A THESIS 
ON 


INVESTIGATION OF ORGANIC METAL COMPLEX ADSORBATES 

Submitted in the partial fulfilment of the requirement for the award of the 
Degree of 


Master of Technology (M.Tech) 

IN 

MATERIALS SCIENCE AND ENGINEERING

 Submitted by 

NEETI UPPAL 

(60702010) 
Under the guidance of 


Dr. Frank Trixler Dr.K.K.Raina 
Ludwig-Maximillians-Universitδt Mόnchen (LMU) Professor and Dean 
And Centre for Nano Science (CeNS) Faculty Affairs and Dean 
Dept. for Earth and Environmental Sciences Resource Planning and Generation 
Section Crystallography, Thapar University 
Theresienstr. 41, 80333 Mόnchen, Germany. Patiala-147004, Punjab, India. 


School of Physics and Material Science 

THAPAR UNIVERSITY 

PATIALA (PUNJAB)-147004 
June 2009 



INVESTIGATION OF ORGANIC METAL COMPLEX ADSORBATES 

Neeti Uppal 


Munich, Germany. 
June, 2009. 



CONTENTS PAGE NUMBER 


Certificate…………………………………………………………………………………….… I 
Acknowledgment……………………………………………………………………………….II 
List of figures…………………………………………………………………………………..III 
Nomenclatures…………………………………………………………………………………IV 
Abstract………………………………………………………………………………………….V 

CHAPTER I 
INTRODUCTION……………………………………………………………………1 

CHAPTER II 
BASICS 

2.1 Organic Solid/Solid Wetting Deposition ……………………………………...4 
2.2 Organic Semiconductors-Pigments……………………………………………5 
2.3 Scanning Tunnelling Microscopy …………………………………………….9 
2.4 Tunnelling Spectroscopy…………………………………………………… 12 
2.5 Raman Spectroscopy…………………………………………………………13 
2.6 Computational Chemistry/Molecular Modelling…………………………….16 
CHAPTER III 
MATERIALS AND METHODS 

3.1 Substrate……………………………………………………………………...22 
3.2 Adsorptive Substances……………………………………………………….23 
3.3 Binder………………………………………………………………………...27 
3.4 Preparations 

3.4.1 Tip……………………………………………………………………28 
3.4.2 Substrate……………………………………………………………...31 
3.5.3 Adsorptives…………………………………………………………...32 
3.5 Scanning Tunnelling Microscope…………………………………………….34 
3.6 Image Analysis (SPIP)……………………………………………………….38 
3.7 Force Filed Calculations……………………………………………………...39 
CHAPTER IV 
SAMPLE EVALUATION –Preliminary Characterizations 

4.1 Energy Dispersive X-ray spectroscopy (EDX)………………………………43 
4.2 Raman Spectroscopy…………………………………………………………49 
CHAPTER V 
RESULTS AND DISCUSSIONS 

5.1 Introduction…………………………………………………………………..51 
5.2 Structural Characterization 
5.2.1 Scanning Tunnelling Microscopy (STM)…………………………….51 
5.2.2 Scanning Probe Image Processor (SPIP)…………………………….56 
5.2.3 Force Field Calculations……………………………………………...59 
5.3 Electronic Characterization (TS)……………………………………………..62 
CHAPTER VI 
SUMMARY………………………………………………………………………….66 

CHAPTER VII 
OUTLOOK………………………………………………………………………….67 


APPENDIX: Tunnelling Spectroscopy parameters………………………………….69 
REFERENCES……………………………………………………………...............73 
PUBLICATIONS……………………………………………………………………76 


List of figures 

CHAPTER I1 
Figure 2.3 (a) : 
Figure 2.3 (b) : 
Figure 2.4 : 
Figure.2.5 (a) : 
Figure 2.5 (b) : 
Figure 2.5 (c) : 
CHAPTER 111 
Figure 3.2 (a) : 
Figure 3.2 (b) : 
Figure 3.2 (c) : 
Figure 3.2 (d) : 
Figure 3.2 (e) : 
Figure 3.2 (f) : 
Figure 3.2 (g) : 
Figure 3.3 (a) : 
Figure 3.3 (b) : 
Figure 3.4.1(a) : 

Interaction of Tip atoms with the Sample atoms 
resulting in a Tunnelling Current and thus producing 
image of the Organic Semiconductor’s Surface. 
Comparison of constant-height and constant-current 
mode for STM. 
Current vs. voltage (I-V) curves characteristic of the 
electronic structure at a specific x,y location on the 
sample surface. 
Energy level diagram for Raman scattering 
Typical Raman spectrum 
WiTec Confocal Raman Microscope 


Structural Formula of PTCDA. 


Alizarin Pigment 


Structural Formula of Alizarin 
Alizarin Krapplack Kremer (Left), Alizarin Krapplack 
Schmincke (Right) 
Structural Formula of ACaAl complex of Alizarin. 


Structural Formula of Alizarin Violet (Alizarin 
Sulphonic Acid Aluminium Complex). 
Basic step involved in synthesis of Alizarin Violet 
Complex. 


Basic Structure of 8CB (left); Chemical formula and 
phase sequence of 8CB. 
8CB used in the lab. Newly ordered (left), old (right). 
Suppliers: Synthon, Aldrich 
Company: Ma TecK; Material: Pt / Ir 90/10 wire 



Figure3.4.1 (b) : Set of cutters and pliers used in making STM tips. 
Figure 3.4.1 (c) : Tungsten wire used to make STM tips. 
Figure 3.4.1 (d) : Experimental set up for etching of tungsten tips. 
Figure 3.4.1 (e) : Etched tungsten tip (left); Etched Tungsten tips 
preserved for days or even weeks (right). 
Figure 3.4.2(a) : Normal Tesa tape used for cleaving graphite and to get 
a fresh smooth cleaved surface to be used as an 
appropriate substrate for organic semiconductors for 
STM analysis. 
Figure 3.4.2 (b) : HOPG with fresh cleaved surface. 
Figure 3.4.3(a) : Mixture of pigments suspended in 8CB 
Figure 3.4.3(b) : A set of heater (left) and shaker (right) used to mix the 
pigment into the 8CB matrix in order to obtain a fine 
suspension of the nanoparticles. 
Figure 3.4.3 (c) : Final application of the droplet of the pigment in 8CB 
on the graphite substrate. 
Figure 3.5 (a) : HUBER STM. The shield minimizes drifts from noise 
in STM results.(left) ;Inside view of HUBER 
STM(right) 
Figure 3.5 (b) : Basic Internal Configuration of HUBER STM 
Figure 3.5 (c) : Control equipment that boasts record-setting low noise, 
high configurability, and operability with scan heads of 
any variety. 
Figure 3.5 (d) : When the tip sample distance is achieved with the help 
of adjusting screws in the HUBER STM, the RHK 
control system shows ΄ In Range΄ signal, after which the 
system is ready for the scans to get started (left) ; The 
Feedback control in RHK system (right). 
Figure 3.5 (e) : XPM Pro Main Menu 
Figure 3.5 (f ) : Real Time Data Acquisition using RHK XPMPro 
Software (left); Navigation window of RHK XPMPro 
Software (right) 
Figure 3.6(a) : SPIP (a) toolbar displaying various modules available 
Figure 3.6 (b) : Raw STM image (left); Auto Correlated STM image in 


SPIP (right). 
Figure 3.6 (c) : FFT analysis (blue) of the STM image (behind) in SPIP. 
Figure 3.6 (d) : Calculation of lattice vectors using SPIP 
Figure 3.7 (a) : Building up of a basic organic semiconductors model 
using molecular modelling. 
Figure 3.7 (b) : Various tools available for Molecular Modeling 
Figure 3.7 (c) : The Ball and Stick style is convenient for molecule 
construction and editing, since atoms and bonds are 
clearly visible. In addition, the bond colour reflects their 
order (left) ; The Stick style is largely for presentations 
(right). 
Figure3.7 (d) : The CPK style is basically preferred for analysis of 
STM patterns. 
CHAPTER IV 
Figure4.1 (a) : Raw STM image of so called labelled Alizarin Tin 
complex by Kremer, showing distinct domains. 
Figure 4.1(b) : EDX of the sample which revealed it to be an Alizarin 
Aluminium complex rather than Alizarin Tin complex 
(No characteristic Tin peak), as mentioned by the 
suppliers. Supplier: Kremer 
Figure 4.1 (c) : EDX of the sample which revealed it to be an Alizarin 
Aluminium complex rather than Alizarin Copper 
complex (No characteristic Copper peak in the spectra) , 
as mentioned by the suppliers. Supplier: Kremer 
Figure4.1 (d) : EDX of Alizarin showing characteristic Carbon and 
Oxygen peaks as expected. Supplier: Fluka 
Figure 4.1 (e) : EDX of Alizarin Aluminium complex (old-Kremer) 
showing a characteristic Aluminium peak. Supplier: 
Kremer 
Figure 4.1 (f) : EDX of Alizarin Sulphur (Alizarin Red S). Supplier: 
Acros 
Figure 4.1(g) : EDX of Alizarin Alumium complex. Supplier: 


Schmincke 

Figure 4.1 (h) : 
EDX of Alizarin Alumium complex (New-Kremer) , 
showing a characteristic Aluminium peak 

Figure 4.1 (i) : 
EDX of Alizarin Violet, showing a characteristic 
Sulphur peak. Since, the complexization involves 
Aluminium ions too; EDX reveals a characteristic 
Aluminium peak besides a Sulphur peak. Supplier: 
Kremer 

Figure 4.2 (a) : 
Raman Spectra of Alizarin pure (left); Alizarin +8CB 
(right) 

Figure 4.2 (b) : 
Alizarin Krapplack pure (left) Alizarin krapplack +8cb 
(right) 

Figure 4.2 (c) : 
Alizarin Violet pure (left); Alizarin Violet +8CB (right) 

CHAPTER V 
Figure 5.2.1(a) : STM image of sample-A-dry deposition (2nm) (left); 
with 8CB (1nm) (right) 
Figure 5.2.1(b) : STM image of Sample-B(Schmincke) under ambient 
conditions (5nm).(left) ; STM image of the same sample 
but from a different pigment company Kremer (1nm) 
(right) 
Figure5.2.1(c) : Raw STM image of Sample-C (left-5nm).; STM image 
of Sample-C (2nm) (right-with graphite atoms at the 
base) 
Figure 5.2.1 (d) : Zoomed STM image of Sample –C (1nm), keeping the 
same value of bias and set point as in Figure 5.2.1(c) 
right image. 
Figure: 5.2.1 (e) : STM image of a surface pattern grown by using a 
sample of 8CB -20nm. 
Figure 5.2.2(a) : SPIP analysis of STM image obtained by using Alizarin 
sample. 


Figure 5.2.2(b) : 
SPIP analysis of STM image obtained by using Alizarin 
Sample. 

Figure 5.2.2 (c ) : 
SPIP analysis of STM image obtained by using Alizarin 
sample. 

Figure 5.2.3 (a) : 
Molecular Modelling of Alizarin without energy 
minised and H-Bonds calculations (left); with energy 
minimised and H-bonds calculations (right) 

Figure 5.2.3(b) : 
Without Energy Minimised calculations (left); With 
Energy minimised calculations (right) 

Figure 5.2.3(c) : 
Energy minimised structure of ACaAl complex viewed 
from different angles. 

Figure 5.2.3 (d) : 
Modelled structure of Alizarin Violet without Energy 
Minimised calculations (left); With Energy minimised 
calculations and H-bonds calculated (right). 

Figure 5.2.3 (e) : 
Alizarin Violet structure modelled with Energy 

minimised calculations-View from different angles 

Figure 5.3 (a) : 
Point Spectroscopy of PTCDA 

Figure 5.3 (b) : 
Point spectroscopy of graphite substrate. 

Figure 5.3(c) : 
Point Spectroscopy of Alizarin 

Figure 5.3(d) : 
Point Spectroscopy of Alizarin Calcium Aluminium 

Complex 

CHAPTER VII 
Figure 7.1: STM Nanomanipulation of ACaAl 
Figure 7.2: Alizarin Sulphonic Acid CaAl Complex 


Nomenclature 

8CB : 4-Octyl-4’-Cyanobiphenyl 
ACaAl : Alizarin Calcium Aluminium Complex 
CAS : Chemical Abstract Service number 
C.I : Chemical Index number 
CRM : Confocal Raman Microscope 
DFT : Density Functional Theory 
Eg : Band Gap 
EDX : Energy Dispersive X-ray analysis 
FFT : Fast Fourier Transform 
HOMO : Highest Occupied Molecular Orbital 
HOPG : Highly Oriented Pyrolytic Graphite or 
Highly Ordered Pyrolytic Graphite 
LUMO : Lowest Occupied Molecular Orbital 
PTCDA : 3, 4,9,10 –Perylentetracarbonsaeuredianhydrid 
Pt-Ir : Platinum-Iridium 
STM : Scanning Tunnelling Microscope 
SPIP : Scanning Probe Image Processor 
TS : Tunnelling Spectroscopy 
OSWD : Organic Solid /Solid Wetting Deposition 


ABSTRACT 


Alizarin is a natural organic compound which occurs mainly as an 
Anthraquinone glycoside in plants. Alizarin tends to form metal chelate complexes, 
which are used as natural pigments since ancient times. One of the earliest known 
complexes is the Calcium Aluminium Complex of Alizarin (ACaAl), first used as a 
pigment in India. 

Organic Solid/Solid Wetting Deposition (OSWD) enables to deposit insoluble 
molecules such as organic pigments and semiconductors on substrate surfaces under 
ambient conditions. The technique enables to grow monolayers of insoluble organic 
molecules without the need for vacuum conditions (as in the case of Molecular Beam 
Epitaxy) or chemical modifications (to achieve solubility). We explore the potential of 
OSWD to grow and manipulate monolayers of biomolecules and their chelates on 
graphite and use Alizarin as a model system. We use for investigation STM, TS and 
Molecular Modelling. 

In the present work attempt has been made to figure out the importance of 
organic metal complexes as semiconductors for organic electronics. The basic 
motivation came from the desire to potentially combine OSWD with the bio-organic 
molecular systems such as Alizarin/ACaAl for applications within the context of 
NanoBioTechnology and the urge to adsorb and self-assemble biomolecules on 
mineral surfaces under ambient conditions without the need for solubility. The goal 
was not only to increase the tool box that could be given to the industry for organic 
electronics or to the medical field as a chelate for chelation therapy, but also to make 
the area of research more simpler and economical in general . 


CHAPTER I 
INTRODUCTION 

The invention of various top down approaches like Nano Imprint Lithography, 
Atomic Layer Deposition etc, gave micro fabrication technology a new turning point. 
But owing to the ultra-precision engineering, costly fabrication processes, and 
complicated equipment design involved, these top down approaches encountered 
physical and economical limitations when approaching the length scale of molecules. 
To overcome the above limitations, bottom up approaches like molecular self 
assembly were looked upon. Again among the intermolecular (mainly weak Van-der-
Waals and hydrogen bonds involved) self assembly and intramolecular (mainly strong 
covalent bonds involved) self assembly , intermolecular or supramolecular self 
assembly gained much importance owing to its simplified way and low cost 
fabrication techniques utilized under ambient conditions. The supramolecular self 
assembly technique not only helps to grow spontaneous monolayers without the aid of 
any external agency, but also offers the possibility of going beyond simple 
miniaturization by introducing dynamic features to surface-supported devices such as 
reconfiguration, self-repairing and self-contacting owing to the reversibility of the 
non-covalent bonds at room temperature. [1] 

Now in building of a monolayer, it’s the interface between the compound 
molecules and the substrate which needs enormous consideration. It’s the interface, 
where the decision is made if the molecule will be adsorbed or not, depending on the 
interaction of the binding energies of the molecules to be transported and that of the 
substrate. Again, if the molecules of the material have a good solubility, they can be 
easily dissolved, and taken from the solution to be transported to the interface. 
However, if the molecules show very poor or no solubility, like several organic 
semiconductors or pigments, the solution method cannot be employed. Molecular 
Beam Epitaxy (MBE) can however be used for such insoluble semiconductors, but 
owing to the high demanding vacuum conditions involved ,it requires tremendous 


Introduction 

instrumentation effort and is most suitable for molecules which are sufficiently stable 
for sublimation. The above drawbacks were overcomed by a simple process, known 
as Organic Solid/Solid Wetting Deposition (OSWD) method. [1] In this technique, 
nanoparticles (pure or suspended) of the respective compound are just brought into 
direct contact with the substrate. When the Binding energy of the molecules to the 
substrate (adsorption energy) exceeds the binding energy of the surface molecules in 
the nanoparticle, single molecules detach themselves from the nanoparticle, adsorb on 
the surface and thus from monolayers under ambient conditions. Eventually, 
combination of thermally activated diffusion and intermolecular forces result in self 
assembly of highly ordered supramolecular structures, if the molecule-substrate 
interaction is not too strong. The behaviour is analogous to the spreading of a liquid 
on a solid, provided the interface tension exceeds the surface tension, thus referred to 
as “Solid-Solid wetting initiated self assembly”[1][2] 

Among the various insoluble organic semiconductors and pigments, Alizarin 
was selected to be analyzed via OSWD process and was used as a model system for a 
bio-organic semiconductor. Alizarin is a natural organic compound which occurs 
mainly as Anthraquinone glycoside in plants. [4] Experiments with Alizarin were 
made via above mentioned simple OSWD phenomenon using graphite substrates .The 
main focus was to figure out if OSWD works successfully with Alizarin. Further 
Tunnelling Spectroscopy and Molecular Modelling experiments were performed to 
determine the properties and structure of Alizarin, and to understand by the simple 
OSWD technique, how and why the behaviour of the organic semiconductor is 
affected. 

After successfully analysing Alizarin using OSWD technique, its chelate 
complexes were studied further. Alizarin tends to form chelate complexes, which are 
used as natural pigments since ancient times. Chelation is a property in which the 
organic semiconductors (chelants) bind with the single metal ions forming a metal 
complex. During the course of it, it inactivates the metal ions so that they cannot 
interact with other elements or ions to produce precipitates or scales. Alizarin is 
known to form such chelates with ions of Aluminium, forming a Calcium Aluminium 
Complex (ACaAl), with ions of sulphur, forming Alizarin Sulphonic Acid complex 
and such complexes with other metal ions too. In the current work, chelate metal 

2 



Introduction 

complexes of Alizarin viz: Alizarin Calcium Aluminium Complex and Alizarin 
Sulphonic Acid Complex have been studied and analysed. 

One of the earliest form complexes of Alizarin is the Alizarin Calcium 
Aluminium Complex (ACaAl) Complex, which was first used as a pigment in India. 
The potential of OSWD to grow and manipulate monolayers of this chelate complex 
on graphite was explored, and experiments prove that OSWD not only works with 
Alizarin, but with its Calcium Aluminium Complex too. Tunnelling Spectroscopy and 
Molecular Modelling experiments were further conducted to determine the behaviour 
of the complex and to understand what the complexization does to the structure and 
properties of the Alizarin molecule. 

On the similar lines, another complex of Alizarin, Alizarin Sulphonic acid 
complex was analysed. It falls under the group of a class of hydroyanthraquinone 
pigments namely metal salts of hydroxyanthraquinone sulphonic acids, and is used as 
an industrial paint, especially throughout USA. Scanning Tunnelling Microscopy 
experiments were made to determine the success of OSWD phenomenon with this 
chelate complex too. Again, Tunnelling spectroscopy and Molecular Modelling 
experiments were conducted to determine the exact behaviour of the complex and to 
estimate the role of different forces which come into play during complexitation, 
sufficient enough to alter the structure and properties of the molecule. 

Thus by studying Alizarin and its chelate complexes, effort has been made to 
increase the tool box for the systems that could be analysed using a simple OSWD 
approach. This would not only bring in the otherwise left out insoluble organic 
semiconductors and pigments into limelight, but also work towards producing 
nanostructures and further nanomanipulating them under fully controlled and ambient 
conditions. 

3 



 CHAPTER II 
BASICS 

2.1 Organic Solid/Solid Wetting Deposition (OSWD) 
Organic Solid/Solid wetting Deposition (OSWD) is a low cost, easily 
available simple technique, which enables to grow epitaxial monolayers of 
particularly insoluble organic semiconductors and pigments, under ambient 
conditions. 

For the simple understanding, consider the case of a liquid droplet in contact 
with a solid surface. The droplet will spread on the solid surface and if the adhesion 
energy between the surface molecules of the droplet and the surface atoms of the 
substrate exceeds the cohesion energy between the molecules of the droplet, the liquid 
droplet will wet the solid surface. [1] 

Now, in case of the crystals of organic semiconductors and pigments, the 
organic molecules are held together within the crystal via weak intermolecular bonds 
(mainly van-der-Waals interactions and hydrogen bonds). Owing to these weak non – 
covalent bonds involved in organic semiconductors and pigments, it could be possible 
that if a direct contact between the surface of the organic semiconductors and the 
inorganic substrate is established, the binding energy of the molecules to the substrate 
(adsorption energy) exceeds the binding energy of the surface molecules in the 
nanocrystals. This results in the detaching of the molecules from the nanocrystal as 
they adsorb on the substrate surface forming monolayers via diffusion (if the 
molecule-substrate interaction is not too strong). 

The behaviour of nanocrystals of organic semiconductors and pigments on the 
substrate surface is analogous to the above mentioned classical case of wetting-the 
spreading of a liquid on a solid surface. Thus this technique is referred to as ‘Organic 
Solid/Solid wetting ‘.However, the occurrence of this effect has only been reported in 

4



Basics 

the special context of inorganic oxide catalysts in a high temperature and time regime 

[3] [22], but not for solid nanoparticles of organic compounds. 
2.2 Organic Semiconductors-Pigments 
Organic semiconductors are a class of organic compounds which have 
semiconducting properties. 

Organics Semiconductors are based on the unusual properties of the carbon 
atom: Among other configurations, it can form the so-called sp2-hybridisations where 
the sp2-orbitals form a triangle within a plane and the pz-orbitals are in the plane 
perpendicular to it. A s -bond between two carbons can then be formed by formation 
of an orbital overlap of two sp2-orbitals. The energy difference between the occupied 
binding orbitals and the unoccupied anti-binding orbitals is quite large and well 
beyond the visible spectral range. Correspondingly, longer chains of bound carbon 
atoms would have a large gap between the highest occupied molecular orbital 
(HOMO) and the lowest unoccupied molecular orbital (LUMO), leading to insulating 
properties. [5] 

However, in the sp2-hybridisation, the pz-orbitals form additionally p -bonds. 
These bonds have much smaller energetic difference between the HOMO and LUMO, 
leading to strong absorption in or near the visible spectral range and to 
semiconducting properties: [5] 

The Organic semiconductors can be further classified into Small-molecule 
organic semiconductors and Polymer organic semiconductors. If carbon atoms form 
larger molecules, typically with benzene rings as the basic unit, the p -bonds become 
delocalized and form a p -system which is often has the extensions of the molecule. 
The gap between occupied and empty states in these p -systems becomes smaller 
with increasing delocalization, leading to absorption and fluorescence in the visible 
region. These substances can be prepared as molecular single crystals. Due to the 
close coupling of the p -systems of the molecules in these crystals, they show in a 
purified form remarkable transport properties. Most of the molecules can also be 
easily evaporated to form polycrystalline (hopping transport with mobilities typically 
around 10-3 cm2/Vs at 300K) or amorphous (hopping with mobilities typically around 

5 



Basics 

10-5 cm2/Vs at 300K) layers. Now if a long chain of carbon atoms is formed, the p-
bonds become delocalized along the chain and form 1-D electronic system. This 
resulting 1-D band has a considerable band width (eV). Thus we have a 1D 
semiconductor with a filled valence band originating from the HOMOs and an empty 
conduction band originating from the LUMOs. [5] 

Pigments cover a wide range of Organic Semiconductors and in the course of 
the last few decades; have experienced rapid growth to become an industry of 
significant commercial importance. [6] The traditional function of organic pigments 
has been to impart colour, and this will remain the major volume use for many years 
to come. 

The building blocks in organic pigments are molecules that determine, directly 
or indirectly, important performance properties of the pigments. Such organic pigment 
molecules are generally characterised by planar conjugated chromophoric systems 
featuring functional groups such as the C=O and NH groups. In certain cases they 
may contain acidic and basic functional groups allowing precipitation of soluble dyes 
via salt and metal complex formation. Organic pigments are classified also according 
to their generic name and chemical constitution. Details of the chemical constitution 
of organic pigments is given in the Colour Index (C.I.) published by the Society of 
Dyers and Colourist’s Each chemical type is characterised by a C.I. number, for 
example, copper phthalocyanine is designated C.I. Pigment Blue 15 (‘C.I. Pigment’ 
generally being omitted for brevity, and P.B., P.G., P.O., P.R. , P.V. and P.Y. etc. 
used to designate blue, green, orange, red, violet and yellow pigments, 
respectively).[2][17] 

We further have Natural Organic Pigments and Synthetic Organic Pigments. 
Natural organic pigments were a significant part of historical pigments before the 
modern era, particularly for bodily ornamentation, cosmetics and textile dyeing. For 
today's artists almost every natural organic pigment has been replaced by a synthetic 
organic alternative. These pigments only survive in their outmoded but quaint 
historical names, which commercial paint companies adopt to lend romance to their 
modern convenience mixtures. [6][17] 

6 



Basics 

Historically, the most important natural organic pigments in watercolours 
included the many rose or crimson dyes from madder root, known since antiquity 
and extracted from the strong smelling powder made from dried, ground roots of 
several varieties of the herbaceous perennial rubia tinctorium, native to Greece and 
cultivated extensively throughout Asia Minor. The plant was brought to Italy by the 
returning Crusaders, but became important as an artists' pigment only after it was 
imported to Holland in the 16th century, which continued to supply most of the 
madder root used in Europe until the late 19th century. Madder was first 
manufactured as a laked pigment (madder lake) in around 1804, which greatly 
improved its permanence, and also afforded an expanded range of colours depending 
on the specific salt or substrate used in the laking process: rose madder or pink 
madder (NR9) in dyes laked on chalk or alum (aluminium hydrate), which can be 
made more brilliant by adding small quantities of stannous salts or by precipitating 
with calcium and sodium phosphates; deep red madder from precipitation on soda or 
potash; violet madder from the addition of iron sulphate; and various shades of brown 
madder from the addition of chromium alum or iron salts. Madder extracts actually 
contain several organic colorants, most of which are fugitive. The two most important 
were first separated and described by the French chemists Robiquet and Colin in 
1826: orange purpurin and deep red alizarin (PR83). Both pigments are impermanent, 
but purpurin is especially fugitive, and is the source of genuine madder's warm, fiery 
colour. The bluest lakes are made by precipitating pure alizarin on alumina. [17] 

Despite the inadequate light fastness and typically dull colour appearance of 
these outmoded historical pigments, the names rose madder, brown madder, carmine, 
Indian yellow, gamboge, sap green, indigo, van dyke brown and sepia are still 
frequently used as marketing monikers for watercolours made with completely 
unrelated and typically much more lightfast synthetic organic pigments. 

The other class of organic semiconductor pigments is synthetic organic 
pigments, which are carbon based molecules manufactured from petroleum 
compounds, acids, and other chemicals, usually under intense heat or pressure. The 
techniques for producing these substances on an industrial scale were invented after 
1860, which created the modern era of consumer colour. Chemical and industrial 

7 



Basics 

innovations increased at an astonishing pace through the end of the 19th century and 
have continued up to the present. 

Among the many dyes created from coal tar (and using ingredients other than 
aniline) the first artificial production took place of a natural dye — alizarin, one of 
two colorants found in natural madder — synthesized in 1868 by the German 
chemists Carl Grδbe and Carl Lieberman, and still sold today as alizarin crimson 
(PR83) and red violet mixtures made with it. 

The reason why so many modern pigments are synthetic organics, is the 
amazing ability of carbon atoms in these organic compounds, to combine with itself 
in a great variety of atomic structures — rings, chains and branches — including the 
most important and basic, the benzene ring of six interconnected carbon atoms. These 
structures in turn can attach to each other or to a variety of other atoms or chemical 
compounds (especially of nitrogen and hydrogen), to produce almost limitless 
molecular variations. Out of this chemical diversity comes a large number of 
molecules with intense colour attributes: of these, the least toxic, most permanent and 
most economically manufactured are used as colorants. 

In recent times, however, organic pigments are finding increased use in a 
number of high technology industries, such as photo-reprographics, opto-electronic 
displays and optical data storage. In some of these applications, the pigment is still 
employed because of its colour imparting capability, while in other cases it performs a 
special function which is not based on its colour. Organic pigments are commonly 
supplied in a number of different commercial forms including powders or granules 
(either surface treated or untreated), aqueous press cakes, predispersed aqueous 
pastes, flushed pigments (dispersions in viscous, aliphatic hydrocarbon-based media), 
resin pre-dispersed pigments, and plastic colour concentrates or masterbatches. The 
commercial performance of a pigment in a vehicle system is defined by a long list of 
its application properties, such as its colouristic performance, rheological behaviour, 
durability and ecological compatibility/acceptability. From the end-user’s point of 
view, the pigments must fulfil certain requirements with regard to such properties. 
The physical and chemical characteristics that control and define the performance of 

8 



Basics 

an organic pigment include its molecular, solid state and particle surface 
characteristics. The pigment manufacturers must design their products, accordingly, 
by judicious choice of the chemistry and solid state pigment elaboration techniques, to 
meet these performance requirements. [6] 

2.3 Scanning Tunnelling Microscopy (STM) 
The scanning tunnelling microscope (STM) is the ancestor of all scanning 
probe microscopes. Invented in 1981 by Gerd Binnig and Heinrich Rohrer at IBM 
Zurich., who were awarded Nobel Prize for it after five years, The STM was the first 
instrument to generate real-space images of surfaces with atomic resolution. STMs 
use a sharpened, conducting tip with a bias voltage applied between the tip and the 
sample. When the tip is brought within about 10Ε of the sample, electrons from the 
sample begin to “tunnel” through the 10Ε gap into the tip or vice versa, depending 
upon the sign of the bias voltage. The resulting tunnelling current varies with tip-tosample 
spacing, and it is the signal used to create an STM image. For tunnelling to 
take place, both the sample and the tip must be conductors or semiconductors. Unlike 
AFMs (Atomic Force Microscopes), STMs cannot image insulating materials. [18] 


Figure 2.3 (a): Interaction of Tip atoms with the Sample atoms resulting in a 
Tunnelling Current and thus producing image of the Organic Semiconductor’s 
Surface. 


9 



Basics 

The tunnelling current is an exponential function of distance; if the separation 
between the tip and the sample changes by 10% (on the order of 1Ε), the tunnelling 
current changes by an order of magnitude. 

The energy-and bias-dependent electron tunnelling transition probability, T, is 
given by: 

2Z 


2m 


.s ..t eV

T . 
exp ( 


. 


. 
E ) ………………………... (2.3)

. 


22 


where fs and ft are the respective work functions of the sample and tip and Z 
is the distance from the sample to the tip. 

This exponential dependence gives STMs their remarkable sensitivity. STMs 
can image the surface of the sample with sub-angstrom precision vertically, and 
atomic resolution laterally. 

There are two modes of STMs viz: constant-height or constant-current mode 
(Figure 2.3 b). In constant-height mode, the tip travels in a horizontal plane above the 
sample and the tunnelling current varies depending on topography and the local 
surface electronic properties of the sample. The tunnelling current measured at each 
location on the sample surface constitutes the data set, the topographic image. In 
constant-current mode, STMs use feedback to keep the tunnelling current constant by 
adjusting the height of the scanner at each measurement point. For example, when the 
system detects an increase in tunnelling current, it adjusts the voltage applied to the 
piezoelectric scanner to increase the distance between the tip and the sample. 

Constant-height mode is faster because the system doesn’t have to move the 
scanner up and down, but it provides useful information only for relatively smooth 
surfaces. Constant-current mode can measure irregular surfaces with high precision, 
but the measurement takes more time. 

In the current work, the mode of operation chosen was constant current mode 
as the organic pigments (powders) analyzed had a relatively irregular surface. 

10 



Basics 


Figure 2.3 (b): Comparison of constant-height and constant-current mode.[19] 

As a first approximation, an image of the tunnelling current maps the 
topography of the sample. More accurately, the tunnelling current corresponds to the 
electronic density of states at the surface. STMs actually sense the number of filled or 
unfilled electron states near the Fermi surface, within an energy range determined by 
the bias voltage. Rather than measuring physical topography, it measures a surface of 
constant tunnelling probability. 

The STM used for the current work was purchased from HUBER; with RHK 
control system and XPMPro Software which are discussed in detail in Materials and 
Methods –STM section. 

Scanning probe microscopes can be operated in a variety of environments like 
ultra high vacuum (UHV), ambient (air), liquid, and electrochemical (EC). The 
easiest, least expensive and thus most popular environment for STMs is ambient, or 
air. STM in air is difficult, since most surfaces develop a layer of oxides or other 
contaminants that interfere with the tunnelling current. One class of materials for 
which ambient STM works well is layered compounds. In graphite, MoS2, Nb3Se, 
and so forth, a clean, “fresh” surface can be prepared by peeling away older surfaces. 

In the present work, STMs are operated under ambient conditions, as Organic 
Solid/Solid Wetting Deposition, in which the insoluble molecules such as organic 
pigments self assemble on their own forming monolayers need no special 
environmental conditions for their organization on a substrate such as graphite. 
Operation under ambient conditions is actually the beauty of OSWD, as it discards the 

11 



Basics 

use of sophisticated and costly experimental set up and hi-tech environmental 
conditions. 

2.4 Tunnelling Spectroscopy (TS) 
Tunnelling spectroscopy (TS) studies the local electronic structure of a 
sample's surface. The electronic structure of an atom depends upon its atomic species 
and also upon its local chemical environment (how many neighbours it has, what kind 
of atoms they are, and the symmetry of their distribution). 

TS encompasses many methods: taking “topographic” (constant-current) 
images using different bias voltages and comparing them; taking current (constantheight) 
images at different heights; and ramping the bias voltage with the tip 
positioned over a feature of interest while recording the tunnelling current. The results 
in current vs. voltage (I-V) curves are the characteristic of the electronic structure at a 
specific x, y location on the sample surface. STMs can be set up to collect I-V curves 
at every point in a data set, providing a three-dimensional map of electronic structure. 


Figure 2.4: Current vs. voltage (I-V) curves characteristic of the electronic structure at 
a specific x, y location on the sample surface. 

With a lock-in amplifier, dI/dV (conductivity) or dI/dz (work function) vs. V 
curves can be collected directly. All of these are ways of probing the local electronic 
structure of a surface using an STM. 

12 



Basics 

The tunnelling current which is measured between the STM tip and the surface 
atoms, is used to image the nano-structures or to determine the local density of states 
of the material under study. The transitions of the electrons excited while applying 
voltage between the STM tip and the sample determine the location of orbital energy 
states. These states presented in the form of a Current vs. Voltage graph as discussed 
earlier, is the basic idea behind Tunnelling Spectroscopy (TS).[20] 

Point Spectroscopy has been used for the current work, for the investigation of 
the electronic structure, in which extensive sets of dI/dV spectroscopy measurements 
have been taken. This is done mainly as the results of the point spectroscopy depends 
drastically on the position on the surface where they were recorded. 

2.5 Raman Spectroscopy 
The Raman effect is an interaction process of electromagnetic waves (light) with 
matter in which a vibrational quantum is excited (Stokes Raman scattering) or 
annihilated (Anti-Stokes Raman scattering). When light of a certain wavelength 
interacts with a molecule, most photons are elastically scattered and therefore have the 
same energy as the incident photons. However, a very small fraction (approximately 1 
in 106 to 107 photons) is in-elastically scattered, which means that the energy of the 
scattered photon is different (usually lower) than the energy of the incident photon. 
This effect is called the Raman effect and was discovered by Sir Chandrasekhara 
Raman in 1928. Raman was awarded the Nobel Prize in 1932 for this discovery. The 
tremendous importance of the Raman effect lies in the fact that the energy shift 
between the exciting and the Raman scattered photon is caused by the excitation (or 
annihilation) of a molecular vibration. This energy shift is characteristic and therefore 
a fingerprint for the type and coordination of the molecules involved in the scattering 
process. [11] 

The basic theory behind the concept, is that in quantum mechanics, the scattering 
process between a photon and a molecule is described as an excitation of a molecule 
to a virtual state lower in energy than a real electronic state and the (nearly 
immediate) de-excitation. The lifetime of the virtual state is extremely short. With 
typical photon energies of 1 - 
2 eV, the lifetime of the excited state is only about 10 

13 



Basics 

to the power -15 seconds. After this extremely short time, the molecule falls back 
either to the vibrational ground state or to an excited state (fig. (2.5 a)). When the 
initial and final states are identical, the process is called Rayleigh scattering. 


Figure.2.5 (a): Energy level diagram for Raman scattering [11] 

If the initial state is the ground and the final state a higher vibrational level, 
one speaks of Stokes scattering, if the initial state is energetically higher than the final 
state of Anti Stokes scattering. The difference in energy between the incident and the 
Raman scattered photon is equal to the energy of a vibration quantum of the scattering 
molecule. A plot of intensity of scattered light versus energy difference is called a 
Raman spectrum. 

The position of a Raman line is usually given in wave numbers (1/cm), which 
is the energy shift, relative to the excitation line: 

―. = (1/ . incident) - (1/ . scattered)…………………… 2.5 

. (incident) and . (scattered) are the wavelengths (in cm) of the incident and Raman 
scattered photons, respectively. 


Figure 2.5 (b): Typical Raman spectrum [11]. 

14 



Basics 

From classical scattering theory one finds, that the intensity I of scattered light 
is proportional to the 4th power of the excitation frequency .Exciting a sample with 
blue light of 400 nm would therefore give a 16 times higher Raman signal than using 
red light of 800 nm. 

The problem of using blue (or even UV) excitation light is fluorescence. Most 
samples show fluorescence when they are excited with blue light. The Raman effect is 
extremely weak compared to fluorescence. If a sample shows fluorescence, obtaining 
a Raman spectrum is usually impossible because of the strong fluorescence 
background. In the red (or even IR) part of the spectrum fluorescence is usually not a 
problem any more, but the excitation intensity has to be much higher. Another 
problem is, that silicon detectors can not be used above 1100 nm (band gap energy of 
Si: 1.12 eV). Other IR detectors (like InGaAs) are extremely expensive; show much 
more thermal noise than silicon and photon counting detectors with a reasonable dark 
count rate are not available up to now. In real experiments one always has to find a 
compromise between detection efficiency and excitation power. 

All measurements for the present work were done using a CRM (confocal 
Raman microscope) alpha300 R (WITec, Jungingen, Germany) with a piezo scan 
stage (100 x 100 x 20 ΅m, PI, Germany). It is not only the most sensitive instrument 
for this purpose, but also combines this sensitivity with an unrivalled spatial 
resolution down to sub-micrometer regime. The system was equipped with a 100x 
micro-scope objective for measuring in air with a working distance of 0.26 mm and a 
numerical aperture NA = 0.90 (Nikon, Dόsseldorf, Germany). The depth of focus was 
about 1 ΅m. The microscope objective was used to focus the excitation beam of a 
2omega–Nd: YAG laser (532 nm emission) onto the surface and to collect the 
scattered light. The zeroth order light was blocked by a long-pass edge filter for 532 
nm. To achieve a confocal setup, the collected light was focused onto the core of a 50 
΅m multimode fibre acting as the pin hole and guiding the light to the lens based 
spectrometer. In the experiments discussed here, we used a 500 nm-blazed diffraction 
grating with 1800 lines/mm. A back thinned, peltier cooled CCD-Chip (1024 x 128 
pixels, cooled to -65 °C) was used to record the spectra at a minimal integration time 
of 19 ms. 

15 



Basics 


Figure 2.5 (c): WiTec Confocal Raman Microscope 

Raman spectroscopy can be employed in various fields of Materials Science, 
Nanotechnology, Semiconductors etc, but in the present work, it was used to examine 
if the Raman peaks of pure AlCaAl complex are different than the peaks obtained by 
analyzing the ACaAl complex suspended in 8CB matrix via Raman Spectroscopy. 
This was done in order to figure out, if mixing the complex with the 8CB matrix 
altered the structural integrity and the complexization of the system under 
consideration. 

2.6 Computational Chemistry/ Molecular Modelling for Organic Chemistry 
Computational chemistry/molecular modelling is a collective term that refers to 
theoretical methods and computational techniques to model or mimic the behaviour of 
molecules. Or in other words, it is the science of representing molecular structures 
numerically and simulating their behaviour with the equations of quantum and 
classical physics. Computational chemistry programs allow scientists to generate and 
present molecular data including geometries (bond lengths, bond angles, torsion 
angles), energies (heat of formation, activation energy, etc.), electronic properties 
(moments, charges, ionization potential, electron affinity), spectroscopic properties 
(vibrational modes, chemical shifts) and bulk properties (volumes, surface areas, 
diffusion, viscosity, etc.). As with all models however, the chemist's intuition and 

16 



Basics 

training is necessary to interpret the results appropriately. Comparison to experimental 
data, where available, is also important to guide both laboratory and computational 
work. 

The various computational techniques are used in the fields of computational 
chemistry, computational biology and materials science for studying molecular 
systems ranging from small systems to large biological molecules and materials 
assemblies. Molecular modelling of any reasonably sized system can be performed 
with the aid of computers. 

As a technique, computational chemistry has the advantage of producing answers 
cheaply and quickly. 

The starting point for many computer assisted molecular design (CAMD) studies 
is generally a two dimensional drawing of a compound of interest say in the form of 
sketches on a piece of paper, where one defines the types of atoms in the molecule, 
their hybridization and how they are bonded to each other 

Currently, there are two ways to approach chemistry problems: computational 
quantum chemistry and non-computational quantum chemistry. Computational 
quantum chemistry is primarily concerned with the numerical computation of 
molecular electronic structures by ab-initio and semi empirical techniques and non-
computational quantum chemistry deals with the formulation of analytical expressions 
for the properties of molecules and their reactions. 

Ab initio [7] (Latin for ‘from scratch’ ) a group of methods in which molecular 
structures can be calculated using nothing but the Schrφdinger equation, the values of 
the fundamental constants and the atomic numbers of the atoms present . 

Semi empirical techniques [8] are use approximations from the empirical 
(experimental) data to provide the input into the mathematical models. 

Molecular mechanics uses classical physics to explain and interpret the behaviour 
of atoms and molecules. It relies on force filed with embedded empirical parameters. I 

17 



Basics 

t is comparatively fast and useful with limited computer resources. Further, it can be 
used for molecules as large as enzymes. 

Ab initio quantum methods compute a number of solutions to a large number of 
equations. While recent publications have reported calculations on large molecules 
[10], the methods are generally limited to compounds containing between ten and 
twenty atoms due to the amount of computer time required for each calculation and 
the large amount of disk space needed to store intermediate data files. 
Physical/theoretical chemists have developed alternative approaches to computing 
structures and properties by simplifying portions of the calculation to circumvent 
these limitations. These methods are referred to collectively as semi empirical 
quantum methods. 

Semi empirical methods utilize approaches which are similar to ab initio 
methods, but several approximations are introduced to simplify the calculations. 
Rather than performing a full analysis on all electrons within the molecule, some 
electron interactions are ignored. These methods include the Huckel approach for 
aromatic compounds (in which the outer electrons in conjugated systems are treated, 
but the inner (or core) electrons are ignored) and the Neglect of Differential Overlap 
formalisms found in the CNDO (Complete Neglect of Differential Overlap) and 
INDO (Intermediate Neglect of Differential Overlap). In these methods, the more 
complex portions of the ab initio calculation are ignored or set to zero. Other semi 
empirical approaches replace complex portions of the calculation with parameters 
which are derived from experimental data. 

While semi empirical methods require less computer resources than ab initio 
methods, they are still compute intensive. In general, calculations are routinely 
performed on compounds which contain up to 100 atoms. The chief drawback of the 
method is that its application is limited to systems for which appropriate parameters 
have been developed. 

Experimental chemists routinely work with compounds which range in size from 
several hundred atoms (drug candidates, monomers, agricultural chemicals, etc.) to 
several thousand atoms (proteins, nucleic acids, carbohydrates, polymers, etc.). The 
computational requirements for quantum mechanical approaches render these 

18 



Basics 

methods unusable for routine analysis of these types of compounds. Thus, a further 
simplification in the way molecular geometries and their associated properties are 
computed is required. This approach is the molecular mechanics or force field 
method. For the present work, Non-computational quantum chemistry using force 
field calculations has been applied. 

Molecular mechanics [9] is a mathematical formalism which attempts to 
reproduce molecular geometries, energies and other features by adjusting bond 
lengths, bond angles and torsion angles to equilibrium values that are dependent on 
the hybridization of an atom and its bonding scheme (this atom description is referred 
to as the atom type). Rather than utilizing quantum physics, the method relies on the 
laws of classical Newtonian physics and experimentally derived parameters to 
calculate geometry as a function of steric energy. The general form of the force field 
equation is 

Epot =.. 
Ebnd + . 
Eang + . 
Etor + . 
Eoop +. 
Enb + . 
Eel ………………….………….2.6 (a) 

Epot is the total steric energy which is defined as the difference in energy between 
a real molecule and an ideal molecule. Ebnd, the energy resulting from deforming a 
bond length from its natural value, is calculated using Hooke's equation for the 
deformation of a spring (E = 1/2 Kb (b -bo)2 , where Kb is the force constant for the 
bond, bo is the equilibrium bond length and b is the current bond length). Eang, the 
energy resulting from deforming a bond angle from its natural value, is also calculated 
from Hooke's Law. Etor is the energy which results from deforming the torsion or 
dihedral angle. Eoop is the out-of-plane bending component of the steric energy. Enb is 
the energy arising from non-bonded interactions and Eel is the energy arising from 
coulombic forces. 

When the terms shown in the general form of the force field are expanded, the 
equation becomes : 

E pot =. 
½ Kb (b-bo) 2 + . 
½ K. 
(.-.0)2 +. 
½ K. 
(1+Cos N.)2 + . 
½ K. 


(.-.o)2 + .((B/r)12 – (A/r) 6) +.(qq/r)……………….2.6 (b) 

19 



Basics 

The manner in which these terms are utilized to build a model is referred to as the 
functional form of the force field. The force constants: Kb ,K. 
,K., K. 
and the 

equilibrium values: b0, .0, k.,K . 
; are atomic parameters which are 

experimentally derived from X-ray, NMR, IR, microwave, Raman spectroscopy and 
ab initio calculations on a given class of molecules (alkanes, alcohols, etc). The 
energy of the atoms in a molecule is calculated and minimized using a variety of 
directional derivative techniques. 

In contrast to ab initio methods, molecular mechanics [7] is used to compute 
molecular properties which do not depend on electronic effects. These include 
geometry, rotational barriers, vibrational spectra, heats of formation and the relative 
stability of conformers. Since the calculations are fast and efficient, molecular 
mechanics can be used to examine systems containing thousands of atoms. 

Each of the methods described above are used to calculate the energy of a 
compound in a specific 3D orientation and to optimize the geometry as a function of 
energy (i.e., adjust the coordinates of each of the atoms and recompute the energy of 
the molecule until a minimum energy is obtained). Coupled with other numerical 
techniques, they also can be used to simulate the time-dependent behaviour of 
molecules (molecular dynamics) and explore their conformational flexibility 
(conformational search). 

Molecular dynamics combines energy calculations from force field 
methodology with the laws of Newtonian (as opposed to quantum) mechanics. The 
simulation is performed by numerically integrating Newton's equations of motion 
over small time steps (usually 10-15 sec or 1 fsec). The simulation is initialized by 
providing the location and assigning a force vector for each atom in the molecule. The 
acceleration of each atom is then calculated from the equation a = F/m where m is the 
mass of the atom and F the negative gradient of the potential energy function (the 
mathematical description of the potential energy surface). The Verlet algorithm is 
used to compute the velocities of the atoms from the forces and atom locations. Once 
the velocities are computed, new atom locations and the temperature of the assembly 
can be calculated. These values then are used to calculate trajectories, or time 

20 



Basics 

dependent locations, for each atom. Over a period of time, these values can be stored 
on disk and played back after the simulation has completed to produce a "movie" of 
the dynamic nature of the molecule. 

21 



CHAPTER III 
MATERIALS AND METHODS 

3.1 Substrate 
An STM specimen needs a substrate that is extremely flat, down to the atomic 
level. If the specimen is uneven, the STM probe will have difficulties in scanning very 
steep pits or ridges. Other defects, such as single atoms sitting on an otherwise flat 
substrate, will also be a problem since the atoms themselves may function as 
unwanted STM probes, destroying the desired image. 

HOPG (Highly Oriented Pyrolytic Graphite or Highly Ordered Pyrolytic 
Graphite crystals are widely used as substrates in STM (Scanning Tunnelling 
Microscopy). The most distinguishing features of HOPG which enable this 
application are a very smooth surface and electro conductivity. 

HOPG, is a relatively new form of high purity carbon, provides surface 
microscopists with a renewable and smooth surface. Unlike mica, HOPG is 
completely non-polar and, for samples where elemental analysis will also be done, it 
provides a background with only carbon in the elemental signature. The extreme 
smoothness of HOPG makes results in a featureless background, except of course, at 
atomic levels of resolution 

Graphite in general and HOPG in particular are described as consisting of a 
lamellar structure, like mica, molybdenum disulphide and other layered materials that 
are composed of stacked planes. All of these examples of lamellar structures have 
much stronger forces within the lateral planes than between the planes, thus 
explaining the characteristic cleaving properties of all of these materials. 

HOPG itself is an interesting object for STM investigations. One can measure 
the surface roughness, microscopic surface features, arrangement of the carbon atoms 
on the HOPG surface, etc. Besides, HOPG images at the atomic level can be used for 


Materials and Methods 

calibrating STM for high-resolution imaging. From the images obtained from the 
STM this experiment of HOPG; one can also measure and interpret the surface 
roughness, microscopic surface features, and the arrangement and interatomic 
distances of the carbon atoms on the HOPG surface. 

Other popular materials that provide large, atomically flat surfaces include 
mica, quartz, and silicon. These materials are insulators, so to be used for STM a thin 
layer of noble metal (mainly gold or platinum) is deposited on the surface. Annealing 
(heating and then slowly cooling) the metal layer helps to smooth the surface and 
produce large flat areas. 

3.2 Adsorptive Substances 
Among the various adsorptive substances, the following substances were 
analysed via OSWD technique on fresh HOPG substrate. 

(i) Perylenetetracarboxylicdianhydride (PTCDA) : 
PTCDA was used initially as a reference material, as to know if it fits well to 
OSWD technique, and if the Tunnelling Spectroscopy data obtained via this 
OSWD technique fits well to the data already published for PTCDA. 

. 
CAS Number : 128-69-8 
. 
Supplier : Lancaster 
. 
Structural Formula: 



Figure 3.2 (a): Structural Formula of PTCDA. 

(ii) Alizarin: 
Bio-Organic Semiconductor Alizarin is an important hydroxyanthraquinone 
pigment, which tends to form metal chelate complexes, which are used as natural 
pigments since ancient times. It has been used as a reference material in the 

23 



Materials and Methods 

current research work, owing to its ability to self assembles into ordered and 
stable supramolecular monolayers under ambient conditions. 


Figure 3.2 (b): Alizarin Pigment 

Alizarin, or 1, 2-dihydroxyanthraquinone, mordant vegetable dye obtained 
originally from the root of the madder plant (Rubia tinctorum), in which it occurs as a 
glucoside. A method for the synthesis of alizarin was first discovered (1868) by Karl 
Graebe and Karl Liebermann, German chemists. With salts of metals the compound 
forms brilliant lakes, although by itself it is a poor dye. Turkey red is produced with 
an aluminium mordant, other shades of red with calcium and tin salts, dark violet with 
iron mordants, and brownish red with chromium. Purpurin, also used in dyeing, 
occurs with alizarin in madder and is produced synthetically. [21] 

Natural dyes from plants (e.g. Madder) added to a white base or substrate. 
Dyes include dozens of hydroxyanthraquinones (e.g., alizarin) from plants. It is one of 
the most stable natural pigments. Madder was formerly used in large quantities for 
dyeing textiles and is still the color for French military cloth. The cultivation of 
madder root almost ceased after a synthetic method for making alizarin was 
discovered by German chemists, Graebe and Liebermann, in 1868. 

. 
CAS Number : 72-48-0 
. 
Supplier : Fluka 
. 
Structural Formula: 



Figure 3.2 (c): Structural Formula of Alizarin. 

24 



Materials and Methods 

(iii) Alizarin Calcium Aluminium Complex (ACaAl): 
Alizarin is known to form colored complexes with a variety of ions, out of which 
Alizarin Calcium Alumium (ACaAl) Complex (Alizarin Krapplack in German) holds 
a dominant place. The phenomenon is referred to as chelation, in which Alizarin 
(chelant) form multiple bonds with a single metal ion of Aluminium. Historically, 
“lakes” referred to the first type of synthetic organic pigments made from water 
soluble dyes by precipitation onto alumina hydrate (aluminium hydroxide). The 
alizarin molecules are capable of forming six-member chelate rings with aluminium 
ions. Colored lakes formed by the metal ions and dye molecules resist extraction by 
water and organic solvents, which readily strip similarly, structured acid dyes. The 
sheer size of the complex may account for some of its insolubility. It is also likely that 
the large complexes are physically trapped within the fibre. [4]. This pigment was first 
of all used in India especially by ancient hermits to colour their clothes. 


Figure 3.2 (d): Alizarin Krapplack Kremer (Left), Alizarin Krapplack Schmincke 
(Right) 

. 
C.I Number : 58000:1 (Kremer) 

. 
Suppliers : Kremer, Schmincke 

. 
Structural Formula : 


Figure 3.2 (e): Structural Formula of ACaAl complex of Alizarin. 

25 



Materials and Methods 

(iv) Alizarin Violet 
Another common chelate complex of Alizarin is Alizarin Violet or Alizarin 
Sulphonate [Al]. It falls under the group of a class of hydroyanthraquinone pigments 
namely metal salts of hydroxyanthraquinone sulphonic acids.[4] 

It is a derivative of hydroxyanthraquinone sulfonic acid, a reddish violet 
Pigment Violet 5:1, 58055:1. 

. 
CAS Number : 1328-04-7 
. 
Supplier : Kremer 
. 
Structural Formula : 



Figure 3.2 (f) : Structural Formula of Alizarin Violet (Alizarin Sulphonic Acid 
Aluminium Complex). [15][16] 


Figure 3.2 (g) : Basic step involved in synthesis of Alizarin Violet Complex. 

Thus, Pigment Violet 5:1 (CAS: 1328-04-7) is an Aluminium complex of Alizarin 
Sulphonate. 

26 



Materials and Methods 

Pigment Violet 5:1 

Commercial interest in P.V.5:1, Constitution No. 58055:1 has declined 
considerably. The pigment continues to be used in industrial paints, especially 
throughout the USA. Its full shade is a brilliant, deep bluish maroon. In white 
reductions, the pigment produces clean, reddish violet shades. It lacks tinctorial 
strength and the coatings are fast to neither acid nor alkali. P.V.5:1 is also not very 
lightfast, which practically precludes its use in products for exterior application, 
particularly in reduced shades. P.V.5:1 is used to a certain extent in PVC. Plasticized 
PVC systems are fast to bleeding and reasonably lightfast in full shades. Addition of 
TiO2, however, markedly affects its light fastness. The pigment is heat stable up to 
170°C. [21] 

3.3 Binder 
The binder used in analyzing the organic semiconductors via STM using solid 
solid wetting approach is normally 8CB. However other binders like oil, epoxy resins 
etc can also be used, but largely their use depends on factors like availability and cost. 
The organic semiconductor can be analyzed on the graphite substrate either by Dry 
deposition method in which the pigment is just deposited onto the graphite substrate 
and is subsequently removed by using a stream of compressed dry air or with the help 
of adhesive tapes. Other method is to mix the pigment which is originally in powder 
form, with a viscous compound such as alkyd resin or the liquid crystal 8CB and 
applied under ambient conditions as a small droplet to the substrate. Here this liquid 
crystal 8CB acts as a binder which only acts as a suspension for the nanoparticles of 
the pigments and not a solvent for them. (Proven by centrifugal experiments which 
reveal that the solubility of the semiconductor pigments in such mixtures is below 
1ppm). [1] 

However the second method is generally preferred owing to the ease of 
handling the pigment mixed in 8CB and also keeping the minimal contamination 
factor in mind. 

27 



Materials and Methods 

Structure: 
4-Octyl-4’-Cyanobiphenyl (8CB) 


Figure 3.3 (a): Basic Structure of 8CB (left); Chemical formula and phase 
sequence of 8CB. 

Cryst = crystalline, SmA = smectic A, N = nematic, Iso = isotropic (right) 


Figure3.3 (b): 8CB used in the lab. Newly ordered (left), old (right). 
Suppliers: Synthon, Aldrich 


3.4 Preparations 
3.4.1 Tip 
Platinum Iridium and Tungsten tips are the most common tips used with RHK 
system. 

Platinum Iridium (Pt-Ir) is preferred for use in air because platinum does not 
easily oxidize. The tiny fraction of Iridium in the alloy makes it much harder. A tip 
made with pure platinum would naturally become blunt in a short time, as the atoms 
on the end of the tip would flow around to minimize the surface. 

28 



Materials and Methods 


Figure 3.4.1(a): Company: Ma TecK; Material: Pt / Ir 90/10 wire; Dimensions: 0.3 
mm* 1m 

The Pt-Ir tips are usually shaped by cutting Pt-Ir wire with a wire cutter. The 
standard technique uses a wire cutter (diagonal cutters) and a pair of pliers. Grab the 
wire with the pliers hold the cutters at an acute angle to the wire and as you start to cut 
into the wire pull with the pliers. 

Ideally as you start cutting through the wire it will weaken and break at the 
end of the point. The idea here is that because the wire broke apart the tip was never 
touched by the cutters, avoiding possible contamination of the tip. 

However, tips with copper wire that have achieved "atomic" resolution on 
graphite can also be made, and independently others have done the same on 
commercial machines. But copper tips don't last as long and at higher bias voltages 
they can quickly oxidize in the surface water contamination. It is not the best for the 
long term but it is cheep and easy. 

Tungsten wire is often used for STM tips. Tungsten (W) is very hard and it is 
easy to electro-chemically etch to a fine point. One drawback Tungsten slowly 
oxidizes in air. 


Figure 3.4.1 (c): Tungsten wire used to make STM tips. 
Tungsten can be electro-chemically etched in KOH or NaOH solutions. 

29 



Materials and Methods 

Preparation of Tungsten Tips: 

1. Wash the pliers and cutters to be used with acetone to avoid any contamination of 
the tips. 
2. Hold one end of the tungsten wire with the pliers and with the help of cutter, cut an 
appropriate length of the wire to be electrochemically etched. 
3. Adjust the tungsten wire in the holder and carefully lower down with the help of 
adjusting screws attached to the etching apparatus, just the tip of the wire in the KOH 
solution .Do not however during the preparation, touch the tungsten wire along the 
length and especially the tip. This is just to avoid any contamination. 
Figure 3.4.1 (d): Experimental set up for etching of tungsten tips. 

4. Gently increase the applied current and let the etching be done for sometime until a 
sharp etching noise is heard. 
5. Do not after this immediately lower the current as this might reduce the sharpness 
of the tips. Reduce the current value slowly to get exactly one molecule at the end of 
the tip. 
6. When the current value is reduced to zero, gently take out the etched tip first by 
unscrewing the screws of the etching apparatus, letting the tungsten wire with the 
etched tip come out of the beaker containing the KOH solution. (This is just to avoid 
any contact of the etched tip with the beaker containing KOH; as it might destroy the 
tip). 
30 



Materials and Methods 

7. Carefully with the help of pliers take out the tungsten wire with the etched tip and 
wash it with distilled water. This is basically done to wash off any hydrogen bubbles 
that might have gone attached to the sides of the tip while etching. 
8. Mount the prepared tips on a piece of thermocol to be used for the STM 
experiments. 
Figure 3.4.1 (e): Etched tungsten tip (left); Etched Tungsten tips preserved for days or 
even weeks (right). 

The main advantage with the Tungsten tips is that they can be used for days and even 
weeks. So at a time, several tungsten tips can be prepared in a row and saved for 
future STM experiments. 

3.4.2 Substrate 
Thus HOPG, because of its layered structure, cleaves almost like mica, 
making its preparation very simple. The usual approach is to take a piece of tape, 
press it onto the flat surface and then pull it off, and the tape invariably takes with is a 
thin layer of HOPG. 


Figure 3.4.2(a): Normal Tesa tape used for cleaving graphite and to get a fresh smooth 
cleaved surface to be used as an appropriate substrate for organic semiconductors for 
STM analysis. 

31 



Materials and Methods 

This freshly cleaved surface is what is used as sample substrate material. 


Figure 3.4.2 (b) : HOPG with fresh cleaved surface. 

As to how many cleavings per sample, cannot be predicted accurately and 
more or less depends on the personal experience. However it largely depends on the 
thickness of the block and the grades desired. For example, per a 2 mm thick block, 
for the best grades, it is reported that one can get 10-20 cleavings. For the lower level 
grades, the number of cleavings per 2 mm thickness will be less, but again, just how 
much less we can not predict with accuracy. 

Once a flat surface has been achieved, it is important to keep it free of 
contamination. A typical dust particle consists of millions of atoms, and could easily 
destroy the STM probe. Other hazards include chemical reactions between the 
specimen and the surrounding air that result in impurities on the substrate. These 
impurities could eventually make the STM probe crash. To prevent these problems, 
many STMs operate in high vacuum. Other techniques include periodic heating of the 
sample in a neutral atmosphere to remove impurities from the surface. 

3.4.3 Adsorptives 
There are two methods for the preparation of Adsorptives on the graphite 
substrate. One is the dry deposition method in which the pigment is directly deposited 
onto the graphite substrate, and is subsequently removed by using a stream of 
compressed air or with the help of adhesive tapes. 

32 



Materials and Methods 

The other method is to mix the pigment, originally in the powder form, with a 
viscous compound such as alkyd resin or liquid crystal 8CB and then apply it under 
ambient conditions as a small droplet onto the HOPG substrate. 

The second method was mainly employed for analysing the adsorptive 
substances chosen for the present work. The following figures give a brief description 
of the adsorptives prepared on the graphite substrate by the second method. 


Figure 3.4.3(a): Mixture of pigments suspended in 8CB 


Figure 3.4.3(b): A set of heater (left) and shaker (right) used to mix the pigment into 
the 8CB matrix in order to obtain a fine suspension of the nanoparticles. 


Figure 3.4.3 (c): Final application of the droplet of the pigment in 8CB on the graphite 
substrate. 

33 



Materials and Methods 

3.5 Scanning Tunnelling Microscopy (STM) 
The scanning tunnelling microscope (STM) is a type of electron microscope 
that shows three-dimensional images of a sample. In the STM, the structure of a 
surface is studied using a stylus that scans the surface at a fixed distance from it. 

It was developed by Gerd Binnig and Heinrich Rohrer in the early eighties, 
and allows the investigation of molecular and also atomic structures. It is the only 
technique with such a high resolution, that even works in air and in liquid.[18] 

The STM consists of a very fine, electrically conducting tip, which is guided 
over a sample surface at an extremely small distance. Owing to an applied voltage a 
current flows between tip and sample, where the variation of the current reveals 
information about the electronic structure of the surface and can also render a height 
relief. A computer is used to collect single scan points and calculates a detailed map 
of the sample surface. 

Today tunnelling microscopy is a standard technique in nanoscience, which is 
not only used to investigate samples at the atomic scale, but can be employed to 
construct structures atom by atom as well. 

The STM used for the current work was from the HUBER systems. 


Figure 3.5 (a) : HUBER STM. The shield minimizes drifts from noise in STM 
results.(left) ;Inside view of HUBER STM(right) 

34 



Materials and Methods 


Figure 3.5 (b): Basic Internal Configuration of HUBER STM 

The adjusting screws provide control over appropriate tip-sample interactions. 
Once the desired tip sample distance for tunnelling is achieved, the shield is lowered 
down and the scan is made to start with the help of RHK system. 

At a separation of a few atomic diameters, the tunnelling current rapidly 
increases as the distance between the tip and the surface decreases. This rapid change 
of tunnelling current with distance results in atomic resolution if the tip is scanned 
over the surface to produce an image. 

RHK (RHK SPM 100) is highly respected for powerful SPM controls, 
thoughtful hardware design, intensive service and lifetime support. [10] 


Figure 3.5 (c): Control equipment that boasts record-setting low noise, high 
configurability, and operability with scan heads of any variety. 

35 



Materials and Methods 


Figure 3.5 (d):When the tip sample distance is achieved with the help of adjusting 
screws in the HUBER STM, the RHK control system shows ΄ In Range΄ signal, after 
which the system is ready for the scans to get started (left) ; The Feedback control in 
RHK system (right). 

The Feedback provides accurate control over the tip sample distance to 
maintain constant tunneling current, and thus avoids any crash that might arise due to 
surface protrusions or steps. A 3D surface map of a conducting material can be 
constructed by monitoring and maintaining the tunneling current using rapid response 
electronic feedback circuits during line scans. 

XPMPro Control Software 

The true scientific work of interpretation and understanding begins after data 
has been acquired. XPMPro offers feature-filled analysis and processing techniques 
that powerfully illustrate every hidden and novel feature awaiting discovery in the 
data. XPMPro is replete with the professional tools that make a seamless transition 
from acquisition to publication. 


Figure 3.5 (e): XPM Pro Main Menu 

RHK launched XPMPro 2.0 software, to supply real-time data acquisition, 
analysis, and image processing for SPM nanotechnology research. XPMPro enables to 
manipulate atoms with more control, automatically track individual atoms moving 

36 



Materials and Methods 

across a surface, compensate for thermal drift in 3 dimensions, and extends advanced 
spectroscopy techniques. 


Figure 3.5 (f): Real Time Data Acquisition using RHK XPMPro Software (left); 
Navigation window of RHK XPMPro Software (right) 


STM thus provides the possibility for probing the local electronic structure of 
metals, semiconductors, and thin insulators on a scale unobtainable with other 
spectroscopic methods. Additionally, topographic and spectroscopic data can be 
recorded simultaneously. 

3.6 Image Analysis (SPIP) 
SPIP (Scanning Probe Image Processor) is primary software package for processing 
and 3D visualisation of images taken by scanning probe microscopes and more. 


Figure 3.6(a): SPIP toolbar displaying various modules available 

37 



Materials and Methods 

Among the various software modules available with this software, the most common 
used for the present work are: 

1. 
Auto Correlation averaging: It is a tool via which an image of the extracted 
repeated structures is obtained. In other words the repeated pattern is enhanced 
in this calculated image. When measuring the nanometer scale, the signal to 
noise ratio is often very small. Traditional filters cannot remove random noise 
without removing parts of the real surface structure. However, by the 
advanced correlation Averaging technique, it is possible to reduce non-
correlated noise and enhance repeated structures at the same time.[13] 
Figure 3.6 (b): Raw STM image (left); Auto Correlated STM image in SPIP 
(right). 

2. 
Extended Fourier analysis: This tool is for the Fourier transform study on the 
periodicities of an image, such as atomic lattice structures and to perform 
advanced filtering. Fourier spectrums contain important information about 
surface structures and distortion phenomenon. By a sub-pixel Fourier 
algorithm SPIP™ provides accurate information about selectable Fourier 
peaks, including wavelengths and the corresponding frequencies in Hz. This is 
particularly useful for diagnosing noise and vibration problems. By defining a 
pair of fourier peaks associated with the reciprocal unit cell, the spatial unit 
cell can be calculated automatically. 
38 



Materials and Methods 


Figure 3.6 (c): FFT analysis (blue) of the STM image (behind) in SPIP. 

For the current work, SPIP was mainly employed to calculate the lattice 
parameters of the unit cell of the adsorptive substances used. 


Figure 3.6 (d): Calculation of lattice vectors using SPIP 

These parameters are essential, as they served an input for further force filed 
calculations. 

3.7 Force field calculations 
Force field calculations are used mainly due to the bigness of the system under 
investigation and the kind of interactions( van -der Waals, H-bridges) involved, 
which otherwise is impossible via ab-initio calculations. Using force field 
calculations, the relative position of the molecules is calculated to decide between the 
rivalising structure-models. The basic implication is Molecular modeling and 
predicting structure and properties. [14] 

39 



Materials and Methods 

The software used for molecular modelling/computational chemistry using force 
filed calculations for this work was CERIUS 2, ACCELRYS INC. 

The model association with a force field is based on the assignment of each atom 
to a molecular mechanics type. The atomic type defines the force field parameters to 
be used in calculations of forces exerted on it. Since different force fields are 
described by different force parameters and different molecular mechanics types, a 
mechanism is required to associate atoms with types and partial charges for each 
supported force field. 


Figure 3.7 (a): Building up of a basic organic semiconductors model using molecular 
modelling. 

Among the various software tools available like, Sketch ring, Sketch atom, 
Adjust Hydrogen, Calculate H-bonds etc, another most important tool is the Display 
settings via which one can change the dispalay style of the model as to Line style, Ball 
stuck style , CPK or Polyhedron , as per user needs. 


Figure 3.7 (b): Various tools available for Molecular Modeling 

40 



Materials and Methods 


Figure 3.7 (c): The Ball and Stick style is convenient for molecule 
construction and editing, since atoms and bonds are clearly visible. In addition, the 
bond colour reflects their order (left) ; The Stick style is largely for presentations 
(right). 


Figure3.7 (d): The CPK style is basically preferred for analysis of STM patterns. 

The fundamental computation at the core of a force field-based simulation is 
the calculation of the potential energy for a given configuration of atoms (and cells, if 
requested and possible). The calculation of this energy, along with its first and second 
derivatives with respect to the atomic coordinates (and cell coordinates), yields the 
information necessary for minimization, harmonic vibrational analysis, and dynamics 
simulations. This calculation is actually performed by the simulation engine, or force 
field-based program. 

Typical use of energy minimization is the optimization of initial geometries of 
models constructed in a molecular modeling program such as Cerius2. 

The Importance of the force field in simulations lies in the fact that they help 
to understand that the force field--both the functional form and the parameters 
themselves--represents the single largest approximation in molecular modeling. The 

41 



Materials and Methods 

quality of the force field, its applicability to the model at hand, and its ability to 
predict the particular properties measured in the simulation directly determine the 
validity of the results. 

Thus, each molecular mechanics method is characterized by its particular force 
field which includes: a series of equations defining the variation of the potential 
energy of a molecule with respect to the positions of its constituent atoms; a series of 
atom types, defining the characteristics of a given chemical element within a specific 
chemical context; the atom type depends on hybridization, charge and the types of the 
other atoms to whcic it is bonded. ; one or more parameters sets that fit the equations 
and atom types to experimental data; these sets define force constants which are 
values used in the equations to relate atomic characteristics to energy components as 
well as structural data such bond lengths, valence and dihedral angles.[14] 

42 



CHAPTER IV 
PRELIMINARY CHARACTERIZATIONS 

4.1 Energy Dispersive Spectroscopy (EDX) 
Before starting with the chosen adsorptive substance for STM experiments, the 
most important preliminary thing is to have an EDX of the desired sample. This 
should be done to be sure of the exact chemical composition of the adsorbate. 

If the condition for binding energies is satisfied, the particular organic 
semiconductor shows self assembled monolayers under STM under ambient 
conditions. One should, however not blindly rely on the pigment suppliers for the 
pigment provided, but to ensure the exactness of the composition of the sample should 
go for EDX characterization first. At times what is supplied by the pigment 
companies, does not have the exact composition, of the sample as is specified. For 
example, refer the following STM image: 


Figure4.1 (a): Raw STM image of so called labelled Alizarin Tin complex by Kremer, 
showing distinct domains. 


Preliminary Characterizations 

EDX of the complex shows no Tin peak, but rather an Aluminium peak, 
proving it to be an Alizarin Aluminium complex rather than a Tin complex. 


Figure 4.1(b) : EDX of the sample which revealed it to be an Alizarin Aluminium 
complex rather than Alizarin Tin complex (No characteristic Tin peak), as mentioned 
by the suppliers. Supplier: Kremer 

On the similar lines, EDX of the sample labelled as Alizarin Copper complex 
was done too, to be sure of the chemical composition. Again the EDX spectra 
revealed it to be an Alizarin Aluminium complex rather than the expected Copper 
complex. 


Figure 4.1 (c) : EDX of the sample which revealed it to be an Alizarin Aluminium 
complex rather than Alizarin Copper complex (No characteristic Copper peak in the 
spectra) , as mentioned by the suppliers. Supplier: Kremer 

44 



Preliminary Characterizations 

Following are the EDX spectra’s of the pigments selected for this work viz: 
Alizarin, Alizarin Calcium Aluminium complex and Alizarin Sulphonic Acid 
complex, purchased from different suppliers. As mentioned above, the EDX 
characterization was essential for these pigments before starting off with the OSWD 
experiments. 

(i) Alizarin: 
Figure4.1 (d): EDX of Alizarin showing characteristic Carbon and Oxygen peaks as 
expected. Supplier: Fluka 

The pigment was confirmed via EDX as the Alizarin compound, and hence 
approved for further studies. 

(ii) Alizarin Aluminium Calcium complex: 
The above complex was ordered from two different companies viz: Kremer 
and Schmincke. From Kremer, again the compound was purchased twice, one referred 
to as Kremer (Old) complex, and the other as Kremer (New) complex. Kremer due to 
the above mentioned discrepancies with Alizarin Tin and Copper complex, was not 
considered very reliable, hence EDX was performed, especially on its products. 

The following figure shows the EDX of ACaAl complex obtained for the first 
time from Kremer, referred to as Kremer Old. 

45 



Preliminary Characterizations 


Figure 4.1 (e): EDX of Alizarin Aluminium complex (old-Kremer) showing a 
characteristic Aluminium peak. Supplier: Kremer 

However, on careful observation of above EDX with ACaAl (Kremer Old) 
complex, one comes across a Sulphur peak too at the right hand side of Aluminium 
peak. This could make one sceptic, on if the presence of Sulphur is as a contamination 
or is it due to maybe some mixture of ACaAl Complex and Alizarin Sulfonic Acid 
Aluminium Complex? 

To understand this, EDX of Alizarin pure Sulphur was made, which was from 
a reliable chemical company Acros. 


Figure 4.1 (f): EDX of Alizarin Sulphur (Alizarin Red S). Supplier: Acros 

On comparison, we observe that there is a S peak along with Na peak, but no 
Ca peak in the EDX of Alizarin Red S. However in the EDX of ACaAl from Kremer 
(old), there is a S peak and a Ca peak, but no Na peak. Now Alizarin Red S is actually 

46 



Preliminary Characterizations 

Alizarin SO3Na [4a], in which the S and Na ions participate in the complexization. So 
from the above EDX results, one can clearly interfere that the S present in ACaAl 
complex supplied by Kremer (old) is not participating in any complexization of the 
compound, and hence altering its behaviour, but it’s rather a contamination due to the 
S remains left during synthesis process, which were not properly washed out. 

Hence, the pigment ACaAl supplied from Kremer (old) can be analysed as an 
Aluminium Calcium complex of Alizarin (and not any sulphonic acid complex), for 
further studies via OSWD technique. 

However, EDX experiments of ACaAl complex obtained from Schmincke 
show characteristic Aluminium and Calcium peaks, characteristic of the pigment. 
Other elements like Na, Si, P and K are present, probably as the left out remains 
during synthesis of the complex, thus approving the above pigment from Schmincke 
for OSWD phenomenon. 


Figure 4.1(g): EDX of Alizarin Alumium complex. Supplier: Schmincke 

Even the ACaAl complex ordered from Kremer the second time (Kremer – 
New), was approved owing to the presence of prominent Al and Ca peaks present in 
the EDX, characteristic of the pigment. 

47 



Preliminary Characterizations 


Figure 4.1 (h): EDX of Alizarin Alumium complex (New-Kremer) , showing a 
characteristic Aluminium peak 

(ii) Alizarin Violet: 
Figure 4.1 (i): EDX of Alizarin Violet, showing a characteristic Sulphur peak. Since, 
the complexization involves Aluminium ions too; EDX reveals a characteristic 
Aluminium peak besides a Sulphur peak. Supplier: Kremer 

On analysing the above EDX, we see that there is no Ca peak, as present in all 
ACaAl complexes. And since Alizarin Violet is actually Alumium Complex of 

48 



Preliminary Characterizations 

AlizarinSO3Na [4], it can be interpreted that S is not present as a contamination, but 
there is indeed an Alumium complex of the derivative of Alizarin Sulphur. 

Also, the above EDX results reveal that in the pure compounds (both Alizarin 
and Alizarin S) C>O, and in all complexes C<O. This proves alizarin violet to be 
indeed a complex, and that the S is not present as a contamination. Again, as Alizarin 
Violet is just an Aluminium Complex and not a Calcium Aluminium Complex [4a] 
(also the fact there is already Na as a Cation), it is reasonable that there is no Ca peak, 
but only a Na peak (from SO3Na). 

Thus, what can clearly be derived from the EDX spectras is complexation, that 
weather the elements present in the sample are participating in the complexization of 
the sample or are they present just as a contamination. 

4.2 Raman Spectroscopy 
To detect the inhomogenity of the mixture (pigment+8CB) which points to a 
suspension rather than a solution, Raman Spectroscopy was made on Alizarin and its 
chelate complexes ordered from different pigment companies. 

In addition, Raman Analysis was preliminary done to compare the peaks of the 
pure pigment and the suspended compound in 8CB to determine if the mixing of the 
complex with 8CB somewhat alters the complexization. 


Figure 4.2 (a): Raman Spectra of Alizarin pure (left); Alizarin +8CB (right) 

49 



Preliminary Characterizations 


Figure 4.2 (b) : Alizarin Krapplack pure (left) Alizarin krapplack +8cb (right) 


Figure 4.2 (c): Alizarin Violet pure (left); Alizarin Violet +8CB (right) 

Discussions: 

Raman Analysis proved that the structural integrity of the complex is not 
affected by the 8CB system as the same fluorescence peaks can be detected both in 
the pigment powder and its mixture with 8CB.. 

The shifting of the peaks to a bit right for pure pigments and to a bit left for 
the pigment+ 8CB is attributed to the drift in the CRM instrument while taking 
measurements, and has nothing to do with the alteration of the pigment by 8CB, 
thereby contributing to a shift. 

Conclusion: 

Thus, it can be concluded that the pigments remain in their nanocrystalline 
state even after mixing with the liquid crystal 8CB. 

50 



CHAPTER V 
RESULTS AND DISCUSSIONS 

5.1 Introduction 
After the samples were confirmed via EDX as Alizarin, Alizarin Alumium 
complex and Alizarin Sulphonic Acid complex, from different pigment companies, 
the next step was the structural and electronic characterization of these trusted 
pigments. For the structural characterization of Alizarin, Alizarin Calcium Aluminium 
Complex and Alizarin Violet; STM, SPIP and Force field calculations were made. For 
the Electronic characterization of the above pigments, Tunnelling Spectroscopy 
experiments were performed. 

5.2 Structural Characterization 
The structural characterization of the pigments under consideration was done 
using STM images, SPIP analysis and Force field energy minimised calculations. 

5.2.1 Scanning Tunnelling Microscopy (STM) 
From the EDX results, it was proved that the samples under consideration 
were Alizarin, Alizarin Aluminium complex and Alizarin Sulphonic Acid complex. 
However, as the samples were mixed with 8CB for STM analysis, one cannot be sure 
if the pattern observed under STM is of the pigment or 8CB or due to some kind of 
contamination. Even though Raman Spectroscopy results revealed that 8CB acts just 
as a matrix for the suspension of nanoparticles and has nothing to do with the 
alteration of the complex, care must be taken while making STM measurements of the 
pigment mixed with 8CB. This is because at times it’s the 8CB pattern or the 
8CB+7CB (which might happen if the matrix is kept for a long time and thus the 8CB 
loses one carbon chain and forms 7CB or a mixture of both) is observed. So, to start 
with we labelled the samples under consideration as Sample-A, Sample-B and 
Sample-C. Also for comparison STM images of pure 8CB were made. 

For all the measurements of the samples with STM , usually the bias voltage 
was kept in between 0.4 V-1.2 V and the setpoint range in between 0.4amperes -1 


Results and Discussions 

amperes. However for viewing graphite, the bias was reduced upto 0.2V-0.1 V and 
setpoint upto 0.2 amperes. 

Results: 

(i) Sample-A: 
Figure 5.2.1(a): STM image of sample-A-dry deposition (2nm) (left); with 8CB 
(1nm) (right) 

(ii) Sample-B: 
Figure 5.2.1(b): STM image of Sample-B (Schmincke) under ambient conditions 
(5nm).(left) ; STM image of the same sample but from a different pigment company 
Kremer (1nm) (right) 

52 



Results and Discussions 

(iii) Sample-C: 
Figure5.2.1(c): Raw STM image of Sample-C (left-5nm).; STM image of Sample-C 
(2nm) (right-with graphite atoms at the base) 


Figure 5.2.1 (d): Zoomed STM image of Sample –C (1nm), keeping the same value of 
bias and set point as in Figure 5.2.1(c) right image. 

Discussions: 

In order to verify that the 8CB matrix does not trigger the adsorption, the 
experiments were repeated without any binder for the nanocrystals. After the direct 
deposition of the pigment powder (Alizarin) on a freshly cleaved HOPG surface and 
subsequent removal of the nanocrystals, supramolecular chain structures can be 

53 



Results and Discussions 

detected as shown in Figure 5.2.1(a) (right). In a similar experiment of direct 
deposition and subsequent removal of the nanocrystalline powder with indigo, no 
adsorption could be detected. [2] 

Another test to confirm if the monolayers obtained from STM are indeed of 
the pigments and not of the 8CB or due to any other contamination present, molecular 
extraction experiments were performed.[1] In this molecules from the self-assembled 
monolayer are extracted when the tip moves along predefined vectors with a 
decreased tip-sample distance of about 0.5 nm with respect to the imaging mode 
distance. The lower tip-sample distance increases the repulsive interaction between 
the tip and adsorbed molecules to an extent that leads to a desorption of molecules 
along the manipulation vectors. A high degree of control over the result of 
nanoextractions can be achieved if the following two basic requirements are 
complied: Firstly, the adsorbate compound may not be forced into relatively strong 
supramolecular networks by hydrogen bonds in order to prevent the collateral 
desorption of adjacent molecules within the network. Secondly, relatively strong non-
covalent bonds between an adsorbed molecule and the substrate (e.g. .-. interactions 
between large, flat aromatic molecules and the graphite substrate) should be present in 
order to prevent unintended extractions/desorptions when the tip-sample distance is 
only slightly decreased with respect to the imaging mode. This combination can be 
achieved by using compounds such as the organic semiconductor Alizarin, ACaAl 
complex and Alizarin Sulphonic Acid complex, besides the well known PTCDA.[23] 

Usually, no modifications are detected after nanomanipulation of monolayers 
at the solid/liquid interface (e.g. pure 8CB on graphite), since the periodic structure 
heals out immediately by filling the gaps with molecules from the liquid. In contrast, 
modifications within self-assembled Alizarin, ACaAl complex and Alizarin Sulphonic 
acid complex, monolayers grown by OSWD via suspended nanoparticles (Figures 
:5.2.1(a),5.2.1(b), 5.2.1 (c) ) are by far more stable, and even after several hours, the 
generated gaps could be identified in STM scans. This degree of stability can be 
explained by the characteristic of OSWD: a precondition for the adsorption of 
molecules via OSWD is a direct, physical contact between organic nanocrystals and 
the substrate. 

54 



Results and Discussions 

However, the gaps, which are usually below 4 nm, are too small to incorporate 
suspended pigment nanocrystals, because the average size of primary particles of 
commercially available pigments is about 50 nm. Thus, the nanocrystals cannot 
achieve a contact with the substrate surface exposed by the gap. This prevents the 
direct resupply of molecules to fill up the gaps. The model predicts that increasing the 
gap width should decrease the stability of the modifications. This is due to the 
increasing fraction of suspended particles with sizes suitable for a direct contact with 
the exposed substrate increases. In fact, this behaviour can be observed in our 
experiments. 

On the other hand, when the molecular extraction experiments were done on 
pure8CB monolayers on graphite substrate, results reveal that the gaps generated heal 
in the second scan itself. This can be attributed to the self healing property of 8CB , 
resulting in immediate refilling of the gaps (in the second scan itself) , thereby 
forming a continious regular pattern all over the surface (Figure: 5.2.1(e) ). 


Figure: 5.2.1 (e) STM image of a surface pattern grown by using a sample of 8CB 20nm. 


The above image shows a regular continuous 8CB pattern scattered all over the 
surface. The middle part is the step in the graphite substrate. The change in angle at 
the bottom of the image in the 8CB pattern is due to a drift in the STM system, and 
must not be confused with any domains of the pigment. 

55 



Results and Discussions 

Also figures 5.2.1(a) . 5.2.1 (b) and 5.2.1(c) show a graphite pattern next to the 
self assembled monolayers of the samples under consideration. This was normally 
achieved by reducing the bias voltage and increasing the set point (current), keeping 
the same scan size. The above setting of parameters reduce the tip sample distance to 
an extent that the upper monolayer is extracted by the tip, revealing a graphite 
(substrate) pattern underneath, at the same scan size. 

As a graphite pattern can always be seen by altering the bias and setpoint 
controls in the same STM image showing the sample monolayers, it can be interpreted 
that the large patterns observed of the samples cannot be an intercalate structures or 
something with HOPG, as peaking through an intercalation or graphite Moiree 
structure (eg. For graphene on graphite, both patterns are shifted with respect to each 
other in a way that a moiree pattern ca be seen) is not possible. Breaking through a 
structure and seeing the smaller structure of graphite tells that this is indeed an 
adsorbate and not an intercalate structure (intercalate: molecules beneath the surface 
layer of graphite, interfering with the graphite density of states and showing you 
pattern in STM). 

Further the zoomed image in case of Sample-C show a larger structure of the 
pattern in the zoomed image , and thus it can be interpreted that the monolayers 
observed are not due to any periodic noise, but is indeed the structure of the sample 
under observation i.e Alizarin Violet. 

Conclusions: 

Hence it can be concluded form the above results and discussions that the 
observed STM monolayers from Sample-A, Sample-B and Sample-C are not of the 
Alizarin, ACaAl complex and Alizarin Sulphonic Acid complex, and not due to any 
participation of 8CB or due to any contamination (like dirt). 

5.2.2 Scanning Probe Image Processor (SPIP) 
After the confirmation of the Samples-A, B and C as Alizarin, ACaAl 
complex and Alizarin Sulphonic Acid complex, SPIP processing was done on the 
obtained STM images. An equivalent graphite image at the same scan range (by 
reducing the bias and increasing the set point) was essential for the SPIP calculations. 

56 



Results and Discussions 

This was mainly because graphite image underneath the monolayer of the pigment at 
the same scan range, which is known to have a hexagonal pattern and thus its lattice 
parameters known ( a=b.c; .=120° ) ; provided the conversion factors for the SPIP 
calculations. Based on these conversion factors obtained from the corresponding 
graphite image, the lattice parameters of the observed monolayer were calculated. 

Results: 

(i) Sample-A: Alizarin: 
Figure 5.2.2(a): SPIP analysis of STM image obtained by using Alizarin sample. 

‘a’= 1.3....0.1nm; ‘b’= 0.745 ....0.1nm; ........2° 

(ii) Sample-B: ACaAl complex: 
Figure 5.2.2(b): SPIP analysis of STM image obtained by using Alizarin sample. 

‘a’= 1.2....0.1nm; ‘b’= 3.3 ....0.1nm; .........2° 

57 



Results and Discussions 

(iii) Sample-C: Alizarin Sulphonic acid complex: 
Figure 5.2.2 (c ) : SPIP analysis of STM image obtained by using Alizarin sample. 

‘a’= 2.8....0.1nm; ‘b’= 3.8 ....0.1nm; .........2° 

Discussions: 

The lattice parameters for pure 8CB as published [24] are: ‘a’ = 3.46 ±0.34nm; 
‘b’=2.55±0.24 nm; .=90±14°. Since the vectors calculated for Alizarin, ACaAl 
complex and Alizarin Sulphonic Acid complex are different from the above values, 
we can further interpret that the STM images used for SPIP anlysis are indeed of the 
pigments under consideration and not because of any interference of 8CB matrix. 

Also, the lattice vectors calculated for Alizarin reveals that a. b; .~90°. SPIP 
results for ACaAl complex and Alizarin Sulphonic acid complex show again that a. b; 
.~90°., making Alizarin and its complexes fall into the same class of Bravais lattices. 
However the vector ‘b’ calculated in case of ACaAl complex is very large as 
compared to vector ‘a’ , which otherwise in case of Alizarin , the lattice vectors do not 
differ to that extent. A similar situation can be observed in case of Alizarin Sulphonic 
acid complex, having lattice vector ‘b’ > lattice vector ‘a’ to a larger extent than in 
pure Alizarin. 

Conclusions: 

Thus it can be concluded that its highly conceivable that the STM pattern of 
sample –A is Alizarin, Sample-B ACaAl complex and Sample-C Alizarin Sulphonic 

58 



Results and Discussions 

Acid complex; and that the STM monolayers observed for the above Samples are not 
due to the presence of 8CB matrix. 

Moreover, it can be concluded that the complexization alters the lattice 
parameters of the actual compound. This may be attributed to the formation of some 
new bonds, breakage of some old bonds or modification in some already present 
bonds, as a result of complexization. Also the type of the metal ion participating in the 
complexization and its valency play an important role, which might alter the actual 
structural behaviour of the compound, resulting in altering of the lattice parameter 
values. 

5.2.3 Force Field Calculations 
A 3D model of Alizarin, ACaAl complex and Alizarin Sulphonic Acid 
complex was made using the Cerius 2 software package. Then H-bonds calculations 
and energy minimised calculations were applied, to see the energy minimised model 
of the structure. 3D rotation further helped in viewing the structure from different 
angles, assisting in the determination of actual arrangement and the relative position 
of the molecules, when energy minimised. 

Results: 

(i) Sample-A: Alizarin: 
Figure 5.2.3 (a) : Molecular Modelling of Alizarin without energy minised and H-
Bonds calculations (left); with energy minimised and H-bonds calculations (right) 


59 



Results and Discussions 

(ii) Sample-B: Alizarin Calcium Aluminium Complex: 
Figure 5.2.3(b): Force field calculations of Sample-B without Energy Minimised 
calculations (left); With Energy minimised calculations (right) 


Figure 5.2.3(c) Energy minimised structure of Sample-B, viewed from different 
angles. 

60 



Results and Discussions 

(iii) Sample-C: Alizarin Violet: 
Figure 5.2.3 (d) : Modelled structure of Alizarin Violet without Energy Minimised 
calculations (left); With Energy minimised calculations and H-bonds calculated 
(right). 


Figure 5.2.3 (e) : Alizarin Violet structure modelled with Energy minimised 
calculations-View from different angles 

Discussions: 

The initial step to force field i.e. modelling of structure and then applying energy 
minimised calculations to the model, revealed that complexization altered the 
structure of the original compound Alizarin. The calculations for ACaAl complex put 
forward that during complexization, two of the Alizarin molecules are in the plane 
and other two out of plane of paper. Similarly, calculations for Alizarin Violet reveal 

61 



Results and Discussions 

that the complexization alters the structure in a way that two of the Alizarin molecules 
are in a plane, above the third molecule. 

For further confirmation of the calculated structure, detailed force field 
calculations using SPIP evaluated lattice parameters are to be employed. The results 
then are arranged on the STM images to see if the pattern modelled and calculated fits 
well to the STM image obtained of the corresponding compound. 

5.3 Electronic Characterization –Tunnelling Spectroscopy(TS) 
PTCDA was used as a reference material, to be sure that the TS experiments work 
with OSWD technique. This was done as PTCDA is a well known organic pigment 
and many papers have been published in its context revealing its band gap. Thus 
PTCDA mixed in 8CB matrix was made to adsorb on the graphite substrate, and then 
TS (point spectroscopy) experiments were done on the STM images obtained. Even 
TS experiments were made on graphite substrate to be sure of the calculations made 
with RHK system. Then , on the similar lines, point spectroscopy of Alizarin and 
ACaAl complex were made to estimate their electronic properties (band gap).TS 
calculations are however to be made for further in depth study of Alizarin Sulphonic 
Acid complex, and were not done for the present work. 

For accuracy of the results, the following parameters must be kept in mind: 

1. The STM images and the TS must always be done simultaneously ( i.e TS 
should be made on the live STM images). The good quality of the STM picture before 
doing a tunneling spectroscopy is the most important parameter to take care of. To 
assure the reliability of the each tunneling spectroscopy, there must be a good STM 
image immediately before and after the point spectroscopy is made. 
2. The another thing to be kept in mind while performing point spectroscopy on 
the STM images is that acquisition of only one tunnelling spectrum per operation 
must be done. This is because if the tunnelling spectrum acquisition is done by several 
measures in the same measuring operation, the tunnelling spectrum data might not get 
repeated and we fail to get the exact value of band gap. This may be due to the 
absence of the control signals while STM is executing the TS measurements, which 
might cause a distance drift between the tip and the samples surface. 
62 



Results and Discussions 

3. The state of the STM tip can change highly after each TS measure. A change 
in the state of tip can give rise two totally different tunnelling spectra even if no 
parameter was changed. For the bandgap determination it is suggested to acquire at 
least 3 independent point tunneling spectra and then to average the them with a 
mathematical software. 
4. The STM parameters like bias voltage and the tunneling current set point 
cause minimal perturbations to the tunneling spectra compared with perturbations due 
those mentioned in the points 1 and 2 above. The reduction of bias voltage give rise to 
a narrowed bandgap region. We recommend to execute tunneling spectroscopy by 
bias voltage values as high as possible with out disturbing STM image. 
Results: 

(i) 
Figure 5.3 (a): Point Spectroscopy of PTCDA 

(ii) Graphite substrate 
Figure 5.3 (b): Point spectroscopy of graphite substrate. 

63 



Results and Discussions 

(iii) Alizarin: 
Figure 5.3(c): Point Spectroscopy of Alizarin 

(iv) Alizarin Calcium Aluminium Complex: 
Figure 5.3(d): Point Spectroscopy of Alizarin Calcium Aluminium Complex 

Discussions: 

The averaged spectrum obtained from the above TS results; show a band gap 
of around 2.2 eV for PTCDA, same as the published value.[25][26][27]. Even, the TS 
measurements with graphite show no band gap, as expected. Averaged tunnelling 
spectrum results for Alizarin show a band gap of 3.2 eV. 

For the ACaAl complex, point spectroscopy experiments show a band gap of 
around 2.0 eV . 

64 



Results and Discussions 

Conclusions: 

Thus we can conclude that the above organic pigments work well with the 
OSWD technique under ambient conditions. Moreover, the band gap values obtained 
from the TS experiments made on the STM images obtained using this simple 
technique of soild/ solid wetting, are reliable (referring to the data obtained for 
PTCDA and graphite). 

Alizarin and ACaAl both act as a wide band gap semiconductors, exhibiting a 
definite band gap. However, the complexization reduces the band gap of Alizarin, 
which may be attributed to some shift in HOMO and LUMO levels during 
complexization. 

65 



CHAPTER VI 
SUMMARY 

It has been shown that polyaromatic molecules can be transferred from a 
nanocrystal, which serves as a precursor, to a solid substrate, just by establishing 
mechanical contact (OSWD). Molecules deposited in this way then form self-
assembled supramolecular structures according to their structure and functional 
groups for hydrogen bonding. The method was demonstrated by means of Alizarin 
and its chelate complexes on graphite, a system which also offers the opportunity for 
rearrangement by guiding the self-assembly process through interaction with the 
scanning probe. 

The experiments with Scanning Tunnelling Microscope(STM), 
Nanomanipulation, Tunnelling Spectroscopy ( TS) and force field calculations; reveal 
that OSWD works also with bio-organic molecules and chelate complexes and that 
the advantages of this approach (self-assembly under ambient conditions in a non-
solvent environment, Nanomanipulation via molecular extraction) can be tapped. 
Moreover, the investigations reveal that Alizarin and Alizarin [Al] properties are well 
suitable for organic electronics and – in case of Alizarin [Al] – for molecular data 
storage. Molecular Modeling and DFT calculations will be applied for further in-
depth analysis of the supramolecular structure of Alizarin, ACaAl and Alizarin 
Sulfonic Acid complex. 

Although some restrictions apply for the solid–solid wetting to occur, namely, 
the adsorption energy of the molecule on the substrate has to exceed the binding 
energy on the surface of the initial nanocrystals, it is still applicable to a wide range of 
interesting compounds. In addition, the ease of preparation renders this novel 
extremely economic preparation method highly interesting for future applications. 
The fact that computationally inexpensive force-field simulations appear to predict the 
applicability of the method for a given system correctly certainly helps to pave the 
road for a new preparation technique for self-assembled molecular monolayers. 


CHAPTER VII 
OUTLOOK 

The experiments show that OSWD (Organic Solid/Solid Wetting Deposition) 
works also with bio-organic molecules and Chelate complexes and that the advantages 
of this approach (interfacial self -assembly under ambient conditions in a non-solvent 
environment, nanomanipulation via molecular extraction) can be tapped. 

Nanomanipulation: A gap within a molecular monolayer can be created by 
reducing the STM tip-sample distance and moving the STM tip along a predefined 
path. The lower tip-sample distance increases the repulsive interaction between the tip 
and adsorbed molecules to an extent which leads to the desorption of molecules along 
the manipulation vectors. [2] 


Figure 7.1: STM Nanomanipulation of ACaAl [2] 

Results as depicted in Figure 7.1 indicate that this approach may in principal 
open up the way for devices which offers a data storage density in the regime of 1 
Tbit/in2 and, at the same time, can both be fabricated and written totally under 
ambient conditions with a low preparational effort. 


Outlook 

The STM images obtained , SPIP and Force filed calculations done specially 
on Alizarin Sulphonic Acid complex, reveal excellent results, thus opening up a way 
for further studies of the complex using Molecular Modelling and DFT calculations, 
thereby making it a promising candidate for better understanding of complexization 
phenomenn via OSWD technique. 


Figure 7.2: STM -Alizarin Sulphonic Acid complex 

Also, Molecular Modelling and DFT calculations will be applied for further 
in-depth analysis of the supramolecular structure of Alizarin, ACaAl and Alizarin 
sulfonic acid complex. 

68 



APPENDIX: Tunnelling spectroscopy parameters. 

. 
The Navigation window is the main control window, via which various 
parameters like scan size, scan speed, scan direction, pulsing etc can be 
applied. The big red square defines the maximum scan area, whereas the small 
yellow square, defines the particular area under investigation. 


. 
A small pulse can be provided, while the scans are running, to improve the tip-
sample interaction. Pulse 1 can be used for weak pulsing, whereas for strong 
pulsing, Pulse 2 is used. 



APPENDIX-Tunnelling Spectroscopy Parameters 

. 
For Tunnelling Spectroscopy, the parameters mainly used in the navigation 
window are Mouse Action: Modify scan area, Add specific Location and 
Drag/Move tip. Another parameter that is essential to TS is the reference 
location: Load image, which loads the live STM image into the yellow square 
of the navigation window, for TS experiments. 


. 
After the STM image has been loaded, settings can be applied on weather 
single point spectrum or multiple point spectrum is required (Point 
Spectroscopy). This is mainly done by ‘Samples/point’ and ‘Spectra to 
acquire’ parameters. Again the Scan mode can be either adjusted to single or 
continuous as per requirements. 

70 



APPENDIX-Tunnelling Spectroscopy Parameters 


. 
Another important parameters involved in TS are the output control tools; 
which help in adjusting the spectroscopy type to either ‘ramp’ or ‘discrete” 
and thereby adjusting the current and voltage values as per the output required. 


71 



APPENDIX-Tunnelling Spectroscopy Parameters 

. 
Display settings in the TS graph can be altered via the Display Settings 
window. It helps in adjusting the title, X-label, Y-label , Background colour of 
the TS graph etc, as per the user requirements . 


72 



REFERENCES 

[1] 
Frank Trixler, Wolfgang M. Heckl, Various approaches to control solid/solid 
wetting self-assembly of organic semiconductors with STM , Modern 
Research and Educational Topics in Microscopy. A. Mιndez-Vilas and J. Dνaz 
(Eds.), 2007 
[2] 
Frank Trixler, Thomas Markert, Markus Lackinger, Ferdinand Jamitzky, 
Wolfgang M. Heckl, Supramolecular Self-Assembly Initiated by Solid–Solid 
Wetting, Chemistry-A European Journal, 2007 
[3] 
E. I. Ko, Role of solid/solid wetting in catalysis, in: Berg, J. C. (ed.): 
Wettability. Dekker, New York (1993). 
[4a] 
W. Herbst, K. Hunger, Industrial organic pigments, Third Edition, Wiley-
VCH, Weinheim, 2004. 

[5] 
Organic Semiconductors-The Basics, OrgWorld 
[6] 
Zhimin Hao , Abul Iqbal , Some aspects of organic pigments , Ciba Specialty 
Chemicals, Pigments Division, CH-1723 Marly, Switzerland 
[7] 
Warren J. Hehre, Leo Radom, Paul v.R. Schleyer and John A. Pople, Ab Initio 
Molecular Orbital Theory, John Wiley & Sons, New York, 1986. 
[8] 
J.J.P. Stewart, Kenny B. Lipkowitz and Donald B. Boyd (editors) Semi 
empirical Molecular Orbital Methods, in Reviews in Computational 
Chemistry, VCH Publishers, 1990, vol. 1 , pages 45-81. 
[9] 
Norman L. Allinger and U. Burkert, , Molecular Mechanics, ACS Monograph 
177, Washington, DC, American Chemical Society, 1982. 

References 
[10] Jerzy Cioslowski , Kenny B. Lipkowitz and Donald B. Boyd (editors), Ab 
Initio Calculations on Large Molecules: Methodology and Applications, , in 
Reviews in Computational Chemistry, VCH Publishers, vol. 4, 1993, , pages 
1-33. 
[11] Operation Manual: Confocal Raman Microscope CRM 200. WITec 
[12] K. Hunger (ed.), Industrial Dyes, Wiley-VCH, 2003, p. 59–67. 
[13] SPIP Brochure: Image Metrology 
[14] Edward J. Maginn., Molecular Modeling and Theory. 
[15] Berneth, H.: Farbstoffe -eine άbersicht. Bayer AG, Leverkusen 2005 
[16] Baars, Gόnther: Das Fδrben von Naturfasern mit Naturfarbstoffen. in: 
Praxis der Naturwissenschaften -Chemie. 47 (1998), 24-32. 
[17] Robert Feller, Roy Ashok, Elisabeth West Fitzhugh, Barbara Berrie, Artists' 
Pigments: A Handbook of Their History and Characteristics , Oxford 
University Press, 1994-2001. 
[18] G. Binnig, H. Rohrer, Ch. Gerber, and E. Weibel, Phys. Rev. Lett. 50, 120 123, 
1983. 
[19] Thomas Mόller, Scanning Tunnelling Microscopy: A Tool for Studying Self-
Assembly and Model Systems for Molecular Devices, (Veeco) 
[20] C. Julian Chen, Introduction to Scanning Tunneling Microscopy, Oxford 
University Press New York (1993). 
[21] E.G. Kiel and P.M. Heertjes, J. Soc. Dyers Col. 79 (1963) 21–27. 

74 



References 

[22] 
S. Gόnther, M. Marsi, A. Kolmakov, M. Kiskinova, M. Noeske, E. Taglauer, 
U. A. Schubert, G. Mestl and H.Knozinger, J. Phys. Chem. B 101 (48), 10004 
(1997). 
[23] 
C. Kendrick, A. Kahn and S. R. Forrest, Applied Surface Science 104/105, 
586 (1996). 
[24] 
F. Stevens, D. L. Patrick, V. J. Cee, T. J. Purcell, and T. P. Beebe Jr., 
Transition from Epitaxial to Nonepitaxial Ordered Monolayers in Pyrolyzed 
8CB Studied by STM, Langmuir, Vol. 14, No. 9, (1998) 
[25] 
N Nicoara, O Custance, DGranados, JMGarc΄ia,, J MG΄omez-Rodriguez1, 
AMBar΄o1 and J M΄endez , Scanning tunnelling microscopy and spectroscopy 
on organic PTCDA films deposited on sulfur passivated GaAs(001), J. Phys.: 
Condens. Matter 15 (2003) 
[26] 
J.B. Gustafsson *, E. Moons, S.M. Widstrand, L.S.O. Johansson, Growth and 
characterization of thin PTCDA films on 3C-SiC(001)c(2 x 2), Surface 
Science 600 (2006) 
[27] 
I.G. Hill a,1, A. Kahn a,), Z.G. Soos b, R.A. Pascal, Jr., Charge-separation 
energy in films of p-conjugated organic molecules, Chemical Physics Letters 
327 (2000). 
75 



PUBLICATIONS 




Publications 


77