Molecular Cut N Paste : Building Molecules with STM

UNIVERSITY OF LJUBLJANA

FACULTY 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. Introduction3

2. Ullman reaction3

3. Basics about bonds, surface, atomic forces 4

3.1. Sigma and Pi bond4

3.2. Metallic bond5

3.3. Surface5

3.4. The role of surface5

3.5. Why atoms gather near step edges ?5

4. Introduction to STM6

4.1. Concept6

4.2. Modes of operation6

4.2.1. Constant Current Mode 6

4.2.2. Constant Height Mode 6

4.3.3. Scanning Tunneling Spectroscopy7

4.3. Technical aspects7

5. Basic molecular manipulation with STM7

6. Berlin team experiment8

7. Basic reaction steps with STM-tip.9

7.1. Controlled molecular diffusion on surfaces9

7.2. Molecular bond breaking10

7.3. Vertical molecular manipulation11

7.4. Molecular bond formation12

8. Single molecule Ullman reaction12

9. Development of one-dimensional band structure in artificial gold chains15

10. Conclusion and future prospects for single molecule engineering17

11. References18

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 CornellUniversity, 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.

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 orbitalsS 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 orbitalsP and P Pi bond

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

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 coordination
number) 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.

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

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 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 processesbecame 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.

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.