Reactions at an organic surface

Dissertation

zur Erlangung des Grades eines Doktors der Naturwissenschaften

der Fakultät für Chemie der Ruhr-Univeristät Bochum

Vorgelegt von

Ketheeswari Rajalingam

Aus Indien

Bochum 2008

Reactions at an organic surface

Tag der mündlichen Prüfung: 19.12.2008

Prüfungskommission:

Referent: Prof. Dr. Christof Wöll

Korreferent: Prof. Dr. Roland. A. Fischer

Vorsitzender: Prof. Dr. Rolf Heumann

Die vorliegende Arbeit wurde im Zeitraum von 2004 bis 2008 am Lehrstuhl

für Physikalische Chemie I der Fakultät für Chemie der Ruhr-Universität

Bochum unter Anleitung von Herrn Prof. Dr. Christof Wöll angefertigt.

Dedicated to my parents

A. Rajalingam and R. Sugunajothi

Abstract

Reactions at an organic surface

The chemical reactions on aromatic dithiol self-assembled monolayers (SAM) adsorbed on

the gold surface has been investigated by infrared reflection absorption spectroscopy

(IRRAS), near edge X-ray absorption fine structure spectroscopy (NEXAFS) and X-ray

photoelectron spectroscopy (XPS). The results show that the reactions on an organic surface

widely differ from the reactions in bulk. The studies on the deacylation reaction highlight the

importance of the quality of substrates used for SAM preparation. The results of the chemical

vapor deposition of palladium on SAMs demonstrate the acceleration of the reaction kinetics

due to the presence of defects. In addition, the results describe the catalytic activity of the

formed palladium metal nanoparticles. This study gives rise to a better understanding of the

chemical reactions on dithiol SAMs and the findings can be extended for the development and

optimization of a suitable surface for metallization purposes.

Reaktionen auf einer organischen Oberfläche

Chemische Reaktionen auf aromatischen Dithiolen, die als selbstorganisierende

Monoschichten (SAM) auf einer Goldoberfläche adsorbiert sind, wurden mittels Infrarot-

Reflexions-Absorptionsspektroskopie, Röntgen-Nahkanten-Absorptionsspektroskopie und

Röntgen-Photoelektronenspektroskopie untersucht. Die Ergebnisse zeigen, dass sich die

Reaktionen auf einer organischen Oberfläche stark unterscheiden von Reaktionen im

Volumen. Untersuchungen der Deacylations-Reaktion heben die Bedeutung der Qualität der

Substrate für die SAM-Bildung hervor. Die Ergebnisse der Gasphasenabscheidung von

Palladium auf SAMs zeigen eine Beschleunigung der Reaktionskinetik in Gegenwart von

Defekten. Außerdem beschreiben sie die katalytische Aktivität der gebildeten Pd-

Nanopartikel. Diese Arbeit führt zu einem besseren Verständnis der chemischen Reaktionen

auf Dithiol-SAMs und die Ergebnisse können für die Entwicklung und Optimierung einer

geeigneten Oberfläche für die Metallisierung eingesetzt werden.

1

Contents

1. Introduction ---------------------------------------------------------------------------------------3

1.1. Scope of the present work------------------------------------------------------------------3

1.2. Surfaces---------------------------------------------------------------------------------------5

1.3. Organic thin films ---------------------------------------------------------------------------6

1.4. Self-assembled monolayers (SAMs)------------------------------------------------------7

1.5. Thiols on Au(111)---------------------------------------------------------------------------8

1.5.1. SAM - Formation kinetics ------------------------------------------------------------9

1.5.2. SAM - Formation mechanism ------------------------------------------------------ 10

1.5.3. Au(111)-------------------------------------------------------------------------------- 10

1.5.4. Structure of thiolates on gold------------------------------------------------------- 11

1.6. Dithiols on Au(111)----------------------------------------------------------------------- 12

1.7. Chemical reactions on self-assembled monolayers ----------------------------------- 13

1.7.1. Deprotection strategy in dithiols --------------------------------------------------- 15

1.8. Metal deposition on SAMs--------------------------------------------------------------- 15

1.9. Palladium precursor----------------------------------------------------------------------- 22

1.9.1. Cyclopentadienyl(allyl)palladium ------------------------------------------------- 23

2. Sample preparation and analytical techniques ---------------------------------------------- 25

2.1. Chemicals ---------------------------------------------------------------------------------- 25

2.2. Preparation of the gold substrates ------------------------------------------------------- 25

2.3. Preparation of SAMs---------------------------------------------------------------------- 26

2.4. Deposition of Cp(allyl)Pd on SAMs --------------------------------------------------- 26

2.5. Spectroscopic methods used in this work ---------------------------------------------- 27

2.5.1. X-ray Photoelectron Spectroscopy------------------------------------------------- 27

2.5.2. Near Edge X-ray Absorption Fine Structure Spectroscopy--------------------- 31

2.5.3. Infrared Reflection Absorption Spectroscopy ------------------------------------ 34

2.6. Analytical equipment --------------------------------------------------------------------- 38

2

3. Self-assembled monolayers of thiol terminated surfaces---------------------------------- 41

3.1. Self-assembled monolayers of terphenyldimethyldithiol ---------------------------- 41

3.1.1. Preparation of TPDMT SAM------------------------------------------------------- 41

3.1.2. Characterization of TPDMT SAM------------------------------------------------- 41

3.2. Self-assembled monolayers of biphenyldimethyldithiol ----------------------------- 49

3.2.1. Preparation of deprotected BPDMAc-1 SAM------------------------------------ 49

3.2.2. Characterization of deprotected BPDMAc-1 SAM------------------------------ 49

3.3. Conclusion --------------------------------------------------------------------------------- 54

4. Deacylation reaction at an organic surface-------------------------------------------------- 55

4.1. Conversion of thioacetate to thiol ------------------------------------------------------- 56

4.2. Chemistry in confined geometries ------------------------------------------------------ 60

4.3. Conclusion --------------------------------------------------------------------------------- 68

5. Metallization of a thiol-terminated organic surface ---------------------------------------- 69

5.1. Deposition of palladium onto a TPDMT-SAM --------------------------------------- 72

5.1.1. XPS of Pd deposited TPDMT-SAM----------------------------------------------- 73

5.1.2. NEXAFS of Pd deposited TPDMT-SAM ---------------------------------------- 80

5.1.3. IRRAS of Pd deposited TPDMT-SAM ------------------------------------------- 83

5.2. Deposition of palladium onto a deprotected BPDMAc-1 SAM--------------------- 87

5.2.1. XPS of Pd deposited deprotected BPDMAc-1 SAM---------------------------- 89

5.2.2. NEXAFS of Pd deposited deprotected BPDMAc-1 SAM---------------------- 94

5.3. Conclusion --------------------------------------------------------------------------------107

5.4. Outlook ------------------------------------------------------------------------------------108

6. Summary----------------------------------------------------------------------------------------112

7. Appendix ---------------------------------------------------------------------------------------116

7.1. List of symbols and abbreviations -----------------------------------------------------116

7.2. List of figures -----------------------------------------------------------------------------117

7.3. List of tables ------------------------------------------------------------------------------120

8. References --------------------------------------------------------------------------------------121

3

1. Introduction

1.1. Scope of the present work The research work described in this thesis focuses on the surface chemical reactions on

aromatic dithiol self-assembled monolayers adsorbed on the gold surface. Self-assembled

monolayers (SAMs) are ordered molecular assemblies formed by the adsorption of

molecules with a specific affinity to a substrate (Fig. 1a). SAMs of �,�-bisfunctionalized

aromatic molecules on gold are a subject of increasing interest as they are robust and

highly stable under mild conditions. Thiols adsorb on gold via gold-thiolate covalent

bond formation. The terminal groups that are exposed to the surface determine the

interfacial properties of the layers. In order to control the surface properties of a SAM, a

variety of functional groups can be introduced.

SAMs with a specific end group pointing towards the ambient can be prepared by two

ways. The first method involves the direct self-assembly of the appropriate functionalized

thiol in a single step. The second route involves the self-assembly of a less reactive

bifunctional thiol followed by a subsequent chemical modification to the desired

functionality. The attachment of functional groups by surface reactions can be carried out

either in vapour phase or in solution phase. Many routine organic reactions have been

carried out on SAM surfaces [1-5]. Some of the reactions that work well in solution

appear to be difficult to perform on surfaces showing that solution chemistry widely

differs from surface chemistry. The presence of reactive thiol functional group at the

SAM-ambient interface in the SAMs made from dithiols offer the possibility to study the

reactions and interactions of such films with external reagents. In particular the

fabrication of thin metallic films on dithiol SAMs with free SH groups at the SAM-

ambient interface is important in organic electronic devices [6].

The main objectives of this work are the following: (a) to prepare thiol-terminated SAM

surfaces, (b) to study chemical reactions namely the conversion of thioester to thiol on

SAM surfaces and (c) to demonstrate the efficient use of organometallic chemical vapour

deposition (OMCVD) for metallization of SAMs. Experiments with thiol-functionalized

surfaces were mainly pursued with regard to the availability of the free thiol groups at the

4

SAM-ambient interface that can act as a suitable platform to perform metal deposition

reactions. The thiol molecules chosen for the present study are the following:

terphenyldimethyldithiol (TPDMT) and biphenyldimethyldithiol (deprotected BPDMAc-

1).The molecular structures are given in Figure 1.

(b)(a) (b)(a)

Figure 1: (a) Schematic of SAM and (b) structure of the molecules used in this study.

Terphenyldimethyldithiol is an oligophenyl dithiol molecule with two reactive thiol

functional groups. The SAMs formed from them are well ordered, highly oriented and

densely packed [7]. The TPDMT SAMs are also found to possess high resistance to

ionizing radiation [8]. Biphenyldimethyldithiol SAMs also belongs to the class of

oligophenyl dithiols. The preparation of high quality TPDMT SAMs by the

straightforward approach proves to be successful whereas the SAMs with a short

oligophenyl backbone (biphenyl) results in the formation of loops or bridge like

constructions [7]. SAMs of biphenyldimethyldithiol with a high degree of molecular

orientation was fabricated from its monoacylated derivative [9]. In the present study, the

first step is to prepare TPDMT and deprotected BPDMAc-1 SAM surfaces with thiol

termination. The next step is to deposit palladium on these thiol-terminated SAMs. The

allylcyclopentadienylpalladium [Cp(allyl)Pd] has been chosen as the precursor for the

deposition of palladium metal. The CVD of metals has significant advantages over

thermal evaporation methods. Palladium has many useful characteristics including

catalytic properties [10]. In this work, Cp(allyl)Pd was chosen for CVD as it is an ideal

precursor (high volatility and easy and high-yield preparation). In this work, various

5

spectroscopic techniques, including infrared reflection absorption spectroscopy (IRRAS),

X-ray photoelectron spectroscopy (XPS) and near edge X-ray absorption fine structure

(NEXAFS) spectroscopy have been used for the characterization purposes.

In spite of a lot of work that has been done on the chemical modifications of SAM

surfaces, a clear understanding of the difference in the reactivity of different surfaces is

lacking. Hence, it is worth putting efforts into the investigation of the reactivity of

organic surfaces. Many open questions on the reactivity of the organic surfaces have been

addressed in this thesis. How does the kinetics of the surface reaction differ from that in

the corresponding solution? Why is the reactivity of a thioester with a base significantly

delayed on the surface? How does the reaction between Cp(allyl)Pd and a thiol group

tethered to the surface proceed? What happens to the monolayer structure in the presence

of catalytically active metal particles? The answers to these questions are discussed in the

coming chapters.

This thesis is organized as follows: An overview of the self-assembled monolayers

(SAMs) and the idea of chemical modifications of the organic surfaces exposed by the

SAM including metal deposition on organic surfaces are given in Chapter 1. The sample

preparation and the analytical tools used in the present study are described in Chapter 2.

The preparation and characterization of the different thiol terminated surfaces are

discussed in Chapter 3. The kinetics of the deacylation reaction (-SCOCH3 to -SH) on a

thio-acetate terminated organic surface has been described in Chapter 4. The

metallization of thiol-terminated surfaces using a palladium precursor is discussed in

Chapter 5. Finally, the results are summarized in Chapter 6.

1.2. Surfaces Atoms or molecules at a surface experience a different environment from those in the

bulk. The effect of having no net force at the surface is that the whole surface region is at

a relatively high energy compared with the bulk. The binding of adsorbates is strongly

favored at the surface, either by the formation of chemical bonds (chemisorption) or by

weak van der Waals type interactions causing physical adsorption (physisorption) [11].

The adsorption of organic molecules on metals and metal oxides alters the interfacial

properties by lowering the free energy of the interface between the metal or metal oxide

6

and the ambient environment. Many chemical processes (such as corrosion and

heterogeneous catalysis) take place at the surface of solids. Organic materials (for

example, thiols and disulphides) adsorbed can resist corrosion, decrease the reactivity of

the surface atoms, or act as an electrically insulating film [12]. An understanding of

interactions at organic surfaces and interfaces is vital to the development of many

technologies like sensors [13], device reliability studies [14], and biological interfaces

[10].

1.3. Organic thin films The research on organic thin films has fairly old roots. In the eighteenth century,

Benjamin Franklin observed the spontaneous spreading of oil on the surface of a pond

[15]. In the nineteenth century, Agnes Pockles and Lord Rayleigh performed studies at

the air-water interface [16]. Irving Langmuir investigated monolayers of amphiphilic

molecules on the water surface [17] and Katherine Blodgett did the first study on the

deposition of long chain fatty acids on solid substrates [18]. Zisman conducted the first

systematic studies related to SAMs of primary aliphatic amines and monocarboxylic

acids on platinum and pyrex substrates [19]. In these earlier studies, the macroscopic

properties (such as surface tension and wetting properties) are explored largely when

compared to the processes at molecular level due to the lack of appropriate tools. With

the spectroscopic and microscopic tools available today, one can attempt to correlate

macroscopic and microscopic properties. There are different ways for the preparation of

organic thin films [20]. Langmuir films are formed by spreading amphiphilic molecules

on a liquid surface. Langmuir-Blodgett (LB) films are built-up monolayer assemblies

prepared by transferring Langmuir films (floating monolayer) onto a solid substrate [21].

The growth of organic thin films in ultrahigh vacuum is referred to as organic molecular

beam deposition or organic molecular beam epitaxy and has an advantage over other

methods in the purity of films formed [22, 23]. Self-assembled monolayers are another

class of organic thin films that can be from solution or from gas-phase. The research

work described within this thesis focuses completely on SAMs and the following is a

brief introduction to SAMs.

7

1.4. Self-assembled monolayers (SAMs) Self-assembly processes are common in nature. Examples include formation of lipid

bilayers, pairing of bases (adenine - thymine and cytosine - guanine), and folding of

proteins. According to Whitesides et al., self assembly are processes that involve pre-

existing components (separate or distinct parts of a disordered structure), are reversible,

and can be controlled by proper design of the components [24]. The process of self-

assembly is driven by both, specific molecular interactions and the drive to minimize the

energy of interaction between molecules. There are two types of self-assembly: static and

dynamic. Static self-assembly involves systems at equilibrium and do not dissipate

energy. In dynamic self-assembly, the formation of ordered state requires the dissipation

of energy. Examples for dynamic self-assembly include galaxies, solar systems, weather

patterns, swarms (ants) and schools (fish). SAMs belongs to the class of systems which

undergo static self-assembly [24].

Self-assembled monolayers (SAMs) are ordered molecular assemblies formed on a solid

substrate by spontaneous organization of molecules [25]. A self-assembling molecule is

defined by three chemical entities (Fig. 2), each of which plays an important role in the

assembly process [26].

Figure 2: Schematic view of SAM.

The first part is the surface-active head group which renders the chemisorption on the

substrate surface. The apparent pinning of the head group to a specific site through a

chemical bond (covalent or ionic) results from strong substrate-molecular interaction.

The second part is the spacer group. The spacer group can be an alkyl chain or an

aromatic backbone. The forces that come into play in simple alkyl molecules and

8

molecules containing polar aromatic groups are van der Waals interactions and

electrostatic interactions, respectively. The third part is the end group. This end group can

be of any desired functionality. The properties of this terminal group define the surface

properties of the assembled monolayer. The macroscopic properties like wettability,

biocompatibility and adhesion of the groups surface can be altered by changing the end

functional groups of molecules that form SAMs [27]. The interplay between the three

components within the molecule determines the order and stability of the final assembled

monolayer.

SAMs can be formed on different substrates like metals, semiconductors and oxides [28].

There are a number of combinations of headgroups and substrates used in the formation

of SAMs. Organic acids on metal oxides [29], alcohols, amines, and isonitriles on Pt,

alkylsilane derivatives on hydroxylated surfaces [25], dithiols, thioesters, dialkyl sulfides,

dialkyl disulfides, thiophenols, mercaptopyridines [30], mercaptoanilines, thiophenes,

cysteines, xanthates, thiocarbamates, thioureas and mercaptoimidazoles on Au, and

alkanethiols on metals such as Au, Ag, Pt, Pd, Hg and Cu, and nonmetals such as GaAs,

InP and InSn oxide [25] are some examples of adsorbate-substrate pairs commonly used

to generate SAMs.

1.5. Thiols on Au(111) Self-assembly of alkanethiols on gold was first reported earlier in 1983 by Ralph G.

Nuzzo and David L. Allara, who described the formation of organized monolayers of

alkyl disulfides and alkanethiols on gold [31]. Since their discovery, SAMs on gold have

been created from many sulfur-containing molecules including alkanethiols, aromatic

thiols, dialkyl disulfides, and dialkyl sulfides. Thiol molecules are good nucleophiles and

bind via strong S-Au interactions. Novel monolayer structures can be obtained using gold

substrates and simple thiol deposition procedures. Thiols are also used to protect metal

nanoclusters and the resulting monolayer protected nanoclusters (MPC) exhibit a great

stability [32].

9

1.5.1. SAM - Formation kinetics

Self-assembled monolayers can be formed from solution or from vapour phase. SAMs

investigated in this work are prepared from solution phase. For most alkanethiols, a

monolayer is formed after just a few minutes of immersion of the substrate into the

corresponding alkanethiol solution. The initial driving force for the assembly is the

chemical affinity between the adsorbates and the substrate. Once the monolayer is

formed, the layer still goes through changes as more alkanethiols pack into the layer and

the molecules rearrange to their optimal configuration. This healing of the monolayer can

take hours to days and will lead to a technically superior monolayer. The amount of time

required to obtain a given level of order within a monolayer will depend on the initial

solution concentration, the temperature, and the characteristics of the alkanethiols being

used. For most monolayers, immersion times of 1 to 2 days will result in an equilibrium

state, where the majority of the molecules are arranged in their final, optimal

configuration [20]. The schematic mechanism for the self-assembly of thiols on Au is

shown in Figure 3.The initial step is the adsorption of molecules onto the substrate and

formation of a lying-down phase or striped phase. The next step is the transition from

lying down to standing-up phase.

1 2 3 41 2 3 4

Figure 3: Schematic sketch of the different steps in SAM formation.

(1) Initial adsorption. (2) Striped phase or lying-down phase. (3) Transition from lying-

down to standing-up phase. (4) Formation of a complete SAM.

10

1.5.2. SAM - Formation mechanism

The adsorption of thiols and disulphides on clean gold gives monolayers through the

formation of gold-thiolate species. The reaction between thiols and gold surface is an

oxidative addition producing surface bound thiolates, followed by a reductive elimination

of the hydrogen (equation 1).

Au + R-SH � Au-SR + ½ H2 (1)

In the case of disulphides, the adsorption reaction is an oxidative addition which proceeds

via the S-S bond cleavage (equation 2).

2Au + RS-SR � 2Au-SR (2)

XPS of the sulphur 2p region have shown that the adsorption of thiols and disulphides on

gold produces thiolate (RS-) species. Raman and infrared spectra show the absence of

strong bands of S-S and S-H (~ 2600 cm-1) vibration. These observations are also

confirmed by laser desorption Fourier transform mass spectrometry and electrochemistry

[33]. Monolayers can be formed from the gas phase in the complete absence of oxygen

and this suggests the evolution of molecular hydrogen. However, the possibility of

formation of water cannot be ruled out in the experiments involving the immersion of the

substrates in solution [28].

1.5.3. Au(111)

Gold is the standard substrate for SAM preparation. There are special properties of gold

that make it a good choice as a substrate for studying SAMs. Gold is a relatively inert

metal. It can be easily manipulated in air with lessened concern for contamination. It does

not react with most chemicals and it does not react with atmospheric oxygen [34, 35]. It

is the most stable metals in the group 8 elements. Few functional groups (thiols or

disulfides) bind strongly to gold and SAMs on gold system is the most studied [36, 37].

As thiols have a high affinity for gold, they also displace adventitious materials from the

surface readily. Gold is easy to obtain as a thin film. It is straightforward to prepare thin

films of gold by physical vapor deposition, sputtering, or electrodeposition. Gold is easy

to pattern by a combination of lithographic tools and chemical etchants. Thin films of

gold are good substrates for spectroscopic studies and are compatible with cells and

organisms. Cells can adhere and function on gold surfaces without evidence of toxicity

11

[10]. Although bulk gold is very popular for being chemically inert, gold nanoparticles

has proven to have catalytic applications [38]. The low index surfaces of gold are (111),

(100) and (110). The thermodynamically stable lowest energy surface of gold is Au(111)

[35]. The reconstructed surface of bare Au(111) is characterized by a 4.3% uniaxial

lateral contraction relative to the bulk layers [39]. The stacking arrangement alternates

between faulted and unfaulted regions delineated by rows of bridging Au atoms. A

(�3x23) surface unit cell is formed and to further reduce the surface energy the pairs form

hyperdomains characterized by alternating 60° bends which is known as herringbone

reconstruction [40]. The nearest neighbour distance in Au(111) is 2.884 Å (Au lattice

constant).

1.5.4. Structure of thiolates on gold

The surface reconstruction of clean Au(111) can be lifted by molecular adsorption.

Alkanethiols adopt commensurate crystalline lattice characterized by a c(4x2)

superlattice of a (�3x�3)R30° consistent with a hexagonal lattice indicating that the

Au(111) reconstruction is lifted in the presence of adsorbates. There are controversies

regarding the specific adsorption site(s) at which the alkanethiolate molecules are placed

on the Au(111) lattice. The different possible adsorption sites for an alkanethiolate

molecule on the Au(111) unit cell are hollow, bridge and atop [41, 42]. The stable

adsorption site was between bridge and fcc hollow sites. Other favourable sites are bridge

and atop sites. The sulphur atoms occupying the hollow sites between the gold atoms are

schematically shown in Fig. 4. The distance between adjacent S atoms is 4.995Å.

12

2.884 Å

4.995 Å

2.884 Å2.884 Å

4.995 Å4.995 Å

Figure 4: Alkanethiolate adlayer (filled circles) on the Au(111) surface (empty circles).

Adapted from reference [43].

The defects in gold-thiol monolayers include domain boundaries, tilt boundaries, stacking

faults, rotational boundaries, antiphase boundaries, Au vacancy islands and molecular

vacancies. Au vacancy islands are pit like defects which were observed in the domain

boundary network. Edinger et al. have shown that the pit depth was �2.5 Å, equal to the

single-atom step height of the Au(111) substrate [44]. This suggests that the pits are

defects in the Au surface layer and not defects in the alkanethiol layer. Poirier et al. have

found evidence for the existence of mobile Au-adatoms during monolayer assembly,

suggesting that the vacancy islands form by ejection of excess Au atom density from the

surface during relaxation of the Au(111) herringbone reconstruction [43].

1.6. Dithiols on Au(111) Dithiols are compounds in which both the headgroup and the endgroup are available for

chemical reactions. SAMs of dithiols are extensively studied in the context of molecular

electronics [20]. Organic dithiols are used as a spacer to bridge nanoparticles and

functionalized nanoparticles results in a well ordered 3D hybrid nano network [45].

SAMs of dithiols are more difficult to handle experimentally than monothiols, because

they oxidize readily. They can form multilayers via disulphide linkages or they can form

looped structures where both ends of the molecule bind to the surface. Oxidation of thiols

to disulphides is the major problem that arises when using dithiols. Because of their high

13

reactivity, thiols need to be protected. The protection of one of the thiol group in dithiols

by an acetyl group is believed to promote the formation of good quality SAMs, suppress

the dimerization, and prevent the multilayer formation [9]. The dithiol SAMs formed

from terphenyldimethyldithiol (TPDMT) and monoacylated biphenlydimethyldithiol

(BPDMAc-1) were investigated in this work.

1.7. Chemical reactions on self-assembled monolayers The reactivity of thioester terminated SAMs on Au(111) towards base hydrolysis and the

reactivity of aromatic dithiol SAMs towards an OMCVD precursor, Cp(ally)Pd has been

investigated in this research work. The discussion that follows includes an overview of

the different chemical reactions that have been studied earlier, followed by a more

detailed look at the deprotection reaction of dithiols.

In principle, chemical reactions such as nucleophilic substitution, free radical

halogenation, oxidation/reduction, etc. can be performed on well-ordered, densely packed

self-assembled monolayers using reaction schemes similar to those observed in the liquid

phase [46-51]. Though chemistry can be done on the organic surfaces exposed by SAMs,

it is quite different from that found in solution. Many organic reactions that work well in

solution appear to be difficult to perform on surfaces. The reactions known from bulk

chemistry cannot simply be transferred to interfaces [1]. Dubois et al. have shown that,

the hydrogen bonding reactions of the surface tethered carboxylic acid with various

amines are perturbed [28]. On the other hand, in solution, simple carboxylic acids rapidly

undergo proton transfer reactions with amines [28]. Furthermore, it is difficult to separate

the product from the byproducts and unreacted materials attached to the surface. This

problem becomes especially acute when monolayers are subjected to a number of

successive reaction steps [3]. The formation of surface-attached by-products at each step

leads to accumulation of defects. Surface amino groups can be easily converted to amides

by coupling with a carboxylic acid in a single step [3]. The SAMs with surface carboxyl

group can be converted to the acid chloride by using gaseous thionyl chloride. These

surfaces can then be converted to an amide linkage by further reaction with an amine

[52]. In this case, the reaction involves two steps.

14

There are several factors affecting the reactivity of functional groups in a self-assembled

monolayer.

(a) Solvent effects: The solvation of functional groups embedded in a monolayer may

differ from the bulk. The local concentration of dissolved reagents near the surface can

also be different. This is especially true for charged surfaces (such as COO-, NH3+) [5].

(b) Steric effects: Many of the reactions show diminished reactivity because of steric

constraints. For example, in a densely packed monolayer, bimolecular nucleophilic

substitution (SN2) reactions may not take place because there is no room for a backside

attack. Reactions requiring penetration of a reagent through a densely packed monolayer

or reactions with bulky transition state may be hindered at surfaces. On the other hand,

enforced favorable orientation or conformation of the reactive functional group in a

monolayer could result in significant acceleration of reaction rates in monolayers.

(c) Electronic and anchimeric (neighbouring group participation) effects: Functional

groups adjacent to the reaction center in the monolayer may affect reactivity through field

effects, hydrogen bonding, or anchimeric participation [5, 53, 54].

Activation of the SAM surfaces for increased reactivity: The functional groups on the

SAM surface can be activated by different approaches. The reactivity can be enhanced by

using a mixed SAM. A molecular component in a mixed SAM can be made shorter

compared to the molecule with the reactive functional group. Microcontact printing is

also another method of adsorbing two different molecules on a substrate. Thus by diluting

the SAMs, the reactivity can be accelerated. Other ways of activation includes the use of

external stimuli, such as electrochemical potentials [55], photoradiation and mechanical

disruption by the SFM probe tip. The activation process transforms the unreactive

functional groups into reactive ones for the subsequent chemical modification [10]. Wang

et al. has investigated the base hydrolysis of a dithiobis(succinimido undecanoate)

monolayer on Au(111) [56]. The rate of the complete transformation of the succinimidyl

terminus to the corresponding carboxylate moiety is approximately 1000 times slower

than the corresponding reaction in solution. The low rate of conversion is explained by

the steric hindrance and the slow surface reaction has been accelerated by the tip-assisted

base hydrolysis. The steric barrier in the SAM is disrupted by the SFM probe tip which

15

facilitates the access of hydroxide ions to the buried acyl carbons. Reactions induced or

affected by the AFM tip belong to a quite different type of reactions, where also catalytic

effects of the perturbing AFM tip have to be considered.

1.7.1. Deprotection strategy in dithiols

There are various approaches to the protection of -SH bond in dithiols [12]. For SAMs,

the thiols have been most commonly protected as thioesters [57, 58]. The protected thiol

has to be deprotected when other functionalities are introduced or modified. The use of

many common protecting groups is limited by the fact that strongly basic conditions are

required for their introduction and acidic or basic conditions are needed in the

deprotection step. Formation of the corresponding disulphide is an expected side reaction

when the thiol group is deprotected under strong basic conditions. The hydrolysis of

thioester by means of a base yields thiols. Bases which are commonly used for

deprotecting thioesters are ammonium hydroxide, sodium hydroxide, triethyl amine,

potassium carbonate and sodium carbonate. Tour et al. investigated the SAMs of rigid

�,�-dithiols which could form assemblies in which one thiols group binds to the surface

while the second thiols moiety projects upward at the exposed surface of the SAM. In situ

deprotection has been performed using NH4OH [59]. Shaporenko et al. have used the in

situ deprotection method using either NH4OH or triethylamine as the deprotection agent

for acetyl-protected biphenyl based dithiol derivatives [60]. Stirling and coworkers have

studied the base catalyzed hydrolysis of esters. It has been shown that the esters which

have the carbonyl function close to the monolayer surface hydrolyze more rapidly

compared to the esters with the carbonyl group buried deeply below the surface [61].

When the access of an external reagent is blocked, the reaction is thought to start at

defect sites and domain boundaries [62].

1.8. Metal deposition on SAMsThe OMCVD of palladium on dithiol SAMs has been studied in this work. The following

sections contain a brief overview on metal deposition on SAMs.

In general, when unreactive metals are deposited on inert SAMs, the deposited metal

diffuse through the SAM to the gold-sulphur interface whereas metals that are more

16

reactive will stick to SAMs with coordinating head groups to form organometallic

complexes. Deposition of metal on organic surfaces involves the reaction between the

end functional group and the deposited metal atoms, the nucleation process and growth

mode of the metal on the modified surface and the final configuration of the deposited

metal with regard to the underlying SAM. In the first step, the metal atoms impinge on

the SAM surface and metal islands are formed on top of the SAM (Fig. 5). Eventually the

deposited metal atoms penetrate into the SAM layer and diffuse to the SAM-substrate

interface. The organic molecules then form SAMs on the buried layer. Diffusion occurs

via defects in the film for example domain boundaries. Surface defects are favored

nucleation centers.

SAM

Gold (111)

Metal atoms Metal islandson top

Metal diffusing to the substrate

Metal buried below SAM

SMetal

H

SAM

Gold (111)Gold (111)

Metal atoms Metal islandson top

Metal diffusing to the substrate

Metal buried below SAM

SMetal

H

Figure 5: Schematic illustration of the deposited metal with regard to the underlying

SAM on the Au(111) surface.

There are several deposition methods available for depositing metals on SAMs that

includes thermal evaporation, atomic layer deposition, physical vapour deposition,

chemical vapour deposition and electrochemical deposition. The following is a brief

description on the different deposition methods. Table 1 lists examples for different

deposition methods. More details can be found in the references quoted. Detailed

literature survey of metallization of SAMs is given in Chapter 5.

Physical vapor deposition: The physical vapor deposition technique is based on the

formation of vapor of the substance to be deposited as a thin film. Vapor deposition of

17

metals onto organothiolate self-assembled monolayers on Au(111) is a common approach

to prepare a metal/SAM/Au sandwich structure [63]. The amount of deposited metal is

commonly monitored by a quartz crystal microbalance. The metal to be deposited is

produced from a vaporization source in an ultra-high vacuum chamber. A variety of

metals can be deposited by this method.

Atomic layer deposition: Atomic layer deposition (ALD) is a process for depositing thin

films by exposing the surface to vapors of two or more reactants [64]. First, the substrate

surface is exposed to one precursor and the excess reactant is pumped away. Then the

system is exposed to the second reactant and the excess is pumped away. This cycle of

steps is repeated to form monolayers of thin films. The surface reactions must be

complementary and self-limiting. The thickness of the layers formed is reproducible as

the thickness depends on the number of reaction cycles. The method is also known as

atomic layer epitaxy.

Chemical vapor deposition: Chemical vapor deposition is a chemical process used for

the deposition of thin films of various materials. The process involves the condensation

of a compound or compounds from the gas phase on to a substrate where a chemical

reaction occurs to produce a solid deposit [65, 66]. The process is shown schematically in

Figure 6.

Figure 6: Schematic representation of a CVD process.

The temperature in the reaction part of the system is generally higher than the vapour

source but considerably below the melting temperature of the deposit. Chemical vapour

deposition of metals can be achieved via thermal decomposition or chemical reduction.

18

Examples for thermal decomposition (equation 3) and chemical reduction (equation 4)

are shown below.

Ni(CO)4(g) � Ni(s) + 2CO2(g) (3)

WF6(g) + 3H2(g) � W(s) + 6HF(g) (4)

In general, the CVD process involves the following key steps: (1) Generation of the

active gaseous reactant species and mass transport of the reactant in the bulk, (2) gaseous

reactants undergo gas phase reactions forming intermediate species, (3) mass transport to

the surface, (4) adsorption on the surface, (5) surface reactions, (6) surface migration, (7)

nucleation and growth of the film, (8) desorption of by-products and (9) mass transport of

by-products in bulk. The unreacted gaseous precursors and by-products will be

transported away from the deposition chamber [65]. Figure 7 shows a schematic

illustration of the reaction mechanism of a CVD process.

Figure 7: Mechanism of chemical vapour deposition.

There are different forms of CVD which can be classified by operating pressures

(atmospheric pressure CVD, low pressure CVD and UHVCVD) or by the energy sources

(thermal CVD, plasma enhanced CVD, microwave plasma assisted CVD, laser assisted

CVD, hot filament CVD, photo CVD, acoustic CVD, metal organic CVD and diamond

CVD).

Metal organic chemical vapor deposition: MOCVD is also referred to as

organometallic vapor phase epitaxy (OMVPE). The growth process occurs via the

19

pyrolysis of the organometallic compounds. The growth process constitutes the

transportation of one or more film constituents to the reaction zone in the form of metal

alkyls and the second constituent are transported as hydrides. The reactions are simple

and the reactants taking part in the reaction are gaseous in nature [67]. Highly pure metal

films have been achieved using special precursors [68]. Examples include M(�3C3H5)3, M

= Rh or Ir, (�5-CH3C5H4)2Ni, Pd(�3CH2CHCH2)2, Pd(�3-CH2C(CH3)CH2)2, (�5-C5H5)-

PtMe3, (�5-CH3C5H4)PtMe3 and �5-C5H5CuPMe3.

Electrochemical deposition: This approach combines elements of currentless and

electrodeposition, and it starts with the complexation between metal ion and the

functional end group of the thiol molecule. This is simply done by immersing the SAM-

covered gold electrode into a solution that contains the metal ions. The gold electrode

with its metal-ion loaded SAM is carefully rinsed and transferred to an electrochemical

cell that contains the supporting electrolyte only, i.e., is free of metal ions. In a

subsequent potential scan in negative direction, the complexed metal ions are reduced

and electrodeposited onto the SAM [69].

Deposition of metals can also be performed in solution. Silver-dithiol-gold multilayer

structures were obtained by using the silver ions from an ethanolic solution of silver

nitrate [70]. Titanium oxide thin films were deposited on a sulphonate functionalized

SAM using TiCl4 solution [71]. Jin et al. have studied the specific adsorption of gold

nanoparticles on the -SH terminated BPDMT molecules in a binary SAM of BPDMT and

octadecane thiol [72]. Cadmium sulfide nanocrystals were attached to metal surfaces

using dithiol SAMs as bridge compounds [73].

20

Table 1: Examples for different metal deposition methods on organic thin films.

Molecule / Substrate Metal Ref.

Thermal evaporation

octadecanethiol, hexanedithiol on Au Ag [74, 75]

octanethiol & HS(CH2)nSH on Au Au [76]

HS(CH2)15X on Au (X = -COOH,-COOCH3 & -CH3) Au, Ti, K [77]

benzenedimethanethiol on Au Au [78, 79]

dodecanethiol & mercaptoundecanoic acid on Au Au [80]

dimercapto-quaterphenyl, -terphenyl, -biphenyl,

monomercapto-terphenyl & hexadecanethiol on Au Au, Al, Ti [81]

HS(CH2)16OCH3 on Au Ti, Ca [82]

HS(CH2)nCOOH on Au Cu [83]

fluorene, biphenyl, nitrobiphenyl on carbon Cu [84]

mercaptohexadecanoate on Au Cr [85]

polyimide films on Pt(111) or Si(100) Au, Ag,

Cu,Pd,Cr,K [86]

phenyltricosanethiol on Au Cr [87]

methoxyhexadecanethiol on Au Mg [88]

TPDMT, BPDMT on Au Ni [6, 89]

Atomic layer deposition

tetrasulphide on SiO2 Pd [90]

Pulsed laser deposition

decanethiol & octadecanethiol on Au Au, Pt, Pd [91]

Metal organic chemical vapor deposition

octadecyltrichlorosilane on TiN, ITO, SiO2, Al2O3,

sapphire and glass Pt, Pd, Cu [92, 93]

Organometallic chemical vapor deposition

biphenyldithiol, biphenylthiol,

mercaptoundecanol & dodecanethiol on Ag Pd [94]

21

Electrochemical deposition

mercaptopyridine, dithiodipyridine on Au Pd, Pt, Rh [95-97]

benzenedimethanethiol on Au Pt [98, 99]

coadsorption of dodecanethiol and a thiolated

derivative of tetraphenylporphyrin on gold Pt [100]

mercaptoethanol, hexanedithiol, ethanethiol,

hexanethiol on Au Ag

[101,

102]

dodecanethiol on Au Rh [103]

(mercaptopropyl)trimethoxysilane on Ag Tl, Pb, Cd [104]

octanethiol, dodecanethiol on Au Cu [105]

aminothiol on Au Co [106]

aminopropyltriethoxysilane on hydroxylated Si Cu [107,

108]

22

1.9. Palladium precursor A major part of the work described in this thesis focuses on the palladium deposition on

SAMs of dithiols using the precursor Cp(allyl)Pd. The following section focuses on

palladium thin film deposition using different Pd precursors followed by a detailed

account on Cp(allyl)Pd.

Palladium is a steel-white, ductile metallic element which is commonly used in

microelectronic devices such as capacitors, resistors, and contacts [109]. It exists in three

states: Pd0, Pd2+ and Pd4+. It can be evaporated onto surfaces using standard techniques.

Palladium reacts reversibly with hydrogen gas to form PdHx. It can react readily with

thiols. SAM of alkanethiolates can be formed on the surface of palladium [110]. Yang et

al. demonstrated the reaction involving Pd2+ ion and alkanethiol ligands through the

synthesis of a Pd-thiolate complex, [Pd(SC12H25)2]6 [111]. Pd is catalytically active and is

used in many hydrogenation reactions [112].

Palladium thin-film deposition was carried out from the known precursors like Pd(allyl)2,

[Pd(Cp)2], Cp(allyl)Pd, Pd(CH3allyl)2, allyl(�-diketonato)Pd, Pd(hfac)(allyl), Pd(hfac)2

and Pd(acac)2 [113-117]. The use of a reactive gas such as dihydrogen led to unexpected

low temperatures of deposition (30-60°C). Catalytic selective hydrogenation reaction of

allylpalladium complexes with H2 has been studied by Carturan et al. [118]. The allyl

groups usually can be removed by hydrogenation. This reaction proceeds readily with the

allyl compounds of nickel, palladium, and platinum when treated with dihydrogen gas at

normal pressure. The products are the free metals and propane. The cyclopentadienyl

(C5H5) and allyl (C3H5) groups are two of the most important ligands in inorganic and

organometallic chemistry [119]. Allyl-transition metal systems can be compared with

cyclopentadienyl-transition metal systems. Cyclopentadienyl metal systems (except

ferrocene) have low catalytic activities because of significant stabilities. Allyl metal

systems are not very stable and as a result the complexes have high catalytic activity

[120].

23

1.9.1. Cyclopentadienyl(allyl)palladium

Cp(allyl)Pd is a labile organopalladium compound useful for preparations of various Pd0

complexes. B.L.Shaw was the first to synthesize Cp(allyl)Pd [121]. It forms red

needlelike crystals and the melting point is around 60 °C. It is diamagnetic and has a low

dipole moment. In the solid state it is fairly stable, although it decomposes gradually at

room temperature to give a black solid. It is an easily sublimed compound with

unpleasant odour [122].

Figure 8: Synthesis of Cp(allyl)Pd precursor.

Preparation of cyclopentadienyl(allyl)palladium: The Cp(allyl)Pd complex (2) was

prepared by the treatment of the bridged complex allyl palladium chloride (1) with

cyclopentadienyl sodium in tetrahydrofuran (Fig. 8). The allyl palladium chloride (1) was

prepared by the reaction of sodium chloropalladate with allyl chloride [123]. All the

cyclopentadienyl and all the allylic carbons are equidistant from the central metal atom

(2.25 and 2.05 Å, respectively). The palladium atom forms two equivalent pi-bonds with

the delocalized one and a half bonds of the allyl group and this interaction is substantially

stronger than with the cyclopentadienyl ring [124, 125]. Particular interest is evoked in

this compound because of its peculiar behavior in chemical reactions. The

cyclopentadienyl ligand is easily eliminated under the influence of a series of

electrophilic and nucleophilic agents, whereas the link with the �-allyl group is stable

even in comparatively severe conditions [126]. The thermal decomposition of

cyclopentadienyl(allyl)palladium is an autocatalytic process [127]. In the first step,

metallic Pd is formed and the liberated Pd0 catalyzes the subsequent process. The allyl

24

radical decomposes to propane, propylene, biallyl and benzene. The cyclopentadienyl

radical decomposes to cyclopentadiene and bicyclopentadiene. Thermolysis of the

Cp(allyl)Pd precursor in the absence of any reactive gas was reported to give a mixture of

propene, cyclopentadiene and traces of hexadiene [128]. Cp(allyl)Pd reacts rapidly with

hydrogen at room temperature to form palladium crystallites [129]. The sandwich

structure of the cyclopentadienyl and the allyl ligands was shown by nuclear magnetic

resonance and IR spectra [130, 131]. The photoelectron spectra (between 21.2 and 60 eV)

of Cp(allyl)Pd has been recorded [132]. The mass spectral data shows evidence for the

relative weakness of the bonding of cyclopentadienyl ring to palladium [133].

Cp(allyl)Pd is a suitable MOCVD precursor because of the properties like low melting

point, low sublimation point, good stability to moisture and air, long shelf life at -10°C,

low decomposition temperature and easy preparation [134-136]. The complex is usually

stable but as often occurs with cyclopentadienyl precursors, the deposited palladium films

contained carbon impurities [116, 137]. High purity Pd films has been obtained by

plasma enhanced CVD of Cp(allyl)Pd [123]. Metallic Pd coatings can be obtained both

by pyrolysis and photolysis of Cp(allyl)Pd [138, 139]. Electron induced decomposition

and subsequent deposition of Cp(allyl)Pd on silicon substrates has been studied by Saulys

et al [140]. Dossi et al. loaded the Pd metal inside zeolite cages by reduction of

Cp(allyl)Pd with H2 gas [141, 142]. The palladium nanoparticles synthesized by the

MOCVD of Cp(allyl)Pd supported on carbon nanofibers [143] and silica [144] show

catalytic activity. Mehnert et al. have used Cp(allyl)Pd to prepare palladium grafted

mesoporous materials by vapor grafting and this catalyst system provides remarkable

activity in Heck carbon–carbon coupling reactions [145, 146].

25

2. Sample preparation and analytical techniques

This chapter describes the experimental details including the sample preparation and

provides a brief description of the analytical techniques used in this work.

2.1. Chemicals The following reagents were used without further purification. Ethanol (Merck),

dichloromethane (Merck), chloroform (Merck) and sodium hydroxide (J. T. Baker). The

thiols, TPDMT and BPDMAc-1 [7, 9] and the organometallic precursor, Cp(allyl)Pd

[121, 122] were synthesized according to the reported procedures. The palladium

precursor and BPDMAc-1 has been provided by Prof. Roland A. Fischer, Anorganische

Chemie II, Ruhr-Universität Bochum. TPDMT has been provided by Prof. Andreas

Terfort, Fachbereich Chemie, Philipps-Universität Marburg.

2.2. Preparation of the gold substrates The gold surfaces were prepared by slow thermal evaporation of pure gold onto a clean

flat surface in ultrahigh vacuum. For the IRRAS, NEXAFS and XPS measurements,

polycrystalline gold substrates were prepared by evaporating 5 nm of titanium with a rate

of 0.5 nm s-1 (99.8%, Chempur) and subsequently 100 nm of gold with a rate of 2 nm s-1

(99.995%, Chempur) onto polished (100) oriented silicon wafers (Wacker) in an

evaporation chamber operated at a base pressure of 10-7 mbar. A thin layer of titanium is

used to promote the adhesion between gold and the silicon substrate. These substrates

were stored in vacuum desiccator until the adsorption experiments were carried out. For

the microscopic measurements, the substrates were prepared by evaporating 150 nm of

gold onto freshly cleaved mica, which had previously been heated to 500 K for 2 days in

the evaporation chamber. After the metal evaporation, the substrates were allowed to

slowly cool down. The substrates were stored in the evaporation chamber and flame

annealed in a propane/oxygen flame immediately before the adsorption experiments were

carried out. This procedure yields gold substrates with very large, atomically flat terraces

exhibiting a (111) surface.

26

When a gold surface is exposed to air, it will be coated with a layer of adventitious

hydrocarbon. The gold surfaces are always rinsed with ethanol before the SAM

preparation. Standard alkanethiols can easily remove the surface contaminants such as

oils, other metals and polymers like polydimethylsiloxane. In this work, freshly prepared

gold surfaces have been used for monolayer formation.

2.3. Preparation of SAMs A typical protocol is described for preparing self-assembled monolayers. Fresh gold

substrates are immersed in to a solution of the appropriate thiol for a period of several

hours to few days. This general protocol is appropriate for most of the thiols, but some

compounds require modifications to the protocol to obtain well ordered SAMs. The most

common solvent is ethanol. Other solvents such as water, dichloromethane, chloroform

and hexane can also be used. Diluted solutions of thiols (mM to μM) are generally used.

The gold substrates were removed from the solution after the incubation time and rinsed

thoroughly with the solvent to remove physisorbed overlayers. Finally, the substrates

were dried in a stream of nitrogen gas. Glass bottles are used and only one sample is

prepared from a bottle in order to prevent substrates from covering or scratching each

other’s surfaces. The labwares used in SAM preparation should be free from

contaminations. The apparatuses to be cleaned are immersed in a base bath [1 kg of KOH

in 15 litres of H2O and 10 litres of isopropanol] for 24 h followed by the immersion in an

acid bath [0.5% HNO3 in 25 litres of H2O] for 24 h. Between the immersion steps

thorough rinsing with water followed by ethanol is performed. Finally, the equipments

are stored in an oven at 60 °C.

2.4. Deposition of Cp(allyl)Pd on SAMs The palladium precursor, [(�3-allyl)Pd(�5-Cp)] was prepared according to the previously

reported procedures and stored at low (-10 °C) temperatures in an inert gas atmosphere

[122]. A schlenk flask has been used for the metal deposition experiment (Fig. 9). The

SAMs were exposed to the precursor (~ 7 - 10 mg) in an Ar atmosphere. The exposure

time was varied between 1 and 24 hours. For the reduction experiments, hydrogen gas

27

has been used. In all the experiments performed, the precursor sublimes without

decomposition.

SAM on Au(111) PrecursorSAM on Au(111) Precursor Figure 9: Schlenk apparatus used for metal deposition.

2.5. Spectroscopic methods used in this work The main surface science techniques employed in this work are infrared reflection

absorption spectroscopy, X-ray photoelectron spectroscopy and near edge X-ray

absorption fine structure spectroscopy. The principles underlying the operation of the

experimental tools are explained. Beside these methods other techniques, namely,

secondary electron microscopy and atomic force microscopy are also used.

2.5.1. X-ray Photoelectron Spectroscopy

Electron spectroscopy is a powerful technique for surface characterization because the

mean free path of electrons in solids is very short and all the signals given by this

technique can give information about the surface [147]. Electron spectroscopic methods

include photoelectron spectroscopy (PES), auger electron spectroscopy (AES), electron

energy loss spectroscopy (EELS) and inelastic electron tunneling spectroscopy (IETS)

[148]. Photoelectron spectroscopy is a technique which frequently involves the

measurement of the kinetic energy of electrons photoionized from a probe of interest by a

monoenergetic photon beam. A photoelectron spectrum is a plot of the number of

electrons emitted versus their kinetic energy. PES has been divided into two areas,

28

depending on the energy of the photon beam used. X-ray photoelectron spectroscopy

(XPS) uses a relatively high energy photon source and involves the ionization of core

electrons. Ultraviolet photoelectron spectroscopy (UPS) uses low energy sources and

involves ionization of valence electrons. Al K� (1486.6 eV) and Mg K� (1253.6 eV) are

the widely used photon sources for XPS. The UPS source is usually the He I and He II

lines at 21.22 eV and 40.80 eV respectively. XPS gives information about non-interacting

core electrons and UPS gives information about chemical bonding valence electrons.

XPS was developed by K.Siegbahn and he was awarded the Nobel Prize for Physics in

1981. The phenomenon is based on the photoelectric effect outlined by Einstein in 1905.

XPS, also called electron spectroscopy for chemical analysis (ESCA), works by

irradiating a sample material with monoenergetic soft X-rays causing electrons to be

ejected ( M h M e� � � � ). Identification of the elements in the sample can be made

directly from the kinetic energies of these ejected photoelectrons. The relative

concentrations of elements can be determined from the photoelectron intensities.

The relationship governing the interaction of a photon with a core level is

KE h BE� � where, KE = Kinetic Energy of ejected photoelectron; h� =

characteristic energy of the X-ray photon; BE = Binding Energy of the atomic orbital

from which the electron originates and � = spectrometer work function. The X-ray

induced electron emission is illustrated in Figure 10.

29

Figure 10: X-ray induced electron emission process.

XPS is not sensitive to hydrogen and helium (H and He have no core electrons) but can

detect all other elements. The XPS technique is surface specific due to the short range of

the photoelectrons that are excited from the solid. The energy of the photoelectrons

leaving the sample is determined using a concentric hemispherical analyzer and this gives

a spectrum with a series of photoelectron peaks. The binding energy of the peaks is

characteristic of each element. The peak areas can be used to determine the composition

of the materials on the surface. The shape of each peak and binding energy can be

slightly altered by the chemical state of the emitting atom. Hence, XPS can provide

chemical bonding information as well. XPS is the most common technique for the

characterization of the chemical composition of surfaces [149-153].

XPS is a widely used experimental tool for the characterization of the molecular structure

of organic films [154]. XPS has been used to characterize the film-substrate bonding. The

terminal groups at the SAM/vacuum interface can be differentiated from the groups lying

on the SAM/gold substrate interface by angular dependent XPS. The typical XPS survey

spectra of BPDMAc-1 SAM on Au(111) is displayed in Figure 11.

30

800 700 600 500 400 300 200 100 0

0

30000

60000

90000

S 2p

Au 4f

Au 4d

Au 4s

Au 4p Inte

nsity

(Cps

)

Binding Energy (eV)

C 1s

Figure 11: XP spectra of BPDMAc-1 SAM on Au(111).

The peaks corresponding to the gold substrate can be easily identified. The elements like

carbon, oxygen and sulphur present in the SAM molecule can also be observed. The

assignment of the photoelectron lines (binding energies, BE) to the corresponding species

is given in Table 2.

Table 2: Assignment of the photoelectron lines.

BE (eV) Assignment BE (eV) Assignment763 Au 4s 165 S 2p1/2 643 Au 4p1/2 164 S 2p3/2 547 Au 4p3/2 110 Au 5s 532 O 1s 88 Au 4f5/2 353 Au 4d3/2 84 Au 4f7/2 335 Au 4d5/2 74 Au 5p1/2 285 C 1s 57 Au 5p3/2

XPS can be used to determine the thickness of the self-assembled monolayers. The

intensities of C 1s and Au 4f7/2 lines have been used to estimate the thickness of the

monolayers. A SAM of known thickness is used as a reference system. The film

thickness is given by the following equation where dreference is the thickness of a known

SAM and dsample is the thickness of the SAM under investigation.

31

� �

� �

sample reference

C1sC AuAu 4f

C1s sample referenceAu 4f

Au C

d d1 exp expI (sample)II d d(reference) exp 1 expI

� � � �� � � �� �� �� � � � � � � �

� � � �� �� � � �

(5)

IC1s and IAu4f are the measured intensities of C 1s and Au 4f7/2 lines. The escape depths

(�) of the electrons for the different kinetic energies were calculated using the NIST

database for inelastic mean free path. �Au = 16 Å at a kinetic energy of 314 eV and �C = 9

Å at a kinetic energy of 115 eV [155].

2.5.2. Near Edge X-ray Absorption Fine Structure Spectroscopy

The fundamental phenomenon underlying NEXAFS is the absorption of an X-ray photon

by a core level of an atom in a solid and the consequent emission of a photoelectron. The

structures near the ionization edge are called XANES (X-ray Absorption Near edge

Structure) and the structures beyond ~ 50 eV above the ionization edge are called EXAFS

(Extended X-ray Absorption Fine Structure). The principle of NEXAFS technique is

depicted schematically in Figure 12. By absorption of a X-ray photon, a core electron is

excited into an unoccupied molecular orbital. The absorption process results in a

photoelectron and a core hole. An electron subsequently fills the hole by either

fluorescent photon emission or Auger electron emission [156].

32

Figure 12: Principle of NEXAFS.

NEXAFS has particular application to chemisorbed molecules on surfaces [157, 158].

Information concerning the orientation of the molecule can be inferred from the

polarization dependence [159, 160]. The information on molecular orientation can be

derived from the experimental data. The intensity of the �* resonance (I) can be

monitored as a function of the X-ray incidence angle (�). The resulting dependence can

be evaluated according to the following equation, where A is a constant, P is a

polarization factor of the X-rays, and � is the average tilt angle of the molecular orbital.

� �� � � � �2 2 2P 1 1I( , ) = A 1+ 3cos 1 3cos 1 1 P sin3 2 2� �� � � � � �� � (6)

NEXAFS spectra are frequently dominated by intra-molecular resonances of � or �

symmetry. The energy, intensity and polarization dependence of these resonances can be

33

used to determine the orientation and intra molecular bond lengths of the molecule on the

surface. Figure 13 displays the NEXAFS spectra of dodecanethiol SAM and TPDMT

SAM. The NEXAFS data for the alkanethiol (C12SH) SAM is dominated by the R*

resonance at 288 eV [161] and the spectra for the aromatic thiol (TPDMT) SAM is

dominated by the intense �* resonance of the phenyl rings at 285 eV and 289 eV. Several

broad �* resonances at higher photon energies are observed for both the thiols.

285

289

288

280 285 290 295 300 305 310 315

0

1

2

3

Solid line - TPDMTDashed line - C12SH

Photon Energy (eV)

Nor

mal

ized

PEY

Figure 13: NEXAFS spectra for C12SH [161] and terphenyldimethyldithiol (TPDMT)

SAMs on gold surface.

NEXAFS can be recorded in different ways which include fluorescent yield (FY), partial

electron yield (PEY), total electron yield (TEY) and Auger electron yield (AEY) [162].

The FY detection requires an appropriate fluorescence detector. The electrons that

emerge from the outermost surface region are detected PEY method. PEY detection is

advantageous over TEY method, where all electrons that emerge from the surface are

detected. In AEY detection method only elastically scattered Auger electrons are

recorded.

34

2.5.3. Infrared Reflection Absorption Spectroscopy

The molecules vibrate and such vibrations can be observed by irradiating the molecules

with infrared light. Different functional groups in a molecule will adsorb IR photons with

specific energies, allowing IR to be used for functional group analysis. The infrared

spectrum is generally acquired using the FTIR technique [163]. Vibrations of molecules

on surfaces can also be investigated by using other methods like electron energy loss

spectroscopy (EELS), surface enhanced Raman spectroscopy (SERS) and surface

electromagnetic wave spectroscopy (SEW). A polyatomic molecule with n atoms has 3n

degrees of freedom. The internal degrees of freedom correspond to normal modes of

vibration. There are 3n-6 modes of vibration for non-linear molecules and 3n-5 modes of

vibration for linear molecules. The vibration of a simple diatomic molecule can be

described in terms of simple harmonic motion. This assumes that the chemical bond

joining the two atoms with atomic masses m1 and m2 acts like a Hooke’s law spring, with

a force constant (k). The vibration frequency () is given by:

1 k2

�� �

and the reduced mass (�) is defined by 1 2

1 2

m mm m

�� �

�.

The vibrational energy levels are given by Ev = (v + ½) h with v = 0, 1, 2,… where v is

the vibrational quantum number. The selection rule for a vibrational transition in the

simple harmonic oscillator is v 1� � � . In practice, the molecule does not always behave

like a simple harmonic oscillator and an anharmonicity results. Because of anharmonicity

the transitions corresponding to v 2� � � , �3, etc., are also observed in the IR spectra.

These are called overtones. The fundamental vibrational frequency (v = 0 to v = 1) is

highly intense and the overtones are of low intensity. The vibration may result in the

stretching and bending of the bonds. The various vibrational modes of H2O and CO2

molecules are shown in Figure 14.

35

Figure 14: Vibrational modes of H2O and CO2.

A molecule is infrared active only if the dipole moment of the molecule changes during

the vibration. IR spectroscopy is also possible on a surface, where the IR beam can be

either reflected off (IRRAS) or introduced via a crystal to give multiple reflections on the

back of a thin metal substrate (attenuated total reflection). The same principal (change in

the dipole moment) as IR in bulk, gas or liquid apply on surfaces. Additionally, the

vibrations which are perpendicular to the surface can only be detected [164]. The

requirements for RAIRS are (a) p-polarized radiation, (b) grazing angles of incidence and

(c) transition dipole arranged along surface normal [165-169]. The oscillating electric

vector of the p-polarized radiation is parallel to the plane of incidence and for the s-

polarized radiation; the electric vector is perpendicular to the plane of incidence. The s-

polarized light is canceled by reflection as it experiences a phase change of 180. The

reflection coefficient for metals is one. The resultant electric field parallel to the surface

is zero (Fig. 15). The p-polarized light is almost doubled by reflection. Only the

vibrations with component dynamic dipole moment aligned perpendicular to surface

plane can interact with (p-polarized) incident light.

36

Surface

E�p

E�s

Ep Es

Plane of incidence

(a)

Ex = 0Ez

-+

+

-

+

-

Ex-+ -

+

Ex will be cancelled outEz will be amplified

Metal Surface

E

Ex

Ez(b)

-180

-90

00 45 90

!

Angle of incidence in degrees

Ph

ase

chan

ge o

n re

flect

ion

in d

egre

es

""

(c)

Surface

E�p

E�s

Ep Es

Plane of incidence

(a)

Ex = 0Ez

-+

+

-

+

-

Ex-+ -

+

Ex will be cancelled outEz will be amplified

Metal Surface

E

Ex

Ez(b)

Ex = 0Ez

-+

+

-

+

-

Ex-+ -

+

Ex will be cancelled outEz will be amplified

Metal Surface

E

Ex

Ez

Ex = 0Ez

-+

+

-

+

-

Ex-+ -

+

Ex will be cancelled outEz will be amplified

Ex = 0Ez

--++

++

--

++

--

Ex-+ -

+Ex-+ -

Ex-+ -

+

Ex will be cancelled outEz will be amplified

Metal Surface

E

Ex

Ez

Metal Surface

E

Ex

Ez

Metal Surface

E

Ex

Ez(b)

-180

-90

00 45 90

!

Angle of incidence in degrees

Ph

ase

chan

ge o

n re

flect

ion

in d

egre

es

""

(c)

-180

-90

00 45 90

!

Angle of incidence in degrees

Ph

ase

chan

ge o

n re

flect

ion

in d

egre

es

""

(c)

Figure 15: (a) Electric vectors of the p- and s-components of radiation incident at a

metal surface. Reflected rays - primed vectors; incident rays-unprimed vectors. (b) The

image-charge effect - parallel dipole (EX) cancellation and perpendicular dipole (EZ)

enhancement. (c) Phase shift for light reflected from surface.

Adapted from reference [168].

37

Figure 16 displays an example for IRRAS of SAMs. The high frequency region (3000

cm-1 to 2800 cm-1) and the low frequency region (2500 cm-1 to 900 cm-1) of decanethiol

SAM on Au substrate are shown in Figure 16. The bands observed at 1382 cm-1 and 1461

cm-1 corresponds to the -CH3 and -CH2 symmetric bending vibration respectively. The -

CH2 symmetric and asymmetric stretching vibrations are observed at 2851 cm-1 and 2921

cm-1 respectively. The -CH3 symmetric and asymmetric stretching vibrations are

observed at 2879 cm-1 and 2966 cm-1 respectively. The negative bands at 2088 cm-1 and

2193 cm-1 correspond to the symmetric and asymmetric stretching of -CD2 (from

perdeuterated docosanethiol) respectively. The band at around 2360 cm-1 corresponds to

CO2 in the sample compartment of the IR spectrometer.

1382

1461

3000 2950 2900 2850 2800

2851

2879

2921

2937

2966

0.002

0.0002

Abs

orba

nce

2400 2200 2000 1800 1600 1400 1200 1000

2339

2361

2074

2088

219322

20

SAM of decanethiol

Wavenumber (cm-1) Figure 16: IRRAS of decanethiol SAM.

38

2.6. Analytical equipment The techniques, XPS, NEXAFS, IRRAS, and SEM were used to characterize the

monolayer films. SEM data were obtained using a LEO 1530 Gemini scanning

microscope. The XPS experiments were performed in two different UHV systems. The

multichamber UHV apparatus located in Bochum was equipped with a modified Leybold

XPS system, an EA11 hemispherical electron energy analyzer, and an Omicron LEED

system. The base pressure of the apparatus was below 1 x 10-10 mbar. X-ray

photoelectron spectra were acquired using a aluminum K� (h = 1486.6 eV) source. The

overview spectra were acquired at pass energy of 199.95 eV and the C 1s, O 1s, S 2p, Pd

3d and Au 4f narrow scan spectra were collected at pass energy of 46.14 eV.

The NEXAFS and some of the XPS measurements were performed in an UHV-system

operated at the HE-SGM beamline of the synchrotron facility BESSY II in Berlin. The

UHV-system consists of a loadlock, a preparation chamber, and an analysis chamber. The

base pressure of the analysis chamber of the UHV-system at BESSY was below 1 x 10-10

mbar. It was equipped with a LEED-optics (Vacuum Generators), a quadrapole mass

spectrometer (Balzer), an ion sputter gun, an Al/Mg twin anode X-ray source (VG), an

energy analyzer (Clam2, VG), and a homemade electron detector based on a double

channel plate (Galileo). The XPS data were acquired at photon energies of 280.0 eV,

400.0 eV and 480.0 eV for the S 2p, C 1s and Pd 3d regions, respectively. The energy

scale of the XPS data was referenced to the Au 4f7/2 peak at 84.0 eV. The XPS data were

fitted using the PeakFit software (Gaussian). The S 2p3/2, 1/2 doublet was fitted using two

peaks with the same full width at half-maximum (FWHM), with a separation fixed at

1.18 eV and a relative ratio of 2. The Pd 3d5/2, 3/2 doublet has been fixed at a separation of

5.3 eV. The same fit parameters were used for identical spectral regions.

The NEXAFS spectra were recorded at the carbon K-edge in the partial electron yield

mode with a retarding voltage of -150 V. The partial electron yield mode was chosen for

its surface sensitivity. The NEXAFS spectra for a particular sample were obtained at

three different angles, 30° (E-vector near surface normal), 55° (Magic angle) and 90° (E-

39

vector in surface plane). Simultaneously with each NEXAFS spectrum, the photocurrent

of a carbon contaminated gold-grid was recorded.

The raw NEXAFS data has to be processed [170, 171]. Normalization of the intensities to

a common scale helps quantitative comparison between different spectra. The substrate

signal is intense in the X-ray absorption spectra of monolayer films with thickness below

10 Å [170]. The following procedure is used in order to separate the adsorbate signal

from the substrate contribution.

In the first step, the raw NEXAFS spectra were normalized to the incident photon flux by

division through a reference spectrum of a clean gold sample recorded at the C K-edge.

This process is performed in order to eliminate the effect of incident beam intensity

fluctuations and monochromator absorption features. Gold has no absorption features in

the operational energy region (Fig. 17). Such a reference spectrum can be considered as a

direct measurement of the number of photons hitting the sample.

280 290 300 310 320

0.50.6

0.7

0.80.9

Ele

ctro

n Y

ield Au transmission

Photon Energy (eV)

Figure 17: Carbon K-edge NEXAFS spectrum of a clean gold substrate as reference.

In the next step, the pre-edge signal at 275 eV is normalized to zero (by subtraction) and

the edge jump at 315 eV is normalized to unity (by division). Finally, the pre-edge and

post-edge signals will be at 0 and 1, respectively (Fig. 18).

For the energy calibration, the spectra were referenced to a characteristic peak at 284.9

eV in the photocurrent spectra of the carbon contaminated gold-grid. The position of this

40

peak was calibrated against the strong �*-resonance of HOPG (highly oriented pyrolitic

graphite) which is located at 285.38 eV.

284.35

270 280 290 300 310 320

0

1

2

3

4

Raw data

C contaminated Au-grid

Ele

ctro

n Y

ield

Photon Energy (eV)270 280 290 300 310 320

0

1

2

3

4

5

Pre-edge normalization

Edge jump normalization

Photon Energy (eV) Figure 18: NEXAFS data treatment.

IRRAS spectra were recorded using a Bio-Rad Excalibur FTS-300 Fourier transform

infrared spectrometer equipped with a grazing incidence reflection unit (Biorad Uniflex)

and a narrow band MCT detector. All spectra were recorded with 2 cm-1 resolution at an

angle of incidence of 80° relative to the surface normal. The baseline correction was done

using the commercial software package. The spectra are presented in absorbance units

which is equal to log(I0/I) where I0 is the intensity of the reference sample and I is the

intensity of the sample under investigation. According to the Lambert-Beer law, the band

intensities are proportional to the concentration and layer thickness.

The two detectors in the spectrometer are MCT and DTGS. The IR spectra for

monolayers are recorded with a liquid nitrogen cooled MCT detector and the spectra for

bulk samples are measured with DTGS detector. The IR spectrometer was purged by dry

air delivered from a commercial purge gas generator. Purging was done to remove the

H2O and CO2 present inside the IR chamber [172]. A perdeuterated docosanethiolate film

on Au was used as a reference sample.

41

3. Self-assembled monolayers of thiol terminated surfaces

This chapter presents the preparation and characterization of thiol-terminated self-

assembled monolayers of oligophenyl dithiols on Au(111). IRRAS, XPS, NEXAFS and

contact angle techniques were used for characterization.

3.1. Self-assembled monolayers of terphenyldimethyldithiol Terphenyldimethyldithiol (TPDMT) belongs to the class of oligophenyldithiols and has a

long aromatic backbone (terphenyl unit). The rigid molecular backbone along with the

methylene (CH2) linkage between the thiol group and terphenyl unit lead to the formation

of highly oriented films on gold substrate. The molecular orientation for the terphenyl

backbone of TPDMT is upright but structural and conformational changes have been

observed upon metal evaporation [89] and on heating the SAM [173]. TPDMT was

synthesized from 4,4��-bis(bromomethyl)-p-terphenyl as previously reported [174]. The

dibromide was converted to dithiol by treatment with an excess of thiourea in ethanol

under reflux and subsequent alkaline hydrolysis in boiling water.

3.1.1. Preparation of TPDMT SAM

Self-assembled monolayers of TPDMT were prepared by immersion of the gold

substrates into a 50 M solution of the aromatic thiol in chloroform at room temperature

[7]. After 1 day of immersion, the sample was thoroughly rinsed with pure chloroform

and dried in a stream of nitrogen. TPDMT is completely soluble in chloroform.

3.1.2. Characterization of TPDMT SAM

(a) Infrared reflection absorption spectroscopy

In Figure 19, the low frequency (1850 cm-1 to 900 cm-1) region of the calculated IR, the

pellet IR and the SAM spectrum of TPDMT are shown (more experimental details can be

found in Section 2.6). For the TPDMT SAM, the in plane parallel bands are located at

1004 cm-1 and 1492 cm-1. Comparison of the SAM spectra with the bulk IR data of

TPDMT reveals the upright orientation of the terphenyl units. The modes with a

transition dipole moment (TDM) oriented parallel to the ring plane and the molecular

42

axis of phenyl unit are present whereas the modes with a TDM oriented perpendicularly

to the ring plane and the molecular axis of the phenyl unit, are absent [174].

1800 1600 1400 1200 1000

1800 1600 1400 1200 1000

1004

1492

100111071396

1481

1595

10011088

1243

1378

1482

1587

1800 1600 1400 1200 1000

(c) TPDMT - SAMA

bsor

banc

e

Wavenumber (cm-1)

0.001

0.4(b) TPDMT - Bulk

0.4(a) TPDMT - Calc.

Figure 19: Low-frequency regions of (a) the calculated spectrum of TPDMT (b) the bulk

spectrum of TPDMT and (c) the SAM spectrum of TPDMT.

The vibrational frequencies have been computed using commercial program package

(Gaussian 98, DFT calculations using the B3LYP-functional) and scaled by a factor of

0.9617. This normalization factor was deduced by comparing the theoretical and

experimental value for the in plane parallel band [Experimental value/Theoretical value =

1481 cm-1/1540 cm-1 = 0.9617].

43

Search for SH stretching mode in IRRAS of TPDMT SAM:

Self-assembled monolayer of TPDMT is SH terminated and the presence of free SH

group is confirmed by IRRAS. The detection of SH in a SAM has difficulties including

oxidation processes and hydrogen bonding with water molecules. The SH signal is broad

and weak [175]. This broadness arises because there are many species apart from the SH

stretching. Perfect SAM background and an environment with less water are needed in

order to observe this peak. Thiols undergoing hydrogen-bonding interactions can shift

their stretching vibration to significantly lower frequencies. This is consistent with the

studies by Long et al, which reported a value of 2412 cm-1 to an induced SH stretching

vibration from associated water at the sulphur atom [176]. The IRRAS experiments in the

following section were carried out in ultra high vacuum (UHV) using Vertex 80v FTIR

spectrometer from Bruker. Molecules like water, carbon dioxide and other hydrocarbons

from ambient can be easily adsorbed on reactive surfaces (like SH terminated SAMs). In

UHV conditions because of the absence of these adsorbates the SH vibrational band can

be observed.

The SH stretching vibrational band is generally observed in the region between 2600 cm-1

and 2500 cm-1 [175]. In Figure 20, the pellet IR of terphenyldimethyldithiol is compared

with terphenyldimethylthiol. The peak at 2555 cm-1 corresponds to the SH stretch of the

thiol functionality of the terphenyldimethyldithiol molecule (Fig. 20a). In the case of

terphenyldimethylthiol, two bands are observed at 2562 cm-1 and 2602 cm-1. The band at

2562 cm-1 is assigned to the SH stretching mode and the peak at around 2602 cm-1 could

be assigned to SH groups bound with molecules from the atmosphere. Intensities of the in

plane parallel band located at 1492 cm-1 is compared with the SH stretching band. In

TPDMT, the intensity of SH band is about 20 times smaller than the in plane parallel

band. In TPMT, the intensity of SH band is about 40 times smaller than the main peak.

The intensity ratios are consistent with the presence of two SH groups in TPDMT and

one SH group in TPMT.

44

14812555

1600 1550 1500 1450 14000,0

0,1

0,2

0,3

0,4

0,5

0,6

0,7

0,8

Wavenumber (cm-1)2650 2600 2550 2500 2450

0,000

0,005

0,010

0,015

0,020

0,025

0,030

0,035

0,040

HS

SH

(a) Terphenyldimethyldithiol-KBr pellet IR

Abs

orba

nce

14922562

2602

1600 1550 1500 1450 14000,00

0,02

0,04

0,06

0,08

0,10

0,12

0,14

Wavenumber (cm-1)2650 2600 2550 2500 2450

0,0000

0,0005

0,0010

0,0015

0,0020

0,0025

0,0030

0,0035

SH

(b) Terphenyldimethylthiol-KBr pellet IR

Abs

orba

nce

Figure 20: Pellet IR spectra of (a) terphenyldimethyldithiol and (b)

terphenyldimethylthiol. Left: Region from 2700 cm-1 to 2400 cm-1; Right: Region from

1550 cm-1 to 1400 cm-1.

45

Figure 21 shows the IRRAS of terphenyldimethyldithiol (TPDMT) SAM and

terphenyldimethylthiol (TPMT) SAM. The experiment of TPDMT SAM has been

reproduced. The SAM spectrum in the case of TPDMT and TPMT is an average of 20480

scans. The monothiol is included as a reference. In Figure 21, the red and orange curves

correspond to the TPDMT SAM. The peak at 2581 cm-1 corresponds to the free SH group

of the SAM and this peak is absent in the case of TPMT SAM. The intensity ratio of the

SH stretching band is roughly 40 times smaller than the in plane parallel band and is

consistent with the presence of one free thiol group at the SAM ambient interface.

2581

1493

2650 2600 2550 2500 2450

0,00000

0,00002

0,00004

0,00006

0,00008

0,00010

Wavenumber (cm-1)

Abs

orba

nce

1600 1550 1500 1450 1400

0,0000

0,0002

0,0004

0,0006

0,0008

0,0010

(1)TPDMT; (2)TPDMT; TPMT

Figure 21: IRRAS of terphenyldimethyldithiol (TPDMT) SAM and terphenyldimethylthiol

(TPMT) SAM. Left: Region from 2700 cm-1 to 2400 cm-1; Right: Region from 1550 cm-1

to 1400 cm-1.

The presence of the free SH group in TPDMT SAMs can also be confirmed by

hydrogen/deuterium exchange experiments between the surface SH of TPDMT SAMs

and deuterium oxide (Fig. 22). The SD stretching band can be observed in the region

46

between 1800 cm-1 and 1900 cm-1. Future experiments involving H/D exchange process

will provide more evidence for the presence of free SH in TPDMT SAM.

Figure 22: Schematic diagram showing the H/D exchange between TPDMT-SAM and

D2O.

(b) X-ray photoelectron spectroscopy

C 1s and S 2p XP spectra of TPDMT SAM are presented in Figure 23. The spectra were

acquired at photon energies of 400 eV (C 1s) and 280 eV (S 2p). The C 1s spectra reveal

a main peak at 284.6 eV and a shoulder at slightly higher binding energies (286.2 eV).

The main peak is assigned to the aromatic TPDMT backbone. In accordance with

previous work the shoulder is assigned to the shake-up processes [174]. The S 2p XPS

data exhibits two doublets at 162.0 eV and 163.2 eV (Fig. 23b). In accordance with

previous work [174], these peaks are assigned to Au-thiolate (-SAu) and to thiol sulphur

species (-SH) exposed at the vacuum side of the SAM. A S 2p3/2 signal centered at 167.3

eV is observed for the TPDMT SAM and this peak is assigned to oxidized sulphur

species. The experimental details and the description of the fit parameters are discussed

in Section 2.6.

Table 3: C 1s and S 2p peak fit data of TPDMT SAM.

BE in eV (total area %) Assignment Colour Carbon 1s (FWHM � 1.3)

284.6 (95.7) Aromatic backbone Black 286.2 (4.3) Shake up process Blue

Sulphur 2p 3/2 (FWHM � 1.1) 161.96 (7.8) S-Au Red

163.20 (80.1) S-H Blue 167.30 (12.1) Oxidized sulphur Gray

47

292 290 288 286 284 282 2800

10000

20000

30000 (a) C 1s XPS region

Inte

nsity

(Cps

)

Binding Energy (eV)

172 170 168 166 164 162 160 1580

400

800

1200

1600(b) S 2p XPS region

Inte

nsity

(Cps

)

Binding Energy (eV)

Expt.Fitted161.96163.20167.30

Figure 23: C 1s and S 2p - XPS of TPDMT SAM.

(c) Near edge X-ray absorption spectroscopy

Figure 24 shows C 1s NEXAFS data recorded for a TPDMT SAM on gold substrate

acquired at different incidence angles of the light with respect to the surface (30°, 55° and

90°). The spectra are dominated by the intense �*-resonance of the phenyl rings at 285.0

eV, another �*-resonance at 289.0 eV and several broad #*-resonances at higher photon

energies. The NEXAFS spectra reveal a pronounced dichroism which suggest a high

degree of orientational order. The difference between the spectra collected at incidence

angles 90° and 30° is also shown in Figure 24. This difference spectrum also highlights

the dichroism. The intensity of the peaks in difference spectrum is the fingerprint of the

molecular orientation.

48

280 285 290 295 300 305 310 315

0

2

4

6

8

10

90° - 30°

Photon Energy (eV)

Nor

mal

ized

PE

YTPDMT

90°

55°

30°

Figure 24: NEXAFS spectra of TPDMT SAM

(d) Contact angle measurements

The water contact angle is 78° for TPDMT SAM on gold. The values are in accordance

with the literature [174]. Low solid-liquid contact angles were observed for hydrophilic

terminated SAMs (e.g., hydroxyl and carboxylic acid) whereas higher contact angles

were observed for more hydrophobic surfaces (e.g., methyl). The contact angle value of

TPDMT SAM is relatively high when compared to acid and alcohol terminated SAMs

and less than the methyl terminated SAMs. The thiol terminated surface can form

hydrogen bonding with water like the -OH terminated SAMs but the high contact angle is

related to the high quality of SAMs.

49

3.2. Self-assembled monolayers of biphenyldimethyldithiol Biphenyldithiol and biphenyldimethyldithiol (BPDMT) has been studied in connection to

molecular electronic devices. However, these molecules do not form well oriented

monolayers. Earlier studies from our group show that they form oligomers with the

biphenyl units linked together by disulphide bond [7]. Due to the presence of disulphide

species the films formed from these molecules are sensitive to oxidation. The straight

forward approach of preparing the BPDMT SAMs leads to disordered monolayers. High

quality monolayers of BPDMT can be prepared by using the monoacetylated derivative

of BPDMT. After SAM formation, the protective thioester group can be deprotected by

using a base. The SAM formed by deprotection method will be mentioned by the term

deprotected BPDMAc-1. The resulting deprotected BPDMAc-1 SAM will be

biphenyldimethyldithiol self-assembled monolayers. BPDMAc-1 (monoacetylated) was

obtained by treating BPDMT with acetyl chloride [9].

3.2.1. Preparation of deprotected BPDMAc-1 SAM

Self-assembled monolayer of BPDMAc-1 was prepared by immersing the gold substrates

into a 50 �M BPDMAc-1 solution in dichloromethane (DCM) at room temperature (RT).

After 4 hours of immersion, the sample was thoroughly rinsed with the solvent (DCM)

and dried in a stream of nitrogen. After formation of the organothiolate adlayer, the

protecting group can be removed by immersion into NaOH solution. The BPDMAc-1

gold SAM was immersed into a 0.01 M NaOH solution in (1:1) ethanol + water mixture

for 3.5 days (~ 84 hours) at room temperature. After removal of the sample from the

solution, it was thoroughly rinsed with ethanol and then dried in a stream of nitrogen.

3.2.2. Characterization of deprotected BPDMAc-1 SAM

(a) Infrared reflection absorption spectroscopy

In Figure 25, the low frequency (1850 cm-1 to 900 cm-1) region of the calculated IR, the

pellet IR and the SAM spectrum of BPDMAc-1 SAM are displayed. The calculated IR

and the SAM spectrum of deprotected BPDMAc-1 are also included in Figure 25. For the

deprotected BPDMAc-1 SAM, the in plane parallel bands are located at 1006 cm-1 and

50

1497 cm-1. The respective spectra of TPDMT look very similar. The band at 1605 cm-1 is

also observed in the BPDMT SAM prepared directly from the corresponding solution.

1800 1600 1400 1200 1000

1006

1497

1605

10051094

1251

1393

1497

1599

1800 1600 1400 1200 1000

(e) deprotected BPDMAc-1 - SAMA

bsor

banc

e

0.0005

Wavenumber (cm-1)

0.4(d) deprotected BPDMAc-1 - Calc.

1800 1600 1400 1200 1000

1800 1600 1400 1200 1000

9591005

1143

13571497

1695

962

100511

40

1261

135313

981497

1699

9621039

1150

130114371549

1694

1800 1600 1400 1200 1000

(c) BPDMAc-1 - SAM

Abs

orba

nce

Wavenumber (cm-1)

0.001

0.4(b) BPDMAc-1 - Bulk

0.4(a) BPDMAc-1 - Calc.

Figure 25: Low-frequency regions of (a) the calculated spectrum of BPDMAc-1 SAM, (b)

the bulk spectrum of BPDMAc-1 SAM, (c) the SAM spectrum of BPDMAc-1 SAM, (d) the

calculated spectrum of deprotected BPDMAc-1 SAM and (e) the SAM spectrum of

deprotected BPDMAc-1.

51

The vibrational frequencies have been computed using commercial program package

(Gaussian 98, DFT calculations using the B3LYP-functional) and scaled by a factor of

0.9677. This normalization factor was deduced by comparing the theoretical and

experimental value for the in plane parallel band [Experimental value/Theoretical value =

1497 cm-1/1547 cm-1 = 0.9677].

(b) X-ray photoelectron spectroscopy

Figure 26 shows the C 1s XPS data. The deprotected BPDMAc-1 SAM shows a peak at

284.5 eV which is assigned to the aromatic biphenyl backbone. S 2p XPS data recorded

for a deprotected BPDMAc-1 SAM is also shown in Figure 26. The peaks at 162.0 eV

and 163.3 eV are assigned to Au-thiolate and to the thiol tail group, respectively.

Oxidation of the organic surface is observed as indicated by the appearance of the peaks

at higher binding energies (168.0 eV, oxidized sulphur species). The details of the fit

parameters are discussed in Section 2.6.

292 290 288 286 284 282 2800

10000

20000 (a) C 1s XPS region

Inte

nsity

(Cps

)

Binding Energy (eV)

172 170 168 166 164 162 160 1580

400

800

1200

1600(b) S 2p XPS region

Inte

nsity

(Cps

)

Binding Energy (eV)

Expt.Fitted161.96 163.35 168.04

Figure 26: XPS of deprotected BPDMAc-1 SAM.

52

Table 4: C 1s and S 2p peak fit data of deprotected BPDMAc-1 SAM.

BE in eV (total area %) Assignment Colour Carbon 1s (FWHM � 1.3)

284.5 (96.0) Aromatic backbone Black 286.3 (4.0) Shake up process Blue

Sulphur 2p3/2 (FWHM � 1.1) 161.96 (18.4) S-Au Red 163.35 (76.0) S-H Blue 168.04 (5.6) Oxidized sulphur Gray

(c) Near edge X-ray absorption spectroscopy

Figure 27 shows C 1s NEXAFS data recorded for a deprotected BPDMAc-1 SAM on

gold substrate acquired at different incidence angles. The spectra are dominated by the

intense �*-resonance of the phenyl rings at 285.0 eV, another �*-resonance at 289.0 eV

and several broad #*-resonances at higher photon energies. The intensities of the

resonances depend on the relative orientation of the corresponding transition dipole

moment relative to the polarization direction of the light. The dichroism is again visible

in the difference spectra shown in Figure 27.

280 285 290 295 300 305 310 315

0

2

4

6

8

10

Nor

mal

ized

PE

Y

Photon Energy (eV)

90°- 30°

30°

55°

90°

Deprotected BPDMAc-1

Figure 27: NEXAFS of deprotected BPDMAc-1 SAM.

53

The monolayer thickness can be estimated from the edge jump in C K-edge NEXAFS.

The change in the edge jump can be used to control the thickness in evaporation

experiments. The edge jump increases with increasing amount of carbon up to saturation.

In Figure 28, the different SAMs, TPDMT, deprotected BPDMAc-1 and BPDMAc-1 are

compared. The gold transmission line is also included. The chemical modification

involves the transformation of -SCOCH3 to -SH. The height of both the deprotected

BPDMAc-1 and BPDMAc-1 should be almost the same. It is clear from the plot that

there is no decrease in the thickness of the BPDMAc-1 thiol film after the treatment with

NaOH solution to remove the acetate group. The thickness estimation clearly shows that

the orientation and the packing density are retained even after the treatment with a strong

base. The edge jump for the TPDMT with three phenyl rings is found to be greater than

deprotected BPDMAc-1 with two phenyl rings.

280 285 290 295 300 305 310 315 320

1

2

3

4

5

6

Deprotected BPDMAc-1

Au transmission

TPDMT

BPDMAc-1

Photon Energy (eV)

Nor

mal

ized

PE

Y

Figure 28: Thickness estimation from the edge jump in C K-edge NEXAFS.

54

3.3. Conclusion The self-assembled monolayers of TPDMT on Au(111) surface were prepared directly

from the TPDMT solution and the SAMs of biphenlydimethyldithiol was fabricated using

a deprotection strategy. A well ordered SAM with a thioester protecting group was

obtained by the self-assembly of BPDMAc-1 which was then deprotected under basic

conditions. This deprotection method yields biphenlydimethyldithiol SAM with high

degree of molecular orientation. The SAMs were characterized with XPS, IRRAS and

NEXAFS. The introduction of aliphatic linker into the aromatic backbone plays an

important role to achieve the high structural quality of the films. The XPS results provide

evidence to the presence of free thiol group at the SAM-ambient interface in both

TPDMT and deprotected BPDMAc-1 SAMs. These free thiol groups are well-suited for

further chemical modifications.

55

4. Deacylation reaction at an organic surface

In this part of the thesis, the kinetics of the reaction involving the conversion of

thioacetate to thiol on an organic surface exposed by a SAM is discussed.

The fabrication of the organic surface exposed by the SAM is attracting an increasing

amount of attention, e.g. in connection with a coupling of biomolecules [177], model

studies regarding biomineralization [178] and to anchor zeolites [179] or metal-organic

frameworks (MOFs) [180-182]. The self-assembled monolayer of thiols adsorbed on

solid substrates offers the possibility to create organic surfaces which can be tailored

easily [28]. The desired organic surface can be obtained by using an appropriately �-

functionalized organothiol and the functional groups at the �-position control the surface

physico-chemical properties. For example, the wettability can be varied smoothly

between hydrophobic and hydrophilic. However, often there are complications resulting

from undesired interactions between either the corresponding functions or the function

and the Au-substrate. The amino, hydroxyl and carboxyl functional groups interact

strongly with themselves via hydrogen bonding. Earlier studies on

mercaptomethylterphenylcarboxylic acid reveal the presence of bilayers in which the first

and the second layers are linked by hydrogen bonds [183]. The formation of monolayers

required the addition of acetic acid. On the other hand, the SAM of

mercaptohexadecanoic acid has significant amount of disorder induced by the hydrogen

bonding between the COOH groups [184]. The interaction of the end functional group

with the gold substrate has been observed in the case of dithiols. In this case, the

formation of disulphide bonds induces the disorder in the SAMs [7]. In order to avoid

such problems, SAMs can be first formed from protected organothiols and a subsequent

deprotection will yield an organic surface with the desired functionality [9].

56

Results and Discussion

4.1. Conversion of thioacetate to thiol The SAMs of biphenyldimethylthiol were prepared by deprotecting the monoacetylated

derivative of BPDMT (BPDMAc-1), an organothiol with a biphenyl backbone and a -SH

group at one end while the other end of the molecule contains a protected S-atom in the

form of a thioacetate (-SCOCH3). After the SAM formation, the thioacetate can then be

cleaved under basic conditions, thus yielding a SH-terminated surface.

S

S

HS

S

S

S

H HSCO C

S

SCO C

S

SCO C

S

HH

H HH

H HH

H

Au (111) Au (111)

0.01M NaOH3.5 days; RT

OH

SCO CH

HH

SH

SC

C HH H

C OOO

HO

CH

HH

R R R

Figure 29: Schematic flowchart illustrating the deprotection mechanism of the

deacylation process.

The deprotection scheme has been illustrated by means of a flowchart (Fig. 29). The

deacylation process was followed by IRRAS, XPS and NEXAFS. In Figure 30, the

IRRAS of BPDMAc-1 was compared with that of the deprotected BPDMAc-1. The

intense vibrational band at 1695 cm-1 in monoacetylated biphenlydimethyldithiol reveals

57

the presence of the carbonyl group. Apart from the C=O stretching vibration, two more

bands, 1143 cm-1 and 1357 cm-1 are related to thioester. The bands at 1497 cm-1 and 1005

cm-1 corresponds to the ring modes of the phenyl units. The absence of the C=O

stretching vibration of the acetate group and other bands related to thioester of BPDMAc-

1 indicates the conversion of thioacetate to thiol.

1006

1497

1605

9591005

1143

1357

14971695

1800 1650 1500 1350 1200 1050 900

Dep. BPDMAc-1

Wavenumber (cm-1)

Abs

orba

nce

0.001

BPDMAc-1

Figure 30: IRRAS of BPDMAc-1 and deprotected BPDMAc-1.

In Figure 31a, the NEXAFS spectra recorded at the C 1s edge for gold substrates, which

were immersed into solutions of BPDMAc-1 and also the spectrum recorded for a

BPDMAc-1 monolayer, after deprotection are displayed. The spectra displayed in Figure

31a was recorded at an incidence angle of 55°. The BPDMAc-1 SAM spectrum exhibits

strong resonances at 285.2, 287.4, 289.1 and 293.8 eV. The deprotection procedure was

followed by the disappearance of the �*-resonance of C=O of BPDMAc-1 at 287.4 eV.

58

The NEXAFS results show only changes at the NEXAFS resonance related to the

carbonyl carbon atom, all other resonances remain unchanged upon deacylation. This

suggests that the deacylation process involves only the uppermost part of the thiol

molecules, i.e., the thioester unit of the BPDMAc-1 molecule whereas the

biphenyldimethyl backbone of the thiol molecule is essentially not affected by the

deacylation process. Furthermore, the NEXAFS results indicate a constant tilt angle for

the molecular backbone of 19�5° relative to the surface normal for both acylated and

deacylated molecules.

280 285 290 295 300 305 310 3150

2

4

6C1s NEXAFS

BPDMAc-1 (55°)

Deprotected BPDMAc-1 (55°)Nor

mal

ized

PEY

Photon Energy (eV)

287.4

Figure 31a: NEXAFS spectra of BPDMAc1 and deprotected BPDMAc-1.

59

280 285 290 295 300 305 310 315

0

2

4

6

8

10 BPDMAc-1

90°

55°

30°

90°- 30°

Nor

mal

ized

PE

Y

Photon Energy (eV)Figure 31b: NEXAFS spectrum of BPDMAc1 at different incidence angles.

NEXAFS data of BPDMAc-1 SAM at different angles are displayed along with the

difference spectrum (90°-30°) in Figure 31b. The blue line corresponds to spectrum

recorded at an incidence angle (angle between the E�

vector of the polarized synchrotron

light and the surface normal) of 30°, whereas the black line represents spectrum taken at

normal incidence of the synchrotron light (angle between the E�

vector of the synchrotron

light and the surface normal of 90°). The intensities of the resonances depend on the

relative orientation of the corresponding transition dipole moment relative to the

polarization direction of the light. The NEXAFS spectra of both BPDMAc-1 (Fig 31b)

and the deprotected BPDMAc-1 (Fig. 27) show a pronounced dichroism, which suggests

good orientational order in these SAMs.

The deprotection was also followed by XPS. The main peak at 284.5 eV corresponds to

the aromatic backbone. The peak at higher binding energy 287.6 eV corresponds to the

C=O of BPDMAc-1. The disappearance of the peak at 287.6 eV in the deprotected

BPDMAc-1 clearly indicates the cleavage of the acetate group (Fig. 32).

60

284.4

287.6

292 290 288 286 284 282 280

BPDMAc-1Deprotected BPDMAc-1

Inte

nsity

(Cps

)

Binding Energy (eV)

5000

Figure 32: XP spectra of BPDMAc1 and deprotected BPDMAc-1.

4.2. Chemistry in confined geometries The chemical reactions at the organic surface of the SAM may proceed quite differently

than the corresponding reaction in solution. The deacylation reaction, which is standard

in solution chemistry, is significantly hindered when confined to a surface. Whereas the

reaction in solution proceeds in minutes [59] the corresponding reaction at the organic

surfaces requires, depending on the conditions, up to 84 hours.

The kinetics of reactions on a SAM is influenced by various factors [10]. The structure of

the SAM influences the reactivity on surfaces. The molecules on the surface are subjected

to certain geometric constraints and environmental variations that are not present in the

solution. The nature of the solution at the interface differs significantly from the bulk

solution [185]. The surface can limit the accessibility of interfacial functional groups to

external reagents. Poor reactivities have been observed for functional groups positioned

within highly ordered organic interfaces. Many studies have demonstrated that the rate of

hydrolysis for the terminal ester groups on well-ordered SAMs depends on the density

and orientation [186, 187]. The reactivity of monolayers was inferior to the

corresponding reactions in solution. The reactivity of a surface is also determined by the

61

steric crowding between the reactive sites within the SAM. The reactivity also depends

strongly on the type of reaction. Reactive sites embedded in the SAM can be less

accessible to reactants in the surrounding medium than the ones positioned at the termini

of the SAM [188, 189].

In the course of a systematic investigation of the surface deacylation reaction, it has been

observed that the time needed for a complete conversion showed an unexpected variation

from sample to sample. The samples were prepared from different gold substrates. The

gold substrates differ in the contact time with the ambient. Generally, freshly prepared

gold substrates are used for preparing SAMs. In order to understand the kinetics of the

deacylation reaction aged substrates are also investigated. The freshly prepared Au

substrates are exposed to ambient (lab conditions) for a considerable time and then the

substrates are used for SAM preparation.

The sample 1 was prepared by immersing a freshly evaporated Au(111) into the

BPDMAc-1 solution. In this case, the substrate was in contact with ambient for less than

30 minutes. The sample 2 was prepared by immersing an aged Au substrate (contact with

ambient for about three days) in the thioester solution. IRRAS were recorded for the two

different Au samples. The BPDMAc-1 SAMs prepared from both the Au samples

(sample 1 and 2) were treated with 0.01M sodium hydroxide solution and the IRRAS has

been recorded at different immersion time in the basic solution (Fig. 33).

The IR results show that in case of the sample 1 the thioester group is present after an

immersion time of 12, 24, 48 and 60 hours. The completion of the deacylation process

occurs after an immersion time of 84 hours. In the case of sample 2, the deacylation

process goes to completion after an immersion time of 60 hours. These observations can

be compared to those obtained for sample 3, a deprotected BPDMAc-1 SAM prepared

from a very aged gold substrate (contact with ambient for more than 3 days) [9].

62

1800 1600 1400 1200 1000

(a) Sample 1

Abs

orba

nce

Wavenumber (cm-1)

84 hrs

60 hrs

48 hrs

24 hrs

12 hrs

BPDMAc-1

0.002

1800 1600 1400 1200 1000Wavenumber (cm-1)

Abs

orba

nce

(b) Sample 2

84 hrs

60 hrs

48 hrs

24 hrs

12 hrs

BPDMAc-1

0.002

Figure 33: IRRAS showing the deacylation reaction at different immersion time in the

basic solution. (a) Sample 1 (Fresh gold substrate); (b) Sample 2 (Aged gold substrate).

The degree of deprotection was determined from the intensity of the acetate vibrational

band of BPDMAc-1 at 1695 cm-1. In Figure 34, the intensity of the CO stretching

vibration band as a function of the immersion time for different Au-samples has been

shown.

63

0 12 24 36 48 60 72 84

0.0

0.2

0.4

0.6

0.8

1.0H

eigh

t of t

he C

=O p

eak

Immersion Time / h

Sample -1 Sample -2 Sample -3

Figure 34: The difference in deprotection kinetics by the change in the nature of the gold

substrate.

Clearly, the kinetics is strongly different. On the most perfect gold surfaces the reaction is

significantly delayed. These results have been reproduced a number of times and they all

indicate that the reaction speed with which the SAM surface is converted depends

strongly on the quality of the substrate. It should be noted that in solution the kinetics of

the deprotection reaction is a fairly fast process, a complete removal of the protection

group in solution requires less than 10 minutes [59].

The base hydrolysis of thioester by sodium hydroxide is also examined by scanning

electron microscopy (Fig. 35). Scanning electron microscopy (SEM) is widely used to

image patterned SAMs. The secondary electron yield of a metal surface can be modulated

by the chemical modification at the surface via adsorption of thin films. The contrast

differences depends on the functionalization of the SAM used. The image contrast in

SEM requires surface regions that contain areas with different chemical composition

64

[190-193]. Mack et al. have examined the adsorption of fibrinogen on hexadecanethiol

SAM by SEM [192]. The image becomes darker on increasing the concentration of the

protein and the adsorption is followed by the increase in the intensity of the image

contrast.

The SEM image of a fresh BPDMAc-1 sample shows an essentially structureless,

homogeneous surface (Fig. 35a). After the samples have been immersed in the basic

solution for three hours small, approximately circular dark regions start to appear (Fig.

35b). This dark spots must correspond to deprotected areas. This observation of an

apparent contrast inversion for ultrathin organic adlayers is, however, in agreement with a

recent thorough study of the mechanism governing the contrast in SEM of SAMs on Au-

substrates [192]. The roundish dark features significantly grow in size for longer

immersion times. The total number of these dark spots also increases (Fig. 35c). This

observation reveals a growth accompanied by coalescence of the deprotected areas. The

process is similar to Ostwald ripening. After 25 hours again an essentially structureless

background is visible (Fig. 35d) indicating the presence of a homogeneous, completely

deprotected surface, in full agreement with the corresponding IR data. The immersion

time is only 25 hours and the deprotection process seems to have completed (Fig. 35d). It

should be noted here that the SEM experiments were done using Au on mica and the

defect density is higher compared to Au on silicon substrates and, accordingly, the

deprotection reaction is carried out faster. The morphological features formed in the

deprotection process closely resemble those seen during wet chemical anisotropic etching

of crystalline silicon, the most widely used processing technique in Si technology [194].

Simulations have shown that in this anisotropic etching process �m-sized, roundish pits

occur which nucleates to shallow features. This is very similar to those seen in the present

experiments. The results shown in Figure 35 clearly demonstrate that under the

conditions reported in Figure captions, the first morphological signs of deprotection can

be seen after three hours of contact time between the organic surface and the basic

solution. By correlating these results with the corresponding IR data, it can be concluded

that the black, spherical areas seen in Figure 35 must correspond to areas, where the

65

deprotection process has already been carried out, i.e. where the thioacetate groups have

been transformed to thiol groups.

Figure 35: SEM images of BPDMAc-1 and deprotected BPDMAc-1 SAM.

Image (a) was recorded for BPDMAc-1 SAM. Images (b) to (d) were recorded for the

deprotected samples prepared by the treatment of BPDMAc-1 SAM with 0.01M NaOH

for different immersion times (b) 3 hours (c) 5 hours and (d) 25 hours.

According to the SEM micrographs the process of hole formation is completed after

about five hours, after that the reaction is so fast that the whole process is completed and

66

SEM images recorded after 25 hours or more show a structure less surface as was the

case for the monolayers before immersion. The deprotection starts at defects within the

SAM, in particular at step-edges which occur e.g. at the edge of the etch-pits created

during the self-assembly process [195].

The rate deceleration can be demonstrated by the model in Figure 36. After a nucleation

center has been created by the removal of a few thioester groups the reaction then

proceeds essentially only at the edges between the deprotected area and the pristine SAM.

The reaction proceeding at the boundaries is much faster than the creation of new

nucleation centers. This is revealed by the SEM images recorded at longer times where

the roundish areas are absent. The reaction proceeds rapidly on low-quality substrates.

This is because of high density of defects in these low-quality substrates which serve as

starting points for the deacylation reaction.

The reaction investigated in the present study occurs at the otherwise unperturbed

interface of an organic surface exposed by a SAM and an aqueous solution. The

BPDMAc-1 SAMs used in the present investigation are not perturbed by any external

means. The difference in the rate of hydrolysis is observed only with the changes in the

nature of the underlying gold substrate. The high density of defects (in low quality

substrates) enhances the rate of the reaction and can be compared with the activation

processes explained in Section 1.7.

On the basis of these observations it can be shown that the removal of the thioester group

at the SAM surface is slower than deacetylation occurring in solution. From the fact that

the process is significantly delayed on very clean surfaces with only a very small content

of contaminations, it is proposed that there must be nucleation centers from which two-

dimensional reaction fronts originate.

67

Figure 36: Schematic model showing the possibility for the attack of the hydroxide ion.

68

4.3. Conclusion The biphenyldimethyldithiol SAM was fabricated from its monoacylated derivative by a

hydrolysis reaction. The reaction kinetics, endgroup chemical nature, and orientational

structure of the deprotected BPDMAc-1 films adsorbed on Au(111) were investigated

with multiple surface science techniques, IRRAS, XPS, NEXAFS and SEM. The

experimental results obtained allow for a better understanding of the chemical reactions

on an organic surface. The results demonstrate that chemical reactions, even simple ones,

can be significantly delayed when one of the reaction partners is confined to a densely

packed, highly ordered organic surface. In the present case of a deacetylation reaction,

the microscopic data suggest that the reaction starts at defects and proceeds at the border

(a one-dimensional entity) between unreacted and deprotected areas. The reaction thus

occurs at a one-dimensional reaction front, the analog to a two-dimensional reaction front

occurring in reactions in three dimensions. An important consequence is that the time

needed for a complete reaction on an organic surface depends strongly on the substrate

quality.

69

5. Metallization of a thiol-terminated organic surface

The deposition of noble metals on organic surfaces has received an increasing amount of

interest in recent years due to its importance for several technological applications [6, 90,

95, 96] e.g., the attachment of electrodes to organic semiconductors [196, 197]. Self-

assembled monolayers provide an ideal model system for the study of inorganic-organic

interface formation. In fact, in addition to serving as model organic substrates, SAMs

may actually be a permanent part of a device, e.g., in organic electronics [198-200].

SAMs are particularly useful in many applications due to their easy preparation methods,

low defect density and strong binding to the underlying substrate. The ability to tailor the

chemistry of the end group helps to determine the physicochemical properties of the

organic surface exposed by the SAM.

The main goal of this work was to deposit metallic palladium by chemical vapour

deposition on top of dithiol self-assembled monolayers. This chapter reports on the

deposition and the subsequent decomposition of Cp(allyl)Pd, on thiol-terminated SAMs

of oligophenyldithiols, terphenyldimethyldithiol (TPDMT) and biphenlydimethyldithiol

(deprotected BPDMAc-1), on Au(111). The interfacial chemical reactions of the vapor-

deposited metal precursor with the pendant thiol group of the SAMs have been studied in

detail using XPS, NEXAFS and IRRAS. This chapter begins by reviewing the metal

deposition on top of SAMs followed by the discussion of the results from the present

work.

Deposition of metal on top of SAMs is a challenging topic. In general, unreactive metals

that are deposited on inert SAMs diffuse through the SAM to the Au/S interface and

reactive metals will stick to SAMs with coordinating head groups to form organometallic

complexes [201]. The deposition of metal on top of passive thiol SAMs mostly results in

penetration of the deposited metal. In order to avoid the diffusion, deposition can be done

at low temperatures. Tarlov has observed the formation of Ag clusters on top of the

octadecanethiol (ODT) SAM, when the deposition was carried out at 90 K whereas at

70

300 K penetration through the film has been observed [75]. The use of reactive functional

groups (-NH2, -COOH, -SH) on the tail of the thiols is another way to prevent diffusion

of deposited metals. This was demonstrated by STM studies of gold deposition on top of

a carboxylate terminated SAM. The deposited gold atoms interacts with the acid group in

the monolayer and this leads to the formation of coalescing clusters on top of the

molecular layer [80, 83]. The penetrating efficiency of metals deposited on monothiol

SAMs has been compared with that of dithiol SAMs in several studies [76, 81]. Jung et

al. have observed the reactivity of the deposited Cr metal on -COOCH3 terminated SAM

resulting in a smooth layer on top of the SAM [85]. The penetration behaviour can be

controlled by modifying the end group and it has been shown that the ionic interactions in

K modified –COOH and –COCH3 SAMs were able to block the diffusion of thermally

evaporated gold [63]. The vapor deposition of K, Ca, Au and Ti atoms on several

alkanethiols and methoxy terminated alkanethiolate self-assembled monolayers was

investigated by Walker et al [82]. The heavy metal atoms generally results in the

penetration of metals toward the Au/S interface whereas the K atom forms a salt with

methoxy group [77, 82]. Czanderna et al. have found that when Cu is vacuum-deposited

on a carboxylic acid terminated SAM, some Cu reacts with the carboxylic acid groups,

although most Cu diffuses through the SAM. When faster deposition rates were used and

the substrate was cooled to 220 K during deposition, penetration of Cu could be slowed

down or even stopped [202-206]. Dronavajjala et al. have studied the ligand exchange

reaction between a cationic Pd organometallic complex, [(Pd(C2H5CN)4](BF4)2)] and a

cyanoterminated alkanethiol (mercaptohexadecanenitrile) SAM and it shows the route for

anchoring a Pd catalyst on a substrate and conducting the polymerization reaction [207].

Electrochemical deposition is also a valuable tool to deposit metals on top of SAMs.

Different metals like Rh, Pd and Pt have been deposited on mercaptopyridine SAMs by

this approach [69, 97, 208]. The metal deposition on SAMs with defects will result in

mushroom like growth [209]. Electroless metallization is also a promising method for

fabricating metal coatings [108]. Electroless deposition is a method in which a pre-

existing catalytically active species are used to form the desired metal on surfaces via

solution electrochemistry [210]. Cobalt islands has been grown by electroless deposition

method on a palladium deposited amine (-NH2) terminated SAM. In the first step, the

71

deposited Pd forms a complex with the amine SAM and later the Pd was reduced. The

presence of Pd islands facilitates the deposition of the second metal, cobalt [106].

Amidst the different functional groups, the thiol groups are promising. SAMs made from

dithiols offer the possibility that the free -SH group binds chemically to the deposited

metals and thus prevents metal diffusing through the SAM. Dithiols can be utilized as a

chemically sticky surface for attachment of metal clusters and layers [99, 211]. De Boer

et al. have demonstrated that Au and Al can penetrate a monothiol SAM whereas they

stick to dithiol SAMs [81]. Ti destroys both kinds of SAMs because of its high reactivity

towards the molecular backbone of the thiols. Oghi et al. have studied the gold deposition

on self-assembled monolayers of thiols and dithiols. In this case, the deposition was done

by evaporating gold [76]. They have observed the penetration of gold atoms in the case of

thiols and formation of gold particles on top of the dithiol SAMs.

The interaction of vapor deposited nickel with TPDMT and BPDMT has been studied

previously by Tai et al. A decrease in molecular tilt resulting in the diffusion of metal to

the SAM substrate interface has been observed. In this study, the deposition was done by

evaporating nickel [89]. Recently, an interesting approach to prevent the metal diffusion

has been demonstrated by Tai et al. The TPDMT SAMs have been irradiated with low

energy electrons to obtain chemical cross-linking between the molecular backbones. It

has been shown that only the cross-linked SAM layers provide an effective barrier for the

penetration of a metal adsorbate [6, 8, 212, 213]. The fabrication of gold nanoparticles on

mixed BPDMT and ODT SAM has shown that the density of nanoparticles can be

controlled by altering the availability of -SH groups [72]. The electrochemical deposition

of platinum on top of a benzenedimethanethiol (BDMT) SAM has been investigated by

Qu et al. [99]. Amidst the different metal deposition techniques, chemical vapor

deposition (CVD) has several advantages over physical vapor deposition processes [214,

215]. In general, the metal deposition on SAMs remains difficult because of the fragile

nature of the SAMs and diffusion of the metal through the SAMs.

72

In this work, an organometallic compound, (�3-allyl)(�5-cyclopentadienyl)palladium

[Cp(allyl)Pd] was used as a Pd precursor. The structure and the properties of Cp(ally)Pd

are given in Chapter 1.

Results

5.1. Deposition of palladium onto a TPDMT-SAM SAMs of terphenyldimethyldithiol (TPDMT) are particularly interesting for the

fabrication of electronic devices. TPDMT is a rigid, conjugated dithiol which can form

SAMs with a free reactive surface that can chemically bind to metals. For the preparation

of electronic devices, another advantage of dithiol SAMs over monothiol SAMs is that

these reactive surface groups will prevent metal diffusing through the SAM. The average

tilt angle of 28° was observed for the terphenyl backbone with respect to the surface

normal [216] and the thickness of the organic adlayer amounts to 19.4 Å [174]. The

intermolecular interaction between the terphenyl backbones favours the highly oriented

structure [217, 218]. Scanning tunneling microscopic (STM) studies on TPDMT SAMs

exhibits an inferior quality when compared to decanethiolate SAMs. The imaging

problems most likely arise from the interaction of the reactive -SH terminated surface

with a metal tip [7].

Figure 37: Illustration of the structure of a TPDMT SAM on gold.

73

In Chapter 3, the preparation and the characterization of TPDMT SAMs on Au(111) are

presented. For the TPDMT SAMs, the IRRAS and NEXAFS data reveal the presence of a

densely packed and highly oriented film with an upright orientation of the terphenyl

backbone (Fig. 37). XPS results strongly indicate that the TPDMT SAM is terminated by

thiol groups. The terphenyldimethyldithiol SAM was exposed to the palladium precursor

vapor at room temperature in a Schlenk flask for times between 1 and 24 hours according

to the procedures described in Chapter 2. Since the precursor is highly sensitive to

moisture and air, the exposures were performed in an Ar atmosphere.

5.1.1. XPS of Pd deposited TPDMT-SAM

The oxidation state of the Pd atom in the intact precursor is +2 and the XPS binding

energies recorded for precursor multilayer amount to 337.7 eV and 343.0 eV for the Pd

3d5/2 and 3d3/2 doublet, respectively [219, 220]. The XPS data recorded for thin films of

elemental palladium obtained from Cp(allyl)Pd exhibits peaks at 335.7 eV and 340.9 eV

for the Pd 3d5/2 and 3d3/2 doublet, respectively [137]. The palladium 3d lines of the intact

precursor are shifted by 2.0 eV toward higher binding energies as compared to the Pd 3d

lines of the metallic palladium. The Pd 3d5/2 line is located at around 338.0 eV for many

Pd(II) compounds. Lin et al. have observed a higher binding energy of 339.1 eV for

Pd(hfac)2 precursor [114]. The higher binding energy is consistent with a larger chemical

shift caused by the more electronegative ligand in the latter complex.

Palladium 3d XPS data: In Fig. 38a, the Pd 3d XPS data for the TPDMT SAM which

was exposed for a short time (one hour) to the precursor is presented. After the exposure

of the SAM to the precursor, the appearance of a Pd 3d signal is clearly visible. The Pd

3d doublet is located at 337.4 eV and 342.7 eV, demonstrating that the Pd is in the +2

oxidation state. Since Cp(allyl)Pd can be easily reduced by dihydrogen gas [94], the

TPDMT SAM which had been treated with the precursor vapor for 1 hour was exposed to

H2 at room temperature. The corresponding XPS data (Fig. 38b) did not reveal any

changes when compared to the data recorded prior to the H2 exposure; a reduction of the

Pd2+ clearly did not take place. In Fig. 39a, the XPS data recorded for the TPDMT SAM

which was exposed to the precursor for significantly longer times, approximately 24

74

hours is displayed. From the XPS results it is clear that again Pd2+ ions are deposited, but

for the longer exposures also Pd0 is present as evidenced by the peaks at 335.6 eV and

340.9 eV, which are a characteristic of metallic Pd [219]. A closer inspection reveals that

the total amount of Pd deposited on SAMs exposed to the precursor for 24 h is

significantly larger, nearly doubled, when compared to the SAMs of shorter (1 h)

exposure time. In contrast to short exposure times, in this case the Pd2+ deposited on the

TPDMT SAM is reduced to metallic Pd upon exposure to H2 as evidenced by the peaks at

335.6 eV and 340.9 eV (Fig. 39b). However, the reduction is not complete; Pd2+, about

25% (peaks at 337.6 and 342.9 eV), is still present after exposure to H2 (Table. 5).

348 344 340 336 332

0

400

800

1200

1600

2000(a)

Pd 3d5/2

337.4Pd 3d3/2

342.7

Binding Energy (eV)

Inte

nsity

(Cps

)

348 344 340 336 332

0

400

800

1200

1600

2000(b)

Pd 3d5/2

337.4Pd 3d3/2

342.7

Binding Energy (eV)

Inte

nsity

(Cps

)

Figure 38: XP spectra of the Pd 3d region of a TPDMT SAM exposed to Cp(allyl)Pd for

(a) 1 hour and (b) the same treated with hydrogen gas.

75

348 344 340 336 332

0

400

800

1200

1600

2000(a)

Pd 3d5/2

335.6

Pd 3d3/2

340.9

Pd 3d5/2

337.4Pd 3d3/2

342.7

Binding Energy (eV)

Inte

nsity

(Cps

)

348 344 340 336 332

0

400

800

1200

1600

2000(b) Pd 3d5/2

335.6

Pd 3d3/2

340.9Pd 3d5/2

337.6Pd 3d3/2

342.9

Binding Energy (eV)

Inte

nsity

(Cps

)

Figure 39: XP spectra of the Pd 3d region of a TPDMT SAM exposed to Cp(allyl)Pd for

(a) 24 hours and (b) the same treated with hydrogen gas.

Table 5: Pd 3d5/2 peak fit data of Pd deposited TPDMT SAM.

Sample Pd 3d5/2 - BE (total area) 1 h to precursor [FWHM � 1.4] 337.40 eV Pd2+ 1 h to precursor + H2 gas [FWHM � 1.4] 337.40 eV Pd2+

Pd2+ 24 h to precursor [FWHM � 1.4] 337.40 eV (84.9%) 335.60 eV (15.1%) Pd0

Pd2+ 24 h to precursor + H2 gas [FWHM � 1.6] 337.60 eV (25.2%) 335.60 eV (74.8%) Pd0

76

Sulphur 2p XPS data: The deposition of Pd is also reflected in the S 2p XPS data. The S

2p3/2, 1/2 doublet was fitted using two peaks with a separation fixed at 1.18 eV and a

relative ratio of 2. TPDMT SAM exhibits two doublets at 162.0 eV and 163.2 eV which

are assigned to Au-thiolate (-S-Au) and to thiol sulphur species (-SH) exposed at the

vacuum side of the SAM (Fig. 23b, Section 3.1.2). The S 2p spectra recorded after

exposure to the precursor for times varying between 1 and 24 hours, respectively are

shown in Figure 40a and 40c. After the exposure to the Pd precursor a new sulphur

species with a S 2p3/2 binding energy of 163.6 eV emerges. This species is assigned to the

sulphur atoms each bound to a single palladium atom (-S-Pd2+-Allyl). The XPS data

recorded after the reduction (exposure to H2) step is displayed in Fig. 40b and 40d. The S

2p XPS signals basically remain unchanged (Fig. 40b) on the sample exposed to

precursor for 1 h even after the reduction step. On the other hand, for the SAMs exposed

for a long time to the precursor, a peak at 162.3 eV is observed after the reduction (Fig.

40d). This species is assigned to palladium thiolate species with the palladium being in

the Pd0 oxidation state in a palladium cluster. Apart from the main peaks at 162.0 eV (-S-

Au), 162.3 eV (-S-Pd0), 163.2 eV (-SH) and 163.6 eV (-S-Pd2+), there are signals located

at higher binding energies which are assigned to oxidized sulphur species. A S 2p3/2

signal centered at 167.3 eV is observed for the TPDMT SAM. For SAMs exposed to Pd

precursor for 1 and 24 h, and for SAMs exposed to the precursor followed by the

treatment with hydrogen gas, a variety of S-O species are observed. The increase of the

signal corresponding to S-O species after H2 gas treatment agrees well with the decrease

of signal intensity at 163.2 eV (Fig. 40d). The decrease in intensity of the signal at 163.2

eV suggests a massive consumption of unbound SH groups by oxidation. The signals at

higher binding energies of 168.5 and 169.2 eV correspond to higher oxides of sulfur (two

and more O atoms per S atom) [221, 222].

77

0400800

12001600

(a)

0200400600800

S 2p XPS data

(c)

Binding Energy (eV)

Inte

nsity

(Cps

)

0200400600800

(b)

172 170 168 166 164 162 160 1580

100200300400

(d)

Figure 40: S 2p spectra of Pd covered TPDMT/Au and hydrogen gas exposed samples.

(a) STE, (b) STE + H2 gas, (c) LTE and (d) LTE + H2 gas. The spectra are decomposed

into the components associated with the S-Au (red), the S-H (blue), the S-Pd2+-allyl

(green), the S-Pd cluster (orange) and the oxidized S groups (see Table 6).

78

Table 6: S 2p peak fit data of Pd deposited TPDMT SAM

Binding energy in eV (total area %) FWHM � 1.1 (a) STE, (b) STE + H2 gas, (c) LTE and (d) LTE + H2 gas

SAM (a) (b) (c) (d) Assignment Colour 161.96 (7.8)

161.96 (13.8)

161.98 (17.9)

161.96 (9.6)

161.94 (6.6)

S-Au Red

163.20 (80.1)

163.00 (39.8)

162.88 (36.9)

162.88 (32.6)

163.00 (12.1)

S-H Blue

- - - 162.34 (15.3)

162.37 (25.2)

S-Pd0 Orange

- 163.60 (37.4)

163.63 (23.6)

163.60 (21.1)

163.70 (8.8)

S-Pd2+ Green

165.00 (7.9)

164.90 (6.1)

164.90 (4.4) Dark gray

166.70 (9.1)

166.70 (9.6)

166.20 (7.4) Gray

167.27 (7.7)

Light Gray

168.45 (13.1)

Light yellow

167.30 (12.1)

166.50 (8.9)

168.00 (4.6)

167.90 (5.7)

169.20 (14.7)

Oxidized sulphur

Magenta

Carbon 1s XPS data: C 1s spectra recorded for TPDMT SAM is presented in Chapter 3

(Fig. 23a, Section 3.1.2). The spectra reveal a main peak at 284.6 eV assigned to the

aromatic backbone and a shoulder at slightly higher binding energies (286.2 eV) assigned

to shake-up processes. The XPS data recorded after the exposure to the Pd precursor for 1

and 24 h are shown in Figure 41a and 41b respectively. The main peak for the aromatic

backbone (284.5 eV) is clearly visible in both cases. The sample which was exposed for

24 h to the precursor and which was subsequently subjected to a H2 gas treatment

exhibits a new peak at around 288.5 eV (Fig. 41d). This high-binding energy reveals the

presence of oxidized carbon species. The spectra are decomposed into a main peak

assigned to the aromatic backbone (black), a shoulder at high-binding energy (blue) and

oxidized carbon species (green) (Table 7).

79

0

10000

20000

30000 (a) TPDMT SAM + Pd (STE)

0

10000

20000 (b) TPDMT SAM + Pd (STE)+ H2 gas

Inte

nsity

(Cps

)

Binding Energy (eV)

0

10000

20000 (c) TPDMT SAM + Pd (LTE)

292 290 288 286 284 282 280

0

10000 (d) TPDMT SAM + Pd (LTE)+ H2 gas

Figure 41: C 1s spectra of Pd covered TPDMT/Au and hydrogen gas exposed samples.

Table 7: C 1s peak fit data of Pd deposited TPDMT SAM.

Binding energy in eV (total area %) (a) STE (FWHM � 1.4), (b) STE + H2 gas (FWHM � 1.4), (c) LTE (FWHM � 1.4) and

(d) LTE + H2 gas (FWHM � 1.5). For SAM the FWHM � 1.3 SAM (a) (b) (c) (d)

284.6 (95.7) 284.5 (92.6) 284.8 (95.9) 284.6 (95.1) 284.5 (72.1) 286.2 (4.3) 286.3 (7.4) 286.3 (4.1) 286.4 (4.9) 286.4 (20.1) - - - - 288.5 (7.8)

80

5.1.2. NEXAFS of Pd deposited TPDMT-SAM

The C K-edge NEXAFS data for a TPDMT SAM is discussed in Chapter 3 (Fig. 24,

Section 3.1.2). NEXAFS spectra of the Pd covered TPDMT SAM and hydrogen gas

exposed samples acquired at different incidence angles are presented in Figure 42. All the

spectra are dominated by the intense �*-resonance of the phenyl rings at 285.0 eV,

accompanied by several broad #*-resonances at higher binding energies.

280 285 290 295 300 305 310 315

0

2

4

6

8

10

12

Nor

mal

ized

PE

Y

Photon Energy (eV)

(a) TPDMT+Pd(STE)

90°

55°

30°

90°- 30°

280 285 290 295 300 305 310 315

0

2

4

6

8

10

Nor

mal

ized

PE

Y

Photon Energy (eV)

(b) TPDMT+Pd(LTE)

90°

55°

30°

90°- 30°

280 285 290 295 300 305 310 315

0

2

4

6

8

10

Nor

mal

ized

PE

Y

Photon Energy (eV)

(c) TPDMT+Pd(STE)+H2 gas

90°

55°

30°

90°- 30°

288.6

280 285 290 295 300 305 310 315

0

2

4

6

8

10

Nor

mal

ized

PE

Y

Photon Energy (eV)

(d) TPDMT+Pd(LTE)+H2 gas

90°

55°

30°

90°- 30°

Figure 42: NEXAFS spectra of Pd covered TPDMT/Au and hydrogen gas exposed

samples.

81

The linear dichroism of the different samples can be followed by the difference spectra.

The difference spectrum is the difference between the spectra acquired at a particular X-

ray incidence angle and another angle taken as a reference [212]. The 90°-30° difference

spectrum for the TPDMT SAM exposed to precursor for 1 and 24 hours and for hydrogen

gas exposed Pd covered SAMs are presented in Figure 42 (green curves). The amplitude

of the difference peaks is a fingerprint of molecular orientation. Comparing the spectra of

the SAMs exposed to the precursor for one hour (STE) with those for the SAMs exposed

to the precursor for 24 h (LTE), it is clear that the short time exposed sample exhibits

high orientational order. The amplitude of the difference peak decreases for the samples

subjected to hydrogen gas treatment. This implies a low orientational order in the films

subjected to reduction with H2 gas. The difference spectrum acquired using the magic

angle of X-ray incidence (55°) as a reference is shown in Figure 43. The intensity of the

absorption resonances decreased significantly, after hydrogen gas treatment of the Pd

covered TPDMT SAMs.

280 287 294 301 308 315

-1.2

-0.8

-0.4

0.0

0.4

0.8

1.2

Photon Energy (eV)

90°- 55°

30°- 55°

Nor

mal

ized

PE

Y

TPDMT

280 287 294 301 308 315Photon Energy (eV)

TPDMT+Pd(STE)

90°- 55°

30°- 55°

280 287 294 301 308 315Photon Energy (eV)

90°- 55°

30°- 55°

TPDMT+Pd(LTE)

280 287 294 301 308 315Photon Energy (eV)

90°- 55°

30°- 55°

TPDMT+Pd(STE)+ H2 gas

280 287 294 301 308 315Photon Energy (eV)

90°- 55°

30°- 55°

TPDMT+Pd(LTE)+ H2 gas

Figure 43: 90°-55° difference spectra of Pd covered TPDMT/Au and hydrogen gas

exposed samples.

82

284.9

286.4

280 285 290 295 300 305 310 315-0.8

-0.4

0.0

0.4

0.8

1.2(a)

Nor

mal

ized

PE

Y

[TPDMT+Pd(STE)] - [TPDMT]

30°55°90°

Photon energy (eV)

284.9

286.3

280 285 290 295 300 305 310 315-0.8

-0.4

0.0

0.4

0.8

1.2(b)

55°90°

30°

[TPDMT+Pd(LTE)] - [TPDMT]

Nor

mal

ized

PE

YPhoton energy (eV)

284.6

287.1

285.1

286.4

280 285 290 295 3000

2

4

6

8

10(d)

Nor

mal

ized

PE

Y

Photon Energy (eV)

C5H6

Cp(allyl)Pd

Figure 44: Difference spectra of precursor exposed samples and the TPDMT SAM.

(a) TPDMT SAM (1 h to precursor), (b) TPDMT SAM (24 h to precursor), (c) For better

presentation, the 55° difference spectra is highlighted and (d) NEXAFS spectrum of

Cp(allyl)Pd and cyclopentadiene (Adapted from reference [219]).

83

In Figure 44, the difference spectrum of precursor exposed samples and the TPDMT

SAM is displayed. The difference spectra is obtained after exposure to Cp(allyl)Pd and

subtracting the spectrum of the original SAM both normalized at the pre-edge. The

spectrum exhibits a resonance at 286.4 eV. On extending the exposure time to 24 hours,

the intensity of this peak increases. In following previous work [219], the resonance at

286.4 eV is assigned to the allyl ligand. The position of the �*-resonance of Cp (285.1

eV) matches the position of the �*-resonance of the phenyl ring (285.0 eV).

5.1.3. IRRAS of Pd deposited TPDMT-SAM

In Figure 45, the IR spectra recorded for the SAMs before and after exposure to the Pd

precursor are displayed. All IR spectra recorded for the Pd precursor treated samples

were normalized by division by the data recorded for a TPDMT SAM (background). The

samples exposed to precursor for one hour exhibit bands at 804 cm-1, 1265 cm-1 and 2932

cm-1. As the exposure of SAMs to the Pd precursor is increased to 24 hours, an increase

in the intensity of the vibration at 2932 cm-1 was observed along with the emergence of

new bands in the region between 2000-800 cm-1. Figure 46 shows the pellet IR and the

calculated IR spectrum of Cp(allyl)Pd. The KBr pellet IR data of Cp(allyl)Pd was

compared with the reported data [131]. The vibrational frequencies have been computed

using commercial program package (Gaussian 98, DFT calculations using the B3LYP-

functional) and scaled by a factor of 0.9339. This normalization factor was deduced by

comparing the theoretical and experimental value for the C-H stretching vibration

[Experimental value/Theoretical value = 3040 cm-1/3255 cm-1 = 0.9339].

Both the pellet IR and calculated spectrum of Cp(allyl)Pd were used to assign the

vibration bands in the SAMs exposed to Pd precursor (Table 8). The bands at 1265 cm-1

and 2932 cm-1 are assigned to the allyl ligand and -CH2 stretching vibrations,

respectively. Increase in the intensity of the vibrations at 2932 cm-1 in the long time

exposed samples indicates the presence of residual allyl and cyclopentadienyl ligands. In

case of the long-term exposed surface, the IRRAS data show new peaks at about 1103

and 1048 cm-1. These signals coincide with the vibrations of RSO2 (typically at about

1030-1100 cm-1) and RSO3 groups (typically at 1140-1250 cm-1), resulting from the Pd-

catalyzed oxidation of terminal thiol groups [223].

84

1600 1500 1400 1300 1200 1100 1000 900 800

1004

1492 TPDMT-SAM

Abs

orba

nce

Wavenumber (cm-1)

0.2

TPDMT+Pd (STE)

1263 804

0.02

82610481103

1265 805TPDMT+Pd (LTE)

0.2

(a)

3100 3050 3000 2950 2900 2850 2800

3030 29282859

TPDMT-SAM

0.02

28582930TPDMT+Pd (STE)

Abs

orba

nce

2965

(b)

2932TPDMT+Pd (LTE)

Wavenumber (cm-1)

0.02

0.2

Figure 45: Infrared spectroscopic data of TPDMT SAM and Pd precursor treated SAMs.

(a) The low frequency (1600 cm-1 to 750 cm-1) and (b) the high frequency regions (3100

cm-1 to 2800 cm-1).

85

Figure 46: IR spectra of bulk Cp(allyl)Pd in KBr (bottom curve) and calculated IR

spectrum of Cp(allyl)Pd (upper curve).

Table 8: Calculated and observed vibrational frequencies of Cp(allyl)Pd and the IR

frequencies of the precursor treated TPDMT SAMs.

C5H5PdC3H5 Calculated x (0.9339)

C5H5PdC3H5KBr Pellet Experiment

STE (1 h)(cm-1)

LTE (24 h)(cm-1) Assignment

3056 3059 - - Cp 3040 3040 - - Cp 2976 2960 2965 2965 Allyl 2952 2934 2930 2932 Allyl 1303 1262 1263 1265 Allyl and Cp 1171 1100 - 1103 Allyl 1007 1012 - - Allyl and Cp 790 806 804 805 Allyl and Cp 724 766 - - Allyl and Cp

86

SEM of Pd deposited TPDMT-SAM

Figure 47 shows a SEM micrograph recorded for the TPDMT SAM exposed to

Cp(allyl)Pd for 24 hours followed by reduction using hydrogen gas. The SEM image

reveals that the surface is covered with Pd clusters (bright spots) with sizes up to 40 nm.

Figure 47b is a zoomed-up view of Figure 47a, where the Pd particles can be observed

clearly.

Figure 47: SEM image of Pd clusters on a TPDMT SAM exposed to Cp(allyl)Pd for 24

hours followed by the treatment with hydrogen gas.

87

5.2. Deposition of palladium onto a deprotected BPDMAc-1 SAM The fabrication of well-ordered SAMs with dithiols has many applications in molecular

electronics. Thiols have high affinity to metals and they can promote the growth of metal

films at the SAM ambient interface. The SAM formation in the case of alkanedithiols

results in stable lying-down arrangements, due to the flexibility of the molecular

backbone [20]. On the other hand, molecules such as oligophenyl dithiols or

oligophenyleneethynylene dithiols with a rigid molecular backbone can form ordered

SAMs. In order to have metal films at the SAM ambient interface, well-ordered SAM is

necessary. Earlier studies on biphenyldimethyldithiol (BPDMT) and biphenyldithiol

show that they do not form well oriented monolayers [7]. A structure with a highly

disordered multilayer, with a significant number of biphenyl units linked by S-S disulfide

bonds has been proposed for both the systems. The disordered structures are possible

through the formation of dimers or higher oligomers with S-S bonds (Fig. 48a). In this

study, chloroform is used as the solvent.

Figure 48a: Illustration of the formation of disordered layers via disulfide linkages for

the BPMDT molecule. Adapted from reference [7].

Tai et al. have demonstrated the formation of a highly oriented and densely packed SAMs

formed from BPDMT solution in tetrahydrofuran (stabilized with 0.1% hydroquinone)

[174]. The quality of the SAMs was related to the solvents used for monolayer

preparation. Poor quality SAMs were obtained when ethanol is used as the solvent

instead of tetrahydrofuran.

88

In the present work, a deprotection approach has been employed to fabricate high-quality

biphenyldimethyldithiol SAM from monoacylated dithiol in which a thioester group (Fig.

48b) protects one of the thiol groups.

Figure 48b: Illustration of the formation of a deprotected BPDMAc-1 SAM on gold.

The biphenyldimethyldithiol (deprotected BPDMAc-1) SAM was obtained by a

deacylation reaction using 0.01M sodium hydroxide. The BPDMAc-1 molecules forms

highly ordered SAM and the biphenyldimethyldithiol SAM formed from BPDMAc-1

SAM retains the quality after the hydrolysis process. The deprotected BPDMAc-1 SAMs

were characterized by IRRAS, XPS and NEXAFS. The results are presented in Chapter 3

and 4. The exposure of the deprotected BPDMAc-1 SAMs to the precursor vapor were

performed using the same procedure as described above for TPDMT.

89

5.2.1. XPS of Pd deposited deprotected BPDMAc-1 SAM

Pd 3d XPS data: Pd 3d region XPS data recorded for the deprotected BPDMAc-1 SAM

exposed to the precursor vapor for short times (1 h) is shown in Figure 49. In this case,

the amount of deposited Pd is considerably less than the amount deposited on TPDMT

SAMs for the same exposure time. In contrast, to the TPDMT SAMs, the reaction

between the precursor and the deprotected BPDMAc-1 SAM is significantly delayed.

348 344 340 336 332

0

100

200

300

400

500

Au 4f7/2

335.0Pd 3d3/2

340.9

Pd 3d5/2

335.6Pd 3d3/2

342.7

Pd 3d5/2

337.4

Inte

nsity

(Cps

)

Binding Energy (eV)

Figure 49: XP spectra of the Pd 3d region of a deprotected BPDMAc-1 SAM exposed to

Cp(allyl)Pd for 1 hour.

For longer exposures (24 h) a substantially larger amount of Pd2+ (Fig. 50a) is seen. After

exposure to dihydrogen gas reduction is observed similar to the case of Pd-deposition on

TPDMT SAMs (Fig. 50b). After contact with hydrogen gas along with metallic

palladium about 29% of Pd2+ is still present, which is possibly due to an oxidation of the

Pd0 clusters upon contact with air.

90

348 344 340 336 3320

500

10001500

2000

25003000

3500

Pd 3d3/2

340.9Pd 3d5/2

335.6

Pd 3d3/2

342.7

Pd 3d5/2

337.4

Inte

nsity

(Cps

)

Binding Energy (eV)

(a)

348 344 340 336 3320

500

10001500

2000

25003000

3500

Pd 3d3/2

340.9

Pd 3d5/2

335.6

Pd 3d3/2

342.7

Pd 3d5/2

337.4Inte

nsity

(Cps

)

Binding Energy (eV)

(b)

Figure 50: XP spectra of the Pd 3d region of a deprotected BPDMAc-1 SAM exposed to

Cp(allyl)Pd for (a) 24 hours and (b) the same treated with hydrogen gas.

Table 9: Pd 3d5/2 peak fit data of Pd deposited deprotected BPDMAc-1 SAM.

Sample Pd 3d5/2 - BE (total area) Pd2+ Pd 0 1 h to precursor [FWHM � 1.6]

337.40 eV (17.2%) 335.60 eV (24.8%) 335.00 eV (58.0%) Au 4d5/2

Pd2+ 24 h to precursor [FWHM � 1.4] 337.40 eV (84.6%) 335.60 eV (15.4%) Pd0

Pd2+ 24 h to precursor + H2 gas [FWHM � 1.6] 337.60 eV (28.8%) 335.60 eV (71.2%) Pd0

91

S 2p XPS data: S 2p XPS data recorded for deprotected BPDMAc-1 SAM is presented

in Chapter 3. The peaks at 161.96 eV and 163.3 eV are assigned to Au-thiolate and to the

thiol tail group, respectively. Figure 51a and 51b show the S 2p XPS data recorded after

exposure of the SAM to the Pd precursor for 1 and 24 hours respectively. In Figure 51c,

the spectra of 24 hour sample after exposure to dihydrogen gas is displayed. The peak at

163.6 eV is assigned to the sulphur-palladium bond formed after exposure to precursor.

Again, oxidation of the SAM surface is observed as indicated by the peaks at higher

binding energies (166.5 eV and 168.5 eV).

Table 10: S 2p peak fit data of Pd deposited deprotected BPDMAc-1 SAM.

Binding energy in eV (total area %) FWHM � 1.1 (a) STE, (b) LTE and (c) LTE + H2 gas

SAM (a) (b) (c) Assignment Colour 161.96 (18.4)

161.96 (19.9) 161.96 (8.5) 161.96 (7.7) S-Au Red

163.35 (76.0)

163.25 (40.1) 163.02 (32.4) 163.02 (12.8) S-H Blue

- - 162.34 (12.2) 162.34 (35.5) S-Pd0 cluster Orange - 163.56 (15.0) 163.70 (17.1) 163.60 (10.9) S-Pd2+ Green

164.90 (5.4) 164.90 (8.9) Dark gray 166.70 (11.0) 166.70 (3.8) Gray

167.90 (5.1) Light Gray

168.04 (5.6)

165.00 (5.4) 166.70 (5.9) 168.20 (13.6) 167.90 (13.4)

168.80 (15.2)

Oxidized sulphur

Light yellow

92

0

300

600

900(a)

172 170 168 166 164 162 160 158

0

200

400

600(c)

0

200

400

600

S 2p XPS data

(b)

Inte

nsity

(Cps

)

Binding Energy (eV) Figure 51: S 2p spectra of Pd covered deprotected BPDMAc-1/Au and hydrogen gas

exposed samples.

(a) STE, (b) LTE and (c) LTE + H2 gas. The spectra are decomposed into the components

associated with the S-Au (red), the S-H (blue), the S-Pd2+-allyl (green), the S-Pd cluster

(orange) and the oxidized S groups (see Table 10).

93

C1s XPS data: Figure 52 shows the C 1s XPS data. The deprotected BPDMAc-1 SAM

and the SAMs exposed to the precursor vapor show a peak at 284.5 eV which is assigned

to the aromatic biphenyl backbone. The samples treated for a long time with the

precursor vapor followed by hydrogen treatment show a peak at around 288.5 eV which

indicates the presence of oxidized carbon species.

0

10000

20000 (a) dep. BPDMAc-1 SAM+ Pd (STE)

0

10000

20000

(c) dep. BPDMAc-1 SAM+ Pd (LTE)+ H2 gas

292 290 288 286 284 282 2800

10000

20000

(b) dep. BPDMAc-1 SAM + Pd (LTE)

Inte

nsity

(Cps

)

Binding Energy (eV) Figure 52: C 1s spectra of Pd covered deprotected BPDMAc-1/Au and hydrogen gas

exposed samples.

Table 11: C 1s peak fit data of Pd deposited deprotected BPDMAc-1 SAM.

Binding energy in eV (total area %) (a) STE (FWHM � 1.4), (b) LTE (FWHM � 1.4) and

(c) LTE + H2 gas (FWHM � 1.4). For SAM the FWHM � 1.3 SAM (a) (b) (c)

284.5 (96.0) 284.6 (89.7) 284.8 (94.4) 284.6 (77.4) 286.3 (4.0) 286.3 (10.3) 286.3 (5.6) 286.3 (15.3) - - - 288.4 (7.3)

94

5.2.2. NEXAFS of Pd deposited deprotected BPDMAc-1 SAM

The C 1s NEXAFS data recorded for the deprotected BPDMAc-1 show a marked linear

dichroism (discussed in Chapter 3). Figure 53 presents the NEXAFS spectra of the Pd

covered deprotected BPDMAc-1 SAM and hydrogen gas exposed samples acquired at

different incidence angles.

280 285 290 295 300 305 310 315 320

0

2

4

6

8

10

Nor

mal

ized

PE

Y

Photon Energy (eV)

90°-30°

30°

55°

90°

(a) dep. BPDMAc-1+Pd(STE)

280 285 290 295 300 305 310 315 320

0

2

4

6

8

10

Nor

mal

ized

PEY

90°

55°

30°

90°-30°

Photon Energy (eV)

(b) dep. BPDMAc-1+ Pd(LTE)

285.2

288.6

280 285 290 295 300 305 310 315

0

2

4

6

8

10 (c) dep. BPDMAc-1+Pd(LTE)+H2 gas

90°

55°

30°

90°-30°

Nor

mal

ized

PE

Y

Photon Energy (eV) Figure 53: NEXAFS spectra of Pd covered deprotected BPDMAc-1/Au and hydrogen gas

exposed samples.

95

As observed in the case of TPDMT, the spectra of samples exposed to precursor for 1 and

24 hours, are dominated by the �*-resonance of the phenyl rings at 285.0 eV,

accompanied by several broad and less intense #*-resonances at higher binding energies.

The difference spectrum (90°-30°) for the dep. BPDMAc-1 SAM exposed to precursor

for 1 and 24 hours and for hydrogen gas exposed Pd covered SAMs are included in

Figure 53 (green curves). The amplitude of the difference peak for the short time exposed

sample is high when compared to the long time exposed sample.

280 287 294 301 308 315-1.2

-1.0

-0.8

-0.6

-0.4

-0.2

0.0

0.2

0.4

0.6

0.8

1.0

1.2

30°- 55°

Nor

mal

ized

PEY

Photon Energy (eV)

90°- 55°

dep. BPDMAc-1

280 287 294 301 308 315

30°- 55°

Photon Energy (eV)

90°- 55°

dep. BPDMAc-1 + Pd(STE)

280 287 294 301 308 315

30°- 55°

90°- 55°

Photon Energy (eV)

dep. BPDMAc-1 + Pd(LTE)

280 287 294 301 308 315

30°- 55°

dep. BPDMAc-1 + Pd(LTE) +H2 gas

90°- 55°

Photon Energy (eV) Figure 54: 90°-55° difference spectra of Pd covered deprotected BPDMAc-1/Au and

hydrogen gas exposed samples.

96

284.9

280 285 290 295 300 305 310 315-0.4

0.0

0.4

0.8

1.2

1.6 (a)N

orm

aliz

ed P

EY

[dep. BPDMAc-1+Pd(STE)] - [dep. BPDMAc-1]

30°55°90°

Photon energy (eV)

285.0

286.4

280 285 290 295 300 305 310 315-0.4

0.0

0.4

0.8

1.2

1.6(b)

55°90°

30°

[dep. BPDMAc-1+Pd(LTE)] - [dep. BPDMAc-1]

Nor

mal

ized

PE

YPhoton energy (eV)

Figure 55: Difference spectrum of precursor exposed samples and the deprotected

BPDMAc-1 SAM.

The difference peak for the sample subjected to hydrogen gas treatment is shown in

Figure 53c. The results suggest a low orientational order in the films subjected to

reduction with H2 gas. The difference spectrum acquired using the magic angle of X-ray

incidence (55°) as a reference is shown in Figure 54. This difference spectrum is also

shows the decrease in the intensity of the absorption resonances after hydrogen gas

treatment of the Pd covered TPDMT SAMs. In Figure 55, the difference spectrum of

precursor exposed samples and the deprotected BPDMAc-1 SAM is displayed. A

resonance at 284.9 eV is observed for the samples exposed to the precursor for one hour.

On extending, the exposure time to 24 h the intensity of the peak at 285 eV increases and

the resonance at 286.4 eV is clearly visible. This peak at 286.4 eV is assigned to the allyl

ligand.

97

Discussion:

The experimental data presented above on the chemical vapor deposition of Cp(allyl)Pd

on dithiol SAMs provide valuable insight to the metallization of SAMs. The reactivity of

Cp(allyl)Pd with terphenyldimethyldithiol (TPDMT) and biphenyldimethyldithiol (dep.

BPDMAc-1) SAMs are discussed in this section.

The analysis of the experimental results reveals that the deposition of palladium on

SAMs exposing a thiol terminated surface using Cp(allyl)Pd consists of two steps. The

initial step is a reaction of the precursor with the free thiol (-SH) groups exposed at the

SAM surface. This complexation reaction proceeds as observed in the bulk. The

reactivity of Cp(allyl)Pd with various thiols in solution has been studied by Weckenmann

et al [94, 224].

Pd Pd

S

S

Pd

R

R

R-SH

R = tBu, [p-CH3C6H4] or p-tolyl

Figure 56: Schematic reaction of Cp(allyl)Pd with thiols in solution.

When the precursor is treated with the solution of t-butyl thiol and p-thiocresol, the

formation of dimeric (allyl)(-thiolato)palladium is observed. Schematic reaction of

Cp(allyl)Pd leading to the formation of dimeric allylpalladiumthiolato complexes is

shown in Figure 56 (Adapted from the reference [94]).

The XPS data (Fig. 38a) conclusively unravel the mechanism of the reaction between the

precursor and the free thiol groups at the SAM surface. When the precursor comes in

contact with the -SH groups on the SAM surface, a Pd2+-S bond is formed leading to the

appearance of a Pd 3d5/2 XPS signal at 337.4 eV. This binding energy is in agreement

98

with the previously reported value of 337.7 eV for the Pd 3d5/2 signal in Cp(allyl)Pd

multilayer deposited on Pd(111) [219]. With regard to the multilayer data, the XPS

results for the monolayer reveal a downshift of 0.3 eV in binding energy. This is

consistent with the presence of different ligands bound to palladium. In the precursor, the

Pd atom is bound to the allyl and to the cyclopentadienyl ligand (337.7 eV) whereas after

the reaction with dithiol SAMs, the Pd atom is bound to the allyl ligand and to the sulfur

from the thiol (337.4 eV). Additionally, the reaction between the thiol and the precursor

leads to a shift in the S 2p signal. It is well-known that the sulfur atoms bound to metal

appear at lower binding energy when compared to the sulfur atoms in the free thiol

groups [94]. In the present study, the S 2p peaks at 162.0 and 163.6 eV are assigned to

Au-S and -S-Pd2+-allyl. The free SH group appears at 163.2 eV.

The allyl-Pd2+ covered TPDMT SAM surface prepared by exposing the SAM to the Pd

precursor for 1 hour (STE) is stable against reduction by dihydrogen gas. The XPS data

do not reveal a significant amount of Pd0 species (Fig. 38b). This is an interesting and

somewhat unexpected observation since the precursor, Cp(allyl)Pd, can be readily

reduced with dihydrogen gas at room temperature [180]. On the other hand the dimeric

(allyl)(-thiolato)palladium complexes (Fig. 56) are stable against reduction [94].

The reactivity of Cp(allyl)Pd with different electrophilic and nucleophilic agents was

studied by Gubin et al [126]. It was shown that the cyclopentadienyl ligand is readily

eliminated whereas the bond of palladium to the allyl group is stable [126]. Bogdanovic

et al. have observed the selective cleavage of the cyclopentadienyl group in a reaction

between hydrogensulphide and Cp(allyl)Pd [225]. The product of this reaction is �3-

allylhydrogensulfidopalladium (similar structure as the product in Fig. 56, R = H). It has

been observed that further reaction of Cp(allyl)Pd with �3-allylhydrogensulfidopalladium

yields an allyl compound with the elimination of Cp ligand [226]. The reaction of

Cp(allyl)Pd with thiols in solution also yields an allyl palladium complex of which the

structure was characterized by single crystal X-ray diffraction studies [94].

99

In the present study, the IRRAS and NEXAFS results show the presence of allyl groups

on the SAM surface. For the TPDMT samples exposed to the precursor for 1 h, the

vibrational bands at 1265 cm-1 and 2932 cm-1 are observed which are assigned to the allyl

ligand. Additionally, in the NEXAFS difference spectra of the samples exposed to

precursor for one hour, a resonance at 286.4 eV is observed which is assigned to the allyl

ligand. In addition, the allyl covered SAM surface is not reduced when treated with

dihydrogen gas similar to the dimeric (allyl)(-thiolato)palladium complexes. This

observation along with the IRRAS and NEXAFS results suggest the cleavage of the

cyclopentadienyl ligand. The cyclopentadienyl ligand is replaced by the sulfur from the

thiol, whereas the allyl ligand is retained (see Fig.59).

On extending the exposure time of the SAMs to the Pd precursor to about 24 h (LTE),

some of the precursor molecules spontaneously decompose on the allyl-terminated SAM

resulting in the formation of a small amount of metallic Pd as is evident from the Pd 3d

XPS data (335.6 eV) (Fig. 39a). However, the amount of metallic Pd formed in this case

is rather small. Once such Pd particles are formed, they can decompose the remaining

Pd2+ centers autocatalytically in the presence of hydrogen gas as has been reported earlier

[127]. The sample exposed to precursor for 24 hours and treated with dihydrogen gas is

found to be readily reduced to metallic Pd. The Pd0 already present before exposure to H2

act as an active site and provides H atoms facilitating the reduction. The XPS data reveal

a small amount of Pd2+ present on the surface after the reduction process. This

observation can be explained either by an incomplete reduction or, more likely, by an

oxidation of the Pd0 particles upon contact with air (during the transfer process into the

spectrometer). After the reduction process, a new S 2p3/2 XPS signal is observed at 162.3

eV which is assigned to S bound to the metal (Pd-thiolate). The SEM micrographs show

Pd clusters in accordance with the Pd0 featured in the XPS data. The particles grow up to

40 nm indicating the occurrence of nucleation and diffusion processes of the reduced

palladium. As the exposure time to the Pd precursor is increased, the catalytic activity of

the small Pd0 particles causes a more unspecific decomposition of the Pd precursor

leading to different carbon residues.

100

Thickness of the monolayers: The relative intensities of the C 1s and Au 4f7/2 lines of

the XPS data have been used to estimate the thickness of the monolayers [216]. XPS data

recorded for a freshly prepared TPDMT and deprotected BPDMAc-1 SAM was used as

reference system for palladium deposited TPDMT and deprotected BPDMAc-1 SAM

samples respectively.

The film thickness is obtained by the following equation. In this equation, dsample is the

thickness of the sample under investigation. In the case of TPDMT SAM samples,

dreference is the thickness of the TPDMT SAM (19.4 Å) and for deprotected BPDMAc-1

SAM samples, dreference is the thickness of the BPDMT SAM (15.5 Å) [7, 174].

� �

� �

sample referenceC1s

C AuAu4f

C1s sample referenceAu4f

Au C

d d1 exp expI (sample)II d d(reference) exp 1 expI

� � � �� � � �� �� �� � � � � � � �

� � � �� �� � � �

(5)

IC1s and IAu4f are the measured intensities of C 1s and Au 4f7/2 lines. The escape depths

�Au = 16 Å at a kinetic energy of 314 eV and �C = 9 Å at a kinetic energy of 115 eV are

used [155]. The thicknesses of the different TPDMT and deprotected BPDMAc-1 SAM

samples are listed in Table 12 and Table 13.

Sample C1s

Au 4f

II dsample (Å)

(a) TPDMT SAM 2.3 19.4

(b) TPDMT SAM + Cp(allyl)Pd for 1 h 1.7 16.0

(c) TPDMT SAM + Cp(allyl)Pd for 1 h + H2 gas 2.4 19.6

(d) TPDMT SAM + Cp(allyl)Pd for 24 h 3.5 25.0 (e) TPDMT SAM + Cp(allyl)Pd for 24 h + H2 gas 0.5 5.6

a b c d e --0

1

2

3

4

5

a b c d e --0

10

20

30

C 1

s/A

u 4f

Thi

ckne

ss

Table 12: Thickness of the Pd covered TPDMT SAM samples.

101

Sample C1s

Au 4f

II dsample (Å)

(a) deprotected BPDMAc-1 SAM 0.33 15.5 (b) deprotected BPDMAc-1 SAM + Cp(allyl)Pd for 1 h 0.28 13.8

(c) deprotected BPDMAc-1 SAM + Cp(allyl)Pd for 24 h 5.14 56.0

(d) deprotected BPDMAc-1 SAM + Cp(allyl)Pd for 24 h + H2 gas 1.86 40

a b c d -- --0123456

a b c d -- --0

102030405060

C 1

s/A

u 4f

Thi

ckne

ss

Table 13: Thickness of the Pd covered deprotected BPDMAc-1 SAM samples.

According to the Table 12, the thickness of the TPDMT SAM sample exposed to

precursor for 1 h is 16.0 Å and after the hydrogen treatment, the thickness is about 19.6

Å. It should be noted that the XPS spectra have been recorded with monochromatized

synchrotron radiation (BESSY). The XPS signal is proportional to the ring current which

varies typically from 250 mA (directly after injection) to 100 mA after 8 hours.

Therefore, absolute intensities will always vary from spectra to spectra. Since the

intensity of the synchrotron radiation changes with time it is rather difficult to provide an

absolute scale for the XPS data. The intensity ratios C 1s/Au 4f, S 2p/Au 4f are plotted in

order to make sure that there are no artifacts in the data (Fig. 57).

SAM

STE

STE+

H

LTE

LTE+

H

0

2

4

6

SAM

STE

LTE

LTE+

H

0

2

4

6 C1s/Au4f S2p/Au4f

Inte

nsity

Rat

io

Dep.BPDMAc-1TPDMT

C1s/Au4f S2p/Au4f

Figure 57: Plot of intensity ratios (C 1s/Au 4f, S 2p/Au 4f).

102

The plot of this intensity ratio shows that within each spectrum the data can be compared.

The difference in the thickness values for the TPDMT SAM sample exposed to precursor

for 1 h is due the variation in the intensity of the synchrotron radiation with time. Taking

this in to consideration it can be concluded that there is no change in the thicknesses for

the TPDMT SAM exposed for 1 h to the precursor and after exposing to hydrogen gas.

Upon extending the exposure time to the palladium precursor to 24 h, an increase in

thickness (~ 5 Å) is observed. Since this increase in thickness cannot be attributed to

deposition of the intact precursor molecule, this increase must be due to a deposition of

palladium/hydrocarbon species on the surface caused by partial decomposition of the

precursor. When the TPDMT SAM exposed to the precursor for 24 h is treated with

hydrogen gas, a prominent decrease of the SAM thickness is observed. This observation

directly demonstrates that a large amount of molecules comprising the SAM has been

removed.

The thicknesses for the palladium covered deprotected BPDMAc-1 samples are displayed

in Table 13. The thickness of the deprotected BPDMAc-1 SAM sample exposed to

precursor for 1 h is 13.8 Å and that of the clean deprotected BPDMAc-1 SAM is 15.5 Å.

There is no change in the thicknesses for the deprotected BPDMAc-1 SAM and the

sample exposed for 1 h to the precursor. The intensity plots (Fig. 57) shows that the

difference in the thickness values for the SAM sample exposed to precursor for 1 h is due

the variation in the intensity of the synchrotron radiation with time. When the exposure

time to the Pd precursor is extended to 24 hours, drastic increase in the thickness is

observed (Table. 13). As in the case of TPDMT SAM, this increase can be attributed to a

deposition of palladium/hydrocarbon species on the surface caused by partial

decomposition of the precursor. When the deprotected BPDMAc-1 SAM exposed to the

precursor for 24 h is treated with hydrogen gas, a decrease of the SAM thickness is

observed.

The thickness results of TPDMT and deprotected BPDMAc-1 SAM samples are

comparable only in the case of samples exposed to palladium precursor for 1 h. In the

case of deprotected BPDMAc-1 sample exposed to precursor for 24 h, thick layers (56 Å)

of palladium/hydrocarbon species is observed whereas in the case of TPDMT sample the

thickness is about 25 Å. Upon extending the exposure time to 24 h, the behaviour differs.

103

This result is also supported by NEXAFS data (Fig. 58). The change in the edge jump is

used to estimate the thickness. In Figure 58a, the SAM samples, TPDMT, TPDMT

exposed to precursor for 1 h (STE) and TPDMT exposed to precursor for 24 h (LTE) are

compared. The gold transmission line is also included. In the case of STE, the chemical

modification involves the transformation of -SH to -S-Pd-Allyl. The height of both does

not differ much. It is clear from the plot that there is no decrease in the thickness of the

TPDMT thiol film after the treatment with Pd precursor (1 h). Figure 58b displays the

deprotected BPDMAc-1 SAM samples, clean SAM, SAM exposed to precursor for 1 h

(STE) and SAM exposed to precursor for 24 h (LTE). There is no decrease in the

thickness of the deprotected BPDMAc-1 thiol film after the treatment with Pd precursor

for one hour. The edge jump for the samples exposed to the precursor for 24 h is found to

be greater than the samples exposed for 1 h (blue curves in Fig. 58b). The results are

consistent with the thickness information obtained from the XPS data.

280 290 300 310 3200

1

2

3

4

5

6

7

8

(b)dep.BPDMAc1+Pd (LTE)dep.BPDMAc1+Pd (STE)dep.BPDMAc1Au transmission

TPDMT+Pd (LTE)TPDMT+Pd (STE)TPDMTAu transmission

Nor

mal

ized

Par

tial E

lect

ron

Yie

ld

Photon Energy (eV)

(a)

280 290 300 310 3200

1

2

3

4

5

6

7

8

Figure 58: Thickness estimation from the edge jump in C K-edge NEXAFS. (a) TPDMT

samples and (b) dep.BPDMAc-1 samples.

104

The decomposition of the precursor molecules and later the SAM molecules itself can be

explained by the catalytic activity of the palladium nanoparticles formed during the

exposure to palladium precursor. Palladium nanoparticles are used as catalysts in

numerous organic and inorganic reactions [227, 228]. Palladium-catalyzed oxidation

reactions are well known in the literature, and effective catalytic activity was observed at

room temperature in ambient environment [229, 230]. Cleavage of the carbon-sulfur

bond from certain thiols and dithioethers can be caused by oxygen by means of a

palladium catalyst in the presence of a co-reductant, either carbon monoxide or hydrogen

[231]. In the present case, the Pd clusters on the surface slowly oxidize first the sulfur

atoms and then the very backbone of the SAM constituents resulting in defect formation.

The oxidation of the aromatic SAM molecules by Pd0 clusters observed here can also be

compared to the oxidation of alkanethiols SAMs formed on a palladium substrate [110].

In principle, the oxidation, decomposition, and subsequent desorption of fragments

leading to a reduction of the SAM thickness can be either caused by the hydrogen gas or

by the ambient since during the transfer of the SAM samples to the XPS apparatuses the

samples are exposed to the ambient for several minutes. With the present experimental

setup, it is not possible to make a final decision. The overall process of the reaction of

Cp(allyl)Pd on TPDMT SAM is summarized in Figure 59. The chemical vapor

deposition of Cp(allyl)Pd on SAMs fabricated from TPDMT results in the formation of

Pd2+-allyl capped surfaces. Clearly, the interaction of the precursor with the SH

terminated surface leads to a break of the Pd-Cp bond. The cyclopentadienyl ligand

leaves the system as cyclopentadiene, and the Pd2+ forms a bond to the surface S atoms.

The Pd2+-allyl capped SAM surface does not react with H2, and metallic Pd can only be

obtained in the presence of small Pd0 particles produced, for example, by prolonged

exposures (24 h) to the Pd precursor. In this process, the allyl ligand is probably

hydrogenated to yield either propene or propane.

105

(b)H2 gas

(d)H2 gas

Pd2+ Pd0

Decomposed Pd precursor molecules

Oxidized TPDMT SAM molecules

(a)Exposure to Cp(allyl)Pd

1 h

(c)Exposure to Cp(allyl)Pd

24 hTPDMT SAM

(b)H2 gas

(d)H2 gas

Pd2+Pd2+ Pd0Pd0

Decomposed Pd precursor molecules

Oxidized TPDMT SAM molecules

(a)Exposure to Cp(allyl)Pd

1 h

(c)Exposure to Cp(allyl)Pd

24 hTPDMT SAM

(a)Exposure to Cp(allyl)Pd

1 h

(c)Exposure to Cp(allyl)Pd

24 hTPDMT SAM

Figure 59: Schematic model showing the deposition of Cp(allyl)Pd and the subsequent

reduction to metallic palladium on TPDMT-SAM.

106

The aromatic dithiols used in the present investigation are analogues to each other. The

reactivity of both TPDMT and deprotected BPDMAc-1 SAM towards the palladium

precursor is expected to be the same. Unexpectedly, the deprotected BPDMAc-1 SAMs

were found to behave quite differently upon exposure to the Pd precursor. After exposure

to the precursor for the same amount of time (1 h), the amount of Pd deposited is

considerably less compared to the TPDMT SAM. It has to be noted here that the SAM

preparation procedures were different. The TPDMT SAM was prepared directly by

immersion of Au substrate in to TPDMT solution whereas biphenyldimethyldithiol SAM

was prepared by a deacylation reaction of BPDMAc-1 SAM. Both the TPDMT and

deprotected BPDMAc-1 SAM surfaces are thiol terminated and this is confirmed by the S

2p XPS data of the respective SAMs. NEXAFS results of the two SAMs shows that they

are highly oriented. No chemical differences are observed between these two SAMs.

Therefore, the reduced reactivity of the deprotected BPDMAc-1 SAMs can be explained

by a very small density of surface defects acting as nucleation centers for the Pd

precursor deposition. The process of formation of palladium thiolate on exposure of the

SAM to the Pd precursor depends on the availability of the –SH units exposed at the

surface, and the density of defects in the SAM accelerates the reaction. Earlier studies

show that the presence of surface H atom was essential for the decomposition of the Pd

precursor on silicon substrates. Clean Si surfaces exhibit the least reactivity whereas the

hydrogen terminated Si surface was highly active [220]. Therefore, the availability of the

hydrogen atoms at the surface is important for the decomposition reaction to take place.

The dependency of reaction speed on surface defect density has been discussed in

Chapter 4. The deacylation reaction on an organic surface by a basic agent was found to

be significantly delayed when the number of defects was reduced. So the efficiency of the

reaction between the Pd precursor and the thiol is mutually related with the availability of

hydrogen atoms on the SAM surface which in turn depends on the packing density of the

SAMs. When the exposure time to the Pd precursor is extended to 24 h, deprotected

BPDMAc-1 exhibits a behavior similar to that observed for TPDMT SAMs. When

treated with hydrogen gas, again a reduction of the Pd2+ species is observed.

107

5.3. Conclusion The experimental results from XPS, IRRAS and NEXAFS spectroscopy presented above

demonstrate that the exposure of thiol terminated organic surfaces fabricated from

terphenyldimethyldithiol to Cp(allyl)Pd results in the formation of an allyl-Pd2+-thiolate

termination. The reaction is found to be similar to analogous reactions in solution.

Exposure of this surface to dihydrogen did not result in a reduction of the Pd2+. It is

concluded that the presence of metallic Pd is required to catalyze the reduction process.

This conclusion is supported by experiments with TPDMT surfaces that were exposed to

the precursor for rather long periods of time, so that small amounts of Pd0 are

spontaneously formed. Such surfaces were found to be readily reduced by exposure to H2

gas, and small metal clusters are formed on the surface. The catalytic activity of the small

Pd cluster, however, also causes the decomposition of the self-assembled monolayer. The

reaction between Cp(allyl)Pd and the deprotected BPDMAc-1 surface is significantly

delayed otherwise, the behavior was found to be rather similar to that of the TPDMT

SAMs. The thiol (-SH) terminated SAMs are thus well suited for a CVD based

metallization.

108

5.4. Outlook The overall process of the reaction of Cp(allyl)Pd on SAMs fabricated from TPDMT is

well understood and the experimental results give a clear picture of the reaction pathway.

On the other hand, the reaction between the precursor and the deprotected BPDMAc-1

surface is delayed. To understand the delay in the reaction time further experiments are

required.

In the present work, the reduced reactivity of deprotected BPDMAc-1 SAM with

Cp(allyl)Pd is explained by the small number of defects in the SAM. In order to have

further evidence, the deposition of Cp(allyl)Pd can be carried out on a diluted deprotected

BPDMAc-1 SAM surface. Diluted SAM of deprotected BPDMAc-1 can be prepared by

mixing it with another thiol with terminal groups that are not reactive with Cp(allyl)Pd.

Methyl terminated thiols can be chosen, as they are inert towards the precursor. Mixed

SAMs can be prepared by displacement or exchange reactions or they can also be

prepared by co-adsorption method. The critical point is to avoid phase separation. On the

other hand, diluting SAMs can be done in a controlled means by microcontact printing.

Microcontact printing (�CP) is a surface patterning technique, which transfers by contact,

a thiol ink from an elastomeric (polydimethylsiloxane, PDMS) stamp to a gold surface,

and if the stamp is patterned, a patterned SAM is formed [232, 233]. Patterned SAMs of

alkanethiols are extensively studied [234-236]. On the other hand, only few studies are

available for the �CP of systems with higher molecular weight. For example,

microcontact printing with heavyweight inks such as calixarene and cavitand tetra

(thioether) derivatives has been studied by Liebau et al [237]. Aromatic inks are not

investigated in detail.

Prior to use, the PDMS stamp (3 �m quadrate) was thoroughly rinsed with ethanol and

dried under a stream of nitrogen. In the present study, two inks, BPDMAc-1 (molecular

weight: 288 g mol-1) and TPDMT (molecular weight: 322.49 g mol-1) are used. The

stamp is inked by the thiol by exposing the stamp to a 1mM solution of either BPDMAc-

1 or TPDMT in ethanol. Both BPDMAc-1 and TPDMT are sparingly soluble in ethanol.

In order to increase the solubility, the solution is subjected to sonication. BPDMAc-1 and

TPDMT molecules are completely soluble in dichloromethane and chloroform but these

organic solvents can diffuse into the PDMS material and cause it to swell. Lee et al have

109

studied the compatibility of polydimethylsiloxane (PDMS) with organic solvents and

ethanol is one among the best solvent for microcontact printing [238].

Then the stamp is taken out of the solution rinsed with ethanol and dried in gentle

nitrogen stream. Before stamping, the stamp is inked again with the inking solution using

a dropper. The stamp is dried until no liquid was visible by eye on the surface of the

stamp, either under ambient conditions, or by exposure to a gentle stream of nitrogen gas.

Following inking, the stamp was applied by hand to a gold surface. Very light hand

pressure aided in complete contact between the stamp and the surface. The stamp was

then peeled gently from the surface. The thiol is transferred to the substrate such that after

removing the stamp thiols are adsorbed exclusively within the contact area. Further

derivatization of unstamped areas can be accomplished by immersing the entire substrate

in a different thiol. In this study, decanethiol is used.

Patterned SAMs terminated by -SCOCH3 are prepared by �CP of BPDMAc-1 on Au on

silicon wafer. Immersing the patterned surface in decanethiol solution results in CH3

terminated SAMs in regions of the gold surface not derivatized by �CP of BPDMAc-1.

Later the patterned SAM surface is treated with a base (0.01M NaOH for 84 h) to

facilitate the conversion of -SCOCH3 to -SH. The scanning electron micrographs showed

a pronounced contrast. The stamped features of the patterned SAM appear bright in the

SEM image (Fig. 60a). The patterned SAMs are exposed to the palladium precursor for

one hour. The SEM micrograph does not reveal any difference after the treatment with

precursor. It is difficult to observe the Pd2+ covered with allyl groups. Only metal clusters

are observed because of edge effect (SEM image not shown here). Control experiments

with TPDMT stamps have also been performed. The SEM images of sample with

stamped TPDMT and backfilled decanethiol show a pronounced contrast. The stamped

features (TPDMT SAM) appear bright in the SEM image (Fig. 60b). In this case, also

after the exposure to Pd precursor for one hour the SEM images do not show any

differences.

110

Figure 60: SEM image of a patterned SAM formed by �CP. Dark squares corresponded

to SAMs terminated by SH; light regions corresponded to CH3 terminated SAMs.

(a) Patterned SAMs of deprotected BPDMAc-1 and (b) patterned SAMs of TPDMT.

The reactivity of the SAMs can be related to the surface defects acting as nucleation

centers. In the patterned SAMs, more defects are expected on the edges of the dark

squares and after exposure to precursor, the edges of the dark squares are expected to be

decorated with Pd precursor molecules. No contrast has been observed inside the dark

squares. Therefore, from the SEM images, no conclusions can be drawn. The thickness

information from XPS and NEXAFS data also confirms that there is no difference in

height before and after exposure to precursor (1 h).

The patterned samples were also characterized by atomic force microscopy (AFM). The

AFM technique has been useful for observing the spatial distribution of different

adsorbates on a surface that differ in terminal functional groups and it can provide

excellent chemical contrast between different molecules. No features are observed in the

height mode AFM images for the patterned SAMs of BPDMAc-1. On the other hand,

height mode AFM of TPDMT SAMs that has been patterned amongst methyl-terminated

decanethiol SAMs (Fig. 61a) shows a pronounced contrast. The thiol-terminated regions

appear brighter when compared to the backfilled decanethiol regions.

111

(a) (b)(a) (b)

Figure 61: AFM images of (a) a patterned SAM of TPDMT after backfilling with

decanethiol and (b) after treatment with Cp(allyl)Pd for one hour.

Figure 61b displays the height mode AFM image obtained after treatment with palladium

precursor for one hour. A height difference of 9.3 Å and 13 Å is observed for patterned

TPDMT SAM backfilled with decanethiol and the same after treatment with precursor

respectively. The expected values are around 3.5 Å and 6.5 Å (Fig. 62). The height

results obtained from AFM are not in accordance with the expected values.

Figure 62: Schematic model illustrating the height difference before and after exposure

to Cp(allyl)Pd for One hour.

These preliminary experiments are encouraging as the patterns are clearly noticeable in

SEM. Future work has to be directed towards finding the appropriate conditions to obtain

patterned SAMs with prominent height difference between the two thiol molecules. For

example, adamantanethiol can be used for backfilling instead of decanethiol. AFM height

mode measurements can be then used to follow the reaction of Cp(allyl)Pd on the SH

terminated surface and the results can provide a better understanding on the reduced

reactivity in the case of deprotected BPDMAc-1 SAMs.

112

6. Summary

The main objective of the research reported in this dissertation is on the investigation of

the chemical reactions on the self-assembled monolayer surface. The topics described in

this thesis can be divided into the analysis of the chemical reaction on a SAM surface in

solution (deacylation reaction) and the interaction of the thiol terminated surface with an

organometallic precursor in vapor phase.

The combination of surface science techniques, infrared reflection absorption

spectroscopy (IRRAS), near edge X-ray absorption fine structure spectroscopy

(NEXAFS) and X-ray photoelectron spectroscopy (XPS) has been used in this work to

investigate the chemical reactions on organic surfaces. These techniques reveal

information about the chemical composition of the monolayers, the oxidation state of the

elements present, the orientational order and the nature of substrate-molecule binding.

The self-assembled monolayers were fabricated from two molecules namely

terphenyldimethyldithiol (TPDMT) and biphenyldimethyldithiol (deprotected BPDMAc-

1). TPDMT is known to form well-ordered SAMs on gold whereas there are some

controversies with the preparation of biphenyldimethyldithiol SAMs.

In this work, the biphenyldimethyldithiol SAMs were prepared from its monoacylated

derivative. The hydrolysis reaction condition for the formation of thiol from thioester was

optimized. The deacylation process (–SCOCH3 to –SH) was performed using a base,

sodium hydroxide. The complete conversion of the thioacetate to thiol required 84 hours.

The reaction was monitored by following the decrease of the infrared intensities of the

CO band 1695 cm-1, on removal of the acyl moieties of the thioester. The conversion of

the thioacetate to thiol was also followed by XPS and NEXAFS. Scanning electron

microscopy (SEM) is also used to follow the deprotection reaction on self-assembled

monolayers adsorbed on gold on mica. This work shows the use of SEM as an analytical

tool for understanding the reactions on SAM surfaces.

113

The deacylation reaction, which is standard in solution chemistry, is significantly

hindered when confined to a surface. Whereas the reaction in solution proceeds in

minutes, the corresponding reaction at the organic surfaces requires, depending on the

conditions, up to 84 hours. The reasons of this unexpected behavior are unraveled using

IRRAS and SEM. The experiments demonstrate that the reaction mainly occurs at

nucleation centers (e.g. defects and step edges) and the edges of reacted regime regions

and that an attack on the perfect organic surface is strongly hindered. The kinetics of the

reaction that is the time needed for the complete conversion of thioester to thiol on an

organic surface strongly depends on the substrate quality.

The metallization of an organic surface with palladium is demonstrated using the self-

assembled monolayers of terphenyldimethyldithiol and biphenyldimethyldithiol. An

organometallic precursor, (�3-allyl)(�5-cyclopentadienyl)palladium [Cp(allyl)Pd] was

used as the palladium source. The deposition and the subsequent decomposition of the

precursor on the thiol terminated self-assembled monolayers were studied using XPS,

NEXAFS and IRRAS.

The experimental results demonstrate that the chemical vapor deposition of Cp(allyl)Pd

on TPDMT SAMs result in the formation of allyl-Pd2+ covered surfaces. The presence of

palladium in the +2 oxidation state was confirmed by XPS measurements. The interaction

of the precursor with the SH terminated surface results in the elimination of the

cyclopentadienyl ligand and the allyl group is retained on the surface. The palladium

forms a bonding between the allyl group and the surface sulphur atoms. The evidence for

the presence of allyl ligand comes from the IRRAS and NEXAFS data. The allyl

terminated surface does not undergo reduction with dihydrogen gas. The reduction was

only observed in the presence of small metallic palladium particles. In this study, the Pd0

particles are formed in-situ by prolonged exposures to the Pd precursor.

The deprotected BPDMAc-1 SAMs were found to behave quite differently upon

exposure to the Pd precursor. The SAM surface was less reactive and considerably a

114

lower amount of palladium was deposited on this surface which is confirmed by XPS. As

TPDMT and dep. BPDMAc-1 are analogues, the reactivity of Cp(allyl)Pd with these

surfaces is expected to be the same. The difference between the two SAMs lies in the

preparation procedures. The terphenyldimethyldithiol SAM was prepared by a

straightforward approach (directly from the TPDMT solution in chloroform) whereas a

deprotection route was employed to prepare the biphenlydimethyldithiol SAM. Apart

from the difference in preparation methods, both surfaces should be similar. The less

reactivity of the SH terminated deprotected BPDMAc-1 surface can be accounted in

terms of small density of surface defects. Upon prolonged exposure to the precursor, the

deprotected BPDMAc-1 SAM exhibits a behavior similar to that observed for TPDMT

SAMs. A Pd2+ surface is obtained which when treated with hydrogen gas, reduction is

observed. The close packing and the steric demands for the availability of the SH groups

can hinder the surface reaction between the palladium precursor and the dep. BPDMAc-1

SAM. The formation of palladium thiolate on exposure of the SAM to the Pd precursor

depends on the availability of the hydrogen exposed at the surface, and presence of

surface H atom was found to be essential for the removal of the Cp group.

The CVD is more advantageous over thermal evaporation methods for metallization of

soft surfaces (SAMs). Generally, the diffusion of metal occurs through the structural

defects in the monolayers. The usage of high quality SAMs (e.g. TPDMT) and

introduction of chemically reactive tail groups (e.g. –SH), which can bind the metal

atoms at the SAM-ambient interface can minimize the penetration of metals. The results

from the present work shows that the deposited metal nanoparticles can be catalytically

active and can destroy the SAM resulting in the accumulation of the metal on the

substrate surface. In the present investigation, a prominent decrease of the SAM thickness

was observed for the SAM samples exposed to the precursor for 24 h followed by

reduction. Large amount of molecules comprising the SAMs has been removed. The

decomposition of the SAM molecules is catalyzed by the metallic palladium particles

formed during prolonged exposure to the palladium precursor. The CVD allows a soft

reaction when compared to physical vapour deposition methods. However, the catalytic

nature of the nanoparticles formed can oxidize the organic SAM molecules.

115

A deeper understanding of the self-assembled monolayer systems is essential in

fabricating functionalized surfaces. The results of the work described in this thesis show

that the reactions on an organic surface widely differs from the reactions in bulk. The

studies on the deacylation reaction highlight the importance of the quality of substrates

used for SAM preparation. The defects in the substrates accelerate the reaction. The

results of the chemical vapor deposition of palladium on SAMs demonstrate the

acceleration of the reaction kinetics due to the presence of defects. In addition, the results

describe the catalytic activity of the formed palladium metal nanoparticles. These

fundamental studies on the chemical reactions on dithiol SAMs widen the understanding

of the molecular behaviour of such surfaces and the findings can be extended for the

development and optimization of a suitable surface for metallization purposes.

116

7. Appendix 7.1. List of symbols and abbreviations

acac - acetylacetonate B3LYP - Becke-3-Parameter-Lee-Yang-Parr BESSY - Berliner elektronen speicherring für synchrotronstrahlung BPDMAc1 - Monoacylated Biphenyldimethyldithiol BPDMT - Biphenyldimethyldithiol Cp(allyl)Pd - Cyclopentadienyl allyl Palladium Cps - Cycles per second CVD - Chemical vapor deposition DCM - Dichloromethane DFT - Density functional theory DTGS - Deuterated Triglycine sulfate EDX - Energy dispersive X-ray spectroscopy Et - ethyl, -CH2CH3 eV - Electron volt ESCA - Electron spectroscopic chemical analysis fcc - Face centered cubic FWHM - Full width at half maximum HESGM - High Energy Spherical Grating Monochromator hfac - hexafluoroacetylacetonato IRRAS - Infrared reflection absorption spectroscopy LB - Langmuir - Blodgett LTE - Long time exposure �M - Micromolar MCP - Microcontact printing MCT - Mercury-Cadmium-Telluride mM - Millimolar NaOH - Sodium hydroxide NEXAFS - Near edge X-ray absorption fine structure OMCVD - Organometallic chemical vapor deposition PDMS - Polydimethylsiloxane PES - Photoelectron spectroscopy PVD - Physical vapor deposition RT - Room temperature SAM - Self-assembled monolayer SEM - Scanning electron microscopy STE - Short time exposure TPDMT - Terphenyldimethyldithiol UHV - Ultra high vacuum XPS - X-ray photoelectron spectroscopy

117

7.2. List of figures Figure 1: (a) Schematic of SAM and (b) structure of the molecules used in this study. ---4

Figure 2: Schematic view of SAM. ----------------------------------------------------------------7

Figure 3: Schematic sketch of the different steps in SAM formation. ------------------------9

Figure 4: Alkanethiolate adlayer (filled circles) on the Au(111) surface (empty circles).

------------------------------------------------------------------------------------------------------- 12

Figure 5: Schematic illustration of the deposited metal with regard to the underlying

SAM on the Au(111) surface. -------------------------------------------------------------------- 16

Figure 6: Schematic representation of a CVD process.-------------------------------------- 17

Figure 7: Mechanism of chemical vapour deposition. --------------------------------------- 18

Figure 8: Synthesis of Cp(allyl)Pd precursor. ------------------------------------------------ 23

Figure 9: Schlenk apparatus used for metal deposition.------------------------------------- 27

Figure 10: X-ray induced electron emission process. ---------------------------------------- 29

Figure 11: XP spectra of BPDMAc-1 SAM on Au(111).------------------------------------- 30

Figure 12: Principle of NEXAFS.--------------------------------------------------------------- 32

Figure 13: NEXAFS spectra for C12SH [161] and terphenyldimethyldithiol (TPDMT)

SAMs on gold surface. ---------------------------------------------------------------------------- 33

Figure 14: Vibrational modes of H2O and CO2. ---------------------------------------------- 35

Figure 15: (a) Electric vectors of the p- and s-components of radiation incident at a

metal surface. Reflected rays - primed vectors; incident rays-unprimed vectors. (b) The

image-charge effect - parallel dipole (EX) cancellation and perpendicular dipole (EZ)

enhancement. (c) Phase shift for light reflected from surface. ------------------------------ 36

Figure 16: IRRAS of decanethiol SAM. -------------------------------------------------------- 37

Figure 17: Carbon K-edge NEXAFS spectrum of a clean gold substrate as reference. - 39

Figure 18: NEXAFS data treatment. ----------------------------------------------------------- 40

Figure 19: Low-frequency regions of (a) the calculated spectrum of TPDMT (b) the bulk

spectrum of TPDMT and (c) the SAM spectrum of TPDMT. -------------------------------- 42

Figure 20: Pellet IR spectra of (a) terphenyldimethyldithiol and (b)

terphenyldimethylthiol. Left: Region from 2700 cm-1 to 2400 cm-1; Right: Region from

1550 cm-1 to 1400 cm-1. --------------------------------------------------------------------------- 44

118

Figure 21: IRRAS of terphenyldimethyldithiol (TPDMT) SAM and terphenyldimethylthiol

(TPMT) SAM. Left: Region from 2700 cm-1 to 2400 cm-1; Right: Region from 1550 cm-1

to 1400 cm-1. --------------------------------------------------------------------------------------- 45

Figure 22: Schematic diagram showing the H/D exchange between TPDMT-SAM and

D2O. ------------------------------------------------------------------------------------------------- 46

Figure 23: C 1s and S 2p - XPS of TPDMT SAM. -------------------------------------------- 47

Figure 24: NEXAFS spectra of TPDMT SAM------------------------------------------------- 48

Figure 25: Low-frequency regions of (a) the calculated spectrum of BPDMAc-1 SAM, (b)

the bulk spectrum of BPDMAc-1 SAM, (c) the SAM spectrum of BPDMAc-1 SAM, (d) the

calculated spectrum of deprotected BPDMAc-1 SAM and (e) the SAM spectrum of

deprotected BPDMAc-1.-------------------------------------------------------------------------- 50

Figure 26: XPS of deprotected BPDMAc-1 SAM. -------------------------------------------- 51

Figure 27: NEXAFS of deprotected BPDMAc-1 SAM.--------------------------------------- 52

Figure 28: Thickness estimation from the edge jump in C K-edge NEXAFS. ------------- 53

Figure 29: Schematic flowchart illustrating the deprotection mechanism of the

deacylation process.------------------------------------------------------------------------------- 56

Figure 30: IRRAS of BPDMAc-1 and deprotected BPDMAc-1. ---------------------------- 57

Figure 31a: NEXAFS spectra of BPDMAc1 and deprotected BPDMAc-1. --------------- 58

Figure 31b: NEXAFS spectrum of BPDMAc1 at different incidence angles. ------------- 59

Figure 32: XP spectra of BPDMAc1 and deprotected BPDMAc-1.------------------------ 60

Figure 33: IRRAS showing the deacylation reaction at different immersion time in the

basic solution.-------------------------------------------------------------------------------------- 62

Figure 34: The difference in deprotection kinetics by the change in the nature of the gold

substrate. ------------------------------------------------------------------------------------------- 63

Figure 35: SEM images of BPDMAc-1 and deprotected BPDMAc-1 SAM. -------------- 65

Figure 36: Schematic model showing the possibility for the attack of the hydroxide ion.67

Figure 37: Illustration of the structure of a TPDMT SAM on gold. ------------------------ 72

Figure 38: XP spectra of the Pd 3d region of a TPDMT SAM exposed to Cp(allyl)Pd for

(a) 1 hour and (b) the same treated with hydrogen gas.-------------------------------------- 74

Figure 39: XP spectra of the Pd 3d region of a TPDMT SAM exposed to Cp(allyl)Pd for

(a) 24 hours and (b) the same treated with hydrogen gas. ----------------------------------- 75

119

Figure 40: S 2p spectra of Pd covered TPDMT/Au and hydrogen gas exposed samples.77

Figure 41: C 1s spectra of Pd covered TPDMT/Au and hydrogen gas exposed samples.79

Figure 42: NEXAFS spectra of Pd covered TPDMT/Au and hydrogen gas exposed

samples.--------------------------------------------------------------------------------------------- 80

Figure 43: 90°-55° difference spectra of Pd covered TPDMT/Au and hydrogen gas

exposed samples. ---------------------------------------------------------------------------------- 81

Figure 44: Difference spectra of precursor exposed samples and the TPDMT SAM. --- 82

Figure 45: Infrared spectroscopic data of TPDMT SAM and Pd precursor treated SAMs.

------------------------------------------------------------------------------------------------------- 84

Figure 46: IR spectra of bulk Cp(allyl)Pd in KBr (bottom curve) and calculated IR

spectrum of Cp(allyl)Pd (upper curve). -------------------------------------------------------- 85

Figure 47: SEM image of Pd clusters on a TPDMT SAM exposed to Cp(allyl)Pd for 24

hours followed by the treatment with hydrogen gas.------------------------------------------ 86

Figure 48a: Illustration of the formation of disordered layers via disulfide linkages for

the BPMDT molecule. Adapted from reference [7]. ------------------------------------------ 87

Figure 48b: Illustration of the formation of a deprotected BPDMAc-1 SAM on gold. -- 88

Figure 49: XP spectra of the Pd 3d region of a deprotected BPDMAc-1 SAM exposed to

Cp(allyl)Pd for 1 hour. --------------------------------------------------------------------------- 89

Figure 50: XP spectra of the Pd 3d region of a deprotected BPDMAc-1 SAM exposed to

Cp(allyl)Pd for (a) 24 hours and (b) the same treated with hydrogen gas.---------------- 90

Figure 51: S 2p spectra of Pd covered deprotected BPDMAc-1/Au and hydrogen gas

exposed samples. ---------------------------------------------------------------------------------- 92

Figure 52: C 1s spectra of Pd covered deprotected BPDMAc-1/Au and hydrogen gas

exposed samples. ---------------------------------------------------------------------------------- 93

Figure 53: NEXAFS spectra of Pd covered deprotected BPDMAc-1/Au and hydrogen gas

exposed samples. ---------------------------------------------------------------------------------- 94

Figure 54: 90°-55° difference spectra of Pd covered deprotected BPDMAc-1/Au and

hydrogen gas exposed samples. ----------------------------------------------------------------- 95

Figure 55: Difference spectrum of precursor exposed samples and the deprotected

BPDMAc-1 SAM. ---------------------------------------------------------------------------------- 96

Figure 56: Schematic reaction of Cp(allyl)Pd with thiols in solution. --------------------- 97

120

Figure 57: Plot of intensity ratios (C 1s/Au 4f, S 2p/Au 4f).--------------------------------101

Figure 58: Thickness estimation from the edge jump in C K-edge NEXAFS. (a) TPDMT

samples and (b) dep.BPDMAc-1 samples. ----------------------------------------------------103

Figure 59: Schematic model showing the deposition of Cp(allyl)Pd and the subsequent

reduction to metallic palladium on TPDMT-SAM.-------------------------------------------105

Figure 60: SEM image of a patterned SAM formed by �CP. Dark squares corresponded

to SAMs terminated by SH; light regions corresponded to CH3 terminated SAMs.------110

(a) Patterned SAMs of deprotected BPDMAc-1 and (b) patterned SAMs of TPDMT. --110

Figure 61: AFM images of (a) a patterned SAM of TPDMT after backfilling with

decanethiol and (b) after treatment with Cp(allyl)Pd for one hour. -----------------------111

Figure 62: Schematic model illustrating the height difference before and after exposure

to Cp(allyl)Pd for One hour. --------------------------------------------------------------------111

7.3. List of tables Table 1: Examples for different metal deposition methods on organic thin films.-------- 20

Table 2: Assignment of the photoelectron lines.----------------------------------------------- 30

Table 3: C 1s and S 2p peak fit data of TPDMT SAM. --------------------------------------- 46

Table 4: C 1s and S 2p peak fit data of deprotected BPDMAc-1 SAM. -------------------- 52

Table 5: Pd 3d5/2 peak fit data of Pd deposited TPDMT SAM.------------------------------ 75

Table 6: S 2p peak fit data of Pd deposited TPDMT SAM ----------------------------------- 78

Table 7: C 1s peak fit data of Pd deposited TPDMT SAM. ---------------------------------- 79

Table 8: Calculated and observed vibrational frequencies of Cp(allyl)Pd and the IR

frequencies of the precursor treated TPDMT SAMs. ----------------------------------------- 85

Table 9: Pd 3d5/2 peak fit data of Pd deposited deprotected BPDMAc-1 SAM.----------- 90

Table 10: S 2p peak fit data of Pd deposited deprotected BPDMAc-1 SAM.-------------- 91

Table 11: C 1s peak fit data of Pd deposited deprotected BPDMAc-1 SAM.-------------- 93

Table 12: Thickness of the Pd covered TPDMT SAM samples. ----------------------------100

Table 13: Thickness of the Pd covered deprotected BPDMAc-1 SAM samples. ---------101

121

8. References

1. O. Dannenberger, K. Weiss, C. Wöll, M. Buck, Phys. Chem. Chem. Phys., 2000,

2, (1509-1514). Reactivity of self-assembled monolayers: formation of organized amino functionalities.

2. V. Chechik, C. M. Stirling, Langmuir, 1997, 13, (6354-6356). Reactivity in Monolayers versus Bulk Media: Intra- and Intermolecular Aminolysis of Esters.

3. X. M. Li, J. Huskens, D. N. Reinhoudt, J. Mater. Chem., 2004, 14, (2954-2971). Reactive self-assembled monolayers on flat and nanoparticle surfaces, and their application in soft and scanning probe lithographic nanofabrication technologies.

4. T. P. Sullivan, W. T. S. Huck, Eur. J. Org. Chem., 2003, (17-29). Reactions on Monolayers: Organic Synthesis in Two Dimensions.

5. V. Chechik, R. M. Crooks, C. M. Stirling, Adv. Mater., 2000, 12, (1161-1171). Reactions and Reactivity in Self-Assembled Monolayers.

6. Y. Tai, A. Shaporenko, H. Noda, M. Grunze, M. Zharnikov, Adv. Mater., 2005, 17, (1745-1749). Fabrication of stable metal films on the surface of self assembled monolayers.

7. W. Azzam, B. I. Wehner, R. A. Fischer, A. Terfort, C. Wöll, Langmuir, 2002, 18, (7766-7769). Bonding and Orientation in Self-Assembled Monolayers of Oligophenyldithiols on Au Substrates.

8. Y. Tai, A. Shaporenko, M. Grunze, M. Zharnikov, J. Phys. Chem. B, 2005, 109, (19411-19415). Effect of Irradiation Dose in Making an Insulator from a Self-Assembled Monolayer.

9. A. Niklewski, W. Azzam, T. Strunskus, R. A. Fischer, C. Wöll, Langmuir 2004, 20, (8620-8624). Fabrication of Self-Assembled Monolayers Exhibiting a Thiol-Terminated Surface.

10. J. C. Love, L. A. Estroff, J. K. Kriebel, R. G. Nuzzo, G. M. Whitesides, Chem.Rev., 2005, 105, (1103-1169). Self-Assembled Monolayers of Thiolates on Metals as a Form of Nanotechnology.

11. E. M. McCash, Oxford Universtiy Press Inc., New York, 2001. Surface Chemistry.

12. D. Witt, R. Klajn, P. Barski, B. A. Grzybowski, Curr. Org. Chem., 2004, 8, (1763-1797). Applications, Properties and Synthesis of �-Functionalized n-Alkanethiols and Disulfides - the Building Blocks of Self-Assembled Monolayers.

13. J. Wang, H. Wu, L. Angnes, Anal. Chem., 1993, 65, (1893-1896). On-line monitoring of hydrophobic compounds at self-assembled monolayer modified amperometric flow detectors.

14. D. L. Angst, G. W. Simmons, Langmuir, 1991, 7, (2236-2242). Moisture absorption characteristics of organosiloxane self-assembled monolayers.

15. B. Franklin, W. Brownrigg, M. Farish, Philos. Trans. R. Soc. London, 1774, 64, (445-460). Of the Stilling of Waves by means of Oil. Extracted from Sundry Letters between Benjamin Franklin, William Brownrigg and the Reverend Mr. Farish.

16. A. Pockels, Nature, 1891, 43, (437-439). Surface tension.

122

17. I. Langmuir, J. Am. Chem. Soc., 1848, 39, (1848-1906). The constitution and fundamental properties of solids and liquids. $$. Liquids.

18. K. Blodgett, J. Am. Chem. Soc., 1934, 56, (495). Monomolecular films of fatty acids on glass.

19. W. C. Bigelow, D. L. Pickett, W. A. Zisman, J. Colloid Interface Sci., 1946, 1, (513-538). Oleophobic monolayers. I. Films adsorbed from solution in non-polar liquids.

20. F. Schreiber, Prog. Surf. Sci., 2000, 65, (151-256). Structure and growth of self-assembling monolayers.

21. G. G. Roberts, Contemp. Phys., 1984, 25, (109-128). Langmuir-Blodgett Films. 22. G. Witte, C. Wöll, J. Mater. Res., 2004, 19, (1889-1916). Growth of aromatic

molecules on solid substrates for applications in organic electronics. 23. S. R. Forrest, Chem. Rev., 1997, 97, (1793-1896). Ultrathin Organic Films Grown

by Organic Molecular Beam Deposition and Related Techniques. 24. G. M. Whitesides, B. Grzyboski, Science, 2002, 295, (2418-2421). Self-Assembly

at All Scales. 25. A. Ulman, Chem. Rev., 1996, 96, (1533-1554). Formation and Structure of Self-

Assembled Monolayers. 26. A. Ulman, Academic Press Inc., San Diego, 1991. An Introduction to Ultrathin

Organic Films: From Langmuir-Blodgett to Self Assembly. 27. E. Delamarche, B. Michel, H. A. Biebuyck, C. Gerber, Adv. Mater., 1996, 8,

(719-&). Golden interfaces: The surface of self-assembled monolayers. 28. L. H. Dubois, R. G. Nuzzo, Annu. Rev. Phys. Chem., 1992, 43, (437-463).

Synthesis, Structure, and Properties of Model Organic Surfaces. 29. A. Badia, R. B. Lennox, L. Reven, Acc. Chem. Res., 2000, 33, (475-481). A

dynamic view of self-assembled monolayers. 30. Q. Jin, J. A. Rodriguez, C. Z. Li, Y. Darci, N. J. Tao, Surf. Sci., 1999, 425, (101-

111). Self-assembly of aromatic thiols on Au(111). 31. R. G. Nuzzo, D. L. Allara, J. Am. Chem. Soc., 1983, 105, (4481-4483).

Adsorption of Bifunctional Organic Disulfides on Gold Surfaces. 32. K. Stolarczyk, R. Bilewicz, Electrochim. Acta, 2006, 51, (2358-2365). Electron

transport through alkanethiolate films decorated with monolayer protected gold clusters.

33. V. Chechick, C. M. Stirling, John Wiley & Sons. Ltd., England, 1999. Gold-thiol self assembled monolayers.

34. M. A. Chesters, G. A. Somorjai, Surf. Sci., 1975, 52, (21-28). The chemisorption of oxygen, water and selected hydrocarbons on the (111) and stepped gold surfaces.

35. M. J. Ford, C. Masens, M. B. Cortie, Surf. Rev. Lett., 2006, 13, (297–307). The application of gold surfaces and particles in nanotechnology.

36. C. D. Bain, E. B. Troughton, Y.-T. Tao, J. Evall, G. M. Whitesides, R. G. Nuzzo, J. Am. Chem. Soc., 1989, 111, (321-335). Formation of monolayer films by the spontaneous assembly of organic thiols from solution onto gold.

37. R. G. Nuzzo, F. A. Fusco, D. L. Allara, J. Am. Chem. Soc., 1987, 109, (2358). Spontaneously Organized Molecular Assemblies. 3.Preparation and Properties of Solution Adsorbed Monolayers of Organic Disulfides on Gold Surfaces.

123

38. M. C. Daniel, D. Astruc, Chem. Rev., 2004, 104, (293-346). Gold Nanoparticles: Assembly, Supramolecular Chemistry,Quantum-Size-Related Properties, and Applications toward Biology, Catalysis, and Nanotechnology.

39. C. Wöll, S. Chiang, R. J. Wilson, P. H. Lippel, Phys. Rev. B 1989, 39, (7988-7991). Determination of atom positions at stacking-fault dislocations on Au(111) by scanning tunneling microscopy.

40. C. B. Carter, R. Q. Hwang, Phys. Rev. B, 1995, 51, (4730-4733). Dislocations and reconstruction of (111) fcc metal surfaces.

41. C. Vericat, M. E. Vela, G. A. Benitez, J. A. M. Gago, X. Torrelles, R. C. Salvarezza, J. Phys.: Condens. Matter, 2006, 18, (R867-R900). Surface characterization of sulfur and alkanethiol self-assembled monolayers on Au(111).

42. C. Vericat, M. E. Vela, R. C. Salvarezza, Phys. Chem. Chem. Phys., 2005, 7, (3258-3268). Self-assembled monolayers of alkanethiols on Au(111): surface structures, defects and dynamics.

43. G. E. Poirier, Chem. Rev., 1997, 97, (1117-1127). Characterization of organosulfur molecular monolayers on Au(111) using scanning tunneling microscopy.

44. K. Edinger, A. Gölzhäuser, K. Demota, C. Wöll, M. Grunze, Langmuir, 1993, 9, (4-8). Formation of Self-Assembled Monolayers of n-Alkanethiols on Gold: A Scanning Tunneling Microscopy Study on the Modification of Substrate Morphology.

45. C. R. Mayer, S. Neveu, V. Cabuil, Adv. Mater., 2002, 14, (595-597). 3D Hybrid nanonetworks from gold funtionalized nanoparticles.

46. N. Balachander, C. N. Sukenik, Langmuir, 1990, 6, (1621-1627). Monolayer transformation by nucleophilic substitution: Applications to the creation of new monolayer assemblies.

47. G. E. Fryxell, P. C. Rieke, L. L. Wood, M. H. Engelhard, R. E. Williford, G. L. Graff, A. A. Campbell, R. J. Wiacek, L. Lee, A. Halverson, Langmuir, 1996, 12, (5064 - 5075). Nucleophilic Displacements in Mixed Self-Assembled Monolayers.

48. T. Vallant, W. Simanko, H. Brunner, U. Mayer, H. Hoffmann, R. Schmid, K. Kirchner, R. Svagera, G. Schügerl, M. Ebel, Organometallics, 1999, 18, (3744-3749). Comparing Reactivities of Metal Complexes in Solution and on Surfaces by IR Spectroscopy and Time-Resolved in Situ Ellipsometry.

49. T. Lummerstorfer, H. Hoffmann, J. Phys. Chem. B, 2004, 108, (3963-3966). Click Chemistry on Surfaces: 1,3-Dipolar Cycloaddition Reactions of Azide-Terminated Monolayers on Silica.

50. J. Luo, S. S. Isied, Langmuir, 1998, 14, (3602-3606). Ruthenium Tetraammine Chemistry of Self-Assembled Monolayers on Gold Surfaces: Substitution and Reactivity at the Monolayer Interface.

51. I. S. Choi, Y. S. Chi, Angew. Chem. Int. Ed., 2006, 45, (4894-4897). Surface Reactions On Demand: Electrochemical Control of SAM-Based Reactions.

52. V. Chechik, C. M. Stirling, John Wiley & Sons. Ltd., England, 1999. Gold-thiol self assembled monolayers.

53. C. J. Michejda, S. R. Koepke, J. Am. Chem. Soc., 1978, 100, (1959-1960). Powerful anchimeric effect of the N-nitroso group.

124

54. F. Ruff, Á. Kucsman, J. Chem. Soc., Perkin Trans. II, 1988, (1123-1128). Electronic effect, steric hindrance, and anchimeric assistance in oxidation of sulphides. Neighbouring-group participation through sulphur-oxygen non-bonded interaction.

55. M. N. Yousaf, E. W. L. Chan, M. Mrksich, Angew. Chem. Int. Ed., 2000, 39, (1943-1946). The kinetic order of an interfacial Diels-Alder reaction depends on the environment of the immolized dienophile.

56. J. Wang, J. R. Kenseth, V. W. Jones, J. D. Green, M. T. McDermott, M. D. Porter, J. Am. Chem. Soc., 1997, 119, (12796-12799). SFM Tip assisted Hydrolyis of a Dithiobis(succinimidoundecanoate) Monplaer Chemisorbed on a Au(111) Surface.

57. D. A. Krapchetov, H. Ma, A. K. Y. Jen, D. A. Fischer, Y. L. Loo, Langmuir, 2005, 21, (5887-5893). Solvent-Dependent Assembly of Terphenyl- and Quaterphenyldithiol on Gold and Gallium Arsenide.

58. Y. Wolman, John Wiley & Sons. Ltd., England, 1974. Protection of the thiol group.

59. J. M. Tour, L. JonesII, D. L. Pearson, J. J. S. Lamba, T. P. Burgin, G. M. Whitesides, D. L. Allara, A. N. Parikh, S. V. Atre, J. Am. Chem. Soc., 1995, 117, (9529-9534). Self- Assembled Monolayers and Multilayers of Conjugated Thiols,Dithiols, and Thioacetyl-Containing Adsorbates.Understanding Attachments between Potential Molecular Wires and Gold Surfaces.

60. A. Shaporenko, M. Elbing, A. Baszczyk, C. Hanisch, M. Mayor, M. Zharnikov, J.Phys. Chem. B, 2006, 110, (4307-4317). Self-assembled monolayers from biphenyldithiol derivatives: Optimization of the deprotection procedure and effect of the molecular conformation.

61. P. Neogi, S. Neogi, C. M. Stirling, J. Chem. Soc., Chem. Commun., 1993, (1134-1136). Reactivity of carboxy esters in gold-thiol monolayers.

62. H. Schönherr, V. Chechik, C. M. Stirling, G. J. Vancso, J. Am. Chem. Soc., 2000, 122, (3679-3687). Monitoring surface reactions at an AFM tip: An approach to follow reaction kinetics in self-assembled monolayers on the nanometer scale.

63. Z. Zhu, T. A. Daniel, M. Maitani, O. M. Cabarcos, D. L.Allara, N. Winograd, J.Am. Chem. Soc., 2006, 128, (13710-13719). Controlling Gold Atom Penetration through Alkanethiolate Self-Assembled Monolayers on Au{111} by Adjusting Terminal Group Intermolecular Interactions.

64. B. S. Lim, A. Rahtu, R. G. Gordon, Nat. Mater., 2003, 2, (749-754). Atomic layer deposition of transition metals.

65. K. L. Choy, Prog. Mater. Sci, 2003, 48, (57-170). Chemical vapour deposition of coatings.

66. W. A. Bryant, J. Mater. Sci., 1977, 12, (1285-1306). The fundamentals of chemical vapour deposition.

67. P. D. Dapkus, Ann. Rev. Mater. Sci., 1982, 12, (243-269). Metal organic Chemical Vapor Deposition.

68. A. Zinn, B. Niemer, H. D. Kaesz, Adv. Mater., 1992, 4, (375-378). Reaction Pathways in Organometallic Chemical Vapor Deposition (OMCVD).

125

69. M. Manolova, V. Ivanova, D. M. Kolb, H.-G. Boyen, P. Ziemann, M. Büttner, A. Romanyuk, P. Oelhafen, Surf. Sci., 2005, 590, (146-153). Metal deposition onto thiol-covered gold: Platinum on a 4-mercaptopyridine SAM.

70. W. Deng, L. Yang, D. Fujita, H. Nejoh, C. Bai, Appl. Phys. A: Mater. Sci. Process, 2000, 71, (639-642). Silver ions adsorbed to self-assembled monolayers of alkanedithiols on gold surfaces form Ag-dithiol-Au multilayer structures.

71. X. Zhongdang, X. Minhua, G. Jianhua, H. Dang, L. Zuhong, Mater. Chem. Phys., 1998, 52, (170-174). Ti-based oxide thin films deposited from solution on self-assembly monolayer.

72. B. Jin, S. Ding, K. Kametani, T. Nakamura, Chem. Lett., 2005, 34, (302-303). The Preparation and Electrochemical Behavior of Density-controlled Gold Nano-particle Self-assembled Interface.

73. V. L. Colvin, A. N. Goldstein, A. P. Alivisatos, J. Am. Chem. Soc., 1992, 114, (5221-5230). Semiconductor Nanocrystals Covalently Bound to Metal Surfaces with Self-Assembled Monolayers.

74. M. J. Esplandiu, P. L. M. Noeske, Appl. Surf. Sci., 2002, 199, (166-182). XPS investigations on the interactions of 1,6-hexanedithiol/Au(111) layers with metallic and ionic silver species.

75. M. J. Tarlov, Langmuir, 1992, 8, (80-89). Silver Metalization of Octadecanethiol Monolayers Self -Assembled on Gold.

76. T. Ohgi, H.-Y. Sheng, H. Nejoh, Appl. Surf. Sci., 1998, 130-132, (919-924). Au particle deposition onto self-assembled monolayers of thiol and dithiol molecules.

77. Z. Zhu, D. L. Allara, N. Winograd, Appl. Surf. Sci., 2006, 252, (6686-6688). Chemistry of metal atoms reacting with alkanethiol self-assembled monolayers.

78. K. Schouteden, N. Vandamme, E. Janssens, P. Lievens, C. V. Haesendonck, Surf.Sci., 2008, 602, (552-558). Single-electron tunneling phenomena on preformed gold clusters deposited on dithiol self-assembled monolayers.

79. N. Vandamme, J. Snauwaert, E. Janssens, E. Vandeweert, P. Lievens, C. V. Haesendonck, Surf. Sci., 2004, 558, (57-64). Visualization of gold clusters deposited on a dithiol self-assembled monolayer by tapping mode atomic force microscopy.

80. Q. Guo, X. Sun, Y. Chen, R. E. Palmer, Surf. Sci., 2002, 497, (269–274). Controlling the formation of Au nanoparticles using functionalized molecular buffer layers.

81. B. deBoer, M. M. Frank, Y. J. Chabal, W. Jiang, E. Garfunkel, Z. Bao, Langmuir2004, 20, (1539-1542). Metallic Contact Formation for Molecular Electronics: Interactions between Vapor-Deposited Metals and Self-Assembled Monolayers of Conjugated Mono- and Dithiols.

82. A. V. Walker, T. B. Tighe, B. C. Haynie, S. Uppili, N. Winograd, D. L. Allara, J.Phys. Chem. B, 2005, 109, (11263-11272). Chemical Pathways in the Interactions of Reactive Metal Atoms with Organic Surfaces: Vapor Deposition of Ca and Ti on a Methoxy-Terminated Alkanethiolate Monolayer on Au.

83. E. L. Smith, C. A. Alves, J. W. Anderegg, M. D. Porter, L. M. Siperko, Langmuir, 1992, 8, (2707-2714). Deposition of Metal Overlayers at End-Group-Functionalized Thiolate Monolayers Adsorbed at Au. 1. Surface and Interfacial

126

Chemical Characterization of Deposited Cu Overlayers at Carboxylic Acid-Terminated Structures.

84. F. Anariba, J. K. Steach, R. L. McCreery, J. Phys. Chem. B, 2005, 109, (11163-11172). Strong Effects of Molecular Structure on Electron Transport in Carbon/Molecule/Copper Electronic Junctions.

85. D. R. Jung, A. W. Czanderna, Appl. Surf. Sci., 1996, 99, (161-168). X-ray photoelectron spectroscopy of Cr/COOCH3 interfaces on self-assembled monolayers of 16-mercaptohexadecanoate.

86. T. Strunskus, M. Grunze, G. Kochendoerfer, C. Wöll, Langmuir, 1996, 12, (2712-2725). Identification of Physical and Chemical Interaction Mechanisms for the Metals Gold, Silver, Copper, Palladium, Chromium and Potassium with Polyimide Surfaces.

87. D. Wacker, K. Weiss, U. Kazmaier, C. Wöll, Langmuir 1997, 13, (6689-6696). Realization of a Phenyl-Terminated Organic Surface and Its Interaction with Chromium Atoms.

88. A. V. Walker, T. B. Tighe, O. Cabarcos, B. C. Haynie, D. L. Allara, N. Winograd, J. Phys. Chem. C, 2007, 111, (765-772). Dynamics of Interaction of Magnesium Atoms on Methoxy-Terminated Self-Assembled Monolayers: An Example of a Reactive Metal with a Low Sticking Probability.

89. Y. Tai, A. Shaporenko, W. Eck, M. Grunze, M. Zharnikov, Appl. Phys. Lett., 2004, 85, (6257-6259). Abrupt change in the structure of self-assembled monolayers upon metal evaporation.

90. J. J. Senkevich, F. Tang, D. Rogers, J. T. Drotar, C. Jezewski, W. A. Lanford, G. C. Wang, T. M. Lu, Chem. Vap. Deposition, 2003, 9, (258-264). Substrate-independent palladium atomic layer deposition.

91. E. A. Speets, B. Dordi, B. J.Ravoo, N. Oncel, A. S. Hallbaeck, H. J. W. Zandvliet, B. Poelsema, G. Rijnders, D. H. A. Blank, D. N. Reinhoudt, Small, 2005, 1, (395-398). Noble metal nanoparticles deposited on self-assembled monolayers by pulsed laser deposition show Coulomb blockade at room temperature.

92. N. L. Jeon, W. Lin, M. K. Erhardt, G. S. Girolami, R. G. Nuzzo, Langmuir, 1997, 13, (3833-3838). Selective Chemical Vapor Deposition of Platinum and Palladium Directed by Monolayers Patterned Using Microcontact Printing.

93. N. L. Jeon, P. G. Clem, D. A. Payne, R. G. Nuzzo, Langmuir, 1996, 12, (5350-5355). A Monolayer-Based Lift-Off Process for Patterning Chemical Vapor Deposition Copper Thin Films.

94. U. Weckenmann, S. Mittler, S. Krämer, A. K. A. Aliganga, R. A. Fischer, Chem.Mater., 2004, 16, (621-628). A Study on the Selective Organometallic Vapor Deposition of Palladium onto Self-assembled Monolayers of 4,4'-Biphenyldithiol, 4-Biphenylthiol, and 11-Mercaptoundecanol on Polycrystalline Silver.

95. O. Shekhah, C. Busse, A. Bashir, F. Turcu, X. Yin, P. Cyganik, A. Birkner, W. Schuhmann, C. Wöll, Phys. Chem. Chem. Phys., 2006, 8, (3375–3378). Electrochemically deposited Pd islands on an organic surface: the presence of Coulomb blockade in STM I(V) curves at room temperature.

96. T. Baunach, V. Ivanova, D. M. Kolb, H. G. Boyen, P. Ziemann, M. Büttner, P. Oelhafen, Adv. Mater., 2004, 16, (2024-2028). A new approach to the

127

electrochemical metallization of organic monolayers:Palladium deposition onto a 4,4' dithiodipyridine self assembled monolayer.

97. M. Manolova, M. Kayser, D. M. Kolb, H.-G. Boyen, P. Ziemann, D. Mayer, A. Wirth, Electrochim. Acta, 2007, 52, (2740-2745). Rhodium deposition onto a 4-mercaptopyridine SAM on Au(111).

98. D. Qu, K. Uosaki, J. Phys. Chem. B, 2006, 110, (17570-17577). Electrochemical Metal Deposition on Top of an Organic Monolayer.

99. D. Qu, K. Uosaki, Chem. Lett., 2006, 35, (258-259). Platinum Layer Formation on a Self-assembled Monolayer by Electrochemical Deposition.

100. T. Hirsch, M. Zharnikov, A. Shaporenko, J. Stahl, D. Weiss, O. S. Wolfbeis, V. M. Mirsky, Angew. Chem. Int. Ed. , 2005, 44, (6775 –6778). Size-Controlled Electrochemical Synthesis of Metal Nanoparticles on Monomolecular Templates.

101. H. Hagenström, M. J. Esplandiu, D. M. Kolb, Langmuir, 2001, 17, Functionalized Self-Assembled Alkanethiol Monolayers on Au(111) Electrodes: 2. Silver Electrodeposition.

102. M. J. Esplandiu, H. Hagenström, Solid State Ionics, 2002, 150, (39– 52). Functionalized self-assembled monolayers and their influence on silver electrodeposition.

103. S. Langerock, H. Menard, P. Rowntree, L. Heerman, Langmuir, 2005, 21, (5124-5133). Electrocrystallization of Rhodium Clusters on Thiolate-Covered Polycrystalline Gold.

104. J. W. F. Robertson, D. J. Tiani, J. E. Pemberton, Langmuir, 2007, 23, (4651-4661). Underpotential Deposition of Thallium, Lead, and Cadmium at Silver Electrodes Modified with Self-Assembled Monolayers of (3-Mercaptopropyl)trimethoxysilane.

105. J. B. Nelson, D. T. Schwartz, Langmuir, 2007, 23, (9661-9666). Electrochemical Factors Controlling the Patterning of Metals on SAM-Coated Substrates.

106. H. Kind, A. M. Bittner, O. Cavalleri, K. Kern, T. Greber, J. Phys. Chem. B, 1998, 102, (7582-7589). Electroless Deposition of Metal Nanoislands on Aminothiolate-Functionalized Au(111) Electrodes.

107. L. N. Xu, J. H. Liao, L. Huang, D. L. Ou, Z. R. Guo, H. Q. Zhang, C. W. Ge, N. Gu, J. Z. Liu, Thin Solid Films, 2003, 434, (121-125). Surface-bound nanoparticles for initiating metal deposition.

108. L. N. Xu, J. H. Liao, L. Huang, N. Gu, H. Q. Zhang, J. Z. Liu, Appl. Surf. Sci., 2003, 211, (184-188). Pendant thiol groups-attached Pd(II) for initiating metal deposition.

109. D. B. Wolfe, J. C. Love, K. E. Paul, M. L. Chabinyc, G. M. Whitesides, Appl.Phys. Lett., 2002, 80, (2222-2224). Fabrication of palladium-based microelectronic devices by microcontact printing.

110. J. C. Love, D. B. Wolfe, R. Haasch, M. L. Chabinyc, K. E. Paul, G. M. Whitesides, R. G. Nuzzo, J. Am. Chem. Soc., 2003, 125, (2597-2609). Formation and structure of self-assembled monolayers of alkanethiolates on palladium.

111. Z. Yang, A. B. Smetana, C. M. Sorensen, K. J. Klabunde, Inorg. Chem., 2007, 46, (2427-2431). Synthesis and Characterization of a New Tiara Pd(II) Thiolate Complex and Its Solution-Phase Thermolysis to Prepare Nearly Monodisperse Palladium Sulfide Nanoparticles.

128

112. A. Tungler, G. Fogassy, J. Mol. Catal. A, 2001, 173, (231-247). Catalysis with supported palladium metal, selectivity in the hydrogenation of C=C, C=O and C=N bonds,from chemo- to enantioselectivity.

113. V. K. Wunder, S. Schmid, N. Popovska, G. Emig, Surf. Coat. Technol., 2002, 151, (96–99). MOCVD of palladium films: kinetic aspects and film properties.

114. W. Lin, T. H. Warren, R. G. Nuzzo, G. S. Girolami, J. Am. Chem. Soc., 1993, 115, (11644-11645). Surface-Selective Deposition of Palladium and Silver Films from Metal-Organic Precursors: A Novel Metal-Organic Chemical Vapor Deposition Redox Transmetalation Process.

115. A. Zinn, L. Brandt, H. D. Kaesz, R. F. Hicks, Wiley-VCH, New York, 1994. Chemical vapor deposition of Platinum, Palladium and Nickel - Chapter 7 of The Chemistry of Metal CVD.

116. Z. Yuan, R. L. Puddephat, Adv. Mater., 1994, 6, (51-54). Allyl(%-diketonato)palladium($$) Complexes as Precursors for Palladium Films.

117. A. Gräfe, R. Heinen, F. Klein, T. Kruck, M. Scherer, M. Schober, Appl. Surf. Sci., 1995, 91, (187-191). Precursor development for the chemical vapor deposition of aluminium, copper and palladium.

118. G. Carturan, G. Strukul, J. Organomet. Chem., 1978, 157, (475-481). Activation of molecular hydrogen with allylpalladium(II) derivatives. Selective catalytic hydrogenation of allene to propene. .

119. R. D. Ernst, Acc. Chem. Res., 1985, 18, (56-62). Metal-Pentadienyl Chemistry. 120. G. Wilke, B. Bogdanovic, P. Hardt, P. Heimbach, W. Keim, M. Kroner, W.

Oberkirch, K. Tanaka, E. Steinrucke, D. Walter, H. Zimmermann, Angew. Chem. Int. Ed., 1966, 5, (151-266). Allyl Transition Metal Systems.

121. B. L. Shaw, Proc. Chem. Soc., 1960, (247). Allyl(cyclopentadienyl)palladium($$). 122. Y. Tatsuno, T. Yoshida, S. Otsuka, Inorg. Synthesis, 1979, 19, (220-223). (�3-

Allyl)palladium($$) complexes. 123. E. Feurer, H. Suhr, Thin Solid Films, 1988, 157, (81-86). Thin Palladium Films

prepared by metal-organic plasma-enhanced chemical vapour deposition. 124. M. K. Minasyan, S. P. Gubin, Y. T. Struchkov, Zh. Strukt. Khim., 1966, 7, (906-

907). Structure of&allylcyclopentadienylpalladium. 125. M. K. Minasyants, Y. T. Struchkov, Zh. Strukt. Khim., 1968, 9, (481-487). Crystal

and molecular structures of allylcyclopentadienylpalladium. 126. S. P. Gubin, A. Z. Rubezhow, B. L. Winch, A. N. Nesmeyanov, Tetrahedron

Lett., 1964, 39, (2881-2887). Cleavage of the cyclopentadienyl-palladium bond in cyclopentadienylallylpalladium.

127. K. G. Shalnova, O. F. Rachkova, I. A. Teplova, G. A. Razuvaev, G. A. Abakumov, Izv. Akad. Nauk SSSR., Ser. Khim., 1978, 10, (2422-2424). Reactivity of allylcyclopentadienylpalladium.

128. J. E. Gozum, D. M. Pollina, J. A. Jensen, G. S. Girolami, J. Am. Chem. Soc., 1988, 110, (2688-2689). Tailored organometallics as precursors for the chemical vapor deposition of high purity Palladium and Platinum thin films.

129. C. S. Jun, K. H. Lee, J. Membr. Sci., 1999, 157, (107-115). Preparation of palladium membranes from the reaction of Pd(C3H5)(C5H5) with H2: wet-impregnated deposition.

129

130. L. A. Leites, V. J. Aleksanyan, T. B. Chenskaya, Dokl. Akad. Nauk SSSR. Phys. Chem., 1974, 215, (634-637). Analysis of �-allyl ligand vibrations in spectra of �-allyl complexes of transition metals.

131. H. P. Fritz, Chem. Ber., 1961, 94, (1217-1224). Spectroscopic investigations on organometallic compounds. IV. Infrared spectra of complexes of some allyl derivatives.

132. X. R. Li, J. S. Tse, G. M. Bancroft, R. J. Puddephatt, K. H. Tan, Organometallics, 1995, 14, (4513-4520). Variable Energy Photoelectron Spectroscopy of (C5H5)M(C3H5) (M=Ni and Pd): Molecular Orbital Assignments.

133. R. B. King, Appl. Spectrosc., 1969, 23, (148-156). Mass spectra of organometallic compounds. V. Some �-Cyclopentadienyl derivatives not contaning carbonyl groups.

134. J. C. Hierso, P. Serp, R. Feurer, P. Kalck, Appl. Organometal. Chem., 1998, 12, (161-172). MOCVD of rhodium, palladium and platinum complexes on fluidized divided substrates:Novel process for one-step preparation of noble-metal catalysts.

135. J. C. Hierso, R. Feurer, P. Kalck, Chem. Mater., 2000, 12, (390-399). Platinum and Palladium Films Obtained by Low-Temperature MOCVD for the Formation of Small Particles on Divided Supports as Catalytic Materials.

136. J. C. Hierso, R. Feurer, P. Kalck, Coord. Chem. Rev., 1998, 178–180, (1811–1834). Platinum, palladium and rhodium complexes as volatile precursors for depositing materials.

137. J. C. Hierso, C. Satto, R. Feurer, P. Kalck, Chem. Mater., 1996, 8, (2481-2485). Organometallic Chemical Vapor Deposition of Palladium under Very Mild Conditions of Temperature in the Presence of a Low Reactive Gas Partial Pressure.

138. G. T. Stauf, P. A. Dowben, K. Emrich, S. Barfuss, W. Hirschwald, N. M. Boag, J.Phys. Chem., 1989, 93, (749-753). Stability and Decomposition of Gaseous Allylcyclopentadienylpalladium.

139. Y. Kim, S. Bialy, G. T. Stauf, R. W. Miller, J. T. Spencer, P. A. Dowben, S. Datta, J. Micromech. Microeng., 1991, 1, (42-45). Photoassisted deposition of conducting palladium films.

140. D. S. Saulys, A. Ermakov, E. L. Garfunkel, P. A. Dowben, J. Appl. Phys., 1994, 76, (7639-7641). Electron-beam-induced patterned deposition of allylcyclopentadienyl palladium using scanning tunneling microscopy.

141. L. Sordelli, G. Martra, R. Psaro, C. Dossi, S. Coluccia, J. Chem. Soc., Dalton Trans., 1996, (765-770). Intrazeolite large palladium clusters prepared by organometallic chemical vapour deposition.

142. C. Dossi, A. Fusi, S. Recchia, M. Anghileri, R. Psaro, J. Chem. Soc., Chem. Commun., 1994, (1245). Novel palladium on magnesium oxide catalysts for alkane aromatisation.

143. C. Liang, W. Xia, H. S. Ahmadi, O. Schlüter, R. A. Fischer, M. Muhler, Chem.Commun., 2005, (282-284). The two-step chemical vapor deposition of Pd(allyl)Cp as an atom efficient route to synthesize highly dispersed palladium nanoparticles on carbon nanofibers.

130

144. S. N. Reifsnyder, H. H. Lamb, Catal. Lett., 1996, 40, (155-161). Pd/silica cluster catalysts: synthesis and reactivity with H2 and C2H4.

145. C. P. Mehnert, J. Y. Ying, Chem. Commun., 1997, (2215-2216). Palladium-grafted mesoporous MCM-41 material as heterogeneous catalyst for Heck reactions.

146. C. P. Mehnert, D. W. Weaver, J. Y. Ying, J. Am. Chem. Soc., 1998, 120, (12289-12296). Heterogeneous Heck Catalysis with Palladium-Grafted Molecular Sieves.

147. S. Ikeda, Trends Anal. Chem., 1984, 3, (115-120). Electron spectroscopy for surface analysis.

148. H. Bubert, J. C. Riviere, Wiley-VCH Verlag GmbH, Germany, 2002. Surface and thin film analysis: Principle, instrumentation, applications - 2. Electron detection.

149. D. M. Hercules, Anal. Chem., 1976, 48, (294R-313R). Electron Spectroscopy: X-ray and Electron Excitation.

150. C. Nordling, Angew. Chem. Int. Ed., 1972, 11, (83-92). ESCA : Electron Spectroscopy for Chemical Analysis.

151. E. I. Solomon, L. Basumallick, P. Chen, P. Kennepohl, Coord. Chem. Rev., 2005, 249, (229–253). Variable energy photoelectron spectroscopy: electronic structure and electronic relaxation.

152. J. M. Hollander, D. A. Shirley, Annu. Rev. Nucl. Sci., 1970, 20, (435-466). Chemical information from Photoelectron and conversion electron spectroscopy.

153. W. E. Swartz, Anal. Chem., 1973, 45, (788A-800A). X-Ray Photoelectron Spectroscopy.

154. A. S. Duwez, J. Electron. Spectrosc. Relat. Phenom., 2004, 134, (97-138). Exploiting electron spectroscopies to probe the structure and organization of self-assembled monolayers: a review.

155. L. Hallmann, A. Bashir, T. Strunskus, R. Adelung, V. Staemmler, C. Wöll, F. Tuczek, Langmuir, 2008, 24, (5726-5733). Self-Assembled Monolayers of Benzylmercaptan and p-Cyanobenzylmercaptan on Au(111) Surfaces: Structural and Spectroscopic Characterization.

156. P. Behrens, Trends Anal. Chem., 1992, 11, (237-244). X-ray absorption spectroscopy in chemistry : II. X-ray absorption near edge structure.

157. G. Haehner, Chem. Soc. Rev., 2006, 35, (1244-1255). Near edge X-ray absorption fine structure spectroscopy as a tool to probe electronic and structural properties of thin organic films and liquids.

158. G. Hähner, M. Kinzler, C. Thümmler, C. Wöll, M. Grunze, J. Vac. Sci. Technol. A, 1992, 10, (2758-2763). The structure of self-organizing organic films: A NEXAFS investigation of thiol-layers adsorbed on gold.

159. J. Stöhr, D. A. Outka, Phys. Rev. B, 1987, 36, (7891-7905). Determination of molecular orientations on surfaces from the angular dependance of near edge x-ray absorption fine structure spectra.

160. J. Stöhr, Springer-Verlag, Berlin, 1996. NEXAFS spectroscopy. 161. M. Badin, A. Bashir, S. Krakert, T. Strunskus, A. Terfort, C. Wöll, Angew. Chem.

Int. Ed., 2007, 46, (3762-3764). Kinetically Stable, Flat-Lying Thiolate Monolayers.

131

162. J. Kawai, S. Hayakawa, Y. Kitajima, Y. Gohshi, Anal. Sci., 1995, 11, (519-524). X-Ray Absorption and Photoelectron Spectroscopies Using Total Reflection X-rays.

163. J. M. Hollas, John Wiley & Sons Ltd., England, 2004. Modern Spectroscopy. 164. A. M. Bradshaw, N. V. Richardson, Pure Appl. Chem., 1996, 68, (457-467).

Symmetry, selection rules and nomenclature in surface spectroscopies. 165. P. Hollins, Vacuum, 1994, 45, (705-714). Surface infrared spectroscopy. 166. V. G. Gregoriou, S. E. Rodman, Mater. Sci., 2002, (1-24). Vibrational

Spectroscopy of Thin Organic Films. 167. F. M. Hoffmann, Surf. Sci. Rep., 1983, 3, (107-192). Infrared reflection-

absorption spectroscopy of adsorbed molecules. 168. R. G. Greenler, J. Chem. Phys., 1966, 44, (310–315). Infrared study of adsorbed

molecules on metal surfaces by reflection techniques. 169. E. M. McCash, Vacuum, 1990, 40, (423-427). Surfaces and vibrations. 170. K. Weiss, J. Weckesser, C. Wöll, J. Mol. Struct., 1999, 458, (143–150). An X-ray

absorption study of saturated hydrocarbons physisorbed on metal surfaces. 171. G. Hähner, M. Kinzler, C. Wöll, M. Grunze, M. K. Scheller, L. S. Cederbaum,

Phys. Rev. Lett., 1991, 67, (851-854). Near Edge X-Ray-Absorption Fine-Structure Determination of Alkyl-Chain Orientation: Breakdown of the "Building-Block" Scheme.

172. R. Arnold, Ph.D. Thesis, Ruhr-Universität Bochum, Germany, 2001. Struktur und Ordnung selbstordnender Monolagen aliphatischer und aromatischer Thiole auf Goldoberflächen.

173. D. Q. Feng, D. Wisbey, Y. Tai, Y. B. Losovyj, M. Zharnikov, P. A. Dowben, J.Phys. Chem. B 2006, 110, (1095-1098). Abnormal Temperature Dependence of Photoemission Intensity Mediated by Thermally Driven Reorientation of a Monomolecular Film.

174. Y. Tai, A. Shaporenko, H. T. Rong, M. Buck, W. Eck, M. Grunze, M. Zharnikov, J. Phys. Chem. B, 2004, 108, (16806-16810). Fabrication of Thiol-Terminated Surfaces Using Aromatic Self-Assembled Monolayers.

175. K. Fathe, J. S. Holt, S. P. Oxley, C. J. Pursell, J. Phys. Chem. A, 2006, 110, (10793-10798). Infrared Spectroscopy of Solid Hydrogen Sulfide and Deuterium Sulfide.

176. D. P. Long, J. L. Lazorcik, B. A. Mantooth, M. H. Moore, M. A. Ratner, A. Troisi, Y. Yao, J. W. Ciszek, J. M. Tour, R. Shashidhar, Nat. Mater., 2006, 5, (901-). Effects of hydration on molecular junction transport. .

177. E. A. Smith, M. J. Wanat, Y. Cheng, S. V. P. Barreira, A. G. Frutos, R. M. Corn, Langmuir, 2001, 17, (2502-2507). Formation, Spectroscopic Characterization, and Application of Sulfhydryl-Terminated Alkanethiol Monolayers for the Chemical Attachment of DNA onto Gold Surfaces.

178. J. Küther, R. Seshadri, W. Knoll, W. Tremela, J. Mater. Chem., 1998, 8, (641-650). Templated growth of calcite, vaterite and aragonite crystals onself-assembled monolayers of substituted alkylthiols on gold.

179. A. Kulak, Y. S. Park, Y. J. Lee, Y. S. Chun, K. Ha, K. B. Yoon, J. Am. Chem. Soc., 2000, 122, (9308-9309). Polyamines as Strong Molecular Linkers for Monolayer Assembly of Zeolite Crystals on Flat and Curved Glass.

132

180. S. Hermes, F. Schröder, R. Chelmowski, C. Wöll, R. A. Fischer, J. Am. Chem. Soc., 2005, 127, (13744-13745). Selective Nucleation and Growth of Metal-Organic Open Framework Thin Films on Patterned COOH/CF3-Terminated Self-Assembled Monolayers on Au(111).

181. O. Shekhah, H. Wang, T. Strunskus, P. Cyganik, D. Zacher, R. Fischer, C. Wöll, Langmuir, 2007, 23, (7440-7442). Layer-by-Layer Growth of Oriented Metal Organic Polymers on a Functionalized Organic Surface.

182. O. Shekhah, H. Wang, S. Kowarik, F. Schreiber, M. Paulus, M. Tolan, C. Sternemann, F. Evers, D. Zacher, R. A. Fischer, C. Wöll, J. Am. Chem. Soc., 2007, 129, (15118-15119). Step-by-Step Route for the Synthesis of Metal-Organic Frameworks.

183. H. J. Himmel, A. Terfort, C. Wöll, J. Am. Chem. Soc., 1998, 120, (12069-12074). Fabrication of a Carboxyl-Terminated Organic Surface with Self-Assembly of Functionalized Terphenylthiols: The Importance of Hydrogen Bond Formation.

184. R. Arnold, W. Azzam, A. Terfort, C. Wöll, Langmuir, 2002, 18, (3980-3992). Preparation, Modification and Crystallinity of Aliphatic and Aromatic Carboxylic Acid Terminated Self-Assembled Monolayers.

185. S. E. Creager, J. Clarke, Langmuir, 1994, 10, (3675-3683). Contact-Angle Titrations of Mixed �Mercaptoalkanoic Acid/Alkanethiol Monolayers on Gold. Reactive Vs Nonreactive Spreading, and Chain Length Effects on Surface pKa values.

186. B. Vaidya, J. Chen, M. D. Porter, R. J. Angelici, Langmuir, 2001, 17, (6569-6576). Effects of Packing and Orientation on the Hydrolysis of Ester Monolayers on Gold.

187. B. Dordi, H. Schönherr, G. J. Vancso, Langmuir, 2003, 19, (5780-5786). Reactivity in the Confinement of Self-Assembled Monolayers: Chain Length Effects on the Hydrolysis of N-Hydroxysuccinimide Ester Disulfides on Gold.

188. Y. Kwon, M. Mrksich, J. Am. Chem. Soc., 2002, 124, (806-812). Dependence of the Rate of an Interfacial Diels-Alder Reaction on the Steric Environment of the Immobilized Dienophile: An Example of Enthalpy-Entropy Compensation.

189. V. Chechik, C. M. Stirling, Langmuir, 1998, 14, (99-105). Reactivity in Self-Assembled Monolayers: Effect of the Distance from the Reaction Center to the Monolayer-Solution Interface.

190. N. Saito, Y. Wu, K. Hayashi, H. Sugimura, O. Takai, J. Phys. Chem. B, 2003, 107, (664-667). Principle in Imaging Contrast in Scanning Electron Microscopy for Binary Microstructures Composed of Organosilane Self-Assembled Monolayers.

191. G. P. Lopez, H. A. Biebuyck, G. M. Whitesides, Langmuir, 1993, 9, (1513-1516). Scanning electron microscopy can form images of patterns in self-assembled monolayers.

192. N. H. Mack, R. Dong, R. G. Nuzzo, J. Am. Chem. Soc., 2006, 128, (7871-7881). Quantitative Imaging of Protein Adsorption on Patterned Organic Thin-Film Arrays Using Secondary Electron Emission.

193. E. W. Wollman, C. D. Frisbie, M. S. Wrighton, Langmuir, 1993, 9, (1617-1620). Scanning electron microscopy for imaging photopatterned self-assembled monolayers on gold.

133

194. M. A. Gosalvez, R. M. Nieminen, New J. Phys., 2003, 5, (100.1-100.28). Surface morphology during anisotropic wet chemical etching of crystalline silicon.

195. E. Cooper, G. J. Leggett, Langmuir, 1999, 15, (1024-1032). Influence of Tail-Group Hydrogen Bonding on the Stabilities of Self-Assembled Monolayers of Alkylthiols on Gold.

196. I. H. Campbell, J. D. Kress, R. L. Martin, D. L. Smith, N. N. Barashkov, J. P. Ferraris, Appl. Phys. Lett., 1997, 71, (3528-3530). Controlling charge injection in organic electronic devices using self-assembled monolayers.

197. D. Bethell, M. Brust, D. J. Schiffrin, C. Kiely, J. Electroanal. Chem., 1996, 409, (137-143). From monolayers to nanostructured materials: an organic chemist's view of self-assembly.

198. C. A. Mirkin, M. A. Ratner, Annu. Rev. Phys. Chem., 1992, 43, (719-754). Molecular electronics.

199. J. M. Tour, Acc. Chem. Res., 2000, 33, (791-804). Molecular Electronics. Synthesis and Testing of Components.

200. J. H. Fendler, Chem. Mater., 2001, 13, (3196-3210). Chemical Self-assembly for Electronic Applications.

201. A. M. Bittner, Surf. Sci. Rep., 2006, 61, (383–428). Clusters on soft matter surfaces.

202. D. R. Jung, A. W. Czanderna, G. C. Herdt, J. Vac. Sci. Technol., A, 1996, 14, (1779-1787). Interactions and penetration at metal/self-assembled organic monolayer interfaces.

203. D. R. Jung, A. W. Czanderna, Crit. Rev. Solid State Mater. Sci., 1994, 19, (1-54). Chemical and physical interactions at metal/self-assembled organic monolayer interfaces.

204. G. C. Herdt, D. E. King, A. W. Czanderna, Z. Phys. Chem., 1997, 202, (163-196). Penetration of deposited Au, Cu, and Ag overlayers through alkanethiol self-assembled monolayers on gold or silver.

205. G. C. Herdt, D. R. Jung, A. W. Czanderna, J. Adhes., 1997, 60, (197-222). Penetration of deposited Ag and Cu overlayers through alkanethiol self-assembled monolayers on gold.

206. G. C. Herdt, A. W. Czanderna, J. Vac. Sci. Technol., A, 1997, 15, (513-519). Metal overlayers on organic functional groups of self-organized molecular assemblies .7. Ion scattering spectroscopy and x-ray photoelectron spectroscopy of Cu/CH3 and Cu/COOCH3.

207. K. D. Dronavajjala, R. Rajagopalan, S. Uppili, A. Sen, D. L. Allara, H. C. Foley, J. Am. Chem. Soc., 2006, 128, (13040-13041). A Simple Technique To Grow Polymer Brushes Using in Situ Surface Ligation of an Organometallic Initiator.

208. V. Ivanova, T. Baunach, D. A. Kolb, Electrochim. Acta, 2005, 50, (4283-4288). Metal deposition onto a thiol-covered gold surface: A new approach.

209. P. L. Schilardi, P. Dip, P. C. dosSantosClaro, G. A. Benitez, M. H. Fonticelli, O. Azzaroni, R. C. Salvarezza, Chem. Eur. J., 2006, 12, Electrochemical Deposition onto Self-Assembled Monolayers: New Insights into Micro- and Nanofabrication.

210. E. A. Speets, P. teRiele, M. A. F. vandenBoogaart, L. M. Doeswijk, B. J. Ravoo, G. Rijnders, J. Brugger, D. N. Reinhoudt, D. H. A. Blank, Adv. Funct. Mater., 2006, 16, (1337–1342). Formation of Metal Nano- and Micropatterns on Self-

134

Assembled Monolayers by Pulsed Laser Deposition Through Nanostencils and Electroless Deposition.

211. J. I. Henderson, S. Feng, G. M. Ferrence, T. Bein, C. P. Kubiak, Inorg. Chim. Acta, 1996, 242, (115-124). Self-assembled monolayers of dithiols,diisocyanides,and isocyanothiols on gold : Chemically sticky surfaces for covalent attachment of metal clusters and studies of interfacial electron transfer.

212. Y. Tai, A. Shaporenko, W. Eck, M. Grunze, M. Zharnikov, Langmuir, 2004, 20, (7166-7170). Depth Distribution of Irradiation-Induced Cross-Linking in Aromatic Self-Assembled Monolayers.

213. H. Noda, Y. Tai, A. Shaporenko, M. Grunze, M. Zharnikov, J. Phys. Chem. B, 2005, 109, (22371-22376). Electrochemical Characterizations of Nickel Deposition on Aromatic Dithiol Monolayers on Gold Electrodes.

214. J. Weiss, H. J. Himmel, R. A. Fischer, C. Wöll, Chem. Vap. Deposition, 1998, 4, (17-21). Self-Terminated CVD-Functionalization of Organic Self-Assembled Monolayers (SAMs) with Trimethylamine Alane (TMAA).

215. P. Serp, P. Kalck, R. Feurer, Chem. Rev., 2002, 102, (3085-3128). Chemical Vapor Deposition Methods for the Controlled Preparation of Supported Catalytic Materials.

216. C. Fuxen, W. Azzam, R. Arnold, G. Witte, A. Terfort, C. Wöll, Langmuir, 2001, 17, (3689-3695). Structural characterization of organothiolate adlayers on gold: The case of rigid, aromatic backbones.

217. D. Q. Feng, Y. B. Losovyj, Y. Tai, M. Zharnikov, P. A. Dowben, J. Mater. Chem., 2006, 16, (4343–4347). Engineering of the electronic structure in an aromatic dithiol monomolecular organic insulator.

218. D. Q. Feng, D. Wisbey, Y. B. Losovyj, Y. Tai, M. Zharnikov, P. A. Dowben, Phys. Rev. B, 2006, 74, (165425-1-165425-11). Electronic structure and polymerization of a self-assembled monolayer with multiple arene rings.

219. A. Niklewski, T. Strunskus, G. Witte, C. Wöll, Chem. Mater., 2005, 17, (861-868). Metal Organic Chemical Vapor Deposition of Palladium: Spectroscopic Study of Cyclopentadienyl-allyl-palladium Deposition on a Palladium Substrate.

220. Q. H. Wu, M. Gunia, T. Strunskus, G. Witte, M. Muhler, C. Wöll, Chem. Vap. Deposition, 2005, 11, (355-361). Deposition of palladium from cyclopentadienyl-allyl-palladium precurser on differently pretreated Sibased substrates: The role of surface Si-OH and Si-H species studied by x-ray photoelectron spectroscopy .

221. M. T. Lee, C. C. Hsueh, M. S. Freund, G. S. Ferguson, Langmuir, 1998, 14, (6419-6423). Air Oxidation of Self-Assembled Monolayers on Polycrystalline Gold: The Role of the Gold Substrate.

222. M. C. Wang, J. D. Liao, C. C. Weng, R. Klauser, A. Shaporenko, M. Grunze, M. Zharnikov, Langmuir, 2003, 19, (9774-9780). Modification of Aliphatic Monomolecular Films by Free Radical Dominant Plasma: The Effect of the Alkyl Chain Length and the Substrate.

223. E. Pretsch, T. Clerc, J. Seibl, W. Simon, Springer-Verlag New York, 1989. Tables of Spectral Data for Structure Determination of Organic Compounds.

224. U. Weckenmann, Ph. D. Thesis, Ruhr-Universität Bochum, Germany, 2002. Selektive Metallorganische Chemische Dampfabscheidung von Gold und Palladium auf Selbstorganisierten Monolagen.

135

225. B. Bogdanovic, M. Rubach, K. Seevogel, Z. Naturforsch., B: Chem. Sci, 1983, 38, (592-598). �'-Allylmetall-Schwefel-Komplexe, IV [1] �'-Allyl-hydrogensulfidopalladium-und -platin-Komplexe.

226. B. Bogdanovic, P. Göttsch, M. Rubach, Z. Naturforsch., B: Chem. Sci, 1983, 38, (599-603). �'-Allylmetall-Schwefel-Komplexe, V [1] Mono- und bimetallische, mehrkernige �'-Allylmetall-Schwefel-Komplexe des Nickels, Palladiums und Platins.

227. Y. Tsuji, T. Fujihara, Inorg. Chem., 2007, 46, (1895-1902). Homogeneous Nanosize Palladium Catalysts.

228. R. Umeda, H. Awaji, T. Nakahodo, H. Fujihara, J. Am. Chem. Soc., 2008, 130, (3240-3241). Nanotube Composites Consisting of Metal Nanoparticles and Polythiophene from Electropolymerization of Terthiophene-Functionalized Metal (Au, Pd)Nanoparticles.

229. M. J. Schultz, C. C. Park, M. S. Sigman, Chem. Commun., 2002, (3034-3035). A convenient palladium-catalyzed aerobic oxidation of alcohols at room temperature.

230. S. S. Stahl, Science, 2005, 309, (1824-1826). Palladium-Catalyzed Oxidation of Organic Chemicals with O2.

231. J. E. Remias, L. E. Grove, A. Sen, Dalton Trans., 2003, (3067-3070). Carbon-sulfur bond cleavage and reduction of thiols and dithioethers under oxidative conditions.

232. S. A. Ruiz, C. S. Chen, Soft Matter, 2007, 3, (168–177). Microcontact printing: A tool to pattern.

233. J. L. Wilbur, A. Kumar, H. A. Biebuyck, E. Kim, G. M. Whitesides, Nanotechnology, 1996, 7, (452-457). Microcontact printing of self-assembled monolayers: applications in microfabrication.

234. G. M. Whitesides, E. Ostuni, S. Takayama, X. Jiang, D. E. Ingber, Annu. Rev. Biomed. Eng., 2001, 3, (335-373). Soft lithography in biology and biochemistry.

235. Y. Xia, G. M. Whitesides, Annu. Rev. Mater. Sci., 1998, 28, (153-184). Soft lithography.

236. R. K. Smith, P. A. Lewis, P. S. Weiss, Prog. Surf. Sci., 2004, 75, (1-68). Patterning self-assembled monolayers.

237. M. Liebau, J. Huskens, D. N. Reinhoudt, Adv. Funct. Mater., 2001, 11, (147-150). Microcontact Printing with Heavyweight Inks.

238. J. N. Lee, C. Park, G. M. Whitesides, Anal. Chem., 2003, 75, (6544-6554). Solvent Compatibility of Poly(dimethylsiloxane)-Based Microfluidic Devices.

Acknowledgments

This thesis would not have been possible without the help and support from a number of

people and I would like to acknowledge all those who have contributed to the realization

of this thesis. First, I would like to express my sincere thanks and gratitude to my thesis

advisor Prof. Christof Wöll for providing me the opportunity to work on this project and

for his encouragement and guidance throughout the course of this work. Thank you for

teaching me many things even beyond science. I would like to thank Prof. Roland A.

Fischer for willingly accepting to be my second referee. Special thanks to his valuable

advices and for the palladium precursor provided by his lab. I owe a great deal of

gratitude to Dr. Thomas Strunskus for his support during the entire course of this work.

He always had time for my questions and problems. I extend my cordial thanks to Dr.

Gregor Witte for inspiring me through his thought-provoking discussions, which have

been valuable to my professional development. I would like to convey my thanks to Dr.

Alexander Birkner (the first person I met from this department) for his friendliness and

fruitful discussions related to microscopic methods. Thanks to Dr. Franziska Traeger and

Dr. Martin Kind for their enormous help in proofreading my thesis. I wish to thank Dr.

Osama Shekhah and Dr. Yuemin Wang for their help in UHV measurements. I would

like to express my deepest gratitude to Dr. P. Engels.

I would like to convey my thanks to Dr. Andreas Terfort for his suggestions and for the

thiol molecules rendered by his lab. Special thanks to Dr. Rolf Neuser who helped me

with the SEM measurements. I am grateful to all the members of Inorganic Chemistry II

and special thanks to Felicitas Schröder who always helped me with the palladium

precursor. I am very grateful to the technicians of the Physical Chemistry I, Mr. Volker

Ader, Mr. Reiner Krause, Mr. Theo Wasmuth, Mr. Gerd Humme, Jennifer Haag and Mr.

Heinz Zwingmann, for their superior technical supports. Thanks to the entire staff at the

Berlin synchrotron facility BESSY II for the excellent technical and scientific support. I

kindly acknowledge the financial support of the IMPRS-SurMat. I am grateful for the

help offered by Mrs. Gundula Talbot, Dr. Angela Buettner and Dr. Rebekka Loschen in

many administrative matters. I would also like to acknowledge my teachers who have

encouraged me all these years.

Many thanks especially to all my colleagues for the friendly working atmosphere and for

their support during my stay in the group. Mihaela Badin, thank you for your company. I

won’t forget our searches for your missing things (tweezers, ethanol, etc,). Kathrin Hänel,

thanks for your friendly mails. Deler Langenberg and Daniel Käfer, thanks for your help

in solving computer problems. Asif Bashir and Rolf Chelmowski, I will never forget our

trip to Italy. Rolf, thanks for sharing a lot of your PDMS stamps with me. David Silber,

Lutz Stratmann, Xia Stammer, Vadim Schott, Jan Götzen, Mira and Sasha - for the

lunchtime chats. Hui Wang, thanks for unforgettable times at Heidelberg. I thank all my

colleagues from SurMat. All of you make me feel at home and this has made life much

easier for me to live in Germany. I want also to thank all my friends in India.

I thank Mrs. Ursula Uhde, Mrs. Bärbel van Eerd, Mrs. Ruth Knödlseder-Mutschler and

Mrs. Angelika Kruse-Fernkorn for all the love and emotional support you have given me

during these years. Special thanks to Mrs. van Eerd, for cheering me up when things were

at low ebb. Thank you for all the happy moments that will stay in my memories for years

to come. I owe special thanks to my friend Kathirvel for his moral support during this

work and for helping me to face challenges in all aspects of my life. Finally, I thank my

parents and my brother for their support throughout these years and for helping me to

realize my dreams. Without their prayers and encouragement, I would not be the person

that I am today. They have made everything possible.

ï¡P

List of publications

1. Chemistry in confined geometries: Reactions at an organic surface

Ketheeswari Rajalingam, Asif Bashir, Mihaela Badin, Felicitas Schröder, Ned

Hardman, Thomas Strunskus, Roland A. Fischer, Christof Wöll

ChemPhysChem, 8, 2007, (657-660)

2. Metallization of a thiol-terminated organic surface using chemical vapor deposition

Ketheeswari Rajalingam, Thomas Strunskus, Andreas Terfort, Roland A. Fischer,

Christof Wöll

Langmuir, 24, 2008, (7986-7994)

Ketheeswari Rajalingam

Date of birth: 01.12.1981

Nationality: Indian

Ph.D. candidate: Chemistry (2004 - 2008)

Ph.D. thesis under the guidance of Professor Dr. Christof Wöll, Physical Chemistry I,

Ruhr University Bochum, Bochum, Germany.

Thesis title: "Reactions at an organic surface".

IMPRS- SurMat Scholarship (2004 - 2007).

Master of Science: Chemistry (2001 - 2003)

Master thesis under the guidance of Professor Dr. S. Arunachalam, School of Chemistry,

Bharathidasan University, Tiruchirappalli, India.

Thesis title: "Studies on emission quenching of *Ru(phen)32+ ion by Cobalt(III) amine

complexes and also studies on various DNA".

Second Rank in M.Sc. degree. Marks obtained: 73%

Summer research fellow (May to June in 2002 & July to August in 2003)

Work under the guidance of late Professor Dr. Bhaskar G. Maiya, School of Chemistry,

University of Hyderabad, Hyderabad, India. Topics include the synthesis of a second-

generation photosensitizer for photodynamic therapy and study on the interactions of

cationic porphyrins with DNA. Summer research fellowship by Jawaharlal Nehru Center

for Advanced Scientific Research, Bangalore, India.

Bachelor of Science: Chemistry (1998 - 2001)

Holy Cross College (Autonomous), Tiruchirappalli, India.

Gold medal for first rank in B.Sc., Chemistry. Marks obtained: 91%

Higher Secondary (1996 - 1998) and Secondary School (1987 - 1996)

Holy Cross Girls Higher Secondary School, Tiruchirappalli, India.

Acknowledgments

This thesis would not have been possible without the help and support from a number of

people and I would like to acknowledge all those who have contributed to the realization

of this thesis. First, I would like to express my sincere thanks and gratitude to my thesis

advisor Prof. Christof Wöll for providing me the opportunity to work on this project and

for his encouragement and guidance throughout the course of this work. Thank you for

teaching me many things even beyond science. I would like to thank Prof. Roland A.

Fischer for willingly accepting to be my second referee. Special thanks to his valuable

advices and for the palladium precursor provided by his lab. I owe a great deal of

gratitude to Dr. Thomas Strunskus for his support during the entire course of this work.

He always had time for my questions and problems. I extend my cordial thanks to Dr.

Gregor Witte for inspiring me through his thought-provoking discussions, which have

been valuable to my professional development. I would like to convey my thanks to Dr.

Alexander Birkner (the first person I met from this department) for his friendliness and

fruitful discussions related to microscopic methods. Thanks to Dr. Franziska Traeger and

Dr. Martin Kind for their enormous help in proofreading my thesis. I wish to thank Dr.

Osama Shekhah and Dr. Yuemin Wang for their help in UHV measurements. I would

like to express my deepest gratitude to Dr. P. Engels.

I would like to convey my thanks to Dr. Andreas Terfort for his suggestions and for the

thiol molecules rendered by his lab. Special thanks to Dr. Rolf Neuser who helped me

with the SEM measurements. I am grateful to all the members of Inorganic Chemistry II

and special thanks to Felicitas Schröder who always helped me with the palladium

precursor. I am very grateful to the technicians of the Physical Chemistry I, Mr. Volker

Ader, Mr. Reiner Krause, Mr. Theo Wasmuth, Mr. Gerd Humme, Jennifer Haag and Mr.

Heinz Zwingmann, for their superior technical supports. Thanks to the entire staff at the

Berlin synchrotron facility BESSY II for the excellent technical and scientific support. I

kindly acknowledge the financial support of the IMPRS-SurMat. I am grateful for the

help offered by Mrs. Gundula Talbot, Dr. Angela Buettner and Dr. Rebekka Loschen in

many administrative matters. I would also like to acknowledge my teachers who have

encouraged me all these years.

Many thanks especially to all my colleagues for the friendly working atmosphere and for

their support during my stay in the group. Mihaela Badin, thank you for your company. I

won’t forget our searches for your missing things (tweezers, ethanol, etc,). Kathrin Hänel,

thanks for your friendly mails. Deler Langenberg and Daniel Käfer, thanks for your help

in solving computer problems. Asif Bashir and Rolf Chelmowski, I will never forget our

trip to Italy. Rolf, thanks for sharing a lot of your PDMS stamps with me. David Silber,

Lutz Stratmann, Xia Stammer, Vadim Schott, Jan Götzen, Mira and Sasha - for the

lunchtime chats. Hui Wang, thanks for unforgettable times at Heidelberg. I thank all my

colleagues from SurMat. All of you make me feel at home and this has made life much

easier for me to live in Germany. I want also to thank all my friends in India.

I thank Mrs. Ursula Uhde, Mrs. Bärbel van Eerd, Mrs. Ruth Knödlseder-Mutschler and

Mrs. Angelika Kruse-Fernkorn for all the love and emotional support you have given me

during these years. Special thanks to Mrs. van Eerd, for cheering me up when things were

at low ebb. Thank you for all the happy moments that will stay in my memories for years

to come. I owe special thanks to my friend Kathirvel for his moral support during this

work and for helping me to face challenges in all aspects of my life. Finally, I thank my

parents and my brother for their support throughout these years and for helping me to

realize my dreams. Without their prayers and encouragement, I would not be the person

that I am today. They have made everything possible.

ï¡P

List of publications

1. Chemistry in confined geometries: Reactions at an organic surface

Ketheeswari Rajalingam, Asif Bashir, Mihaela Badin, Felicitas Schröder, Ned

Hardman, Thomas Strunskus, Roland A. Fischer, Christof Wöll

ChemPhysChem, 8, 2007, (657-660)

2. Metallization of a thiol-terminated organic surface using chemical vapor deposition

Ketheeswari Rajalingam, Thomas Strunskus, Andreas Terfort, Roland A. Fischer,

Christof Wöll

Langmuir, 24, 2008, (7986-7994)

Ketheeswari Rajalingam

Date of birth: 01.12.1981

Nationality: Indian

Ph.D. candidate: Chemistry (2004 - 2008)

Ph.D. thesis under the guidance of Professor Dr. Christof Wöll, Physical Chemistry I,

Ruhr University Bochum, Bochum, Germany.

Thesis title: "Reactions at an organic surface".

IMPRS- SurMat Scholarship (2004 - 2007).

Master of Science: Chemistry (2001 - 2003)

Master thesis under the guidance of Professor Dr. S. Arunachalam, School of Chemistry,

Bharathidasan University, Tiruchirappalli, India.

Thesis title: "Studies on emission quenching of *Ru(phen)32+ ion by Cobalt(III) amine

complexes and also studies on various DNA".

Second Rank in M.Sc. degree. Marks obtained: 73%

Summer research fellow (May to June in 2002 & July to August in 2003)

Work under the guidance of late Professor Dr. Bhaskar G. Maiya, School of Chemistry,

University of Hyderabad, Hyderabad, India. Topics include the synthesis of a second-

generation photosensitizer for photodynamic therapy and study on the interactions of

cationic porphyrins with DNA. Summer research fellowship by Jawaharlal Nehru Center

for Advanced Scientific Research, Bangalore, India.

Bachelor of Science: Chemistry (1998 - 2001)

Holy Cross College (Autonomous), Tiruchirappalli, India.

Gold medal for first rank in B.Sc., Chemistry. Marks obtained: 91%

Higher Secondary (1996 - 1998) and Secondary School (1987 - 1996)

Holy Cross Girls Higher Secondary School, Tiruchirappalli, India.