Single Atom Substitution for Marking and Motion Tracking of Individual

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J. Phys. Chem. C 2008, 112, 14058–14063

Single Atom Substitution for Marking and Motion Tracking of Individual Molecules by Scanning Tunneling Microscopy Guillaume Schull,† Herve´ Ness,† Ludovic Douillard,*,† Ce´line Fiorini-Debuisschert,† Fabrice Charra,† Fabrice Mathevet,‡ David Kreher,‡ and Andre´-Jean Attias‡ CEA, IRAMIS, SerVice de Physique et Chimie des Surfaces et Interfaces, F-91191 Gif-sur-YVette, France, and UniVersite´ Pierre et Marie Curie, Laboratoire de Chimie Macromole´culaire, CNRS-UMR 7610, 4 Place Jussieu F-75252, Paris cedex 05, France ReceiVed: April 7, 2008; ReVised Manuscript ReceiVed: July 9, 2008

We report on a simple way to mark and track individual molecules self-assembled on a surface by scanning tunneling microscopy. The tracer mechanism consists in a minimal one-atom chemical substitution. While this substitution leads to significant modifications in the STM signature of the molecules, no substantial changes of the physics of self-assembling are observed when using the modified or unmodified molecular building blocks. This allows us to follow the intrinsic dynamical properties of the self-assembled molecular patterns. Introduction microscopies1

and more especially scanning Scanning probe tunneling microscopy2 (STM) have revolutionized the real space imaging of surfaces at the atomic scale level. For the study of molecules adsorbed on surfaces, early pioneering works3-6 have mostly been focused on direct imaging of single molecules. Now a constant trend is to go beyond simple imaging in order to achieve a better discrimination at the molecular level. One natural way along this line is the use of specific chemical STM marking groups.7,8 STM marking groups are functional groups exhibiting unusual contrast in the STM images relative to the rest of the molecule moieties. Experimental investigations carried on substituted long-chain molecules have identified several groups with interesting properties. Some groups can increase the tunneling probability,8-13 such as thiol group -SH, sulfur atoms S, iodine atoms I, amino group -NH2, amide group -OdC-NH2 and so on; some can decrease it,12,14-16 for example, fluorine atoms F, carboxylic group -COOH, cyano group -CN and so forth; or some can present an alternate contrast depending on the different molecular configurations on the surface,17,18 such as bromine atoms Br. Other successful approaches include addition or elimination of molecular moieties,19 tip functionalization,20-23 and various spectrometric investigations, for example, scanning tunneling spectroscopies21,24,25 or inelastic tunneling spectroscopies.26,27 In this work, we present a simple way to single out and track individual molecules self-assembled on graphite surface by STM applying STM marker concepts in conjunction with first principle calculations. The tracer mechanism we used consists in labeling a molecule by a minimal one-atom chemical substitution. In this way, while the STM signature of the substituted molecule exhibits significant intramolecular modifications, the self-assembling physics remains the same when using the modified or unmodified molecular blocks. Application of this singling out method is demonstrated here * To whom correspondence should be addressed. Present address CEA Saclay Baˆt. 466 DSM\IRAMIS\SPCSI, F-91191 Gif sur Yvette, France. Tel. +33-(0)1 69 08 36 26. Fax +33-(0)1 69 08 64 62. E-mail: ludovic. [email protected]. † CEA, IRAMIS. ‡ Universite ´ Pierre et Marie Curie.

by direct observation of the intrinsic dynamics of recently obtained nanoporous assemblies acting as 2D molecular sieves.28-31 On a more general basis, the present work represents a valuable contribution to studies performed by scanning tunneling microscopy and aiming at the recognition of specific molecular events that are pivotal to surface dynamics such as surface diffusion,32,33 domain boundary motion.34,35 and so forth. Results and Discussion A. Single Atom Substitution and Its Effects on SelfAssembling. We start with star-shaped stilbenoid compounds, namely a 1,3,5-tristyrylbenzene conjugated core and decyloxy peripheral chains in 3 and 5 positions (1,3,5-tris[(E)-2-(3,5didecyloxyphenyl)-ethenyl]benzene, denoted TSB; see Figure 1A.1. This class of compounds36 self-assembles on highly oriented pyrolytic graphite (HOPG Goodfellow) as a honeycomb structure leaving empty cavities as illustrated in Figure 1A.3. Note that all reported images correspond to room-temperature (RT) scanning tunneling pictures acquired in the constant height mode at the liquid/solid interface on a homemade instrument allowing high scanning rates up to ∼0.5 frame/s. The solvent used is 1-phenyloctane (Fluka, purum g98%). STM tips are mechanically cut from a 90% Pt, 10% Ir wire 0.25 mm in diameter (Goodfellow). Typical settings for tunneling current and bias voltage (sample) are 15 pA and -1.0 V. During experiments the tip is maintained at zero potential. All presented STM images are routinely observed and correspond to highly reproducible molecular features. In all images, individual molecules appear as a bright three-arm pattern; see Figure 1A.2. This star-shaped signature corresponds to the delocalized π-electrons of the TSB conjugated core. Moreover, the intramolecular features are typical of a molecular-orbital assisted nonresonant tunneling regime, and mostly reflect the highest occupied frontier orbitals (HOMOs) of the molecule. More experimental details have been reported elsewhere.28,30 It has been shown that the obtained supramolecular matrix acts as a two-dimensional molecular sieve for various organic guest molecules.30 Depending of the lengths of the alkoxy peripheral chains, the size and shape selectivities of the

10.1021/jp8030013 CCC: $40.75  2008 American Chemical Society Published on Web 08/19/2008

Tracking of Individual Molecules by STM

Figure 1. (A.1) Model structure of the TSB molecule. (A.2) Highresolution STM image of one single TSB molecule. (A.3) Honeycomb supramolecular network obtained by self-assembling of TSB molecules on HOPG surface. (B.1) Model structure of the N-substituted TSP molecule. (B.2) High-resolution STM image of one single substituted TSP molecule. (B.3) Honeycomb supramolecular network obtained by self-assembling of the TSP molecules on HOPG surface. The unit cell corresponds to a p(241x241 R3.2°) surface reconstruction. All STM images are recorded in the variable current (constant height) mode at RT. The initial setpoint current is 15 pA, the sample bias is -1.0 V, and the scanning rate 350 nm/s. A largest contribution in the molecular contrast is originated from the highest occupied frontier orbital (HOMO). The white scale bar is 3 nm.

supramolecular networks can be tuned to a specific guest molecule.30,31 Because the sieving properties rely on the intrinsic dynamics of the host matrix any further investigation requires precise knowledge of the behavior of each individual molecular block. In an attempt to achieve direct visual discrimination between individual TSB molecular units within the honeycomb structure, a minimal change in the skeleton of the TSB molecules has been adopted. The modification consists in the replacement of one carbon atom of the central conjugated core by a nitrogen atom, namely the inner benzene ring is replaced by a pyridine core (Figure 1A.1,B.1). Details regarding the synthesis routes leading to both molecular entities are available in the Supporting Information section. As illustrated in Figure 1B.3, 1,3,5tristyrylpyridine (TSP) molecules self-assemble on graphite in a way identical to the TSB ones, forming a long-range regular honeycomb lattice. From a crystallography point of view, the supramolecular networks obtained using either TSB or TSP molecules as elementary building blocks are nondiscernible and adopt a p(241x241 R3.2°) surface reconstruction.31 However, at the intramolecular level, the individual STM signatures of both molecules exhibit subtle differences. In particular, the pyridine inner core appears with an asymmetric shape in the STM images, as can be seen in Figure 1A.2,B.2. Owing to the high spatial resolution of STM, the intramolecular features of a TSP molecule seem to lack one of its central lobes in comparison to the TSB molecules. Overall, a TSP molecule departs from the well-balanced star shape signature of a TSB molecule to adopt an asymmetric arrowlike configuration pointing to a specific direction. Since both building blocks differ by the substitution of only one atom, the STM images suggest a reduction of the occupied density of states at the position of the nitrogen atom. B. First-Principle Calculations. To achieve a better understanding of the system at the molecular level, quantum me-

J. Phys. Chem. C, Vol. 112, No. 36, 2008 14059 chanical calculations of the ground-state electronic structure and total energy of model systems have been performed using a first-principle method. The aim of the calculations is to get information about the adsorption properties of a TSB/TSP like molecule on a graphite substrate and to calculate STM images from the electronic structure. Previous first-principle calculations have shown a qualitative correlation between the STM contrast and the energy spacing between the electronic levels of the surface and of the molecular adsorbates.37 In some cases, the energy spacing between these levels might be further enhanced by the tip-induced electric field in the tunnel junction.37,38 In our calculations, we have used the ab initio code package ABINIT,39 which is a density-functional theory based code. In order to reduce the computing time and the memory space required, the calculations are performed for molecules whose alkoxy peripheral chains are considerably shortened. Although, the length of the alkoxy chains plays an extremely important role in the auto-organization of the molecules on graphite surfaces,31,40 we believed that these chains play a minor role on the STM contrast observed above the conjugated core of the molecule. Indeed, we have checked from calculations on isolated molecules that the electronic density in the conjugated core is not strongly modified when the alkoxy chains are modeled by a single H atom or by a methyl group. Furthermore the graphite surface is modeled by a single graphene sheet (see Figure 2) whose 200 carbon atoms are kept at fixed positions during the calculations, though all the other atoms of the molecule are allowed to relax their positions to reach the equilibrium ground-state. The two different kinds of TSB-/TSP-like molecules are considered, as well as two different adsorption sites of the molecules on graphene (see Figure 2 for detailed explanations). For convenience, the theoretical molecules considered are respectively called CoreCH (60 atoms) and CoreN (59 atoms). The calculations are performed within the local density approximation (LDA), for Troullier-Martins norm-conserving pseudopotentials41 with a plane wave energy cutoff of 25 Rydbergs and for a sufficiently large unit cell. The results of the calculations show that both molecules CoreCH and CoreN stay mostly flat upon adsorption on graphene. They mainly keep their free-standing planar conjugated conformation. The mean-averaged distances d between the molecules and the surface and the corresponding adsorption energies Eads are reported in Table 1 for two different adsorption sites denoted A and B (see Figure 2). Site A is energetically more favorable than site B. Note that substituting the CH group in CoreCH by a N atom in CoreN does not affect significantly the values of both the equilibrium molecule-surface distances and the adsorption energies. However d and Eads are dependent on the adsorption site. Furthermore one should note that the values of Eads are rather small when normalized to the number of atoms in the molecules. Indeed, a rough estimate of the adsorption energy per sp2 C atom amounts to 63 meV for CoreCH on site A. This estimation neglects the relative contribution of both hydrogen and oxygen atom and thus overestimates the contribution of C atoms. The small adsorption energy corresponds to a weak molecule-surface interaction (van der Waals forces) and is in close agreement with the measured value of 52 ( 5 meV/C atom for the graphene exfoliation energy determined by thermal desorption.42 Note that in the present calculations we do not consider the presence of a supernatant solution. While we expect that the absolute values of the adsorption energy will be different in the presence of the solvent (i.e., presence of an extra solvation

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Schull et al.

Figure 2. First-principle calculations. (A) Ball and stick model for the model molecules (A.1) (left) Molecule denoted CoreCH in which each C10H21 peripheral chain bonded to the oxygen atoms is replaced by one H atom. For the molecule CoreN, one of the CH groups of the central ring (the right one) is substituted by an N atom. (A.2) (right) Single graphene sheet on top of which the molecules are deposited. Site A corresponds to the center of the central ring of CoreCH/N located above a C atom of the graphene and the N (C atom of the CH group) of the molecule CoreN (CoreCH) also located above a C atom of the graphene. Site B, the center of the central ring of CoreCH/N, is located above an atom of the graphene layer and the N (C atom of the CH group) of the molecule CoreN (CoreCH) is located above a hollow site of the graphene layer. (B) Constant current STM images of the molecules CoreCH and CoreN on graphene for adsorption site A. The TH approximation is used to calculate the STM images for a theoretical bias of -0.73 V. The current flows from the surface to the tip, i.e. only the HOMO-n states participate to the tunneling current. (B.1) (left) STM image for CoreCH. The overall shape of the molecule is in good agreement with the experiments. (B.2) (right) STM image for CoreN. Note the strong reduction of the STM current above the N atom (blue colored ball in the central ring) in agreement with the experiments, though the overall shape of the molecule is only partially reproduced.

TABLE 1: Calculated Mean-Averaged Distances d (Å) and Adsorption Energies Eads (eV) between the CoreCH and CoreN Molecules on a Graphene Surface for Both A and B Sites site A

site B

molecule name distance d (Å) Eads (eV) distance d (Å) Eads (eV) CoreCH CoreN

3.30 3.30

1.88 1.86

3.33 3.34

1.66 1.66

energy) we believe that the effects of the supernatant solution will be equivalent for both CoreCH and CoreN molecules and both adsorption sites. Hence one will probably keep the same relative difference between adsorption energies in the presence and in the absence of the solvent. Experimental supports along this line are the equivalent self-assembling products of TSB molecules obtained on graphite either at the liquid-solid interface or under ultra high vacuum conditions.30 Now that we have shown that changing “one atom” in the molecule (CoreCH T CoreN) does not affect too much the adsorption properties of these molecules, we turn on to the effects of such a substitution on the corresponding electronic

structures. Several HOMO (highest occupied molecular orbitals) and LUMO (lowest unoccupied molecular orbitals) states have been computed for both molecules in different sites. The isodensity plots (see Supporting Information) of these electronic states around the Fermi energy show significant differences in the shape when changing “one core atom” in the molecule and for the adsorption sites A and B. These differences are even more noticeable in the calculated STM images. The STM images are calculated within the Tersoff-Hamann (TH) approximation,43 i.e., the tunneling current is taken to be proportional to the integrated density of states at the position of the tip. Images at constant (arbitrary) current are shown in Figure 2B.1,B.2 for an applied sample bias corresponding to the experimental conditions. One obtains a rather good agreement with the experiments as far as the overall shape of the molecules is concerned. Most importantly, a strong decrease of the tunneling current just above the N atom of CoreN molecule is obtained (with respect to the case of the CoreCH molecule) as observed experimentally. It is interesting to note that the observed STM images appear to contain also a nonzero weight from the empty states (see Supporting Information) although the current flows from the surface to the tip. This might be due to the fact that the graphite surface is semimetallic and that the tails of the molecular resonances of the empty states overlap more than expected with the Fermi level of the surface. Nonperturbative STM calculations44 would be needed to clarify this point. C. On the Use of Individual Molecule Marking and Tracking. The ab initio calculations confirm that changing one atom in the core of a TSB like molecule can be indeed observed by STM. Similarly, the fact that the chemical C T N substitution does not influence the self-assembling process in anyway is consistent with the almost degenerate calculated adsorption energies on the HOPG surface. Further validation of the marker mechanism requires that the substituted molecules can be fully recognized within a self-assembled matrix. To that respect Figure 3A displays one typical STM topograph of the honeycomb network obtained when selfassembling TSP molecules on graphite. In contrast with the orientation degenerated TSB network (see Figure 1A.3), the exact orientation of individual TSP molecules is readily accessible. Indeed, each individual molecular signature exhibits a clear delta shape pointing into one of the six possible directions associated with the honeycomb lattice symmetry. For convenience, molecules of equivalent orientations are represented with identical symbol in Figure 3A. The full set of recorded STM images permits us to perform a statistical analysis on a population of 584 molecules. Within one standard statistical error, an equiprobable distribution for the six molecular orientations is obtained (see histogram in Figure 3B). The statistical measurements further confirm that the chemical substitution has no effect whatsoever on the physics of the self-assembling of TSB like molecules. In particular the permanent dipole associated to the pyridine core does not lead to any peculiar physical effect. A rough estimate of the electrostatic potential energy between the selfassembled TSP molecules supports this observation. Indeed, at their closest distance two TSP molecules constitute a pair of aligned and antiparallel permanent dipoles separated by a distance R ) 3/3 × cell parameter, i.e., R ) 1.26 nm. Considering a permanent dipole value of 1.0 D (1 D ) 3.335 10-30 C · m), one obtains a potential energy of 6.2 10-4 eV which is negligible in comparison to the characteristic energy kT at room temperature kT ∼ 1/39 eV (k is the Boltzmann

Tracking of Individual Molecules by STM

Figure 3. Individual molecule marking. (A) Honeycomb supramolecular network obtained by self-assembling the substituted TSP molecules on HOPG. The STM images are acquired in the current (constant height) mode at RT. The initial setpoint current is 25 pA, the sample bias is -1.0 V, and the scanning rate is 300 nm/s. A largest contribution in the molecular contrast is originated from the highest occupied frontier orbital (HOMO). The white scale bar is 3 nm. Each colored circle identifies a TSP molecule in one of the six possible directions associated with the honeycomb lattice symmetry. As a guide for the eyes, the orientation of each arrowlike pyridine core is represented by a black arrow on the figure caption (right side). (B) Histogram of the six possible molecule orientations. The total molecule population is 584. The solid black line represents the population average per orientation. The dotted green lines correspond to ( one standard statistical deviation σ from the average value.

constant and T the absolute temperature 300 K). Furthermore the TSP molecules are adsorbed on a semimetallic substrate which partially screens the molecular dipoles through the formation of image dipoles. Therefore the charge distributions to consider are not dipolar but quadrupolar in nature leading to a further reduction of the above estimate of the electrostatic interaction between polarized molecules. Tracking the motion of individual molecular units within a self-assembled matrix permits us to investigate the intrinsic dynamics of network. Indeed, we can study the rotational and translational motions, as well as a measure of the residence time8 of one individual molecular block on the HOPG surface for different numbers and lengths of the alkyl end chains and substrate temperatures. As one example, Figure 4 shows the self-assembling product of TSP molecules on graphite. A close-up of the two STM images shows one TSP molecule in two different orientation states (blue colored molecule). The rotation(s) of the molecular unit occur(s) during the mean time of the acquisition of one STM picture (here 80 s). Similarly, Figure 5A,B shows the self-assembling product resulting from a coadsorption of TSB and TSP molecules. Figure 5B has been recorded immediately after Figure 5A. Because of the almost degenerate adsorption energies on HOPG surface, the surface

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Figure 4. In-plane rotation tracking of TSP molecules. (A.1) Honeycomb supramolecular network obtained by self-assembling the TSP molecules on HOPG surface. For convenience, the TSP molecule of interest is outlined in blue. (A.2) CPK (Corey, Pauling, and Koltun) model zoomed on one rotating molecule in panel A1. (B.1) Same as panel A.1, but after in-plane rotation(s) of the outlined TSP molecule. (B.2) CPK model corresponding to the rotated molecule in panel B.1. All STM images are recorded in the current (constant height) mode at RT. The scanning rate is 164 ms/line (512 × 512 pixels2 image acquisition time is 80 s). The initial setpoint current is 15 pA and the sample bias is -1.0 V. The largest contribution in the molecular contrast is originated from the highest occupied frontier orbital (HOMO). The white scale bar is 3.8 nm.

Figure 5. Mixture of TSP and TSB molecules self-assembled on a HOPG surface. (A) Honeycomb supramolecular network obtained by self-assembling of a mixture of TSP and TSB molecules in a 1:10 concentration ratio. For convenience the visible TSP molecules of interest are outlined in blue. The unit cell corresponds to a p(241 × 241 R3.2°) surface reconstruction. (B) Same as panel A, but after in-plane rotation(s) of two of the outlined TSP molecules. (C) Image processing difference between the STM signatures of TSB and TSP molecules (taken from B). STM images recorded in the current (constant height) mode at RT. The initial setpoint current is 15 pA and the sample bias is -1.0 V. The scanning rate is 174 ms/line (512 × 512 pixels2 image acquisition time is 90 s). A largest contribution in the molecular contrast is originated from the highest occupied frontier orbital (HOMO). The white scale bar is 3.8 nm.

stoechiometry between the two parented molecules reflects their respective molecular fractions in solution, namely TSP/ TSB ∼ 1/10. As for the case of TSP molecules, the mixture of TSP and TSB molecules self-assembles on the HOPG basal plane as a honeycomb structure according to a p(241 × 241 R3.2°) surface reconstruction.31 One can single out four marked TSP molecules embedded in the regular honeycomb lattice of TSB molecular units. Again close examination of

14062 J. Phys. Chem. C, Vol. 112, No. 36, 2008 Figure 5A,B reveals the rotation(s) of two TSP molecular units during the acquisition time of the STM pictures (here 90 s). In complement, the sequence in Figure 5C displays the image processing difference between the STM signatures of TSB and TSP molecules acquired in equivalent condition (taken from Figure 5B). The image difference clearly shows the missing central lobe characteristic of the intramolecular features of the TSP molecule in comparison to the TSB molecule. Hence, the specific contrast arising from the single C T N substitution is kept for equivalent scanning tunneling settings, in particular any significant influence of the tip or adsorption site can be discarded. These results confirm our method as a pertinent marker mechanism. Regarding the network dynamics, the time of rotational motions (tens of seconds) is longer than the characteristic residence time of guest molecules in one cavity of the nanoporous network (ms range) because of the stronger interactions between the interdigitated alkyl chains and the steric confinement. Owing to the low concentration in TSP molecules, the measurements performed on mixtures rule out the desorption-readsorption process as a physical explanation. Hence, the origin of this motion has to be looked for in the high mobility reported for close-packed assemblies of n-alkane chains on graphite at RT.45 Temperature-programmed desorption experiments carried out on linear n-alkanes46,47 and n-alkane derivatives48 have shown the dynamic nature of the alkyl chain physisorption on graphite at RT. On average47 for a C10H22 alkane chain physisorbed on graphite under ultra high vacuum condition two of the ten methylene groups are detached from the surface at T ) 300 K; a ratio that would certainly be larger in the presence of a supernatant solution. This aspect supports an in-plane rotation mechanism of individual molecular blocks. It may also play a significant role in the dynamics of guest molecules in 2D molecular sieves.28 A detailed study of the influence of the mobility of the alkyl peripheral chains on the dynamics of compact self-assembled matrix is currently in progress. Conclusion In conclusion, we have devised a marking procedure to achieve direct visual discrimination and tracking of individual molecules in a self-assembled layer by using scanning tunneling microscopy. The marker mechanism consists in the minimal substitution of one carbon atom by a nitrogen one in the central conjugated core of the target molecule. Both theoretical and experimental investigations ascertain the pertinence of our marking and tracking procedure. This method allows us to probe the dynamics of individual molecular blocks within a selfassembled monolayer. The investigation of rotational and translational motions as well as the measure of the residence time of individual molecular blocks on the HOPG surface for different numbers and lengths of the alkyl interdigitated chains and substrate temperature are now possible. While we have shown the usefulness of our marking/tracking method on a specific stilbenoid compound self-assembled on graphite, recent studies49,50 suggest that this mechanism, based on the use of the respective carbon/nitrogen contrast in high resolution STM imaging, is of more general interest for surface science. Supporting Information Available: (i) Synthesis routes yielding to the unmarked (benzene core TSB) and marked (pyridine core TSP) molecular building blocks. (ii) Full description of the first-principle calculations carried on. This material is available free of charge via the Internet at http://pub.acs.org.

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