Stable room temperature molecular assembly of zwitterionic organic dipoles guided by Si(111)-7x7 template effect **
(Result of the month 02/2008)

The adsorption of functional molecules on surfaces plays a vital role for the emerging field of nanoelectronic.[1] In this context, molecular and supramolecular ordering, which are key-steps for the development of complexes architectures, are controlled by a balance between intermolecular forces and molecule-substrate interactions.[2] The restructuring is often driven by cooperative molecule-substrate interactions involving many molecules, and is not directly related to the shape of individual molecules. This is still a challenge to deposit organic molecules and to preserve their entire skeleton, especially on semiconductor surfaces.
However, much progress has been made in the development of metallic surface-based devices with organic molecules at low temperature because the molecule/surface interactions are weak and diffusion remains low.[3] However, the use of metallic substrates has less attractive potential applications with regards to semiconductors, especially in the field of nanoelectronic. Thus, the deposition of molecules on a semiconductor surface at room temperature with complete control of the adsorption site and without alteration of their aromatic behaviour is still a challenge in view of the development of complex architectures.[4] For example, Polanyi et al. have shown that the adsorption of chlorododecane on Si(111)-7x7 at room temperature leads to the formation of bistable dimeric corral of self-assembled molecules. On-off electronic switching of single silicon adatom by molecular field effects has been demonstrated.[5] In addition, the authors have described a new strategy to prevent the dissociation of halogenoalkanes on Si(111)-7x7 until elevated temperature (373K). This stability is ensured thanks to dimeric formation of circular corrals for overriding molecules-substrate interaction. [5] In this paper, we propose a new concept for the successful deposition at room temperature of π-conjugated organic molecules, without any modification of their electronic structure, in specific adsorption sites of the semiconductor Si(111)-7x7 surface.
Our solution consists to adsorb π-conjugated zwitterionic molecules on this semiconductor surface. The presence of negative charge on the target molecules offsets the electrophilic character of the Si(111)-7x7 adatoms and preserves the π-skeleton of organic molecules after the deposition. The half-cells of Si(111)-7x7 act as a template for guiding the molecular assembly of achiral molecules as it is proved by the induction of chirality in the modified areas. Experimental STM images as well as theoretical calculations are in perfect agreement with the proposed concept. The electronic properties of molecules are often modified during their adsorption on the Si(111)-7x7 interface. Indeed, Si-C σ-bonds are usually formed by the reaction of electron-deficient silicon adatoms of Si(111)-7x7 with electron-rich carbon atom of organic molecules.[6] We propose an original concept to turn off the cycloadditions by using the negative site of zwitterionic molecule as a shield (by electrostatic interactions) for the molecule on the electrophilic adatoms of Si(111)-7x7. Zwitterionic molecules seem to be ideal candidates since they are neutral but they carry formal positive and negative charges on different atoms. In principle, the surface should offset its electronic lack with the negative charge of molecules instead of its extended electron-rich π-conjugated system. To prove our concept, we have synthesised the 4-methoxy-4’-(3-sulfonatopropyl)stilbazolium (MSPS) which is ended by the negative sulfonato (SO3-) group as depicted in Figure 1a as a model of zwitterionic organic molecule. Experiments were carried out in an ultra-high vacuum chamber with a pressure lower than 2.10-10 mbar. Molecules are sublimed from a kundsen cell at 390K onto the Si(111)-7x7 kept at room temperature. STM images were acquired in the usual constant current mode at room temperature. Figures 1b and 1c exhibit STM images in two opposite polarities with atomic resolution on both Si(111)-7x7 reconstruction and molecules. For both filled and empty states, a half-cell exhibits an original threefold star at the center of images. Each arm of the star consists in two matched protrusions, one being more intense than the other. The length between centers of two paired protrusions (0.67 nm) strongly deviates from the length of one free MSPS molecule (1.3 nm).
However, this difference can be explained by a change of conformation due to the MSPS-substrate interactions (see below for details). Three protrusions are located exactly atop of corner adatoms and the three others are between a rest-atom and an adjacent center adatom. In the filled states (Figure 1b), the brighter protrusions are situated exactly atop of corner adatoms whereas, in the empty states (Figure 1c), the brighter protrusions appear between a rest-atom and a center adatom. In the MSPS, the sulfonato moiety possesses a negative charge and the methoxy group is electron-poor due to the conjugation with pyridinium ring. Therefore, the intense protrusions observed in the filled states atop corner adatoms are attributed to the sulfonato groups (Figure 1b) and the intense protrusions observed in the empty states between a rest-atom and an adjacent center adatom are assigned to the methoxy groups (figure 1c). Thanks to both polarities in STM images, MSPS molecules position in the assembled edifice can be undoubtedly defined. The star shape in a 7x7 half-cell could be attributed to the assembly of three MSPS. The molecule-substrate interactions have led to modify the conformation of three molecules which have been shrivelling up in from trans to cis conformation.
The proposed structural model of the 7x7 superimposed to the STM images is shown in Figure 1d. For very low molecule coverage, the star shape adsorption occurs preferentially on the faulted half-cell known to be the more reactive (Figure 1b).[7] The occupied half-cells are only filled by three MSPS as described previously. This experimental assembly process implies high molecule diffusion onto the surface at room temperature to form a stable structure of three assembled MSPS in a half-cell.

The assembly of three molecules in this particular star-shape can be explained by the template effect of the surface which possesses a threefold symmetry. The formation of a star-shape by assembly is probably guided by the transfer of symmetry from substrate to molecular reconstruction. Moreover, for each polarity, the intensities of the protrusions are not too much affected by the variations of bias voltage.
These phenomena are incompatible with the well-known formation of C-Si σ-bonds between the molecules and the substrate as it is described in the literature.[6, 8] The nature of the MSPS adsorption on Si(111)-7x7 surface has been investigated by ab initio calculations with extended density functional theory (DFT) using the Vienna Ab Initio Simulation Package (VASP).[9] In order to simulate the entire system MSPS+Si(111)-7x7, we have first optimised geometry of one free MSPS in vacuum in the cis conformation using GAUSSIAN 03 at the Hartree-Fock 6-31G(d) level of theory.[10]
Then, the three optimised molecules have been positioned in the cis conformation thanks to the help of the high resolution STM images aforementioned. Adsorption energy variation has been conducted at room temperature for different assembled molecules/surface distances d, which correspond to the separation between Si-adatoms and sulphur atom of the sulfonato group. Finally, the local densities of states (LDOS) have been determined with the Tersoff-Hamann scheme,[11] in each point for a constant current value and at respectively, -2V and +2V bias voltages.

The adsorption energy for the entire system is depicted in Figure 2a as a function of the distance d. The equilibrium distance, corresponding to the minimum of energy equal to -2.66 eV (i.e. -0.887eV per molecule), is close to 0.26 nm, in agreement with a physisorbed state. The LDOS images calculated at the equilibrium distance compare well with the experimental STM images (Figure 2b and 2c). Figure 2d represents the DOS of the whole stable system at d = 0.26 nm.
Two weak interactions are observed, corresponding to a very small electronic transfer, respectively, from the sulfonato groups to the corner adatoms and from methoxy moieties to Si-atoms. Therefore, there is no bond formation between only one oxygen atom and any silicon adatom. Nonetheless, the interaction between molecular edifice and substrate exists but depends only on the distance, in agreement with a weak electrostatic interaction between the oxygen anions of the sulfonato moieties and the electrophilic Si-adatoms.
Consequently, we have developed a new strategy to stabilise zwitterionic π-conjugated molecules on Si(111)-7x7 surface thanks to the electrostatic interactions between silicon adatoms and anionic atoms of molecules. However, these interactions are enough strong to stabilise the molecular edifice at room temperature and act as a template effect of Si(111)-7x7 surface in order to impose the cis conformation to MSPS molecules on the Si(111)-7x7 half-cells.

Figure 3 shows two half-cells, which are image one of the other by a mirror plane, containing each three assembled MSPS molecules. Therefore, the threefold stars are chiral even if free MSPS molecules are achiral. The chirality of the assembled molecular edifice is explained by the template effect of the Si(111)-7x7. The sulfonato group can swivel upon the corner adatom whereas the surface forces the methoxy moieties to be exactly adsorbed between a rest-atom and a center adatom (Figure 3). In this case, two enantiomers are possible, in accordance with a clockwise or anticlockwise folding and named, respectively (P)-enantiomer and (M)-enantiomer.
Besides, most of previous studies about chiral structures are concentrated on metal surfaces,[12] whereas relatively little work was spent on semiconductor surfaces.[13] However, in the previous studies on semiconductor, the chirality is due to the formation of at least one stereogenic center after the chemisorption (i.e. via cycloaddition) of molecules on silicon or germanium atoms. This is, to our knowledge, the first report of chiral assembly of achiral molecules on Si(111)-7x7. In conclusion, the results reported in this paper are remarkable from different points of view: molecular assembly of organic dipoles at room temperature, chirality of the edifice, stability and conservation of the π-conjugated skeleton at room temperature on semiconductor surface.
The zwitterionic strategy may become a major advance to deposit π-conjugated molecules successfully: The sulfonato group acts as an electrostatic shield for the protection of the π-skeleton of organic molecules versus the dangling bonds of semiconductor surfaces.