ATOMISTIC INTERACTIONS IN STM ATOM MANIPULATION

A dissertation presented to

the faculty of

the College of Arts and Sciences of Ohio University

In partial fulfillment

of the requirements for the degree

Doctor of Philosophy

Aparna Deshpande

March 2007

This dissertation entitled

ATOMISTIC INTERACTIONS IN STM ATOM MANIPULATION

by

APARNA DESHPANDE

has been approved for

the Department of Physics and Astronomy

and the College of Arts and Sciences by

Saw-Wai Hla

Associate Professor of Physics and Astronomy

Benjamin M. Ogles

Dean, College of Arts and Sciences

Abstract

DESHPANDE, APARNA, Ph.D., March 2007, Physics

ATOMISTIC INTERACTIONS IN STM ATOM MANIPULATION (125 pp.)

Director of Dissertation: Saw-Wai Hla

This thesis describes the study of two diverse systems, a cluster of silver atoms, and

individual silver and bromine atoms, deposited on a metallic single crystal Ag(111)

substrate, in the domain of atomic and molecular manipulation techniques, using a

custom-built ultrahigh vacuum low temperature scanning tunneling microscope.

A cluster of silver atoms was created by a controlled tip-sample contact. Single atoms were extracted from the cluster by using STM tip induced lateral manipulation. To

investigate the mechanism of extraction in detail, atom extraction was carried out for

different values of manipulation voltage and current. The threshold distance to pull an

atom out from the cluster was determined. The tip-cluster distance proved to be the

governing factor for the atom extraction mechanism.

Lateral manipulation of a metal atom, silver, and a halogen atom, bromine, was

carried out on a silver substrate with a silver coated tip apex. Silver atoms were extracted

from a cluster of atoms, and bromine atoms were extracted from a cobalt porphyrin

molecule using tunneling electron-induced bond dissociation technique. The threshold

distance necessary to manipulate the silver atom and the bromine atom was determined.

The lateral manipulation signals provided a value of the angle made by the tip with the

surface at the first jump of the atom during manipulation. The interaction energy curves

for these atoms were calculated using density functional theory. From a combination of

all these results, a numerical value of force was obtained. This force corresponds to the

threshold force necessary to move a silver atom and a bromine atom on the surface. The

values of force provide an insight into the ionic and metallic interactions on the surface at the single atom level.

The manipulation capability of the scanning tunneling microscope to build

nanostructures was demonstrated by constructing a parabolic corral using locally

extracted atoms. Since the surface vacancies and defects created during construction can

be sealed off with the atoms and clusters after construction, this procedure resembles an

atomic scale analog of a macroscale construction site.

Approved:

Saw-Wai Hla

Associate Professor of Physics and Astronomy

Acknowledgments

I am grateful to my advisor for his mentorship. His crucial input at every stage of my

projects, his wisdom, scientific and otherwise, and his pedagogy have helped me all

along. Thank you for your patience and for the opportunity to be involved in the

construction of a sophisticated system.

My thesis committee members for devoting a share of their precious time to read my thesis. A special note of thanks to Prof. Elizabeth who was willing to be on the committee at a late notice.

Dr. Kai-Felix Braun for his help with the STM instrumentation, standing wave pattern calculation program, and insightful discussions.

For all the physics classes and the professors who gave them, thank you.

Prof. Sergio for letting me participate in the theory group meetings and the chance to broaden my physics and world outlook.

Prof. Nancy for being a friend and a great listener.

Ennice, Ruth, Tracy, Chris and Roger for all their help over the years.

Violeta for the enriching friendship.

To all my team mates in the Hla group for the camaraderie.

Swati for the good times, Deepshikha for the fun get togethers and the fantastic Indian food, Anand for sharing the passion for movies and music.

Collins for the love, friendship and the stoic support that I have always counted on.

My Kaku and Kaka for making me a part of their family and for their continued love and affection.

My Baba for always being there. Thank you for being a great parent, for instilling the value of education and for letting me follow my dreams.

My Tai for the love and emotional support, Tejas for the wonderful growing up years.

Suhita for being my pillar of strength.

Dedicated to Suhita 8 Table of Contents

Page

Abstract……………………………………………………………………………………3

Acknowledgments…………………………………………………………………………5

Dedication…………………………………………………………………………………7

List of Table...... ….11

List of Figures……………………………………………………………………………12

Chapter 1. Introduction...... 19

Chapter 2. Instrumentation ...... 24

2.1 Operating Principle of STM ...... 24

2.2 UHV-LT-STM System ...... 31

2.2.1 UHV System ...... 32

2.2.2 STM Unit ...... 34

2.2.3 STM Hardware and Software ...... 36

Chapter 3. Background ...... 38

3.1 STM Manipulation Techniques ...... 38

3.1.1 Lateral Manipulation...... 39

3.1.2 Vertical Manipulation ...... 43

3.1.3 Inelastic Tunneling Electron Induced Excitations ...... 46

3.2 Atomistic Interactions...... 48

3.2.1 Types of Interactions...... 48

3.2.2 Interactions in STM Manipulation...... 51 9 3.3 Materials ...... 52

3.3.1 Substrate...... 53

3.3.2 Molecule ...... 55

Chapter 4. Atom Extraction by Controlled Tip-Cluster Interaction ...... 57

4.1 Introduction...... 57

4.2 Experimental Details...... 60

4.3 Atom Extraction...... 60

4.3.1 Lateral Manipulation for Extraction ...... 61

4.3.2 Threshold Resistance ...... 64

4.4 Modeling...... 67

4.5 Discussion...... 70

Chapter 5. Atomistic Constructions...... 72

5.1 Construction Scheme ...... 72

5.2 Reconstruction Scheme...... 78

5.3 Discussion...... 79

Chapter 6. Atom Selective Force Measurement ...... 81

6.1 Introduction……………………………………………. …………………81

6.2 Force Measurement Strategy ...... 82

6.3 Experimental Details...... 84

6.4 Br Atoms...... 87

6.4.1 Extraction of Br Atoms...... 87

6.4.2 Threshold Resistance Measurement of Br Atoms ...... 90

6.4.3 Lateral Manipulation for Angle Measurement ...... 94 10 6.4.4 Height Correction for Br Atoms ...... 96

6.4.5 Numerical Value of Force...... 97

6.5 Ag Atoms...... 100

6.5.1 Extraction of Ag Atoms...... 100

6.5.2 Threshold Resistance Measurements for Ag Atoms...... 101

6.5.3 Lateral Manipulation for Angle Measurement ...... 104

6.5.4 Numerical Value of Force...... 105

6.6 Discussion...... 108

Chapter 7. Conclusions and Outlook ...... 111

Bibliography……………………………………………………….…………………....115

Appendix A List of Publications………………………………………………………..122

Appendix B List of Contributed Talks and Posters in Conferences………………....…124

11 List of Tables

Page

Table 1. Values of energy and distance from the Ag-Br interaction energy curve……...99

Table 2. Values of total force and lateral force calculated using equation (1) and values from Table 1……………………………………………………………………………...99

Table 3. Values of energy and distance from the Ag-Ag interaction energy curve…….108

Table 4. Values of total force and lateral force calculated using equation (1) and values from Table 3…………………………………………………………………………….108

Table 5. Values of threshold lateral force, total force and threshold resistance for Ag and

Br atoms………………………………………………………………………………...109

12 List of Figures

Page

Figure 2.1 Illustration of a scanning tunneling microscope. (a) The STM tip is attached to

a piezo tube. By applying an appropriate voltage to the piezo tube, the tip can be

moved in x, y, and z directions on the sample. (b) Illustration of electron

tunneling at the tip-sample junction at an applied sample bias ‘V’. Here φ is the

work function of the material, Ef is the Fermi level and E vac is the vacuum

energy. ………………………...... 25

Figure 2.2 Schematic representation of STM operation in constant current mode (a) and

constant height mode (b)…………………………………………………………26

Figure 2.3 Schematic of direction of electron flow based on polarity of applied bias…..28

Figure 2.4 Energy diagram for elastic and inelastic tunneling mechanisms through an

adsorbate on the surface along with the corresponding form of I-V, dI/dV and

d2I/dV2 spectra that represent the processes. A change in I-V curve appears as a

step-like change in dI/dV signal, which in turn produces a peak in d2I/dV2 signal.

Figure from [17] …………………………………………………………..……..29

Figure 2.5 Tunneling resistance as a function of tip-sample distance acquired from an I-Z

spectroscopy at a fixed bias. A reduction in resistance leads to an increase in the

tunneling current. A red line is drawn for the eye guidance of the ohmic

contact……………………………………………………………………………31

Figure 2.6 Homebuilt UHV-LT-STM system…………………………………………...33 13 Figure 2.7 A close up of the STM unit attached to the base of the

cryostat………………………………………………...... 34

Figure 2.8 Schematic of cryostat, radiation shields, and STM unit. Picture from [22]….35

Figure 3.1 Illustration of lateral manipulation. Picture from [22]…………………….... 39

Figure 3.2. Competing forces during pulling mode of atom manipulation on the periodic

surface potential………………………………………………………………… 41

Figure 3.3 Pushing mode of lateral manipulation………………………………………. 41

Figure 3.4 Characteristic lateral manipulation signals………………………………….. 42

Figure 3.5 Illustration of vertical manipulation. Picture from [22]……………………...43

Figure 3.6 Illustration of an atomic switch with the double well potential for Xe atom and

vibrational energy levels. Picture from [36]……………………………………..44

Figure 3.7 Vertical manipulation. (a) The double potential well becomes a single

potential well by reducing the tip-atom distance to a contact point (b). By

retracting the tip, the manipulated atom moves vertically……………………….45

Figure 3.8 Illustration of adsorbate-induced resonance state for an adsorbate on a metal

substrate. Picture adapted from [30]……………………………………………..46

Figure 3.9 Bond dissociation using tunneling electrons. Picture from [38]...... 47

Figure 3.10 (a) Dipole formation for bonding. (b) Lennard-Jones potential. (c) Transfer of

electrons for an ionic bond formation between two atoms. (d) Energy E vs.

distance r plot for ionic interaction. (e) Sharing of electrons in a covalent bond. (f)

Metallic bonding…………………………………………………………………49 14 Figure 3.11 STM image showing atomic resolution of Ag(111) surface. The surface

directions used for manipulation are marked. The three-fold hollow site favored

by adatoms Ag and Br for adsorption is highlighted by circles…………………53

Figure 3.12 (a) Ag(111) surface state bear the fermi level in the bulk band dispersion

diagram. Picture from [45], (b) dI/dV spectrum showing the onset of the surface

state at -65 mV…………………………………………………………………...54

Figure 3.13 Standing waves on Ag(111) surface created by scattering of surface state

electrons off a step edge and Ag atoms that act as point scatterers……………...55

Figure 3.14 Chemical structure of cobalt porphyrin molecule…………………………..56

Figure 3.15 STM image of cobalt porphyrin molecule showing the central porphyrin ring

lifted by the 4 lobes. Size of the molecule is 15 Å x 15 Å………………………56

Figure 4.1 Illustration showing the tip-sample distance of operation of different types of

scanning probe microscopes using the Lennard – Jones potential………………58

Figure 4.2 Creation of a cluster of Ag atoms by tip-sample contact. Image (a) shows a

bare Ag(111) surface. Image (b) shows an Ag nanocluster created after contact.

Image parameters: V= 50 mV, I= 1 nA, image size 400 Å x 180 Å, and cluster

size 70 Å x 24 Å………………………………………………………………….59

Figure 4.3 STM images of atom extraction before and after the extraction process. A ball

model of the tip marks the site of extraction. Image parameters: V= 30 mV, I= 1

nA, dimensions of the cluster: height 6 Å, width 30 Å, length 100 Å…………...61

Figure 4.4 Lateral manipulation signal recorded during the atom extraction process…...62

Figure 4.5 Signature of atom extraction from a cluster. Ball models explain the peaks in

the signals with reference to the jump height of the tip………………………….63 15 Figure 4.6 Probability of atom extraction as a function of current at fixed bias

voltage...... 64

Figure 4.7 Threshold resistance Rth to extract an atom from the cluster………………...65

Figure 4.8 Threshold distance corresponding to the threshold resistance for atom

extraction is obtained from the curve. A model shows the correlation of this

distance with the tip-cluster framework………………………………………….66

Figure 4.9 Effect of the tip on the energy barriers at adatom sites. Picture from

[50]……………………………………………………………………………….67

Figure 4.10 Model system for atom extraction along with the path taken by the atom

down the slope of the cluster. Picture from [51]………………………………....68

Figure 4.11 Lowering of the tip-cluster energy barrier due to the presence of the tip...... 69

Figure 5.1 An illustration of the nanoscale construction scheme. A controlled tip crash

creates holes and clusters on the surface (1-2), the atoms are extracted from the

cluster by using lateral manipulation (3), the atoms are arranged in desired

geometry (4), the holes are sealed with the unused clusters (5), and the tip is

retracted to imaging height (6). Picture from [51] ………………...... 74

Figure 5.2 Constant current image of a corral constructed on Ag(111) surface. Image

parameters: (a) V= 30 mV, I= 1nA; image size 220 Å x 240 Å; (b) V= -30 mV, I

= 1 nA; image size 220 Å x 240 Å………………………………………………75

Figure 5.3 Constant current image of a parabola constructed by an assembly of 15 Ag

atoms. Image parameters: (a) V= 40 mV, I= 1nA; image size 170 Å x 270 Å; (b)

V= -60 mV, I= 1 nA; image size 170 Å x 270 Å………………………………...76 16 Figure 5.4 dI/dV maps at (a) 30 mV and (b)-30 mV generated using scattering

theory…………………………………………………………...... 78

Figure 5.5 Reconstruction of a surface at an atomic level by filling the holes on the

surface using atoms and clusters. Picture from [57]……………………………..79

Figure 6.1 Atomistic force measurement strategy. An STM tip-height signal

(manipulation signal) shows single atomic site hopping of the atom on Ag(111)

surface when the atom is manipulated along a close-packed surface direction. The

drawings indicate the changes of vertical and lateral force components during

manipulation. Initially only a vertical force component exists but when the tip

traces the atom contour, the lateral force component increases. When the lateral

force component overcomes the surface force, the atom hops to the next surface

site. Here, ‘φ’ is the force vector angle and ‘r’ is the tip-atom distance.

……………………………………………………………………………………83

Figure 6.2 A series of images before tip crash (a) and after tip crash (b), showing a

sharper image resolution after the tip crash. The crash site is marked by a circle.86

Figure 6.3 CoTBrPP molecules on Ag(111) surface seen in domains (a) and in a cluster

arrangement (b)…………………………………………………………………..86

Figure 6.4 STM image of CoTBrPP single molecule taken at V= 1000 mV, I= 1 nA

(Image size 38 Å x 28 Å) along with a ball model based on the chemical structure

of the molecule…………………………………………………………………...88

Figure 6.5 Dissociation of phenyl in CoTBrPP molecule by I-V spectroscopy showing an

abrupt drop in the current the breaking of the C-Br bond………………………..89 17 Figure 6.6 Dissociation of CoTBrPP molecules on Ag(111). The dissociated Br atom is

seen in the image. Image parameters are: V= 1000 mV, I= 1.2 nA, size 52 Å x 32

Å………………………………………………………………………………….90

Figure 6.7 A series of images showing dissociation of Br atom and its subsequent lateral

manipulation. Image parameters: V= 1000 mV, I = 0.44 nA, size 90Å x 40 Å…91

Figure 6.8 Probability plots for Br atom manipulation at positive

voltages…………………………………………………………………………..92

Figure 6.9 Probability plots for Br atom manipulation at negative voltages…………….93

Figure 6.10 Linear relationship between current and voltage during Br atom

manipulation……………………………………………………………………..94

Figure 6.11 LM curve for the Br atom during manipulation at positive

voltage……………………………………………………………………………95

Figure 6.12 LM curve for the Br atom during manipulation at negative voltage………..95

Figure 6.13 Height correction scheme for atoms………………………………….……..96

Figure 6.14 Interaction energy between Ag-Br atoms as a function of the separation

between the atoms is shown in (a). The plot is rescaled to Ag-Br bond energy and

to the distance between outer Van der Waal radii of the two atoms as shown in

(b).………………………………………………………………………………..97

Figure 6.15 Measurement of angle φ as a function of total force between the tip and the

Br atom…………………………………………………………………………...98

Figure 6.16 Extraction of Ag atoms from an Ag cluster. (Image parameters: V= 50 mV,

I= 1 nA, size 90 Å x 30 Å)……………………………………………………...101

Figure 6.17 Ag atom manipulation at positive voltages………………………………..102 18 Figure 6.18 Ag atom manipulation at negative

voltages…………………………………………………………………………103

Figure 6.19 Linear relationship between the current and voltage during Ag atom

manipulation……………………………………………………………………104

Figure 6.20 LM curves to measure the angle made by the tip and the Ag atom during

lateral manipulation…………………………………………………………….105

Figure 6.21 Interaction energy between Ag-Ag atoms as a function of the separation

between the atoms (a). The plot is rescaled to Ag-Ag bond energy and to the

distance between outer Van der Waal radii of the two atoms, shown in (b)…...106

Figure 6.22 Measurement of angle φ as a function of total force between the tip and the

Ag atom…………………………………………………………………………107 19

Chapter 1

Introduction

The field of surface science has seen consistent path breaking developments since the

1960s. Every new technological breakthrough in areas as diverse as vacuum technology and semiconductor microelectronics contributed to a better understanding of surfaces and

interfaces. The invention of the scanning tunneling microscope (STM) in 1982 attracted a

great deal of attention and appreciation as it was the first instrument with the fine lateral

resolution and vertical resolution necessary to image single atoms in real space [1] .

However the operation of STM was not limited to imaging. The technique of scanning

tunneling spectroscopy explored the capability of an STM to resolve the energy states of

a surface at a fixed position [2].

The operation of an STM in ultrahigh vacuum and at low temperatures (UHV-LT-

STM) broadened the scope of its applications. One remarkable achievement was the

technique of atom manipulation where a precise control of interactions between the tip

and the adsorbed atom on the surface could move the atoms to different locations on the

surface [3]. A bidirectional vertical transfer of the atom between the tip and the surface

demonstrated the function of the atom as a switch [4]. It introduced the concept of using

atoms as active elements in an electronic circuit, one of the key features of bottom-up

nanotechnology. Construction of corrals using atoms made it possible to visualize the 20 standing wave patterns within the corral created by an interference of the confined

electrons. A fascinating corral experiment exploited the geometry of the corral and the

physics of the Kondo effect to create a quantum mirage from the localized spectroscopic

response of a magnetic atom [5].

Manipulation techniques have made a significant contribution to a detailed

understanding of molecules by probing chemistry at length scales comparable to bond

lengths in a molecule. Individual bonds in the molecule can be dissociated using energy

provided by tunneling electrons from the tip [6]. Vibrational spectroscopy using STM can

`fingerprint’ the molecule by identifying the chemical bonds in the molecule [7].

Chemical reactions performed in the confines of a laboratory can be actualized on a metal substrate. The Ullman reaction is a spectacular example of this demonstration [8]. Lateral manipulation of molecules can probe the mechanical stability of a molecule and record the intramolecular dynamics in response to the tip [9]. The switching behavior of molecules can be studied for possible applications in molecular electronic devices [10].

Thus, the extent of STM applications is interdisciplinary in nature.

Lateral manipulation of an atom involves different types of interactions and forces that come into play when the atom encounters energy barriers of different magnitude and character. The surface on which the atom is adsorbed acts as the host providing a potential energy landscape for the atom to bind to the surface either by physisorption or chemisorption. The corrugation of the surface presents a barrier for diffusion of the atom.

The tip acts as a highly localized perturbation that modifies the potential energy landscape and affects the state of the adsorbed atoms. Under the influence of the tip, the atoms experience either attractive or repulsive interactions. The lateral movement of the 21 atoms on the surface is guided by the nature of this interaction. When the atom

acquires enough energy from the tip-induced interaction to overcome the diffusion

barrier, it jumps to the next energetically favorable site. The dynamics of all these

processes are controlled by tuning the distance between the tip and the atom.

The interactions between the tip and the surface can be controlled to carry out local

surface modifications. A controlled tip crash can create single atoms and reshape the tip

apex making the tip sharper for a better resolution of images [11]. The STM tip can be

used as a construction tool to dig out clusters from a metal surface. The manipulation

technique used to move a single atom on the surface can be employed to extract an atom

from a three dimensional cluster.

The complexity of such phenomena and the precision with which an STM can

attempt to explore and understand them makes the field of STM manipulation a very

challenging enterprise and an equally intriguing pursuit. The wide spectrum of

applications of STM: imaging, manipulation and spectroscopy, makes it an ideal tool to communicate with the nanoworld.

A part of this dissertation explores the rich physics of interactions between the STM tip and a metallic cluster using a homebuilt UHV-LT-STM. A single atom can be extracted from a cluster of silver atoms using the STM lateral manipulation technique.

The extracted atom is initially bound to the other atoms inside the cluster. The presence of the tip enhances the interaction between the tip and the cluster. The atom is pulled out from the cluster by breaking the bonds within the cluster. What are the driving forces behind this mechanism? At what critical tip-cluster distance is this mechanism feasible? 22 How does the potential energy landscape of the cluster change due to the presence of the tip? These are some of the questions explored in this study.

Another interesting area probed in this dissertation is the extensive manipulation study of two different types of atoms – a metal atom (silver) and a halogen atom

(bromine) on a metallic substrate (Ag(111)). Under identical conditions of manipulation, using the same tip and the substrate, how does the chemical nature of the atom manifest itself? What is the threshold force necessary for lateral manipulation of these atoms? An attempt is made to answer these questions with a systematic study using STM manipulation. With this objective in mind, the organization of this dissertation is as follows:

Chapter two describes the instrumentation used for the projects and the basic functions of an STM. The UHV-LT-STM is a custom-built system. The experience of being involved in the construction of this machine helped to understand the intricacies of

such a sophisticated and powerful tool. The operating principle of STM is explained and

different spectroscopic techniques are introduced.

Chapter three gives an account of the manipulation techniques since the projects

carried out here are based extensively on atomic and molecular manipulation. Different

types of interactions between the tip and the adsorbate are discussed to help focus the

analysis and interpretation of the experimental results. The substrate and the molecule

used for the experiments are introduced.

Chapter four is a detailed study of the process of extracting a single atom from a

metallic cluster using the technique of lateral manipulation. The cluster is created from

the substrate material by a controlled tip sample contact. The interactions between the 23 STM tip and the cluster are investigated by determining the threshold tip-cluster distance essential for a successful atom extraction.

Chapter five is an account of creating nanostructures on the surface by an atom-by- atom assembly. The atoms are extracted from a metallic cluster. The holes created on the surface during a tip-sample contact can be sealed with the extracted atoms. The ability of the scanning tunneling microscope to build structures at the nanoscale, analogous to a macroscopic construction project, is thereby demonstrated.

Chapter six is an exhaustive investigation of two different types of atoms, Ag and Br, on a metal substrate. The Ag atoms are obtained from the substrate and a vapor deposited porphyrin molecule is the source of Br atoms. Lateral manipulation trials of Ag and Br give a value of threshold resistance necessary for manipulation. The threshold force required to move these atoms is also estimated.

Chapter seven summarizes the significant conclusions of this study and provides a broad outlook of the projects carried out in this dissertation.

24 Chapter 2

Instrumentation

The construction of a low temperature ultrahigh vacuum scanning tunneling microscope

(UHV-LT-STM) was undertaken in the first year of my research. This chapter describes

the principle of operation of an STM and the spectroscopic techniques followed by the

UHV-LT-STM construction.

2.1 Operating Principle of STM

The scanning tunneling microscope, invented by Binnig and Rohrer in early 1980s,

marked a pivotal contribution to the study of surfaces and was recognised by the award of

a Nobel Prize in 1986. The realization of a scanning tunneling microscope (STM) was the result of a classic combination of surface science and engineering[1]. The field of surface science was revolutionized by STM due to its unprecedented resolution. The high resolution of STM is the result of the quantum mechanical phenomenon of tunneling.

When a sharp metallic tip is placed a few angstroms away from a conducting sample and a bias voltage is applied between the tip and the sample, electrons can tunnel at this junction (Figure. 2.1), thereby tunneling current flows between the tip and the sample. If 25 the applied bias is positive, (for positive bias the sample is positive with respect to the tip, negative bias implies that the sample is negative with respect to the tip), then the electrons tunnel from the tip to the sample, while a negative bias directs the flow of electrons from the sample to the tip. The current varies exponentially with the distance between them and is given by:

−z ϕ I ∝ V ⋅ ρ s ⋅ e

V, ρs and φ represent the bias voltage, density of states of the sample at the Fermi level and the workfunction of the sample. The distance between the tip and the sample is denoted by z. The basic set up of STM is represented in Figure 2.1.

(a) (b)

Figure 2.1 Illustration of a scanning tunneling microscope. (a) The STM tip is attached to a piezo tube. By applying an appropriate voltage to the piezo tube, the tip can be moved

in x, y, and z directions on the sample. (b) Illustration of electron tunneling at the tip-

sample junction at an applied sample bias ‘V’. Here φ is the work function of the

material, Ef is the Fermi level and E vac is the vacuum energy.

26 By keeping the current constant using a feedback loop, a topographic STM image

is generated when the tip scans the surface of the sample; this image reflects the constant

local density of states of the sample surface. Alternatively, it is also possible to obtain an

STM image by keeping the tip at a constant height with the feedback loop turned off; the

image thus recorded is a snapshot of the variation in the tunneling current at each point

on the sample [12]. Figure 2.2 illustrates these two operational modes.

Figure 2.2 Schematic representation of STM operation in constant current mode (a) and

constant height mode (b).

STM imaging provides information about the electronic states of the sample over the

spatial extent of the image. It is also possible to study the local electronic structure of the sample at a specific x,y location by keeping the tunneling gap constant and applying a

voltage ramp on the tunneling junction. This technique is known as scanning tunneling

spectroscopy (STS). Most commonly used spectroscopy techniques are current-voltage

spectroscopy [I-V], conductance spectroscopy [dI/dV - V] and vibrational spectroscopy

[d2I/dV2 – V]. I-V spectroscopy provides information about the transport of electrons between the tip and the surface as a function of varying voltage. dI/dV probes the local 27 electronic energy states of the sample whereas d2I/dV2 signal probes the vibrational energy states.

The tunneling current measured by STM is an integral of the density of states of the

tip ρT and density of states of the sample ρs close to the Fermi level within an energy

range eV. The expression for tunneling current is given by

eV

IEeVEd∝−++∫ ρερεεsf()()Tf 0

When the tip density of states is constant, then the differential tunneling conductance

(dI/dV) is proportional to the sample density of states [13, 14]

dI ∝−ρ ()EeV dV sf

The dI/dV spectrum records the peaks at energies where the electrons tunnel through

the specific electronic states between the tip and the sample for different values of

applied bias voltage. At a negative bias voltage the electrons tunnel from the sample to

the tip, providing information about the occupied electronic states in the sample. For a

positive bias voltage, the electrons tunnel from the tip to the sample, providing

information about the unoccupied electronic states of the sample. This is illustrated in

Figure 2.3. 28

Figure 2.3 Schematic of direction of electron flow based on the polarity of applied bias.

To record the tunneling spectrum the feedback loop is interrupted. An ac bias modulation of few mV is added to the dc bias using a lock-in amplifier. The first and second harmonics of the tunneling current are detected by the lock-in amplifier as the dc bias is swept over the selected energy range. The differential conductance dI/dV is proportional to the first harmonic while the d2I/dV2 is proportional to the second

harmonic of the tunneling current.

Depending on the energy of the tunneling electrons, tunneling spectroscopy is

categorized into two types: elastic tunneling spectroscopy and inelastic tunneling

spectroscopy. In case of elastic tunneling spectroscopy the electrons tunnel without any

loss of energy; this is generally seen in spectroscopic studies of semiconductors and bare

metal surfaces [2, 15, 16] .When the electron tunnels into a vibrational energy state of the

adsorbate, there is an induced excitation in the adsorbate with a concomitant energy loss

by the electron. Such a process is inelastic in nature and is known as inelastic electron 29 tunneling spectroscopy (IETS) [17]. A schematic of this description is shown in Figure

2.4.

Electronic spectra of adsorbates contain features related to energy levels of the substrate and adsorbate whereas vibrational spectra are characteristics of chemical bonds

in the molecules [7]. Scanning tunneling spectroscopy is hence an indispensable tool for

exploring physics and chemistry at the atomic and nanoscale.

Figure 2.4 Energy diagram for elastic and inelastic tunneling mechanisms through an adsorbate on the surface along with the corresponding form of I-V, dI/dV and d2I/dV2 spectra that represent the processes. A change in I-V curve will appear as a step-like change in dI/dV signal, which in turn produces a peak in d2I/dV2 signal. Figure from [17].

The variation of tunneling current with the width of the tunneling junction between the

tip and the sample is exponential in nature. However, there is a transition from the 30 tunneling regime to a point contact marked by a sharp increase in the current at a specific distance between the tip and the sample. The STM can be used to measure this change in the tunneling current as a function of the tip-sample distance. This technique is known as I-z spectroscopy. For I-z measurement, the tip height is set by a small value of voltage. The feedback is turned off and the tip is approached towards the sample by varying the distance between the tip and the sample in small steps. As the tip approaches the surface, it is attracted towards the surface whereas the atoms of the surface underneath the tip are pulled towards the tip. Strong adhesive forces between these two metals, i.e the tip and the surface at distances of the order of bond lengths, are responsible for this phenomenon. At a specific distance the tip jumps to contact with the surface followed by an abrupt increase in the tunneling current (Figure 2.5). The relationship

between the current and voltage in this regime is ohmic in nature [18-20]. The current at

each point of the tip trajectory can be converted to resistance, thus each value of junction

resistance can be assigned to the corresponding tip-sample distance. I-z spectroscopy can

thus be used for calibration of the tip height in STM measurements.

31

Figure 2.5 Tunneling resistance as a function of tip-sample distance acquired from an I-z

spectroscopy at a fixed bias. A reduction in resistance leads to an increase in the

tunneling current. A red line is drawn for the eye guidance of the ohmic contact.

2.2 UHV-LT-STM System

Manipulation of single atoms on a surface requires an atomically clean surface and low surface temperatures to prevent diffusion of the adsorbates due to thermal energy.

Operation of an STM in an ultrahigh vacuum (UHV) condition keeps the sample clean for a longer period of time whereas cooling the STM to low temperatures (LT) greatly

reduces the drift. Our UHV-LT-STM consists of 3 main units: the UHV system, the

STM, and the hardware and software that operate the STM. These units are described in

brief below.

32 2.2.1 UHV System

The vacuum chamber comprises of three main parts- a sample preparation chamber, a

load lock chamber, and a liquid helium bath cryostat. The sample preparation chamber

bears ports that can be utilized for different functionalities like an ion gun port for

sputtering facility, view ports for optical access, and a residual gas analyzer to check the

gas components in ultrahigh vacuum. The crucial component of this chamber is the

manipulator arm that holds the sample during cleaning and deposition of molecules, and

transfers the sample into the STM chamber. The manipulator includes facilities for the x,

y, z travel, rotation, as well as cooling (20 K) and heating (1100 K) of the sample. The

load lock chamber is connected to the sample preparation chamber via a gate-valve and it contains a Knudsen cell for vapor deposition of molecules. The cryostat consists of a tall cylindrical unit with electrical feedthroughs at the top. The STM is attached to the base of

the cryostat which holds the coolants- liquid nitrogen and liquid helium. 33

Figure 2.6 Custom-built UHV-LT-STM system.

All the constituents of the UHV-LT-STM, preparation chamber, cryostat and STM

were assembled. as seen in Figure. 2.6. Vacuum is achieved by pumping the chamber

using a set of pumps in ascending order of pumping capabilities- rotary pump, turbo pump, titanium sublimation pump and ion pump. A pressure below 10-10 torr can be

attained with these pumps. The filling of the cryostat with coolants further lowers the

base pressure to 10-12 torr (normal atmospheric pressure is 760 torr or 760 mmHg). To reach ultrahigh vacuum pressure, the chamber needs to be `baked’, i.e. heated to about

150ºC.

34 2.2.2 STM Unit

The design of the STM scanner unit is based on the Besocke-beetle type [21]. It

consists of a base plate that holds three coarse piezo tubes and one main piezo tube in the center to which the tip is attached at its base with a magnetic tip holder. The tip is made of electrochemically etched tungsten wire. A Cu disc machined with three equidistant ramps rests on the coarse piezo tubes, supported by sapphire balls. See Figure 2.7 for a photo of the STM unit.

Figure 2.7 A close up of the STM unit attached to the base of the cryostat.

By applying a voltage to the piezo tubes, movement in the x,y direction is achieved

by displacement of the piezos in the same direction. For z-movement all three piezos are 35 moved in a sequential order to execute a rotation of the ramp. A finer displacement in z direction is achieved by applying a voltage to the center piezo tube that holds the tip. The tip wire is a stainless steel wire with shielding. The wiring between the scanner and electrical feedthroughs is done with specialized Kapton insulated fine NiCu wires for low thermal conductivity. For mechanical vibration isolation, the STM scanner unit is suspended from the base of the cryostat with stainless steel springs. The STM is then surrounded by two concentric radiation shields (75 K and 4.2 K temperatures, respectively) to ensure effective thermal isolation (Figure 2.8). The base plate of the scanner has three magnets for eddy current damping. The entire system frame rests on four Newport vibration isolators for vibration isolation from ambient disturbances.

Figure 2.8 Schematic of cryostat, radiation shields and STM unit. Picture from [22].

The sample and sample holder geometry is designed to match with the STM scanner.

The sample, circular in shape, 8mm in diameter and 1mm high, is mounted on top of a 36 button heater using a tantalum cap. The sample holder is made of oxygen-free copper.

It has two electrical ports that line up with sample contacts for electrical connection when mounted in the STM system and align with the manipulator arm during sputtering and

annealing of the sample.

For temperature measurements, two silicon diodes are used; one at the base plate of

the scanner reads sample temperature. The other diode wired at the base of the cryostat

records the cryostat temperature that serves as a guide to refill the coolants.

2.2.3 STM Hardware and Software

STM software contains all the commands for data acquisition, ranging from imaging

to manipulation and spectroscopy. Image processing and 3D image rendering can also be

done using the same program. The STM feedback system is digitally controlled by the

program with appropriate settings selected by the operator.

The real-time electronic control system of the STM includes a PC-32 digital signal

processing (DSP) board for analog to digital and digital to analog transfer (AD and DA)

operations, and low noise high-voltage amplifiers with variable gain setting for the x, y,

and z piezo tubes, that controls the movement of the tip in all three dimensions. The

output channels of the DSP board control piezo voltages and sample bias and the input

channels register tunneling current and dI/dV signal from an external lockin amplifier. A

Femto preamplifier is used to amplify the tunneling current signal which in effect adjusts

the feedback loop to maintain a constant current during imaging and manipulation. 37 Alternatively, this loop can be disabled during dI/dV and I-z spectroscopy. The preamplifier gain can be varied over a wide range to utilize the manipulation capabilities of the system.

38 Chapter 3

Background

This chapter gives an introduction to the manipulation techniques used in atomic and

molecular manipulation followed by an overview of basic types on interactions between

atoms. The substrate and the molecule used for the experiments are introduced in the

final section.

3.1 STM Manipulation Techniques

One of the striking features of the design of this custom-built UHV-LT-STM is its

ability to manipulate atoms and molecules. Atom manipulation, a precursor for bottom- up nanotechnology, focuses on the use of atoms for construction of nanostructures with specific functionality and for exploration of properties of matter at nanometer scale [23-

26]. The pioneers of this field, Eigler and Schweizer, wrote the letters `IBM’ by precise

positioning of xenon atoms on a Ni(110) surface [3]. This technique has adapted itself

well to molecules of different sizes to exploit their potential for applications in molecular

electronics [10, 27-29]. 39 Manipulation techniques can be broadly classified into three types: lateral manipulation, vertical manipulation, and inelastic tunneling electron-induced excitations.

3.1.1 Lateral Manipulation

When the adsorbate moves in a direction parallel to the substrate, the technique is referred to as lateral manipulation. The key element of lateral manipulation is the tuning of interactions between the tip and the adsorbate by reducing the tunneling barrier between the two. This is actualized by increasing the tunneling current. The tip is thus approached closer to the adsorbate. In the constant current mode of manipulation, the current is maintained at a fixed value. The tip is then assigned a path from the adsorbate to the substrate. Based on the nature of tip-adsorbate interaction, the adsorbate moves under the influence of the tip. Once the trajectory assigned to the tip is covered, the adsorbate is relocated to a new position on the substrate. The tip is then retracted to imaging height. The subsequent image reveals the new location of the adsorbate (Figure

3.1).

Figure 3.1 Illustration of lateral manipulation. Picture from [22] 40

The adsorbate is bound to the substrate either by physisorption or chemisorption. In the case of physisorption, the adsorbate is weakly bound to the surface. If the adsorbate binds to the substrate by forming a chemical bond, then it is considered to be chemisorbed and the binding is much stronger. The depth of the physisorption potential energy well is small (~ 25meV) compared to chemical bond energies (~1 eV) [30]. It is therefore logical that a stronger interaction is necessary to move a chemisorbed species as compared to a physisorbed species. A sign of stronger interaction is that the tip needs to be in close proximity to the adsorbate, which effectively implies that manipulation is successful at a higher current or lower junction resistance. A physisorbed atom can be moved at a lower current or a higher junction resistance. This has been observed in case of lateral manipulation of different types of atoms. A threshold resistance of 5 MΩ was necessary to move Xe atoms physisorbed on Ni(110) surface, Pt atoms chemisorbed on

Pt(111) could only be manipulated with a threshold resistance of 20 kΩ [31].

An extensive study of lateral manipulation of Cu and Pb atoms and CO molecules on a Cu(211) surface was crucial in categorizing the types of lateral manipulation based on an attractive or repulsive interaction between the tip and the adsorbate [32]. Three manipulation modes, pulling, sliding and pushing modes were established. The interaction between the tip and the atom is attractive in the pulling mode. To move the atom to the next surface site, it must overcome the diffusion barrier encountered by the atom. During the manipulation process in the pulling mode, the tip first follows a part of the manipulated atom contour. By doing so, the vertical force component F┴ gradually decreases while the lateral force component F// increases. When F// overcomes the 41 diffusion barrier, the atom hops to the next surface site under the tip. This action

“alerts” the STM feed-back system and the tip retracts in order to maintain the constant

current, thus producing an abrupt increase in the tip height. Repeating this movement of atom along the manipulation path produces a saw-tooth like signal (Figure 3.2).

(a) (b) (c)

Figure 3.2 Competing forces during pulling mode of atom manipulation on the periodic surface potential.

In the pushing mode, however, the repulsive interaction between the atom and tip drives the atom movement. In this case, the atom moves to the next surface site before the tip reaches to the maximum contour height, so the tip needs to be moved forward toward the surface. This produces a rapid decrease in tip height. The atom still moves in a discontinuous manner on the surface but the manipulation signal in this case produces a reverse saw-tooth pattern of the pulling (Figure 3.3).

(a) (b)

Figure 3.3 Pushing mode of lateral manipulation. 42 When the atom follows the tip by being bound to the substrate during the entire

time of the trajectory, the movement is continuous and the atom is located under the tip.

This produces a smooth tip-height signal unlike the previous manipulation cases. This

can be understood in terms of the formation of a van der Waals trap between the tip and

the atom. If the magnitude of this trap is less than the physisorption well, the atom stays its course on the surface [33]. The atom is thus equally attracted to the tip and the surface.

This mode of manipulation is known as the sliding mode.

Lateral manipulation is generally carried out by maintaining a constant current at the tunneling junction. As the adsorbate moves under the influence of the tip, the current

changes due to varying interactions between the tip and the adsorbate. The feedback loop

in its effort to maintain a constant current adjusts the height of the tip accordingly. The

feedback loop signature is recorded as the variation of tip height versus the lateral

distance traversed by the tip. This lateral manipulation signal is characteristic to each of the three modes of manipulation, pushing, pulling and sliding, irrespective of the

adsorbate in most cases (Figure 3.4).

Figure 3.4 Characteristic lateral manipulation signals. 43 The nature of the tip movement provides information on the type of interactions between the tip and the adsorbate. The lateral distance between the consecutive jumps of the atom reveals the direction along the atomic rows on the substrate traversed by the atom. Based on the direction assigned for manipulation of a single atom, diverse signals

can be recorded which convey the intricate details of the manipulation process [34, 35].

3.1.2 Vertical Manipulation

When there is a vertical transfer of an adsorbate between the tip and the substrate, the

manipulation technique is known as vertical manipulation (Figure 3.5).

Figure 3.5 Illustration of vertical manipulation. Picture from [22].

This transfer can be bidirectional; the adsorbate can be transferred to the tip and vice

versa. The energy barrier encountered by the adsorbate for the transfer depends on the

separation between the tip and the surface. The adsorption energy of the adsorbate has to

be overcome to ensure its transfer to the tip. There are various ways to tune this energy

barrier. By applying a voltage pulse the atom can be transferred to the tip. Reversal of the

bias polarity transfers the atom back to the surface. This technique was first demonstrated 44 by Eigler by repeated transfer of a Xe atom between the tip and the Ni(110) surface

[4]. Such a process can be understood by considering the Xe in a double well potential; one well represents the bonding with the substrate and the other well represents the bonding with the tip (Figure 3.6).

Figure 3.6 Illustration of an atomic switch with the double well potential for Xe atom and vibrational energy levels. Figure from [36].

The Xe atom transfer from Ni(110) surface to the tip is marked by an inelastic electron tunneling process. The adsorbate-substrate bond is broken by gaining energy from tunneling electrons. This energy input brings about an excitation of vibrational energy levels of the adsorbate-substrate bond. The rate of atom transfer is given by

~ VB R ≈ nΓ↑ exp(− ) k B Γυ

~ Γ where VB is (n-1)ħΩ, close to the actual barrier height VB, ↑ is the excitation rate between the vibrational ground state and first excited state, and Tυ is the characteristic 45 temperature that justifies the atom transfer mechanism to be a vibrational heating

mechanism.

Other examples of vertical manipulation include the transfer of covalently-bonded Si

atoms using a combination of high voltage pulses typical to field evaporation and tip-

sample interactions [37, 38]. CO molecules can be transferred to the tip by using 2.4 V

voltage pulses. The molecules can also relocate to adjacent sites on the adsorbate [39].

Another vertical atom transfer mechanism is based on the direct tip-atom contact. By

reducing the tip-height, the distance between the double potential wells representing the

manipulated atom and the tip-apex atom reduces. At sufficiently close tip-atom distance,

this double potential well becomes a single well (Figure 3.7). Note that the vertical tip- manipulated atom distance here needs to reach the contact point, thus it is much less than the vertical tip-atom distance used in lateral manipulation. The manipulated atom is then bound to the tip. By retracting the tip back to an image height the manipulated atom,

which is now adsorbed to the tip is moved vertically away from the surface.

(a) (b) (c)

Figure 3.7 Vertical manipulation. (a) The double potential well becomes a single

potential well by reducing the tip-atom distance to a contact point (b). By retracting the tip, the manipulated atom moves vertically. 46 3.1.3 Inelastic Tunneling Electron-Induced Excitations

Inelastic tunneling electron-induced excitations can be used to manipulate atoms and

molecules as well. In particular, a rich variety of manipulations, such as rotation,

conformational changes, and dissociation can be performed on the molecules. Bond

dissociation, the breaking of a bond between two atoms in a molecule, can be carried out

by injecting low-energy tunneling electrons into the molecule by an adsorbate-induced

resonance state. The presence of an adsorbate on a substrate modifies the energy levels of

both the adsorbate and the substrate. The atomic states in the adsorbate are broadened

into a resonance state that is accessible to the electrons tunneling into the metal from the

STM tip. This is illustrated in Figure 3.8.

Figure 3.8 Illustration of the concept of an adsorbate-induced resonance state for an adsorbate on a metal substrate. Picture adapted from [30].

The tunneling electron energy can be transferred to the molecule through the adsorbate induced resonance state by means of a temporary electron attachment to the 47 molecule. The incident electrons occupy an available molecular orbital during the

lifetime of this resonance state and lead to changes in the molecule, depending on energy

provided by the electrons [40, 41]. This is done by positioning the STM tip above the molecular bond to be dissociated by applying low bias voltage pulses. The electrons can be injected from the tip or the substrate depending on the polarity of the bias (Figure 3.9).

The changes in tunneling current provide information about the event of dissociation.

This technique is known as Inelastic electron tunneling spectroscopy (IETS). The rate of dissociation can be determined from the relation

R α IN

where R is the dissociation rate, I is the tunneling current, and N is the number of

electrons involved in the IET dissociation process [6, 42].

Figure 3.9 Bond dissociation using tunneling electrons. Picture from [38].

Tunneling electrons can also provide the energy necessary for a chemical association of two species resulting in the formation of a chemical bond between them. A classic demonstration of this process was shown in the formation of Fe(CO) and Fe(CO)2

complexes [43] and in C-C bond formation in the case of two phenyl groups [8]. 48 3.2 Atomistic Interactions

The interaction between the two atoms, one at the tip-apex and the other on the

surface, is central to STM manipulation of atoms. The interaction between the tip-apex

atom and manipulated atom is exploited in a controlled manner for both lateral and

vertical manipulation processes. This part of the chapter presents a brief overview of

different types of interactions that govern the bonding between atoms and molecules. The

interactions are then discussed in the context of STM manipulation.

3.2.1 Types of Interactions

Depending on the chemical nature of atoms, the binding between two atoms can be

based on four different types of interactions [44]: van der Waals interaction, ionic interaction, covalent interaction, and metallic interaction. In case of inert gases/closed shell atoms, there is an interaction between atoms due to an induced dipole moment that is attractive in nature and characterized by an overlap of individual charge distributions.

When the interatomic separation is lower than the bonding distance between the atoms, electronic repulsion sets in as a result of the Pauli exclusion principle. Refer to Figure

3.10 for an illustration of the concepts underlying each interaction. 49

Figure 3.10 (a) Dipole formation for bonding. (b) Lennard-Jones potential. (c) Transfer of electrons for an ionic bond formation between two atoms. (d) Energy E vs. distance r plot for ionic interaction. (e) Sharing of electrons in a covalent bond. (f) Metallic bonding.

The effective interaction in a covalent bond is modeled by Lennard Jones Potential. It represents the change in the interaction between two atoms as a function of their distance, given by 50 12 6 ⎡⎛ σσ⎞ ⎛ ⎞ ⎤ Vr()= 4ε⎢⎜ ⎟ − ⎜ ⎟ ⎥ ⎣⎝ rr⎠ ⎝ ⎠ ⎦ where r is the separation between two atoms, σ and ε are parameters that can be fit to experimental data related to gas phase ionization potential. Here, the term

12 6 ⎛ 1⎞ ⎛ 1⎞ ⎜ ⎟ describes the repulsive part of the interaction while ⎜ ⎟ represents the attractive ⎝ r ⎠ ⎝ r ⎠ part of the interaction (Fig. 3.10b).

Ionic interaction arises from the electrostatic attraction of positively and negatively charged ions. Two atoms participate in the interaction, one being the electron donor and the other being the acceptor, leading to the formation of an ionic bond. The classic example of an ionic bond is a sodium chloride (NaCl) molecule (Figure 3.10c). The interaction energy between the ions can be expressed as a sum of a repulsive potential

2 −r/ρ q λe , (λ and ρ are empirical parameters) and a coulomb potential ± . A r graphical representation is drawn in Figure 3.10d.

Covalent bonds are formed by sharing of electrons between two atoms. They are known for their strength and directionality and are ubiquitous in organic compounds.

Sigma (σ) bonds and pi (π) bonds are the types of covalent bonds that play an active role in hybridization of orbitals and bond formation, and are highly directional. In the case of hydrogen molecule, the covalent bond between two hydrogen atoms is formed by an overlap of wavefunctions of the electron in each atom. The bond formation depends on the spin orientation of the electrons, as dictated by the Pauli exclusion principle. 51 A bond, specific to a hydrogen atom, is the hydrogen bond which involves bonding

between hydrogen, and oxygen, fluorine, or nitrogen. It is seen in water molecules and in proteins and nucleic acids. It is weaker than an ionic bond or a covalent bond.

In the case of metals, the valence electrons are delocalized from the respective atoms and the positive ions are immersed in a sea of electrons (Figure 3.10f). The high electrical conductivity of metals is an outcome of this uniform distribution of electrons. A metallic bond can also be classified as a non-directional and non-polar covalent bond. In the order of bond strength covalent bonds are the strongest (metallic

3.2.2 Interactions in STM Manipulation

STM provides access to surfaces of metals and semiconductors at atomic length

scales abundant with interplay of different short range forces. The force between the tip

and the sample originates from the distance-dependent interactions between them. Based

on this distance the force can be categorized as van der Waals force, resonance force or

the repulsive force [14]. Van der Waals force follows a power law and is always present

in normal STM operation. But the dominant force is the attractive force between the tip

and the sample that arises from an overlap of the tip and the sample wavefunctions, also

known as resonance force.

Lateral manipulation of atoms using an STM is a direct technique to explore this

regime of attractive interactions. For an identical tip and substrate, manipulation of atoms

of different types can provide insight about the nature of attractive interactions. 52 To move an atom adsorbed on a surface there are various energy considerations.

The adsorbed atom binds to the surface either by physisorption, eg. Xe on Pt(111) [31],

or chemisorption as is the case for Cu on Cu(111), and Ag on Ag(111) [32, 34]. During manipulation, when the interaction between the tip and the atom is strong enough, the atom overcomes the binding with the substrate and follows the tip till the end of the trajectory of the tip. The atom then localizes its position to the closest available energy minimum on the substrate. It is possible to estimate the threshold distance necessary for manipulation. In case of Ag atom manipulation on an Ag(111) surface the critical tip- atom distance is experimentally determined to be 1.3 Å between the van der Waals radii of the two atoms. This is the distance where the electronic wavefunctions between the

two atoms overlap and the attraction between the two atoms originates from temporary

chemical bonding. Since both the manipulated atom and tip-apex atom are silver atoms,

this bonding should be metallic in nature. One could speculate, based on this result, that

the extensive manipulation of halogen atoms would have a strong contribution from ionic

interactions. Thus lateral manipulation can be seen as a selective technique to probe

interactions at an atomic level.

3.3 Materials

For the projects carried out in this dissertation a single crystal Ag(111) surface was

used as the main substrate. The characteristic features of the sample are discussed below.

The molecule used for one of the projects is also introduced. 53 3.3.1 Substrate

The Ag(111) surface is composed of a hexagonal arrangement of atoms with a nearest neighbor atom distance of 2.89 Å along the close-packed row directions, i.e. [110] surface directions. The atoms used for the manipulation in this dissertation, Ag and Br, are normally adsorbed on the surface at three-fold hollow sites. Refer to Figure 3.12.

Figure 3.11 STM image showing atomic resolution of Ag(111) surface. The surface directions used for manipulation are marked. The three-fold hollow site favored by adatoms Ag and Br for adsorption is highlighted by circles.

The surface of a crystal represents a planar termination of the bulk. Electronic structure calculations reveal the existence of surface states in the projected bulk band gap of metals [30, 45]. Figure 3.12 shows the location of these states and their characteristic free-electron parabolic energy dispersion curve. Scanning tunneling spectroscopy (STS) measurements on a bare Ag(111) surface show the onset of the surface state at -65 mV with respect to EF. 54

Figure 3.12 (a) Ag(111) surface state near the Fermi level in the bulk band dispersion diagram, picture from [45], (b) dI/dV spectrum showing the onset of the surface state at

-65 mV.

These states disperse parallel to the surface and contribute to the local density of states (LDOS) at the surface. The surface state electrons bounce off the defects like step 55 edges or other adsorbates on the surface and give rise to standing waves created by

oscillations in the local density of states of Ag(111) surface (Figure 3.13). At the ground

state the distance between the two peaks of the waves, 39 Å, corresponds to half of the

Fermi wavelength of Ag(111) surface state.

Figure 3.13 Standing waves on Ag(111) surface created by scattering of surface state

electrons off a step edge and Ag atoms that act as point scatterers.

3.3.2 Molecule

For manipulation of Br atoms, instead of depositing Br atoms on the surface, Br

atoms were extracted using the technique of bond dissociation from a cobalt porphyrin molecule. The molecule 5,10,15,20-Tetrakis-(4-bromophenyl)-porphyrin-Co(II),

(C44H24Br4CoN4) has been extensively investigated in our research group [29]. It consists

of a central porphyrin ring with the magnetic cobalt atom at the center of the ring. Four

bromophenyl groups are attached to the molecule. Figure 3.14 shows the chemical

structure of the molecule. 56

Figure 3.14 Chemical structure of cobalt porphyrin molecule.

The molecules are vapor deposited on to the Ag(111) surface. STM image of the molecule shows four lobes that correspond to the phenyl groups. The central porphyrin ring is elevated from the surface by these lobes. The C-Br bond is located at the edge of the lobes. This bond is dissociated using tunneling electrons to extract the Br atom. An

STM image of the molecule is shown in Figure 3.15.

Figure 3.15 STM image of cobalt porphyrin molecule showing the central porphyrin ring lifted by the 4 lobes. Size of the molecule is 15 Å x 15 Å.

57 Chapter 4

Atom Extraction by Controlled Tip-

Cluster Interaction

This chapter focuses on the interactions between the STM tip and a bare Ag(111) surface at 4 K. An indentation of the tip on the surface coats the tip apex with Ag atoms.

When such indentations penetrate a few atomic layers on the surface, clusters of Ag atoms are created. By tuning the tip-cluster interaction single atoms can be extracted from the cluster. A modeling study carried out using interaction potentials from Embedded

Atom Method (EAM) shows that the proximity of the tip to the cluster leads to a lowering of the potential barrier between the tip-cluster system and aids the extraction mechanism.

4.1 Introduction

Scanning probe microscopy explores the interaction between a probe tip and a sample surface at different distance regimes. The parameter that controls this interaction is 58 specific to the type of probe microscopy. For example, in case of atomic force

microscopy (AFM), the deflections of a cantilever record the force between the cantilever

and the sample surface. For a scanning tunneling microscope the tunneling current

between the tip and the sample controls the interactions. The different parts of the

Lennard-Jones potential energy curve are relevant to the operation of STM and AFM

(Figure 4.1).

Figure 4.1 Illustration showing the tip-sample distance of operation of different types of

scanning probe microscopes using Lennard – Jones potential.

The interaction between an Ir tip and an Ir sample in an STM set up probed as a

function of the tip-sample distance was found to be attractive, originating from short-

range metallic adhesion forces [46]. The tip-sample interaction between a semiconductor

surface, Si(111) and a tungsten tip was used to transfer silicon atoms and clusters

between the tip and the surface by tuning electrostatic and chemical forces using voltage pulses [37]. An interesting theoretical study of single Al atom extraction from Al(111) sample surface attributed the mechanism to a chemical interaction between the tip and 59 substrate as a function of applied bias [47]. All these studies focus on a vertical tip approach towards the sample and are unique and insightful.

In the present work, a controlled tip-sample contact is indeed employed. But the semblance to previous studies ends at this point. The tip-sample contact is highly localized. The tip penetrates a few atomic layers of the sample and creates a nanometer size cluster of Ag atoms upon retraction (Figure 4.2).

Figure 4.2 Creation of a cluster of Ag atoms by tip-sample contact. Image (a) shows a bare Ag(111) surface. Image (b) shows an Ag nanocluster created after contact. Image parameters: V= 50 mV, I= 1 nA, image size 400 Å x 180 Å, and cluster size 70 Å x 24 Å.

Single atoms are then extracted from this cluster using the technique of lateral manipulation. The extraction of atoms from a metallic cluster using lateral manipulation is a unique and novel application of LM as this technique has been generally used for single atoms and molecules [8, 24, 31]. Here the tip can interact with the 3D contour of the cluster. Prior to extraction, the atom is bound to the other atoms inside the cluster. 60 The tip-cluster interaction during manipulation needs to be strong enough to break the

interatomic bonds within the cluster. Once the atom is pulled off the cluster, it moves

along the uneven terrain of the cluster following the tip till it reaches its final destination

on the terrace away from the cluster.

4.2 Experimental Details

For this experiment a bare Ag(111) sample is cleaned in situ by sputtering and

annealing. It is then cooled to 4 K. The tungsten tip is coated with Ag by gently crashing

the tip on the surface [11]. This restructures the tip apex for better imaging and the

chemical identity of the apex, Ag in this case, is established.

4.3 Atom Extraction

With a well-defined tip apex a silver cluster is deposited on the surface. A suitable voltage is applied to the z piezo tube. A controlled tip-sample contact is thereby achieved.

This results in the deposition of a cluster. The topography of the cluster is analyzed in

3-D and any protrusions on the cluster are preferred for extraction. The cluster serves as a repository of single atoms.

61 4.3.1 Lateral Manipulation for Extraction

Once the Ag cluster is imaged, the manipulation mode of STM operation is invoked.

Manipulation is carried out at constant current, which implies that the tip is maintained at

a constant height by setting a suitable current. The height of the tip is lowered from that

in the imaging mode to the parameters set in the manipulation mode. The tip is then assigned a specific path from the cluster to the surface. The increase in tip-cluster interaction leads to the breaking of the bonds within the cluster effective enough to `free’

a single atom. This atom then continues to follow the tip to the final destination on the

surface. The extracted atom can be seen in the image recorded after the extraction trial is

completed. Refer to Figure 4.3 for the STM images.

Figure 4.3 STM images of atom extraction before and after the extraction process. A ball model of the tip marks the site of extraction. Image parameters: V=30 mV, I =1 nA; dimensions of the cluster: height 6 Å, width 30 Å, and length 100 Å.

The dynamics of this atom extraction process can be inferred from the STM manipulation signal shown in Figure 4.4. To comprehend the atomistic behavior during 62 this process, every detail of the manipulation signal needs to be analyzed. The manipulation signal shows a peak at the topmost location of the cluster caused by sudden changes of vertical tip position. Over hundreds of repeated atom extraction trials confirm that such peaks can be associated with a successful atom extraction. Since the extracted atom is a constituent of the cluster, removing it from the original position involves severing the bonds with neighboring atoms within the cluster. Thus the appearance of such peaks in the manipulation signal can be caused by a sudden removal of the atom from its original location. This event leads to a re-adsorption of the atom at the next favorable site at the downward slope of the cluster. Several subsequent atom removals occur along the lateral tip movement providing more peaks in the manipulation signal. At the flat terrace, the tip height suddenly increases followed by a smooth manipulation curve. This event is associated with the positioning of the extracted atom under the tip apex. The atom then moves together with the tip as in the case of sliding mode [32]. In the sliding mode, the manipulated atom is temporarily bound to or trapped under the tip, and both the tip and the atom move together smoothly across the surface.

Figure 4.4 Lateral manipulation signal recorded during the atom extraction process.

63 The pattern of sharp peaks along the contour of the cluster followed by a relatively smooth trace is seen repeatedly in the extraction trials. Figure 4.5 shows some lateral manipulation signals along with a ball model explaining the peaks with reference to the

tip height. The tip jump height is dictated by the cluster geometry in general. Extraction

can be carried out from clusters of various sizes and shapes. No constraint is posed by the

dimensions of the cluster.

Figure 4.5 Signature of atom extraction from a cluster, ball models explain the peaks in

the signals with reference to the jump height of the tip.

A range of bias voltages from 10mV to 35 mV was used during the manipulation.

Since the tip apex itself is composed of silver atoms due to the in situ tip-preparation 64 process the possibility of atom extraction from the tip cannot be completely ruled out

[11].

4.3.2 Threshold Resistance

To get a quantitative feel for atom extraction as a function of the current and

voltage used in manipulation the value of the threshold tunneling resistance (Rth) is determined from the probability of atom extraction. The probability here is defined as the ratio between the distance traveled by the atom (Latom) and the lateral tip movement

distance (Ltip). The values of Latom/Ltip for atom extraction events are determined by

varying the tunneling current at several fixed tunneling biases.

Figure 4.6 Probability of atom extraction as a function of current at fixed bias voltage. 65 The probability plots can be interpreted as follows: consider the plot for 18 mV in

Figure 4.6, the ratio Latom/Ltip is zero below 400 nA tunneling current. This means that no

atom has been extracted below that value. Above 400 nA, however, the Latom/Ltip value is

~1 and implies that the atom can be successfully extracted. In a few cases, Latom/Ltip remains zero even at current values higher than 400 nA, indicating that not all extraction events are successful. We find a success rate of ~85% from all the trials in the experiment. All the plots shown in Figure 4.6 show a characteristic step-function with a definitive current threshold for the voltages used.

The procedure of determining threshold current is carried out for different bias voltages and the results are displayed in Figure 4.7 as a plot of threshold current versus bias voltage. Here, each data point is determined by plotting the probability plot for a specific bias voltage that gives a specific threshold current as shown in Figure 4.6. The value of threshold resistance, Rth comes out to be 47 ± 2 kΩ from the inverse of the slope of this curve.

Figure 4.7 Threshold resistance Rth to extract an atom from the cluster. 66 Tunneling resistance is a measure of both the tip-cluster distance and the tip-cluster

interaction strength. A lowering of the tunneling resistance causes a reduced tip-cluster

distance and consequently, an increased tip-cluster interaction. The Rth value can be

related to the threshold tip-cluster distance necessary to extract an atom via a tip-height versus tunneling resistance curve, shown in Figure 4.8. The threshold tip-cluster distance corresponding to Rth = 47 ± 2 kΩ is determined to be 0.6 Å. This analysis shows that a

distance of 0.6 Å or less between the edges of van der Waals radii of the tip-apex atom

and the cluster atom is necessary for a successful atom extraction; a model is shown in

Figure 4.8 for clarity.

Figure 4.8 Threshold distance corresponding to the threshold resistance for atom

extraction is obtained from the curve. A model shows the correlation of this distance with

the tip-cluster framework.

Within the bias range explored here, the threshold tunneling current varies linearly

with the bias (Figure 4.7). This linear relationship is indicative of the lack of contribution

from tunneling electron-induced excitation or local heating effects. Furthermore, since

low voltages (< 35 mV) are used in the atom extraction scheme, the contribution of 67 electric field in this process is negligible [11, 19]. Therefore, the tip-cluster interaction

should be the governing mechanism in this case.

At the length scales of the cluster, typically few tens of Å, the tip apex is more

localized with respect to the cluster geometry in general. So the tip proximity influences

the extraction process.

4.4 Modeling

The STM tip plays a crucial role in manipulation experiments. It acts as an active

element that brings about a dynamical change in the location of adatoms by modifying the energy barriers responsible for manipulation. This phenomenon is illustrated in Figure

4.9. Such a scenario has been explored in case of lateral and vertical manipulation of single atoms on metal surfaces using total energy calculations with interaction potentials from the embedded atom method [48-50].

Figure 4.9 Effect of the tip on the energy barriers at adatom sites. Picture from [50].

68 The extraction of a single atom from the cluster using the tip was exposed to a

similar theoretical treatment [51]. The changes in the potential energy landscape due to

the tip-cluster interaction were explored using embedded atom method and molecular

dynamics simulations. The prototypic system used for the total energy calculations

consists of a silver tip composed of 35 silver atoms, and a 28-atom silver cluster on

Ag(111) as shown in Figure 4.10. The Ag(111) substrate under the cluster is formed by

six atomic layers with 80 silver atoms in each layer. Initially, the entire system is allowed

to relax to its minimum energy configuration using the conjugate gradient method. Since

only small biases are used in the experiment, the electric field effect is not included in the

calculation. The total energy calculations provide the potential energy landscape of the

system while the molecular dynamics simulation introduces the motion of the atom and

the minimum atom movement path.

Figure 4.10 Model system for atom extraction along with the path taken by the atom down the slope of the cluster. Picture from [51].

The energy required to extract the atom from the cluster can be defined as the energy barrier to move the atom from its original location, A, to the next site, B, within the 69 cluster as shown in Figure 4.8. The barriers are altered by the presence of the tip as the tip modifies the energy landscape of the system drastically [50].

The lateral position of the tip apex atom and the adatom is equally significant for the extraction process in the simulations. The adatom moves towards the tip only at a lateral distance of 2.7 Å. The energy barrier for the atom to jump from site A to site B (Figure

3.9) is reduced from 0.29 eV to 0.03 eV as the tip approaches the adatom from a height of

3.23 Å to 2.43 Å (Figure 4.11).

Figure 4.11 Lowering of the tip-cluster energy barrier due to the presence of the tip.

Picture from [51].

Thus the modeling study predicts that the lowering of the energy barrier due to the tip-cluster proximity is the key factor in the extraction of a single atom from the cluster.

The results from the simulations are in qualitative agreement with experimental findings.

70 4.5 Discussion

The interaction between the STM tip and a metallic cluster was investigated. The

metallic cluster was created in situ by a controlled tip-sample contact. Single atoms were

extracted from the cluster using the technique of lateral manipulation. The ability of the

tip to break a single atom from the cluster, and direct it from the three dimensional

uneven terrain of the cluster onto the substrate marks novelty of the experiment in

comparison with lateral manipulation of atoms on a flat terrace. The variation of tip

height with the lateral distance covered during manipulation gives insight into the

atomistic mechanism of the process. The interaction induced by the proximity of the tip

to the cluster breaks the bond within the atoms in the cluster to extract a single atom. The

extracted atom continues to readsorb on different sites of the cluster while following the

tip. Once it is totally free from the cluster, the atom slides onto the flat terrace keeping its

position underneath the tip constant until it reaches the final destination on the terrace.

Quantitative parameters, like the threshold resistance and threshold tip-cluster distance

for extraction, were determined. A linear relationship between the current and voltage

used for extraction rules out the contribution of tunneling electron-induced excitations or

local heating effect to the extraction mechanism. A critical distance of 0.6 Å between the tip apex and the cluster is essential for successful atom extraction. Thus the proximity of the tip to the cluster gives rise to a series of attractive and repulsive interactions that

guide the extraction process. A modeling study of atom extraction attributes the extraction mechanism to the tip-induced changes in potential energy landscape of the tip- 71 cluster system. In conclusion, the detailed investigation of atom extraction from a cluster provides a fundamental understanding of the process and is a reliable way to

produce single atoms for atomistic constructions. 72

Chapter 5

Atomistic Constructions

The role played by the STM tip in atom manipulation on metal surfaces can be compared to a construction tool in the real world. With a high degree of precision the tip can create a metallic cluster from the substrate, extract single atoms from the cluster, and build nanostructures by positioning the atoms in predetermined locations on the surface.

The holes created during tip-surface contact to extract debris from the substrate for construction can be sealed with unused atoms or clusters. This chapter describes the construction and reconstruction schemes that demonstrate the potential of STM manipulation for nanoscale engineering of surfaces.

5.1 Construction Scheme

For a demonstration of atomic level constructions and reconstructions, the choice of substrate continues to be a single crystal Ag(111) metal surface. Surface states are present in the projected bulk band gap for noble metal (111) surfaces [52]. The electrons in these surface states form a two dimensional electron gas. The interaction of step edges or 73 defects on the surface with the surface state electrons gives rise to oscillations in the

charge density on the surface, also known as Friedel oscillations. STM images of metal

surfaces, Au(111) and Cu(111), provided the first real space image of the wave-like

interference patterns of these oscillations due to the scattering of electrons [53, 54]. The

wave patterns are isotropic and waves around the adsorbates on the surface scatter

uniformly around them. This is a reflection of the free electron-like behavior of surface

state electrons. The oscillations are characterized by a period λF/2 at the ground state,

1/2 where λF is the Fermi wavelength. These waves decay in the order of 1/x as the distance

x from the step edge decreases [53, 54].

Manipulation of atoms using an STM allows precise positioning of atoms on the

surface. The atoms can be arranged in specific geometries that dictate the scattering of

the electron waves. Such an arrangement of atoms, commonly known as a quantum

corral, gives rise to spectacular standing wave patterns in electron density caused by the

constructive or destructive interference of the electron waves. These patterns can be

interpreted as eigenstates of the structure using a particle-in-a-box model [55]. By

changing the applied bias voltage various energy eigen states of the structure can be probed.

The geometry of the corral makes a significant contribution while exploring different phenomena on metal surfaces. An elliptical quantum corral with a magnetic cobalt atom

located at one focus could project the Kondo signature at the other empty focus, creating

a quantum mirage [5]. Calculations for parabolic corrals of different geometries suggest

their role as possible quantum beacons to transmit information in quantum structures

[56]. 74 In the present construction scheme a corral of Ag atoms was constructed using Ag

atoms. Single Ag atoms were extracted from clusters created in situ by tip-sample contact. The concept of atomistic construction is described in Figure 5.1.

Figure 5.1 An illustration of the nanoscale construction scheme. A controlled tip crash

creates holes and clusters on the surface (1-2), the atoms are extracted from the cluster by

using lateral manipulation (3), the atoms are arranged in desired geometry (4), the holes

are sealed with the unused clusters (5), the tip is retracted to imaging height (6). Picture

from [57].

This scheme involves the following systematic steps. A construction site is chosen on

the surface by taking STM images. By dipping the STM-tip into the substrate, debris and

holes are formed. The debris normally is composed of substrate materials. By controlling

the tip-cluster interaction, individual atoms are extracted from the clusters. The extracted

atoms are then repositioned to the desired locations on the surface with atomic precision

to construct various nanostructures. The remaining holes are filled back with the 75 atoms/clusters to ‘reconstruct’ the surface. The tip is retracted back to the normal

imaging height.

To position the atoms precisely at predetermined locations on the substrate, the

technique of lateral manipulation is used [22]. 17 Ag atoms extracted from a Ag cluster were arranged in the form of a parabolic corral. The surface state electrons are scattered

by Ag atoms resulting in characteristic standing wave patterns at the set bias voltage.

Figure 5.2 Constant current image of a corral constructed on Ag(111) surface. Image

parameters: (a) V= 30 mV, I= 1nA, image size 240Å x 220 Å; (b) V= -30 mV, I= 1 nA;

image size 240 Å x 220 Å).

Another example of such a construction is a single parabola of 15 atoms shown in

Figure 5.3. 76

Figure 5.3 Constant current image of a parabola constructed by an assembly of 15 Ag atoms. Image parameters: (a) V= 40 mV, I= 1nA, image size 270 Å x 170 Å; (b) V= -60 mV, I= 1 nA; image size 270 Å x 170 Å.

The STM images shown in Figure 5.2 and Figure 5.3 are taken in constant current mode. So they represent an integrated local density of states from 0 mV to 30 mV above

Ef in 5.2(a), 5.2(b) shows all energy states 30 mV below Ef. Figure 5.3(a) contains energy states from 0 mV to 40 mV above Ef and 5.3(b) represents all energy states 40 mV below

Ef.

The standing wave patterns within the corral can be explained using multiple scattering theory [23, 26]. The atoms can be considered as point scatterers and the wave patterns can be calculated using a program based on multiple scattering theory [26]. The concepts involved in the calculations are explained in the following description.

The tip is modeled as a point source emanating a circular wave. The atoms are modeled as point scatterers. The electron wave from the tip experiences a phase shift δi due to the scatterers, and the amplitude of the wave decreases, represented by absorption

αi . These parameters are used in the scattering T matrix: 77

(α e2iδi −1) t = i i 2

A silver atom emits an s wave that travels to the other scatterers or to the tip. Interference of the `tip’ wave and the `atom’ wave is responsible for the intensity seen in the dI/dV maps generated by the program. Using the T matrix in the Schrodinger equation, the solution is given by:

→T ~ → −1 LDOS α Re[ aT • (1− A) • a ]

→ → where aT and a refer to vectors of dimension N , N is the number of Ag adatoms,

→ → akrTi() and akrii() are values of the vectors aT and a and represent the value of the

~ circular wave with wave vector k and tip-adatom distance ri, A is an N X N matrix , aij = ai(krij) are the off diagonal elements of the matrix and the diagonal elements are zero.

The dI/dV maps corresponding to the corral shown in Figure 5.2 were calculated for same voltages used in the constant current mode of STM imaging. These maps are shown in Figure 5.4. These maps reveal the density of states within the corral at a specific energy of 30 mV above the Fermi level, 5.4 (a) and at 30 mV below the Fermi level,

5.4(b). Hence no identical match between the STM images and calculated dI/dV map is expected here. 78

Figure 5.4 dI/dV maps at (a) 30 mV, (b) -30 mV generated using scattering theory.

5.2 Reconstruction Scheme

The area on the surface perturbed by the creation of the cluster and subsequent

atomistic constructions can be `reconstructed’ using the remnants of the cluster or atoms,

thereby demonstrating a remarkable nanoscale analog of a real world construction scheme. Using lateral manipulation procedure the tip is approached close enough to the

cluster to ensure an interaction strong enough to direct the cluster towards the hole or a

crater. The tip is then assigned a path that terminates at the center of the hole to be filled.

This is repeated in steps till the hole is sealed and the surface `reconstruction’ leaves no

mark of the indentations executed at the site.

The craters or holes are the defects on the surface and usually have a stronger binding

to the adsorbate than a normal terrace. When the cluster reaches at the periphery of the

crater during the manipulation process, it is adsorbed by the crater. The sequence of

images A-F in Figure 5.5 shows the step-by-step filling of the crater using the debris,

which originated from the same area during the tip-crash. After completing the process, 79 the final area has no recognizable imprint of the crater [57]. This renders the surface

area defect free for further measurements if required.

Figure 5.5 Reconstruction of a surface at an atomic level by filling the holes on the

surface using atoms and clusters. Figure from [57].

5.3 Discussion

The surface state electrons of noble metal surfaces provide an ideal platform to study

the scattering mechanisms on the surface perpetrated by the charge density of these electrons. Scattering off step edges and defects gives information about the oscillatory

nature of the charge density fluctuations. The scattering is isotropic in nature which is a 80 characteristic of the surface being probed. Lateral manipulation of atoms with an STM takes this study further by creating artificial nanostructures (quantum corrals) using single atoms. Characteristic standing wave patterns are generated within these structures due to the constructive and destructive interference of the electrons waves. The constituent atoms of the corrals act as point scatterers with equal participation from the tip waves. Multiple scattering theory based on these concepts can generate wave patterns within these structures.

The atoms and clusters created in situ for the nanoscale constructions can leave craters on the surface as a result of trials that involve tip-surface contact. These craters can be filled after the construction using unused atoms or clusters and the surface imperfections can be erased for aesthetics and measurements demanding a defect-free area.

In conclusion, manipulation techniques carried out using a UHV-LT-STM bring out the versatility of STM and broaden the scope of exploration of metal surfaces.

81

Chapter 6

Atom Selective Force Measurement

This chapter takes the study of single atom manipulation to a quantitative force

measurement. Two types of atoms, a metal atom, Ag and a halogen atom, Br are chosen

for this experiment. Extensive lateral manipulation measurements are carried out to

determine the minimum threshold distance between the Ag-Ag and Ag-Br necessary for manipulation. From the lateral manipulation signals the specific angle at which the atom

moves is measured. The interaction energy between these atoms is obtained from density

functional theory calculations. A combination of these results yields a numerical value of

threshold lateral force required to move these atoms. The experiment is described in

detail followed by a discussion of the results.

6.1 Introduction

Lateral manipulation (LM) of the atoms controls the interaction between the tip and

the atom to bring about a change in the spatial location of the atom. Atoms adopt

different modes of manipulation in their attempt to balance the competing interactions

presented by the proximity of the tip and the substrate corrugation [32]. The presence of 82 the tip modifies the potential energy landscape of the surface in such a way that the atom overcomes the barriers presented by the surface and moves on to the next favorable site [49]. Intricate pathways traced by atoms when manipulated at different directions on an fcc(111) surface prove to be insightful in understanding the mechanisms involved in manipulation [34]. A comprehensive investigation of LM for metal atoms like Ag and Au reveals a linear relationship between threshold tunneling current and tunneling voltage for small values of bias [19, 34]. In the present work, a metal atom, Ag and a halogen atom Br, is each subjected to several LM trials to understand how the chemical nature of the atom is reflected under identical manipulation conditions, with same tip and substrate.

The lateral force necessary for manipulation is then determined.

6.2 Force Measurement Strategy

Lateral manipulation of an atom is recorded as the variation of tip height with the lateral distance traversed by the atom on the surface when the manipulation is carried out with a closed feedback loop [32, 34]. Under competing influences of the substrate and the tip, the atom jumps under the influence of the tip and follows the trajectory assigned to the tip. The contour of the first jump of the atom makes a characteristic angle φ with the surface (Figure 6.1).

83

Figure 6.1 Atomistic force measurement strategy. An STM tip-height signal

(manipulation signal) shows single atomic site hopping of the atom on Ag(111) surface when the atom is manipulated along a close-packed surface direction. The drawings indicate the changes of vertical and lateral force components during manipulation.

Initially only a vertical force component exists but when the tip traces the atom contour, the lateral force component increases. When the lateral force component overcomes the surface force, the atom hops to the next surface site. Here, ‘φ’ is the force vector angle and ‘r’ is the tip-atom distance.

84 The cosine of this angle is a crucial factor for determination of lateral force needed

for manipulation. The numerical value of the lateral force is obtained by using equation

(1) and the total force is given by equation (2):

dU (r) dU (r) F = × cosϕ F = Lat dr ------(1), Tot dr ------(2) where U(r) is the interaction energy between the atoms

r is the separation between the atoms

φ is the angle between the tip and the atom

U(r) is obtained from density functional theory (DFT) calculations. The distance between the atoms is obtained from threshold resistance measurements of Ag and Br atoms.

Extensive lateral manipulation trials (925 trials for Ag, 1150 trials for Br) are carried out to determine the threshold resistance. The angle φ is measured from LM signals. Using equation (1) and (2) a numerical value of the lateral force and total force is calculated respectively.

6.3 Experimental Details

The present experiment involves the study of Br and Ag atoms on an Ag(111)

surface. Distinction between two different types of adsorbed atoms in an STM image is

difficult without the assistance of an additional investigative technique. Cu and Co atoms

on Cu(111) could be distinguished by detecting Kondo signal from Co atom using 85 tunnelling spectroscopy. Single Ag atoms have been imaged on Ag(111) surface at 4K and they appear as protrusions on the surface [20, 26, 34]. There is no known characteristic of a Br atom to identify and distinguish it from an Ag atom. Also single Br atoms have not been investigated on Ag(111) to date. Hence codeposition of these atoms would present itself with the complexity of identification of these atoms from the topography in the STM image. To circumvent this issue these atoms were extracted from obtained by bond dissociation of a cobalt porphyrin molecule.

The experiment was performed using our homebuilt ultrahigh vacuum scanning tunneling microscope. A single crystal Ag(111) sample was cleaned by several cycles of sputtering and annealing. This was followed by vapor deposition of cobalt porphyrin molecules, (5,10,15,20-Tetrakis-(4-bromophenyl)-porphyrin-Co(II)), referred to as

CoTBrPP henceforth. The sample was then transferred to the STM chamber and cooled to 4K for the manipulation experiment.

In an STM experiment it is important to have a reliable tip apex for unambiguous data and reproducibility of results. Standard methods of tip preparation involve electrochemical etching but once the tip is in imaging environment the control over its apex structure diminishes rapidly. In our experimental setup we can modify the tip apex by tip-sample indentations prior to the experiment and even in the midst of it [11]. This coats the tip apex with silver atoms and improves the resolution of the image as shown in

Figure 6.2. 86

Figure 6.2 A series of images before tip crash (a) and after tip crash (b) showing a sharper image resolution after the tip crash. The crash site is marked.

Cobalt porphyrin molecules selfassemble on Ag(111) in various patterns forming domains with characteristic ordering on the terrace and along the step edges as well. They

can also be seen in random clusters (Figure 6.3). They are chemisorbed on the surface.

Figure 6.3 CoTBrPP molecules on Ag(111) surface seen in domains (a) and in a cluster arrangement (b).

87 6.4 Br Atoms

Br atoms are extracted from CoTBrPP molecules. Lateral manipulation of Br atoms is

carried out on the Ag(111) surface along the closepacked row direction [110] for

different values of manipulation voltage and current. The threshold resistance to move a

Br atom is obtained from this data. The distance between the tip and Br atom

corresponding to this resistance is read from Iz spectroscopy curve. A height correction is made to this distance r. Then by using the Ag-Br interaction energy curve, the energy

U(r) corresponding to r is traced. The angle φ is determined from a LM curve. Using all these values in equation (1) a numerical value of force is obtained. All these steps are described in detail in the following sections.

6.4.1 Extraction of Br Atoms

The individual CoTBrPP molecule is seen as four lobes. In accordance with the

chemical structure of the molecule, the 4 lobes correspond to the phenyl groups that are

attached to the central porphyrin ring. The region of interest in this molecule is the C-Br

bond which is a constituent of the phenyl lobes. So in principle each molecule can

provide four Br atoms (Figure 6.4). 88

Figure 6.4 STM image of CoTBPP single molecule taken at V=1000 mV, I = 1nA (Image

size 38 Å x 28 Å) along with a ball model based on the chemical structure of the

molecule.

The Br atom can be thereby obtained by scission of this bond. Dissociation of

molecules using tunneling electrons is a powerful technique and can be carried out with a great degree of precision [6, 58]. Br atom is attached to the phenyl ring. The bonds in this

region of interest include C-C, C-H and C-Br. The C-Br bond has the lowest strength out

of all 3 bonds [58]. To estimate the bond dissociation energy for the C-Br bond dissociation was performed by positioning the tip above one of the lobe of the molecule.

The voltage was ramped from -1.5 V to 2 V. The corresponding tunnelling current 89 showed an abrupt drop at 1.8 V. Thus it was established that the C-Br bond

dissociation needs a minimum energy of 1.8V (Figure 6.5).

Figure 6.5 Dissociation of phenyl in CoTBrPP molecule by I-V spectroscopy showing an

abrupt drop in the current the breaking of the C-Br bond.

To extract the Br atom, the C-Br bond was dissociated using a voltage pulse of 2 V.

The variation of tunnelling current with time showed the characteristic change in the current. The images of CoTBPP before and after dissociation show the change in the

molecule at the dissociation site along with the extracted bromine atom. The images and the trace showing a drop in the tunnelling current is shown in Figure 6.6. 90

Figure 6.6 Dissociation of CoTBPP molecules on Ag(111). The dissociated Br atom is seen in the image. Image parameters are: V= 1000mV, I= 1.2nA, size 52 Ǻ x 32 Ǻ.

6.4.2 Threshold Resistance Measurement of Br Atoms

The Br atom obtained from bond dissociation is used for extensive lateral

manipulation measurements. The atom is moved along the closepacked row direction

[110] of Ag(111) surface (Figure 6.7). 91

Figure 6.7 A series of images showing dissociation of Br atom and its subsequent lateral

manipulation. Image parameters: V=1000 mV, I = 0.44nA, size 90 Å x 40 Å.

To get the current-voltage relationship during manipulation, a value of threshold

resistance Rth is determined from the probability of Br atom manipulation. The probability of Br atom manipulation is obtained from the ratio between the distance

traveled by the atom (Latom) and the lateral tip movement distance (Ltip). The values of

Latom/Ltip are plotted as a function of tunneling current. The plots show a characteristic

step function form. There is a specific value of current for each value of voltage marking

the onset of manipulation. This is repeated for different values of manipulation voltage.

92 A set of the probability plots for manipulation at positive voltage are shown in

Figure 6.8 plots for manipulation at negative voltage are shown in Figure 6.9.

Figure 6.8 Probability plots for Br atom manipulation at positive voltages. 93

Figure 6.9 Probability plots for Br atom manipulation at negative voltages.

The threshold current values recorded at each bias voltage are plotted as a function of

the bias voltage. The plot is linear and an inverse of the slope gives the value of threshold

resistance. This value is 499±11 kΩ. The linear nature of the plot implies an ohmic

relationship between the current and voltage during manipulation (Figure 6.10). 94

Figure 6.10 Linear relationship between current and voltage during Br atom

manipulation.

6.4.3 Lateral Manipulation for Angle Measurement

Lateral manipulation signals for Br atom manipulation are used to obtain the value of

the angle φ. Figure 6.11 shows the signals at positive voltage; Figure 6.12 shows the signals at negative voltage. 95

Figure 6.11 LM signals during manipulation at positive voltage.

Figure 6.12 LM signals during manipulation at negative voltage. 96 6.4.4 Height Correction for Br Atoms

The junction resistance in an STM experiment is a measure of the distance between the tip and the sample. The calibration is done by Iz spectroscopy as explained in Chapter

2. Based on this distance calibration a threshold resistance of 499 kΩ corresponds to a distance of 1.7 Å. However as the tip-sample distance calibration is done for Ag atoms,

the difference in the height of Br atoms a need to be accounted for as the tip approaches

Br atoms. The difference in height of Ag and Br atoms from STM images is 0.6 Å. This

implies that the tip needs to approach the Br atom at a closer distance to get the set

tunneling current. The same scenario prevails for lateral manipulation in a constant

current mode. Hence the real distance for manipulation is corrected to 1.27 Å (Figure

6.13).

Figure 6.13 Height correction scheme for Br atoms.

97 6.4.5 Numerical Value of Force

The potential energy curve for Ag-Br is calculated using GAMESS package [64]. For

the present calculation B3LYP hybrid density functional theory was used with SBKJC basis set which uses pseudopotentials for core level electrons [59]. A 4-atom-ag-cluster was used to represent the Ag(111) surface with a Br atom on the three-fold hollow site.

The total energy of the system was calculated as a function of interatomic seperation

(Figure 6.14).

Figure 6.14 Interaction energy between Ag-Br atoms as a function of the separation

between the atoms is shown in (a). The plot is rescaled to Ag-Br bond energy and to the

distance between outer Van der Waal radii of the two atoms, shown in (b).

The numerical value of the lateral force is obtained using equation (1) from Section 6.2

dU (r) F = ×cosϕ Lat dr ------(1) 98 The total force is given by

dU (r) F = Tot dr ------(2)

The values of r are read from the R-z calibration curve, Figure 4.8. The values of U(r) corresponding to r are read from the rescaled energy curve, Figure 6.14 (b). For different

LM curves, the angle φ is determined. The total force is calculated using equation (2).

The angle φ is plotted as a function of the total force as shown in Figure 6.15.

Figure 6.15 Measurement of angle φ as a function of total force between the tip and the

Br atom.

The angle φ is almost constant for the small tip-atom distance variation range, mean

φ=84º, cos φ =0.1045. The lateral force Flat is obtained using equation (1), the average 99 lateral force amounts to 50 pN for Br atoms. The total force Ftot is obtained using

equation (2), the average value is 478 pN.

Refer to Table 1 and Table 2 for the values of U(r), r, Ftot and Flat. The description of the

tables is as follows:

R kΩ is the threshold resistance measured from the experiment.

r Å is the distance between the outer Van der Waal radii of the atoms Ag and Br.

ΔE eV is the energy in eV corresponding to r obtained from the rescaled interaction energy curve in Figure 6.14(b).

U(r) = - ΔE

Ftot = U(r)/r in pN

Flat = Ftot cos φ, mean φ=84º, cos φ =0.1045

Table 1. Values of energy and distance from the Ag-Br interaction energy curve.

R kΩ r Ǻ ΔE eV U(r) eV 510 1.274 -0.3758 0.3758 499 1.265 -0.3779 0.3779 488 1.258 -0.3805 0.3805

Table 2. Values of total force and lateral force calculated using equation (1) and equation

(2) and values from Table 1.

R kΩ Ftotal =[U(r)/r] pN Flat = [Ftot cos φ] pN 510 472 49.3 499 478 49.9 488 484 50.6

Thus, to conclude, the total force between the Ag atom at the tip and Br atom under

manipulation is 478 pN. To overcome the surface forces in order to move the Br atom

from one atomic site to the other, a lateral force of 50 pN is necessary. Manipulation 100 carried out at negative or positive bias does not influence the force required for

manipulation. This is also reflected in the threshold resistance measurement results, the

plot is linear for both positive and negative manipulation voltages.

6.5 Ag Atoms

The study of Ag atoms on Ag(111) surface follows the same steps as those for Br atoms. The following sections describe the Ag atom manipulation in detail.

6.5.1 Extraction of Ag Atoms

The technique for extraction of Ag atoms is similar to the one described in Chapter 4.

A cluster of Ag atoms is created from the substrate by a controlled tip-surface indentation

[51]. Then the interaction between the tip and the cluster is increased using lateral

manipulation technique. The tip is moved along a protrusion on the cluster to the

substrate. The strong tip-cluster interaction causes local bond breaking to remove a single

atom from the cluster. The extracted atom is seen in the next image (Figure 6.16). 101

Figure 6.16 Extraction of Ag atoms from an Ag cluster. (Image parameters: V= 50 mV,

I= 1 nA, size 90 Å x 30 Å).

6.5.2 Threshold Resistance Measurements for Ag Atoms

Manipulation of Ag atoms is carried out at positive and negative bias voltages. For each value of voltage the threshold current at which the atom moves is determined. The probability of atom manipulation defined by the ratio Latom/Ltip is plotted versus the current. Figure 6.17 shows some plots for manipulation at positive voltages and Figure

6.18 shows some plots for manipulation at negative voltages.

102

Figure 6.17 Ag atom manipulation at positive voltages.

103

Figure 6.18 Ag atom manipulation at negative voltages.

The threshold current values for each manipulation voltage are plotted as a function of the applied voltage (Figure 6.19). 104

Figure 6.19 Linear relationship between current and voltage during Ag atom manipulation.

The threshold resistance is obtained from the inverse of the slope of this plot. The value is 255±3 kΩ. This corresponds to a distance of 1.3 Å from Iz spectroscopy curve.

6.5.3 Lateral Manipulation for Angle Measurement

The angle for lateral manipulation is read from the lateral manipulation curves. Figure

6.20 shows two curves used to determine the corresponding angle. 105

Figure 6.20 LM curves to measure the angle made by the tip and the Ag atom during lateral manipulation.

6.5.4 Numerical Value of Force

The potential energy curve for Ag-Ag is calculated using GAMESS package [64]. A

4-atom-ag-cluster was used to represent the Ag(111) surface with an Ag atom on the three-fold hollow site. The total energy of the system was calculated as a function of interatomic seperation (Figure 6.21). 106

Figure 6.21 Interaction energy between Ag-Ag atoms as a function of the separation between the atoms (a). The plot is rescaled to Ag-Ag bond energy and to the distance between outer Van der Waal radii of the two atoms, shown in (b).

The numerical value of force is obtained using equation (1) and equation (2) as discussed in Section 6.2

dU (r) F = ×cosϕ Lat dr ------(1)

The total force is given by

dU (r) F = Tot dr ------(2)

The values of r are read from the R-z calibration curve, Figure 4.8. The values of U(r) corresponding to r are read from the rescaled energy curve, Figure 6.21 (b). For different

LM curves, the angle φ is determined. The total force is calculated using equation (2).

The angle φ is plotted as a function of the total force as shown in Figure 6.22.

107

Figure 6.22 Measurement of angle φ as a function of total force between the tip and the

Ag atom.

Refer to Table 3 and Table 4 for the values of U(r), r Ftot and Flat . The description of the

tables is as follows:

R kΩ is the threshold resistance measured from the experiment

r Å is the distance between the outer Van der Waal radii of the atoms Ag and Ag.

ΔE eV is the energy in eV corresponding to r obtained from the rescaled interaction energy curve.

U(r) = - ΔE

Ftot = U(r)/r in pN

Flat = Ftot cos φ, mean φ=80.5º, cos φ =0.1650

108 Table 3. Values of energy and distance from the Ag-Ag interaction energy curve.

R kΩ r Ǻ ΔE eV U(r) eV

258 1.298 -0.2661 0.2661 256 1.294 -0.2725 0.2725 253 1.290 -0.2797 0.2797

Table 4. Values of total force and lateral force calculated using equation (1) and equation

(2) and values from Table 3.

R kΩ Ftotal =U(r)/r pN Flat = [Ftot cos φ] pN 258 328 54.1 256 337 55.6 253 347 57.2

From Table 4, a lateral force of 55 pN is necessary to move an Ag atom on an

Ag(111) surface. The interaction between Ag-Ag is metallic in nature [44]. It is

delocalized and weaker than an ionic or covalent bond. In comparison with the total force required for Br atom manipulation, Ag atoms need less force for manipulation on an

Ag(111) substrate.

6.6 Discussion

Interactions between two types of atoms, Ag and Br, on an Ag(111) surface were

investigated using the homebuilt UHV-LT-STM. The Ag and Br atoms were extracted

from two different sources in situ. Lateral manipulation trials of these atoms were carried

out for different values of applied bias voltage. The threshold resistance and the 109 necessary for manipulation were determined. The minimum lateral force required for manipulation on Ag(111) surface was calculated. Table 5 summarizes these results.

Table 5. Values of threshold lateral force, total force and threshold resistance for lateral manipulation of Ag and Br atoms.

Parameter Ag atoms Br atoms

Flat pN 55 50

Ftot pN 337 478

Rth kΩ 255 499

The interaction between Ag and Br is ionic in nature and more localized [60-63].

Hence a stronger lateral force is essential to overcome the barrier posed by this interaction. The metallic Ag-Ag interaction is weaker in comparison and delocalized. The

Ag atom can be manipulated with a smaller force. The most important finding of this study is that the interaction between the tip and atom carries an imprint of the inherent bonding nature of the atom.

The structure of the tip apex can influence the manipulation of single atoms. Also the manipulation trials are repeated for different tip shapes and for a large number of Br and

Ag atoms to minimize the error induced by this entity.

Although force and interactions between the tip and the sample have been investigated using STM, our results present the first systematic enquiry of these short range forces scaling down to a single atom. The threshold lateral force necessary to move the atom is quantitatively estimated. This study can be extended to a combination of 110 different types of atoms thereby paving the way for probing interactions at an atomic level. It boosts the potential of single atom manipulation to a new frontier where tuning and control of interactions for applications using the bottom up approach of nanotechnology can be developed further.

111

Chapter 7

Conclusions and Outlook

In this dissertation we have explored two diverse systems in the purview of atomic

and molecular manipulation techniques. These systems, a cluster of metal atoms and

single atoms, were subjected to a comprehensive investigation by using STM tip induced

manipulations. The entire study was carried out on a metallic silver substrate using our

homebuilt ultrahigh vacuum low temperature scanning tunneling microscope.

For an inquiry into tip-cluster interactions, a cluster of silver atoms was created by a

controlled tip-sample contact. The technique of lateral manipulation was used to extract

single silver atoms from the cluster. The proximity of the tip to the cluster was changed

by tuning the manipulation parameters. The lateral manipulation signals provided an

insight into the dynamics of the event. The relationship between the current and voltage

parameters used for extraction was found to be linear. The threshold distance necessary to

pull an atom out from the cluster was determined. This distance was found to be much

smaller than the threshold distance required to move a single atom on the surface. This

proves that atom extraction from the cluster demands a much stronger interaction than

that required for the relocation of an atom on the surface. The sole mechanism guiding

the extraction was the tip-cluster distance. The geometrical size of the cluster did not pose any constraints for the extraction process. A modeling study was carried out for 112 such a tip-cluster system. The presence of the tip was responsible for a modification in the potential energy surface of the cluster. This led to a lowering of the energy barrier between the tip-cluster system that facilitated the extraction of the atom from the cluster.

The results from the modeling study are thus in agreement with the experimental results.

This study of atom extraction from a metallic cluster presents a novel application of the lateral manipulation technique. The precise control over the process at the nanoscale can be seen as one of the ways to produce single atoms for a manipulation experiment.

We have used lateral manipulation to explore the interactions between the STM tip and two atoms of different chemical identity adsorbed on a metal substrate. With a silver atom at the tip apex, a silver atom and a bromine atom adsorbed on Ag(111) surface were investigated. The silver atom was extracted from a cluster of silver atoms. The bromine atom was dissociated from a cobalt porphyrin molecule using the vertical manipulation technique. Lateral manipulation of these atoms was carried out for different values of voltage and current. The threshold distance necessary to move these atoms was determined from the manipulation trials. The angle marking the first jump of the atom in response to the tip was measured from the lateral manipulation curves. The interaction energy curves for Ag-Ag and Ag-Br atoms were calculated using density functional theory. The interaction energy corresponding to the threshold manipulation distance for

Ag and Br was measured from these curves. A numerical value of force was obtained using a combination of all these parameters. This force represents the threshold force necessary to move a silver atom and a bromine atom on the surface. The values of the force obtained carry a signature of the intrinsic bonding nature of the atom. The interaction between the tip apex silver atom and the silver atom on the surface is metallic 113 in nature. The interaction between the silver atom at the tip apex and the bromine atom is a combination of ionic and metallic character. We find that a stronger force is necessary to move the bromine atom as compared to the silver atom. The interaction of the atoms with the substrate plays a significant role in directing their response to the atom at the tip apex. The choice of same substrate and same tip for manipulation of both atoms is crucial to sense the details of the inherent nature of the atom. Our study presents the first quantitative force measurement at an atomic level the STM lateral manipulation on a metal surface.

We have also exploited the potential of the STM manipulation techniques to construct nanostructures on the surface. Single atoms were assembled on predetermined locations on the surface using lateral manipulation; the source of atoms was a cluster of silver atoms extracted from the native substrate. The holes or imperfections on the surface created during the construction were sealed by using these atoms. This demonstrates the role of the STM tip as a construction tool at the nanoscale.

In future the strategy of exploring interactions at the atomic level demonstrated in this work could be extended to magnetic systems. For example, using a magnetic atom at the tip apex for the manipulation of a magnetic atom on a metallic substrate, the spin-spin interaction between these atoms could be probed at a single atom level. This would further the current understanding of magnetic interactions on a metal surface. Another interesting application would be to determine the force necessary to manipulate molecules on a metallic substrate. New experiments are being initiated in this direction.

Lateral manipulation of molecules induces conformational changes in the molecule [28].

The ability of a molecule to switch between the conformations in response to STM tip 114 induced manipulation provides a new research direction to explore the functional aspect of molecules from the viewpoint of device applications [10]. The technique of force measurement could be applied for various conformations of the molecule.

Depending on the adsorption of the molecule on the substrate and the related conformations, a suitable manipulation technique could be selected to change the conformation of the molecule. The threshold force necessary for a conformational change could provide relevant information about interaction between the molecule-substrate system. 115

Bibliography

1. Tersoff J. and Hamann D.R., Theory of the scanning tunneling microscope. Phys.

Rev. B. 31, 805 – 813 (1985).

2. Feenstra R.M., Stroscio J.A., and Fein A.P., Tunneling spectroscopy of the

Si(111)2 x 1 surface. Surf. Sci. 181, 295-306 (1987).

3. Eigler D.M. and Schweizer E.K., Positioning single atoms with a scanning

tunnelling microscope. Nature 344, 524-526 (1990).

4. Eigler D.M., Lutz C.P., and Rudge W.E., An atomic switch realized with the

scanning tunnelling microscope. Nature 352, 600-603 (1991).

5. Manoharan H.C., Lutz C.P., and Eigler D.M., Quantum mirages formed by

coherent projection of electronic structure. Nature 403, 512-515 (2000).

6. Stipe B.C., et al., Single-Molecule Dissociation by Tunneling Electrons. Phys.

Rev. Lett. 78, 4410 – 4413 (1997).

7. Stipe B.C., Rezaei M.A., and Ho W., Single-Molecule Vibrational Spectroscopy

and Microscopy. Science 280, 1732-1735 (1998).

8. Hla S.-W., et al., Inducing All Steps of a Chemical Reaction with the Scanning

Tunneling Microscope Tip: Towards Single Molecule Engineering. Phys. Rev.

Lett. 85, 2777 – 2780 (2000).

9. Moresco F., et al., Recording Intramolecular Mechanics during the Manipulation

of a Large Molecule. Phys. Rev. Lett. 87, 088302 (2001). 116 10. Iancu V. and Hla S.-W., Realization of a four-step molecular switch in

scanning tunneling microscope manipulation of single chlorophyll-a molecules

PNAS 103, 13718-13721 (2006)

11. Hla S.-W., et al., Single-Atom Extraction by Scanning Tunneling Microscope Tip

Crash and Nanoscale Surface Engineering. Nano Lett. 4, 1997-2001 (2004)

12. Hansma P.K. and Tersoff J. Scanning tunneling microscopy. J. Appl. Phys 61,

R1-R24 (1987).

13. Lang N.D., Spectroscopy of single atoms in the scanning tunneling microscope.

Phys. Rev.B, 34, 5947 – 5950 (1986).

14. Chen C.J., Introduction to Scanning Tunneling Microscopy., New York, Oxford

University Press. 412 (1993).

15. Feenstra R.M., Scanning tunneling spectroscopy. Surf. Sci. 299-300, 965-979.

(1994).

16. Li J., Schneider W.-D., and Berndt R., Local density of states from spectroscopic

scanning-tunneling-microscope images: Ag(111). Phys. Rev. B. 56, 7656 - 7659.

(1997.

17. Hipps U.M., Inelastic electron tunneling: an alternative molecular spectroscopy.

J. Phys. Chem 97, 30 (1993).

18. Gimzewski J.K. and Moller R., Transition from the tunneling regime to point

contact studied using scanning tunneling microscopy. Phys. Rev. B. 36, 1284 –

1287 (1987)

19. Braun K.-F., et al. Force, Current and Field Effects in Single Atom Manipulation.

AIP Conference Proceedings 696, 109 (2003). 117 20. Limot L., et al., Atom Transfer and Single-Adatom Contacts. Phys. Rev. Lett.,

94, 26102 (2005).

21. Besocke K., An easily operable scanning tunneling microscope. Surf. Sci. 181,

145-153, (1987).

22. Hla S.-W., Scanning tunneling microscopy single atom/molecule manipulation

and its application to nanoscience and technology. J Vac. Sci & Tech B 23, 1351-

1360 (2005).

23. Heller E.J., et al., Scattering and absorption of surface electron waves in quantum

corrals. Nature 369, 464-466 (1994).

24. Stroscio J.A. and Celotta R.J., Controlling the Dynamics of a Single Atom in

Lateral Atom Manipulation. Science 306, 242-247 (2004).

25. Stroscio J.A., et al., Electronically Induced Atom Motion in Engineered CoCun

Nanostructures. Science 313, 948-951 (2006).

26. Braun K.-F. and Rieder K.-H., Engineering Electronic Lifetimes in Artificial

Atomic Structures. Phys. Rev. Lett. 88, 096801 (2002).

27. Braun K.-F., Hla S, W, Probing the conformation of physisorbed molecules at the

atomic scale using STM manipulation. Nano Lett. 5, 73-76 (2005).

28. Hla S.-W., et al., Controlled Low-Temperature Molecular Manipulation of

Sexiphenyl Molecules on Ag(111) Using Scanning Tunneling Microscopy. Phys.

Rev. Lett. 93, 208302 (2004).

29. Iancu V., Deshpande A., and Hla S.-W., Manipulating Kondo Temperature via

Single Molecule Switching. Nano Lett. 6, 820-823 (2006).

30. Zangwill A., Physics at surfaces. Cambridge University Press. (1988). 118 31. Stroscio J.A. and Eigler D.M., Atomic and Molecular Manipulation with the

Scanning Tunneling Microscope. Science 254, 1319-1326 (1991).

32. Bartels L., Meyer G., and Rieder K.-H., Basic Steps of Lateral Manipulation of

Single Atoms and Diatomic Clusters with a Scanning Tunneling Microscope Tip.

Phys. Rev. Lett. 79, 697 – 700 (1997).

33. Bouju X., et al., van der Waals atomic trap in a scanning-tunneling-microscope

junction:Tip shape, dynamical effects, and tunnel current signatures. Phys. Rev.

B. 55, 16498 – 16498 (1997).

34. Hla S.-W., Braun K.-F., and Rieder K.-H., Single-atom manipulation mechanisms

during a quantum corral construction. Phys. Rev. B. 67, 201402. (2003).

35. Kuhnle A., et al., Understanding atom movement during lateral manipulation

with the STM tip using a simple simulation method. Surf. Sci. 499, 15-23 (2002).

36. Gao S., Persson M., and Lundqvist B.I., Theory of atom transfer with a scanning

tunneling microscope. Phys. Rev. B. 55, 4825 – 4836 (1997).

37. Lyo I.-W. and Avouris P., Field-Induced Nanometer- to Atomic-Scale

Manipulation of Silicon Surfaces with the STM . Science 253, 173-176 (1991)

38. Hla S.-W. and Rieder K.-H., STM control of chemical reactions: Single-Molecule

Synthesis. Annu. Rev. Phys. Chem. 54, 307-330 (2003).

39. Bartels L., et al., Dynamics of Electron-Induced Manipulation of Individual CO

Molecules on Cu(111). Phys. Rev. Lett. 80, 2004 – 2007 (1998).

40. Gadzuk J., Resonance-assisted, hot-electron-induced desorption. Surf. Sci. 342,

345-358 (1995). 119 41. Walkup R.E., Newns D.M. and Avouris P., Role of multiple inelastic

transitions in atom transfer with the scanning tunneling microscope. Phys. Rev. B

48, 1858-1861 (1993).

42. Sloan P.A. and Palmer R.E., Two-electron dissociation of single molecules by

atomic manipulation at room temperature. Nature 434, 367-371 (2005).

43. Lee H.J. and Ho W., Single-Bond Formation and Characterization with a

Scanning Tunneling Microscope Science 286, 1719-1722 (1999).

44. Kittel C., Introduction to Solid state physics. Wiley Eastern (1976).

45. Hsieh T.C., Miller T., and Chiang T.-C., Probing the Wave Function of a Surface

State in Ag(111): A New Approach. Phys. Rev. Lett. 55, 2483 – 2486 (1985).

46. Durig U., Zuger O., and Pohl D.W., Observation of metallic adhesion using the

scanning tunneling microscope. Phys. Rev. Lett. 65, 349 – 352 (1990).

47. Wang FH., Yang J.L., and Li J.M., Theoretical study of single-atom extraction

using STM. Phys. Rev. B. 59, 16053 – 16060 (1999).

48. Daw M.S. and Baskes M.I., Embedded-atom method: Derivation and application

to impurities, surfaces, and other defects in metals. Phys. Rev. B 29, 6443 - 6453

(198).

49. Kurpick U. and Rahman T.S., Tip Induced Motion of Adatoms on Metal Surfaces.

Phys. Rev. Lett. 83, 2765 – 2768 (1999).

50. Ghosh C, Kara A, and Rahman T, Theoretical aspects of vertical and lateral

manipulation. Surf. Sci. 502-503, 519-526 (2002).

51. Deshpande A, et al., Atom-by-atom extraction using scanning tunneling

microscope tip-cluster interaction. Phys.Rev.Lett. 98, 028304 (2007). 120 52. Kevan S.D. and Gaylord R.H., High-resolution photoemission study of the

electronic structure of the noble-metal (111) surfaces. Phys. Rev. B. 36, 5809–

5818 (1987).

53. Hasegawa Y. and Avouris P., Direct observation of standing wave formation at

surface steps using scanning tunneling spectroscopy. Phys. Rev. Lett. 71, 1071 –

1074 (1993).

54. Crommie M.F., Lutz C.P., and Eigler D.M., Imaging standing waves in a two-

dimensional electron gas. Nature 363, 524-527 (1993).

55. Crommie M.F., Lutz C.P., and Eigler D.M., Confinement of Electrons to Quantum

Corrals on a Metal Surface. Science 262, 218-220 (1993).

56. Trallero-Giner C., Ulloa S.E., and Lopez-Richard V., Local density of states in

parabolic quantum corrals. Phys. Rev. B. 69, 115423 (2004).

57. Deshpande A., et al., Atomistic constructions using a scanning tunneling

microscope tip. 6th IEEE Conference on Nanotechnology, Conference

proceedings (2006).

58. Hla S.-W., Meyer G., and Rieder K.H., Selective bond breaking of single

iodobenzene molecules with a scanning tunneling microscope tip. Chem. Phys.

Lett. 370, 431-436 (2003).

59. Ratner M.A and Schatz G.A., Introduction to Quantum Mechanics in Chemistry,

Prentice Hall (2001).

60. Schott J.W. and White H.S., Halogen chemisorption on Silver(111). Scanning

tunneling microscopy of Coadsorbed Halogen Atoms. Langmuir 10, 486-491

(1994). 121 61. Schott J.W. and White H.S., Halogen Adlayers on Ag(111). J. Phys. Chem 98,

291-296 (1994).

62. Bagus P.S., Pacchioni G., and Philpott M.R. Bond ionicity of the halogen--silver

interaction. J. Chem. Phys. 90, 4287-4295 (1989).

63. Lang N.D., and Williams A.R., Theory of atomic chemisorption on simple metals.

Phys. Rev. B. 18, 616 – 636 (1978).

64. GAMESS (General Atomic and Molecular Electronic Structure System) is a

general ab initio quantum chemistry package, maintained by the members of the

Gordon research group at Iowa State University, available free online.

122 Appendix A

List of Publications

ƒ Aparna Deshpande, Kai-Felix Braun, Saw-W. Hla, “Piconewton force

measurement in single atom manipulation”, submitted

ƒ Aparna Deshpande, Dandapani Acharya, Joel Vaughn, Saw-W. Hla, Handan.

Yildirim, Abdelkader Kara, Talat Rahman, “Atom-by-atom extraction using

scanning tunneling microscope tip-cluster interaction”, Phys. Rev. Lett. 98 (2007)

028304.

ƒ Aparna Deshpande, Kendal Clark, Dandapani Acharya, Joel Vaughn, Kai-F.

Braun, Saw-W.Hla, “Atomistic Constructions by using Scanning Tunneling

Microscope Tip”, IEEE-NANO 2006, 6th IEEE Conference on Nanotechnology,

Conference proceedings.

ƒ Violeta Iancu, Aparna Deshpande, Saw-W. Hla, “Manipulating Kondo

Resonance in Two-Dimensional Molecular Self-Assembly”, Phys. Rev. Lett. 97

(2006) 266603.

ƒ Violeta Iancu, Aparna Deshpande, Saw-W. Hla, “Manipulating Kondo

Temperature via Single Molecule Switching”, Nano Lett. 6 (2006) 820-823.

ƒ Violeta Iancu, Aparna Deshpande, Saw-W. Hla, “Controlling formation of

nanodots and nanocavities using scanning tunneling microscope”, IEEE-NANO

2006, 6th IEEE Conference on Nanotechnology, Conference proceedings. 123 ƒ Saw-W. Hla, Kai-Felix. Braun, Violeta Iancu, Aparna Deshpande, “Single

atom extraction by scanning tunneling microscope tip-crash and nanoscale surface

engineering”, Nano Lett. 4 (2004) 1997-2001. Appeared in ‘Science News’,

‘Smashing the Microscope: Tiny crashes harnessed for nanoconstruction’,

11/06/2004. 124

Appendix B

List of Contributed Talks and Posters in

Conferences

ƒ “Atomistic constructions using Scanning tunneling microscope tip”, Oral

Presentation at the 6th IEEE Conference on Nanotechnology, July 2006

ƒ “Controlling Formation of Nanodots and Nanocavities Using Scanning

Tunneling Microscope”, Oral Presentation at the 6th IEEE Conference on

Nanotechnology, July 2006

ƒ “Force measurement with STM”, Poster Presentation Ohio Center for

Technology and Science (OCTS) summit, April 2006

ƒ “Atom selective force measurement with STM”, Oral Presentation at APS

March meeting, March 2006

ƒ “Atom-by-atom extraction by controlling a scanning tunneling microscope tip-

cluster interaction”, Oral Presentation at APS March meeting, March 2005

ƒ “Atom-by-Atom Extraction using Scanning Tunneling Microscope Tip-Cluster

Interaction”, Poster Presentation Ohio Center for Technology and Science

(OCTS) summit, March 2005 125 ƒ “In-situ tip preparation and nanoscale surface modification using STM

manipulation”, Poster Presentation AVS 50th International Symposium and

Exhibition, November 2003

ƒ “Atomic-scale surface modification and in-situ tip preparation using STM

manipulation”, Poster Presentation APS March Meeting, March 2003