ellipsometric characterisation of anisotropic thin organic films · 2017-10-26 · ellipsometric...
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Ellipsometric characterisation of anisotropic thin organic films
vorgelegt von
MSc Phys.
Dana - Maria Rosu
aus Hunedoara, Rumänien
von der Fakultät II - Mathematik und Naturwissenschaften
der Technischen Universität Berlin
zur Erlangung des akademischen Grades
Doktor der Naturwissenschaften
- Dr. rer. nat. –
genehmigte Dissertation
Promotionsausschuss:
Vorsitzender: Prof. Dr. Birgit Kanngießer
Berichter: Prof. Dr. Norbert Esser
Berichter: Prof. Dr. Christian Thomsen
Berichter: Prof. Dr. Georgeta Salvan
Tag der wissenschaftlichen Aussprache: 17.06.2010
Berlin 2010
D 83
2
Parts of this work have been already published in:
Journals:
Dana M. Rosu, Jason C. Jones, Julia W. P. Hsu, Karen L. Kavanagh, Dimiter Tsankov,
Ulrich Schade, Norbert Esser, Karsten Hinrichs, Langmuir 25 (2009) 919: Molecular
orientation in octanedithiol and hexadecanethiol monolayers on GaAs and Au measured
by infrared spectroscopic ellipsometry.
Reports:
K. Hinrichs, M. Gensch, G. Dittmar, S. D. Silaghi, D.-M. Rosu, U. Schade, D.R.T.
Zahn, S. Kröning, R. Volkmer and N. Esser, BESSY ANNUAL REPORTS, 285 (2006):
IR - Synchrotron Mapping Ellipsometry for Characterisation of Biomolecular Films.
3
Table of contents
Introduction 5
Einleitung 7
1. Theoretical background 10
1.1 Polarized light………………………………………………………………10
1.2 Ellipsometric quantities…………………………………………………….12
1.3 Mathematical description of polarized light……………………………..…15
1.4 Electronic spectra. Franck-Condon principle………………………………20
2. Experimental techniques 23
2.1 Spectroscopic ellipsometry (SE)…………………………………………...23
2.2 Synchrotron mapping ellipsometry………………………………………...24
3 Optical modelling 27
3.1 Cauchy model………………………………………………………………27
3.2 Gaussian oscillator model…………………………………………………..28
3.3 Lorentz model………………………………………………………………29
4 Self assembled monolayers of alkanethiol 31
4.1 Sample preparation…………………………………………………………32
4.2 IRSE characterisation of alkanethiol thin films…………………………….33
4.3 IR synchrotron mapping ellipsometry..…………………………………….42
5 Cytosine 44
5.1 Sample preparation…………………………………………………………45
4
5.2 AFM characterisation of cytosine films……………………………………46
5.3 Visible spectroscopic ellipsometry…………………………………………47
5.4 Infrared spectroscopic ellipsometry……………………………………….51
5.5 Synchrotron mapping ellipsometry………………………………………..60
6. Concluding remarks 63
References 65
List of figures 70
List of tables 73
Acknowledgements 74
5
Introduction
The aim of the present work was to investigate the structural properties of
organic molecules on different substrates using different optical spectroscopic
techniques. The two studied systems were: self assembled monolayers of alkanethiols
on GaAs and Au and cytosine thin films on H-passivated Si(111) surface. As it will be
introduced in chapters 4 and 5, the studied organic molecules are very attractive due to
their application in various fields, ranging from biosensors to optoelectronic devices.
Characterisation of the molecular orientation and molecular packing in systems
as biological sensors, electronic and optical organic devices, novel solid lubricants,
corrosion inhibitors, as well as hydrophobic and hydrophilic coatings has gained
considerable attention [Ulm91, Tre94, Fra98]. Various surface sensitive methods have
been applied over time in order to study the packing and orientation of organic
molecules on different substrates. Standard investigation techniques for quantifying
molecular orientation and packing in organic thin films include reflection infrared
absorption spectroscopy (RAIRS) [Tol03], UV- visible and infrared spectroscopic
ellipsometry [Lec98], X-ray photoelectron spectroscopy (XPS) [Yan99], scanning
tunnelling microscopy (STM) [Sch00], near-edge X-ray absorption fine structure
(NEXAFS) [Stö92, Gie99], polarized ultraviolet (UV) spectroscopy [Kai99], angle-
resolved photoelectron spectroscopy (ARUPS) [Oku99], near-infrared (NIR) Fourier
transform surface-enhanced Raman spectroscopy [Wu99], and grazing-incidence X-ray
diffraction (GIXD) [Pra86].
The main investigation technique used to obtain the results presented in this
work was infrared spectroscopic ellipsometry. Ellipsometric technique in the visible
(VIS) as well as in the infrared (IR) spectral range is a typical method for thickness
determination and structural investigation of thin films. The ellipsometric experiment is
non-invasive, contact-free, and does not depend on special requirements such as (ultra-
high) vacuum. Depending on the photon energy, electronic or vibrational properties are
6
investigated. Since many organic compounds do not exhibit characteristic electronic
transitions in the VIS spectral range, a detailed structural characterisation is often not
possible from VIS ellipsometric spectra. On the other hand IR ellipsometry is
extensively used for this purpose because characteristic IR bands associated with
vibrations of specific molecular groups are noticed. The band amplitudes and shapes in
the IR ellipsometric spectra are directly related with the directions of transition dipole
moments of specific molecular vibrations, thus enabling determination of the molecular
orientation [Hin02, Par92, Deb84, Ros09].
The current work is structured in 6 chapters as follows:
Chapter 1 introduces the notion of polarized light, presents the description of the
spectroscopic ellipsometry technique and the mathematical formalism that describes the
propagation of the light in stratified media.
In chapter 2 the experimental set-ups used in order to obtain the desired
information about the studied samples are in detail presented.
Self assembled monolayers of octanedithiol and hexadecanemonothiol on GaAs
and Au are the topic of the 4th chapter. The orientation of the molecules on the substrate
was determined from simulations on spectroscopic measurements in the mid infrared
range. The inhomogeneity of the organic layer was proved by infrared mapping
ellipsometry.
Chapter 5 is dedicated to the investigation of cytosine thin films with different
thicknesses deposited on Si(111) substrates. Various investigation techniques were used
in order to determine the optical and structural properties of the organic layers. The
thickness of each layer was determined using visible ellipsometry while the molecular
orientation was deduced from the ellipsometric measurements in the infrared spectral
range.
The conclusions of this work are summarized in the last chapter.
7
Einleitung
Das Ziel der vorliegenden Studie war es, die strukturellen Eigenschaften von
organischen Molekülen auf verschiedenen Substraten mit verschiedenen optischen
spektroskopischen Methoden zu untersuchen. Die folgenden zwei Systeme wurden
untersucht: Selbstorganisierende Monoschichten aus Alkanthiolen auf GaAs und Au,
sowie dünne Cytosinschichten auf H-Si(111) Oberflächen. Wie in Kapitel 4 und 5
eingeführt wird, sind die untersuchten organischen Moleküle aufgrund ihrer
Anwendung in verschiedensten Bereichen, von Biosensoren bis hin zu
optoelektronischen Bauelementen sehr attraktiv.
Die Charakterisierung der molekularen Orientierung und Packung der Moleküle
in biologischen Systemen wie Sensoren, elektronischen und optischen organischen
Bauelementen, neuartigen Festschmierstoffen, Korrosionsinhibitoren, ebenso wie
hydrophobe und hydrophile Beschichtungen hat beträchtliche Aufmerksamkeit
gewonnen [Ulm91, Tre94, Fra98]. Verschiedene oberflächenempfindliche Methoden
wurden im Laufe der Zeit angewendet, um die Packung und die Orientierung von
organischen Molekülen auf verschiedenen Substraten zu untersuchen. Zu den
Standarduntersuchungsmethoden zur Quantifizierung molekularer Orientierung und
Packung in den organischen dünnen Schichten gehören Reflexions-
Infrarotabsorptionsspektroskopie (RAIRS) [Tol03], Ellipsometrie im UV-sichtbaren
Spektralbereich und spektroskopische Infrarotellipsometrie [Lec98], Röntgen-
Photoelektronenspektroskopie (XPS) [Yan99], Rastertunnelmikroskopie (STM)
[Sch00], Röntgen Nahkanten Absorptionsspektroskopie (NEXAFS) [Stö92, Gie99],
polarisierte UV-Spektroskopie [Kai99], Winkel-Photoelektronen-Spektroskopie
(ARUPS) [Oku99], oberflächenverstärkte Nah-Infrarot (NIR) Fourier Transform
Ramanspektroskopie [Wu99] und Röntgendiffraktometrie unter streifendem Einfall
(GIXD) [Pra86] .
Die Hauptuntersuchungstechnik, die verwendet wurde um die Ergebnisse dieser
Arbeit zu erzielen war die spektroskopische Infrarotellipsometrie. Ellipsometrie im
8
sichtbaren (VIS) als auch im infraroten (IR) Spektralbereich ist eine typische Methode
zur Bestimmung der Dicke und zur strukturellen Untersuchung von dünnen Schichten.
Die ellipsometrischen Messungen sind nicht-invasiv, berührungslos und nicht auf
spezielle Anforderungen wie (ultra-hohes) Vakuum angewiesen. Abhängig von der
Photonenenergie wurden elektronische Eigenschaften oder Schwingungseigenschaften
untersucht. Weil viele organische Verbindungen keine charakteristischen elektronischen
Übergänge im VIS-Spektralbereich zeigen, ist eine detaillierte strukturelle
Charakterisierung durch VIS-ellipsometrische Spektren oft nicht möglich. Aus diesem
Grund wird IR-Ellipsometrie hauptsächlich für diesen Zweck verwendet, weil
charakteristische IR-Banden auftreten, welche den Vibrationen der spezifischen
molekularen Gruppen zugeordnet sind. Die Amplituden und Formen der
Absorptionsbanden in den IR-ellipsometrischen Spektren stehen in direktem
Zusammenhang mit den Richtungen der Übergangsdipolmomente von spezifischen
molekularen Schwingungen, wodurch die Bestimmung der molekularen Orientierung
möglich ist [Hin02, Par92, Deb84, Ros09].
Die aktuelle Arbeit ist wie folgt in 6 Kapitel unterteilt:
Kapitel 1 führt den Begriff des polarisierten Lichtes ein und liefert eine
Beschreibung der spektroskopischen Ellipsometrie, sowie des mathematischen
Formalismus, der die Ausbreitung von Licht in mehrlagigen Medien beschreibt.
In Kapitel 2 werden die angewendeten experimentellen Setups, die verwendet
wurden um die gewünschten Informationen über die untersuchten Proben zu erhalten,
detailliert vorgestellt.
Selbstorganisierende Monoschichten von Octanedithiol und
Hexadecanemonothiol auf GaAs und Au sind das Thema des 3. Kapitels. Die
Orientierung der Moleküle auf dem Substrat wurde durch Simulationen zu
spektroskopischen Messungen im mittleren Infrarotbereich bestimmt. Die
Inhomogenität der organischen Schicht wurde durch Infrarot-Mapping Ellipsometrie
gezeigt.
Kapitel 4 widmet sich der Untersuchung von dünnen Cytosinschichten, welche
mit unterschiedlichen Dicken auf Si(111) Substraten aufgedampft wurden.
Verschiedene Untersuchungstechniken wurden verwendet um die optischen und
strukturellen Eigenschaften der organischen Schichten zu bestimmen. Die Dicke der
einzelnen Schichten wurde unter Verwendung von sichtbarer Ellipsometrie bestimmt,
9
während die molekulare Orientierung aus den ellipsometrischen Messungen im
Infraroten Spektralbereich abgeleitet wurde.
Die Schlussfolgerungen dieser Arbeit sind in dem letzten Kapitel
zusammengefasst.
10
Chapter 1
Theoretical background
Ellipsometry is a reflection technique that allows us to perform contact-free non-
destructive in situ studies of surfaces. The ellipsometric methods in the visible (VIS) as
well as in the infrared (IR) spectral range are standard methods for structural
investigation and thickness determination of thin films [Hin05, Rös01, Asp85, Rös96].
Depending on the photon energy, electronic or vibrational properties are examined.
Since many organic compounds do not exhibit characteristic electronic transitions in the
VIS spectral range, a detailed structural characterisation is often not possible from VIS
ellipsometric spectra. On the other hand, IR ellipsometry is widely used for this purpose
because characteristic IR bands associated with vibrations of specific molecular groups
are observed. The band amplitudes and shapes in the IR ellipsometric spectra are
directly related with the directions of transition dipole moments of specific molecular
vibrations, thus enabling determination of the molecular orientation[Hin02, Par92,
Deb84]. In the recent years, Infrared Spectroscopic Ellipsometry (IRSE) has proven to
be well suited for analysis of thin functional organic films on metal and semiconductor
substrates by providing information about thickness and molecular structure.
1.1 Polarized light
Light can be defined as an electromagnetic wave described by Maxwell's theory.
Light is characterized by two mutually perpendicular vectors: E, the electric field, and
B, the magnetic field. Both E and B are also perpendicular to the direction of
propagation z, given by the wave vector k . The electromagnetic wave is described by
its amplitude and frequency in complex form:
11
)]([0
)]([0
kxti
kxti
eBB
eEE (1.1.1)
where E0 represents the maximum amplitude of the electric field E that propagates into
the z direction, ω is the angular frequency, t is the time, and k is the wave vector. When
light has completely random orientation and phase, it is considered unpolarized. When
two orthogonal light waves are in-phase, the resulting light will be linearly polarized.
Circularly polarized light consists of two perpendicular waves of equal amplitude that
differ in phase by 90°. When the mutually perpendicular components of polarized light
are out of phase, the light is called elliptically polarized [Tom05]. The representation of
the polarized states is presented in figure 1.1.1.
Figure 1.1.1: a) linearly polarized light; b) elliptically polarized light
12
1.2 Ellipsometric quantities
Figure 1.2.1 presents an optical model constructed for a multilayer isotropic thin
film structure on a substrate. Each optical layer is represented by a complex refractive
index and the thickness of the layer. Incident light will reflect and refract at the interface
of two adjacent layers.
Figure 1.2.1: Sketch of polarized light propagation in stratified media
Light can be separated into orthogonal components with respect to the plane of
incidence. Electric fields parallel and perpendicular to the plane of incidence are
considered p- and s- polarized, respectively. These two components are independent and
can be calculated separately. The amount of light reflected at the interface between
isotropic materials is given by the Fresnel coefficients rp and rs :
11
11
11
11
coscos
coscos
coscos
coscos
mmmm
mmmms
mmmm
mmmmp
nn
nnr
nn
nnr
(1.2.1)
Here φm represents the angle of incidence, φm+1 the angle of refraction and n
the
complex refractive index. rp is the ratio of the electric field amplitudes after and before
reflection of light with the electric field in the plane of incidence. rs is the same ratio,
13
but for light with the electric field perpendicular to the plane of incidence. The ratio of
the two complex Fresnel reflection coefficients determines a new complex quantity ρ,
which defines the ellipsometric parameters tanΨ and Δ (0 ≤ Ψ ≤ 90°, 0 ≤ Δ ≤ 360°).
tanΨ stands for the amplitude ratio and Δ for the phase shift difference of the two
orthogonally polarized components of the reflected wave (rs and rp).
ii
s
pi
s
p
is
ip
s
p eer
re
r
r
er
er
r
rsp
s
p
tan)(
(1.2.2)
The s- and p-polarized reflectances are defined by Rp= |rp|2 and Rs= |rs|
2. The reflection
absorbance of a thin film is defined by -log(R/R0), where R0 is the reflectance of the
clean substrate.
The dielectric function and the refractive index are complex numbers and related
to each other through the following equation:
nkikniknni
iknn
n
2)()(ˆˆ
ˆ
ˆˆ
222221
2
(1.2.3)
If the investigated sample is isotropic and the interface between the ambient and the
material is abrupt (no roughness), they can be directly calculated [Bor80] by:
2
200
2
2
22202
022
1
cos2sin1
sin4sin)tan(sin2
)cos2sin1
)sin2sin2(costan1()(sin
nk
kn
(1.2.4)
and
][2
1
][2
1
122
21
122
21
k
n (1.2.5)
where n and k are the real and the imaginary part of the complex refractive index n .
The correlation between the reflected waves is evaluated using a parameter called
polarisation degree. The polarisation degree value decreases with the decrement in
correlation. For ideal samples, the polarisation degree is 1. The polarisation degree is
calculated using the formula:
2222sincos2sin2cos P (1.2.6)
where 2cos , 2sin , cos , sin represent the mean experimental quantities.
14
The degree of phase polarisation Pph [Rös92] is defined as the sum of the
average terms of <cosΔ>2 and <sinΔ>2:
22sincos phP (1.2.7)
For anisotropic materials, the optical constants cannot be directly calculated
from the measurements and a proper optical model that describes the interaction
between the light and the sample has to be chosen. References [Ber72, Azz77, Sch96]
present a detailed description of the 4x4 matrix method used to study the propagation of
polarized light in stratified anisotropic media. In the present work, a short introduction
will be exposed.
Teitler and Henvis first introduced the 4X4-matrix technique [Tei70], and it was
developed two years later by Beremann in [Ber72]. Maxwell’s equations in Gaussian
units and chartesian coordinates can be written:
z
y
x
z
y
x
z
y
x
z
y
x
B
B
B
D
D
D
tc
H
H
H
E
E
E
zy
xz
yz
xy
xz
yz
1
0000
0000
0000
0000
0000
0000
(1.2.8)
where E, D, H, B represent the electromagnetic field vectors and c is the velocity of
light in vacuum. The equation can be abbreviated:
Ctc
RG
1
(1.2.9)
If nonlinear effects are not taken into account, the relation can be rewritten:
MCG (1.2.10)
where M is a 6x6 matrix and contains the anisotropic properties of the medium. First
and third quadrants of the matrix represent optical rotation tensors ρij and ρ´ij. The
second quadrant is the dielectric tensor ij and the fourth is the permeability tensor μij.
Equation 1.2.10 and (1.2.10) can be combined and rewritten:
15
Mc
iR
(1.2.11)
where Γ denotes the spatial part of G.
The particular problem considered involves the reflection and transmission of a
monochromatic plane wave incident from the isotropic ambient medium (z<0) onto an
anisotropic planar structure (z>0) stratified along z–axis. The symmetry of the problem
suggests that there is no variation along the y direction of any field component Gi so
that ∂Gi/∂t=0. If kx represents the x component of the wave vector of the incident wave,
the variation of the fields in x direction is xik xe and xikx
[Azz77]. Beremann
derived the equation:
x
y
y
x
x
y
y
x
H
E
H
E
SSSS
SSSS
SSSS
SSSS
c
i
H
E
H
E
z
23222421
33323431
13121411
43424441
(1.2.12)
The last relation can be abbreviated:
c
i
z (1.2.13)
The elements of S and Δ are given in reference [Ber72]. If matrix Δ is independent of z
over a finite distance h in the direction of z axis, equation 1.2.13 can be integrated and
we obtain:
)()()( zhLhz (1.2.14)
where L represents the partial transfer matrix of the layer and is given by:
....!3
1
!2
1)( 3
32
2
c
h
c
h
c
hiIhL
(1.2.15)
with I being the identity matrix.
1.3 Mathematical description of polarized light
There are two ways of describing mathematically, how an electromagnetic wave
interacts with a sample: the Jones matrix and the Mueller matrix formalism. When no
depolarisation occurs, both formalisms are fully consistent. Therefore, for non-
depolarizing samples the simpler Jones matrix formalism is sufficient. If the sample is
16
depolarizing the Mueller matrix formalism should be used, because it gives additionally
access to the amount of depolarisation.
1.3.1 Jones matrix formalism
In this formalism, it is assumed that the light is totally polarized, thus the
polarisation state does not fluctuate. According to [Fuj03], the Jones vector is defined
by the electric field vectors in the x and y directions. The Jones vector is given by:
)exp(
)exp()(exp
)(exp
)(exp),(
0
0
0
0
yy
xx
yy
xx
iE
iEkzti
kztiE
kztiEtzE
(1.3.1.1)
The equation can be simplified to
y
x
E
EtzE ),( (1.3.1.2)
where
)exp(
)exp(
0
0
yyy
xxx
iEE
iEE
(1.3.1.3)
The light intensity is given by
2220
20 yxyxyx EEEEIII (1.3.1.4)
In optical measurements, only relative changes in amplitude and phase are taken
into account. Consequently, the Jones vector is generally expressed by the normalized
light intensity (I = 1). In this case, linearly polarized waves parallel to the x and y
directions are expressed by
0
1,xlinearE
1
0, ylinearE (1.3.1.5)
17
If we normalize light intensity, linearly polarized light oriented at 45° is written as
1
1
2
145E (1.3.1.6)
The Jones matrix of the sample is defined by:
s
p
r
rJ
0
0 (1.3.1.7)
where rp=Erp/Eip and rs=Ers/Eis represent the Fresnel reflection coefficients for p and s
polarized light. Eis, E
ip are the components of the incident electric field vector while E
rs,
Erp
are the components of the reflected light from the sample.
The Jones matrix for a rotation of the coordinate system has the form:
cossin
sincosJ (1.3.1.8)
1.3.2 Stokes parameters and Mueller matrix formalism
In order to describe unpolarized or partially polarized light, Stokes parameters
(vectors) are used. Some physical phenomena that generate partially polarized light
upon light reflection are: surface light scattering caused by a large surface roughness of
a sample [Lee98], incident angle variation originating from the weak collimation of
probe light
[Rös92, Zoll00], thickness inhomogeneity in a thin film formed on a substrate
[Lee98,Zoll00, Jell92] or backside reflection that occurs when the light absorption of a
substrate is quite weak (k~0) [Yan95, Joe97, Rös92]. The Stokes parameters enable us
to describe all types of polarisation. In actual ellipsometry measurement, these Stokes
parameters are measured. In the Stokes vector representation, optical elements are
described by the Mueller matrix.[Fuj03]
The Stokes parameters are described by the equations:
LR
yx
yx
IIS
IIS
IIS
IIS
3
45452
1
0
(1.3.2.1)
18
S0 represents the total intensity of the light beam, Iy corresponds to the light
intensity of linear polarisation in the y direction and Ix in the x direction. The light
intensity of a linear polariser rotated by ± 45° is noted I45° and I -45° respectively. Finally,
IR and IL are the light intensities of the right and left circularly polarized light.
The Stokes parameters can be expressed by using electric fields by the following
equations:
sin2
cos2
003
0045452
20
201
20
200
yxLR
yx
yxyx
yxyx
EEIIS
EEIIS
EEIIS
EEIIS
(1.3.2.2)
Figure 1.3.2.1: a) Representation of the elliptical polarisation by (Ψ,Δ) coordinate
system; b) Representation of a point on the Poincare sphere with the radius S0
In case of totally polarised light, the state of polarisation can be represented as a point
on a sphere with the radius S0 in the coordinate system formed by S1, S2 and S3.
Between the Stokes parameters the next relations can be deduced:
sin2sin
cos2sin
2cos
03
02
01
23
22
21
20
SS
SS
SS
SSSS
(1.3.2.3)
The degree of polarisation can be defined using Stokes parameters by:
19
0
23
22
21
S
SSSP
(1.3.2.4)
For totally polarized light P=1, in case of unpolarized light P=0 and for partially
polarized light 23
22
21
20 SSSS .
One can describe the Stokes parameters using a vector representation, known as the
Stokes vector.
3
2
1
0
S
S
S
S
S (1.3.2.5)
The transformation of a Stokes vector after the light passes an optical element can be
described with the help of Müller matrices. For example, the Müller matrix for an ideal
analyzer/polarizer is given by:
0000
0000
0011
0011
MS (1.3.2.6)
while the relation for a non-ideal polarizer becomes more complex:
2sin000
02sin00
0012cos
002cos1
2
22yx
idealnon
ttS (1.3.2.7)
After the reflection from a sample, the change in the polarisation state of the light is
described by the matrix:
cos2sinsin2sin00
sin2sincos2sin00
0012cos
002cos1
SS (1.3.2.8)
20
1.4 Electronic spectra. Franck-Condon principle
The vibrational transitions which accompany electronic transitions are referred
to as vibronic transitions. In an absorption process, most of the molecules will be,
initially, in the ν’’=0 state of the ground electronic state. The selection rule governing
these vibronic transitions is completely unrestrictive.
Although the selection rule allows transitions with all values of ν’, it is the
intensity distribution along the progression that determines which transitions are
sufficiently intense to be observed. This distribution is governed by the Franck-Condon
principle [Fra26].
Figure 1.4.1 depicts the nuclei potential curves of a diatomic molecule in the
ground state, and one electronic excited state. Both, the ground state (E0) and the
excited state (E1) support a large number of vibrational levels, which contain rotational
levels (not presented in the figure).
Figure 1.4.1: Diagram of Frank-Condon principle. E0 represents the electronic ground
state, E1 denotes the first excited electronic state.
The Franck-Condon principle states that the most probable vibronic transition is
a vertical transition between positions on the vibrational levels of the upper and lower
21
electronic state at which the vibrational wave functions have maximum overlap.
Electronic transition takes place on such short time scale (10-15 s) that the nuclei are
considered frozen during a transition. The energies of vibrational transitions do not
change during the electronic transition. They will change after the electronic transition,
because the nuclei adjust their position to minimize the total energy of the new electron
configuration.
Electronic transitions to and from the lowest vibrational states are often referred
to as 0-0 transitions. In the absorption spectrum of a polyatomic molecule, the vibronic
transitions from ν’’=0 form a progression with the band origin at the frequency
corresponding to the (0-0) transition. A typical electronic band presents many
vibrational structures that extend over a few thousand cm-1. The vibronic structure of
molecules in a cold, dispersed gas is most clearly visible due to the absence of
inhomogeneous broadening of the individual transitions. For large molecules in
condensed state at room temperature, the vibrational structure is overlapped and
combines into what is called Franck-Condon envelope.
Figure 1.4.2: Vibronic fine structure of 1,2,4,5-tetrazine. I Gas phase at room temperature, II In isopentane-methylcyclohexane matrix at 77K, II In cyclohexane at
room temperature, IV In water at room temperature
Figure 1.4.2 presents the comparison between the vibronic fine structure of 1,2,4,5-
tetrazine in different states. As expected, the best resolved vibronic structure was found
22
for the gas phase, while in case of the molecule solved in water, no vibrational structure
could be distinguished.
23
Chapter 2
Experimental technique
In the present work, two in-house build experimental set-ups were used: the
ellipsometer attached to a BRUKER 55 located in our laboratory [Rös02] and the
synchrotron mapping ellipsometer attached to a BRUKER IFS 66/v located at the IR
beamline at the BESSY II synchrotron facility [Gen03], both operating in the mid-IR
spectral range. The working principle will be described in the current chapter.
2.1 FT-IR ellipsometer at ISAS Berlin
The general working principle of the FT-IR ellipsometer at ISAS is summarized
in Figure 2.1.1.
Fig
ure 2.1.1: Measurement principle of the FT-IR ellipsometer at ISAS Berlin [Rös02]
24
The incident radiation is modulated in the interferometer and linearly polarized
by polarizer P1. The electric vector forms an azimuthal angle α1 with the plane of
reflection. In the general case, the beam reflected from the sample surface is elliptically
polarized. The resulting change in the state of polarisation is determined by measuring
the reflected radiation through an analyzer P2 with its vector at azimuths α2.
In our case, the ellipsometric parameters Ψ and Δ are obtained from intensity
measurements at four azimuthal angles of the polarizer α1= 0°, 90°, 45°, 135° and at a
fixed position of the analyzer α2=45°:
)135()45(
)135()45(cos2sin
)0()90(
)0()90(2cos
II
II
II
II
(2.1.1)
2.2 FT-IR synchrotron mapping ellipsometer at BESSY II
The FT-IR synchrotron mapping ellipsometer works according to the principle
of photometric ellipsometry described in the previous section. The differences between
the two set-ups consists in the source used, laboratory set-ups use globar as a source
while the IRIS beamline uses synchrotron light.
Figure 2.2.1 Infrared mapping ellipsometer at BESSY II Berlin[Gen03]
25
For synchrotron light, the emitted radiation in the infrared wavelength region is some
orders of magnitude more brilliant than standard thermal sources (e.g. globar) - it emits
more photons per unit area into a unit solid angle [Sch98].
Figure 2.2.1 presents the synchrotron mapping ellipsometer at BESSY II.
Measurements at incidence angles between 20° and 90° can be performed. The
ellipsometer is equipped with a 2-dimensional mapping stage, autocollimation and
microfocus unit. In cooperation with Sentech Instruments, the IR synchrotron mapping
ellipsometer was upgraded with a rotating retarder in order to measure both
ellipsometric parameters during the mapping. No manual operation is required during
measurements, control of the set-up being made using OPUS software of the
spectrometer.
The purpose of using a synchrotron radiation source is in particular to analyze
smaller sample areas than are possible with conventional equipment or to achieve higher
lateral resolution when mapping a large sample. Our mapping system provides a lateral
resolution below 1 mm2 and enables the investigation of thin film samples with
monolayer sensitivity.
To get a better feeling about the difference between a lab measurement and a
measurement performed at BESSY, the area investigated on a sample is sketched in
figure 2.2.2.
Figure 2.2.2: Measurement scheme at a certain incidence angle: Grey spot represents
the beam spot on the studied sample for the measurements performed in the lab. Each
black dot represents one illuminated spot on the sample for the measurements
performed with the mapping ellipsometer at BESSY II.
The diameter of the spot on the sample for the lab measurements is
approximately 50 mm2, much bigger than the one at BESSY: < 1 mm2. Each of the
26
black dots represents one measured point on the sample, therefore a spectrum. From the
obtained spectra, one can calculate tanΨ and Δ maps as it follows.
As shown in figure 2.2.3, tanΨ maps represent the amplitude of a characteristic
vibrational band of the studied material. Δ maps are obtained from the average value of
Δ in the non absorbing range of the spectra.
Figure 2.2.3: Calculation of tanΨ maps from a vibration band
From the determined maps one can obtain valuable information about thickness
and structure variation.
27
Chapter 3
Optical simulation
From the data analysis of spectroscopic ellipsometry, the dielectric function of a
certain material is derived. For this, the optical response of the investigated samples was
modelled in a 4x4 matrix formalism [Azz92] by building a suitable optical model. The
experimental ellipsometric data were fitted using the Levenberg-Marquardt algorithm
[Pres92] implemented in the WVASE software for the cytosine organic layers and in the
MATLAB software in the case of the self assembled monolayers of alkanethiols.
3.1 Cauchy model
The Cauchy model is adequate for determining the refractive index of a film in
the transparent energy range. For a certain transparent material, the Cauchy equation
makes the connection between the refractive index and the wavelength of the light. The
form of the equation [Tom05] is:
...)(42
CB
An (3.1.1)
where n is the refractive index, λ the wavelength and A, B and C are fit parameters.
Usually just the two terms of the equation are considered, thus the Cauchy equation
becomes:
.)(2
BAn (3.1.2)
A and B are directly connected with the physical meaning of the refractive index of the
fitted material.
28
Oscillator model. Kramers-Kronig consistency
The real and imaginary parts of the complex dielectric function are not
independent of each other but they are linked by the Kramers-Kronig relation, if the
dielectric function is analytical and 0)( for . The Kramers-Kronig
relation allows calculating the real part of the dielectric function, when the imaginary
part is known in the whole definition range and vice versa
0
'22'
'
2
0
'22'
''
1
)(Re2)(Im
)(Im21)(Re
dP
dP
Similar equations can be written for n and k. The examination of the
denominator shows that the integrand is not contributing significantly unless ω′ is very
close to ω, such that absorption processes far removed from the photon energy of
interest do not contribute strongly to the dispersion of the real part of the dielectric
constant at that energy.
The broadening of electronic transitions in solids is often more closely fit using a
Gaussian oscillator while the bands corresponding to vibrational transitions in the
infrared spectral range are fitted using a Lorentz oscillator.
3.2 Gaussian oscillator model
The model presents the dielectric function of a film (ε) as a sum of real or
complex terms:
),,,( 3332
222
222
1
121 BEAEGaussian
EiBEE
A
EE
Ai
(3.2.1)
where Ai, B
i, and E
i are the amplitude, broadening and energy position, respectively
corresponding to the oscillator “i”.
29
3.3 Lorentz model
As the name is suggesting, the model was introduced by Lorentz and it considers
electrons and atoms in matter to be an ensemble of harmonic oscillators. A molecular
vibration can be described by a harmonic oscillator with the quasi-elastic force
KrF , with K being the elasticity coefficient and r the displacement of the particle
from its equilibrium position. When one of the oscillators is exposed to an
electromagnetic field it becomes polarized and the electric polarisation has the form:
Ep
0ˆ (3.3.1)
where represents the electric polarizability of the medium. In the linear case, the
electric polarisation of an ensemble of oscillators will be:
rNQENpPi
i
0ˆ (3.3.2)
where N represents the number of harmonic oscillators.
Knowing [Kit96] that
EPED
ˆ00 (3.3.3)
the dielectric function can be determined:
ˆ1ˆ N (3.3.4)
This equation is the bridge between the macroscopic optical properties, described in
terms of the local dielectric function, and the microscopic parameter characterizing
polarisation of each specific oscillator under the action of the external electric field.
If a harmonic oscillator is placed in an external time dependent electric field
described by tieEE 0
, the electric field will redistribute charges and a dipole moment
will be induced. The elastic force F restricts this process and produces a restoring force (
rm2
0 ). The Newton equation for the motion of the harmonic oscillator [Yu96] is:
dt
rdmrmEQ
dt
rdm
*** 202
2
(3.3.5)
30
where r
is the displacement of the oscillator with respect to the equilibrium position, γ
is the damping constant and ω02 is the resonant frequency and Q the charge of the
harmonic oscillator. Integrating the equation one can obtain the displacement:
jj i
Em
Q
r
22
,0
*
(3.3.6)
From equations (3.3.2), (3.3.4) and (3.3.6) the following representation of the dielectric
function is deduced:
jj i
m
NQ
22
,0
0
2
*1ˆ (3.3.7)
For ω » ω0, ε→1 and for ω « ω0, ε→0
2
1
NQ . In infrared spectral range, the radiation
field appears to be static to the electrons and therefore high–energy contributions due to
electronic transitions can be considered constant. The electronic contribution is denoted
and is known as high frequency dielectric constant.
The representation of the complex dielectric function will be:
j jj
j
j jj
jj
i
F
i
S)()(ˆ
22,0
22,0
2,0
(3.3.8)
where Γ represents the damping constant. The dimensionless parameter Sj represents the
oscillator strength and is proportional with the number of oscillators N, the reduced
mass m*, the resonance frequency ω0, and the effective charge Q and has the form:
200
2
* m
NQS . If one substitutes in equation 3.3.8 ω by using the relation:
c
2,
the following relations are calculated:
][2
)2(
1
22
20
cmc
cmc
SF
(3.3.9)
31
Chapter 4
Self assembled monolayers of alkanethiols
Self-assembled monolayers are ordered molecular assemblies that are formed
spontaneously by the adsorption of a surfactant with a specific affinity of its headgroup
to a substrate. Figure 4.1 presents a sketch of an alkanethiol self assembled monolayer
structure.
Figure 4.1: Schematic representation of self assembled monolayer
Alkanethiols are molecules with an alkyl (CH2-CH2)n chain as the back bone, a
tail group called also functional group, and a thiol (S-H) head group. Research on the
properties of n-alkanethiol monolayers is of high relevance due to their potential use in
a variety of applications: lubrication in micromechanical systems, chemical passivation
in microelectronic devices, and chemical biosensing [Dor95, Goo99, Lio99]. The
control of wetting properties is one of the first applications of organic monolayers. By
selectively modifying the end group (hydrophilic vs. hydrophobic), control of the
wetting properties can be achieved [Bai89], [Eng95]. Particularly, mixed SAMs are
attractive for this purpose, since they allow a continuous change of the contact angle as
a function of concentration [Atr95, Tam97]. Besides the adsorption properties for
simple wetting agents, the selective adsorption of large, bio-related molecules is of great
interest. Several studies have shown possible directions of bio-compatible applications
32
[Pri91, Sin94, Hig00, Wir97]. Since SAMs form the link between organic and inorganic
matter, they are ideal for interfacing biological materials.
While the adsorption of the n-alkanethiols on metal substrates was intensively
studied, the study of the adsorption of these molecules on GaAs is limited despite the
wide potential for such films in electronic and optoelectronic devices.
In a recent study on the ordering of chain molecules relative to the substrate
[McG06] a 14° tilt angle of the methylene chains for octadecanethiol on GaAs(001)
using a combination of RAIRS and XPS techniques is reported. A tilt angle lower than
15° was calculated from XPS measurements by Nesher et al. in a study of the electronic
properties of a GaAs-alkylthiol monolayer- Hg junction [Nes06].
In this chapter, the results of orientation studies of monolayers formed by
octanedithiol and hexadecanethiol (HDT) on GaAs and on Au are presented.
4.1 Sample preparation
Molecular monolayers on GaAs substrates were prepared by Jason C. Jones at
Sandia National Laboratories in Albuquerque as presented in [Jun06]. The 1,8-
octanedithiol (Aldrich, 97 %) or hexadecanethiol (HDT,Fluka, > 95%) monolayers were
deposited from solution (5 mM in ethanol) onto bulk n+-GaAs wafers (Si-doped, 3x1018
cm-3), previously etched with a combination of 1:20 NH4OH: deionised water and 1:10
HCl:ethanol solutions to remove the native oxide. Octanedithiol and hexadecanethiol
were used as received without any further purification. The same deposition procedure
was used to form monolayers on Au films (50 nm) that were e-beam evaporated on Si
substrates with a Ti adhesion layer (2.5 nm). Prior to thiol deposition, the Au films were
cleaned with UV ozone for 20 min and rinsed with ethanol to remove possible
contaminations. The root mean square roughness of the cleaned GaAs substrates was
determined by AFM measurements over an area of 1 μm2 to be 0.5 nm. SAMs
developed by the chemisorption of the head group onto a substrate followed by a slow
organization of the tail groups. Even though self-assembled monolayers form rapidly on
the substrate, it is necessary to use adsorption times larger than 15 h to obtain well-
ordered, defect-free SAMs. Multilayers do not form, and adsorption times of two to
three days are optimal in forming highest-quality monolayers.
33
4.2 Infrared spectroscopic ellipsometry
The samples were investigated using IRSE. We used the two ellipsometers
presented in chapter 2, operating in the mid-IR spectral range and using a photovoltaic
mercury-cadmium-telluride (MCT) detector.
For defined reflectance measurements the incidence angle was set either to 60°
or to 65°. These incidence angles assure that the probed spots are definitely smaller than
the sample size (7x19 mm2). We avoided using bigger incidence angles because at the
same experimental settings the irradiated spot would become larger than the sample
size. Additionally, the lower incidence angles reduce the error due to the opening angle.
Setting the incidence angle at 80° or above would increase the error due to non-linearity
of the p-polarized reflectance.
The frequencies of the CH2 stretching modes of hydrocarbon chains are very
sensitive to the conformational ordering of the chains in a layer and therefore the
analysis of the CH2 stretching bands provides information about the average
conformation and orientation of the methylene backbone of alkanethiols. The
investigation of the band shapes and amplitudes of the stretching vibrations via optical
simulations of IR ellipsometric spectra determines the average molecular orientation of
the organic molecules on the substrates. All the measured spectra were baseline
corrected. The weaker bands due to Fermi resonances at about 2890-2900 cm-1 and
2932 cm-1 were not taken into account in our calculations.
The orientation of an alkanethiol molecule in the laboratory cartesian frame
(where the z-axis is perpendicular to the substrate and the y-axis along the direction of
the s-polarisation) is defined by three Euler angles (Fig. 4.2.1): the tilt angle γ (between
the chain and the z-axis), the azimuth angle φ (between the projection of the chain axis
onto the xy-plane and the x-axis), and the twist angle δ (rotation about the long axis of
the molecule). The transition dipole moment of )( 2CHs vibration lies in the plane of
the back bone while the transition moment of the )( 2CHas is parallel to it. For our
simulations the uniaxial symmetry (nx=ny) was considered and the angle φ was
considered to be 45°. The in-plane isotropy of the prepared alkanethiol films was
34
s
a
experimentally proved by comparison of ellipsometric measurements of the same
sample rotated by 90 °.
.
Figure 4.2.1: Schematic of the geometric model of HDT molecules used for the
simulations. The tilt angle and the twist angle δ are marked. In order to account for
the uniaxial symmetry (nx = ny) of the studied samples, the angle φ (rotation in x, y
plane) was set to 45°. The directions of the transition dipole moments of the symmetric
and antisymmetric stretching vibrations of the CH2 group are shown in the inset.
For well defined organic film on a substrate, a three-phase optical layer model is
most frequently used [Azz77, Hin02]. In the current simulations the Lorentz model
presented in chapter 3 is used. The vibrational bands are described by Lorentzian
oscillators with wavenumber ( ~i0 ), parameters for the oscillator strengths (Fi) and full
width at half maximum FWHM (i) to yield the complex dielectric function '''
with:
35
i ii
iiF2222
0
220
)~()~~(
)~~('
(4.2.1)
i ii
iiF2222
0 )~()~~(
~
(4.2.2)
Uniaxial symmetry was assumed for the investigated samples, which assumes isotropic
properties in directions parallel to the surface plane (x, y plane in Figure 4.2.1). The
dielectric function components in the j = x, y, z directions are represented by: x = y z.
The refractive index is defined as n .
A fundamental problem in case of quantitative spectral interpretation of ultrathin
organic films is that the parameters for the oscillator strengths of characteristic
vibrational bands are usually unknown. The film thickness and the high frequency
refractive index can be determined from VIS-ellipsometric measurements. A set of
oscillator parameters, necessary for IR ellipsometric simulations is often derived from
evaluation of IR or ellipsometric spectra of reference samples. As stated by Parikh and
Allara [Par92] for polycrystalline reference samples, the situation of identical inter- and
intramolecular interactions, and electronic structure and packing density between the
reference and the studied film is never met exactly, but is still a very useful
approximation. In the present work the oscillator parameters are taken from the
evaluation of polarized reflectance spectra of a HDT monolayer.
The parameter F in eqs (4.2.1) and (4.2.2) can be transformed into the
dimensionless oscillator strength S (as already explained in paragraph 1.2) by dividing it
by the square of the oscillator position in wavenumbers ( ~i02). The parameters of the
oscillator strengths Fi are related to the transition dipole moments Mi by [Tol03]:
2~ ii MF (4.2.3)
36
At a particular orientation of the oscillators (s and as of CH2 group), the single
components of the transition dipole moments in the molecular coordinate system (j = x,
y, z) (Fig. 4.2.1) are related to the principal transition dipole moment Mmax as
iiz
iiiy
iiix
MM
MM
MM
22max
2
222max
2
222max
2
cos
sinsin
cossin
i=ss, as (4.2.4)
where and are the Euler angles. Since thetransition dipole moments of the
symmetric and the antisymmetric stretching vibrations of CH2 group are mutually
orthogonal and both are perpendicular to the chain axis when all-trans conformation
exists, the tilt angle of the chain can be determined from the measured tilts of the
methylene stretching vibrations (θs, θas) using the following equation [Tol03]:
1coscoscos 222 chainass
where chain is the tilt angle of the methylene chain. Assuming uniaxial orientation
2
1sincos 22 ii and the tilt angles (i) can be determined from the ratio of x, y
and z components in eq. (4.2.4):
i
i
iz
ix
iz
ix
M
M
F
F
2
2
2
2
cos2
sin
(4.2.6)
As described at the beginning of this section, the parameters of the oscillator strengths
are determined from simulation of the measured ellipsometric or polarisation dependent
reflection spectra within optical layer models.
Monolayer of HDT on GaAs
In figure 4.2.2 measured and simulated polarized reflectance spectra together
with the corresponding tanΨ spectra of a HDT monolayer on GaAs are presented.
Within the simulation procedure, first the s-polarized and then the p-polarized spectra
were fitted. The procedure is described in detail in [Hin02]. For n∞ = 1.41 and a
monolayer thickness of 2.3 nm (corresponding nearly to the extended length of HDT) a
tilt angle of =19° and a twist angle of δ = 45° were calculated. It is well known from
literature that when the chains in the monolayer are in all-trans zigzag conformation and
highly ordered, the narrow absorption bands νas(CH2) and νs(CH2) appear at around
37
2918 ± 1 and 2850 ± 1 cm−1, respectively [Tol03]. The band frequencies observed in
case of the monolayer of HDT on GaAs, 2851 cm-1 νs(CH2) and 2919 cm-1 νas(CH2), are
characteristic for a well-packed all-trans zigzag conformation. These data support the
assumption that the HDT film is highly ordered and comparable to a self-assembled
monolayer. From the theoretical calculation, the following parameters were determined
for the symmetric and asymmetric CH2 stretching vibrations: F1x(2919 cm-1) = 40000
cm-2 ; F1z(2919 cm-1) = 5000 cm-2 , Г1 = 17 cm-1; F2x(2851 cm-1) = 67500 cm-2, F2z(2851
cm-1) = 6500 cm-2, Г2 = 16 cm-1. Substituting these values in (4.2.6), a molecular tilt
angle of 19° was calculated from (4.2.5).
Figure 4.2.2: Simulated (red) and measured (black) reflection spectra (top: p-polarized
reflection absorbance; middle: s-polarized reflection absorbance, bottom: tan) of a
HDT monolayer on GaAs. The incidence angle was set to 60° in order to ensure defined
reflectance measurements in which the probed spot was smaller than the sample size
(7x19 mm2).
38
Assuming about 10 % uncertainty in the determined oscillator strengths (when
correlated to the noise level in the s- polarized reflectance spectra), the uncertainty for
the calculated tilt angle remains within ±2°. The error in the estimation of the molecular
orientation might be higher since the anisotropy of the high frequency refraction indices
is not known and because of effects of inhomogeneity. The determined values for F1 =
85000 cm-2 and F2 = 141500 cm-2 (from Fi = Fix+Fiy+Fiz) are similar to the parameter of
oscillator strengths as used for the calculations of polycrystalline polyethylene in
reference [Roo08] (Fi = 3Fiiso): F1 = 61000 cm-2; Г1 = 17.4 cm-1; F2 = 151000 cm-2; Г2 =
15 cm-1. The oscillator parameters of the weaker CH3 bands cannot be determined with
sufficient accuracy and were therefore not included in the simulations. The determined
tilt angle for HDT on GaAs is slightly higher than but still in good agreement with the
values reported previously [McG07, Nes06]. The slight deviation (about 4°) from the
documented values in above mentioned references can be assigned to the already
discussed uncertainties as well as to the different measurement conditions in the
different experiments.
Molecular orientations in HDT and octanedithiol monolayers on GaAs
The comparison between the experimental tanΨ spectra of octanedithiol and
hexadecanemonothiol on GaAs is shown in Figure 4.2.3.a. Figure 4.2.3 b presents the
simulated monolayer spectra of HDT based on the optical constants already previously
determined. The appearance of the weak CH3 stretching band at 2966 cm-1 in the
measured spectra of the octanedithiol film on GaAs might designate the contamination
of the sample (most likely octanethiol) which excludes a quantitative interpretation of
the tanΨ spectra of octanedithiol on GaAs.
39
Figure 4.2.3 a) Measured tanΨ spectra of octanedithiol monolayer on GaAs (bottom)
and HDT monolayer on GaAs (top). The baseline was corrected for convenience. The
incidence angle was 65°; b) spectra for tilt angles of 12°, 18°, 24°, 30°, 36° and 42°
simulated based on the optical constants used for HDT on GaAs.
The comparison of the experimental spectra (Fig. 4.2.3 a) with the simulations made for
several tilt angles in Fig. 4.2.3 b implies that the weak negative bands for octanedithiol
on GaAs could be qualitatively interpreted by a larger tilt angle (>30°) compared with
the one determined for HDT. Such characteristic band shapes are well known for
differently oriented molecular films [Hin05]. As already mentioned before, the positions
of CH2 stretching vibrations in the tanΨ spectra are sensitive to the ordering of the
alkanethiol chains on the substrate. In the tanΨ spectrum of octanedithiol a shift of the
positions of CH2 stretching vibrations to higher frequencies was noticed. Figure 4.2.3.b
shows a wavenumber shift of maximum 4 cm-1 in the simulated spectra for which the
same oscillator frequencies have been used for the calculations at different tilt angles.
This indicates that part of this wavenumber shift is a pure optical effect, which occurs
when the tilt angle becomes larger than about 30°. The band shape upon change from
positive to negative passes through a derivative like band shape at about 30° tilt. For the
hexadecanemonothiol layer, the position of the asymmetric stretching of the CH2
stretching vibration is 2928 cm-1, shifted with about 9 cm-1 compared to HDT on GaAs.
This shift is a consequence of the formation of gauche rotomers. This is due to a
coupling between the carbon atoms and a methylene hydrogen, which, due to
40
conversion around the C−C bond, is positioned in the plane defined by the carbon
atoms, resulting in an increased force constant for this C−H bond [Tol03]. In contrast,
for the all-trans conformation, all methylene hydrogens are out of plane [Par95]. In
general, the order of the hydrocarbon chains decreases with decreasing chain length
[Ger93]. Gauche defects are expected to be concentrated near the free ends of the
chains, and this has been experimentally confirmed by Nuzzo et al. [Nuz90, Dub90].
Beside the CH, stretching bands in the region 2800-2950 cm-1 there are other
bands sensitive to the change in the ordering of the chains in the layer in the range
1000-1500 cm-1.
Figure 4.2.4: Comparison between tanΨ spectra of C8DT and HDT on GaAs. The
spectra were referenced to clean GaAs and shifted for a better understanding
Figure 4.2.4 presents the measured tanΨ spectra of octanedithiol and
hexadecanemonothiol on GaAs. The assignment of the bands in the range 1400-1700
cm-1 is not completely clear, though the band at 1460 cm-1 is usually assigned to the
CH3 deformation. Due to the fact that the bands appear in all the samples, including the
reference sample, one can suppose the bands come from a contamination of the
substrate. The bands at ~1111 cm-1 and 1264 cm-1 are assigned to CH2 wagging modes
and the sign of the bands is reversed for the two alkanethiol layers, a new sign for the
different orientation of the molecules on the substrate.
1200 1400 1600
1112
C8DT on GaAs C16MT on GaAs
tan
wavenumber / cm-1
1111 1264
1265 1408 1555
1462
41
Molecular orientation in HDT monolayer on Au
Figure 4.2.5 a) Simulated (black) and measured (grey) tan spectra of a HDT
monolayer on gold. The incidence angle was set to 65°. b) Simulations for tilt angles
from 12° to 42°.
The comparison between the experimental and simulated tanΨ spectra of HDT
on Au is shown in Figure 4.2.5. The same oscillator parameters which were determined
for HDT on GaAs were used as input for the calculations. For the fit of the spectra
shown in Fig. 4.2.4.a only the z-values for the parameters of the oscillator strength were
adjusted: F1z(2919 cm-1) = 6100 cm-2, F2z(2851 cm-1) = 9600 cm-2. From these values
the tilt angle of 22° and the twist angle of 45° are calculated. This tilt angle is consistent
with published values determined from RAIRS [Par92, Por86]. The similar results
found for the HDT film on GaAs and Au imply a similar organisational structure of the
HDT film on both substrates. Owing to the so called surface selection rule [Hay87] the
bands in tanΨ spectra of thin organic films on metallic substrates look like typical IR
bands in transmission spectra (Fig 4.2.4 b). These rules allow only absorption of
incident IR radiation by vibrational modes whose transition dipole moment components
are perpendicular to the surface plane.
42
4.3 IR synchrotron mapping ellipsometry
In order to study the homogeneity of the organic layer in more detail, the
samples were mapped using the FT-IR ellipsometer attached to a BRUKER IFS 66/v at
BESSY II. A detailed description of the set-up can be found in reference [Gen06].
Figure 4.3.1: Interpolated 2D map of the CH2 band amplitude at 2922 cm-1,
which was taken from tanΨ spectra: a), HDT on Au, b) HDT on GaAs. The step width
was 1 mm.
2D tanΨ maps for two different samples are shown in Figure 4.3.1. The maps were
calculated after the procedure described in chapter 2 and represent the band amplitude
of the CH2 stretching vibration. The 2D maps indicate some large-scale inhomogeneity
of the molecular layers, which was deduced from the variation of the band amplitude at
2922 cm-1. For the film on Au, the change of the band amplitude could be assigned to a
thickness variation of about ± 0.4 nm. It is important to note that in the lab
measurements a sample area of at least 24 mm2 or larger is probed. These data provide
information about the average values for tilt angle and thickness of the investigated
area. In the infrared optical simulations, the roughness of the substrates (typically 0.5
nm for GaAs and 2 nm for Au) is not taken into account in the idealized layer models.
Due to the long wavelengths in the IR spectral range, the influence of roughness on
phase shift and depolarisation is much smaller than in the VIS spectral range.
43
Nevertheless, the microscopic roughness may lead to a variation of the molecular
orientation on a microscopic scale.
Summarizing, the interpretation of IR spectra can only give average values for
tilt angles and thicknesses for the probed area, which in our case in the lab experiments
typically is between 24-50 mm2 and between 0.3-1 mm2 in the synchrotron experiments.
Figure 4.3.2: Sketch presenting the orientation of the studied molecules on the
substrates
The obtained orientation of the alkanethiol chains relative to the perpendicular to the
substrates is schematically drawn in figure 4.3.2.
44
Chapter 5
Cytosine
The crystal structure of cytosine has been determined by D.L. Barker and R.E.
Marsh in the reference [Bar64]. The crystals are orthorhombic with space group P212121
and unit-cell with a=13.041 Å, b=9.494 Å, c=3.815 Å. Molecules are tilted about 27.5°
with respect to ab plane and adjacent molecules make a dihedral angle of
approximately 15°.
Figure 5.1: Crystalline structure and unit cell of cytosine
Previous studies showed that DNA bases (guanine, cytosine, adenine and thymine)
could be successfully used in biomolecular electronic devices as charge transport
molecules. Electrical transport measurements on DNA molecular films [Oka98] and on
micrometer-long DNA ropes [Fin99] suggest that DNA has a metallic conductivity.
Conversely, in the reference [Por00] the authors prove the semiconducting behaviour
with a large band gap of double-stranded DNA polymer. Charge transfer through DNA
takes place via the overlap of the π orbitals in adjacent base pairs in a single strand.
45
Hydrogen bonding plays a universal role in molecular recognition [Cha09] of DNA
base paring. In DNA, adenine and thymine as well as cytosine and guanine form
hydrogen bonded base pairs. Recently, scanning tunnelling microscopy demonstrated
hydrogen-bonding-based recognition [Cha09]. These effects provide new mechanism
for designing sensors that transduce a molecular recognition event into an electronic
signal [Cha09].
Cytosine is the smallest molecule between the DNA bases and is used in storing and
transporting genetic information within a cell. The pyrimidine molecule contains 13
atoms (C4H
5N
3O) and binds to guanine molecule via hydrogen bridges forming the
second strand poly (C-G) in the double helix of the DNA molecule.
Because the optical properties are correlated to the electrical properties of devices,
investigating the optical behaviour of the organic layer and determining the optical
constants is vital in order to improve efficiency of devices.
5.1 Sample preparation
Flat p-type (B-doped) silicon (111) surfaces were used as substrates. The one-
side polished flat silicon substrates were provided by Wacker Siltronic. Prior to
biomolecular deposition, the substrates were hydrogen terminated via a wet-chemical
procedure. The flat substrates were first degreased in isopropanol and deionised water in
order to remove organic contaminants. Afterwards the substrates were dipped for 10
min in 5% HF, 10 min in piranha solution (98% H2SO4: 30% H2O2 = 1 : 1), 8 min in
40% NH4F, washed with deionised water and dried with N2.
High-purity cytosine powder was purchased from Across Organics. The material
was evaporated under high vacuum conditions (~10-8 mbar) from a Knudsen cell at a
temperature of approximately 400 K and an evaporation rate between 0.2 and 0.3
nm/min. The biomolecular film was deposited on silicon substrates maintained at RT.
The evaporation rates were in situ monitored via a quartz crystal microbalance and then
ex situ calibrated via film thickness measurements using VIS ellipsometry. Five samples
with different thicknesses (13.7 nm, 20.9 nm, 57.4 nm, 75.9 nm and 127.6 nm) were
prepared in similar conditions.
46
5.2 Atomic force microscopy (AFM) characterisation of cytosine films
The AFM measurements were performed in contact mode with a tip of
approximately 15 nm diameter provided by Veeco System. Figure 5.2.1 shows in
comparison AFM images of cytosine thin films with thicknesses between 13.7 nm and
127.6 nm.
Figure 5.2.1: 2D and 3D 5μm AFM images of different cytosine film thicknesses
For the thinnest cytosine film it is clearly seen that the film is not completely
closed while in case of the 20.9 nm film random oriented chains are observed. For the
next three thicknesses, grains structures with the dimension decreasing with the
thickness increment are observed. The 57.4 nm sample forms grains with a diameter of
approximately 320 nm, the 75.9 nm film forms 201 nm diameter grains and finally 210
nm grains are observed for the 127.6 nm cytosine film.
47
5.3 Visible spectroscopic ellipsometry
Ex–situ ellipsometric measurements were performed on cytosine films with
thicknesses between 13.7 and 127.6 nm. Variable angle spectroscopic ellipsometry
(VASE) in the energy range of 1.33-5 eV was used under different angles of incidence
(55°-65°). Figure 5.3.1 presents experimental and calculated Ψ and Δ spectra of
cytosine films with different thicknesses. Film thickness and roughness values were
obtained by fitting the ellipsometric data in the transparent range 1.33- 2.7 eV using an
anisotropic Cauchy model. The obtained information is summarized for the five
samples in Table 5.3.1. The exception is the 13.7 nm thick cytosine layer for which an
isotropic Cauchy model was applied.
Sample 1 2 3 4 5
Thickness(nm) 127.62 75.95 57.43 20.95 13.71
Roughness(nm) 16.25 1.99 - - -
An IP 1.71 1.72 1.74 1.65
1.49 OOP 1.51 1.51 1.50 1.55
Bn IP 0.011 0.017 0.007 0.027
0.019 OOP 0.007 0.011 0.021 0.017
Table 5.3.1: Film thickness and roughness values determined for the 5 cytosine
samples
Due to significant structural and optical properties of the cytosine layers, multi-
sample analysis was not possible to be applied. Using the thickness and roughness in
table 5.3.1 and applying a uniaxial oscillator model, the optical constants in the visible
range 1.33-5 eV (1198 fitted experimental points) were determined and are plotted in
Figure 5.4.2. The parameters of the Gaussian oscillators involved in the optical model
are summarized in Table 5.3.2.
48
Figure 5.3.1: Experimental and calculated Ψ and Δ spectra of cytosine films on
Si(111)
2 3 4 5
20
30
40
Experiment 65° Experiment 60° Experiment 55° Oscillator model
°
Energy / eV
2
2 3 4 50
30
60
90
°
Energy / eV
Oscillator model Experiment 65° Experiment 60° Experiment 55°
3
2 3 4 5-100
0
100
200
3003
Energy / eV
Experimental 65° Experimental 60° Experimental 55° Oscillator model
2 3 4 5-100
0
100
200
3004
Energy / eV
Experiment 65° Experiment 60° Experiment 55° Oscillator model
2 3 4 5-100
0
100
200
300 5
°
Energy / eV
Experiment 65° Experiment 60° Experiment 55° Oscillator model
2 3 4 50
30
60
90 5
Energy / eV
Experiment 65° Experiment 60° Experiment 55° Oscillator model
2 3 4 5
18
27
36
°
Energy / eV
Experiment 65° Experiment 60° Experiment 55° Oscillator model
1
2 3 4 590
120
150
1801
Energy / eV
Experiment 65° Experiment 60° Experiment 55° Oscillator model
2 3 4 5
30
60
90 4
Energy/ eV
Experiment 65° Experiment 60° Experiment 55° Oscillator model
2 3 4 5
90
120
150
180
Experiment 65° Experiment 60° Experiment 55° Oscillator model
°
Energy / eV
2
49
An exception is the thin film sample with a thickness of 13.7 nm for which an
isotropic model with a sum of two oscillators was applied. The following parameters
were determined: for oscillator 1, Amplitude1=0.977 eV2, Energy1=4.4891 eV,
Broadening1=0.786 eV and for oscillator 2, Amplitude2=1.7533 eV2, Energy2=5.755
eV, Broadening2=1.0315 eV.
Sample 1 2 3 4
Oscillator 1
IP
Amplitude(eV2) 0.97 1.61 1.11 1.21
Energy(eV) 4.59 4.78 4.67 5.185
Broadening(eV) 0.87 0.49 0.31 1.43
OOP
Amplitude(eV2) 0.35 0.55 0.69 0.92
Energy(eV) 4.26 4.26 4.26 4.25
Broadening(eV) 0.0725 0.072 0.064 0.06
Oscillator 2
IP
Amplitude(eV2) 2.26 2.67 7.57
Energy(eV) 6.25 6.26 9.93
Broadening(eV) 2.4 2.40 2.85
OOP
Amplitude(eV2) 0.25 0.59 0.50 1.10
Energy(eV) 4.37 4.34 4.36 4.36
Broadening(eV) 0.082 0.16 0.16 0.24
Oscillator 3
IP
Amplitude(eV2)
Energy(eV)
Broadening(eV)
OOP
Amplitude(eV2) 0.16 0.53 0.20 1.42
Energy(eV) 4.49 4.49 4.54 4.54
Broadening(eV) 0.071 0.27 0.31 0.49
Oscillator 4
IP
Amplitude(eV2)
Energy(eV)
Broadening(eV)
OOP
Amplitude(eV2) 3.18
Energy(eV) 4.90
Broadening(eV) 0.41
Table 5.3.2: Oscillator parameters determined for the four thicker cytosine
samples
50
The first Gaussian oscillator corresponds to the HOMO→LUMO gap of
cytosine, a π-π* energy transition type.
The in-plane and out-of-plane optical constants of cytosine are presented in
figure 5.4.2.
Figure 5.3.2: In plane (dotted line) and out of plane (continuous line) optical
constants of cytosine thin films determined in the visible spectral range by an
anisotropic oscillator model
The excitation of a molecule from the ground electronic state to an excited
electronic state gives rise to a broad absorption peak in the visible region of a spectrum.
In the process of inducing an electronic transition, the energy is usually sufficient to
induce also vibrational transitions. Therefore, a fine structure resulting from the
vibrational transitions can be noticed in the electronic spectrum. In this case we speak
about a vibronic spectrum. Very well resolved vibronic spectra can be obtained by
51
studying material in gas phase or single crystals at low temperature. Surprisingly, in the
present work was for the first time noticed such a structure at room temperature for a
thin film of cytosine deposited on Si. As it can be noticed in figure 5.4.2, the spectrum
consists of a succession of Frank-Condon vibronic transitions. The spectra are not as
well resolved as known from low temperature measurements on cytosine monohydrated
single crystal in references [Step93, Sho70], but in a good agreement. Shoup and Van
der Hart observed in the vibronic spectra a progression with the origin at 4.4 eV and a
vibrational interval of 750 ± 100 cm-1. In the present work, the absorption band at 4.25-
4.26 eV is assigned to the pure electronic transition (0-0) that is the origin of a single
vibronic progression. Compared with the above mentioned papers, in the presented
spectra, just two vibrational components were noticed, but their position is in agreement
with reference [Step93, Sho70]. The energetic separation of the vibrational components
is determined and interpreted for each sample. The first vibrational interval differs for
the different thicknesses and has the value in the interval 0.08-0.12 eV. This
corresponds to approximately 645.2 - 806 cm-1, in good agreement with the values from
the references previously cited. If we compare the obtained result with the tanΨ
spectrum obtained in the infrared energetic range, this can be assigned to the breathing
vibration of cytosine ring, which appears in IR at 799 cm-1. This suggests that the
electronic excitation causes remarkable enlargement of the ring [Step93]. Important to
mention is that an error of 0.01 eV in determining the energy position of the Gaussian
oscillators induces a shift of 80.7 cm-1. Following the rules of a linear progression and
the harmonic oscillator theory, the next vibronic structure should appear at 1451±100
cm-1. This vibration would correspond to another ring vibration that appears in our
infrared spectra at 1461-1471 cm-1. From our vibronic structures, the energetic
separation is 0.12-0.18 eV that corresponds to 1209-1451.8 cm-1. No infrared
vibrational band corresponding to the band at 4.9 eV in the visible range was found.
5.4 Infrared spectroscopic ellipsometry
The five samples were investigated using infrared spectroscopic ellipsometry
(IRSE) in the mid-IR spectral range. The incidence angles were set to 55°, 60° and 65°.
In Figure 5.5.1 tanΨ spectra measured at 60° are plotted.
52
Figure 5.4.1: tanΨ spectra of cytosine thin films measured at an incidence angle of
60°
The vibrational band assignment for cytosine is controversially discussed in
literature. In the table 5.4.1 the assignments collected from different scientific studies
are summarised [Öst05, Szc88, Sub97].
13.71 nm
20.95 nm
57.43 nm
75.95 nm
127.6 nm
53
Östblom KBr
Szczesniak KBr
Subramanian
Present work (experimenta
l) film
frequency
(cm-1)
assignment
frequency
(cm-1) assignment
frequency
(cm-1)
assignment
frequency (cm-1)
792 δop ring 791 ring, ωC4H,
ωC6H 784 νC2O, δring 794
815 δop ring 820 ring, ωN1H 834
878 δring 885 sqz ring, δNH2,N2H
964
996 ωC5H,C6H
1010 δring 1088 δNH2
1100 δN1H,C5H 1130 δC5H, νC6N1
1149
δs N7H9,
N7H10 1150 δN7H9,N7H10 1198
δC6H,N1H, νC6N1
1237 δring 1238 νN1C2,C2N3 1237 νC2N3 1235
1277 δNH 1278 δNH,CH 1275.5
1364 δs
N1H,C5H,C6 1363 δN1H,C5H,C6H 1340 νC4N, δC5H 1362
1463 δring 1463 ring(νN1C6,N3C
4) 1423 δN1H 1460
1503
δsc NH2,
C4N7 1505 βNH2,νC4NH2 1475 νN3C4,βC6H 1506
1540
δring, N1H 1540 ring(νC4C5), δC4H,N2H
1539 νN3C4, νC4C5
1538
1640 (sh)
νC5=C6 1640 ring(νC5C6),
βNH2 1602 βNH2 1628
1663 νC2=O 1662 νC2O, βNH2,
δN1H 1653
1700 (sh)
δsc NH2 1700 νC2O, βNH2,
δNH2 1730
ring(νC5C6
) 1708
3179
3380 νN7H9,N7H10 3457 νsNH2 3388
Table 5.4.1: Assignment of the vibration bands in the mid infrared spectral range.
The marked band will be used in the future theoretical calculations.
54
In the work of Östblom the band at about 1700 cm-1 is assigned to an in-plane
vibration mainly related to the scissoring vibration of the NH2 group as mixed x, y
mode (Fig. 5.4.2) [Öst05]. The band at 1663 cm-1 is assigned to the C=O stretching
vibration in y-direction, while the band at about 1640 cm-1 is related to a C=C vibration
mainly in x direction with a y component. In the case of the band observed at 1461 cm-1,
this is related to the in-plane deformation vibration of the ring in y-direction.
Figure 5.4.2: Molecular structure of cytosine; red=oxygen, blue= nitrogen, green=
carbon, white= hydrogen
The assignment plays a crucial role for the further simulation using an optical
model and influences the interpretation of the obtained results. In the present work the
spectral interpretation presented in reference [Öst05] will be considered.
Comparing the tanΨ spectra of the five samples, big changes are noticed for the
in-plane ring vibration band at ~1461 cm-1(0.1813 eV). The sign is changing from
positive to negative passing through derivative like shape for the 20.9 nm thick sample.
A special attention was accorded to this band in order to determine the orientation of the
molecules relative the substrate. The orientation of the molecules can be determined
from the ring vibration mode because the transition dipole moment for the vibration at
1461 cm-1 is in the plane of the molecule.
55
Figure 5.4.3: Sketch of the geometric model of cytosine used for the simulations.
The tilt angle is marked. For the supposed uniaxial model the angle φ (rotation in x, y
plane) was set to 45°.
Figure 5.4.4 presents the infrared spectra of cytosine on Si(111) in the energy
range 0.178 eV – 0.183 eV (1435-1475 cm-1) for the molecular layer with a thickness of
approximately 57.4 nm, 75.9 nm and 127.6 nm respectively. For the optical simulation a
uniaxial oscillator model was used (nx=ny≠nz). Lorentz oscillators with amplitudes Fi
and broadening Γi characterized the in-plane vibration of the ring. The square
amplitudes of the oscillators obtained from the optical simulation are proportional with
the components of the transition dipole moment. Thus, one can obtain the orientation of
the molecules (γ) relative to the substrate using the formula:
yx
z
F
F
,2
2
cos
sin2
(5.4.1)
The thickness, roughness and refractive index values used were the ones
determined from visible ellipsometry.
56
Figure 5.4.4: tanΨ and Δ spectra of cytosine on Si(111). Scattered chart represents the
experimental measurements, red continuous line the model fit.
A multi-sample analysis was not possible indicating that a different optical
response was obtained for the differently thick organic layers. Thus, the samples were
fitted separately. The oscillator parameters are summarized in the table 5.4.2. The
average tilt angle of the molecules on the substrate was determined and a similar
1440 1450 1460 1470
0.40
0.44
0.48
0.52 127.62 nm
wavenumbers/ cm-1
tan
Model fit Experiment 55° Experiment 60°
1440 1450 1460 14700.36
0.40
0.44
0.48
Model fit Experiment 55° Experiment 60°
75.95 nm
tan
wavenumers/ cm-1
1440 1450 1460 1470
164
168
172
176
Model fit Experiment 55° Experiment 60°
127.62 nm
wavenumbers/ cm-1
1440 1450 1460 1470
0.38
0.40
0.42
0.44
0.46
0.48
0.50
tan
wavenumbers/ cm-1
57.43 nm
Model fit Experiment 55° Experiment 60°
1440 1450 1460 1470171
174
177
Model fit Experiment 55° Experiment 60°
75.95 nm
wavenumbes/ cm-1
1440 1450 1460 1470
174
176
178
wavenumbers/ cm-1
57.43 nm
Model fit Experiment 55° Experiment 60°
57
orientation of the molecules was determined for the three samples. 12° tilt angle was
determined for the 57.4 nm cytosine film, 11.5° tilt for 75.9 nm thick film and 10.8° for
127.6 nm cytosine film.
Thickness (nm) 127.62 75.95 57.43
Oscillator
strength
IP 6.927 6.362 7.249
OOP 0.5094 0.529 0.6547
Tilt (°) 10.8 11.5 12
Tabel 5.4.2: Oscillator parameters and calculated tilt angle for three different
cytosine thicknesses
For the 20.9 nm thick cytosine layer on Si(111) determining the orientation of
the molecules relative to the substrate seems to be more difficult. A simultaneous fit of
the parameters tanΨ and Δ using a similar model like for the other three samples will
result in a high value of the mean square error. One reason could be that even though
from AFM measurements the film looks like a closed layer, the existence of holes in the
depth of the layer cannot be excluded. Though, the fitted tanΨ spectra for an incident
angle of 55°, 60° and 65° is presented in figure 5.4.5.
Figure 5.4.5: Experimental and calculated tanΨ spectra of 20.9 nm cytosine on
Si(111)
1450 1460 1470 1480 1490
0.28
0.32
0.36
0.40
0.44
Model fit Experiment 55° Experiment 60° Experiment 65°
tan
Energy / eV
58
Following a similar procedure like for the previous samples, an average tilt angle
of 22° was calculated. The bigger angle was expected since the band at 1460 cm-1 has a
derivative shape compared with an upright oriented band in case of the thicker samples.
In the case of the isotropic cytosine layer with the thickness of 13.7 nm, a random
orientation of the molecules is considered and the average molecular orientation of the
dipole moment with respect to the electric field gives rise to the magic angle of 54.7°
[Sch95].
Figure 5.4.6: Sketch presenting the orientation of the cytosine molecules on the Si(111)
substrates
The obtained orientation of the cytosine molecules with respect to the substrate for the
five layer thicknesses studied is schematically drawn in figure 5.4.6.
Investigating the tanΨ spectra of the cytosine layers to higher wavenumbers, a
new indicator of the change in the orientation with the thickness was found.
59
Figure 5.4.7: tanΨ spectra of cytosine layers on Si(111) in the range 3000-3600 cm-1
In figure 5.4.7 the NH2 symmetric and antisymmetric stretching band are shown. The
assignment of the bands was made in concordance to reference [Roz04]. The
antisymetric stretching vibration changes the shape from downward pointing band for
the thin cytosine layers (13 nm and 20.9 nm) to upward oriented bands for the other
three samples suggesting a change in the orientation of the transition dipole moment
corresponding to this vibration. The NH2 symmetric stretching vibration is shifting from
3169 to 3185 cm-1 while the NH2 antisymmetric stretching vibration presents a
maximum between 3381 and 3390 cm-1. For the antisymmetric vibration, this shift is
just due to an optical effect appearing at the change in the sign of the bands. In case of
the symmetric stretching vibration, there is no change in the sign of the bands and
therefore the big gradual shift could be interpreted as a shift induced by the change in
the lineshape of the antisymmetric vibration. This explanation is reasonable if we think
that the two bands are very broad and are positioned relatively close.
If we compare the change in the orientation of the NH2 antisymetric stretching
bands with the deformation band of the ring at 1460 cm-1 a consistency in the change
was noticed. An explanation for this could be that the transition dipole moment of νsNH2
has approximately the same direction like the transition dipole moment induced by the
ring deformation. The orientation of the transition dipole moment of the NH2 stretching
vibrations with respect to the permanent dipole moment direction was determined
3000 3150 3300 3450 3600
0.28
0.30
0.32
13 nm 21 nm 57 nm 76 nm 127 nm
tan
wavenumber/cm-1
60
experimentally and theoretically by Dong et al in [Don02] and [Cho05] and presented in
figure 5.4.8.
Figure 5.4.8: The transition dipole moment of NH2 stretching vibrations (dotted arrows)
is pictured with respect to the permanent dipole moment (red arrow)
From the theoretical calculation, it is expected that the transition dipole moment
corresponding to νssNH2 is rotated with 88° with respect to the permanent dipole moment
while for the transition dipole moment induced by νasNH2 the rotation is 6°.
For the vibrational bands at 1663 cm-1 and 1700 cm-1 corresponding to C=O
stretching vibration and NH2 deformation a very interesting behaviour is observed. The
ratio of the amplitudes of the C=O band and NH2 band is decreasing with increasing the
thickness of the cytosine layer, supporting the change in the molecular orientation with
the thickness mentioned before.
5.5 Synchrotron mapping ellipsometry
The homogeneity of the samples was studied using the synchrotron mapping
ellipsometer at BESSY II in Berlin. During the measurements, the incidence angle was
fixed at 65° and the set-up was purged with dry air in order to avoid the absorption of
the infrared radiation by the water molecules in the studied area. A photovoltaic
mercury-cadmium-telluride (MCT) detector with a detector element smaller than 1 mm2
was used.
NH2SS
NH2AS
61
Figure 5.5.1: tanΨ and Δ maps calculated for the five cytosine samples
62
The maps were measured with a 1 mm step and the investigated area was
between 12 and 20 mm2. From the measured spectra tanΨ and Δ maps were calculated
and presented in figure 5.5.1.The detailed description of the method used to obtain the
maps is presented in Chapter 2 of the present work TanΨ maps were calculated from the
band amplitude at 1461 cm-1. Δ maps were derived from Δ spectra in the non absorbing
range 2700-2800 cm-1. The maps give information about the variation in thickness and
morphology of the organic layers. If one assumes that the variation in Δ is only due to a
thickness variation, the maps can be translated in a thickness variation of the organic
layer. The maximum variation in Δ is approximately 1.8 ° that corresponds to a change
in the layer thickness of approximately 3 nm for the four thicker samples. The thickness
variation for the 13 nm thick cytosine is not studied because, as obtained from AFM
investigation, the organic layer is not closed.
63
Concluding remarks
This work proves that spectroscopic ellipsometry (SE), in the visible spectral
range as well as in the mid-infrared spectral range, is suitable for the characterisation of
organic layers with thicknesses between 1 monolayer and some hundred nanometers.
The advantage of using this method is that one obtains a variety of information about
the studied sample. The thickness and the high frequency refractive index of an organic
layer can be estimated from the obtained Δ values while the tanΨ parameter gives
information about the structure of the molecular layer as well as about the orientation of
the molecules on the substrate. The homogeneity of a layer and the presence of defects
were in more detailed investigated by synchrotron mapping ellipsometry.
Two different systems were chosen for investigation using spectroscopic
ellipsometry.
First, the functionalization of GaAs and Au substrates using alkanethiol
molecules was studied. Highly ordered monolayer films on the substrate was expected
to be obtained. It was proved that in the case of long alkanethiol chains
(hexadecanemonothiol) a very well ordered self-assembled monolayer on both
substrates is obtained. The average orientation of the molecules on the substrate is 19°
for the molecules on GaAs and 22° for the molecule on Au. The tilt angle was
calculated with respect to the perpendicular to the substrate. The positive results
indicate hexadecanemonothiol monolayers as a successful candidate for further
industrial applications. In case of the short chain molecule (octadecanedithiol) a
quantitative interpretation could not be done due to the presence of defects and possible
contamination of the substrate. Qualitatively, an average tilt angle bigger than 30° was
indicated.
A thickness dependent study of the optical properties was performed for
cytosine layers on passivated Si(111). Using visible spectroscopic ellipsometry the
thickness of the organic layer and the high frequency refractive index were determined.
The vibronic structure observed in the visible energetic range was discussed and
64
correlated with results obtained from ellipsometric measurements performed in the
infrared range. The change in the average orientation of the molecules with respect to
the substrate was determined from optical calculations in the infrared range. A gradual
change in the tilt angle was obtained by investigating the orientation of the transition
dipole moment of the ring deformation at 1461 cm-1. The calculations were done using a
separate optical model for each sample, as an optical model that takes into account
gradual optical changes with the thickness does not exist. The successful preparation of
the samples was proved by synchrotron mapping ellipsometry that indicated a
maximum thickness variation of 3 nm.
65
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List of figures
Figure 1.1.1: a) linearly polarized light; b) elliptically polarized light…………..……11 Figure 1.2.1: Sketch of polarized light propagation in stratified media……………….12 Figure 1.3.2.1: a) Representation of the elliptical polarisation by (Ψ,Δ) coordinate system; b) Representation of a point on the Poincare sphere with the radius S0………………………………………………………………………………………..18 Figure 1.4.1: Diagram of Frank-Condon principle. E0 represents the electronic ground state, E1 denotes the first excited electronic state…………………………………..…..20 Figure 1.4.2: Vibronic fine structure of 1,2,4,5-tetrazine. I Gas phase at room temperature, II In isopentane-methylcyclohexane matrix at 77K, II In cyclohexane at room temperature, IV In water at room temperature………………………………..….21 Figure 2.1.1: Measurement principle of the FT-IR ellipsometer at ISAS Berlin [Rös02]……………………………………………………………………………..…..23 Figure 2.2.1: Infrared mapping ellipsometer at BESSY II Berlin[Gen03]………….....24 Figure 2.2.2: Measurement scheme at a certain incidence angle: Grey spot represents the beam spot on the studied sample for the measurements performed in the lab. Each black dot represents one illuminated spot on the sample for the measurements performed with the mapping ellipsometer at BESSY II………………………………..25 Figure 2.2.3: Calculation of tanΨ maps from a vibration band……………………..…26 Figure 4.1: Structure of self assembled monolayer………………………………...….31 Figure 4.2.1: Schematic of the geometric model of HDT molecules used for the simulations. The tilt angle and the twist angle δ are marked. In order to account for the uniaxial symmetry (nx = ny) of the studied samples, the angle φ (rotation in x, y plane) was set to 45°. The directions of the transition dipole moments of the symmetric and antisymmetric stretching vibrations of the CH2 group are shown in the inset……..…..34 Figure 4.2.2: Simulated (red) and measured (black) reflection spectra (top: p-polarized reflection absorbance; middle: s-polarized reflection absorbance, bottom: tan) of a
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HDT monolayer on GaAs. The incidence angle was set to 60° in order to ensure defined reflectance measurements in which the probed spot was smaller than the sample size (7x19 mm2)……………………………………………………………………………..37 Figure 4.2.3 a) Measured tanΨ spectra of octanedithiol monolayer on GaAs (bottom) and HDT monolayer on GaAs (top). The baseline was corrected for convenience. The incidence angle was 65°; b) spectra for tilt angles of 12°, 18°, 24°, 30°, 36° and 42° simulated based on the optical constants used for HDT on GaAs…………………….39 Figure 4.2.4: Comparison between tanΨ spectra of C8DT and HDT on GaAs. The spectra were referenced to clean GaAs and shifted for a better understanding………………………………………………………………………..…40 Figure 4.2.5: a) Simulated (black) and measured (grey) tan spectra of a HDT monolayer on gold. The incidence angle was set to 65°. b) Simulations for tilt angles from 12° to 42°…………………………………………………………………………41 Figure 4.3.1: Interpolated 2D map of the CH2 band amplitude at 2922 cm-1, which was taken from tanΨ spectra: a), HDT on Au, b) HDT on GaAs. The step width was 1 mm……………………………………………………………………………….…….42 Figure 4.3.2: Sketch presenting the orientation of the studied molecules on the substrates……………………………………………………………………………….43 Figure 5.1: Crystalline structure and unit cell of cytosine………………………..……44 Figure 5.2.1: 2D and 3D 5μm AFM images of different cytosine film thicknesses……………………………………………………………………………..46
Figure 5.3.1: Experimental and calculated Ψ and Δ spectra of cytosine films on Si(111)……………………………………………………………………………...…..48 Figure 5.3.2: Optical constants of cytosine thin films determined in the visible spectral range……………………………………………………………………………………50 Figure 5.4.1: tanΨ spectra of cytosine thin films measured at an incidence angle of 60°………………………………………………………………………..…………….52 Figure 5.4.2: Molecular structure of cytosine…………………………………………54 Figure 5.4.3: Sketch of the geometric model of cytosine used for the simulations. The tilt angle is marked. For the supposed uniaxial model the angle δ (rotation in x, y plane) was set to 45°……………………………………………………………………55 Figure 5.4.4: tanΨ and Δ spectra of cytosine on Si(111). Scattered chart represents the experimental measurements, red continuous line the model fit…………..……………56 Figure 5.4.5: Experimental and calculated tanΨ spectra of 21 nm cytosine on Si(111)……………………………………………………………………………...…..57
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Figure 5.4.6: Sketch presenting the orientation of the cytosine molecules on the Si(111) substrates…………………………………………………………………………..…..58 Figure 5.4.7: tanΨ spectra of cytosine layers on Si(111) in the spectral range 3000-3600 cm-1…………………………………………………………………………………….59
Figure 5.4.8: The transition dipole moment of NH2 stretching vibrations (dotted arrows) is pictured with respect to the permanent dipole moment (red arrow)…………………………………………………………………………………..60 Figure 5.5.1: tanΨ and Δ maps calculated for the five cytosine samples………..…….61
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List of tables
Table 5.3.1: Film thickness and roughness values determined for the 5 cytosine samples………………………………………………………………………..………..47 Table 5.3.2: Oscillator parameters determined for the 5 cytosine samples….…….…..49 Table 5.4.1: Assignment of the vibration bands in the mid infrared energetic range….53 Tabel 5.4.2: Oscillator parameters and calculated tilt angle for three different cytosine thicknesses…………………………………………… ………………………………57
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Acknowledgements
I am grateful to many people who made the completion of this research work
possible and I hope I will remember and mention all of them.
Firstly, I would like to thank prof. Norbert Esser who offered me the opportunity
to join the Interface Spectroscopy group at ISAS in Berlin and use the excellent research
facilities of the institute.
I am grateful to Dr. Karsten Hinrichs for his guidance and support during my
stay at ISAS as well as for the proofread of my PhD thesis.
Special thanks go to the two persons I shared the office most of the time and that
were a great help with the proofreading of my thesis, Dennis and Simona. Dennis,
thanks a lot for your help in the difficult situations more or less related with research
activities. BESSY beamtimes were much easier to endure in two. Last but not least, I
would like to thank you for helping me understand how men brain works. Many thanks
to Simona for very valuable scientific discussions and for her being ready to help me
any time I needed it. I am also thankful for the moral support, the friendship and for
helping me not to forget speaking Romanian.
I would like to acknowledge Dr. Jörg Rappich and Xin Zhang for the preparation
of the H terminated Si substrates.
For interesting scientific discussions I thank to prof. Dimiter Tsankov.
My appreciation goes to Karen Kavanagh and Julia Hsu for the fruitful
cooperation in the research of self assembled monolayers on Si and Au surfaces.
For technical support in the laboratories at ISAS and during the beamtimes in
BESSY, I am grateful to Ilona Fischer and Ulrich Schade.
I am grateful to Christian Friedrich for the introduction to AFM set-up.
I would also like to thank all the colleagues at ISAS for their support with
technical, electronic and administrative problems.
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Many, many thanks to my family, my mother, my father and Diana for their
constant support and understanding even when, because of the stress I became
unbearable. Multumesc parintilor mei pentru suportul neconditionat, pentru educatia
care a pus bazele a ceea ce sunt astazi si surorii mele pentru increderea si incurajarile
permanente.