UNIVERSITY OF LJUBLJANAFACULTY OF MATHEMTICS AND PHYSICS

Molecular cut’n’paste : building molecules with STM

Mitja Majerle

Mentor : prof. dr. Igor Muševič

Ljubljana, april 2003

Figure 1: Schematic illustration of an STM tip induced single molecule engineering process. Preparation of molecular building blocks by dissociation of larger molecules with the STM tip (1), relocation of molecular building blocks to the assembling site by lateral manipulation (2) and by vertical manipulation (3), assembling of new molecules with the STM tip (4)[1].

Abstract

During the last decade, atomic and molecular manipulations with the scanning tunneling microscope (STM) lead to fascinating advances: Probing local physical and chemical properties of atoms and molecules on surfaces together with prototypic fabrication of artificial atomic scale structures with atomic scale precision lead to the possibility of new local studies of quantum phenomena. Recent achievements in inducing all basic steps of a chemical reaction with the STM open up entirely new opportunities in chemistry on nano scale. We will review the basics about atomic interaction, basics of STM, molecular manipulation techniques and Ullman reaction based on STM. Prospects for future opportunities of single molecule chemical engineering are discussed as well.

Contents

1. Introduction 32. Ullman reaction 33. Basics about bonds, surface, atomic forces 4

3.1. Sigma and Pi bond 43.2. Metallic bond 53.3. Surface 53.4. The role of surface 53.5. Why atoms gather near step edges ? 5

4. Introduction to STM 64.1. Concept 64.2. Modes of operation 6

4.2.1. Constant Current Mode 64.2.2. Constant Height Mode 64.3.3. Scanning Tunneling Spectroscopy 7

4.3. Technical aspects 75. Basic molecular manipulation with STM 76. Berlin team experiment 87. Basic reaction steps with STM-tip. 9

7.1. Controlled molecular diffusion on surfaces 97.2. Molecular bond breaking 107.3. Vertical molecular manipulation 117.4. Molecular bond formation 12

8. Single molecule Ullman reaction 129. Development of one-dimensional band structure in artificial gold chains 1510. Conclusion and future prospects for single molecule engineering 1711. References 18

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1. Introduction

Scientists have long wanted to carry out chemical reactions one molecule at a time. They've also hoped they might find ways to create novel compounds that are impossible to make by conventional means. They have anticipated assembling molecules that might be useful as nanometer-scale devices.

In 1995, Avouris and his coworkers[2] used electrons from an STM to selectively snip molecular bonds, those between silicon and hydrogen atoms. November 2000 at Cornell University, physicists Wilson Ho and Hyojune Lee[3] reported the first example of inducing a single atom, iron, and a single molecule, carbon monoxide, to bond – again using an STM.

To crone to this successes followed soon with the experiment from Berlin. For the first time, researchers have duplicated with individual molecules the full sequence of steps in a widely used chemical reaction. What's more, they've made a photo album of the molecular makeover as it unfolds.

Karl-Heinz Rieder, Saw-Wai Hla, and their colleagues at the Free University of Berlin [4,5]

have miniaturized a century-old chemical transformation known as the Ullman reaction. Laboratories and industry use that process to link two iodobenzene molecules. Each contains a six-carbon ring known as a phenyl, so a barbell-shaped biphenyl results.

This experiment was a great success in modern physics. Engineering of single molecules may require creation of basic building blocks, bringing them together to an assembling place and then joining them to form a desired molecule. This entire process is somewhat similar to the assembling process of automobiles or electronic commodities such as TV, computer etc. in a factory production line and there were hundreds of ideas how to use it before German physicists show them the way.

2. Ullman reaction

Almost all chemical reactions we know today are studied in large scale experiments, where enormous numbers of molecules are involved. The corresponding chemical equations are based on these experiments. Normally, the Ullman reaction proceeds in beakers or larger vessels inside which copper, a catalyst, blends countless reacting molecules. The Ullmann reaction is a basic chemistry textbook case and an important aromatic-ring coupling reaction widely used in synthetic chemistry. Almost a century ago, Ullmann and coworkers discovered that heating a mixture of C6H5I liquid and Cu powder to ~400 K resulted in formation of C12H10. From this experiment, they derived the following formula:

There are three elementary steps involved in this reaction after adsorption of C6H5I on Cu: dissociation of C6H5I into phenyl (C6H5) and iodine, diffusion of phenyl to find its reaction partner another phenyl and then, association to form a biphenyl. Cu acts as a catalyst in this reaction. Naturally, the Ullmann reaction is triggered by thermal excitations. Dissociation of C6H5I occurs at 180 K and biphenyl is formed at 400 K. Iterations of this reaction can produce multi-ring polymers.

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3. Basics about bonds, surface, atomic forces

Now that we know the reaction with which we are going to deal in next chapters, let us have a closer look in physical background of solid matter. As we know from Solid state physics, several bonds exist betweens atoms in crystal : molecular, covalent, metallic, hydrogen, ionic. We will review the basics of covalent sigma and pi bond, for better understanding of single molecule Ullman reaction; metallic bond, as STM is useful only on metals; we will discuss some details of crystal growth and tell why there are step edges on surfaces of such crystals and how are they useful.

3.1. Sigma and Pi bond

The first covalent bond formed between two atoms is always a sigma. Sigma bonds exhibit cylindrical symmetry to the internuclear axis. They are formed when two s orbitals, one s and one p orbital, two p orbitals, or two d orbitals overlap.

Figure 2: Unbonded S and S orbitals S and S Sigma bond

A bond formed by the sideways overlap of two parallel p orbitals. Pi bonds result from the concentration of electron density above and below the bond axis and exhibit bimodal planar symmetry. The second and third bonds formed are pi bonds.

Figure 3: Unbonded P and P orbitals P and P Pi bond

We meet these two types of bonds in our “working” molecules: C6H5I, biphenyl, CuI.

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3.2. Metallic bond

Of all crystals metals have the best properties for use in STM. These properties include malleability and ductility and most are strong and durable. They are good conductors of heat and electricity. Their strength indicates that the atoms are difficult to separate, but malleability and ductility suggest that the atoms are relatively easy to move in various directions. The electrical conductivity suggests that it is easy to move electrons in any direction in these materials. The thermal conductivity also involves the motion of electrons.

These properties suggest that their atoms posses strong bonds, yet the ease of conduction of heat and electricity suggest that electrons can move freely in all directions in a metal. The general observations give rise to a picture of "positive ions in a sea of electrons" to describe metallic bonding.

This description is used for surfaces on which molecular cut’n’paste is performed (Cu(111), Ni(110), NiAl(110),…). Single metallic atoms on the surface (Au on NiAl(110) at 12K!) are probably also bound to the surface with something that can be explained as the metallic bond, but the exact model of these bonds are not yet known.

3.3. Surface

Usually surfaces play the role of the catalysator in chemical reactions. Molecules gather on them, are localized with Van der Waals or other interactions on the surface and are waiting there for reactants. In our case the surface has preserved its role of catalysator, but as this is not a large scale experiment it must be carefully prepared.

Cu (or other) crystals are grown from liquid state Cu which is slowly cooled down. Such crystals are cut in specific direction (X-ray diffraction is used to determine right directions), the surface is then optically polished and finally cleaned with ionic beams.

Molecular cut’n’paste are mainly performed on few types of surfaces – Cu(111), Ni(110), NiAl(110), … It could be done on any surface, but the three listed above have the advantage, that are almost flat for STM at certain voltages. So an atom adsorbed on the surface is easily seen as a hill on a flat surface on a STM scan at operating voltages in this experiment.

3.4. Why atoms gather near step edges ?

The atom on a terrace has a certain number of nearest neighbours (its coordinationnumber) and the bonding to these neighbours provides stability for that atom. As it reaches the edge of a terrace, it suddenly has fewer neighbours, and the resulting decrease in the binding energy is manifested as a barrier for diffusion over the edge. If it reaches the edge from the lower terrace, he has more neighbors, more binding energy and will stay there if thermal excitations do not exceed binding energy. That is also why we always get steps when growing a crystal.

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4. Introduction to STM

4.1. Concept

The Scanning Tunneling Microscope (STM) was introduced by G. Binnig and W. Rohrer at the IBM Research Laboratory in 1982[6] which was honoured by the Noble Prize in 1986. It has become widely used as an important instrument for real space analysis in surface science.

The basic idea is to bring a fine metallic tip in close proximity (a few Å) to a conductive sample. By applying a voltage (U~several Volts) between the tip and the sample, a small electric current (0.1pA-50nA) can flow from the sample to the tip or reverse, although the tip is not in physical contact with the sample. This phenomenon is called electron tunneling. The exponential dependence of the tunneling current on the tip to sample separation results in a high vertical resolution. By scanning the tip across the surface and detecting the current a map of the surface can be generated with a resolution of the order of atomic distances. It has to be mentioned that the image cannot just be interpreted as a topographic map as the tunneling current is influenced by the lateral and vertical variation of the electronic state density at the particular point on the surface. The lateral resolution is about 1Å whereas a vertical resolution up to 0.01Å can be achieved. The STM can be used in ultra high vacuum, air or other environments, even liquids.

4.2. Modes of operation

4.2.1. Constant Current Mode

By using a feedback loop the tip is vertically adjusted in such a way that the current always remains constant. As the current is proportional to the local density of states, the tip follows a contour of a constant density of states during scanning. A kind of a topographic image of the surface is generated by recording the vertical position of the tip. Figure 4 : STM operating in constant current mode

4.2.2. Constant Height Mode

In this mode the vertical position of the tip is not changed, equivalent to a slow or disabled feedback. The current as a function of lateral position represents the surface image. This mode is only appropriate for atomically flat surfaces as otherwise a tip crash would be inevitable. One of its advantages is that it can be used at high scanning frequencies (up to 10 kHz). In comparison, the scanning frequency in the constant current mode is about 1 image per second or even per several minutes. Figure 5 : STM operating in constant

height mode

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4.3.3. Scanning Tunneling Spectroscopy

Further information from STM can be gathered by using spectroscopic modes of operation where the voltage dependence of the tunneling current is studied. The polarity of the applied bias voltage determines whether electrons tunnel into the unoccupied states of the sample or out of the occupied states. The amount of the applied bias voltage determines which electronic states can contribute to the tunneling current.The density of states can be deduced by

Modulation of the bias voltage Current-Imaging Tunneling Spectroscopy (CITS): The tip is scanned in the constant

current mode to give a constant distance to the sample. At each point the feedback loop is disabled and a current-voltage curve (I/V curve) is recorded.

4.3. Technical aspects

A probe tip typically made out of tungsten (see Figure 6) is attached to a piezodrive, which is a system of very sensitive piezo crystals which will expand or contract in reaction to an applied voltage. By using the piezo to position the tip within a few angstroms of the sample, the electron wave functions in the tip and the sample overlap, leading to a tunneling current flow when a bias voltage is applied between the tip and the sample. The tunneling current is amplified and fed into the computer while processing a negative feedback loop to keep the current constant. The computer, by collecting the z distance data, can on-screen image a three dimensional plot. This plot will represent the electron density of the sample surface. This electron density plot can then in turn be interpreted as the general arrangement or positioning of atoms on a conductive surface.

Figure 6: SEM (scanning electron microscope) picture of STM tungsten tip above the scan surface[7].

5. Basic molecular manipulation with STM

The dream of constructing individual molecules from various basic building blocks has recently come close to reality, at least on a substrate surface, by using the scanning tunneling microscope (STM) tip as an engineering tool. Often experimenters experienced perturbations during STM imaging caused by interactions between the STM tip and adsorbates. It did not take a

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long time that these unwanted perturbations became one of the most fascinating tools to be pursued by scientists: Manipulation of individual atoms and molecules on surfaces using STM tip-adsorbate interactions. During the last decade, various STM tip induced manipulation techniques have been developed. Single atoms or molecules can be manipulated by using atomic forces or the electric field between the STM tip and the sample, or by employing the tunneling electrons. With the advances in manipulation procedures, the fundamental surface reaction steps such as dissociation, diffusion, desorption, re-adsorption and association processes became possible to be induced at a single molecule level. In many (metal) catalyzed reactions – where the initial reactants are transformed into new molecular species with the help of a substrate catalyst – one or more of these phenomena are involved as elementary steps. By choosing a suitable combination of manipulation techniques with an STM tip, a sequence of processes constituting a complete chemical reaction was recently induced employing single molecules in a controlled step by step manner leading to the synthesis of product molecules on an individual basis.

6. Berlin team experiment

In its experiment, the Berlin team began with just two molecules of iodobenzene. These were placed near the step on a copper surface and chilled to 20 kelvins. The researchers then used flows of electrons from the sharp tip of a scanning tunneling microscope to break up the molecules. The tip dragged the fragments around, and its electron bursts provided the energy to rejoin the phenyl rings[4,5].

Because the STM is able to sense the electron clouds that protrude from individual atoms, the researchers also used the instrument to image each step of the reaction. In the end, they checked their work by tugging one ring of the biphenyl product and finding that the other followed along.

In general, these STM manipulations must take place at extremely low temperatures to keep the reactant molecules from diffusing around. In the new experiment, the deep chill also squelched the thermal energy that drives the breaking and reforming of bonds in a conventional, larger-scale Ullman reaction. The STM electron bursts provided that energy.

Now that they have demonstrated molecular manipulation with a familiar reaction, the Berlin researchers have set their sights on molecular constructions never made before, especially ones that might behave like nanometer-scale transistors or other minuscule devices.

If we simplify the process, we have four molecular manipulations, which give us together a chemical reaction : Lateral manipulation, molecule dissociation, vertical manipulation and bond formation (Figure 7).

Figure 7: Manipulation procedures used in single molecule engineering processes

Lateral manipulation (a),

molecule dissociation (b),

vertical manipulation (c)

bond formation (d).7. Basic reaction steps with STM-tip.

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7.1. Controlled molecular diffusion on surfaces

Diffusion of atoms or molecules on surfaces naturally occurs by thermal excitation causing adsorbates to move across the surface in a random fashion. The STM manipulation procedure close to this phenomenon but at temperatures low enough that the molecules are immobile is known as ‘lateral’ manipulation. It applies tip-molecule interactions to laterally move the molecule across a surface. This procedure involves approaching the tip towards the target molecule at its initial location to increase the tip-molecule interaction force, and then to move the tip along a desired path until it reaches a predetermined destination. The molecule moves along with the tip and when the tip retracts back to the normal imaging height, it is left behind on the surface. A nice example for this kind of controlled manipulation was first demonstrated by Eigler and Schweizer in 1990[8]. They wrote ‘IBM’ with 35 Xe atoms on a Ni(110) surface (Figure 8). Because an extremely fine control of the tip-molecule interactions is a necessary ingredient to achieve atomic scale precision, cryogenic substrate temperatures are favored in most experiments in order to reduce thermal excitation and drift. However, also room temperature manipulation is possible for larger molecules such as ‘Cu-tetra-(3,5 di-tertiary-butyl-phenyl) -porphyrin’ (CuTBPP) or C60 molecules.

Figure 8: ‘IBM’ written with 35 Xe atoms on a Ni(110) surface by Eigler and Schweizer in 1990 (13 years ago !)[8].

A fascinating aspect of this technique is that one can extract further information – such as how the molecule moves and what kind of interactions are involved during manipulation – from the corresponding STM feed-back or tunneling current signals. Based on the strength of the tip-molecule interactions, three basic manipulation modes, pushing, pulling and sliding can be distinguished. Attractive interactions lead the molecule to follow the tip in the pulling mode while repulsive tip-molecule interactions cause pushing. The molecule is strongly bound to the tip during a ‘sliding’ mode operation. Molecular ‘pulling’ is dominant for small and medium sized molecules such as diiodobenzene (C6H4I2) and biphenyl (C12H10) on Cu surfaces. However for large molecules, such as porphyrin based systems, ‘pushing’ is the main manipulation mode. A typical pulling operation of a single diiodobenzene molecule on Cu(111) is illustrated in Figure 9. A molecular art work demonstrating the abilities for precise positioning of molecules is

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presented in Figure 10 where the millennium number 2000 is written by using 47 CO molecules on Cu(211). Further detailed experimental and theoretical investigations of the manipulation signals of single molecules can even reveal how the molecules behave during their movements such as internal conformational changes or movement of the molecules relative to the tip.

a b c

Figure 9 : A diiodobenzene molecule on Cu(111) (upper left corner in a) is laterally moved to a new position (b).The CO molecule (darker circle) is used as a landmark. The manipulation operation is illustrated in (c): The tip first makes a trial scan at a height of about 6 Å along the manipulation path and records the initial molecule position (A), then the actual manipulation was performed by reducing the tip height by 3.5 Å. A sudden increase in tip-height (shown by the arrow) occurs due to molecule hopping towards the tip. The vertical line is drawn to show the initial molecule position. The molecule follows the tip in pulling mode with mostly single hops (2.55 Å). The tip is retracted at the final position and re-scanned along the manipulation path to check the successful manipulation of the molecule to the location (B)[4].

Figure 10: “New millennium is celebrated in our group by writing 2000 with single CO molecules on Cu(211)”. Each protrusion represents an individual CO molecule; the back ground vertical lines are the intrinsic Cu step-edges. The image was acquired with CO functionalized tip[9].

7.2. Molecular bond breaking

Tunneling electrons from the STM tip can be used to break the bonds inside a molecule. Based on the electron energy, two regimes; field emission and inelastic tunneling can be distinguished. High electron energies (roughly >3 eV) are involved in field emission regime where the tip acts as an emission gun. The dissociation process in this regime is less controllable. Early examples include dissociation of adsorbed B10H14

[10] and O2[11] on Si(111) with voltages ~4V

and ~6V, respectively.In the case of inelastic tunneling, low energy tunneling electrons are usually involved in bond

breaking. To break a bond, the tip is positioned above the molecule or at the location of the bond at a fixed height and then the tunneling electrons are injected into the molecule. The tunneling electron energy can be transferred to the molecule through resonance states and when the transferred energy exceeds the specific bond-dissociation energy, the respective bond is broken. The corresponding tunneling current can be monitored and current changes can be associated with the dissociation event. This process was demonstrated in the dissociation of diatomic

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oxygen molecules on Pt(111)[12]. However, controlled dissociation of poly-atomic molecules is more complex because more than one bond is involved. In case of benzene and HCCH dissociation on Cu(100), the C-H bonds of the molecule can be broken while leaving the C=C and C~C bonds intact. The selective breaking of a specific single bond inside a poly-atomic molecule was demonstrated in the case of the C-I bond scission from C6H5I molecule on Cu(111). This can be achieved due to the inherent differences in bond energies inside the molecule where the C-I bond is the weakest. The lesson of this example is that, by choosing a proper molecular system, specific bond breaking can be performed. An example for molecular dissociation is shown in Figure 11 where the two C-I bonds of a C6H4I2 molecule on Cu(111) have been broken by using inelastic tunneling process.

Figure 11: Iodine abstraction via molecular bond-breaking[13]:

A p-diiodobenzene (C6H4I2) molecule adsorbed at a screw dislocation on Cu(111) (a).

After breaking the two C-I bonds of the molecule using inelastic tunneling electrons, the two iodine atoms remain adsorbed. The other fragment of the parent molecule, C6H4, diffused away after breaking of the second C-I bond (b).

The two abrupt changes in the tunneling current signals (shown with arrows) correspond to the each bond-breaking event. Inset shows the C-I bond dissociation probability collected from 70 dissociation events (c).

7.3. Vertical molecular manipulation

Vertical manipulation involves transfer of molecules between the tip and the substrate and vice versa. Closely related surface phenomena for this case are the desorption and re-adsorption processes. An ‘atomic switch’ operated by repeatedly transferring a ‘Xe’ atom between the STM tip and a Ni(110) substrate[14] and improvement of the STM resolution using a Xe-tip were the first examples to prove this kind of manipulation. Further work on vertical molecular manipulation includes C6H6, CO and C3H6. During manipulation, the STM-tip is positioned exactly above the molecule and voltage pulses are applied. The excitation with tunneling electrons and/or the electric field causes breaking of the molecule-substrate bond. The molecule then desorbs and is re-adsorbed at or near the tipapex.

In case of CO vertical manipulation, the CO/Cu bond is broken by attachment of an electron to the CO state[15]. The resultant excited CO molecule can either jump to nearby Cu surface sites or toward the tip. One useful application of this technique is the ‘functionalization’ of the STM tip with a molecule. The tip plays a crucial role in STM imaging and usually it is difficult to know what kind of chemical element exists at the tip apex. By deliberate transfer of a molecule to the tip apex, the tip becomes sharper and yields good image contrast. Additionally, now the tip

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becomes well defined with respect to its chemical constitution. The application of functionalized tips has proven useful in molecular recognition imaging. For example, CO and oxygen can be distinguished when CO functionalized tips are used. An application is demonstrated in Figure 12.

Figure 12: Imaging with CO molecule functionalized tip. STM images showing the number ‘0’ formed with 8 CO molecules on Cu(211). CO molecules appear as indentation (a) when imaged with a normal tip and protrusions (b) when imaged with a CO functionalized tip. An unknown adsorbate (shown with arrow) is still remains as indentation in both images, thus chemical contrast can be achieved[16].

7.4. Molecular bond formation

The STM tip can also be used for molecular bond formation processes. In fact, the transfer and redeposition processes in vertical manipulation can be considered as forming a bond between the molecule and the tip or the substrate, respectively. Additional bond formation was demonstrated by Lee and Ho by forming Fe(CO)2 on Cu(100)[17]. They used vertical manipulation to deposit a CO molecule over an adsorbed Fe atom on Cu surface. Then another CO molecule was brought with the tip and the process repeated. Because the adsorbed Fe atom can accommodate more than a CO molecule, an additional bond could be formed. The bond formation process between two radicals on a surface was first demonstrated by creating a biphenyl molecule out of two phenyl radicals on Cu(111). This process is mediated by excitation with tunneling electrons on two closely located phenyls. It involves breaking of the two phenyl-substrate bonds so that the two phenyls are free to form a stable biphenyl molecule.

8. Single molecule Ullman reaction[4,5]

As mentioned in chapter 2 Ullman reaction looks like that :

One more time : There are three elementary steps involved in this reaction after adsorption of C6H5I on Cu: dissociation of C6H5I into phenyl (C6H5) and iodine, diffusion of phenyl to find its reaction partner another phenyl and then, association to form a biphenyl. Cu acts as a catalyst in this reaction. Naturally, the Ullmann reaction is triggered by thermal excitations. Dissociation of C6H5I occurs at ~180 K and biphenyl is formed at ~400 K.

Thus it is necessary to conduct single molecule experiments at low temperatures to avoid thermal influences. Figure 13 demonstrates an example for the single molecule Ullmann reaction sequence induced at 20K by using the STM tip. This sequence is different from the case published previously, because here an iodine functionalized tip was used to induce most of the basic reaction steps. The use of an iodinated tip does not effect the detailed tunneling parameters such as tunneling voltage or current for the reaction steps, but has the advantage, that the image contrast is enhanced thus allowing more precise tip positioning.

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The reaction was started with two C6H5I molecules adsorbed at the lower part of a Cu(111) step-edge (Figure 13a). The first reaction step, dissociation, was performed by injecting 1.5 eV energy tunneling electrons into the molecule. A single tunneling electron energy transfer to the molecule causes breaking of the C-I bond. Altogether 175 molecules were dissociated at four different tunneling currents of 0.01, 0.02, 0.03, and 0.6 nA, respectively. The linear dependence of the dissociation rate on the tunneling current (Figure 14a) shows that the energy transfer from a single electron causes the breaking of the C-I bond. It is not possible to break the C-H and C-C bonds with a single electron process at this voltage, especially as their bond energies are about 2 and 3 times higher than the C-I bond. Upon dissociation, resultant species change their positions from the original location under the tip. This effectively terminates tunneling through the fragments (as observed in the drop of the tunneling current); no further dissociation of the C-H and C-C bonds was observed.

The resulting fragments, phenyl and iodine, are separated by 2.5a0 for the left and 3.5 a0 for the right molecule (a0= 2.55 Å denotes the Cu nearest neighbor distance) (Figure 13b). The phenyl appears larger in the STM images and can be dissociated further into smaller fragments using biases >3 V and high currents. This is in good agreement with experiments on benzene on Cu(001) where the C-H bonds can be broken only with tunneling voltages >2.9 ± 0.1 V. Because of the high bias requirement to decompose both phenyl and benzene, dehydrogenation does not occur during the initial iodine abstraction process. Then the abstracted iodine atom at the far left was transferred to the tip-apex using vertical manipulation (Figure 13b and 13c). Now the tip becomes sharper and the image contrast is improved (Figure 13c).

Figure 13: Single molecule Ullmann reaction[4]:Two iodobenzene molecules are adsorbed at a Cu(111) step (a).

After dissociation with tunneling electrons, two phenyl radicals (larger bumps) and two iodine atoms are adsorbed at the Cu step-edge (b).

After the iodine at the far left (indicated by a green arrow) has been transferred to the tip apex via vertical manipulation, the image contrast improves (c).

The two phenyls are moved via lateral manipulation towards each other (d).

When the two phenyls are in closest distance, a splash of electrons with 500 meV is supplied to excite them for biphenyl formation (e).

Then, the newly synthesized biphenyl is pulled by the tip to the left side of the image proving successful chemical association (f).

Finally, the iodine from the tip-apex is transferred back to the substrate (g) (indicated by a green arrow).

The second reaction step, diffusion, was performed by using the lateral manipulation technique. Both phenyls are moved towards each

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other (Figure 13d) until they were closely located (Figure 13e). We employed the “soft” lateral manipulation technique, which uses only tipadsorbate forces. First we chose the manipulation path for phenyl along the Cu(111) straight step edge. This path has the advantage that due to the higher binding energy and well defined geometry of the step edge as compared to the plane surface, it is more convenient to move the adsorbates along the step with the STM tip without losing them. To perform lateral manipulation, we first surveyed the initial and final locations of the phenyl to be moved by scanning the STM tip along the chosen path with a tunneling current of 0.53 nA at 170 mV sample bias. The actual movement was accomplished by increasing the tunneling current by a factor of 200 at its initial site to reduce the tip-phenyl separation. Then the tip was moved along the predetermined path in constant current mode. The corresponding tip height curves during manipulation (Figure 14b) show typical pulling behavior with hops equal to a0 or 2 a0 along the step edges. Stronger tip-adsorbate forces (lower tunneling gap resistance) are necessary to move a phenyl compared to an iodobenzene. We attribute this to the C-Cu bonding of phenyl to the step edge in addition to its interaction with the terrace.

If necessary, the iodine atoms were also pulled by the tip to further separate them from the phenyls and to clear the manipulation path. Lateral manipulation was continued until two phenyls were located close to each other. The shortest achievable distance between the centers of two phenyls is 3.9 ± 0.1 Å, as determined from the STM images. We emphasize that even though the two phenyls are brought together spatially they do not join at our working temperature (20 K) unless further measures are taken: In attempts to laterally manipulate the phenyl couple, the two phenyls are always separated again. Therefore we assume that both phenyls are still bound to the step edge via their C-Cu bonds at this stage.

To realize the third reaction step, association, the phenyl couple at Figure 13c was excited by applying 500 meV voltage pulses for 10 sec. We suggest the following explanation for the association process: Since the two adjacent phenyls are initially tied up to the step edge, both of their C-Cu bonds are pointing towards it. If the phenyls are activated by the tunneling current, this can also lead to their in-plane rotation. A slight rotation points the reactive C- atoms out of the step edge normal. As Zheng et al. explained, this can lead to the formation of a C-Cu bond, if the initial rotation is sufficiently energetic. By exposing the phenyls to the 500 meV electrons of the tunneling current the necessary activation energy is supplied. The observed process can be initiated only by using voltages =<0.5 V. Since the bias necessary for association is as small as 0.5 V, dehydrogenation during the association process can be ruled out. Formation of biphenyl was confirmed by pulling the synthesized molecule from its front end with the STM tip (Figure 13f). Since the entire unit follows the tip from behind in the pulling mode, this verifies the successful chemical association of the two phenyls to form a biphenyl molecule. Finally, the iodine atom from the tip-apex was transferred back to the substrate (Figure 13g) by applying reverse voltage pulses. In the sequence of Figure 13, the first image (13a), showing two adsorbed C6H5I molecules on Cu, exactly represents the left side of the Ullmann reaction while the final image (13g), a biphenyl molecule and two iodine atoms on Cu, exactly represents the right side of the equation. Thus the whole chemical equation can be visualized with individual reactants for the first time. Additionally, the important role of step-edges in catalytic reactions is reflected in this atomic scale reaction sequence.

Although already in 1929 one dimensional defects were proposed as the catalytically active-sites in the ‘Adlineation Theory’ by Schwab and Pietsch, only a few detailed studies for metal-catalyzation at step-edges have emerged. During our experiment, we found that it is much easier to induce the reaction at Cu step-edges, especially at very low molecule coverages, because of the following reasons; (1) Adsorption: Due to their mobility, most C6H5I molecules are adsorbed at

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the Cu step-edges even at ~20 K. Therefore they are easy to locate. (2) Dissociation: Due to the stronger binding at the step-edges than on the terraces, the phenyls attach to the step edges after dissociation. (3) Diffusion: Again due to the stronger binding, it is easier to laterally manipulate the phenyls along step-edges without losing them. Step-edges were therefore also used as navigation aid for the manipulation paths. Moreover, there is a higher probability for phenyls to meet a reaction partner, another phenyl, at the step-edges. (4) Association: Because the step-edge locks the closely located phenyl couple, it is easier for them to join.

Figure 14: Investigations concerning the mechanisms of dissociation, manipulation, and association[5]. (a) A double logarithmic plot of the dissociation rate of iodobenzene versus the tunneling current shows a slope close to unity indicating a single electron process. (b) Tip height curve during lateral movement of a phenyl corresponding to pulling the phenyl molecule by the STM tip. During pulling adsite hops of distances a0 and 2a0 can be observed. (c) A background subtracted STM image with a phenyl couple in its center. The upper and lower parts correspond to the stages before and after the chemical association. The tip height profile across the centers of the synthesized biphenyl molecule is indicated.

9. Development of one-dimensional band structure in artificial gold chains

Another interesting example of manipulating atoms on surface was experiment made by Nilius, Wallis and Ho[18,19]. They built linear Au chains on NiAl(110) with STM, adding one atom at a time, measured their electronic properties from scanning tunneling spectroscopy (STS) and revealed the evolution of a 1D band structure from a single atomic orbital.

The experiments were carried out in an ultrahigh-vacuum STM operated at 12K on the NiAl(110) single crystal surface. Single Au atoms, deposited on NiAl(110) at 12 K, appear as protrusions in topographic STM images. A single Au atom can be moved across the surface, jumping from one to the next adsorption site as it follows the trajectory of the tip (“pulling mode”). The controlled manipulation of Au atoms is used to build 1D chains along the Ni troughs, which serve as a natural template. The atom-atom separation is given by the distance between adjacent Ni bridge sites (2.89 Å) and matches the nearest neighbor distance in bulk Au (2.88 Å). For every atom added to the structure, the measured chain length increased by ~3 Å. Individual Au atoms in a chain are indistinguishable in STM images, indicating a strong overlap of their atomic wave functions.

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Figure 15:

(a)STM topographic image showing single Au atoms on NiAl surface.

(b) Structure model of a Au7 chain and an Au atom on a NiAl(110).

(c) STM image showing intermediate stages of building a Au20 chain.

The electronic properties of the Au chains were determined by STS, which detects the derivative of the tunneling current as a function of sample bias with open feedback loop. The tunneling conductance (dI/dV) gives a measure of the local density of states (DOS) available for tunneling electrons. Probing the empty states of NiAl(110) at positive sample bias reveals a smooth increase in conductivity, reflecting the DOS of the NiAl sp-band (Fig. 16).

In contrast, STS of a Au monomer is dominated by a Gaussian-shaped conductivity peak centered at 1.95 V. The resonance is reproduced with different tips and shows a spatial extension comparable to the size of the atom in topographic images. The enhanced conductance is attributed to resonant tunneling into an empty state in the Au atom.

Moving a second Au atom into a next neighbor position on the Ni row leads to a dramatic change of the electronic properties. The single resonance at 1.95 V splits into a doublet with peaks at 1.50 and 2.25 V, indicating strong coupling between the two atoms (Fig. 16). The energy splitting appears to be analogous to the well-known example of two hydrogen 1s states forming a bonding and an antibonding level in a H2 molecule.

The formation of a linear Au trimmer shifts the low energy peak to 1.1 eV and the high-energy peak to 2.6 eV. A third peak emerges at 1.8 V, as predicted in molecular orbital theory from the overlap of three initial Au orbitals.

Individual conductivity resonances become indistinguishable for chains containing more than three atoms, because of the overlap between neighboring peaks and the finite peak width of 0.35

V. However, adding more atoms to the chain causes a continuous downshift of the lowest energy peak from 0.95 eV for Au4 to 0.75 eV for a 20-atom chain. Reproducing the experiment with different STM tips gives an identical relation between peak energy and chain length.

Figure 16:

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Conductivity spectra for bare NiAl and for Au chains with different lengths. Spectra were taken in the center of the chains and are offset for clarity. The tunneling gap was set at Vsample=2.5V, I=1nA. Electronic resonances of Au3 are marked with arrows.

The experiment described here demonstrates an approach to studying the correlation between geometric and electronic properties of well-defined 1D structures.

10. Conclusion & future prospects for single molecule engineering

We learned basics of STM and demonstrated that by employing the STM tip as an engineering tool on the atomic scale all steps of a chemical reaction can be induced: Chemical reactants can be prepared, brought together mechanically, and finally welded together chemically. We also learned about another experiment, where scientists collected Au atoms in a chain and measured electronic properties of this chain.

By inducing the chemical reactions with the STM tip, the detailed underlying reaction processes can be studied on atomic level. Chemical relationships like the Ullmann equation, can be checked and confirmed. However, one should be cautious in making direct relationships between the natural and tip-induced reactions. Under the influence of the tip, reactions can be forced to proceed which otherwise may not occur in nature. But this is exactly the advantage for nano-technology since synthesis of individual man-made molecules, never before seen in nature or made in chemical reactors, may eventually become a possibility. Molecules with specific functions, to be used in nano-electronic and nano-mechanic devices, may be possible to be constructed and their physical and chemical properties may be studied in-situ with STM spectroscopy techniques on an individual basis. Thus, with these achievements in molecular manipulation possibilities with the STM, an entire new dimension for future nano-science and technology is now wide opened.

11. References

[1] Hla SW, Rieder KH, Engineering of single molecules with a scanning tunneling microscope tip, SUPERLATTICE MICROST 31 (1): 63-72 JAN 2002 [2] Dujardin G, Walkup RE, Avouris P, Dissociation of individual molecules with electrons from the tip of a scanning tunneling microscope, SCIENCE 255 (5049): 1232-1235 MAR 6 1992

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[3] Lee HJ, Ho W, Single-bond formation and characterization with a scanning tunneling microscope, SCIENCE 286 (5445): 1719-1722 NOV 26 1999 [4] Hla SW, Meyer G, Rieder KH, Inducing single-molecule chemical reactions with a UHV-STM: A new dimension for nano-science and technology, CHEMPHYSCHEM 2 (6): 361-366 JUN 18 2001[5] Hla SW, Bartels L, Meyer G, et al., Inducing all steps of a chemical reaction with the scanning tunneling microscope tip: Towards single molecule engineering, PHYS REV LETT 85 (13): 2777-2780 SEP 25 2000[6] Binnig G, Rohrer H, Gerber C, et al., PHYS REV LETT 49 (57): 120-123 1982[7] http://www.uni-saarland.de/fak7/hartmann/projects/nano_stm.html[8] Eigler DM, Schweizer EK, Positioning single atoms with a scanning tunneling microscope, NATURE 344 (6266): 24-526 APR 5 1990 [9] Meyer G, Repp J, Zöphel S, Braun KF, Hla SW, Fölsch S, Bartels L, Moresco F, Rieder KH, SINGLE MOLECULES, 1, 79-86, 2000[10] Dujardin G, Walkup RE, Avouris P, Dissociation of individual molecules with electrons from the tip of a scanning tunneling microscope, SCIENCE 255 (5049): 1232-1235 MAR 6 1992[11] Martel R, Avouris P, Lyo IW, Molecularly adsorbed oxygen species on Si(111)-(7x7): STM-induced dissociative attachment studies, SCIENCE 272 (5260): 385-388 APR 19 1996 [12] Stipe BC, Rezaei MA, Ho W, et al., Single-molecule dissociation by tunneling electrons, PHYS REV LETT 78 (23): 4410-4413 JUN 9 1997 [13] Saw-Wai Hla, Angelika Kühnle, Gerhard Meyer, Karl-Heinz Rieder, Detailed Mechanisms of Single Atom Motion During STM Manipulation, http://www.physik.fu-berlin.de/~hlas/iodine.htm[14] Eigler DM, Lutz CP, Rudge WE, An atomic switch realized with the scanning tunneling microscope, NATURE 352 (6336): 600-603 AUG 15 1991 [15] Bartels L, Meyer G, Rieder KH, et al., Dynamics of electron-induced manipulation of individual CO molecules on Cu(III), PHYS REV LETT 80 (9): 2004-2007 MAR 2 1998 [16] J. Repp, M.Sc thesis, Free University of Berlin (Germany), 1999.[17] Lee HJ, Ho W, Single-bond formation and characterization with a scanning tunneling microscope, SCIENCE 286 (5445): 1719-1722 NOV 26 1999 [18] Wallis TM, Nilius N, Ho W, Electronic density oscillations in gold atomic chains assembled atom by atom, PHYS REV LETT 89 (23): art. no. 236802 DEC 2 2002 [19] Nilius N, Wallis TM, Ho W, Development of one-dimensional band structure in artificial gold chains, SCIENCE 297 (5588): 1853-1856 SEP 13 2002 [20] Saw-Wai Hla, Gerhard Meyer, Karl-Heinz Rieder, Inducing Single-Molecule-Ullmann Reaction with Iodine Functionalized STM-Tip, http://plato.phy.ohiou.edu/~hla/1.pdf[21] Hla SW, Rieder KH, Engineering of single molecules with a scanning tunneling microscope tip, SUPERLATTICE MICROST 31 (1): 63-72 JAN 2002 [22] Hla SW, Meyer G, Rieder KH, Selective bond breaking of single iodobenzene molecules with a scanning tunneling microscope tip, CHEM PHYS LETT 370 (3-4): 431-436 MAR 14 2003 [23] http://www.phy.ohiou.edu/~hla/publication.html

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