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Self-Assembled Monolayers on Gold Substrates made
from Functionalized Thiols and Dithiols
Dissertationzur Erlangung des Grades
eines Doktors der Naturwissenschaftender Fakultät für Chemie
der Ruhr-Univeristät Bochum
Vorgelegt von
Mihaela Georgeta Badin
Aus Brasov/Rumänien
Bochum 2007
Self-Assembled Monolayers on Gold Substrates made
from Functionalized Thiols and Dithiols
Tag der mündlichen Prüfung:
23.11.2007
Prüfungskommission:
Referent: Prof. Dr. Ch. Wöll
Korreferent: Prof. Dr. R. Fischer
Vorsitzender: Prof. Dr. R. Heumann
Die vorliegende Arbeit wurde im Zeitraum von Dezember 2003 bis März 2007 am Lehrstuhl
für Physikalische Chemie I der Fakultät für Chemie der Ruhr-Universität Bochum unter
Anleitung von Herrn Prof. Dr. Christof Wöll angefertigt.
Dedicatie
A plecat de langa noi si s-a dus printre straini,
Sa patrunda-n miezul cartii, in adancul ei cuvant.
S-a luptat sa faca totul ca sa fie la-naltime,
Sa se multumeasca-n sine si pe noi cei dragi parinti,
Ca asa e bine-n viata, sa le faci cum se cuvine.
A fost munca si sudoare si o grija permanenta,
Ca sa faca totul bine si sa fie foarte-atenta.
A fost greu, dar a trecut si-a ajuns unde-a dorit.
Acum drumul e deschis, ca sa faca fapte mari,
Si sa fie printre lume, cu dorinte tot mai tari.
Dupa-atata straduinta si cu un bagaj frumos,
O sa mearga inainte, ca sa-i fie de folos.
Dar sa fie foarte-atenta, ca sfarsitu-abia incepe,
Si ca viata ii ofera multe griji si bucurii,
Ca sa fie foarte tare si sa urce, fara nici-o ezitare.
Stelian Badin
Dedicated to my parentsAurica and Stelian Badin
Table of Contents
I
Table of contents
Table of contents ___________________________________________________________ I
Chapter One _______________________________________________________________ 1
Introduction _______________________________________________________________ 1
1. Motivation and Objective of the Work _______________________________________ 1
2. Outline of the Thesis _____________________________________________________ 3
Chapter Two _______________________________________________________________ 5
Basics and Techniques Used in This Work_______________________________________ 5
2.1. Infrared Spectroscopy __________________________________________________ 5
2.1.1. The Electromagnetic Spectrum 5
2.1.2. Molecular vibrations 7
2.1.3. Stretching vibrations 9
2.1.4. Infrared Spectrometer 12
2.1.4.1. Principle of Operation of FTIR- Spectrometer __________________________ 12
2.1.4.2. Rinsing Gas Supply and its Influence on the Measurement ________________ 14
2.1.4.3. RAIRS- Setup ____________________________________________________ 15
2.2. X-ray Photoelectron Spectroscopy (XPS) __________________________________ 17
2.3. Near Edge X-ray Absorption Fine Structure (NEXAFS)_______________________ 20
2.4. Scanning Tunneling Microscopy (STM) ___________________________________ 23
2.5. Ellipsometry (SE) ____________________________________________________ 25
2.6. Water contact angle (CA) ______________________________________________ 26
2.7. UV-VIS Spectroscopy _________________________________________________ 28
Chapter Three_____________________________________________________________ 30
Self-Assembled Monolayers and Sample Preparation _____________________________ 30
3.1. Self-Assembled Monolayers ____________________________________________ 30
3.1.1. Introduction_______________________________________________________ 30
Table of Contents
II
3.1.2. Self-Assembly Kinetics and Mechanism _________________________________ 31
3.1.3. Self-Assembled Monolayer Structure ___________________________________ 32
3.2. Preparation and Characterization of Gold Substrates ________________________ 35
3.2.1. Introduction_______________________________________________________ 35
3.2.2. Preparation and Characterization of Gold on Silicon Wafers ________________ 35
3.2.3. Preparation and Characterization of Gold on Mica Substrates_______________ 36
3.3. Preparation of Self-Assembled Monolayers Films ___________________________ 36
3.4. Preparation of Bulk Pellets for the IR measurements_________________________ 37
3.5. Chemicals used in this work ____________________________________________ 37
3.6. Laboratory Equipment ________________________________________________ 38
Chapter Four _____________________________________________________________ 39
Triptycenethiol-based Self-Assembled Monolayers _______________________________ 39
4.1. Introduction and Objective of the Work Presented in this Chapter ______________ 39
4.2. Self-Assembly Process of Triptycenethiol on Au(111) ________________________ 40
4.2.1. Introduction_______________________________________________________ 40
4.2.2. Results ___________________________________________________________ 41
4.2.2.1. XPS and Ellipsometry _____________________________________________ 41
4.2.2.2. IRRAS _________________________________________________________ 43
4.2.2.3. NEXAFS _______________________________________________________ 46
4.2.2.4. STM ___________________________________________________________ 48
4.2.3. Discussion ________________________________________________________ 49
Chapter Five ______________________________________________________________ 52
Influence of the Leaving Group in case of Triarylaminethiols ______________________ 52
5.1. Introduction and Objective of the Work Presented in this Chapter ______________ 52
5.2. Self-Assembly Process of the Triarylaminethiols on Au(111)___________________ 54
5.2.1. Introduction_______________________________________________________ 54
5.2.2. Results ___________________________________________________________ 54
Table of Contents
III
5.2.2.1. IRRAS _________________________________________________________ 54
5.2.2.2. XPS ________________________________________________________ 57
5.2.2.3. NEXAFS _______________________________________________________ 58
5.2.2.4. Deprotection Process _____________________________________________ 60
5.2.2.5. STM ___________________________________________________________ 62
5.2.3. Disscussion _______________________________________________________ 64
Chapter Six _______________________________________________________________ 66
Formation of Self-Assembled Monolayers from Alkane Thioacetates ________________ 66
6.1. Introduction and Objective of the Work Presented in this Chapter ______________ 66
6.2. Preparation of the SAMs of C12SAc ______________________________________ 67
6.2.1. Introduction_______________________________________________________ 67
6.2.2. Results ___________________________________________________________ 67
6.2.2.1. IRRAS _________________________________________________________ 67
6.2.2.2. Water contact angle ______________________________________________ 71
6.2.2.3. Ellipsometry ____________________________________________________ 71
6.2.2.4. XPS ___________________________________________________________ 71
6.2.2.5. NEXAFS _______________________________________________________ 73
6.2.2.6. STM ___________________________________________________________ 74
6.2.2.7. Re-immersion of C12SAc-SAMs into thiol solutions ______________________ 78
6.2.3. Discussion ________________________________________________________ 80
Chapter Seven_____________________________________________________________ 83
Determination of Trans/Cis Isomerization of Azobenzene Molecules_________________ 83
7.1. Introduction and Objective of the Work Presented in this Chapter ______________ 83
7.2. Preparation of the solutions containing the azobenzene molecules ______________ 85
7.2.1. Results ___________________________________________________________ 85
7.2.1.1. UV/VIS Spectroscopy _____________________________________________ 85
7.3. Preparation of the SAMs on gold surfaces (111) ____________________________ 86
Table of Contents
IV
7.3.1. Results ___________________________________________________________ 87
7.3.1.1. IR spectroscopy __________________________________________________ 87
7.3.1.2. Water contact angle (CA) __________________________________________ 91
7.3.1.3. STM ___________________________________________________________ 93
7.4. Discussion __________________________________________________________ 95
Chapter Eight _____________________________________________________________ 98
Summary and Conclusions __________________________________________________ 98
Chapter Nine_____________________________________________________________ 102
Appendix 103
9.1. List of figures 103
9.2. List of tables 106
9.3. List of references 110
Chapter One Introduction
1
Chapter One
Introduction
1. Motivation and Objective of the Work
Self-assembled monolayers (SAMs) consist of densely packed long-chain organic molecules,
which are chemisorbed on metal substrates through a sulfur head group, which has a specific
affinity for these surfaces [1]. The gold surface has been used in this work as a substrate,
because the gold surface is inert to oxidation and can be handled with few precautions and
does not require specialized facilities. For STM measurements the Au/mica substrate is very
adequate, because of the atomically flat and large terraces consisted by this gold surface.
These monolayers are closely related to many important technological applications such as
corrosion inhibition, adhesion promotion/inhibition [2], nano-fabrication and supra-molecular
assembly, molecular recognition [3], and bio-sensors [4], resulting in a broad interest in
SAMs from many subjects. Self-assembled monolayers are very complex, because of the
various interactions in the process of including the interactions between headgroup and
substrate, the interaction endgroup-endgroup, endgroup and substrate and the chain-chain
interactions.
Techniques employed in the characterization of the SAMs include ellipsometry [5, 6],
reflectance infrared spectroscopy (IRRAS) [5, 7], x-ray photoelectron spectroscopy (XPS),
near edge x-ray absorption fine structure [8], and scanning probe microscopy [9, 10] etc.
The purpose of this study was to investigate the arrangement and the structure of self-
assembled monolayers containing aromatic moieties, which have been given less attention
due to the synthetic difficulties and poor solubility and also to understand how the molecular
backbone will affect the structure of the monolayer. A lot of interest has been given by the
molecules protected with an acetyl group, to understand how the leaving of this group will
affect the kinetic of monolayer formation [11].
Thus, different adsorbates have been investigated in this work, including aromatic thiols,
aromatic thiols protected with acetyl groups, aliphatic thiol protected with acetyl groups and
aromatic dithiols SAMs on gold substrate, as shown in Figure 1. The molecular structure of
the first group contains triptycene moiety as a rigid molecule and also with a methylene
Chapter One Introduction
spacer between the aromatic moiety and the sulfur group. The second group of thiols contains
triarylamine groups and and all these molecules are protected by acetyl groups as a
termination of the sulfur group. The third group contains an aliphatic moiety protected by
acetyl group and the last group of investigated molecules contains an azobenzene
photoresponsive moiety and is terminated by dithiols.
Apart from the investigation of the films also an evaluation of applicability of the methods
used for the investigation is necessary.
2
Figure 1: Structure of thiols used in this study.
In this study, to permit an efficient ordering within the monolayers, the molecules chosen
were derived from triptycenes, which have not only an axis of higher symmetry (C3) but also
permit a coaxial attachement of both, the anchoring group (in our case a sulfur atom) and the
headgroup [12]. It is very interesting to understand how the nature of the triptycene molecular
backbone influences the structure of these monolayers.
The triarylaminethiols protected with the acetyl groups have been selected to achieve a better
understanding about the kinetic stabilization which is formed by the leaving of the thioacetate
group during the deprotection process. These SAM structures can then serve as excellent
model systems for studying bridge mediated electron transfer (ET) [13].
To achieve a better understanding about this deprotection reaction, we continue with the
investigation of a simple aliphatic thioacetates like C12SAC compared with C12SH. The
adsorption of C12SAc on gold substrate (111) is investigated using a broad set of experimental
Triptycenethiol
Triarylaminethiol
Dodecyl thioacetate
Azobenzene dithiol-carboxylate
Triptycenethiol
Triarylaminethiol
Dodecyl thioacetate
Azobenzene dithiol-carboxylate
Chapter One Introduction
3
techniques likewise in all chapters of this study, gracing incidence infrared spectroscopy, x-
ray photoelectron spectroscopy, contact angle measurements, XPS, and STM. Altogether the
experimental results allow for a very consistent description of the adsorption behavior. The
objective of this work was to give an explanation for the kinetic stabilization of flat lying
molecules or so-called striped phase, which is formed by the loss of the acetyl group.
Dithiols containing an azobenzene moiety have attracted considerable attention as a
possibility for creating photoresponsive materials [14-16]. The azobenzene molecules have
been selected because they are photoisomerizable from trans- to cis isomers and reversible
from cis to trans- isomers due to alternating the irradiation of UV light and blue light. The aim
was to understand how the structure of these SAMs will change by the irradiation, if this
process is really reversible.
2. Outline of the Thesis
To achieve a better understanding of the basic experimental findings described in this work,
the fundamental principles of the applied techniques will be given in chapter two. The
operation principle of reflection-absorption infrared spectroscopy (RAIRS) or FT-IR will be
presented first followed by the principles of x-ray photoelectron spectroscopy (XPS), near
edge x-ray adsorption fin structure (NEXAFS), scanning tunneling microscopy (STM),
ellipsometry (SE), water contact angle (CA) and finally UV/VIS spectroscopy.
In chapter three a small introduction into self-assembled monolayers is presented, their
kinetics and adsorption mechanism followed by the preparation of the gold substrates used in
this work, likewise gold deposited on silicon wafer used in case of RAIRS measurements,
contact angle, ellipsometry, XPS and NEXAFS. For measurements in the STM gold
evaporated on mica is suitable, because of the large flat (111) terraces separated by
monoatomically height steps (2.4 Å). This chapter highlights also the preparation of the
SAMs films, chemicals, technical equipment used in this study.
Chapter four reports the study of triptycene films like C0T, C1T and C3T using ellipsometry
(SE), reflection absorption infrared spectroscopy (RAIRS), X-ray photoelectron spectroscopy
(XPS) near-edge X-ray absorption fine structure spectroscopy (NEXAFS) and scanning
tunnelling microscopy (STM) techniques. Chapter five describes the formation of (SAMs)
from triarylaminethiols onto gold (111) substrates studied by using IR, XPS, NEXAFS and
STM techniques.
Chapter One Introduction
4
In chapter six it has been found that the monolayers derived from the thioacetate (C12SAc)
have a significantly different structure and are compared to the ones obtained from the
corresponding alkanethiol (C12SH).
Finally the chapter seven gives the results for azobenzene molecules under alternating the
irradiation with UV and blue light using the UV/VIS spectroscopy measured in case of
prepared solutions of these molecules and the investigations by the contact angle and STM on
prepared SAMs from azobenzene molecules.
Chapter Two Basics and Techniques Used in This Work
5
Chapter Two
Basics and Techniques Used in This Work
2.1. Infrared Spectroscopy
An important tool of the organic and inorganic chemist which was frequently used in this
work is Infrared Spectroscopy, or IR. This covers a range of techniques, the most common
type is absorption spectroscopy. IR is used to get information of the structure of a compound
and to determine the purity or composition of the sample [17, 18].
2.1.1. The Electromagnetic Spectrum
Infrared refers to that part of the electromagnetic spectrum between the visible and microwave
regions [19].
The radiation is characterized by its frequency or wavelength, which are connected through eq.
1. Frequency, ν is measured in Hz, where 1 Hz = 1/sec. Wavelength, λ is the length of one
complete wave period. It is often measured in cm (centimetres).
Eq. 1
c
and
c
,
where c is the speed of light, 103 10 cm/sec.
Energy is related to wavelength and frequency by the following formulas:
Eq. 2
hc
hE ,
where h=Planck’s constant, 6.6 10-34 joules-sec.
Note that energy is directly proportional to the frequency and inversely proportional to
wavelength.
The IR region is divided into three regions: the near, mid, and the far IR (see Figure 2). The
mid IR region contains wavelengths between 3 × 10-4 and 3 × 10-3 cm.
A wavenumber is the inverse of the wavelength in cm:
Chapter Two Basics and Techniques Used in This Work
6
Eq. 3
1
,
where is in units of cm-1 and is in units cm and now:
Eq. 4 hcE
The mid IR range corresponds to 4000-400 cm-1 (wavenumber). Infrared radiation is absorbed
by molecules and converted into energy of molecular vibration, when the radiant energy
matches the energy of a specific molecular vibration.
Figure 2: The IR regions of the electromagnetic spectrum.
The adsorption of the light to the properties of the material through which the light is
travelling is called Lambert Beer law [20, 21]:
cdA , where A is the absorbance, is the molar
extinction coefficient, c the concentration and d the distance that the light travels through the
material. Band intensities can also be expressed as absorbance (A), which is the logarithm, to
the base 10, of the reciprocal of the transmittance (Figure 3):
)1(log10 TA
Chapter Two Basics and Techniques Used in This Work
7
Certain groups of atoms absorb energy and therefore, give rise to bands at approximately the
same frequencies. The chemist analyzes a spectrum with the help of tables which correlate
frequencies with functional groups. The theory behind this relationship is discussed in the
next section on molecular vibrations.
2.1.2. Molecular vibrations
There are two types of molecular vibrations, stretching and bending. A molecule consisting of
n atoms has a total of 3 n degrees of freedom, corresponding to the Cartesian coordinates of
each atom in the molecule. In a nonlinear molecule, 3 of these degrees are rotational and 3 are
translational and the remaining corresponds to fundamental vibrations; in a linear molecule, 2
degrees are rotational and 3 are translational [22]. The net number of fundamental vibrations
for nonlinear and linear molecules is consequently:
Table 1: Number of vibrational degrees of freedom of nonlinear and linear molecules.
3000 2900 280070
75
80
85
OctadecanethiolSAM
Tra
nsm
itta
nce
/%
Wavenumber (cm-1)
3000 2900 2800
0.012
0.013
0.014 OctadecanethiolSAM
Ab
so
rban
ce
Wavenumber (cm-1)
Figure 3: The IR spectrum of octadecanethiol, plotted as transmission (left) and
absorbance (right).
Molecule Vibrational
nonlinear 3n - 6
linear 3n - 5
Chapter Two Basics and Techniques Used in This Work
The fundamental vibrations for H2O are given in Figure 4. Water, which is nonlinear, has
three fundamental vibrations, symmetrical and asymmetrical stretching modes and one of
scissoring (bending) vibration.
Carbon dioxide, CO2 is a linear molecule and exhibits four fundamental vibrations. The
asymmetrical stretch of CO2 gives a strong band in the IR at 2350 cm-1. Since CO2 is present
in the atmosphere this band will appears in all IR spectra, if the IR light passes through air.
The two scissoring or bending vibrations have the same frequency and are degenerate,
appearing in the IR spectrum both at 666 cm-1.
Th
no
sp
th
Symmetrical stretching Asymmetrical stretching Scissoring (bending)
Figure 4: Stretching and bending vibrational modes for H2O.
Figure 5: Stretching and bending vibrational modes for CO2.
8
e symmetrical stretch of CO2 (Figure 5) is inactive in the IR because this vibration does
t produce a change in the dipole moment of the molecule. The selection rules of the IR
ectroscopy are that to be IR active, a vibration must cause a change in the dipole moment of
e corresponding molecule. In general, if the dipole moment change is larger, the intensity of
Chapter Two Basics and Techniques Used in This Work
9
the band will be stronger in the IR spectrum [22].
An oscillating electric or magnetic moment can be induced in an atom or molecular entity by
an electromagnetic wave. Its interaction with the electromagnetic field is resonant if the
frequency of the latter corresponds to the energy difference between the initial and final states
of a transition (DE = hυ). The amplitude of this moment is referred to as the transition
moment.
The stretching and bending vibrations of the important organic group -CH2 are illustrated in
Figure 6 as follows:
Twisting, out-of-plane Rocking, in-plane Wagging, out-of-plane
1350-1150 cm-1 720 cm-1 1350-1150 cm-1
Figure 6: Stretching and bending vibrational modes for a –CH2 group.
The 3n – 6 rule does not apply since the –CH2 group represent only a portion of a molecule.
The bending vibrations occur at lower frequencies than corresponding stretching vibrations.
2.1.3. Stretching Vibrations
The stretching frequency of a bond can be approximated by Hooke’s Law. Two atoms are
treated as a simple harmonic oscillator composed of two masses joined by a spring:
Symmetrical stretching Asymetrical stretching Sccisoring, in-plane
2850 cm-1 2925 cm-1 1465 cm-1
Chapter Two Basics and Techniques Used in This Work
According to Hooke’s
Eq. 5
where k is the force co
In the classical harmon
of the spring. If this mo
Figure 7: Harmonic a
The vibrational energy
Eq. 6
where is the frequen
the force constant of th
be than E1 = 3/2h .
According to the selec
anharmonic potentials
10
m1 m2
law, the frequency of the vibration is related by the formula:
m
k
2
1 ,
nstant, m is the mass and is the frequency of the vibration.
ic oscillator the energy ishkxE 2
2
1
, where x is the oscillation
del was true, a molecule could absorb energy of any wavelength [22].
pproximation via potential of the oscillator V(r) [23].
is quantized and only the transitions must fit the formula:
20 )(
2
1)()()
2
1( rrkrVnEhn ,
cy of the vibration, n is the quantum number (0, 1, 2, 3, ….) and k is
e bond. The lowest energy level is E0 = 1/2h and the next level will
tion rule, only transitions to the next energy level are permitted. For
also transitions like 2 h , 3 h can be observed. These are called
Chapter Two Basics and Techniques Used in This Work
11
overtones in an IR spectrum and they are usually of lower intensity than the fundamental
vibration bands.
A record consequence of the molecule being an anharmonic oscillator is that the energy levels
become more closely with increasing interatomic distance and dissociation is possible.
If for a molecule the mass m is replaced by the reduced mass (for two atomic
molecules21
21
mm
mm
) eq. 5 turns into:
Eq. 721
21 )(
2
1
mm
mmf
c
,
where is the vibrational frequency (cm-1)
m1 and m2 are the mass of the atoms (g)
c is the velocity of the light (cm/s)
f is the force constant of the bond (dyne/cm)
As the force constant increases, the vibrational frequency (wavenumber) also increases.
Examples of the forces constant: single bond 5 × 105 dyne/cm
double bond 10 × 105 dyne/cm
triple bond 15 × 105 dyne/cm
As the mass of the atoms increases, the vibrational frequency decreases.
The regions of an IR spectrum where stretching vibrations are seen, depend on whether the
bonds are single, double, triple or bonds to hydrogen.
Table 2: Absorption by single, double and triple bonds observed in an IR spectrum.
Bond Absorption region, cm-1
C-C, C-O, C-N 800-1300
C=C, C=O, C=N, N=O 1500-1900
C≡C, C≡N 2000-2300
C-H, N-H, O-H 2700-3800
Chapter Two Basics and Techniques Used in This Work
12
2.1.4. Infrared Spectrometer
In the following the equipment to measure IR spectra will be presented:
Since the measured radiation contains the optical functions of all components of the
spectrometer, first of all a spectrum of I0 ( ) without sample is taken, which is called
reference or background. Subsequently (or parallel), a spectrum I ( ) but this time with
assigned sample is recorded with otherwise identical configuration of the spectrometer. By
computation of the absorbance
Eq. 8)(
)(lg)( 0
I
IA
one receives an appropriate spectrum, which corresponds to the Lambert-Beer law [21] and its
band intensities are proportional to the concentration and to the layer thickness. If sample and
reference are identical, then one receives a “zero-line” over the entire spectral region. It
defines the baseline of the spectrum.
2.1.4.1. Principle of Operation of FTIR- Spectrometer
In contrast to the classical spectrometers, where the spectral absorption of a sample is being
scanned, Fourier-Transform Infrared (FTIR) spectroscopy is an interferometric method. An
FTIR spectrometer consists in principle of an infrared source, an interferometer, the sample,
and the infrared detector.
The interferometer is the heart of the spectrometer and consists in its simplest form of a beam
splitter, a fixed mirror, and a moving mirror scanning back and forth. Therefore, the spectrum
is not directly measured but its interferogram, i.e. the IR intensity reaching the detector as a
function of the mirror position. The spectrum is subsequently obtained by Fourier
transformation of the interferogram from the time domain into the frequency domain [23].
Chapter Two Basics and Techniques Used in This Work
13
Figure 8: Schematic setup of FTIR- Spectrometer [23].
The major advantages of FTIR spectroscopy, as compared to conventional dispersive IR
spectroscopy, are the so-called multiplexing advantage (Felgett advantage: all the wavelength
are simultaneously collected) and the high energy flux reaching the detector (Jacquinot
advantage), therefore the FTIR spectrometers have a stronger intensity of light, which leads to
an improved signal to noise ratio and permits faster measurements. The schematic setup of the
FTIR spectrometer is shown in the Figure 8. The light which is leaving from the light source 1
is focussed with an ellipsoid mirror 2 into an aperture 3. With the help of the aperture 3 the
extension of the light source can be adapted. Afterwards the light will be reflected from the
paraboloic mirror 4 into the Michelson-Interferometer, where the KBr beam splitter will split
up the collimated light in two beams. After reflection 6 will comes the moveable mirror 7 and
the flat mirror 8. It is used only for the redirection of the light. On the other hand the
paraboloic mirror 9 will focus the light to the plane of the sample 10. Afterwards the ellipsoid
mirror 11 reflects the light to one of the two detectors 12. One of the detector is DTGS
(Deuteriertes Triglycinsulfat, D2N-(CD2-CO-ND)2-CH2-COOD) and the other one MCT
(Mercury-Cadmium-Telluride). The better signal to noise ratio of some orders of magnitude is
necessary for the measurement of self-assembled monolayers.
Chapter Two Basics and Techniques Used in This Work
14
In addition the expanding of a Monomode HeNe laser 13 (15803 cm-1) with the help of a
plane mirror 14 is linked into the polychromatically bundle and go together through the
interferometer. Mirror 8 possesses an opening and lets so the laser light to the three detectors
15 arranged in the triangle perpendicularly to the laser bundle.
The source of light is constructed to give large intensity and the adjustment takes place via
attenuation on the necessary intensity [24].
2.1.4.2. Rinsing Gas Supply and its Influence on the Measurement
Figure 9: Set up of rinsing gas supply.
Air consists to 79% of nitrogen (N2) and 21% of oxygen (O2) and these molecules are not IR
active. Therefore air would be a good environment for the IR measurements if the small
portions of water vapour and carbon dioxide would be absent. These two substances because
of their high polarity show a very high absorption in the IR spectrum. Therefore it is
necessary to use dry air in the spectrometer, to remove C02 and water as far as possible from
the air. Compressed air made available from the central supply 1 with an operating pressure of
0.5 MPa is supplied after passing a stop valve 2 to the rinsing gas producer. The rinsing gas
producer contains two adsorption columns, which are alternately and automatically switched
on in the air flow. The manometer 4 serves for the monitoring of the minimum pressure
necessary for the operation of the generator of 0.4 MPa. The air regulator 5 limits the flow to
12 l/min, which is controlled by the flow meter 6. The main compartiment of the IR
spectrometer is dried with a blue gel cartridge and the flowing air will be held under a small
pressure (Figure 9). Therefore the major part of the flowing air serves for the air interchange
in the sample area.
Chapter Two Basics and Techniques Used in This Work
15
3900 3600 2400 2100 1800 1500 1200
0.00
0.05
0.10
0.15
H2O asym/sym
3657/3756 cm-1 H
2O Sccis.
1595 cm-1
CO2asym.
2349 cm-1
Ab
sorb
an
ce[A
U]
Wavenumber[cm-1]
Figure 10: Spectrum of air in the sample area.
Figure 10 shows the regions of the water vapour and carbon dioxide in the sample area. After
an initial rinsing time of approximately 300 s an almost stationary condition is reached. It is
therefore reasonable not to start immediately a measurement after inserting the sample into
the spectrometer, but to wait until the IR spectrometer is purged and most of the H2O and CO2
are removed. Therefore was selected for the initial of all admission IR spectrums a waiting
period of 5 min [23].
2.1.4.3. RAIRS- Setup
Measurements of thin films on metal surfaces must take place in reflection so called Infrared
Reflection Absorption Spectroscopy (RAIRS) or External Reflection Spectroscopy (ERS)
[25]. Additional on metal substrates these techniques are limited by the surface selection rules.
Chapter Two Basics and Techniques Used in This Work
16
Figure 11: Deduction of the surface selection rules at metallic surfaces [23].
The most frequently used technique for the determination of the orientation is the
determination of the dichroism of the vibrations by means of IR spectroscopy. This means
that on electrically conductive surfaces all electrical field components (E-field) parallel to the
surface are repressed (Figure 11). In the result only normal E-field components are available
and this means that only molecule vibrations with the TDM (Transition Dipole Moment) Δp
perpendicular to the surface are IR active and for the band intensities A it follows:
Eq. 9 2
max
)(p
p
A
Az
Amax – means that the TDM orientation is perpendicular and the band intensities are
measurable. By the surface selection rules, the direct analysis of the orientation becomes
impossible from the IR spectra.
The setup (Figure 12) which is used into the sample area of the spectrometer follows:
Figure 12: Measuring accessories of the “Uniflex” of the Bio-Rad FTS-3000 [23].
The incident light is reflected by means of the plane mirrors 1 and 2 as well as the ellipsoid
Chapter Two Basics and Techniques Used in This Work
17
mirror 3 on the sample lying from the sample table 4. After reflection at the sample the light
leaves over the ellipsoid mirror and the plane mirrors 6 and 7 the sample area toward detector.
All optical elements are installed on the two base plates 8 and 9. They are tiltable around the
optical axis of the light in the sample area, thus the angle of incidence can be varied (Figure
12, right) continuously. Since only the normal component of the E-field can contribute to the
spectrum, the incident light is polarized by the polarizer 10 parallel to the plane of incidence
(p-polarization). The aperture 11 limits the opening angle of the incident light beam. All the
IR spectra were measured in this work on SAMs with an angle of incidence of 80° with
respect to the surface normal. The diameter of the spots of the sample with perpendicular
incidence was measured with a heat sensitive foil. It amounts to about 10 mm. The field
aperture 12 reduces the diameter of the spots to half, which is covered by a diameter of a
sample of (2 cm × 4 cm). The measurements were started 5 min after mounting a new sample.
The resolution used was set to 2 cm-1 and 2000 scans were accumulated, averaged, and
transformed by using triangular apodization. For the bulk samples one has to use the DTGS
detector, averaged over 100 scans, and also transformed by using a triangular apodization [24].
2.2. X-ray Photoelectron Spectroscopy (XPS)
X-ray Photoelectron Spectroscopy (XPS), also known as Electron Spectroscopy for Chemical
Analysis (ESCA) is a widely used technique to investigate the chemical composition of
surfaces based on the photoelectric effect [26]. XPS is a surface sensitive method with typical
information depth of 1-5 nm, determined by the mean free path of electrons in the solid state.
This technique was developed in the mid 1960s by K. Siegbahn and his research group. He
was awarded for his work in XPS with Nobel Prize for physics in 1981.
The energy of the incident radiation used in XPS is usually more than 1000 eV. For XPS, Al
Kα (1486.6 eV) or Mg Kα (1253.6 eV) are often the photon energies of choice [27]. The XPS
technique is highly surface specific due to the short range of the photoelectrons that are
excited from the solid. When a sample in UHV is bombarded with x-rays of characteristics
energy, electrons from the core levels of the sample are emitted. The kinetic energy
distribution of the emitted photoelectrons (i.e. the number of emitted photoelectrons as a
function of their kinetic energy) can be measured using an appropriate electron energy
analyser and a photoelectron spectrum can thus be recorded.
Chapter Two Basics and Techniques Used in This Work
18
Figure 13: Energy pattern of x-ray photoelectron spectroscopy.
The process of photoionization can be considered in several ways: one way is to look at the
overall process as follows:
Eq. 10 eAhA
Conservation of energy:
Eq. 11 )()()( eEAEhAE
Since the electron's energy is present solely as kinetic energy (KE) this can be rearranged to
give the following expression for the KE of the photoelectron:
Eq. 12 )]()([ AEAEhKE
The final term in brackets, representing the difference in energy between the ionized and
neutral atoms is generally called the binding energy (BE) of the electron (as shown in the
Figure 14) - this then leads to the following commonly quoted equation:
Eq. 13 BEhKE
The binding energy (BE) of the photoelectron is a “fingerprint” of the elements in the material
and their chemical environment, the peaks appear in an XPS spectrum at distinct values of BE.
CCoonndduuccttiioonn BBaanndd
VVaalleennccee BBaanndd
LL22,,LL33
LL11
KK
FFeerrmmii
LLeevveell
FFrreeee
EElleeccttrroonn
LLeevveell
IInncciiddeenntt XX--rraayyEEjjeecctteedd PPhhoottooeelleeccttrroonn
11ss
22ss
22pp
Chapter Two Basics and Techniques Used in This Work
19
XPS is a quantitative chemical spectroscopy, because the area of a photoemission peak is
proportional to the number of emitters in the analysis volume.
Figure 14: Schematic diagram of the photoelectronic spectroscopy.
The BE is now taken to be a direct measure of the energy required to just remove the electron
from its initial level to the vacuum level and the KE of the photoelectron is again given by :
Eq. 14 BEhKE
The binding energies (BE) of energy levels in solids are conventionally measured with respect
to the Fermi-level of the solid, rather to the vacuum level. This involves a small correction to
the equation given above in order to account for the work function ( ) of the solid. In this
work XPS was used to identify the elemental composition of the SAMs and to determine the
thickness of the SAMs. The film thickness can be calculate by the using of the relative
intensities of the Au 4f7/2 and C 1s peaks and by using a thiol with known thickness on Au as
a reference system (Ex: Au =36.5 Å at a kinetic photoelectron energy of 1169 eV for MgKα)
and carbon (Ex: c =30 Å at 996 eV for MgKα) [28].
By applying the equation 15, one can get the film thickness (d sample):
Eq. 15
)(exp1
)(exp
)(exp
)(exp1
)(
)(
cc
reference
Auc
reference
Auc
sample
cc
sample
Au
c
Au
c
E
d
E
d
E
d
E
d
referenceI
I
sampleI
I
Chapter Two Basics and Techniques Used in This Work
20
The XPS spectrum of C18 thiol (Figure 15) is presented as follows, where one can observe
the core level electron energy states of the Au and peaks of C and S can be seen as well:
800 700 600 500 400 300 200 100 00
50
100
150
200
250
Au
4f
7/2
Au
4f
5/2
S2p
C1s
Au
4d
5/2
Au
4d
3/2
Au
4p
1/2
Au
4s
Au
4p
3/2
C18 on Au(111)
Inte
nsit
y[k
cp
s]
Binding energy [eV]
Figure 15: XPS overview spectrum of octadecanethiol (C18) on Au(111).
2.3. Near Edge X-ray Absorption Fine Structure (NEXAFS)
A further important technology for surface analysis is near edge x-ray absorption fine
structure or NEXAFS, which refers to the absorption fine structure close to an absorption
edge, about the first 30eV above the actual edge. This region usually shows the largest
variations in the x-ray absorption coefficient and is often dominated by intense, narrow
resonances. NEXAFS is also called X-Ray Absorption Near Edge Structure, XANES [29]. In
our days NEXAFS is typically used for soft x-ray absorption spectra and XANES for hard x-
ray absorption spectra.
Chapter Two Basics and Techniques Used in This Work
21
Figure 16: Energy pattern of NEXAFS spectroscopy.
The measurement principle is illustrated in Figure 16. This method uses monochromatic,
linear polarized x-rays of a synchrotron, which are absorbed in the material by excitation of
core electrons into unoccupied molecular orbitals. Each excited electron leaves a core hole
into which another electron relaxes. The relaxation energy is transferred thereby in the form
of fluorescence or transferred to a further electron, which is emitted as Auger electron. Since
the Auger process dominates for light elements, it is used as indirect proof of the excitation.
In NEXAFS the x-ray energy is scanned and the absorbed x-ray intensity is measured. As
illustrated in the Figure 17 below, NEXAFS spectra can be recorded in different ways. The
creation of secondary electrons is the principle of the electron yield measurements.
Figure 17: Different methods of recording x-ray absorption spectra.
Chapter Two Basics and Techniques Used in This Work
22
The detection of the entire swarm of electrons (TEY, Totally Electron Yield) contains more
frequently diffuse electrons of deeper layers of the sample. It is not very surface sensitive. A
good signal/noise relationship and sufficient sensitivity for the monomolecular adsorbate
layers can be reached by measuring in the "Partial Electron Yield" mode, whereby only
electrons emitted near to the surface can be acquired. All spectra presented here are measured
with a backlash potential of 150 V in the PEY mode, due to ensure of a good surface
sensitivity by the mean of the free path of the electrons of only unite nanometers. Regarding
by the measurements of the carbon edge, a gold lattice is used, the organic impurities, of
which give rise to π*-resonances.
In this work NEXAFS was used to determine the orientation of the molecules of the SAMs as
shown in the Figure 18.
The intensities I of the suggestions of resonances are described by transition probabilities P by
the Fermi’s Golden rule:
Eq. 162
2
1~ ipEf
EI
where i is the initial state (one C 1s orbital) and f the final state (can be σ* or π* molecule
orbital) of the electrical field E
of the stimulatory radiation and of the dipole operator p̂ .
Under definition of the TDM of the ipfp arises:
Eq. 17 ),(cos2 TDMEIpEI
NEXAFS spectra of a particular film are measured for at least two different angles of the
Figure 18: Definition and orientation of the angles in the surface coordinate system of
the NEXAFS experiment. E║ and E┴ are the p and the s-polarized portions of the
incident light, and TDM is the situation of the dipole transition moment of the excited
transition.
Chapter Two Basics and Techniques Used in This Work
23
incident e-field to the surface normal of the sample, so one can determine the middle
orientation of the TDMs from the observed dichroism of the spectra. In the case of triple
substrate symmetry (gold substrates) all orientations are averaged around the surface
normal, one receives only the middle tilting angle of the TDM. In the context of this work
for the determination of the middle tilt angles, one has to considered the π*-resonances. It is
incidental angle dependence in the case of two fold substrate symmetry:
Eq. 18 )sin)(sin1()cossincos(cos 222222
* PPI , the intensity
of the NEXAFS resonances depends on the angle of incidence , the adsorption angle of
the adsorbed molecules and on the angle of the adsorbed molecule for the azimuth direction
of the substrate.
The angle dependence in the case of three fold substrate symmetry:
Eq. 19 22222
* sin)1()sinsin2
1cos(cos PPI ,
the intensity of the NEXAFS resonances depends in the case of three fold substrate symmetry
on the angle of incidence , the adsorption angle of the adsorbed molecules.
In this work are presented NEXAFS and XPS spectra, which were measured at the HE-SGM
beam-line (resolution: E = 0.4 eV at 300 eV) of the BESSY II synchrotron in Berlin.
2.4. Scanning Tunneling Microscopy (STM)
Scanning tunnelling microscopy (STM) is a scanning probe technique, based on the quantum-
mechanical effect of the electron tunnelling. It has become an important instrument for real
space analysis in surface science. The Scanning Tunneling Microscope (STM) was introduced
by G. Binnig and W. Rohrer at the IBM Research Laboratory in 1982 which was honoured by
the Noble Prize in 1986.
The importance of the STM was realized in 1982 when images for the (7×7) reconstructed
structure of Si(111) were acquired [30]. The STM is used for the investigations of clean metal
surfaces, the atomic resolution imaging of these surfaces and surface defects [31].
The basic idea is to bring a fine metalic tip in close proximity (a few Å) to a conductive
sample. By applying a voltage (U~4V) between the tip and the sample a small electric current
(0.01nA-50nA) can flow from the sample to the tip or reverse, although the tip is not in
Chapter Two Basics and Techniques Used in This Work
24
physical contact with the sample. This phenomenon is called electron tunneling.
Figure 19: Principle of the imaging process by the STM. The lower part shows a band
structure diagram for a tunnel contact between the tip and the sample.
In scanning tunnneling microscopy a small bias voltage V is applied so that due to the electric
field the tunneling of electrons results in a tunneling current I. The height of the barrier can
roughly be approximated by the average workfunction of sample and tip.
Eq. 20 )(2
1tipsample
The electrons can never leave the metal unless they are given the necessary energy to go over
this potential barrier, if they tunnel. In the example presented in Figure 19, the electrons
tunnel from occupied states of the sample into empty states of the tip (in case Pt-Ir). The
system used in STM measurements is a piezolelectronic drive system and a feedback loop
with those can be obtained a topography map of the corresponding surface.
The relation of the tunnelling current to the gap distance is shown in the following expression:
Eq. 21 )exp( 21
0 dkI st
where, Φ is the average work function of the sample and the tip, d is the distance between the
Chapter Two Basics and Techniques Used in This Work
25
sample and the tip, ρt and ρs are the densities of the states of tip and sample, respectively, and
κ and k are constants. The tunnelling current decreases exponentially with the separation
between the tip and the sample. Changes in the separation such as 1Å result in measurable
changes in the tunnelling current [32, 33]. Alternatively the height of the tip over the sample
can be kept constant and the tunnelling current can be used as topography information
(constant height mode). More resuming details about the STM can be found in the technical
literature [34-37]. The STM measurements in this work were carried out in air, using a Jeol
JSPM 4210 microscope. The tips were prepared mechanically by cutting a 0.25mm Pt0.8Ir0.2
wire (Goodfellow). All data were collected in a constant-current mode with a tunneling
current of (60-90 pA) and a sample bias of (450-500mV). For these tunnelling conditions no
tip-induced changes were observed.
2.5. Ellipsometry (SE)
The characterization of the optical constants and thickness of self-assembled monolayers
(SAMs) is a part of our research, and ellipsometry is the best method to determine these
quantities. There are three types of data typically acquired with the ellipsometer, transmission
and reflection intensity and of course change of polarization [38].
Ellipsometry measures the change in polarisation state of light reflected from the surface of a
sample, expressed as Ψ and Δ. These values are related to the ratio of Fresnel reflection
coefficients, Rp and Rs. for p and s-polarized light, respectively [39].
Eq. 22s
pi
R
Re )tan(
Figure 20: Schematic of the geometry of an ellipsometry experiment.
Chapter Two Basics and Techniques Used in This Work
26
Because ellipsometry measures the ratio of two values, it can be very accurate and nicely
reproducible. The s-direction is taken to be perpendicular to the direction of propagation and
parallel to the sample surface. The p-direction is taken to be perpendicular to the direction of
propagation and contained in the plane of incidence (shown in the Figure 20).
Optical constants:
The optical constants define how light interacts with a material. The index of refraction, n,
defines the phase velocity of light in material.
Eq. 23n
c
where, υ is the speed of the light in the material and c is the speed of light in vacuum. The
extinction coefficient, k, determines how fast the amplitude of the wave decreases. The
extinction coefficient is directly related to the absorption of a material and is related to the
absorption coefficient by:
Eq. 24
k4
where, α is the adsorption coefficient and λ is the wavelength of light [40].
Ellipsometric measurements were performed using an ellipsometer SE 400 (Sentech
Instruments GmbH) under an incidence angle of 70° at a wavelength of 633 nm. While the
substrate parameters for each spot were determined before immersion, a refractive index of n=
1.45 was assumed for the organic layers.
2.6. Water contact angle (CA)
Contact angle measurement is a well-known technique, which is being used to control
adhesion, surface treatments, and polymer film modification. The wetting of solid substrates
by liquids is a basic element in many natural and commercial processes.
The contact angle between a liquid and a solid is a measure of the energetic interaction
between the solid and the liquid. This is usually determined using the sessile droplet method
[41].
In this case, a tangent is drawn and the angle between the solid and the surface is called as the
contact angle. The contact angle can be determined from the droplet contour by means of
calculational methods (for example using the Young-Laplace equation).
Chapter Two Basics and Techniques Used in This Work
27
As shown in Figure 21, when a liquid drop is settled on a solid surface, the contact angle of
the drop on the solid surface is defined by the mechanical equilibrium, of the drop under the
action of three interfacial tensions (solid, vapour and liquid). The equilibrium relation is
known as Young’s equation:
Eq. 25 YVLSLSV cos
where, θY is the Young contact angle, which is suited in Young’s equation; SV = contact
angle between the interfacial tensions of solid and vapour; SL = contact angle between solid
and liquid and VL = contact angle between vapour and liquid interfaces.
In practice, the contact angle measured in the laboratory could not be exactly the Young
contact angle because of the following experimental errors:
1. Any gravitational effect during the drop is set on the solid surface
2. Any volume reduction of the drop when the syringe is detached from the liquid drop
after the drop is set on the solid surface
3. Heterogeneity of the solid surface
4. Any absorption of the liquid phase of the drop by the solid
5. Any reaction between the liquid phase and the solid phase or any variation of the
liquid surface tension due to the adsorption of a surface active materials or impurities
when the liquid phase is not pure
6. Effect of the line tension produced at the solid/liquid/gas contact line (drop size effect)
7. Any experimental errors on the drop profile observation during the measurement
The line tension is defined as the specific free energy of the three-phase contact line as a force
operating in the three-phase line. The mechanical equilibrium condition for any point at the
Figure 21: Schematic of a sessile-drop contact angle system.
Chapter Two Basics and Techniques Used in This Work
28
three-phase contact line can be given as:
Eq. 26 Rlvslsv cos
where, R is the radius of the three-phase contact circle [41].
Sessile water-drop contact angle (CA) measurements were obtained by using a video camera-
based commercial apparatus (Surface & Optics Co., Ltd, Korea; Phoenix 150). The reported
value is the average of three measurements with deionized water on each substrate of the
SAM.
2.7. UV-VIS Spectroscopy
UV-VIS spectroscopy is the measurement of the wavelength and intensity of absorption of
near-ultraviolet and visible light by a sample. Ultraviolet and visible light are energetic
enough to promote outer electrons to higher energy levels. UV-vis spectroscopy is usually
applied to molecules and inorganic ions or complexes in solution. The concentration of an
analyte in solution can be determined by measuring the absorbance at some wavelength and
applying the Beer-Lambert Law [21].
The photon energies are sufficient to promote or excite a molecular electron to a higher
energy orbital. Consequently, absorption spectroscopy carried out in this region is sometimes
called "electronic spectroscopy".
Figure 22: Electronic excitations for an organic molecule.
A diagram showing the various kinds of electronic excitation that may occur in organic
molecules is shown in Figure 22. Of the six transitions outlined, only the two lowest energy
ones (left-most, colored blue) are achieved by the energies available in the 200 to 800 nm
Chapter Two Basics and Techniques Used in This Work
29
spectrum.
Molar absorptivities from n* transitions are relatively low, and range from 10 to100 liter
mol-1 cm-1. * transitions normally give molar absorbtivities between 1000 and 10,000
liter mol-1 cm-1. The solvent in which the absorbing species is dissolved also has an effect on
the spectrum of the species. Peaks resulting from n* transitions are shifted to shorter
wavelengths (blue shift) with increasing solvent polarity. Often (but not always), the reverse
(i.e. red shift) is seen for * transitions. This is caused by attractive polarisation forces
between the solvent and the absorber, which lower the energy levels of both the excited and
unexcited states. This effect is greater for the excited state, and so the energy difference
between the excited and unexcited states is slightly reduced - resulting in a small red shift.
This effect also influences n* transitions but is overshadowed by the blue shift resulting
from solvation of lone pairs.
An optical spectrometer records the wavelengths at which absorption occurs, together with the
degree of absorption at each wavelength. The resulting spectrum is presented as a graph of
absorbance (A) versus wavelength analogue to infrared spectra presented in sec.2.1.
Chapter Three Self-Assembled Monolayers and Sample Preparation
30
Chapter Three
Self-Assembled Monolayers and Sample Preparation
3.1. Self-Assembled Monolayers
3.1.1. Introduction
Organic films for instance the deposition of long chain carboxylic acids were first studied by
K. Blodgett and I. Langmuir [42, 43]. At that time, the amphiphilic monolayers were already
used to control the wetting behaviour of metal condenser plates in steam machineries [44-46].
Further research on systems related to self-assembled monolayers were done later by Zisman
et al. [47], see also the history of organic thin films summarized by [48].
Besides applications in the classical field of technology, organic thin films can play an
important role in interfacing bio-technological devices [13].
In comparison to the Langmuir-Blodgett films, which are formed by a mechanical process,
SAMs are formed spontaneously by the immersion of an appropriate substrate into a solution
of an active surfactant in an organic solvent [47, 49].
As shown in the Figure 23, Langmuir films consist of amphiphilic molecules spread on a
liquid surface like water [50, 51]. The hydrophilic headgroup has an affinity to the water
Figure 23: Compariosn between LB films and SAMs films.
Chapter Three Self-Assembled Monolayers and Sample Preparation
31
whereas the hydrophobic endgroup sticks out on the other side. These Langmuir films are
transferred onto a solid substrate and they are called Langmuir-Blodgett films (LB) [48].
The self-assembled monolayers are strongly bound on solid substrates due to specific affinity
of the headgroup to the solid surfaces.
Since their discovery in 1983 by Nuzzo and Allara [52], self-assembled monolayers of thiols
and disulfides on gold (111) have been studied for their potential applications in molecular
technologies like chemical sensors, nonlinear optical materials [48], microelectronics, and
computer technology [53-56]. One can stabilize the surface with a desired functionality and
this idea is also used in wetting studies of SAMs [57] which also serve as a model for polymer
films. Furthermore chemical reactions at surfaces can be studied under controlled conditions
[58].
3.1.2. Self-Assembly Kinetics and Mechanism
Much of the recent work on self-assembling organic monolayers at metal surfaces has focused
on the adsorption kinetics of alkanethiolate/gold system, where alkanethiols adsorb
spontaneously onto the metal surface to form a highly ordered array [5, 7, 59-63].
For the examination of these monolayers little effort has been spent on understanding the
elementary steps in the formation of the monolayers. Most of these studies have suggested a
two-step kinetic model for alkanethiolate on gold surfaces, a fast initial adsorption step in
some minutes and a slow adsorption step with a time scale of hours or days [9, 64-66].
All spectroscopic methods used to characterize these self-assembled monolayers provide only
spatially averaged information about the adsorption process, which lead to a request for
molecular level information during the self-assembly process. Using the scanning probe
microscopy (STM/AFM) the process of adsorption kinetics of self-assembled monolayers of
thiols deposited on gold surfaces (111) has been studied and well understood [67-70].
Figure 24 shows that the thiol molecules will adsorb on the gold surface and they first will
form a so called striped-phase with their molecular axis parallel to the surface. The adsorption
process of thiols onto gold can be divided into two or three steps, the first is fast, and the
following steps are much slower [71]. The first step takes less than 10 s to finish (sulfur
adsorption) and 10 h to complete the second step (orientation ordering). The orientation
ordering step is governed by the interchain interactions [72, 73].
Chapter Three Self-Assembled Monolayers and Sample Preparation
32
3.1.3. Self-Assembled Monolayer Structure
Figure 25: Schematic diagram of a SAM. Shaded circle indicates adsorbed or
chemisorbed headgroup and open circle endgroup, which can be chosen from variety of
chemical functionalities.
Figure 24: Schematic mechanism diagram for the self-assembly of thiols on Au(111): a)
Initial adsorption. b) Striped phase or lying-down phase. c) 2D phase with a transition
from lying-down to standing-up phase. d) Formation of a complete SAM [74].
Chapter Three Self-Assembled Monolayers and Sample Preparation
33
Figure 26: Schematic diagram of different energies in the adsorbed SAM [71]
Self-assembled monolayers (SAMs) are ordered, chemically and thermally stable two-
dimensional aggregates that are formed spontaneously by the adsorption of surface active
molecules onto a solid.
The surface active molecule should feature a head group, suitable for strong interactions or
even chemical bonding with the surface, a molecular backbone moiety responsible for the 2D
packing and favorable lateral interactions with the next neigbors and a tail or end group
determining the properties of the newly formed solid surface as shown in the Figure 25. The
SA of a film is a concerted interplay of various forces. The overall stability of a SAM is
determined by all inter- and intramolecular forces in the film. (as shown in the Figure 26
ΔEads stands for adsorption energy, ΔEcorr corrugation of substrate potential experienced by
molecule, ΔEhyd van der Waals interaction of (hydrocarbon) tails, and ΔEg energy of gauche
defect or deviation from the fully stretched backbone [71]).
A gold surface can simply be coated with an SAM by immersing the substrate into a dilute
solution of thiol or disulphide [75] The formation of the SAMs may be considered formally as
an oxidative addition of the S-H bond to the gold surface, followed by a reductive elimination
of hydrogen. X-ray photoelectron spectroscopy experiments suggest that chemisorption of
alkanethiols on gold(0) surfaces yields the gold(I) thiolate (R-S-) species [76]. The adsorption
chemistry is:
R-SH + Aun0 → R-S- - Au+ + ½ H2 + Aun-1
0
The bonding of the thiolate group to the gold surface is very strong (the homolytic bond
strength is approximately 160 kJ/mol) [1].
A schematic model as in Figure 27 of the (√3×√3)R30° overlayer structure formed by
alkanethiolate SAMs on Au(111) shows that in S…S distance are in the order of 4.99 Å,
which is a result from their tilt to reestablish the vdW interchain interactions [53, 68]. This tilt
angle is found to be ~30° with respect to the surface normal towards the nearest neighbour
direction [71].The angle can be deduced using FTIR spectroscopy (shown in the Figure 28 ).
Chapter Three Self-Assembled Monolayers and Sample Preparation
34
Figure 27: Constant-current STM topograph of an octanethiol monolayer on Au(111)
which shows a c(4 x 2) superlattice of a R3033 )( overlay structure [68].
From the theoretical calculations for alkanethiolate on the Au(111) [77-80], it has been
concluded that the angle between gold and the S-C bond is about 180° if the the S atom is sp
hybridized and about 104° if the S atom is sp3 hybridized [81].
Z
Y
X
t
Figure 28: The tilt angle Θt of the alkanethiol chain relative to the surface normal [71].
Chapter Three Self-Assembled Monolayers and Sample Preparation
35
3.2. Preparation and Characterization of Gold Substrates
3.2.1. Introduction
The self-assembled monolayers formed from organic molecules like thiols, have a very high
affinity to gold substrates [53] These films of SAMs deposited on the Au (111) are the
principal topic of this work. Gold substrates have some better properties in comparison with
others substrates like glass [82, 83], copper [84], silver [85] and mercury [86] because upon
the exposure to the air they are inert to oxidation. For the sensitive measurements of IRRAS
or XPS, these substrates have to be contamination free. Therefore, gold substrates must be
handled using some preventive measures to keep them clean and without surface impurities.
3.2.2. Preparation and Characterization of Gold on Silicon Wafers
IR-, NEXAFS-, XPS and contact angle measurements were possible on evaporated gold
surfaces. These gold surfaces show some closed layers [87, 88], which are showing the
orientation (111) [89].
As substrates were used Si(100)-Wafer (Fa.Wacker). Au was evaporated at 10-7 mbar in a
commercial equipment (Leybold Univex 300 with two thermal evaporators): after twelve
hours of annealing the wafers at 300°C in vacuum, they were coated with 50 Å titanium
(Chempur, 99,8%) with a rate of 5 Å/s and subsequently with 1000 Å gold (Chempur,
99,995%) with a rate of 20 Å/s. Afterwards the measurement of the layer thickness took place
with a quartz balance ( Leybold, Inficon XTM/2). All the silicon wafers were prepared in the
same way and before use they were kept in desiccator under argon.
Figure 29: AFM (atomic force microscopy) image of gold evaporate on Si(100)-Wafer
(1μm × 1μm).
Chapter Three Self-Assembled Monolayers and Sample Preparation
36
3.2.3. Preparation and Characterization of Gold on Mica Substrates
For STM studies, the substrate has to be atomically flat to distinguish and characterize any
deposited species [90] and this can not be achieved by using the silicon wafers substrates.
Therefore gold substrates were produced on mica as reported in [91, 92].
Figure 30: STM images of Au/Mica (111) and Au/Si (111).
A freshly cleaved sheet of mica was deposited in the evaporation chamber (Leybold) for 72h
and was heated up to 300°C and then 1000 Å gold was deposited at a pressure of
approximately 10-7 mbar. These substrates were flame annealed in a butane/oxygen gas flame
for some seconds. They reveal large terraces of about 0, 5 μm to 1 μm width and orientation
Au (111). Afterwards the samples were cooled down in air before immersing into ethanolic
solution. Also the (2√3×3) reconstruction of the gold surface [93] can be observed [94].
3.3. Preparation of Self-Assembled Monolayers Films
Films are prepared by immersion into thiol solutions. The gold substrates have to be handled
with preventive measure to keep them clean and without contaminations.
The dimensions of substrate pieces have to be: 0.5 cm × 0.5 cm for the STM, 3 cm × 2 cm for
the IR, contact angle and ellipsometry and 1 cm × 1 cm for XPS and NEXAFS and these
small pieces have to be immersed into appropriate thiol solution. The immersion time depends
on the thiol and the goal of the study, but normally for a good quality of the SAMs, the small
pieces of gold are immersed into the solution for 24 h.
The concentrations of these solutions, used in this work, vary from 10-20 μM to 0.1 mM
depending on the solubility of each thiol substances. After approximately 24 h the gold
substrates were removed from the incubation solutions and rinsed carefully with absolute
ethanol or dichloromethane and then again with ethanol to remove the physisorbed overlayers.
Afterwards the substrates were dried in a nitrogen stream.
Chapter Three Self-Assembled Monolayers and Sample Preparation
37
3.4. Preparation of Bulk Pellets for the IR measurements
The pellets which are used for the IR measurements are made by grinding approximately 0.3
g of pure KBr, and 2 mg of the corresponding thiol as a powder into the capsule. For the
grinding, one can use the vibrating mill (Perkin-Elmer) for 30 s or also hand mortar in order
to obtain homogeneous dispersion. Afterwards the pellet is produced with a diameter of 13
mm [95].
3.5. Chemicals used in this work
In this work, the following solvents with the given purities for the preparation of the self-
assembled monolayers films:
Chemical Source Purity
Ethanol absolute, p.a.,
Reag. ISO.
Riedel-de Haen 99.8%
Dichloromethane,
analytical reagent
(stabilized with 0.1%
Ethanol)
VWR 99.84%
Diethylamine, for synthesis Merck 99%
KBr (for Pellets) Aldrich 98.3%
The thiols used in this work are listed in the following (they were already presented in
Chapter one):
Substance Substance
1. C0T 9-triptycenethiol 7. AH-4
2. C1T (9-triptycenyl)-methanethiol 8. C12SAc dodecyl thioacetate
3. C3T 3-(9-triptycenyl)propane-1-thiol 9. C12SH dodecanethiol
4. AH-10 10. Azo 1 azobenzene
5. VK-55 11. Azo 2 azobenzene
Chapter Three Self-Assembled Monolayers and Sample Preparation
38
3.6. Laboratory Equipment
A very important step is to clean all the items, which are used in the laboratory. After purging
with first bath of KOH/H2O2/2-propanol (15/15/1) and finally a second H2O/HCl (50/1) bath
have to be used. The items are immersed in each bath for 24 h. Between the two steps of
immersion, the items were precleaned with water provided from the filter system and with
ethanol (for the cleaning one can use technical ethanol). Afterwards the equipment is stored in
the oven at 60° for drying and then the bottles have to be rinsed with ethanol or another
solvent and then filled with the solvent needed for preparing the samples.
Chapter Four Triptycenethiol-based Self-Assembled Monolayers
39
Chapter Four
Triptycenethiol-based Self-Assembled Monolayers
In this chapter, the SAMs formed from triptycenethiol (C0T), mercaptomethyltriptycenethiol
(C1T), and mercaptopropyltriptycenethiol (C3T) on polycristalline Au/Si and Au/mica are
characterized by ellipsometry (SE), infrared reflection absorption spectroscopy (IR), X-ray
photoelectron spectroscopy (XPS) and near-edge X-ray absorption fine structure spectroscopy
(NEXAFS) and scanning tunnelling microscopy (STM) and the results are following
described.
4.1. Introduction and Objective of the Work Presented in this Chapter
Self-assembled monolayers (SAMs) in particular of thiolates on gold have frequently been
used to tailor surface properties [53, 96, 97]. Of particular interest are surfaces with sensing
properties, usually attained by directed substitution at the exposed part of the molecules (the
so called end group) with a suitable recognition group [98]. A major problem arises from the
fact that most recognition groups are relatively bulky compared to the carbon-backbone of the
SAM-forming molecules: e.g. the frequently used, comparatively small biotinyl-group still
has a cross section about threefold as the one of the frequently used alkanethiole chains [1].
The problem becomes even more significant if one considers the size of the typical analytes,
biomolecules, which easily have diameters of 10 nm or more. The usual approach for the
design of monolayers suitable for the efficient accommodation of such bulky end groups is
the production of so called diluted monolayers, in which the molecules carrying the
recognition groups are singled out within the monolayers by a huge excess of inert, diluting
molecules. In the best cases, this approach results in a statistical distribution of the relevant
molecules, while in worse cases either a preferential deposition of the minority species at the
grain boundaries within the SAM [99] or a complete phase segregation of the two kinds of
molecules occurs [100, 101].
In contrast we suggest the use of molecules with a bulky backbone for the generation of self-
assembled monolayers consisting of only one species, which allow for the accommodation of
bulky headgroups in a defined, periodic manner. To permit an efficient ordering within the
monolayers, the molecules chosen were derived from triptycenes, which have not only an axis
of higher symmetry (C3) but also permit a coaxial attachement of both, the anchoring group
Chapter Four Triptycenethiol-based Self-Assembled Monolayers
40
(in our case a sulfur atom) and the headgroup [12].
This coaxial arrangement allows for an unambiguous positioning of the molecules within the
SAMs as shown in Figure 31 (all three possible rotamers are equivalent) and also fits well
with the threefold symmetry of the commonly used Au(111) surface [99].
The aim was to understand better the intermolecular interactions and their effect on the
morphology and also the molecular orientation of these rigid aromatic thiols. We expected
that these rigid SAMs molecules will form high degree of order and packing structures. The
influence of the methylene spacer employed between the trip- unit and the sulfur atom, will
play also a very important role in their adsorption process on account of this we examined the
influence of this methylene spacer on the molecular arrangement. In the following the
formation of the triptycene SAMs are presented.
4.2. Self-Assembly Process of Triptycenethiol on Au(111)
4.2.1. Introduction
The aromatic rings and the rigidity of the aromatic system determine the molecular orientation
and orientational order of the adsorbed thioaromatic molecules. In C1T and C3T the insertion
of the methylene group creates a conformative flexibility which is important to yield high
quality films.
Measurements using IR, XPS and NEXAFS confirm that these molecules form SAMs on the
substrate surface. C1T and C3T molecules show a tilted orientation with respect to the surface
normal.
Figure 31: Molecular structures of C0T, C1T and C3T (triptycene molecules).
Chapter Four Triptycenethiol-based Self-Assembled Monolayers
41
4.2.2. Results
4.2.2.1. XPS and Ellipsometry
The thicknesses of the films were determined using an ellipsometer SE 400 (Sentech
Instruments GmbH) under an incidence angle of 70° at a wavelength of 633 nm. A refractive
index of n= 1,45 was assumed for the organic layers, while the refractive index of the
substrate was determined before film formation on each spot separately [71].
C0T C1T C3T
XPS 7.4 7.8 10.3
Ellipsometry 4.4 8.0 9.2
Calculated 6.1 7.5 10.0
Photo-electron spectroscopy (XPS) is a suitable method to determine the chemical species
within self-assembled monolayers. The energy scales of all spectra were referenced to the
Au4f7/2 peak located at the binding energy 84.0 eV. If the reaction of the triptycene thiols
with the gold surface proceeds as reported in the literature for aliphatic and aromatic thiols,
the carbon signals (C 1s at 284 eV) would show an unchanged carbon backbone [99], while
the shift of the sulphur signals (S 2p of 162 eV) should indicate the formation of a thiolate
species.
From the intensities of the Au 4f and the C 1s signals the thickness of the organic layers could
be determined (see Eq.15 from sec. 2.2) using a mean free path of 27 Å for the C 1s electrons
and 35Å for the Au 4f electrons [102]. The results are presented in Table 3 together with the
values determined by ellipsometry and the calculated thicknesses. While the values for C1T
and C3T agree well, a significant deviation larger than the typical error (±1Å) can be seen for
C0T. C0T molecule shows a discrepance not only in ellipsometry, but likewise in XPS shown
in the Figure 32. Here in the C 1s region the spectra of C0T, C1T and C3T are compared with
alkanethiol ODT (octadecanethiol). The C 1s peak in the case of aromatic thiols like ours
thiols is at ~284 eV and for the alkanethiol located at 285 eV.
Table 3: The layer thicknesses (in Å) as determined by XPS and ellipsometry as well as
the expected values for molecules standing upright on the substrate.
Chapter Four Triptycenethiol-based Self-Assembled Monolayers
42
Figure 32: XP spectra of C 1s and S 2p regions of the C0T, C1T and C3T molecules in
comparison with an alkanethiol ODT.
Examination of the spectrum in the S 2p region showed an extremely broad and asymmetric
peak with a binding energy maximum at 162.3 eV. Only the C0T molecule is different and
shows an easily deviation from this binding energy to higher binding energies. The chemical
shift of C0T spectrum is shown in Figure 33, whereas the doublet at 161.4 eV is assigned to a
metal thiolate species and the second doublet at ~163 eV is related to unbound thiol molecules
or the thiols are showing oxidized sulphur [103].
ODT
ODT
]
ODT
ODT
]
Chapter Four Triptycenethiol-based Self-Assembled Monolayers
In
gr
m
co
re
pe
ar
pr
ob
tri
do
or
Th
Th
Figu
area
re 33: XPS S 2p spectrum of C0T adsorbed onto gold/Si. Two S 2p doublets with 2:1
43
4.2.2.2. IRRAS
frared spectroscopy at interfaces not only provides insight into the presence of functional
oups but – in case of metallic substrates - also permits to determine the orientation of the
olecules on the surface. Due to the shielding by the electron gas in the metal, the
mponents of the transition dipole moment parallel to the surface become invisible in the
spective thin-film spectrum. For comparison, the bulk spectra of the triptycene thiols in KBr
llets were recorded. As can be seen in Figure 34, the bands appearing in the surface spectra
e also visible in the bulk spectrum (in the case of C3T and C0T), suggesting an adsorption
ocess without decomposition, although some bands are somewhat shifted or are not
served in the SAM spectra. This small shift might result from a different packing of the
ptycene moieties in the film as compared to the bulk. In fact, the bulk structure of triptycene
es not show any coaxial alignment of the units [12, 104] as would be expected in an
dered film.
e peak assignment of the bands in the case of triptycene SAMs (C3T) is shown in Table 4.
e production of the preparation solutions was done as follows: 2 mg of the respective
ratios and splittings of 1.2 eV were used to fit experimental spectrum.
Chapter Four Triptycenethiol-based Self-Assembled Monolayers
44
Triptycenethiols was dissolved in 100 ml Et-OH after 5 min. under ultrasonic effect. The
saturated solutions were cooled down in the refrigerator, then filtered and diluted 1:1 with the
ethanol solvent. Then the immersion of the substrates took place for 24 hours, then rinsing,
drying and measuring the samples. The positions and intensities of the measured oscillation
transitions are likewise in the tables of the appendix [23].
For the C0T there are problems in the reproducibility by the IR measurements. Because of the
rigidity of this molecule (inflexibility) differences in the orientation of the C0T on the gold
surface occur as shown in the Figure 35 [105].
Figure 34: Infrared spectra of KBr and SAM of C0T, C1T and C3T in ethanolic
solution (concentration for the solutions: 70 M).
Chapter Four Triptycenethiol-based Self-Assembled Monolayers
Figure 35: Infrared spectra of C0T molecule showing the problem of the
reproducibility on the gold substrates.
(C-H)
(C-H)
(C=C
(CH2
s(CH2
as(CH
as(CH
s(CH2
Table 4: The assignm
Mode assignment SAM(cm-1)
, trip vibration op ~756
, trip vibration , op ~947
), trip vibration ip// axis 1150
sci) and trip vibration 1458
) 2908
2) 2961
2)-20a ~3052
)-20b ~3071
45
ent of the peaks in the SAM of C3T molecule.
Chapter Four Triptycenethiol-based Self-Assembled Monolayers
46
4.2.2.3. NEXAFS
To obtain a more quantitative measure for the average molecular tilt of the molecules,
NEXAFS data were recorded. Briefly, if the degree of polarization P of the incident
synchrotron light is known, the intensity Iif of a NEXAFS resonance on substrates with 3-fold
symmetry can be described by sec. 2.3 [29].
Iif P(1-cos2 cos2 + ½ sin2 sin2 ) + (1- P) 1/2(1 + cos2 )
Here, denotes the angle of the parallel electrical field vector component relative to the
surface normal and represents the angle of the transition dipole moment for the transition in
question relative to the surface normal. Thus, the variation of the intensity upon change of the
angle of the incident light with respect to the surface normal is characteristic for different
orientations of the transition dipole moment.
Figure 36 shows three representative C 1s NEXAFS spectra for each of the triptycene thiol
films on gold (111). The spectra were normalized to the absorption step height of the C 1s
edge and referenced to the *-resonances at 285.1 eV and 288.4 eV and σ*- resonances at
292.1 eV and 298 eV. The anisotropy of the intensity of these *-resonances was used for the
determination of the tilt angles of the respective transition dipole moments and therefore of
the molecular orientation. It should be mentioned that the transition dipole moments of all
three rings become averaged by the C3-symmetry of the triptycene moiety. From the intensity
modulation, the C0T and C3T show “no dichroism”, in contrast to the others spectra from
C1T.
280 290 300 310 320 330
0
1
2
3
4
C0T
1
*1
*
Photon Energy[eV]
Inte
nsity
[Un
its
ofe
dg
e-j
um
p] 30°
55°90°
Chapter Four Triptycenethiol-based Self-Assembled Monolayers
47
280 290 300 310 320 3300
1
2
3
4
C1T
1
*1
Inte
nsity
[Units
ofed
ge-j
um
p]
Photon Energy[eV]
*
30°55°90°
280 290 300 310 320 330
0
1
2
3
4
C3T
Inte
nsity
[Un
its
ofe
dg
e-j
um
p]
Photon Energy[eV]
1
*1
*30°55°90°
Figure 36: NEXAFS spectra of C0T, C1T and C3T thiolates for different angles of
incidence of the synchrotron light. The solvent used for the solutions was EtOH.
Chapter Four Triptycenethiol-based Self-Assembled Monolayers
48
4.2.2.4. STM
Figure 37: STM image of C0T molecule on Au(111) at room temperature.
For the STM studies gold on mica, which was described in chapter 3.2.3, was prepared and
then immersed in ethanolic solution of triptycene thiol. Figure 37 shows the STM
measurement of C0T molecule, which is a very rigid molecule and Figure 38 and Figure 39
show the measurement of C1T molecule with a rate of flexibility due to the inserted
methylene group as shown in Figure 31. All the images are showing highly packed films on
the surface, but one can not observe specific structures as observed at other thiol SAMs on Au
(111) like a significant amount of holes in the morphology of the substrate [9].
As we can observe in the Figure 38 the morphology of the C1T film at room temperature is
characterized by a lot of islands (the small brighter points) and their height correspond to an
atomic step of the gold substrate. After annealing of the sample at 60°C one can observe that
these small islands are now bigger and wider.
Figure 38: STM image of C1T
molecule on gold (111) at room
temperature
Figure 39: STM image of C1T molecule
on gold (111) at high temperature
Chapter Four Triptycenethiol-based Self-Assembled Monolayers
49
From the imaging with the STM it is apparent that all three molecules are forming densely
packed films on the gold surface. One can not determine the molecular orientation of the
molecules due to formation of the islands and the impossibility to get high molecular
resolution. C1T shows very rough surfaces and because of the insertion of the methylene
group one can expected that C1T and C3T are tilted away from the surface normal.
4.2.3. Discussion
Between IR measurements of pellets and SAMs on gold substrates there is an agreement
between the bands. Therefore one can deduce that the triptycenethiols are adsorbed on the
surface, without destruction of the molecules. Some bands like in the case of the C0T
molecule, the trip- band from ~950 cm-1 show a clear shift. These are suggesting different
crystal configurations of the SAMs compared with those of the pellets and the Figure 40
shows the crystal configurations of the triptycenes [12]. The individual molecules within the
unit cell do not exhibit a preferential plane, according to which the molecules of the
triptycenethiols can orient them self at the favourably energetically surface [23].
The measured vibrational transitions are done on basis of the assignment of the bands shown
in the Appendix. The calculations were made for respectively one (isolated) molecule,
therefore they stand for gaseous phase spectra.
As shown in the Figure 35 the reproducibility of the C0T spectra is not obtained, some bands
reveal a representative shift in comparison with others spectra of the same molecule and the
same concentration of the solution. Definitively C0T molecules because of the pronounced
rigidity of the trip- frame have a different orientation of the molecule on the Au (111)
substrates. The bands from 1450 cm-1 are showing a good agreement, the vibrations between
2900 cm-1 and 3100 cm-1 are somewhat deviated because of the limitations of the calculations.
In the finger print we have big deviations between the calculated spectra and the measured
spectra, which could be explained by the effect of crystallization.
The determination of the molecular orientation is only possible on basis of the more intensive
bands of the spectrum, because only these bands can be measured with a reasonable intensity
and quality on the surface. The most intensive bands however are consisting of an overlap of
several vibrational transitions with differently oriented transition dipole moments.
Chapter Four Triptycenethiol-based Self-Assembled Monolayers
50
Figure 40: The crystal structure of the triptycene [12, 23].
DFT calculations of the IR spectra were done to identify better the bands and to assign the
directions of the transition dipole moments (TDM). For the calculation of the spectra of the
triptycene molecules B3LYP/6-31G(d) functionals were used and the calculated spectra are
compared with Ref. [106]. The comparison shows a good agreement of the bands only with
small deviations in the case of C1T and C3T molecules. By C3T molecule exist a strong
interconnection between aromatic vibrations of triptycene with the propylene chain, therefore
one can not allocate the orientations (TDMs) to the vibrations of the benzene rings. On the
basis of IR measurement it is not possible to determine the molecular orientation of these
triptycene molecules.
The determination of the molecular orientation, therefore, was done with the help of NEXAFS
measurements. The π*-resonances show in the case of C0T molecule a very small dichroism,
which means that C0T show a disorder of the molecules on the surface. In case of C1T and
C3T one can observe differences in intensity because of the dependence in angle of incidence.
From these measurements result a tilt angle of 42 ± 2° in case of C1T molecule and 46 ± 2° in
case of C3T shown in Table 5. The angles refer to a tilting of the triple symmetry axis of the
triptycene frame against to the surface normal [107].
The confirmation of the chemisorption and the determination of the thickness take place with
C0T C1T C3T
Au(111) Very small dichroism 42 ± 2° 46 ± 2°
Table 5:Tilt angles of the triptycene units with respect to the surface normal in the
triptycene thiol films on gold
Chapter Four Triptycenethiol-based Self-Assembled Monolayers
51
XPS (see Table 3). The S 2p region are showing the formation of the thiolates with a position
of the gold-sulfur-bond specific at 161.4 eV [108, 109] and the second doublet at ~163 eV is
related to unbound thiol molecules or the thiols are showing oxidized sulphur shown in Figure
33. In comparison with an alkanethiol like ODT taken as a reference, demonstrate that only
C1T and C3T form thiolates as ODT molecules and only C0T molecule exhibit two different
S 2p doublets. One can not clamp if the C0T molecule remains thiol or not. In C 1s region
with the exception of C0T molecule, the positions of the aromatic carbon species agree with
the literature. The value of C0T thickness is too high, in case of C3T the value agrees and for
C1T they were found some discrepancies. From XPS one can conclude with exception of C0T
molecule, that monolayers are formed on the substrates.
The STM images (Figure 37, Figure 38 and Figure 39) confirm the formation of the densely
packed films on the Au (111). The determination of the molecular orientation it is not possible
without molecular resolution. One can say about the C0T molecule that it does not form
laterally arranged structure, and perhaps they are tilted away on the surface with an angle of
55° (magical angle) because of the discrepancies resulted from IR, XPS and NEXAFS
measurements. Possible are additional arrangements with different tilting, whose average
value corresponds to the orientation measured at 55°. In case of C1T and C3T because of the
inserted methylene between the trip- frame and the sulphur group the distance between the
molecule and surface is bigger and the molecules are more flexible on the surface. These
densely packed films exhibit well ordered structure based also on the LEED (low energie
electron diffraction) data. They form (m3 x n3) R30° structure, where m and n can be
possibly 2 [23].
Figure 41: Model for the arrangement of the C1T on gold surface.
Chapter Five Influence of the Leaving Group in Case of Triarylaminethiols
52
Chapter Five
Influence of the Leaving Group in case of Triarylaminethiols
In this chapter, the formation of self-assembled monolayers (SAMs) from triarylaminethiols
onto gold (111) substrates has been studied by using gracing incidence infrared spectroscopy,
X-ray photoelectron spectroscopy, near-edge X-ray absorption spectroscopy, and scanning
tunneling microscopy with or without deprotection of these triarylaminethiols molecules. We
found by using gracing incidence infrared spectroscopy that the monolayers derived from the
deprotected thioacetate have a similar structure compared to the ones obtained from the
corresponding triarylaminethiols without deprotection.
5.1. Introduction and Objective of the Work Presented in this Chapter
The research topic of self-assembled monolayers (SAMs) has witnessed tremendous growth
in synthetic sophistication and depth of characterisation over the past 20 years [48]. The
reasons for the large interest in SAMs are their great advantages compared to Langmuir-
Blodgett (LB) films [43, 110]. Chemisorption involves relatively large heats of bond
formation (40 – 160 kJ/mol) and has two advantages: firstly, the chemical reaction displaces
any previously formed physically attached adsorbates or impurities from the surface.
Secondly, the adsorbed species, once bonded, is difficult to remove from the surface.
However there are three disadvantages of chemisorption: the uncertain degree of coverage,
the possibility of further chemical reactions, e. g. thiolates on gold slowly oxidise to
sulfoxides in high-humidity environment, and the formation of surface dipoles [111]. While
the early days of SAM research were almost exclusively devoted to the investigation of the
formation, structure and physical properties of alkanethiols on gold, in the past decade the
function of such SAMs moved into the foreground.
Of the numerous kinds of monolayer systems, the one of organothiols on gold have been
proved to be the most popular ones due to their reliable formation and almost predictable
structure. While for monolayer formation most often organothiols or organodithiols are being
used, in a number of cases also organothioacetates or organodithioacetates have been utilized
[62, 98]. For example most studies on so-called break junctions, where single molecules are
attached in between two gold electrodes in order to directly measure the electrical
characteristics of these molecules, dithioacetates have been used as precursors for the
Chapter Five Influence of the Leaving Group in Case of Triarylaminethiols
53
resulting dithiolates [112, 113]. Nevertheless, the reported results on the adsorption chemistry
of thioacetates on gold surfaces are somewhat controversially discussed [114]. An early paper
[115], reported that organothiolate adlayers formed from thioacetates have a similar quality as
the ones obtained from the respective thiols. The authors speculated that some of the
thioacetate molecules are hydrolysed in solution followed by deposition onto the gold. In
contrast to this, a more recent paper [114] finds that it is not possible to grow well-defined
self-assembled monolayers of a biphenyl-based organodithioacetate by immersing gold
samples in the corresponding solution. Since thioacetates are used in many papers [116-118]
for the preparation of monolayers on metals, we decided to carry out a detailed study on the
formation of self-assembled monolayers from aromatic thioacetates in particular on gold. The
widespread interest in triphenylamine (TPA) derivatives is due to their actual use as hole
transporting materials in electroluminescent multilayer light emitting devices based on
molecular organic compounds [119-122]. In their pioneering work on triphenylamine based
compounds Sakanoue et.al [123] pointed out that the reorganization energy is one of the most
important factors to determine the hole transport mobility, and a good hole transporting
material must have a small reorganization energy in an ionization process. For investigation
we chose substituted triarylamines- shown in the Figure 42 which have the great advantage
that the distance of the redox centres from the electrode, the chemical surrounding of the
redox centres as well as the type of the molecular bridges can be varied systematically.
These SAM structures can then serve as excellent model systems for studying bridge
AH-10 VK-55 TS-10 AH-4
Figure 42: Molecular structures of substituted triarylamine- AH-10, VK-55, TS-10 and AH-4.
Chapter Five Influence of the Leaving Group in Case of Triarylaminethiols
54
mediated ET (electron transfer processes). This was the aim of the project [13] to synthese
these substituted triarylaminethiols to use them as redox centres connected to donor- or
acceptor-substituted aromatic bridge units with saturated or unsaturated spacers. On the other
hand the important characterization of the SAMs was done using a broad set of experimental
techniques, gracing incidence infrared spectroscopy, x-ray photoelectron spectroscopy,
contact angle measurements, XPS, and STM. Altogether the experimental results allow for a
very consistent description of the adsorption behavior.
5.2. Self-Assembly Process of the Triarylaminethiols on Au(111)
5.2.1. Introduction
The experimental conditions of self-assembly were adjusted to optimize the formation of the
triarylaminethiols SAMs with or without deprotection. The adsorption of the substituted
triarylaminethiols layer(s) with deprotection was carried out by immersing the gold substrates
into 50 M solution of the compounds in dichloromethane at room temperature together with
10 mM of diethylamine. Acetyl protected thiols were deprotected during the formation of the
SAMs. Self-Assembled Monolayers formed on the gold surface in a solution of 50 M
without using the deprotection of the acetyl protected are further described.
After one day of immersing, the samples were efficiently rinsed with the solvent used for
deposition and dried in a stream of nitrogen to remove physisorbed overlayers. The
measurements were then carried out within the next 18- 24h.
5.2.2. Results
5.2.2.1. IRRAS
IRRAS spectra of substituted triarylaminethiols AH-10, TS-10, AH-4 and VK-55 have been
recorded for polycrystalline gold substrates prepared by immersion into ethanolic solution at
room temperature. In Figure 43, the low frequency regions of the IRRAS spectra are shown
together with the corresponding bulk spectra recorded using KBr pellets. All peaks in these
spectra can be assigned using data in the literature [17, 23], and the results are summarized in
Table 6.
Due to the selection rules on metallic substrates, only the vibrations with a transition dipole
moment component (TDM) perpendicular to the surface plane can be observed in the spectra.
As can be seen in Figure 43, the bands appearing in the surface spectra are also visible in the
Chapter Five Influence of the Leaving Group in Case of Triarylaminethiols
55
bulk spectrum, suggesting an adsorption process without decomposition, although some bands
are somewhat shifted. This shift might result from a different packing of the substituted
triarylamine- moieties in the film as compared to the bulk spectra. The compounds of
triarylaminethioacetate were deprotected during the formation of the SAMs using 10mM
(C2H5)2NH [13] and the process was successful, because in all four spectra of the monolayers
the vibration υ(C=O) around 1700 cm-1 disappeared.
While an exact tilt angle determination for the thiol-derived films was not possible with this
method, one can say with the help of selection rules of the IR that substituted triarlyamine-
molecules are not oriented perpendicular on the surfaces of gold.
Vibration band Literature(cm-1) Pellet(cm-1) SAM(cm-1)
υ (C≡C) 2100-2250 ~2199 ~2210
υ (C=O) 1710-1720 ~1707 -
υ (C=C)in ring 1500-1600 1504-1600 1510-1600
υ (C-N) 1200-1350 ~1240 ~1247
υ (C-N) 1200-1350 ~1289 ~1289
δ(C-H)oop 800-860 ~826 ~804
Table 6: Positions and assignment of the IR-modes In case of Au surface and KBr pellet.
Chapter Five Influence of the Leaving Group in Case of Triarylaminethiols
56
Figure 43: Infrared spectra of substituted triarylaminethiols AH-10, TS-10, AH-4 and
VK-55. The red trace displays are IRRAS spectra of the monolayer and the black trace
measured for a KBr pellet.
Chapter Five Influence of the Leaving Group in Case of Triarylaminethiols
57
5.2.2.2. XPS
Figure 44: XP spectra recorded for polycristalline gold substrates showing the carbon 1s,
nitrogen 1s, sulfur 2p and oxygen 1s region for the triarylaminethiols AH-10, TS-10,
VK-55 and AH-4.
X-ray photoelectron spectroscopy was used to confirm the adsorption of the triarylamienthiols
molecules on the Au (111) surfaces. The samples which are used for XPS measurements are
exactly prepared as those used for the IR measurements, the four compounds are deprotected
during the formation of the SAMs using 10mM (C2H5)2NH [13].
In the Figure 44, one can find the XPS spectra of the four SAMs in different regions measured
after 24 h of immersion in the ethanolic solution. The energy scales of all spectra were
referenced to the Au 4f7/2 peak located at the binding energy 84.0 eV. In case of S 2p region
only the spectrum of VK-55 shows a strange behaviour due to this shift to higher binding
energy. Examination of the spectrum S 2p region of the AH-10 SAM (see Figure 45) showed
168 166 164 162 160 158
0.0
0.1
0.2
S 2p regionah 10ts 10vk 55ah 4
Inte
nsit
y[c
ps]
Binding energie [eV]
406 404 402 400 398 396 394
0.00
0.04
0.08
0.12
Inte
nsit
y[c
ps]
N 1s regionah 10ts 10vk 55ah 4
290 288 286 284 282 2800.0
0.5
1.0
1.5
C 1s regionah 10ts 10vk 55ah 4
Inte
nsit
y[c
ps]
538 536 534 532 530 528
0.0
0.1
0.2
0.3
O 1s regionah 10ts 10vk 55ah 4
Inte
nsit
y[c
ps]
Binding energy [eV]
Chapter Five Influence of the Leaving Group in Case of Triarylaminethiols
58
two chemically different species S 2p(1) at 161.7 eV and S 2p(2) at ~163 eV. The two
doublets are having ratios of 2:1 and splittings of 1.2 eV, predetermined intensity ratio.
Figure 45: XPS S 2p spectrum of AH-10 adsorbed onto gold/Si. Two S 2p doublets with
2:1 area ratios and splittings of 1,2 eV were used to peak fit experimental spectrum.
Whereas the doublet at 161.7 eV is assigned to a metal thiolate species and the second doublet
at ~163 eV is related to unbound thiol molecules or the thiols are showing oxidized sulphur
[103].
The C 1s region for AH-10, TS-10 and AH-4 showed a single symmetric peak centred at
almost 284 eV and only the sample VK-55 shows a strange behaviour due to this shift of the
C 1s peak to the higher binding energy of ~ 285 eV.
The oxygen 1s region showed a broader peak with a binding energy of ~ 533.6 eV and only
for the VK-55 film exist a shift of the peak to lower binding energy. In case of the nitrogen 1s
region the AH-10 film shows a strange behavior due to a shift of the peak to lower binding
energy of ~ 398 eV comparisons to the others spectra, which are having their peak around 399
eV.
5.2.2.3. NEXAFS
To obtain information about the orientation of the molecules on the Au/Si surface, NEXAFS
spectra were recorded (see Figure 46). The samples which are used for NEXAFS
measurements are prepared as those used for IR and XPS measurements. If the degree of
polarization P of the incident synchrotron light is known, the intensity Iif of a NEXAFS
Chapter Five Influence of the Leaving Group in Case of Triarylaminethiols
resonance on substrates with 3-fold symmetry, see sec. 2.3 [29].
Figure 46: NEXAFS C 1s spectra of TPA (triphenylaminethiols) AH-10, AH-4, TS-10 and
59
The spectra were normalized to the “edge jump” height of the C 1s edge and we observe the
*-resonances at 285.1 eV, Rydberg resonances (R*) at ~ 287.7 eV and σ*- resonances at
292.1 eV. The anisotropy of the intensity of these *-resonances was used for the
determination of the tilt angles of the respective transition dipole moments and therefore of
the molecular orientation. For the phenyl ring, the symbol “*C=C” is used to denote the
delocalized * structure in the phenyl ring for typographical convenience [124]. The origin of
the energy shift of core→ * transitions in different functional groups is due to differences in
the unoccupied orbital energy as well as that of the C 1s core level [29].
The C 1s→ *C=C transitions are dominating and the C 1s peak is assigned at 285 eV,
indicating that the E vector of the X-rays is parallel to the macromolecular backbone, which is
observed for these four SAMs.
VK-55 at different angles of incidence of the synchrotron light.
Chapter Five Influence of the Leaving Group in Case of Triarylaminethiols
60
One can observe in case of these four TPA compounds that “no dichroism” is present in the
NEXAFS spectra and therefore one can not analyze the orientation of the TDM and
simultaneously the orientation of these four molecules on the surface.
5.2.2.4. Deprotection Process
In chapter 5.2.2.1 presented above, IR measurements for the four compounds of
triphenylaminethiols (TPA) using the deprotection process were shown [13]. The process was
effective, because in all four spectra of the monolayers the vibration corresponding to υ(C=O)
around 1700 cm-1 disappeared. Now there are surface bound via an aromatic thiol unit, thus
there is no potentially insulating alkyl fragment between the aromatic moieties and the gold
[115].
In this chapter IR data of the same samples of triphenylamine thiols AH-10, TS-10 and AH-4
without using the deprotection process during the formation of the SAMs will be presented.
The monothioacetyl moiety could even be used, without deprotection by using the 10mM
(C2H5)2NH, to generate the SAM directly.
In case of the direct adsorption or amine-promoted adsorption ((C2H5)2NH)) of the thioacetyl-
terminated systems, the IR results confirmed that the SAMs were similar in their composition
to the SAMs generated by the using of 10mM (C2H5)2NH.
Chapter Five Influence of the Leaving Group in Case of Triarylaminethiols
61
Figure 47: IRRAS spectra of AH-10, TS-10 and AH-4. The red lines are showing
the spectra without deprotection process and the black lines the spectra with
deproctection (used 10mM (C2H5)2NH) [13].
Chapter Five Influence of the Leaving Group in Case of Triarylaminethiols
62
From Figure 47 it is obvious that there are no differences between the IR spectra measured
after deprotection during the formation of the SAMs and the spectra measured without using
the 10mM (C2H5)2NH agent. The most important and surprising effect was that the vibration
corresponding to υ(C=O) around 1700 cm-1 disappeared in both cases.
In the following chapter STM measurements on these triarlyaminethioacetates are presented,
which will show the influence of the deprotection process.
5.2.2.5. STM
For these measurements gold on mica was used, prepared as descriebed in the chapter 3.2.3.,
and then immersed in the ethanolic thiol (AH-4-conformative flexibility) solution for 24 h.
The measurements were done at room and elevate temperature on samples prepared with and
without using the deprotection process (the amine-promoted adsorption).
Figure 48: STM measurements on the AH-4 molecule. Conditions: with deprotection,
10-20 µM DCM solution; Ut= 600 mV, It= 70 pA.
Figure 48 shows measurements of AH-4 molecule done at the room temperature and using the
deprotection conditions. This molecule is rather flexible due to the inserted methylene group
and the monolayer shows the typical atomically flat terraces of the Au substrate, which has a
height of 2.4 Å [9]. One can observe specific structures as observed for other thiol SAMs on
Au (111) like holes in the morphology of the substrate [9] only in a lower number of them.
Chapter Five Influence of the Leaving Group in Case of Triarylaminethiols
63
Figure 49: STM measurements on the AH-4 molecule. Conditions: with deprotection at 60°,
10-20 µM DCM solution; Ut= 650 mV, It= 65 pA
Figure 49 shows STM measurements on the same SAM and in the same condition of
deprotection but an elevated temperature of 60°. In the large-scale image one can observe
many terraces separated by monoatomic steps characteristic to the thiols on Au (111). The
morphology of the structure slightly changed and now the SAMs are denser on the gold (111)
substrate. It was impossible to record images, showing AH-4 compounds in the molecular
resolution.
Figure 50: STM measurements on AH-4 molecule. Conditions: without
deprotection, 10-20 µM DCM solution; Ut= 600 mV, It= 70 pA.
Chapter Five Influence of the Leaving Group in Case of Triarylaminethiols
64
Figure 50 shows STM measurements of AH-4 SAMS formed without the deprotection
process. The deprotection has been done by the molecules themselves during the bond of the
sulfur to the gold surface, without the amine-promoted adsorption.
In the large-scale image one can observe many terraces separated by the steps and more holes,
which are characteristics for other thiols on Au (111). By zooming in the region indicated in
Figure 50 one can not observe many differences, in detail there are the same lower number of
the so-called edge pits in comparison with the images shown in Figure 48 where the
deprotection process was used. It was impossible to reach high resolution, however, and one
can say that these molecules are not forming highly ordered monolayers.
5.2.3. Disscussion
From the IR measurements between the bands of the pellets spectra and the SAM spectra
measured on the gold substrate there is good agreement. By the comparison between SAM
spectra measured after deprotection and SAM spectra measured without deprotection one can
observe that these spectra are almost similar and in very good agreement. The peak around
~1700 cm-1 disappeared in both cases, which means that the protecting acetyl group was
easily removed [125]. It is deduced that triphenylaminethiols (TPA) adsorbed on the surface
in both cases if the deprotection process was used or not. These molecules are able to
deprotect themselves with a longer and slower reaction by the bounding of the sulfur
compound to the gold (111) surface compared to the normal adsorption process of
alkanethiols [115].
From the STM measurements it is concluded that these molecules are not forming highly
ordered SAMs, perhaps the molecules are lying down (striped phase) on the surface or they
are tilted from the surface normal, but the determination of the molecular orientation it is not
possible without molecular resolution and with these variations arise from the measurements.
Also from the NEXAFS measurements (Figure 46) it is difficult to understand the orientation
of TPA molecules. The π*-resonances do not show any dichroism, which means that the
triphenylaminethiols molecules do not show any angle dependence, perhaps they exhibit a
disorder on the surface. The confirmation of the chemisorption takes place with XPS shown in
Figure 44 and Figure 45.
Examination of the spectrum S 2p region of AH-10 molecule showed two chemically
different species S 2p(1) at 161.7 eV [108, 109] and S 2p(2) at ~163 eV. The peak at 161.7 eV
is assigned to a metal thiolate species and the second peak at ~ 163 eV is related to unbound
Chapter Five Influence of the Leaving Group in Case of Triarylaminethiols
65
thiol molecules or the thiols contain oxidized sulphur [103].
The spectrum of VK-55 shows a shift and one can not say if this molecule remains thiol or not.
In C 1s region three samples showed a single symmetric peak centred at almost 284 eV in
agreement with the literature. Only the VK-55 SAM shows a strange behaviour with the C 1s
peak shifted to the higher binding energy of ~ 285 eV.
From the XPS measurements one can conclude that monolayers are formed on the gold
substrates, with exception of the VK-55 molecule.
Because it is difficult to characterize the structure of these SAMs as we observed in STM
measurements and from NEXAFS measurements we can not determine the orientation of the
molecules on the gold surface, in the following an eventual model of the arrangement of one
molecule of AH-4 on the Au (111) will be presented.
Figure 51: Model of an AH-4 molecule on the Au (111) surface flat lying or tilted away
from the surface.
Chapter Six Formation of Self-Assembled Monolayers from Alkane Thioacetates
66
Chapter Six
Formation of Self-Assembled Monolayers from Alkane Thioacetates
In this chapter, the growth of self-assembled monolayers (SAMs) from dodecyl thioacetate
C12SAc onto gold (111) substrates has been studied by using gracing incidence infrared
spectroscopy, X-ray photoelectron spectroscopy, contact angle measurements, ellipsometry,
near-edge X-ray absorption spectroscopy, and scanning tunneling microscopy. We found that
the monolayers derived from the thioacetate have a significantly different structure compared
to the ones obtained from the corresponding alkanethiol (C12SH) and are further described.
6.1. Introduction and Objective of the Work Presented in this Chapter
Although self-assembled monolayers are already known for a couple of decades, they still
receive a lot of attention, since they slowly start making their way into a variety of technical
applications. Of the numerous kinds of monolayer systems, the one of organothiols on gold
have been proved to be the most popular ones due to their reliable formation and almost
predictable structure. While for monolayer formation most often organothiols or
organodithiols are being used, in a number of cases also organothioacetates or
organodithioacetates have been utilized [62, 98]. For example most studies on so-called break
junctions, where single molecules are attached in between two gold electrodes in order to
directly measure the electrical characteristics of these molecules, dithioacetates have been
used as precursors for the resulting dithiolates [112, 113]. Nevertheless, the opinion on the
adsorption chemistry of thioacetates on gold surfaces is somewhat controversial [114].
An early paper [115], reported that organothiolate adlayers formed from thioacetates have a
similar quality as the ones obtained from the respective thiols. The authors speculated that
some of the thioacetate molecules are hydrolysed in solution followed by deposition onto the
gold. In contrast to this, a more recent research work [114] finds that it is not possible to grow
well-defined self-assembled monolayers of a biphenyl-based organodithioacetate by
immersing gold samples in the corresponding solution. Since thioacetates are used in several
works [116-118] for the preparation of monolayers on metals, we decided to carry out a
detailed study on the formation of self-assembled monolayers from thioacetates in particular
on gold. As a model substance we chose dodecyl thioacetate, CH3(CH2)11SCOCH3 (C12SAc),
since the monolayers of the corresponding thiol are well known and thoroughly characterized
Chapter Six Formation of Self-Assembled Monolayers from Alkane Thioacetates
67
[126, 127]. In order to rule out any interference from small contaminations by free thiols, we
synthesized a high purity thioacetate virtually free of any thiol. Note that in the past, trace
amounts of thiols in the starting materials lead to wrong conclusions about the monolayer-
forming properties of dialkylsulfides [115]. The adsorption of C12SAc is investigated using a
broad set of experimental techniques, gracing incidence infrared spectroscopy, x-ray
photoelectron spectroscopy, contact angle measurements, XPS, and STM. Altogether the
experimental results allow for a very consistent description of the adsorption behavior.
We found that the monolayers derived from the thioacetate have a significantly different
structure compared to the ones obtained from the corresponding alkanethiol (C12SH). The
objective of this work was to understand better why this difference between thioacetate and
the corresponding thiol occurs, and to find the explanation for a kinetic stabilization of the flat
lying phase the structure, which is formed by the separation of the acetyl group.
6.2. Preparation of the SAMs of C12SAc
6.2.1. Introduction
The experimental conditions of self-assembly were adjusted to optimize the formation of
C12SAc-SAMs. The adsorption of the dodecanethiolate and dodecyl thioacetate layer(s) was
carried out by immersing the substrates (gold substrates) into 10-20 M solution of the
compounds in ethanol or dichloromethane at room temperature. Self-assembled monolayers
of dodecanethiol (C12SH) were grown as reference.
After one day of immersing, the samples were efficiently rinsed with the solvent used for
deposition (ethanol or dichloromethane, respectively) to remove physisorbed overlayers and
dried in a stream of nitrogen. The measurements were then carried out within the next 18- 24h.
All the measurements confirm that the thioacetate C12SAc adsorb on the surface as a striped
phase in comparison with the normal thiol of C12SH.
6.2.2. Results
6.2.2.1. IRRAS
Figure 52 displays gracing incidence IR spectra recorded from films obtained by immersion
of gold substrates in solutions of C12SH and C12SAc, respectively. The spectra obtained of
similarly prepared samples of these two substances are superimposed for comparison. The
Chapter Six Formation of Self-Assembled Monolayers from Alkane Thioacetates
68
spectra for C12SH films resemble closely those reported earlier for the same system [126]. The
spectra recorded for C12SAc are clearly different from those obtained for the C12SH and
indicate that much less material has adsorbed on the gold surface. To make sure that this is
not an effect for significant slower film formation kinetics for C12SAc, the experiments were
repeated with very long immersion times (120 h), resulting in virtually unchanged spectra for
both the thiol and the thioacetate (Figure 52c).
Due to the dipole selection rules on metallic substrates, only the vibrations with a transition
dipole moment component (TDM) perpendicular to the surface plane absorb the IR radiation
and can be seen in the spectra. As described in detail in previous publications [95, 128] the
order and – if applicable – the tilt angle of the molecules in the films can be determined from
the relative intensity of the CH3 and CH2 bands because of their differently oriented TDMs. In
Table 7, we assign the guide frequencies together with the data fitted for the C12SH spectra
using Gaussian curves as shown in the Figure 53.
Using these data, it can be concluded that the films deposited from dichloromethane (DCM)
consist either of much less material (C12SAc) or are more disordered (C12SH) than the ones
generated from ethanolic solution. We therefore focus on films deposited from ethanol in the
following.
While a tilt angle determination for the thiol-derived films was possible, an obvious change in
the TDMs of the vibrations for the thioacetate made this impossible. This kind of changes in
the vibrational spectra has been described earlier for molecules lying flat on metal surfaces
and is caused by the electronic coupling to the electron gas of the metal [129].
Chapter Six Formation of Self-Assembled Monolayers from Alkane Thioacetates
69
Figure 52: Infrared spectra of C12SH and C12SAc a) in ethanolic solution, b) in ethanolic
solution for five days and c) in dichloromethane solution.
Chapter Six Formation of Self-Assembled Monolayers from Alkane Thioacetates
70
Stretching mode Max [cm-1] Fit [cm-1] Lit. [cm-1]
CH2 sym (d+) 2850.5 2850.5 2850
CH3 sym (r+) 2878.8 2879.1 2876
CH2 sym FR(d+FR) 2899.5 2900.8 2895
CH2 asym (d-) 2918.8 2918.7 2917
CH3 sym FR(r+FR) 2937.4 2937.7 2932
CH3 asym ip (r-) 2964.2 2964.3 2968
Table 7: The assigment of the peaks of C-H stretch mode vibrations from Figure 53.
The peaks were fited by Gaussian (Origin 7) [23].
3000 2900 2800
0
1
2
3
296
4.3
293
7.7
2918.7
29
00
.4
28
79.1
28
50.5
C12
SH
Ab
so
rban
ce
[10
3 AU
]
Wavenum ber (cm-1
)
Figure 53: RAIRS spectra of C12SH on the gold substrate (111) showing the region
of C-H stretch mode vibrations and the approximation of these peaks.
Chapter Six Formation of Self-Assembled Monolayers from Alkane Thioacetates
71
6.2.2.2. Water contact angle
Contact angle measurements are an effective and relatively effortless means to gain
information about macroscopic surface properties of molecular films [130]. Since these
measurements are extremely surface sensitive, they allow to distinguish between surfaces
exposing alkyl chains in different orientations [84, 131]. The advancing contact angle for
water on dense self-assembled monolayers of C12SH on gold have been reported to be larger
than 103° [132]. This corresponds very well with the value found for the C12SH monolayers
deposited from ethanol (104°), while deposition from DCM results in layers with contact
angles of 97°, hinting on a diminished homogeneity of the surface endgroups.
The monolayers of thioacetate were found to be much more hydrophilic, exhibiting contact
angles of about 65° independently from the immersion time in the ethanolic solution. A
similar value has been found for methylene-group terminated SAMs, suggesting that the
layers generated from C12SAc do not expose CH3 groups, but their central chains [84]. This
could either be the effect of strong disorder or of flat-lying molecules.
6.2.2.3. Ellipsometry
One of the most convenient possibilities to characterize thin films is the determination of the
film thickness by optical ellipsometry. This very fast method effectively gives an idea about
the properties of the respective systems. Within minutes the layers derived from the reference
system C12SH reach a final thickness (6 Å vs 18 Å) as has been reported in the literature for
closely packed films with almost upright molecules [61]. Although the films derived from
C12SAc also reach their final thickness within minutes, which suggests the formation of
incomplete SAMs from C12SAc with a thickness of 30% relative to the thickness of the C12SH.
This situation remains unchanged even after 120 h of immersion.
6.2.2.4. XPS
In Figure 54 we show results obtained by x-ray photoelectron spectroscopy for the C 1s, S 2p,
Au 4f and O 1s regions. The recording time for the spectra was as short as possible. As seen
in the S 2p data, even under these precautions a certain amount of beam damage already
occurred what has to be considered when analyzing the data. Besides this damage effect, only
one sulfur species with a binding energy of 161.8 eV can be found, being consistent with the
formation of thiolate upon adsorption for both films [133]. The data recorded in the Au 4f
region show Au core-level lines which are much more intense in the case of the C12SAc than
for C12SH, revealing that the adlayers of the thioacetate are considerably thinner. This is
Chapter Six Formation of Self-Assembled Monolayers from Alkane Thioacetates
72
supported by the C 1s spectra showing much lower signal intensity for the monolayers
deposited from the thioacetate, hinting on highly tilted molecules. In the case of the C 1s
spectra one also notes a significant difference in the energy of the core-level lines: The
observed C 1s binding energy for the monolayers derived from the thioacetate is about 0.4 eV
lower than for the thiol-derived monolayers. This effect has been observed before for
molecules lying flat on metal surfaces [129].
The reason for this shift is probably final state effects, lowering the binding energy of the C 1s
core hole in case of flat-lying molecules because of the better screening by the metal
electrons [134]. Consistent with this are the observations in the O 1s regime: while in the
monolayer generated from the thiol only trace amounts of oxygen can be found, the layers
made from C12SAc contain about one oxygen atom for every three molecules. Since this
Figure 54: XP spectra recorded for polycristalline gold substrates showing the carbon
1s, gold 4f, oxygen 1s region and sulfur 2p region for thioacetate (C12SAc) and thiol (C12SH)
immersed in ethanol solution.
Chapter Six Formation of Self-Assembled Monolayers from Alkane Thioacetates
73
cannot result from the adsorption of intact thioacetate molecules (for which a ratio of 1:1
would be expected), we believe that the oxygen atoms rather stem from the oxidation of the
monolayer after formation during manipulation and transfer into the XPS set-up. It has been
reported in the past that the sulfur atoms of flat-lying thiolates are rather prone to oxidation by
atmospheric oxygen [135].
6.2.2.5. NEXAFS
To obtain more detailed information about the orientation of the thiolate molecules in the two
kinds of monolayers, NEXAFS spectra were recorded (Figure 55). The spectra of the C12SH
SAM very closely resemble earlier NEXAFS results reported for alkanethiolate-based SAMs
[136].
In the spectrum for the C12SH the resonance denoted R* has been shown to result from an
excitation into unoccupied orbitals with stronger R character [137, 138]. These signals show a
pronounced variation of the resonance intensity with the angle of incidence. A quantitative
analysis of the linear dichroism reveals a tilt angle of θ = (63 ± 5)°. For the C12SAc-based
SAM, the NEXAFS spectra are quite different. While the R* resonance is much less
pronounced, an additional resonance labeled as * can be seen at energy of 285 eV. This
resonance is attributed to a small amount of C=C double bonds, possibly generated by some
beam damage. Since the spectra as well as their angle dependency are significantly different
compared to the ones for the thiol-derived monolayers, the orientation of the alkyl chains in
the adlayers obtained by immersion in C12SAc must be considerably different. Note, that in
previous work it has been found that if alkane chains are in direct contact with a metals
surface, the R* resonance is modified in a way similar to that seen in the figure obtained here
for the C12SAc layers [139].
Therefore, the NEXAFS results are consistent with a monolayer in which the axes of the
hydrocarbon chains are parallel to the gold surface.
Chapter Six Formation of Self-Assembled Monolayers from Alkane Thioacetates
74
Figure 55: NEXAFS spectra of a) C12SAc and b) C12SH thiol for different angles of
incidence of the synchrotron light. The solvent used for the solutions was EtOH.
6.2.2.6. STM
Since the presence of an alkanethiolate-based SAM with the alkyl chains orientated parallel to
the substrate not as an intermediate [68, 140] but as the final state appears to be in conflict
with previous reports (see above) additional experiments were carried out using high-
resolution scanning tunneling microscopy (STM).
The STM data reproduced in Figure 56 clearly demonstrate the presence of a striped phase, a
typical signature of low-density, intermediate SAM phases. In Figure 56 (a and b) we show
large scan area STM micrographs recorded for Au substrates covered with monolayers of
Chapter Six Formation of Self-Assembled Monolayers from Alkane Thioacetates
75
C12SH and C12SAc, respectively, formed after 48 hours from 10-20 M solutions in ethanol.
At this lengths scale no major differences are seen, both images are dominated by the terraces
of the gold substrate and small circular depressions, which in earlier work have been
identified as vacancy islands [9].
The only difference might be a somewhat lower number of depressions for the film derived
from the thioacetate, although we have not quantified this amount.
While the high resolution STM for the monolayers derived from the thiol solution show the
same patterns of a densely packed SAM as reported earlier (not shown here), those of the
thioacetate clearly show the presence of two different phases. The dominant one is a striped
phase exposing three different orientations on the gold substrates Figure 56 (c), exhibiting a
close similarity to the results reported in previous papers [68, 140-145]. A high resolution
micrograph like the one shown in Figure 56 (d) allows to determine the distance between
adjacent rows, resulting in 15-16 Å. This value closely agrees with the length of extended
dodecanethiolate molecules, suggesting straight, flat-lying molecules in a parallel order. The
distance between the parallel molecules, as shown by the line scan in Figure 56 (d), is 5 Å,
suggesting a rectangular (p×2√3) unit cell containing two molecules, with the larger value
being predominantly determined by the length of the molecule. It should be mentioned that in
case of an orientation of the molecules parallel to the longer vector (thus being oriented
perpendicular to the rows of neighboring sulfur atoms) the value of p should be 6 resulting in
a calculated unit-cell length of 17.3 Å.
Although a number of different flat-lying phases are already described [68, 140-145] and even
a phase diagram has been established by Poirier [68], this particular phase has, to the best of
our knowledge, not been observed before. All previously known striped phases either show a
head-to-head arrangement with a stripe width significantly larger than the alkanethiolate
length (up to twice) or an alternating (intercalating) ordering with a pairing of the sulfur atoms
in form of double rows, resulting in a typical elongated ‘plaid’ pattern.
The second structure to be found in the C12SAc films is shown in Figure 57. This structure is
basically identical with those found for high-quality SAMs prepared by immersion of Au(111)
surfaces into alkanethiol solutions. As in previous publications on dodecanethiol monolayers
[68], we find a unit cell (Fig. 7b-d) described by a rectangular c(4×2) superlattice. It is
interesting to note that these areas of apparently upright orientated molecules are always
located at domain boundaries or other defects of the striped phase. For prolonged immersion
times the relative area of this phase was observed to slowly increase, but even after two days
the relative area of this upright orientated phase did not exceed 40 % of a monolayer.
Chapter Six Formation of Self-Assembled Monolayers from Alkane Thioacetates
76
Figure 56: (a) Constant-current STM micrographs showing the gold substrate after
immersion into a 10-20 µM ethanolic solution of C12SH at 273 K for 48 h. Tunneling
parameters: (a) Ut= 600 mV, It= 70 pA. (b) Constant-current STM micrographs showing
the gold substrate after immersion into a 10-20 µM ethanolic solution of C12SAc at 273 K
for 48 h. Tunneling parameters: (b) Ut= 650 mV, It= 80 pA.(c) Constant-current STM
micrographs showing the stripe phase with the three different orientational domains.
Tunneling parameters: (c) Ut= 1000 mV, It= 65 pA. High resolution STM micrographs
Chapter Six Formation of Self-Assembled Monolayers from Alkane Thioacetates
77
showing the stripe phase on one of orientational domains. Tunneling parameters:
(d) Ut= 1000 mV, It= 65 pA.
Figure 57: Constant-current STM micrographs showing the gold surface after immersion
into a 10-20µM ethanolic solution of C12SAc at 273 K for 48 h. In (b), the unit cell of the
(2√3×4)R30° structure is marked by the rectangular box. Tunneling parameters: (a) Ut=800
mV, It= 95 pA; (b) Ut= 1000 mV, It= 75 pA.
Chapter Six Formation of Self-Assembled Monolayers from Alkane Thioacetates
78
6.2.2.7. Re-immersion of C12SAc-SAMs into thiol solutions
Since the layers derived from the thioacetate remain virtually unchanged even after prolonged
immersion times in the C12SAc solution, we wanted to understand whether inhibition of the
addition of further molecules was a general phenomenon or was specifically for the
thioacetate molecules. For this, we re-immersed the monolayers formed from C12SAc into a
solution of the corresponding thiol, C12SH (for 24h). The IRRAS measurements are shown in
Figure 58.
The IR spectra reveal a close similarity to the ones obtained for dense thiolate SAMs, which
also indicate the presence of a saturated hydrocarbon chain with its C-C-C backbone
orientated parallel to the substrate (Figure 58). The XP spectra obtained after this re-
immersion step are presented in Figure 59. The monolayers now contain much more material
and are now very similar to the ones obtained by immersion of the plain gold substrates into
Figure 58: C-H vibrational area of the IRRA spectra of the monolayers formed from C12SAc,
C12SH, as well as of the C12SAc-derived monolayer after re-immersion into C12SH solution.
The significantly lower intensity of the signals in the C12SAc-derived monolayer hints on a
much lower coverage, while re-immersion of this layer forms monolayers similar to the ones
obtained directly from C12SH.
Chapter Six Formation of Self-Assembled Monolayers from Alkane Thioacetates
79
the C12SH solution, as demonstrated with the C 1s signal. In this particular experiment the
amount of beam damage, as can be seen in the S 2p area, is much more pronounced due to
experimental reasons. It nevertheless becomes clear that the re-immersed samples are densely
packed monolayers since they show an O 1s signal much smaller than even the monolayers
directly prepared from C12SH.
Figure 59: XP spectra recorded for polycristalline gold substrates showing the carbon
1s, oxygen 1s and sulfur 2p region for thioacetate (C12SAc) reimmersed for 24 h in the
thiol (C12SH) solution (solvent:EtOH).
Also the macroscopic properties of these re-immersed samples become similar to the ones of
C12SH monolayers: the contact angle of 102° indicates the formation of a well ordered SAM
with almost upright molecules.
Chapter Six Formation of Self-Assembled Monolayers from Alkane Thioacetates
80
6.2.3. Discussion
All together the results obtained by the different techniques allow to put forward a structure
model for the C12SAc films as presented in Figure 60. On the basis of our results we can
conclude, that in contrast to C12SH SAMs, (upright molecules), the C12SAc do not form a
SAM within almost upright orientation of the alkanethiolate films but that the adsorption
stops at an earlier state. Essentially the surface is covered by the so called flat lying phase.
This phase has first been identified in early STM measurements by Poirier et al [144]. The
STM data reported here are in full agreement with the striped phase consisting of lying-down
molecules. Obviously the adsorption of further molecules must be kinetically strongly
hindered when this first layer is present on the surface. The structure model proposed in Fig.9
for the alkanethiolate SAMs derived from C12SAc is fully consistent with the fact that in the
XPS data the C 1s core-level is shifted by 1.6 eV to lower binding energy. In earlier work this
effect has been demonstrated in case of mono- and multilayers of alkanes adsorbed on Cu
surface and have been explained by final state screening effects, which are stronger for carbon
atoms in close proximity to metal surface. Already for a bilayer of saturated hydrocarbon on a
Cu(100) surface the C1s binding energy is reduced by almost 1 eV [146]. Also the spectral
features in the NEXFAS data are fully consistent with such a phase of flat lying molecules.
Since in earlier work it has been shown that in particular the prominent R* resonance
dominating the NEXFAS spectra of alkanethiolate based SAMs is strongly affected if the
hydrocarbon chain is in direct contact with the metal surface. It should be noted that in the
spectra recorded for the C12SAc there is some similarity with the SAMs obtained from C12SH
solutions after short immersion times in very diluted solutions [147]. Probably the most
conclusive evidence for the presence of such striped phase comes from the STM data where
clearly stripes with an average distance of 15-16 Å can be seen. This value corresponds very
well to the lengths of the hydrocarbon chain in the C12SAc molecule and also corresponds
very well to the results obtained by Poirier et al obtained for decanethiol on Au(111). The
fact that the (2√3×3)-islands (appearing higher in the STM micrographs) are always localized
at the domain-boundaries of the striped phase (Figure 60) or near surface defects (in particular
step edges) suggests that the transformation of the striped-phase containing flat-lying
molecules into the dense, upright (2√3×3) phase is significantly hindered. Since the latter
phase should be the thermodynamically more stable, we conclude that there must be a kinetic
limitation hindering the formation of adsorbed thiolates from the thioacetate.
Chapter Six Formation of Self-Assembled Monolayers from Alkane Thioacetates
81
Figure 60: Model of the surface layer formed upon adsorption of C12SAc (top view). The
surface is dominated by the flat-lying phase with the molecules lying next to each other
with alternating orientation. At domain boundaries or defects the (2√3×3) structure with
upright molecules can be formed due to the accessibility of the gold surface for further
C12SAc molecules.
After having established the structure model for the C12SAc based SAMs we can now turn to
the discussion of the reasons why the adsorption apparently stops at a coverage, which is
significantly lower than that of a high quality SAM with almost upright molecules as obtained
by immersing the gold films in a solution of the alkanethiol, C12SH. The flat lying phase
sketched in Fig.9 corresponds to the lowest coverage where the gold surface is completely
covered by molecules. When this coverage is reached, molecules interacting with the surface
will first have to find small areas of the bare gold surface where the sulfur of the thioacetate
group can get closely enough to the gold surface to form a chemical bond to the substrate and
to break the chemical bond to the acetate group. We propose that this adsorption on the
surface is strongly hindered after the striped phase has fully developed. Such a kinetic
limitation is strongly supported by a closer investigation of the STM data [148]. These data
show that for prolonged immersions in the C12SAc solution small areas developed which can
be identified as regions with upright orientated molecules. Although the area of these small
Chapter Six Formation of Self-Assembled Monolayers from Alkane Thioacetates
82
patches is to small to allow a spectroscopic characterization with IR, NEXAFS or XPS, the
high resolution STM data clearly allow an assignment to areas with upright ordered
molecules. It is very interesting to note that these small patches of upright orientated
molecules are only observed at defects, e.g at domain boundaries between perfect areas of the
striped phase. This is in full accord with the kinetic limitations proposed above. After the
striped phase has formed the solvated C12SAc molecules can only react with the gold surface
at defects like etch pits, domain boundaries and possibly step edges. This explanation based
on a kinetic stabilization of the flat lying phase is strongly supported by the experiments
where C12SAc based SAMs were immersed in a solution of the corresponding alkanethiol,
C12SH. IR spectra and XPS spectra as well as contact angle measurements recorded after this
second immersion are basically indistinguishable from the corresponding data recorded for
C12SH based SAMs. This result is expected since for the corresponding alkanethiol much less
space is needed for getting the sulfur in contact with the gold. Although in this case a two step
adsorption process has been observed, where first a highly disordered film is formed and this
is followed by significantly slower second step where the orientational order is introduced,
immersion in the solutions of alkanethiols generally results in the formation of upright
oriented films [136].
We have obtained experimental data for gold substrates immersed into solutions of C12SAc
with high purity which demonstrate that alkanethiolate SAMs obtained by immersion into
organo-thioacetate has a significantly different structure from SAMs obtained by immersion
into alkanethiol solutions. The SAMs obtained by immersion into the thioacetates correspond
to a low coverage phase, which has also been observed previously for the alkane thiols.
Further adsorption after the completion of the low coverage phase is strongly hindered by
kinetic effects. Re-immersion into alkane thiol solutions leads to the formation of SAMs,
which are indistinguishable from those obtained after immersion into thiols. We speculate that
small modifications of the thioacetate group, e.g adding a more bulky hydrocarbon group,
may show further strong effects on the SAM formation process.
Chapter Seven Determination of Trans/Cis Isomerization of Azobenzene Molecules
83
Chapter Seven
Determination of Trans/Cis Isomerization of Azobenzene Molecules
Photo-induced trans–cis isomerization of N- [4-(Phenylazo)phenyl]-1,2-dithiolan-4-
carboxamid (Azo 1) and 4-(Phenylazo)phenyl]-1,2-dithiolan-4-carboxylat (Azo 2) were
investigated in this work in ethanol. The results of infrared spectroscopy, contact angle
measurements and scanning tunnelling microscopy obtained by the investigation of the SAMs
of these azobenzene molecules, were cross-correlated with the trans–cis isomerization
determined from UV–visible spectra in solution. The kinetics of the photoisomerization
reaction of the trans- species under UV light irradiation is described by a simple first order
exchange between the trans and cis forms of the molecules. The cis-to-trans reversion in the
absence of irradiation is about 3% of the back reaction under irradiation [149].
7.1. Introduction and Objective of the Work Presented in this Chapter
The azobenzene chromophore continues to attract considerable interest as it offers the
potential for creating photoresponsive materials [14-16]. The properties of these molecules
may be altered reversibly by irradiation at selected wavelengths or by the temperature.
Recently, the introduction of azobenzene into SAMs has been examinated, resulting in unique
SAM structures [150]. It is known that azobenzene is photoisomerizable from trans to cis
isomers and from cis to trans isomers upon irradiation with UV light (366 nm) and with vis
light (436 nm), respectively. SAMs containing a azobenzene moiety could have the potential
for photoresponse(shown Figure 61) [151]. This isomerization results not only in a change of
geometry and dipole moment but also in a change in its optical properties.
Nevertheless, the introduction of the azobenzene in the SAMs could not produce a
photoisomerizable monolayer because there is not enough space to photoisomerize in close-
packed molecular films. This means that a passage volume is necessary for the isomerization
of the azobenzenes, even in a monolayer [152] and a suitable spacer in order to reduce the
metal substrate-azobenzene interaction. In the cis configuration the footprint area is twice as
large as for trans configuration, that means for a efficient photoisomerization in the film one
needs larger free volume [153].
Chapter Seven Determination of Trans/Cis Isomerization of Azobenzene Molecules
84
UV light
Visible light
Trans form Cis form
Figure 61: Conformational change of azobenzene [151].
In this work, the photoresponse of the solutions Azo 1 and Azo 2 (Figure 62) was investigated
by using UV/VIS spectroscopy. The photoreactivity and the effects on the structure of the
SAMs formed from the same molecules has been observed on the basis of the measurements
of static contact angles [154], IRRA spectroscopy and scanning tunneling microscopy.
The purpose of this work was to develop further our studies on structural characterization of
these SAMs and to evaluate the possibility to credible distinguish cis and trans azobenzene
isomers due to the reversibility of the irradiation process.
NN
OO
S S
NN
NHO
S S
Azo 2 Azo 1
Figure 62: Azo 1 and Azo 2 molecules.
NN
NN
Chapter Seven Determination of Trans/Cis Isomerization of Azobenzene Molecules
85
7.2. Preparation of the solutions containing the azobenzene molecules
The experimental conditions of the solutions were adjusted to optimize the reversibility of the
irradiation process and to distinguish the trans and cis isomers in both solutions, Azo 1 and
Azo 2. The preparation of the solution takes place in a dark room, in ethanol and the
concentration of the solutions is about 0.1 mM. There the solutions were irradiated with UV
light of 366 nm and to bring the molecules back in the ground state, they were irradiated with
Vis light of 440 nm. UV–visible spectra were recorded using a SPECORD 200 UV-visible
spectrometer. Samples were contained in quartz cuvettes and spectra were collected in single
beam mode over a wavelength range of 200 nm to 600 nm.
7.2.1. Results
7.2.1.1. UV/VIS Spectroscopy
As outlined in the previous section, the reversible photo-induced trans– cis isomerization of
solutions Azo 1 and Azo 2 were investigated by UV–visible spectroscopy as shown in Figure
63.
Figure 63 shows the UV-vis spectra of the both solutions against the irradiation process. The
unirradiated sample solutions show two important absorption bands, an intense one at 345 nm
in the case of Azo 1 and for Azo 2 at 320 nm attributed to the π- π* electronic transition of the
trans-azobenzene moiety and the second band very weak at 442 nm for Azo 1 and at 435 nm
for Azo 2, which are assigned to the forbidden n- π* electronic transition [149].
After the irradiation with UV light (the red curves), one can observe that the bands
corresponding to the trans-azobenzene moiety are decreased for both solutions. This means
that the cis form of the isomers in the solutions are formed. To demonstrate that the irradiation
process is reversible, the solutions were then irradiated with the vis light for 1h and
subsequently again irradiated with UV light. In the Figure 63 one can observe that the second
cis-spectrum (the green curve) is very similar to the first one, which means that the irradiation
process is reversible and the reproducibility of the measurements was successfully
demonstrated.
Chapter Seven Determination of Trans/Cis Isomerization of Azobenzene Molecules
86
Figure 63: UV-VIS spectra of Azo 1 and Azo 2 solutions in the ground state of trans
isomers and after irradiation with the UV light.
7.3. Preparation of the SAMs on gold surfaces (111)
The ordered monolayers of azobenzene molecules (Azo 1 and Azo 2) on gold have been
prepared by the self-assembling technique [155]. The molecules are bound covalently to the
gold through the disulfide group, which will break upon adsorption of the molecules on the
gold surfaces. Figure 64 shows the azobenzene chains on the gold substrates in the case of
Azo 1 and Azo 2 in the trans and cis form. It is important to note that the orientation of the
azobenzene unit is almost perpendicular to the substrate normal [150, 153, 156].
Chapter Seven Determination of Trans/Cis Isomerization of Azobenzene Molecules
The freshly prep
azobenzene molec
in a nitrogen atmo
The samples were
controlled by sca
confirmed by the
7.3.1. Result
7.3.1.1. IR
IR spectra for KB
observe that the in
peaks located at
azobenzene grou
antisymmetric str
respectively. Tab
SAM.
Figure 64: Trans
87
ared gold substrates were dipped into 0.1 mM ethanol solutions of
ules for 24 h. Finally, the substrates were rinsed with pure ethanol and dried
sphere.
investigated by infrared spectroscopy [157] and the sample quality was also
nning tunnelling microscopy. The switching ability of the molecules was
contact angle change between the trans and cis configuration.
s
spectroscopy
r, calculated, and SAM of Azo 1 are shown below in Figure 65. One can
tensity of the peaks appearing below 1400 cm-1 is very low compared to the
1600 cm-1. The low-frequency region is dominated by modes of the
p and the high-energy is mainly governed by the symmetric and
etching modes of the CH2 group at 2855, 2927, 2960 and 3075 cm-1,
le 8 contains the assignment of the more intense peaks in the case of Azo 1
- and cis-Azo 2 on the gold substrate.
Chapter Seven Determination of Trans/Cis Isomerization of Azobenzene Molecules
F
[
88
igure 65: KBr, calculated and SAM IR spectra in low and high frequency regions
157].
Chapter Seven Determination of Trans/Cis Isomerization of Azobenzene Molecules
89
Mode assignment SAM(cm-1)
(C-H), ring op 756
(C-H), Ring , op 17b 812
(C-H), Ring , op 10a 845
(C=C), ip// axis 1002
(18)a ring, // axis 1022
=N-Ph 1156
(C-N)+Ring, ip 1,4-axis 1262
-N=N- + Ring, ip 1,4-axis 1409
Ring, ip// 1,4-axis 1478
(C-N) 1509
(N-H)+ (C-N) 1543
Benzene stre. // ring (8a) 1597
s (CH2) 2855
as(CH2) 2927
as(CH2) 2960
s (CH2) 3075
Table 8: The assignment of the more intense peaks in the SAM of Azo 1.
The broad peak around 1466-1525 cm-1 correspond to the overlap between the vibrations of
(N-H)+ (C-N), the peak at 1408 cm-1 is due to the –N=N- sym and the peak around 1156
cm-1 is due to =N-Ph. These peaks are showing that the SAM is consisting of N-H, –N=N-, C-
N, and =N-Ph. This rule out the possibility of the reduction of –N=N- to –NH-NH-.
For determination of the molecular orientation we are interested in the peaks, located firstly at
845, 812, 762 cm-1, these peaks having transition dipole moment (TDM) out of plane
perpendicular to the molecular axis and to the benzene plane. Secondly, the peaks located at
1022 and 1002 which having TDM parallel to the molecular axis. By comparing the op/ip
peak intensities (take 845/1020 cm-1) in KBr and SAM spectra, a large reduction in the ratio is
observed in the SAM spectrum. The latter suggest that the azobenzene moiety is tilted by a
certain degree from the surface normal. The C=O vibration around 1700 cm-1 is absent in the
SAM spectrum of Azo 1, which exhibit a parallel orientation of the C=O vibration to surface
[157].
Chapter Seven Determination of Trans/Cis Isomerization of Azobenzene Molecules
Figure 6
region.
The pea
(C-O-C)
SAM an
The N-H
2 SAM.
90
6: Comparison between Azo 1 and Azo 2 SAMs in low and the high frequency
ks which appear in Azo 2 SAM at about 1200 and 1225 and 1252 cm-1 are due to as
and (Ph-O-C) vibrations. The (C=O) peak located at 1750cm-1 appears in Azo 2
d this means that the orientation of the C=O group is not parallel to the surface.
peak located at 1540 cm-1 which appears in Azo 1 SAM is not observed for the Azo
Chapter Seven Determination of Trans/Cis Isomerization of Azobenzene Molecules
91
7.3.1.2. Water contact angle (CA)
A solid surface modified with photochromic azobenzenes is a promising material to control
the surface free energy with light, because trans–cis photoisomerization of azobenzenes is
accompanied by reversible changes in the physicochemical properties of the chromophores
such as dipole moment and geometrical molecular structure [158, 159].
The action of liquid droplets of water was examined by placing them on the photoresponsive
surface, alternating irradiation with homogenous UV and blue light to push the isomerization
of the azobenzene moieties assembled on the surface. The sessile contact angle of the droplets
(shown in Table 9) was changed in the case of Azo 1 from 72° in trans form to 71° after 1 h of
irradiation with UV light and then the sample was irradiated again with the blue light to show
the reversibility of this process. After 1 h of irradiation with the blue light the sessile contact
angle was 77°. By the Azo 2 SAM, the static contact angle in trans form was changed from
72° to the cis form of 69° after 1 h of irradiation with UV light and by the irradiation with the
blue light the contact angle increased again to 72°. The reversible changes of sessile contact
angles were maintained within experimental error after 3-4 cycles of alternating
photoirradiation.
Azo 1 Trans 1h irradiated UV light
(Cis)
1h irradiated VIS
light (Trans)
Sample 1 72; 71; 72. (72) 71; 70; 72 (71) 77; 76; 77. (77)
Sample 2 74; 74; 73. (74) 72; 74; 74. (73) 75; 75; 73. (74)
Azo 2 Trans 1h irradiated UV light
(Cis)
1h irradiated VIS light
(Trans)
Sample 1 72; 73; 74. (72) 70; 70; 68 (69) 73; 71; 71. (72)
Sample 2 74; 74; 75. (74) 69; 69; 70. (69) 75; 74; 73. (74)
The values were within an experimental error of ± 2°.
Table 9: Contact angles of Azo 1 and Azo 2 before and after irradiation (liquid: water).
Figure 67 shows the reversible process of a droplet of the water on the Azo 2 SAM upon
alternating irradiation with UV and blue light. The sessile contact angle of the droplet was
changed from 80° to 65° after UV irradiation (a difference of 15° between trans- and cis- was
not always observed, the measurements were not always reproducible).
Chapter Seven Determination of Trans/Cis Isomerization of Azobenzene Molecules
F
U
T
p
th
ir
F
th
th
T
T
ir
In
c
UV light
Vis light
trans
igure 67: Droplet of water on Azo 2 SAM before
V light.
his discrepance between the measurements presen
resented in the Table 10 might be interpreted by th
e mobility of the molecular tails possibly makes th
regular [160].
urther, we continue to prepare samples of Azo 1 a
e contact angle was measured again in the stable
e UV light (cis form).
he values were within an experimental error of ± 2°
Azo 1 Trans
Sample 1 57
Sample 2 54
Azo 2 Trans
Sample 1 59
Sample 2 58
able 10: Contact angle of annealed Azo 1 and Az
radiation with the UV light.
case of annealing the samples at 60 °C we obse
ompounds in trans- form, from 72° (see Table 9)
92
(80°) and after irradiation (65°) with
ted in Figure 67 and the measurements
e disordered film structure as well, where
e photoresponse on the SAM unclear and
nd Azo 2 by annealing at 60 °C and then
form trans- and after irradiation 1 h with
.
1h irradiated UV light
(Cis)
56
54
1h irradiated UV light
(Cis)
59
57
o 2 at 60 °C, before and after
rved a decreasing of the values for both
to 57°(see Table 10). The photoresponse
Chapter Seven Determination of Trans/Cis Isomerization of Azobenzene Molecules
93
from trans- to cis form by the irradiation with the UV light does not exist, which reveal that
the comportation of the SAMs by annealing at 60°C is different from the comportation at
room temperature presented above.
7.3.1.3. STM
Figure 68 shows STM images of the Azo 2 molecules in the trans position after different
times of immersion in ethanolic solution, at room temperature and at 60° under ambient
conditions.
We find a densely packed monolayer consisting of small domains ( Azo 2- 1 day and Azo 2- 4
days) without so-called “etch pits”, which are known from SAMs of simple alkanethiols and
are caused by the relaxation of the Au(111) surface reconstruction upon adsorption of the
thiol group [68]. After 1 day and 4 days of immersion in ethanolic solution the monolayer
shows the typical atomically flat terraces of the Au substrate, which has a height of 2.4 Å [9]
but Azo 2 is unable to form a highly ordered monolayer at room temperature, or it is because
of the impossibility to image these films at the molecular resolution. At elevated temperature
of 60 °C, one can observe a big difference between the monolayers, the domains are bigger
and full of the so-called “etch pits”. In general it was problematic to image these SAMs,
which can be interpreted by the disordered film structure of the Azo 2 conjugated molecules
and one can speculate that the azobenzene group plays a critical role in the SAM formation
and in the structure of the SAM [161].
In the following we tried to image with the STM in situ the photoisomerisation of these Azo 2
molecules prepared at 60 °C by the irradiation with UV light. By the irradiation of these Azo
2 SAMs prepared at elevated temperature we expected a different arrangement of the
molecules within the unit cell. As presented in the image above one can observe that the
morphologie of the surface changed and present a plenty of so-called “edge pits”, which are
showing a normal comportation of adsorption of these molecules on the Au substrate.
Chapter Seven Determination of Trans/Cis Isomerization of Azobenzene Molecules
94
Figure 69: STM images of Azo 2 SAM prepared at elevated temperature of 60 °C: A)
Before irradiation with UV light. B) After irradiation with UV light during 1h.
The STM measurements shown in Figure 69, exhibit the same morpfologie of the surface
Figure 68: STM images showing the a SAM of Azo 2 on Au(111): the first row after 1 day
immersion in the ethanolic solution, after 4 days immersion and after 1 day at elevated
temperature of 60 °C.
Chapter Seven Determination of Trans/Cis Isomerization of Azobenzene Molecules
95
before and after irradiation with UV light. We expected to see some differences because of
the photoisomerization of the molecule from the stable form trans to the cis form, more at the
limits of the domains or at the defects of the substrate.
7.4. Discussion
The present work demonstrates the use of light on a photoresponsive solid surface and in
solution. The detailed preparation and structural characterization of the solutions and SAMs
made from two azobenzene molecules (Azo 1 and Azo 2) are presented in this chapter.
The molecules change their conformation between trans and cis forms under visible (Vis,
440nm) and ultraviolet (UV, 360 nm) light. Therefore, when functional molecules are
modified using this moiety, new functions associated with the switching mechanisms can be
added to the original functions such as molecular recognition, sensing and memory as shown
in Figure 70 (b).
Figure 70: a) Schematic of photoisomerization of azobenzene molecule. b) Schematic of
functional control using an azobenzene molecule [162].
In the case of solutions containing azobenzene molecules Azo 1 or Azo 2, we saw with the
help of UV/VIS spectroscopy that the photoirradiation process is reversible and the molecules
are very sensitive to day light (blue light). After measuring two cis-spectra with alternating
irradiation of UV light and blue light, one can conclude that the reproducibility of the
switching process is very high.
SAMs were prepared by immersing the gold substrates in ethanolic solutions of the azo-
molecules for 24 h. In the cis configuration the footprint area is twice as large as for trans
configuration, that means for a efficient photoisomerization in the film one needs larger free
volume [153].
Chapter Seven Determination of Trans/Cis Isomerization of Azobenzene Molecules
96
From the IR measurements one can deduce that the azobenzene molecules Azo 1 and Azo 2
are adsorbed on the surface. The bands in the KBr pellet spectra and the bands in the SAM
spectra of the Azo 1 molecules measured on a gold substrate show a good agreement. In IR
measurements obtained after irradiating the samples with UV light one can not observe a
difference between the stable trans form and cis-form that should have been formed after
irradiation (the measurements are not shown in this work) [157, 163].
The IR spectra indicate that the azobenzene units are tilted from the surface normal and form
ordered monolayers on the gold substrates. These SAMs show a photoresponse that is
reflected in a change of the static contact angle measurements indicating that there is a free
space for the isomerization of the azobenzene moieties. To increase the stability of the SAMs,
ordered and densely packed structures are needed, whereas on the other hand free space is
necessary to achieve a reproducible molecular transformation due to photoisomerization, as is
observed in the case of the contact angle measurements [154, 160]. Towards to this
circumstance, by annealing the samples at 60 °C they show by the contact angle
measurements a decreasing in the values and the effect of photoisomerization is missing
completely.
The STM measurements are indicating the formation of densely packed monolayer at room
temperature, but at increased temperature the surface shows a difference. The domain size is
increased and the number of the so-called “etch-pits” is also increased. We can say that this
phase is dependent on the temperature, but in both cases it was impossible to get the
molecular resolution. This observation indicates that the substituent on the azobenzene
moieties is also an important factor in regulating the photoreactivity (as described in section
7.3.1.2 part) as well as the SAM structures shown in section 7.3.1.3. Regarding the STM
measurements of Azo 2 using in situ irradiation with UV light for 1h, the sample looks the
same before and after using the UV light. The STM measurements are in good agreement
with the contact angle measured for samples prepared at 60 °C, where the effect of
photoisomerization is missing. Concerning the STM measurements at elevated temperature of
60 °C and NEXAFS measurements (are not presented in this work) of Azo 1 and Azo 2
molecules, where the calculated tilt angle from the surface normal of the azobenzene moiety
and it has been found to be 275° [157] a model of the trans- and cis form is shown below.
Chapter Seven Determination of Trans/Cis Isomerization of Azobenzene Molecules
Figure 71: Model possibility of Azo 2 molecules on the gold (111) in trans- isomerization
(tilting of ~ 275° from the surface normal).
97
Figure 72: Model possibility of Azo 2 molecules on the gold (111) in cis- isomerization
(disorder of the molecules).
Chapter Eight Summary and Conclusions
98
Chapter Eight
Summary and Conclusions
The purpose of this work was to investigate and characterize the structure and the ordering of
self-assembled monolayers made from alkane thioacetates, aromatic and rigid thiols as
triptycenethiol, and triarylaminethiols based on a tertiary amine bonded to three phenyl rings
and the investigation of the photoswitching in the case of azobenzene disulfides by using UV
light and blue light.
For the preparation of the gold substrates two methods have been used: the evaporation of
gold onto silicon wafers and evaporation of gold onto mica (see sec.3.2). All the
measurements have been done on gold surfaces, because gold is an inert material which is not
oxidized in comparison to silver and copper under atmospheric conditions [164]. The gold on
silicon wafer is suitable for IR measurements, ellipsometry, contact angle, x-ray photoelectron
spectroscopy and near-edge x-rax absorption fine structure but is not suitable for the STM
measurements which need atomically flat gold surface with terraces separated by one atomic
layer of Au (111). High quality gold on mica substrates are prepared and imaged at an atomic
level using STM measurements.
Therefore, SAMs from the bulky triptycenethiol molecules have been prepared and the results
reveal that triptycenethiols adsorb on the surface. The reproducibility of C0T is showing
difficulties because of the high rigidity of the molecule, which plays an important role. About
C0T and their orientation one can conclude that, because in the NEXAFS measurements the
C0T spectra are not showing any dichroism this molecule did not present a dependence of the
angle, and C1T and C3T are presenting a tilting of the triple symmetry axis of the triptycene
frame against to the surface normal [107] due to the methylene spacer inserted between
sulphur and the triptycene frame and in NEXAFS spectra they are showing an angular
dependence, which is not observed for the C0T films. About the structure of the SAMs made
by triptycenethiol, one can conclude from the STM measurements that these thiols are
forming densely packed monolayers on the Au (111). The arrangements of these molecules
present differences between the surface morphology of C0T, C1T and C3T and based on
LEED data [23] the C1T and C3T form (m3 x n3) R30° structure, where m and n can be
possibly 2. For future work, the formation of highly ordered monolayers should be attemped.
The experiments on substituted triarylamines show that these protected molecules with an
Chapter Eight Summary and Conclusions
99
acetyl group are able to deprotect themselves during a longer and slower reaction [115, 116].
The objective of this work was to understand better why there is almost no difference between
protected triarylaminethioacetate and the corresponding thiol after deprotection and to find the
explanation of a kinetic stabilization which occurs upon the leaving of the thioacetate group
during the deprotection process.
The IR measurements are showing that the quality of the SAMs formed after deprotection by
themselves is really similar with the quality of the SAMs deprotected by using the 10mM
(C2H5)2NH, to generate the SAM directly. The IR and XPS measurements possess
information about the chemisorption of substituted- triarylaminethiols on the gold surface.
The determination of the orientation of these molecules on the surface was impossible to
understand through NEXAFS, where these films are not showing even a small dichroism and
by the performance of the STM measurements one can conclude that these molecules are not
forming highly ordered monolayers, one can suppose that these molecules are still in the lying
down phase or disordered on the surface.
To understand better the effect of the deprotection process without using any acid or base, it
has been done the investigation of a simple alkanethioacetate likewise dodecyl thioacetate
C12SAc onto gold (111). These measurements were done in comparison with the
measurements of the corresponding alkanethiol (C12SH). While ellipsometry suggests the
formation of incomplete SAMs from C12SAc with a thickness of 30% relative to the C12SH
reference system, (6 Å vs 18 Å), the water contact angle of 65° for the C12SAc SAMs implies
the presence of an organic surface exposing methylene groups (as opposed to high density
dodecanethiolate SAMs with a contact-angle of ~110° characteristic for the presence of CH3-
groups [84]. This could either be the effect of strong disorder or of flat-lying molecules
(shown in Figure 73).
More definitive clues can be found in the XPS and NEXAFS data, where a shift of the C1s
core-levels and unoccupied orbital resonances, respectively, indicates the presence of n-alkyl
chains adsorbed in a flat geometry on a metal surface [134, 139]. Also the IR spectra reveal
significant differences to those obtained for dense thiolate SAMs, which also indicate the
presence of a saturated hydrocarbon chain with its C-C-C backbone orientated parallel to the
substrate. The STM data reproduced in sec. 6.2.2.6 clearly demonstrate the presence of a
striped phase, a typical signature of low-density, intermediate SAM phases, which appears in
conflict with previous reports [140, 141, 145]. This behavior can be rationalized by the notion
that for the transformation of C12SAc into the binding thiolate some reagent must be present,
since these molecules are chemically stable in pure ethanol. In our case this reagent is the gold
Chapter Eight Summary and Conclusions
100
surface, facilitating the cleavage by formation of the stable Au-S bond (the leaving acetyl
group probably reacts with the ethanol). As soon as the gold surface is covered by the low
density monolayer, the contact between the gold surface and the C12SAc molecules is
hindered, suppressing the quick formation of the denser phase. Only on domain boundaries or
structural defects the gold substrate is sufficiently exposed to permit a further generation of
thiolate molecules, eventually leading to the formation of the upright phase in these places.
Figure 73: The time dependence of the apparent thickness (as determined by ellipsometry)
as well as the contact angle (advancing, for water) show that the monolayer obtained from
the thioacetates must mostly consist of flat lying molecules and remains stable even after
prolonged immersion times [11].
Instead, the thioacetates form a highly-ordered striped phase with flat-lying molecules anti-
parallel to each other, a structure which has not yet been reported for SAMs formed from the
corresponding alkanethiols and the presence of leaving-group effects on the structure and
quality of organothiolate SAMs opens a new possibility to control the properties of this
versatile class of materials.
In the category of the photoswitching exhibiting behavior we investigated the azobenzene
molecules (Azo 1 and Azo 2) by alternating the irradiation with UV light (366 nm) and blue
light (440 nm) in the solutions and also by the SAMs prepared on gold substrate. The
azobenzene molecules are very representative photoresponsive molecules, therefore one can
find several reports about azobenzene on hybrid material with mesoporous silica [165].
Chapter Eight Summary and Conclusions
101
By investigation the photoswitching exhibiting in the solutions of Azo 1 and Azo 2 it has been
used a UV/VIS spectrometer to show if the irradiation process by alternating UV light and
blue light is reversible. The UV/VIS spectra shown in the sec.7.2.1.1. are indicating that the
irradiation process is reproducible and one can reach very easy the cis isomerisation of the
azobenzene molecules.
In case of the SAMs prepared from azobenzene molecules, is not easy to reach the expected
photoresponse, because on the surface the azobenzene molecules need more space and a
larger free volume. From the IR measurements one can observe that these molecules adsorbed
rapidly in the trans form on the gold surface. After irradiation with the UV light it is
impossible to observe the isomerization to the cis form. One can also conclude from the IR
spectra that the azobenzene moiety is almost tilted from the surface normal.
The photoswitching of the SAMs is suitable for the contact angle measurements, because after
several cycles of alternating the irradiation with UV and blue light the photoresponse of Azo 1
and Azo 2 is reversible and reproducible.
By STM measurements in the trans stable form, these molecules form up densely packed
monolayers at room temperature, but with the increasing of the temperature the domains
become larger and the number of so-called “etch-pits” is incrementing. Regarding the STM
measurements proceeded on Azo 2 prepared at 60 °C and continued to irradiate the sample
with UV light for 1h, the sample looks the same before and after using the UV light.
The impossibility to obtain the high resolution of these azobenzene monolayers indicate that
Azo 1 and Azo 2 do not form highly ordered monolayers.
Chapter Nine Appendix
102
Chapter Nine
9.1. List of figures
Figure 1: Structure of thiols used in this study. ......................................................................... 2
Figure 2: The IR regions of the electromagnetic spectrum. ..................................................... 6
Figure 3: The IR spectrum of octadecanethiol, plotted as transmission (left) and absorbance
(right). ........................................................................................................................................ 7
Figure 6: Stretching and bending vibrational modes for a –CH2 group. .................................. 9
Figure 7: Harmonic approximation via potential of the oscillator V(r) [23].......................... 10
Figure 8: Schematic setup of FTIR- Spectrometer [23]. ........................................................ 13
Figure 9: Set up of rinsing gas supply. ................................................................................... 14
Figure 10: Spectrum of air in the sample area. ....................................................................... 15
Figure 11: Deduction of the surface selection rules at metallic surfaces [23]....................... 16
Figure 12: Measuring accessories of the “Uniflex” of the Bio-Rad FTS-3000 [23]. ............ 16
Figure 13: Energy pattern of x-ray photoelectron spectroscopy. ............................................ 18
Figure 14: Schematic diagram of the photoelectronic spectroscopy....................................... 19
Figure 15: XPS overview spectrum of octadecanethiol (C18) on Au(111)............................. 20
Figure 16: Energy pattern of NEXAFS spectroscopy. ............................................................ 21
Figure 17: Different methods of recording x-ray absorption spectra. ................................... 21
Figure 18: Definition and orientation of the angles in the surface coordinate system of the
NEXAFS experiment. E║ and E┴ are the p and the s-polarized portions of the incident light,
and TDM is the situation of the dipole transition moment of the excited transition................ 22
Figure 19: Principle of the imaging process by the STM. The lower part shows a band
structure diagram for a tunnel contact between the tip and the sample. ................................. 24
Figure 20: Schematic of the geometry of an ellipsometry experiment..................................... 25
Figure 21: Schematic of a sessile-drop contact angle system. ................................................ 27
Figure 22: Electronic excitations for an organic molecule. .................................................... 28
Figure 23: Compariosn between LB films and SAMs films. .................................................... 30
Figure 24: Schematic mechanism diagram for the self-assembly of thiols on Au(111): a)
Initial adsorption. b) Striped phase or lying-down phase. c) 2D phase with a transition from
lying-down to standing-up phase. d) Formation of a complete SAM [74]. ............................. 32
Figure 25: Schematic diagram of a SAM. Shaded circle indicates adsorbed or chemisorbed
headgroup and open circle endgroup, which can be chosen from variety of chemical
functionalities. .......................................................................................................................... 32
Chapter Nine Appendix
103
Figure 26: Schematic diagram of different energies in the adsorbed SAM [71]..................... 33
Figure 27: Constant-current STM topograph of an octanethiol monolayer on Au(111) which
shows a c(4 x 2) superlattice of a R3033 )( overlay structure [68]. ................................. 34
Figure 28: The tilt angle Θt of the alkanethiol chain relative to the surface normal [71]. .... 34
Figure 29: AFM (atomic force microscopy) image of gold evaporate on Si(100)-Wafer (1μm
× 1μm). ..................................................................................................................................... 35
Figure 30: STM images of Au/Mica (111) and Au/Si (111). .................................................... 36
Figure 32: XP spectra of C 1s and S 2p regions of the C0T, C1T and C3T molecules in
comparison with an alkanethiol ODT. ..................................................................................... 42
Figure 36: NEXAFS spectra of C0T, C1T and C3T thiolates for different angles of incidence
of the synchrotron light. The solvent used for the solutions was EtOH. .................................. 47
Figure 37: STM image of C0T molecule on Au(111) at room temperature............................. 48
Figure 38: STM image of C1T molecule on gold (111) at room temperature ......................... 48
Figure 39: STM image of C1T molecule on gold (111) at high temperature .......................... 48
Figure 40: The crystal structure of the triptycene [12, 23]. .................................................... 50
Figure 41: Model for the arrangement of the C1T on gold surface. ....................................... 51
Figure 42: Molecular structures of substituted triarylamine- AH-10, VK-55, TS-10 and AH-4.
.................................................................................................................................................. 53
Figure 43: Infrared spectra of substituted triarylaminethiols AH-10, TS-10, AH-4 and VK-55.
The red trace displays are IRRAS spectra of the monolayer and the black trace measured for
a KBr pellet. ............................................................................................................................. 56
Figure 44: XP spectra recorded for polycristalline gold substrates showing the carbon 1s,
nitrogen 1s, sulfur 2p and oxygen 1s region for the triarylaminethiols AH-10, TS-10, VK-55
and AH-4. ................................................................................................................................. 57
Figure 45: XPS S 2p spectrum of AH-10 adsorbed onto gold/Si. Two S 2p doublets with 2:1
area ratios and splittings of 1,2 eV were used to peak fit experimental spectrum................... 58
Figure 47: IRRAS spectra of AH-10, TS-10 and AH-4. The red lines are showing the spectra
without deprotection process and the black lines the spectra with deproctection (used 10mM
(C2H5)2NH) [13]....................................................................................................................... 61
Figure 48: STM measurements on the AH-4 molecule. Conditions: with deprotection, 10-20
µM DCM solution; Ut= 600 mV, It= 70 pA............................................................................. 62
Figure 49: STM measurements on the AH-4 molecule. Conditions: with deprotection at 60°,
.................................................................................................................................................. 63
Figure 50: STM measurements on AH-4 molecule. Conditions: without deprotection, 10-20
Chapter Nine Appendix
104
µM DCM solution; Ut= 600 mV, It= 70 pA............................................................................. 63
Figure 51: Model of an AH-4 molecule on the Au (111) surface flat lying or tilted away from
the surface. ............................................................................................................................... 65
Figure 52: Infrared spectra of C12SH and C12SAc a) in ethanolic solution, b) in ethanolic ... 69
Figure 53: RAIRS spectra of C12SH on the gold substrate (111) showing the region of C-H
stretch mode vibrations and the approximation of these peaks. .............................................. 70
Figure 54: XP spectra recorded for polycristalline gold substrates showing the carbon ....... 72
Figure 55: NEXAFS spectra of a) C12SAc and b) C12SH thiol for different angles of incidence
of the synchrotron light. The solvent used for the solutions was EtOH. .................................. 74
Figure 56: (a) Constant-current STM micrographs showing the gold substrate after............ 76
Figure 57: Constant-current STM micrographs showing the gold surface after immersion into
a 10-20µM ethanolic solution of C12SAc at 273 K for 48 h. In (b), the unit cell of the
(2√3×4)R30° structure is marked by the rectangular box. Tunneling parameters: (a) Ut=800
mV, It= 95 pA; (b) Ut= 1000 mV, It= 75 pA. ........................................................................... 77
Figure 58: C-H vibrational area of the IRRA spectra of the monolayers formed from C12SAc,
.................................................................................................................................................. 78
Figure 59: XP spectra recorded for polycristalline gold substrates showing the carbon ....... 79
Figure 60: Model of the surface layer formed upon adsorption of C12SAc (top view). ........... 81
Figure 61: Conformational change of azobenzene [151]........................................................ 84
Figure 62: Azo 1 and Azo 2 molecules..................................................................................... 84
Figure 63: UV-VIS spectra of Azo 1 and Azo 2 solutions in the ground state of trans isomers
and after irradiation with the UV light. ................................................................................... 86
Figure 64: Trans- and cis-Azo 2 on the gold substrate............................................................ 87
Figure 65: KBr, calculated and SAM IR spectra in low and high frequency regions [157]. .. 88
Figure 66: Comparison between Azo 1 and Azo 2 SAMs in low and the high frequency........ 90
Figure 67: Droplet of water on Azo 2 SAM before (80°) and after irradiation (65°) with UV
light........................................................................................................................................... 92
Figure 68: STM images showing the a SAM of Azo 2 on Au(111): the first row after 1 day
immersion in the ethanolic solution, after 4 days immersion and after 1 day at elevated
temperature of 60 °C. ............................................................................................................... 94
Figure 69: STM images of Azo 2 SAM prepared at elevated temperature of 60 °C: A) Before
irradiation with UV light. B) After irradiation with UV light during 1h. ................................ 94
Figure 70: a) Schematic of photoisomerization of azobenzene molecule. b) Schematic of
functional control using an azobenzene molecule [162]. ........................................................ 95
Chapter Nine Appendix
105
Figure 71: Model possibility of Azo 2 molecules on the gold (111) in trans- isomerization
(tilting of ~ 275° from the surface normal). ........................................................................... 97
Figure 72: Model possibility of Azo 2 molecules on the gold (111) in cis- isomerization
(disorder of the molecules)....................................................................................................... 97
Figure 73: The time dependence of the apparent thickness (as determined by ellipsometry) as
well as the contact angle (advancing, for water) show that the monolayer obtained from the
thioacetates must mostly consist of flat lying molecules and remains stable even after
prolonged immersion times [11]. ........................................................................................... 100
Chapter Nine Appendix
106
9.2. List of tables
Table 1: Number of vibrational degrees of freedom of nonlinear and linear molecules........... 7
Table 2: Absorption by single, double and triple bonds observed in an IR spectrum. ............ 11
Table 3: The layer thicknesses (in Å) as determined by XPS and ellipsometry as well as the
expected values for molecules standing upright on the substrate. ........................................... 41
Table 5:Tilt angles of the triptycene units with respect to the surface normal in the triptycene
thiol films on gold..................................................................................................................... 50
Table 6: Positions and assignment of the IR-modes In case of Au surface and KBr pellet. .... 55
Table 7: The assigment of the peaks of C-H stretch mode vibrations from Figure 53. .......... 70
Table 8: The assignment of the more intense peaks in the SAM of Azo 1. ............................... 89
Table 9: Contact angles of Azo 1 and Azo 2 before and after irradiation (liquid: water). ..... 91
Table 10: Contact angle of annealed Azo 1 and Azo 2 at 60 °C, before and after irradiation
with the UV light. ..................................................................................................................... 92
Chapter Nine Appendix
107
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ACKNOWLEDGEMENTS
I would like to express my gratitude to Prof. Dr. Christof Wöll for his great support and
encouragement during this study. His suggestions and critical advices in the course of
numerous fruitful discussions we had - were and are highly appreciated and were also a
significant contribution to the success of this work.
Prof. Dr. Roland Fischer I would like to thank for taking over the part of the co-referee and its
with-stated interest in the present work.
I am also indebted to Dr. Andreas Terfort for his assistance, guidance and motivation during
my entire doctoral study. His enthusiasm, exploratory mind and his friendship have been truly
inspiring.
Special thanks I would like to express to Dr. Waleed Azzam for his help and support in all
what self-assembled monolayers means and for the good atmosphere which we had during his
visit in Germany.
I would like to give special thanks to Dr. Thomas Strunskus for the comprehensive scientific
collaboration, for reviewing important parts of this manuscript, as well as for the numerous
suggestions he gave me related to the spectroscopy methods.
I would like to thank Dr. Alexander Birkner for introducing me to the field of scanning
tunnelling microscopy at the very beginning of my doctoral studies and Dr. Gregor Witte for
his fruitful and critical discussions about the scientific work during the course of my studies.
A critical review of the manuscript was carried out also by Dr. Franziska Träger and by Dipl.
Phys. Dorothee Meier, - their comments are highly appreciated.
Dorothee Meier I would like to thank for her guidance and patience to introduce me to the
field of atomic force microscopy and for her friendship, which means a lot to me.
I would further like to thank all my collegues in the Physical Chemistry group, especially to
Asif Bashir, Deler Langenberg, Dr. Kathrin Hänel, Ketheeswari Rajalingam, Jennifer Haag,
Milusche Krzikalla, Jan Götzen and Dr. Carsten Busse to whom I owe countless valuable
discussions and advice, and - last but not least - great fun in the course of my work.
Special thanks are reserved to all technicians from the Physical Chemistry department for
their very good support with the equipments and for their technical assistance.
Very, very special thanks I would like to express to the secretaries’ chair, Mrs. Uhde, Mrs.
van Eerd, Mrs. Knoedleseder Mutschler and Mrs. Kruse Fernkorn (second Mom) for the
assistance of the administrative questions, for their friendship, motivation and for their
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122
“warmness”. These four ladies are very special to me and one of the brightest things which
happened to me in Germany.
I would like to express special thanks to my partner Marius Pesavento for supporting and
motivating me in the course of my doctoral study and for his faith in me.
Finally, I would like to express thanks and gratitude to my both parents, Aurica and Stelian
Badin and to my lovely sister Simona Mocanu. Without their help and support I would never
arrived here, where I am now.
Chapter Nine Appendix
123
List of publication
1. Kinetically Stable, Flat Lying Thiolate Monolayers
M. G. Badin, A. Bashir, S. Krakert, Th. Strunskus, A. Terfort and Ch. Wöll, Angewandte.
Chemie, Int. Ed. 46 (2007) 3762-3764
2. Chemistry in confined geometries: Reactions at an organic surface
K. Rajalingam, A. Bashir, M. Badin, F. Schröder, N. Hardman, Th. Strunskus, R. A. Fischer,
Ch.Wöll, ChemPhysChem 8 (2007) 657-660
Chapter Nine Appendix
124
Curriculum Vitae
Family name: BADIN
First name: MIHAELA GEORGETA
Adress: Seippelstr. 2, 44803 Bochum
Email: [email protected]
Date of birth: 20.09.1978
Nationality: Romanian
Academic degrees:
1997-2002: Studies at the University „Politehnica” Temesvar, Romania, Faculty of Industrial
Chemistry and Environmental Engineering, department of „Knowledge and engineering
science of the oxide materials- Silicates”. Degree: Diploma engineer
Diploma Thesis: „Thermally steady pigments in the system CoO-ZnO-Al2O3-TiO2” and
„Development of the methods for the evaluation of the thin coatings”.
Since April 2007: Process Engineer in Air Quality Control Systems, Hitachi Power
Europe, Duisburg.
Dec. 2003- March 2007: doctorand by Prof. Dr. Christof Wöll, Lehrstuhl für
Physikalische Chemie I, Ruhr-Universität Bochum.
March 2002-July 2002: Scholarship "Socrates Erasmus" at the University of Applied
Sciences Gelsenkirchen, department of Recklinghausen, Germany.
Oct. 1997-Sept. 2002: Studies at the University „Politehnica” Temesvar, Romania,
Faculty of Industrial Chemistry and Environmental Engineering, department of
„Knowledge and engineering science of the oxide materials- Silicates”
Sept. 1993-June 1997: High school: Theoretical lyceum „C.D.Nenitescu”, Brasov,
Romania.
Sept. 1985-June 1993: Primary school Brasov, Romania.