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Imaging Bond Formation Between a Gold Atom and Pentacene on an Insulating Surface

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Science  26 May 2006:
Vol. 312, Issue 5777, pp. 1196-1199
DOI: 10.1126/science.1126073

Abstract

A covalent bond between an individual pentacene molecule and a gold atom was formed by means of single-molecule chemistry inside a scanning tunneling microscope junction. The bond formation is reversible, and different structural isomers can be produced. The single-molecule synthesis was done on ultrathin insulating films that electronically isolated the reactants and products from their environment. Direct imaging of the orbital hybridization upon bond formation provides insight into the energetic shifts and occupation of the molecular resonances.

Electron transport through single molecules in contact with metal electrodes has turned out to depend crucially on the details of the contact geometry (1), resulting in poor reproducibility of experiments in different setups. Control on the contact formation will not only have to include the atomic-scale geometry itself, but also coherent (strong coupling) versus incoherent (weak coupling) electron transport, coupling with respect to the molecular orbitals, and possibly also the phase of the orbital wave function at the contact point.

We show here that such control can be achieved for connecting metal atoms to π-conjugated molecules on insulating NaCl films by means of single-molecule chemistry (25) in a scanning tunneling microscope (STM) junction. The atomic precision in STM manipulation and single-molecule chemistry can be exploited to create different kinds of contacts between a gold atom and a pentacene molecule. The gold atom can be brought into various positions a few angstroms away from the molecule, which facilitates an electron tunneling current between the atom and the molecule (weak coupling). Alternatively, the gold atom can be covalently bound to the pentacene molecule to form a metal-organic complex, which is accompanied by a strong and coherent electronic coupling between the two constituents, as can be deduced from STM images. Moreover, the possibility of creating different structural isomers by bringing together the reactants in different orientations enables control of the phase of the molecular orbital at the contact point. The influence of the contact formation on the electronic structure of the complex is evident from the different frontier orbitals of the different isomers, which can be directly seen in the corresponding STM images (6). Frontier orbitals have previously been imaged for the case of pentacene alone. We complement our results by using density functional theory (DFT) calculations.

The experiments were carried out with a home-built low-temperature STM operated at 5 K. NaCl was evaporated thermally onto clean Cu(111) and Cu(100) single-crystal samples at room temperature so that defect-free, (100)-terminated NaCl islands of two atomic layers in thickness were formed (7). Individual pentacene molecules and gold atoms were adsorbed at a sample temperature of T ∼5 K, with the sample located in the STM. Bias voltages refer to the sample voltage with respect to the tip. All experimental data refer to the NaCl/Cu(100) system, except where stated otherwise.

Single-molecule chemistry by means of STM on an insulating surface follows a different route compared with the well-established manipulations on metal substrates, on which a single-molecule synthesis can be separated into two distinct steps (35). On a flat metal surface, the first step, in which the reactants are brought close to each other by lateral manipulation (8), is relatively easily achieved because of the small diffusion barrier–to–binding energy ratio. In the second, more-complex bond-formation step, much higher energy barriers must be overcome. Thus, this step is initiated by means of nonthermal excitation of the reactants with inelastic electron tunneling (IET). In the case of an insulating substrate, as discussed here, the diffusion barrier–to–binding energy ratio is much larger, thus requiring an excitation by IET to induce the lateral movement. Such IET excitation is most efficient on insulating films, because of the longer electronic lifetimes (7, 9, 10). The actual bond formation between the metal atom and the molecule, however, requires a smaller activation energy, such that the IET excitation process applied to achieve lateral movement is already sufficient to also initiate the synthesis.

Figure 1 shows the bond formation between a pentacene molecule and a gold atom on a bilayer of NaCl. In Fig. 1A, the reactants are already located close to each other. The bond was formed by IET (11), and the resulting complex (Fig. 1B) has a mirror plane that is perpendicular to the long axis of the molecule, indicating that the gold atom is attached to the central ring of pentacene (6-gold-pentacene) (Fig. 1, C and D). The bond was broken again by IET-induced excitation of the entire complex. The next image (Fig. 1E) shows the two constituents separated again; namely, the gold atom and the pentacene molecule. In a subsequent step, they were bonded to each other again, but this time the gold atom was attached to the pentacene molecule in a different position. Judging from the dark feature in the STM image of the complex (Fig. 1F), the gold atom is slightly off-center (5-gold-pentacene).

Fig. 1.

Making and breaking a chemical bond between a single pentacene molecule and gold atom on an NaCl bilayer supported by a Cu(100) substrate. (A) STM image showing the molecule and the gold atom before bond formation. (B) Image showing a molecule-metal complex (6-gold-pentacene) after resonant tunneling through the LUMO of the pentacene molecule. The sphere models show a cut perpendicular to the long molecular axis (C) and a top view (D) of the calculated geometry of the adsorbed 6-gold-pentacene complex. C, H, and Au atoms are represented by gray, white, and gold spheres, respectively. The Au-Cl and Au-C interatomic distances are 2.4 and 2.1 Å, respectively. The metal atom can be detached (E) and reattached again (F) in a different position, forming another structural isomer of the complex (5-gold-pentacene). All STM images are 26 by 22 Å in size and taken at a bias of +0.34 V.

The reversibility of the complex formation suggests that it is an addition reaction of the gold atom to one of the pentacene's aromatic rings and involves neither the substitution of a hydrogen atom nor a defect creation in the substrate. The complete reversibility was substantiated in an experiment in which, after forming and breaking the bond again (as seen in the STM image of Fig. 1E), the molecular orbitals of the pentacene (6) and the charge bistability of the gold atom (7) on the NaCl/Cu(111) surface could be observed at unchanged experimental parameters. This finding indicates that the gold atom, the pentacene molecule, and the underlying substrate were not permanently modified.

The differential conductance signal (dI/dV, where I is current and V is voltage) acquired with the STM tip above the 6-gold-pentacene complex in Fig. 2D exhibits two pronounced peaks at –1.5 and +1.2 V and a broad gap in between. As in the case of isolated pentacene (6), images taken at different bias voltages corresponding to the gap region (in-gap conditions) and to the peaks in dI/dV spectra (resonance conditions) differ greatly. The images in Fig. 2, A and C, show pronounced intramolecular resolution and a large apparent height of 2.0 and 2.6 Å, respectively. In contrast, for in-gap conditions, the apparent height measures only 1.0 Å (Fig. 2B). The orbital structure of the complex is delocalized over the entire complex including the gold atom, indicating a covalent bond between the pentacene molecule and the gold atom. For comparison, Fig. 2, E to G, show the STM images of an isolated pentacene molecule for bias voltages corresponding to the highest occupied molecular orbital (HOMO), in-gap conditions, and the lowest unoccupied molecular orbital (LUMO), respectively. When the gold atom is very close to a pentacene molecule but not bound to it, the corresponding STM image (Fig. 2H) exhibits no sign of bonding or common orbital structure but is just a superposition of the unperturbed LUMO of the pentacene molecule and the protrusion of the gold atom. In this configuration, the Au atom is adsorbed at a distance of 6 Å from the long molecular axis.

Fig. 2.

Bias-dependent STM images and differential conductance (dI/dV) spectra of various structures of a gold atom and a pentacene molecule on the NaCl film. The dI/dV spectrum of the 6-gold-pentacene complex (D) exhibits two distinct peaks at -1.5 and +1.2 V (solid line). For easy reference, the plot also shows the dI/dV signal of an isolated pentacene molecule (dashed line). At biases corresponding to the two peaks and the broad gap region of the dI/dV spectrum, the 6-gold-pentacene complex and the isolated pentacene molecule yield three different STM images: (A to C) and (E to G), respectively. The 5-gold-pentacene isomer shows an almost identical dI/dV spectrum, but the corresponding in-gap (I) and resonance (J) images are different from those of the other complex. For comparison, in an arrangement of the Au atom and molecule corresponding to Fig. 1A, the image of the molecular resonance (H) shows just the unperturbed LUMO of the pentacene molecule and the protrusion of the Au atom, indicating a nonbonded arrangement. All images are 22-by-19 Å in size and acquired with a pentacene molecule attached to the tip (6) to enhance the intramolecular resolution. pos., positive; arb. u., arbitrary units.

The 5-gold-pentacene complex (Fig. 2I) exhibits two peaks in its dI/dV spectrum, almost identical to those of the 6-gold-pentacene isomer (the peak at positive bias is slightly lower in energy by ∼0.05 V). The corresponding image in Fig. 2J also shows a covalent bond formation, with distinct differences to the pentacene's LUMO, which are predominant near the gold atom. In addition, there is a very strong enhancement of the orbital structure at the end of the complex that is closer to the gold atom. This enhancement in the STM image is expressed in a height difference of about 1 Å of the two outmost protrusions.

Because electrons can still tunnel through the ultrathin NaCl film, the charge state of the complex after its formation is not clear a priori (7, 12). Therefore, the charge state of the 6-gold-pentacene complex was experimentally investigated and found to be neutral because of the absence of scattering of the NaCl/Cu(111) interface-state electrons at the complex (9). Thus, the complex accommodates an odd number of electrons and has a singly-occupied molecular orbital (SOMO) near the Fermi level (EF). This result explains why the orbital structure looks almost the same for both polarities of the bias voltage in Fig. 2, A and C. In both cases, the electrons tunnel through the same orbital, either temporarily emptying it (V < 0) or temporarily filling it with a second electron (V > 0) (13, 14).

Thus, the broad gap in the dI/dV spectra of the complexes is not a HOMO-LUMO gap, but is solely attributed to the Coulomb energy associated with adding or removing an electron to or from the same orbital of the complex. Thus, the separation of the two peaks labeled SOMO gives a simple and direct measure of this important parameter. In the case of isolated pentacene, the HOMO-LUMO peak separation is much larger [4.1 eV (6)]. This value can be regarded as the sum of the energy needed to excite an electron from the HOMO to the LUMO, plus a similar Coulomb energy associated with adding or removing an electron to or from the very same orbital.

To gain deeper insight into the nature of the 6-gold-pentacene complex on the NaCl film, we have carried out spin-polarized DFT calculations (15) of the complex adsorbed on an NaCl bilayer supported by a Cu(100) surface (7, 16). We used the projector augmented wave method (17) as implemented in the Vienna Ab initio Simulation Package (VASP) code (18). STM images were simulated in the Tersoff-Hamann approximation (19) as topographies of constant, local density of (Kohn-Sham) states (LDOS) integrated over the range of energies allowed by the applied bias.

With the DFT calculations, we have identified a geometrically stable configuration of the 6-gold-pentacene complex (Fig. 1, C and D) with an interesting metal-ligand interaction. The pentacene molecule in the complex has the same adsorption site on the NaCl film as does the single molecule in previous studies (6). The molecule is aligned parallel to one of the polar <011> directions of the NaCl(100) films with its center located on top of a Cl ion. The Au atom is bonded to both a Cl and a C atom in the central ring of the molecule (Fig. 1, C and D). This C atom is henceforth referred to as the C′ atom. The H atom is tilted upward so that the C′ atom is in a nearly tetrahedral bond configuration with respect to its four neighbors—the Au atom, the H atom, and the two adjacent C atoms—indicating a sp2-to-sp3 rehybridization of the C′ atom. The bonding of the Au atom to the pentacene molecule results in sizeable relaxations in the NaCl film only for the Cl bonded to the Au atom and the Na+ below.

A comparison between simulated and observed STM images of the complex provides strong support that the calculated geometry corresponds to the one imaged in experiments. The simulated image (Fig. 3A) reproduces all of the details of the experimental image (Fig. 2C). An analysis of the LDOS reveals that the “half-moon” around the Au atom in the STM image originates from the Au 6s state and the protrusion above the Au atom from one of the C′ sp3-hybridized states. To understand the detailed molecular orbital character of the STM image and the formation of the complex and its bonding to the surface, we need to scrutinize the electronic structure of the complex and its fragments.

Fig. 3.

Simulated STM images of the adsorbed 6-gold-pentacene (A) and 5-gold-pentacene (B) complexes as given by the topographic image of the constant, integrated LDOS. The energy range of the LDOS integral (EFEF + 0.5 eV) includes the unoccupied part of the SOMO. The apparent heights are about 3 Å. The positions of the C atoms and the Au atom are indicated by diamonds and a circle, respectively. The image sizes are 15-by-23 Å. (C) Schematic diagram of the calculated one-electron energy levels and density maps of the frontier orbitals participating in the formation of the 6-gold-pentacene. This orbital set includes the HOMO and LUMO of the pentacene molecule; the HOMO, LUMO, and SOMO of the adsorbed complex; and the Au (6s)-derived orbital. All energies and density maps refer to adsorption on a NaCl bilayer on Cu(100). Unoccupied and occupied states are represented by open and filled circles, respectively. The density maps are 16-by-10 Å in size and correspond to LDOS maps taken at a distance of ∼0.8 Å above the molecular plane.

First we need to understand the bonding of the fragments to the NaCl film. The closed-shell structure of the pentacene molecule results in a weakly adsorbed state for the molecule on the NaCl bilayer. The HOMO and the LUMO experience small energy shifts and have a negligible overlap with the metal substrate states. The characteristic nodal structures of these π-orbitals are shown in the left column of Fig. 3C. The bonding of the Au atom to the NaCl film can result in two different charge states (7). In the (nearly) neutral state, the Au atom is weakly adsorbed on the film and the Au(6s) state of the adsorbed gold atom [henceforth referred to as Au(6ŝ)] is partially occupied and pinned to EF of the substrate.

The addition of an Au atom in its neutral state to the pentacene molecule results in a radical complex with an odd number of electrons, with predominant orbital interactions being among their frontier orbitals. The HOMO and LUMO of the molecule and the Au(6ŝ) state (Fig. 3C) interact and form three new orbitals whose characters can be rationalized in a simple three-state model. The HOMO of the complex is predominantly a bonding combination of the Au(6ŝ) state with the HOMO of pentacene, whereas the LUMO is an antibonding combination with the pentacene's LUMO. The remaining SOMO is a linear combination of the Au(6ŝ) state with both the HOMO (with antibonding character) and the LUMO (with bonding character). The apparent sideways bending of this state is purely an electronic effect. This bending and the nodal structure of the STM image are understood from the mixing of the HOMO and LUMO in the given phase relation, resulting in an enhanced amplitude on the side of the long axis of the pentacene molecule that is opposite from the Au atom. Furthermore, we find that the addition of the Au atom to the molecule is electrophilic, as there is a small net electron transfer to Au due to the larger electronegativity of the Au atom than of the pentacene molecule.

The calculations also show a stable adsorption configuration for the 5-gold-pentacene. The simulated STM image of this complex (Fig. 3B) is similar to the experimental image shown in Fig. 2J. The large difference in the apparent height between the ends of the complex is an electronic rather than a geometric effect, because the complex lies almost parallel to the surface.

Finally, DFT calculations on free gold-pentacene complexes without the NaCl/Cu(100) substrate reveal that these complexes are also stable and have similar geometric configuration and bond lengths, as well as orbitals and charge redistribution, to the adsorbed complexes. The main difference is an upward energy shift of the LUMO of the adsorbed complexes compared with a free complex because of their interaction with the occupied Cl 3p states.

Our DFT analysis confirms that the bond formation is an addition reaction of the gold atom to a pentacene's benzene ring, with a covalent character to create a radical complex. Aromatics usually prefer substitution over addition reactions that maintain their delocalized π-electronic system (20). However, in contrast to a reaction taking place in solution, the hydrogen atom in our case would have no alternate bonding partner.

Apart from the aspects of a contact formation, our findings also show new routes to selectively alter the electronic structure and chemical reactivity of large molecules with a delocalized electronic system. Control of the energetics of molecular resonances has been demonstrated before by the doping of a single molecule (21). The organometallic bond formation in our experiment even transforms a closed-shell molecule into a radical. This “engineering” of the orbital structure by creating different isomers controls both the nodal structure itself as well as the relative weight of the probability distribution in different parts of the molecule.

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