLE 2a B5OTF syn-syn (MD) a b q c d u total energy van der Waals energy dipole-dipole energy adsorption energy
syn-anti (MD)
3.75 ( 0.05 1.20 ( 0.04 88.3 ( 5.6 1.20 ( 0.05 1.05 ( 0.08 55.2 ( 6.5 246.0 ( 6.9 -802.0 ( 4.6 15.3 ( 0.2 -1314.8 ( 2.8
3.77 ( 0.04 1.20 ( 0.04 89.1 ( 6.1
anti-anti (MD)
Lattice Parameters
3.76 ( 0.05 1.20 ( 0.04 88.3 ( 7.7
Sulfur Lattice Parameters c1 ) 1.20 ( 0.05 c2 ) 1.20 ( 1.20 ( 0.06 d1 ) 0.99 ( 0.05 d2 ) 0.80 ( 0.12 0.80 ( 0.14 u1 ) 56.0 ( 7.0 u2 ) 72.8 ( 9.8 69.7 ( 5.1 238.7 ( 5.9 245.8 ( 6.7 -798.8 ( 3.6 -785.5 ( 4.2 7.0 ( 0.2 0.9 ( 0.1 -1315.9 ( 2.4 -1311.8 ( 2.6
STM 3.90 ( 0.56 1.21 ( 0.13 89.0 ( 9.3 c1 ) 1.21 ( 0.08 d1 ) 0.78 ( 0.09 u1 ) 52.6 ( 7.0
c2 ) 1.20 ( 0.08 d2 ) 0.78 ( 0.09 u2 ) 62.8 ( 5.8
a The theoretical structural data (in nm) correspond to the average values and standard deviations over the 400 ps MD run, after equilibration. The energetic values (in kcal/mol) correspond to the average and standard deviation over the optimized points along the MD runs for the whole lattice containing 20 molecules.
conformers would hardly be distinguished on the images recorded at room temperature based on their expected STM signature. Modeling the Self-Assembled Structures We have modeled the self-assembly of the three possible conformers (syn-syn, syn-anti, and anti-anti) for the B4OTF and B5OTF molecules on the graphite surface. The observed supramolecular structures result from the interplay among several dispersive forces: CH-π interactions, π-π stacking, and packing forces. The calculations using molecular mechanics (MM) and molecular dynamics (MD) provide information about the lattice parameters and the adsorption energy (see the theoretical methodology section). The calculations also provide a detailed decomposition of the total energy in terms of several components: bonding, angle, torsion angle, dipole-dipole, and Van der Waals interactions. Since the bonding, angle, and torsion angle contributions are equivalent in the three conformations, the two main energetic contributions that rule the selfassembly are the dipole-dipole interactions and the Van der Waals interactions. The energies reported in Tables 1 and 2 for B4OTF and B5OTF systems, respectively, are expressed in kcal/ mol and refer to the whole lattice considered in the calculation (20 molecules). Figures 6 and 8 show snapshots of the molecular dynamics for the assemblies of the three conformers of B4OTF and B5OTF, along with the lattice parameters. It is also very useful to draw the dipole moment on each fluorenone and on each thiophene unit and to represent the lattice formed (in yellow
in Figures 6 and 8) by the sulfur atoms between adjacent rows of molecules, in order to better understand the dipole-dipole interactions between rows of molecules. For B4OTF, we obtain lattice parameters in good agreement with the STM measurements regardless of the molecular conformation (Table 1). For the syn-syn conformation, we observe a large standard deviation for the b parameter ((0.15 nm) and for the angle q ((20°), due to the fact that the molecules are linear and so can slide on the surface with respect to each other along their long axis. The consequence of this sliding is a nonstable lattice. In contrast, the syn-anti and antianti molecules are bent, which prevents any long-range motion within the layer. The relative positions of the thiophene rings and the interaction of the dipoles localized on those thiophene rings are very different for the three systems (Figure 6). For the syn-syn conformation, the thiophene rings form a lattice of 1.25 nm × 0.63 nm and the angle between the two directions is about 64°. In the anti-anti conformation, the thiophene rings form a lattice of 1.20 nm × 0.53 nm and the angle between the two directions is about 77°. The most favorable dipole-dipole interactions would occur for dipoles with an antiparallel arrangement between adjacent molecular rows, i.e., if the angle of the “dipole lattice” would be close to 90°. Therefore, the dipole-dipole interaction is more favorable in the anti-anti layer than in the syn-syn layer (-4.5 vs +8.9 kcal/mol for the whole assembly). In the syn-anti layer, we find the two different lattices; as a consequence, the contribution to the total energy from dipole-
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Figure 4. Potential energy surface for the rotation of a thiophene ring with respect to the fluorenone core, calculated at the B3LYP/6-31+G(d) level. The zero of the energy scale is defined as the energy of the 30° conformer.
Figure 5. HOMO and LUMO for the syn-syn, syn-anti, and anti-anti conformers, computed at the B3LYP/6-31+G(d) level.
dipole interactions is intermediate between those of the synsyn and anti-anti systems. A detailed analysis of the structure of the assemblies also shows that in the anti-anti layer the contact area for interactions between alkyl chains of adjacent molecules is larger than in
the syn-syn layer. In other words, the number of methylene groups of adjacent molecules facing each other is larger in the anti-anti configuration than in the syn-syn one. This can explain why the Van der Waals interaction is more favorable in the anti-anti system than in the syn-syn system. As
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Figure 6. Snapshots of the MD simulations for the (a) syn-syn, (b) syn-anti, (c) anti-anti conformations of B4OTF. The pink and green arrows represent the dipoles on the thiophene and fluorenone units, respectively. The arrows represent the effective orientation of the local dipoles on the thiophene and fluorenone units as can be readily anticipated from the relative electronegativity of the involved atoms.
Linares et al. expected, the Van der Waals interactions in the syn-anti assembly are intermediate between those of the two extreme cases. To conclude, for B4OTF, the anti-anti layer is the one most likely to form on the graphite surface. Indeed, its energy is lower than the energy of the other two systems, by about 1 kcal/mol per molecule, because of favorable dipole-dipole and Van der Waals interactions. On that basis, we can focus on the origin of the different contrast in the STM images of B4OTF monolayers (lines I and II in Figure 2c). Our results indicate that a slightly asymmetric positioning of B4OTF molecules self-assembled on HOPG in the anti-anti lattice accounts both for the existence of brighter lines of thiophene pairs and for the observation of chiral domain boundaries. An STM image of an interface between such enantiomeric domains, where the right side appears as the mirror image of the left side, is displayed in Figure 7c. For achiral compounds, that is in the case of B4OTF, chirality in monolayers has been frequently reported.19-23 It arisesfrom a loss of mirror plane symmetry when the molecule is restricted to a 2D surface, which can stem from several causes. For instance, adsorption on one side or the other of the molecule can break the symmetry and result in the formation of chiral domains. In some other cases, the molecules arrange forming chiral elementary repeating units. Symmetry breaking upon adsorption can occur at the single-molecule scale, which is actually the situation for B4OTF on HOPG as discussed hereafter. As mentioned above, it has been shown that alkyl side chains can play a major role in such phenomena.12 In this study, either due to the very high packing of the short molecules or to other effects (such as thermal agitation), the alkyl side groups are not clearly resolved even from the STM images at the submolecular level. However, from the modeling of the anti-anti assembly (see Figure 6c), we find that the angle between the two directions of the alkyl chains is about 140° (γ). Therefore, if one alkyl group of the B4OTF molecules follows one graphite axis, as often observed for alkylated molecules on HOPG and confirmed by the threefold symmetry observed on large-scale STM images (Figures 2a and 3a), the other alkyl group cannot match with the graphite axis (Figure 7d), because the energy cost to deform the molecule to reach an angle of 120° would be too high. In turn, the two thiophene units of a given B4OTF molecule become slightly asymmetrically (Figure 7b-d) positioned over the graphite lattice, which can account for the contrast observed between lines I and II in STM images. It is reasonable to assume that the overlap between graphite and the thiophene π-orbitals is affected by the adsorption-induced asymmetry, giving rise to enhanced contrast variations in the STM topographic images. On that basis, the chirality of B4OTF layers originates clearly in the molecular symmetry breaking upon adsorption on HOPG, as illustrated in Figure 7. Note that, for the syn-syn assembly, the molecules are linear, so both alkyl chains can be properly oriented with respect to one main axis of the graphite, and consequently, we would expect the same contrast for both thiophene rings (the case of the synanti assembly is similar to the anti-anti system). For B5OTF, the calculated lattice parameters for the three systems are also in good agreement with the STM measurements (Table 2). In contrast to B4OTF, we do not observe a large standard deviation for the lattice parameters in the syn-syn layer. B5OTF molecules are less linear than B4OTF molecules; therefore, they appear to be “locked” in the self-assembly and cannot slide with respect to each other. As in B4OTF, the dipole-dipole interactions are more favorable in the anti-anti layer than in its syn-syn counterpart.
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Figure 7. B40TF monolayer chirality induced by molecular symmetry breaking upon adsorption on HOPG. (a) If B4OTF molecules were perfectly symmetric on HOPG (the thiophenes rings of a single molecule are equivalent, represented in red color), it would be possible to insert the mirror image of the elementary repeating unit within the lattice by a simple translation, which is the case for an achiral assembly. (b) B4OTF monolayers are chiral on HOPG, due to symmetry breaking upon adsorption: only one alkyl chain per B4OTF molecule matches the substrate (see Figure 6c and text). The thiophene units of a given molecule are also asymmetrically positioned over the HOPG, as highlighted by their different colors (yellow and red). It is then impossible to insert the mirror image of the elementary repeating unit within the lattice by a simple translation. (c) STM image of a B4OTF domain boundary. 14 × 14 nm2, 700 × 700 pixels, It ) 31 pA, Vg ) 0.9 V. The two domains on each side of the boundary are enantiomers. (d) Schematic model for the boundary. For each B4OTF molecule, only one alkyl chain matches the substrate. The thiophene units with an alkyl side chain in epitaxy on HOPG (forming lines I, see text) are highlighted by red circles.
The angle of the lattice formed by the thiophene rings in the syn-syn layer is about 55°, which is the closest to 45°, i.e., the worst case for dipole-dipole interactions. In the anti-anti layer, the lattice angle is about 70°, which is much more favorable (i.e., closer to 90°). As in B4OTF, we find the two types of lattice in the syn-anti layer; as a consequence, the energetic contribution from dipole-dipole interactions is again intermediate between those of the syn-syn and the anti-anti systems. However, contrary to B4OTF, the Van der Waals interactions are more favorable in the syn-syn layer than in the anti-anti layer. Figure 8 clearly shows that the interaction area between alkyl chains is larger in the syn-syn assembly than in the antianti assembly. This difference with respect to B4OTF illustrates the importance of the position of the alkyl chains on the thiophene ring on the self-assembly process. As expected, the Van der Waals interactions in the syn-anti system are intermediate between those of the two extreme cases. For B5OTF, it therefore appears that the two main interactions (dipole-dipole and Van der Waals) do not follow the same trend: the Van der Waals interactions are increasingly favorable in the series anti-anti, syn-anti, syn-syn; while the dipoledipole interactions are increasingly favorable in the series synsyn, syn-anti, anti-anti. As a consequence, the syn-anti
assembly is the most stable and should be the one forming on the graphite surface. However, the other two assemblies (synsyn and anti-anti) are very close in energy, and we cannot exclude finding them locally on the surface. Two sets of parameters were extracted from the STM images for the sulfur lattice, which could be consistent either with the syn-anti model or with a more complex assembly involving several conformations. As the syn-anti conformation is prochiral, one should expect the existence of chiral domains, which were never observed for B5OTF assemblies. This suggests a more complex organization, which is also consistent with the absence of welldefined lines formed by the thiophene rings in the STM images at large scales. An additional indication is given by the 12 nm modulation in the b direction whose value is an integer multiple of the b lattice constant (12 nm ) 10 × b). As this phenomenon cannot be accounted for by the syn-syn, syn-anti, or antianti models, several conformations may participate in the formation of a long-range ordered (i.e., at scales larger than that of the 10 × b modulation) self-assembly. At this stage, modeling of such an organization is beyond the limits of the formalisms employed in this work. Further studies, including measurements after in situ annealing, are in progress to get a deeper understanding of the exact nature of the short-range and
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Linares et al. long-range organization of B5OTF assemblies. Preliminary measurements reveal that the self-assembly is dramatically affected by annealing at moderate (above 60 °C) temperatures, which suggests that the B5OTF assemblies are at the limit of structural instability in ambient conditions. Conclusion The 2D self-assembly of B4OTF and B5OTF thiophenefluorenone conjugated oligomers on HOPG has been investigated by a combination of STM imaging at the submolecular level, conformational DFT calculations, and adsorption MM/ MD simulations. The formation of highly ordered assemblies on HOPG is ruled by the interplay between weak interactions resulting from the relative orientation of the dipole on the thiophene and fluorenone units, and from the position of the alkyl chains grafted to the conjugated backbone. For both B4OTF and B5OTF on the graphite surface, the lattice parameters calculated for the three possible conformers (syn-syn, syn-anti, and anti-anti) are close to those deduced from STM measurements. The simulations indicate that for B4OTF molecules the anti-anti conformation is preferred, due to more favorable dipole-dipole and Van der Waals interactions. Remarkably, B4OTF adsorption on graphite induces a loss of symmetry, which can be explained by a simple model where only one side chain matches the underlying substrate. This model accounts well for the contrast observed in the STM images and for the existence of chiral domains formed from achiral B4OTF molecules on achiral HOPG. Changing the position of the side groups from C4 to C5 position dramatically impacts the self-assembly process. Due to the competition between dipole-dipole and Van der Waals interactions, the syn-syn, syn-anti, and anti-anti 2D assemblies become very close in energy for B5OTF. From the comparative analysis between the experimental data and the modeling, and taking into account the existence of an additional long-range modulation, it has been suggested that several conformers are in fact involved in the self-assembly process of B5OTF. Material Synthesis
Figure 8. Snapshots of the MD simulations for the (a) syn-syn, (b) syn-anti, (c) anti-anti conformations of B5OTF. The pink and green arrows represent the dipoles on the thiophene and fluorenone units, respectively. The arrows represent the effective orientation of the local dipoles on the thiophene and fluorenone units as can be readily anticipated from the relative electronegativity of the involved atoms.
All the starting materials and solvents were purchased from Aldrich (except the palladium catalyst purchased from Acros) and used as received. All the compounds were characterized by 1H/13C NMR and FTIR-ATR spectroscopies and elemental analysis. NMR spectra were recorded on an AC200 spectrometer (Bru¨cker). Chloroform-d containing tetramethyl silane (TMS) as internal standard was used as solvent. Elemental analyses were carried out by the Analytical Service of CNRS-Vernaison (France). FTIR-ATR spectra were recorded on a Paragon 500 (Perkin-Elmer) spectrometer (wavenumber range 4000-400 cm-1, resolution 4 cm-1) equipped with a Golden Gate Diamond Single Reflection ATR accessory (Specac). The synthetic method applied for the synthesis of 2,7-bis(4-octyl-thien-2-yl)-fluoren-9-one (B4OTF), and 2,7-bis-(5octyl-thien-2-yl)-fluoren-9-one (B5OTF) involves the conventional Suzuki palladium cross-coupling reaction between 2,7dibromofluoren-9-one and the appropriate R-boronate esters of 3-octylthiophene and 2-octylthiophene, respectively. The general procedure can be briefly described as follows. 2,7-Dibromofluoren-9-one (1.92 mmol) and the appropriate R-boronate ester (4.34 mmol, 2.25 equiv), prepared as described in detail in ref 24, were placed in anhydrous DMF (20 mL). The mixture was stirred under argon for 10 min, then K3PO4 (4.24 mmol, 2.2
2D Self-Assembly of Thiophene-Fluorenone Oligomers equiv) and Pd(P(Ph)3)4 (0.173 mmol, 0.09 equiv) in 10 mL of DMF were added. The mixture was kept at 100 °C for an additional period of 20 h with constant stirring and then allowed to cool to room temperature. The product was then purified by precipitation and filtration. All the characterization data of B4OTF were identical to those reported in ref 24. 2,7-Bis-(5-octyl-thien-2-yl)-fluoren-9-one (B5OTF). 1H NMR (CDCl3, 200 MHz, ppm): δ 7.75 (d, 2H, J ) 1.75 Hz), 7.56 (dd, 2H, J ) 7.79 and 1.75 Hz), 7.52 (d, 2H, J ) 7.79 Hz), 7.10 (d, 2H, J ) 3.63 Hz), 6.67 (d, 2H, J ) 3.63 Hz), 2.74 (t, 4H, J ) 7.66 Hz), 1.57-1.68 (m, 4H), 1.10-1.40 (m, 20H), 0.75-0.95 (m, 6H). 13C NMR (CDCl3, 50 MHz, ppm): 193.45 (CdO), 146.56 (2C), 142.39 (2C), 140.36 (2C), 135.65 (2C), 135.08 (2C), 131.12 (2C), 125.22 (2C), 123.35 (2C), 121.07 (2C), 120.55 (2C), 31.84 (2C), 31.57 (2C), 30.27 (2C), 29.32 (2C), 29.20 (2C), 29.09 (2C), 22.63 (2C), 14.05 (2C). FT-IR (powder, ATR mode): 3080 (w), 2956 (m), 2919 (s), 2849 (s), 1722 (CdO, s), 1600 (m), 1583 (m), 1488 (s), 1465 (s), 1454 (s), 1430 (m), 1266 (m), 1172 (s), 834 (m), 800 (s), 782 (s), 721 (s). Elemental analysis: Calcd. for C37H44OS2: C, 78.12%; H, 7.80%; S, 11.27%. Found: C, 77.90%; H, 7.74%; S, 11.30%. Scanning Tunnelling Microscopy. B4OTF and B5OTF films with monolayer coverage were prepared by drop-casting from 10-4 M CHCl3 solution on freshly cleaved highly oriented pyrolytic graphite (HOPG) substrates. STM experiments were performed in the low-current mode, at room temperature, under ultrahigh-vacuum conditions (base pressure below 5 × 10-11 mbars), using a VT Omicron system and in situ cleaned W tips. The scanner tube was calibrated by realizing atomically resolved images of the reconstructed Si(111)-7 × 7 surface. In this setup, the bias voltage Vg is applied to the tip and the sample is grounded. All the images were obtained in the constant current mode (tip bias voltages and tunneling currents are given in the figure captions), and postacquisition treatment consisted only of slope subtraction. The lattice parameters for B4OTF and B5OTF assemblies were estimated by means of statistical analysis performed on several sets of images (the values were averaged and the error bars correspond to the standard deviation). Theoretical Methodology. For the self-assembly, all the computations were done with the molecular package TINKER25 and the MM3 force field, which has been recently modified26 with new parameters to take into account weak interactions. We use periodic boundary conditions to perform calculations on an infinite adsorbed layer, with a unit cell containing 20 molecules assembled on a two-layer-thick slab of graphite. The self-assembly is built by alternating the orientation of molecular rows in order to alternate the orientation of the molecular dipoles. For each system, we perform molecular dynamics (MD) simulations in the canonical ensemble (constant NVT), with an equilibration time of 400 ps. Then, during the next 400 ps, we follow and record the lattice parameters (distance and angle between oxygen atoms) of the assembly. By optimizing the geometry extracted from several snapshots along the MD trajectory, we can obtain information about the total energy of
J. Phys. Chem. C, Vol. 112, No. 17, 2008 6859 the full system. Performing the same calculations after removal of the graphite substrate yields energetic information about the assembled layer itself, which then allows determination of the adsorption energy. Acknowledgment. The modeling work in Mons has been supported by the European Commission Marie Curie Research Training Network CHEXTAN (MRTN-CT-2004-512161), by the Interuniversity Attraction Pole program of the Belgian Federal Science Policy Office (PAI 6/27) and by FNRS-FRFC. D.B. is Research Director of FNRS. SPM facilities used for the experimental work in Grenoble have been funded by the French Ministry of Research under the grant “RTB: Post CMOS Mole´culaire 200 mm”. References and Notes (1) Puigmarti-Luis, J.; Minoia, A.; Uji-i, H.; Rovira, C.; Cornil, J.; De Feyter, S.; Lazzaroni, R.; Amabilino, D. B. J. Am. Chem. Soc. 2006, 128 (39), 12602-12603. (2) Neher, D. Macromol. Rapid. Commun. 2001, 22 (17), 1366-1385. (3) Grice, A. W.; Bradley, D. D. C.; Bernius, M. T.; Inbasekaran, M.; Wu, W. W.; Woo, E. P. Appl. Phys. Lett. 1998, 73 (5), 629-631. (4) Arias, A. C.; Mackenzie, J. D.; Stevenson, R.; Halls, J. J. M.; Inbasekaran, M.; Woo, E. P. Macromolecules 2001, 34 (17), 6005-6013. (5) Demadrille, R.; Firon, M.; Leroy, J.; Rannou, P.; Pron, A. AdV. Funct. Mater. 2005, 15, 1547-1552. (6) Porzio, W.; Destri, S.; Pasini, M.; Giovanella, U.; Motta, T.; Iosip, M. D.; Natali, D.; Sampietro, M.; Franco, L.; Campione, M. Synth. Met. 2004, 146 (3), 259-263. (7) Porzio, W.; Destri, S.; Giovanella, U.; Pasini, M.; Motta, T.; Natali, D.; Sampietro, L.; Campione, M. Thin Solid Films 2006, 492 (1-2), 212220. (8) Porzio, W.; Destri, S.; Giovanella, U.; Pasini, M.; Marin, L.; Iosip, M. D.; Campione, M. Thin Solid Films 2007, 515 (18), 7318-7323. (9) Jaramillo-Isaza, F.; Turner, M. L. J. Mater. Chem. 2006, 1, 8389. (10) Qiu, D. L.; Ye, K. Q.; Wang, Y.; Zou, B.; Zhang, X. Langmuir 2003, 19 (3), 678-681. (11) Xu, S.; Zeng, Q.; Lu, J.; Wang, C.; Wan, L.; Bai. C.-L. Surf. Sci. 2003, 538, 451-459. (12) Wei, Y.; Kannappan, K.; Flynn, G. W.; Zimmt, M. B. J. Am. Chem. Soc. 2004, 126, 5318-5322. (13) Charra, F.; Cousty, J. Phys. ReV. Lett. 1998, 80, 1682-1685. (14) Cai, Y.; Bernasek, S. L. J. Am. Chem. Soc. 2004, 126, 1423414238. (15) Rabe, J. P.; Buchholz, S. Science 1991, 253, 424-427. (16) De Feyter, S.; De Schryver, F. C. J. Phys. Chem. B 2005, 109 (10), 4290-4302. (17) Pan, G. B.; Cheng, X. H.; Hoger, S.; Freyland, W. J. Am. Chem. Soc. 2006, 128 (13), 4218-4219. (18) Nakanishi, T.; Miyashita, N.; Michinobu, T.; Wakayama, Y.; Tsuruoka, T.; Ariga, K.; Kurth, D.G.; J. Am. Chem. Soc. 2006, 128 (19), 6328-6329. (19) Tao, F.; Bernasek, S. L. J. Am. Chem. Soc. 2005, 127, 1275012751. (20) Gong, J. R.; Wan, L. J. J. Phys. Chem. B 2005, 109, 18733-18740. (21) Weigelt, S.; Busse, C.; Petersen, L.; Rauls, E.; Hammer, B.; Gothelf, K.; Besenbacher, F.; Linderoth. T. Nat. Mater. 2006, 5, 112-117. (22) France, C. B.; Parkinson, B. A. J. Am. Chem. Soc. 2003, 125, 127112-127113. (23) Plass, K. E.; Grzesiak, A. L.; Matzger, A. J. Acc. Chem. Res. 2007, 40, 287-293. (24) Demadrille, R.; Divisia-Blohorn, B.; Zagorska, M.; Quillard, S.; Lefrant, S.; Pron, A. Electrochim. Acta 2005, 50, 1597. (25) http://dasher.wustl.edu/tinker/. (26) Ma, B. Y.; Lii, J. H.; Allinger, N. L. J. Comput. Chem. 2000, 21 (10), 813-825.
