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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

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Page 1: Ellipsometric characterisation of anisotropic thin organic films · 2017-10-26 · Ellipsometric characterisation of anisotropic thin organic films vorgelegt von MSc Phys. Dana -

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

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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.

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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

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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

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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

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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.

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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

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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,

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9

während die molekulare Orientierung aus den ellipsometrischen Messungen im

Infraroten Spektralbereich abgeleitet wurde.

Die Schlussfolgerungen dieser Arbeit sind in dem letzten Kapitel

zusammengefasst.

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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:

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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

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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,

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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.

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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:

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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

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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)

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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)

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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:

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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)

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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

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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

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for the gas phase, while in case of the molecule solved in water, no vibrational structure

could be distinguished.

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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]

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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]

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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

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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.

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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.

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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”.

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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)

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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)

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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

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[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.

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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

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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:

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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)

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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

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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).

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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.

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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

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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

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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.

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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.

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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.

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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.

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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.

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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.

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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.

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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

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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

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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

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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.

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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

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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.

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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.

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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.

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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°

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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

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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.

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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

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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

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Figure 5.5.1: tanΨ and Δ maps calculated for the five cytosine samples

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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.

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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

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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.

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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.