Growth and Structural Characterization of Self-Assembled Monolayers (SAMs) on Gold made from Functionalized Thiols and Selenols

Transcription

1 Growth and Structural Characterization of Self-Assembled Monolayers (SAMs) on Gold made from Functionalized Thiols and Selenols Dissertation zur Erlangung des Grades eines Doktors der Naturwissenschaften der Fakultät für Chemie der Ruhr-Universität Bochum Vorgelegt von Asif Bashir Aus Wah Cantt/Pakistan Bochum 2008

2 Growth and Structural Characterization of Self-Assembled Monolayers (SAMs) on Gold made from Functionalized Thiols and Selenols Tag der mündlichen Prüfung: Prüfungskommission: Referent: Prof. Dr. Ch. Wöll Koreferent: Prof. Dr. R. Fischer Vorsitzender: Prof. Dr. R. Heumann

3 Die vorliegende Arbeit wurde im Zeitraum von Januar 2005 bis April 2008 am Lehrstuhl für Physikalische Chemie I der Fakultät für Chemie der Ruhr-Universität Bochum unter Anleitung von Herrn Prof. Dr. Christof Wöll angefertigt.

4 Dedicated to my loving Parents

5 Abstract The use of organic thin layers as active component in materials science and electronic devices is presently considered a potential alternative to conventional semiconductor based nano scale electronics since it directly provides precise well-defined nano-scale components for electronic devices which eventually allows for simple processing and device fabrication. In the area of interface and surface science covalently bound Self- Assembled Monolayers (SAMs) became of significant importance. In particular aromatic based materials became of paramount interest, since they exhibit strong intermolecular interactions, chemical stability and charge transport properties across metal-organic interface. In the present thesis the SAMs of different systems are investigated by microscopic and spectroscopic investigation. The dependence of protecting group on thiol (-SH) moiety and the structure of resulting SAMs demonstrated experimentally which offers new possibilities to control the SAMs structure. The differently anchored (thiols and selenols) aromatic molecules are studied, to explore the anchoring-ordering interrelation with particular emphasize on their microstructure with the goal to correlate the molecular ordering and packing with the bulk structure. Improvement in the growth and lateral ordering in the SAMs are developed which is the prerequisite for the application in the molecular electronics and organic devices. Finally, the self-assembly and electron transport properties of π-conjugated (macro) molecular architectures on Au(111) are explored. Within the present course of work, the enhanced long range ordering in the SAMs that have been developed are not only of interest for nanoconstructions on solid surfaces, but also exhibit properties that render them candidates for applications in the field of molecular electronics.

6 Chapter 1 Table of contents 1.1 Introduction Self-Assembled Monolayers Head Group Molecular Backbone Terminal Group Mechanism and kinetics of SAM Structural Characterization of Thiol Monolayer Energetics of SAM Formation Outline of the Thesis Chapter Scanning Tunneling Microscopy (STM) Historical Background Introduction Theory Basic Principle Working Principle Modes of Operation Constant-Current Mode Constant-Height Mode Calibration of STM Current Imaging Tunneling Spectroscopy (CITS) Methodology of Working Reflection-Absorption Infrared Spectroscopy (RAIRS) X-ray Photoelectron Spectroscopy (XPS) Low-Energy Electron Diffraction (LEED) Near-Edge X-ray Absorption Fine Structure (NEXAFS) Chapter Introduction Substrates Muscovite Mica Gold Herringbone Reconstruction Gold Substrates Preparation and Characterization of Gold Substrates Ultra-flat Gold Substrates (UFGS) Introduction Preparation of Ultra-flat Gold Substrates Characterization of Ultra-flat Gold Substrates

7 3.4.4 Surface Morphology of Ultra-flat Gold Substrates Characterization of Alkanethiol Monolayer on UFGS Preparation of Self-Assembled Monolayers (SAMs) Preparation of KBr Disk for RAIR Studies Cleaning of Glassware and Laboratory Equipment Chemical and Reagents Chapter Introduction Objective of Work Presented in this Chapter Adsorption Process of TPn SAMs on Au(111) Results Infrared Spectroscopy Scanning Tunneling Microscopy Odd-Numbered TPn (TP1, TP2, TP5) Monolayers Structural Model for Odd-Numbered TPn SAMs (TP1, TP2, TP5) Even-Numbered TPn SAMs (TP2, TP4, TP6) Monolayers Summary of Structures Adopted by TPn SAMs Exchange of TP2 SAM in C10 Matrix Introduction Molecular Exchange Results STM NEXAFS Discussion Common Feature For All TPn SAMs Odd-Numbered TPn Monolayers Even-Numbered TPn Monolayers Effect of Aliphatic Part in Molecular Packing Effect of the Solution Temperature Influence of Aromatic Part in Molecular Packing Chapter Introduction Objective of Work Presented in this Chapter Adsorption of Dodecyl thioacetate SAMs on Au(111) Results Infrared Spectroscopy STM XPS Re-immersion of C12SAc-SAMs into Thiol Solution Structural Model Discussion

8 Chapter Introduction Objective of the Work Presented in this Chapter Results STM of Benzenethiol SAMs Structural Model of BT SAMs STM of Benzeneselenol SAMs Structural Model of BSe SAMs Monolayer of Anthracene-2-Selenoate (AntSe) on Au(111) Fabrication of AntSeSAMs Microscopic Results Growth of AntSe SAMs Growth of AntSe SAMs by Gently Heating Saturated Phase of AntSe SAMs Structural Model Spectroscopic Results RAIRS and XPS NEXAFS Discussion Monolayer of BT Monolayer of BSe Monolayer of AntSe Chapter Introduction Objective of the Work Presented in this chapter Monolayer of Mono-thiol Substituted Hexabenzocoronene Formation of HBC-C3-SAc SAMs STM RAIR Structural Model Lateral Transport Through Organic Layers Introduction Results HBC-C 3 -thiol Islands in An Alkanethiol Matrix Monolayer of Hexabenzocoronene-ethynyl-benzyl Thiol Formation of P-HBC-SAc SAMs STM Current Imaging Tunneling Spectroscopy (CITS) Model for electron Transport Discussion Monolayer of HBC-C 3 -thiol Monolayer of P-HBC-thiol Electron transport in discotic molecules

9 Chapter Preparation of Gold Substrates Influence of the Temperature of the Thiol Solution Effect of the Aliphatic Part in the Molecular Structure of TPn Effect of the Protecting group on Molecular Structure Effect of the Anchor group on Molecular Ordering Molecular Arrangement of HBC-C 3 -thiol Molecular Arrangement of P-HBC-thiol Current-Voltage Characteristic of Discotic molecules List of Figures Reference

10 Chapter One Self-Assembled Monoalyers Chapter One Self-Assembled Monolayers 1.1 Introduction Thin and ultra thin layers are films with a thickness ranging from micrometers down to few angströms. The Langmuir-Blodgett method was the first technique that allowed to construct thin ordered molecular assemblies [1], and it is based on the preparation of monolayers at the water-air interface. A Langmuir monolayer is generally prepared by placing a known number of amphiphilic molecules on the surface of a sub phase, which usually is deionized water. Langmuir and Blodgett deposited these films on solid surfaces by dipping a solid slab in water that was pre-covered with a monolayer of long-chain carboxylic acids, causing the hydrophobic part of the molecule to adhere to the surface [2,3]. In rare cases also mercury and other materials, as well as glycerol, have also been used as sub phases [4]. In the 1940 s, Zisman et al. discovered that an alkanoic acid is self-organizing a monolayer on a clean platinum surface driven by chemisorption from a solution phase [5] and that these films are more stable than those organic films prepared by Langmuir-Blodgett method [2]. Hitherto the most commonly used method to prepare well ordered, robust thin films is the method of self-assembled monolayers (SAMs). SAMs are formed spontaneously by immersion of an appropriate substrate into a dilute solution of an surface active agent (surfactant) having specific affinity of its head group to the substrate in an organic solvent or by gas phase deposition in vacuum, which is in contrast to Langmuir-Blodgett films, which are formed by a mechanical process. There are various types of SAMs that have been synthesized and studied in detail including organo silanes on oxidized surfaces (SiO 2 on Si, Al 2 O 3 on Al, glass etc), trifunctional alkylsiloxane monolayers on SiO 2 surfaces [6], alkanethiol on metallic surfaces like Au, Ag and Cu, alcohols and amines on Pt, dialkyl sulphide and dialkyl disulphide on Au, and carboxylic acids on Al 2 O 3 and Ag [7]. 1

11 Chapter One Self-Assembled Monoalyers The discovery of SAMs in particular the identification of thiol/au pioneering work of Nuzzo and Allara in 1983 [8], have been intensively studied in research focusing on interfacial properties and also for their potential applications in molecular technologies. SAMs made up of thiols on Au(111) have been used to study important fundamental phenomena and processes such as adhesion [9,10], control of surface wetting [11-13], friction and lubrication [14,15], biocompatibility [16,17], protein and cell adhesion [18-20], interfacial electron transfer [21-24] and catalysis [25]. Self-assembly is the spontaneous molecular arrangement without the aid of external factors/guidance, uses the inherent chemical and physical properties of molecules to form controlled ordered and organized geometries on a variety of substrates. The inherent chemical, physical and thermodynamic properties of molecules can be exploited as a facile route to fabricate and to control surfaces at the molecular level using the selfassembly techniques [26]. Since their inception, much progress has been made in the formation of SAMs and considered as a major contributors in many types of molecular assemblies because their ease of preparation, stability and high structural order [27-29]. SAMs have been used as insulating layers and as 2D-matrices in which other molecules can be studied by following the mechanism of insertion into SAM matrices [30-32]. Self-assembled monolayers (SAMs) can be formed from a variety of molecules differing in size and functionality [33-38] and are more versatile than the thin films prepared from molecular beam epitaxy [39] or chemical vapor deposition [27, 40]. 2

12 Chapter One Self-Assembled Monoalyers 1.2 Self-Assembled Monolayers Self-assembled monolayers (SAMs) are formed by the spontaneous adsorption of amphiphilic adsorbates onto noble metallic substrates. The molecules which are capable of forming SAMs are mainly consisting of the three parts as shown in fig. 1.1, which influence significantly on the stability of resulting SAM structure: a head group, a molecular backbone and a terminal group. Figure 1.1: Self-assembly of amphiphilic adsorbates on solid surface, depiction of alkanethiol adsorbates on gold Au(111) showing the terminal group, molecular backbone and head group Head Group The first and main part consists of the thiol moiety (-SH) and is referred to as the head group. The chemisorption of head group to the substrate is the most important and most energetic process in the monolayer formation. Head group in the thiol molecules has the strong affinity to make the covalent bond to a specific site on the surface. Indistinguishable monolayers apparently forming the Au(1) thiolate (RS-) species result 3

13 Chapter One Self-Assembled Monoalyers from chemisorption of alkanethiols or di-alkyl disulfides on gold [41,42]. The cleavage and oxidative addition of S-S bond to the gold surface is possibly the mechanism of SAM formation from the disulfides: RS - RS Au n RS Au.Au n (1.1) In the case of thiol, the reaction may be formally considered as an oxidative addition of S-H bond to the gold surface, followed by a reductive elimination of the hydrogen: R - S - H + Au n R - S Au.Au n + 1 H 2 2 (1.2) The formation of H 2 thought to be exothermic which may be important in the chemisorption energetics. The bonding of head group (thiolate) is very strong and the hemolytic bond strength has been estimated to be approximately 40 kcal per mol [43] Molecular Backbone The second part consist of aliphatic or aromatic moiety plays an important role in the determination of the ordering and structure in the self-assembled monolayers. Once molecules adsorbed on the surface, the formation of ordered and closely packed arrangement starts which then depends upon the intermolecular interactions, such as van der Waals, dipole or π-π interaction. The contribution of intermolecular interaction depends upon the spacing between the molecular backbone and the anchor group [44, 45]. Van der Waals interactions are the main forces in the case of simple alkyl chains ( C n H 2n+1 ). Recently aromatic thiols have also moved into the focus of interest since they represent an interesting alternative to alkane-based thiol SAMs. While the purely aromatic thiol exhibits low solubility which yield SAMs of fairly low structural quality significantly lower than the well know aliphatic SAMs [46-49]. Because of their higher rigidity in the molecular backbone and stronger π-π interactions, aromatic thiols offer the chance of better control over the structure of SAMs [27,50-55]. By the insertion or varying the 4

14 Chapter One Self-Assembled Monoalyers length of alkyl spacer between the thiol head group and aromatic moiety, which introduces additional interactions and degrees of freedom, affects substantially the free energy of the SAMs, yields to a high structural quality in ordering of SAMs [29,33,56-58]. Figure 1.2: Schematic presentation of an alkanethiol molecule adsorbed on a gold surface. Angles Θ, Ψ, Φ refer to tilt angle, twist angle and tilt direction respectively, used to describe the molecular orientation Terminal Group The third part comprises of terminal moieties which are useful to functionalize the thiol based SAMs. This offers the possibility for successive adsorption (anchoring) [59,60] or the chemical reaction on top of SAMs [48,61-64]. Functionalized self-assembled monolayers on Au(111) with a variety of functional group such as fluorocarbon [65,66], OH, COOH [67-69], NH 2, SH, CN [70] have been studied with respect to their potential applications. A small change in the end group is strongly capable to change the physical and chemical properties of the organic thin layers/ SAMs [1,71,72]. Thus, -CH3 and -CF 3 groups turn the SAMs surface hydrophobic, metallophobic and highly anti-adherent, while -COOH, -NH2 or -OH groups yield hydrophilic surfaces with good metal ion and protein binding properties [73,74]. A huge body of literature which deals with phase separation in mixed SAMs [75], binary mixed SAMs containing different terminal groups obtained by mixing differently terminated thiols in preparative solution to vary surface 5

15 Chapter One Self-Assembled Monoalyers properties such as wetting and reactivity [76,77]. These functionalized SAMs have the wide range of application in surface engineering [78,79], sensor development [80,81], organic field-effect transistor [82,83], electronic properties [84,85] and nano particles [86-89]. 1.3 Mechanism and kinetics of SAM There are two ways to adsorb thiol molecules onto Au(111) surface: Solution-phase monolayer formation and Gas-phase monolayer formation. a) Solution-phase monolayer formation The adsorption mechanism and kinetics of thiols onto Au(111) in solution were investigated thoroughly by using different surface analysis techniques. These include ellipsometry [72], near-edge X-ray adsorption fine structure (NEXAFS) [90], surface plasmon resonance (SPR) [91], second harmonic generation (SHG) measurements [92], sum frequency generation (SFG) [93], mass spectrometry [94] and helium atom diffraction [49]. Bain et al. first investigate the kinetics of thiol-based SAMs on gold substrates [72]. Most of studies have suggested that two distinct kinetic regimes are responsible for alkanethiol film formation. The first regime took place within the time scale of seconds to a few minutes, during which % of the monolayer is formed (fast regime). The second regime took place with a time scale of minutes to hours (slow regime) during which the molecular backbone of the monolayer undergoes orientational ordering leading to saturated phase [49,90,91,95]. The purity and cleanliness of both thiols and solutions are the primary concern for monolayer formation. Most of the studies have found that rate of monolayer formation increases with increasing concentration of thiol in solution. The thiol concentration in the solution has to be controlled precisely, particularly when comparing the kinetics of SAM formation from different solutions. The presence of contamination either adsorbed from solution or preadsorbed onto the substrate, can severely influence the adsorption mechanism and process since the thiol adsorbates must immediately displace the contaminants to chemisorb. Indeed, the presence of contaminants has been reported which induce the significant role to delay the monolayer formation [52]. 6

16 Chapter One Self-Assembled Monoalyers Figure 1.3: Schematic illustration for self assembly of thiols on Au(111). (a) Immersion of Au(111) substrate into the thiol solution. (b) The adsorbate molecules in solution approach the surface, which is pre-coated with a layer of physisorbed molecules. (c) Lying-down phase. (d) Additional adsorbates incorporate into lying-down phase and initiate a transition to an upright orientational phase. (e) Formation of saturated phase complete SAM formation. 7

17 Chapter One Self-Assembled Monoalyers b) Gas-phase monolayer formation The kinetics of monolayer formation by adsorption from the gas-phase is a more straightforward process than in the solution phase, since the solvent interaction can be excluded and the cleanliness of substrates can be precisely controlled and monitored by using the variety of in situ surface analysis techniques. Schreiber et al. studied gas-phase deposition of C10-SAM on Au(111) with x-ray photoelectron spectroscopy (XPS), low energy helium atom diffraction (LEAD), grazing incidence x-ray diffraction (GIXD) suggesting that full coverage phase proceed through a two step process, involving a rapid initial step followed by a step that was ~500 times slower. The have reported that first step involves the formation of a striped phase in which the adsorbate molecules lie down on the substrate with their alkyl chains parallel to the surface in p(11 3 ) phase, followed by the final step in which molecules are oriented nearly perpendicular to the Au(111) surface. The molecules are adsorbed in c(4 2) superlattice of ( 3 3)R30 hexagonal overlayer structure on Au(111) [96]. G. Poirier reported a very decent STM study which further provides evidence for this mechanism of C10-SAM on Au(111). In this work both the striped (lying down phase) and standing-up phase were nicely imaged and presented. Additionally, a number of different intermediate phases were observed [97]. The observation of these ordered phase during the intermediate states by STM can be rationalized by the fact that STM is sensitive to local structure, while the diffraction and spectroscopic studies gather information over large area. The major difference between solution-phase and gas-phase monolayer formation arises from the presence of solvent molecules [95,98]. Generally, the energy of adsorption (i.e. difference in energy of free and adsorbed molecules) for the solution-phase will be less than that of gas phase as a result of attractive interaction with the solvent. In addition, the kinetics of film growth can also be influenced by the presence of solvent. For example, the formation and persistence of the striped-phase during solution phase formation can be limited due to already present solvent molecules on the surface. Prior to thiol adsorption, a layer of physisorbed solvent molecules exist on gold surface. These solvent molecules 8

18 Chapter One Self-Assembled Monoalyers must be displaced in order to enable the adsorption of thiol molecules. The number of displaced solvent molecules required for the thiol molecules to adsorb in the lying down orientation is greater than that needed to adsorb in a standing up orientation. Furthermore, the energy gained upon replacing physisorbed solvent molecules with a physisorbed lying-down phase can be smaller than the energy gained upon replacement of upright chemisorbed thiolate. Consequently, saturated standing up phase directly from solution might, in some cases, be favored. 9

19 Chapter One Self-Assembled Monoalyers 1.4 Structural Characterization of Thiol Monolayer Although the main aim of this thesis does not focus on the structural characterization of n-alkanethiol SAMs, it is useful to have a model to which to refer. Hitherto the most thoroughly characterized SAMs are alkanethiol C10-SAMs on Au(111) (see Fig. 1.4 and 1.5). Figure 1.4: (a) Constant-current STM images of decanethiol SAM on Au(111). The white and black arrows in (b) correspond to etch pits and domain boundaries respectively. (c) A typical high resolution depicting the unit cell. Tunneling parameters: (a) U t = 600 mv, I t = 110 pa; (b) U t = 640 mv, I t = 120 pa; and (c) U t = 750 mv, I t = 90 pa. 10

20 Chapter One Self-Assembled Monoalyers Figure 1.5: Schematic presentation of decanethiolate SAM structure on Au(111). (a) A side view showing the tilt to maximize van der Waals interactions in trans-extended conformation (b) A top view depicting the unit cell of underlying Au(111) substrate along with the ( 3 3 )R30 hexagonal lattice and the p( 2 3 3) superlattice of adlayer. The darker and lighter molecules representing the c(4 2) superstructure. 11

21 Chapter One Self-Assembled Monoalyers Fabrication of C10-SAMs carried out from thiols or disulfides via a variety of methods, carried out by spontaneously adsorption of thiol (R-SH) molecule as a thiolate (R-S-Au) on Au(111). The formation of SAMs occurs by a fast adsorption process within the first few seconds of exposure of Au(111) to thiol or disulfide solution, followed by the much slower adsorption-desorption exchange process with the molecule in the solution, during which the molecules interact with each other and order to form a densely packed saturated phase [47,61]. As illustrated in the Fig. 4a the surface morphology after the adsorption of C10 molecules forming the holes, vacancy islands or etch pits. During the adsorption process, the morphology of Au(111) surface is changed by the ejection of Au atoms, causing one atom deep vacancy islands having a depth of 2.4 Å. Later, Poirier showed that this type of vacancy islands also occurs when a SAMs was grown from gas-phase [47,48]. The formation of these depression/vacancy islands can be explained by two different mechanism based on the experimental results: shrinkage of gold surface lattice constant due to thiol adsorption [99] and ejection of excess Au atoms from the surface during relaxation of Au(111) herringbone reconstruction [100]. The growth of a low-symmetry structure obtained from monolayers on to a high symmetry Au(111) substrate leads to various domain boundaries including tilt boundaries, rotational and antiphase boundaries. Areas with the densely packed phase are separated by domain boundaries (see back arrows in Fig. 4b). The domains differ from its neighbors by difference in translation, rotation or tilt each causing different variety of domain boundaries. In the case of n- alkanethiol SAMs on Au(111), spectroscopic and diffraction studies revealed that the alkyl chains are tilted 30 from the surface normal. These studies revealed that there are twelve equivalent azimuth orientations, 3-fold-orientational degeneracy of the unit cell and 3-fold tilt degeneracy [101]. 12

22 Chapter One Self-Assembled Monoalyers 1.5 Energetics of SAM Formation Several approaches have been used to obtain the energetics of SAM formation. To obtain the information about the energetics of SAMs formation, it is convenient to consider the following simplified reaction: 1 RSH + Au RSAu + H 2 2 (1.3) There are several steps involve in the formation of SAMs: cleavage of RS-H bond, formation of the RS-Au bond, removal of hydrogen as H 2, with the bond dissociation energies are: RS-H kcalmol -1, RS-Au --40 kcal mol -1, H-H kcal mol -1. From the above values, the free energy of the reaction ( Δ G ads ) is calculated to be -5 kcalmol -1, suggesting an exothermic adsorption process. Karpovich et al. proposed that the modest value of ( Δ G ads ) indicates a balance between the entropic and enthalphic contributions to adsorption [95]. The enthalpy of adsorption ( Δ H ads ) for an alkane thiol on gold was assumed to be -28 kcalmol -1. These values are related to the entropy of adsorption ( Δ G ads ) by following equation: Δ Gads =ΔHads TΔ Sads (1.4) The relatively large and negative value of ( Δ S ads ) apparently indicates the great degree of ordering that takes place as the alkanethiols molecules change from randomly distributed orientation and motion in solution to highly oriented two-dimensional (2D) crystalline lattice on the surface. 13

23 Chapter One Self-Assembled Monoalyers 1.6 Outline of the Thesis The brief introduction of the basic experimental techniques used in this work will be given in the chapter two. Theoretical background and working principle of scanning tunneling microscopy (STM) will be presented first followed by its calibration. Later the introduction to reflection-absorption infrared spectroscopy (RAIRS), principles of x-ray photoelectron spectroscopy (XPS), low-energy electron diffraction (LEED), near edge x- ray adsorption fine structure (NEXAFS), and finally current imaging tunneling spectroscopy (CITS) will be described. Chapter 3 details the preparation of gold films on silicon wafers and on mica and their characterization by STM. The basic requirement of STM studies is the large terraces of atomically flat substrates which depend on the preparation conditions. It was found that the gold on silicon wafer films were dominated by small grains that are appropriate for spectroscopic studies. However, the gold substrates produced by evaporating gold onto mica showed large atomically flat (111) terraces separated by the monotonic steps having the height of 2.4 Å is the prerequisite for STM studies. The preparation and characterization of ultra flat gold substrates (UFGS) will be discussed. Moreover, this chapter highlight on the preparation of the self-assembled films, chemicals, glass wares and technical equipment used in this work. Chapter four reports the study on the homologous series of terphenylalkanethiol (TPn, where n = 1-6) using reflection absorption infrared spectroscopy (RAIRS) and scanning tunneling microscopy (STM) techniques. The importance of solvent temperature was investigated by using two different temperatures (298 K, 333 K), which result in the enhanced improvement in the lateral ordering and different packing density of the resulting SAMs. In chapter five it has been found that the monolayers derived from the thioacetate (C 12 SAc) have a significantly different structure as compared to the ones obtained from the corresponding alkanethiol (C 12 SH). In contrast to previously reported results the high-purity thioacetates do not form self-assembled monolayers with the same (2 3 3) structure that is obtained from the corresponding thiols. Instead, the thioacetates form a 14

24 Chapter One Self-Assembled Monoalyers highly ordered striped phase with flat-lying molecules antiparallel to each other forming a (p 2 3) unit cell, a structure that has not yet been reported. Chapter six describes the molecular scale investigation of differently anchored aromatic SAMs made from benzenethiol (BT), benzeneselenol (BSe) and anthracenethiol (AntSe) on Au(111) studied by using STM, LEED, IR, XPS, and NEXAFS. In contrast to long range ordered selenols based SAMs consisting of closed packed, upright standing molecules, the SAMs of benzenethiol characterized by the loose packing of largely tilted molecules appears only in small domains. The chapter seven reports the results obtained for the films of large discotic, aromatic conjugated molecules (hexa-peri-hexabenzocoronene modified thiol). The effect of soft and stiffer anchoring on the resulting SAMs structure will be highlighted by using STM and RAIS techniques. Finally describes the results of the electron transport through the HBC core within the SAMs by using current imaging tunneling spectroscopy (CITS). 15

25 Chapter Two Experimental Techniques Chapter Two Experimental Techniques 2.1 Scanning Tunneling Microscopy (STM) Historical Background The concept of vacuum tunneling dates back to the beginning of tunneling spectroscopy [102]. Attempts to measure a vacuum tunneling current were made by various scientists [103,104]. The main limitation to this kind of experiments was the vibration transmitted to the tunneling unit, which render the distance between the two electrodes and thus the tunneling current very instable. In 1982 Binning and Rohrer et al. reported on reproducible results on tunneling through the well defined vacuum gap between the tungsten tip and platinum plate [105]. They had overcome the problem of vibration by a mechanically isolation of system. The research of Binning and Rohrer had been prompted by a major issue in the semiconductor industry at this time, which was the problem of inhomogeneities at nanometer scale. Such inhomogeneities had become increasingly important due to the progressive miniaturization of electronic devices. The original idea of Binning and Rohrer was actually to perform vacuum tunneling spectroscopy to study inhomogeneities in thin oxide layers on metals on a local scale (<100 Å) [106,107]. But soon they have realized that scanning over a surface with a positionable tip could yield topographic image. The concept of surface scanning with a tip was in fact already applied much earlier by Young et al. [108]. Young et al. constructed a machine called Topografiner to measure the micro topography of a metal surface. They measured the field emission current between the tip and surface while scanning. Using a tungsten tip and a platinum surface Young et al. even observed tunneling currents [109]. Binning and Rohrer, apparently without knowing of the work of Young et al. [109] developed their scanning tunneling microscopes (STM) and published first time the images of surface reconstruction and monatomic steps of CaIrSn 4 (110) and Au(110) were published in 1982 [105]. A large part of scientific community remained, however, skeptical about the physical reality of 16

26 Chapter Two Experimental Techniques results until Binning and Rohrer could present high resolution measurements of the (7x7) reconstruction of Si(111) in 1983 [110]. At this time they had built and STM working in UHV that was protected against the vibrations by a double stage spring system with eddy-current damping. They achieved atomic resolution, did first chemical imaging [111], and performed first scanning tunneling spectroscopy (STS) measurements [112,113]. Other groups started to build STMs. Imaging under ambient-air pressure and in liquids became possible and first low temperature STM was developed [114], followed later on by first variable-temperature STM [115]. Furthermore, the tunneling spectroscopy microscope has evolved from a merely measuring device to a tool allowing surface manipulation on the nano scale [116]. At the same time it is increasingly being used in field of material science and biology. With its unique capability of measuring surface properties on an atomic scale, STM has become one of the most important tools in surface physics and nano-science Introduction Scanning tunneling microscopy (STM) is a powerful scanning probe technique, based on the quantum-mechanical effect of electron tunneling, used for obtaining real space information about surface on atomic scale. Since the first invention by G. Binning, H. Rohrer and coworkers in 1981, STM has been revolutionized into powerful surface and interface analysis technique, capable of imaging at atomic level [105]. In 1986, a Nobel Prize was awarded for scientific progress made by G. Binning, H. Rohrer five years earlier on a microscope based on electron tunneling. This high resolution instrument allows atomic information not from an average over many atoms, but over atom by atom under the tunneling mechanism governed by the externally and reproducibly adjustable vacuum gap [117]. The significance of STM figured out when (7 7) reconstructed structure of Si(111) were documented. Till date this surface has been used as a model system in device application, chemical configuration of organic molecules on silicon surfaces [118]. Since after the discovery of STM, a great deal of research has been focused on clean metal surface including surface reconstruction, surface defects, atomic/molecular resolution of clean/coated metallic surfaces, chemical reaction and modification on the substrates, 17

27 Chapter Two Experimental Techniques spectroscopy and current-voltage (I-V) characteristics of adsorbates. In contrast to conventional electron microscopy, STM can be performed in air, in liquids and in ultrahigh vacuum (UHV) Theory If a voltage is applied between tip and sample, electron may tunnel from filled tip states to empty sample states or vice versa as depicted in Fig In order to calculate this tunneling current, first one needs to exactly know the electronic states of tip and sample as well as the electron potential in the tunneling gap region. Apart from the fact that detailed information is missing, in particular on the shape and the chemical composition of the tip apex and thus its electronic properties, only rough approximation calculation can be made due to the complexity of the issue. A few models have, however, been developed during the past twenty years. Figure 2.1: Schematic illustration of tunneling process. The tip-sample distance is d and a voltage V is applied between tip and sample. Φt and Φs are the work functions of tip and sample, respectively. An electron can elastically tunnel from tip electronic state Eµ into a sample electronic state Ev. First, Tersoff and Hamann [119,120] applied Bardeen s [121] formalism to the tunneling microscope. The tunneling current is given to first order by 18

28 Chapter Two Experimental Techniques 2π e 2 I = f( E ev) [ 1 f( E )] M δ ( E Ev) μ v μv μ h μ. v (2.1) where f(e) is the fermi function, V is the applied voltage, M µv is the tunneling matrix element between states ψ µ of the tip and ψ v of the surface, and E µ is the energy of the state ψ µ in the absence of tunneling. The main problem is then to evaluate the matrix element M µv. The starting point for Tersoff and Hamann s calculation was given by Bardeen [121] : M 2 h r ur ur * * = ds Ψ Ψ Ψ Ψ μv μ v v μ 2m.( ) (2.2) where, the integral goes over any surface lying entirely within the region between tip and surface. Tersoff and Hamann made the crucial assumption of a spherical tip shape in the tunnel gap region. They considered the tip of radius R with center of curvature at r 0. the wave function of tip extending into tunneling gap are then assumed to have a spherical forms. For simplicity the work function Φ of the tip is assumed to be equal to that of sample. Tersoff and Hamann calculated M µv under these conditions by expanding the wave function of tip and surface in Fourier space. In the case of tunneling at small voltages and at room temperature or below, this leads to r 2 2 ρ (, 2 kr I VR e r E 0 F ) with ρ ( r, E 0 ) Ψ ( r ) δ v 0 ( E E v ) r v r (2.3) Note that only sample and no tip wave function appear in this equation. In fact, ρ ( r, EF ) is simply the surface local density of states at the Fermi energy at point r r. Finally the surface wave function ψ υ decays exponentially within the tunnel gap: r which results in: ψ r 2 2 k( r+ d) ( r ) e v 0 (2.4) 2 2kd I VR e (2.5) 19

29 Chapter Two Experimental Techniques Thus the tunneling current depends exponentially both on tip-sample distance and on the inverse decay length. For a typical value of Φ 4eV, the current decrease by roughly one order of magnitude for each angstrom increase in tip-sample distance. The tunneling current is also proportional to number of electronic states of the sample at the Fermi level Basic Principle Metals are good conductors of heat and electricity since they exhibit unfilled space in the valence energy band. Fig. 2.1 illustrates the existence of electrons in a metal within the energy range which represent the atomic core electron levels and metallic conduction electron levels. In metal, the electrons at the Fermi energy (E F ) are held by an energy barrier, the work function (Φ 1 ). If a second metal having work function (Φ 11 ) at the Fermi energy (E F 11) is brought closer to the first one, slightly imbalance develop by applying an external voltage (ΔV), the slope of energy will be changed leading to flow of electrons across the barrier. Figure 2.2: A one dimensional schematic view of tunneling process between two metals. 20

30 Chapter Two Experimental Techniques In classical mechanics it is impossible that electrons overcome the potential barrier to leave the metal unless energy is provided to them. However, in Quantum mechanics, electrons near the Fermi energy can pass through the potential barrier via tunneling process if the two metals brought sufficiently close to each other Working Principle The main feature of STM can be seen in fig A sharp metallic tip (in this work 80% Pt, 20% Ir) is brought into close proximity of a metallic sample surface until a gap of only few angstroms is formed. A voltage difference (ΔV, tunneling voltage) of up to a few volts is applied. Due to the overlap of the electronic wave functions of tip and sample, which extend into gap, a current referred to as tunneling current can flow between the tip and samples depending upon the polarities of applied voltage. The tunneling current can flow from the occupied electronic state near the Fermi level of one metal to the unoccupied states of other metal. This current crucially depends on the distance between the tip and sample, i.e. the tunneling gap width, which is always affected by thermal instabilities and mechanical vibrations. To control the tip-sample distance the measured tunneling current is fed into a feedback loop. The tunneling gap width is then readjusted by means of a piezoelectric transducer. Figure 2.3: Working principle of STM 21

31 Chapter Two Experimental Techniques Modes of Operation The STM can be constructed to operate in different modes Constant-Current Mode The original first and most often used mode [122], in which STM uses a feedback loop that enables the tunneling current to be constant by adjusting the height of the scanner at each location of surface during measurement as is shown in Fig. 2.3 (a). The variation in geometric height and variation in electronic structure is responsible for change in current. Therefore, while scanning the actual current is continuously measured and compared to the set current and the feedback loop in the electronic circuit leads to a retraction or approach of tip with respect to the sample whenever the current exceed or falls below its set point. The height adjustment of the tip (Z-signal) this reflects the local electronic and geometric properties of surface. It can give a nearly topographic image of the sample surface in case where the geometric induced height variations scanning over a surface with a positionable tip could deliver topographic images. (a) (b) Figure 2.4: (a, b) A one dimensional schematic view of tunneling process in constantcurrent mode and in constant-height mode, respectively Constant-Height Mode In this mode tunneling current is monitored as the tip scanned parallel or horizontally to the surface. The Z-position (height) of the tip is kept constant over the sample surface as is shown in fig. 2.4 (b), while the feed back loop is slow down or turned off completely. The dependence of tunneling current and local electronic properties of surface a topographic image is obtained. 22

32 Chapter Two Experimental Techniques Each mode has advantages and disadvantages. Constant-height mode is faster as system does not have to move the scanner up and down, but it works only for the relatively ultra smooth samples. Constant-current mode can measure irregular surfaces with high precision, but the measurement takes more time and lateral resolution that can be achieved is usually smaller due to the difficulty in setting the proper feedback loop which allows the contemporary to tip follow the surface prosperities not to induce the periodic noise in the data set Calibration of STM Highly oriented pyrolytic graphite (HOPG) is one of the most studied surfaces by STM, because it is relatively easy prepare and to image the lattice of carbon atoms at its surface. In addition, atomic-level images of HOPG can be used to calibrate the STM for high-resolution imaging. The STM image normally obtained looks like a close packed hexagonal array; in this array, each atom is surrounded by six nearest neighbors. The distance between any two of these atoms is nm. The surface C atoms depicted in schematic sketch could be imaged by the STM reveal hexagonal close packed arrangement. In this work the all presented STM data were cross calibrated by imaging HOPG with atomic resolution. Figure 2.5: Constant-current STM image of HOPG (right) and schematic sketch of layer structure of HOPG (left). 23

33 Chapter Two Experimental Techniques 2.2 Current Imaging Tunneling Spectroscopy (CITS) The most direct way to obtain the information about the electronic structure, next to imaging at different tunneling biases, is the measurement of current-voltage characteristic. This specific frequently used STM mode is called current imaging tunneling spectroscopy (CITS). Here, the feedback loop and the lateral scanning are temporarily switched off and during this time the tip should remain at a fixed position above the sample surface. Normally linear sweep in tunneling voltage is performed while recording the tunneling current. Very often, especially if one has to deal with the small variations in current, it is preferable to measure the first and/or second derivative of the current with respect to voltage by using lock in technique. The resulting spectroscopic data yield the information about the local electronic structure of sample surface convoluted with the the STM tip [123]. The intriguing feature of combined STM/CITS study is the high spatial and energetic resolution that can be obtained simultaneously which is an exceptional property among techniques for surface characterization. The above mentioned modes can also work in parallel. One can perform tunneling spectroscopy after measuring each step during the surface scan Methodology of Operation CITS can be performed by positioning the STM tip over the region of interest as close as possible to the most recently scanned line in order to minimize the effect of drift. After the few seconds, which allows the system to adjust the tip-sample separation such that the actual current met the setpoint value, the feedback loop switched off and I-V curves can be measured by running a desired voltage ramp with 128 equidistance values. The spectroscopic data can only be reliable and accepted if there is no changes observe in the surface morphology observed by STM images before and after CITS. The obtained I-V curves meet the settings of feedback loop used before switching off the feedback loop (correct current at the tunneling bias within 10%). Finally, the obtained I-V curves average over the number of molecules on the different part of the surface. 24

34 Chapter Two Experimental Techniques 2.3 Reflection-Absorption Infrared Spectroscopy (RAIRS) This technique is well established for the identification and characterization of the chemical state and structure of molecules and organic thin films adsorbed on metallic (in this study SAMs) and non-metallic surfaces. Vibrational spectra are used as characteristic fingerprints for adsorbate molecule, adsorption configuration and structures. RAIRS covers the wavelength range from µm or cm -1. Unlike spectrophotometer or actually most other techniques which respond to the electronic structure of a molecule, the IR-based probes give information of molecular structure, orientation and intermolecular bonding. The relatively high IR adsorption cross section (compared to Raman and non-linear optical probes) and the relative ease in interpretation of IR spectra contributes to making RAIRS most generally useful for studying thick films. For the characterization of ultra thin films or SAMs the approach of external reflection geometry at grazing incidence results in sensitivity even adequate for submonolayer detection. Besides obtaining the IR spectrum from ultrathin films on metal surfaces it is widespread used as a tool to extract the detailed structural information, ordering and orientation within the SAMs. If molecule has a dipole moment, that is one end of molecule has a partial positive charge and the other end a partial negative charge then the molecule is capable for absorbing the IR light, but only at certain fixed frequencies. Hence an infrared spectrum of light reflected from surface will show absorption peaks that are characteristic of molecule and it mode of bonding to surface. This is the basis RAIRS technique. RAIRS provides the information about the molecular structure and the orientation of molecules in organic thin films based on the direction of transition dipole moments present in the sample. The incident electromagnetic radiation interacts with the molecules inside the sample layer, excites molecular vibrations, and thereby loses intensity at spectral energies that are characteristic for the functional groups of the molecules under investigation. The intensity of each single absorption band in the spectrum depends on the amplitude of the electric field, the orientation of the transition dipole moment relative to the electric field vector, and on the amount (i.e. concentration) of absorbing functional groups interacting with the radiation. 25

35 Chapter Two Experimental Techniques From the selection rules in infrared spectroscopy, those molecules which undergo the change in the dipole moment are infrared active. In order to absorb infrared radiation, a molecular vibration mode must cause a change in or an introduction of the appropriate dipole moment of the molecule. Figure 2.6 demonstrates that the in case of metal surface, the electrical field vector E of the incident electromagnetic radiation beam is separated into two orthogonal components which are parallel plane of incidence. E x and perpendicular E Z to the Figure 2.6: Schematic illustration shows the electric field E at a metal surface. The plane of incidence is defined as the (x,z)-plane, with x as the direction of the propagation radiation and z as surface normal. Only the perpendicular field component, E Z, survives at the metal surface [124]. When incident light is reflected from a metallic surface, phase shifts occur to both the and E Z. According to the calculations from Fresnel s equation [125], E x E x undergoes a phase shift of 180 at all angles of incidence. With this phase shift, the interference between the incident and reflected zero intensity at the reflection interface. Therefore, confined to the substrate. E x component is destructive. This means that E x has E x can not interact with the species E Z also suffers a phase shift upon reflection, but the degree of shift is dependent on the angle of incidence. It was found that the best angle of incidence for highest reflection intensity is around 80 [125]. Under this condition the light amplitude is increased so that the signal to noise ratio is enhanced. This selection rule is called the surface dipole selection rule on metal surfaces. Therefore, vibration modes with an electric dipole moment aligned parallel to the plane of incidence will not be 26

36 Chapter Two Experimental Techniques excited. Only vibrational modes that are at least partially aligned perpendicular to the surface normal will appear with enhanced intensity. The determination of the molecular orientation within a SAM on a surface using IR spectroscopy is not straightforward due to the screening of electric field vectors parallel to the surface E x by the electrons of a metal surface. However, two indirect methods have been proposed to determine the molecular orientation within a SAM. The first method is so called absolute method [126] based on the determination of the absolute excitation probabilities of a vibrational mode in the bulk and in a SAM spectrum. For this method to be applicable, the intensity of only one band in the SAM spectrum having a transition dipole moment along the chain axis of the molecule under investigation and the corresponding one in the bulk spectrum are required to be known. The second method is called a relative method [127] that is based on the comparison between the relative excitation probabilities of two or more vibrational modes with different orientations of their transition dipole moments in the SAM spectrum and the corresponding ones in the bulk spectrum. For the case of monolayers generated from thiol based compounds exhibit the special symmetry, in which the transition dipole moments (TDMs) are either along the chain axis or out of plane parallel or perpendicular to the ring plane. In this special case the TDMs are not only different oriented, but also they are orthogonal. This makes using the relative method more easily and convenient than the absolute method for these SAMs because only simple trigonometric formulas are needed to set up and solve an equation system and to eliminate the unknown concentration in bulk and at surface. Based on this comparison, the tilt angle can be determine by using the following equation [128]. I I Θ (2.6) I I 2 tan = bulk 1 bulk 2 SAM 2 SAM 2 where, and bulk I 1 and bulk I 2 are the intensities of bands 1 and 2 in the bulk spectrum and SAM I 2 are the intensity of the corresponding one in the SAM spectrum. SAM I 1 27

37 Chapter Two Experimental Techniques 2.4 X-ray Photoelectron Spectroscopy (XPS) X-ray photoelectron spectroscopy (XPS) is a powerful technique widely used for the surface analysis of materials. At low energy resolution it provides qualitative and quantitative information on the elements present. At high energy resolution it gives information on the chemical state and bonding of those elements. XPS is based on the photoelectric effect used for obtaining qualitative and quantitative information about the elemental composition and of the surface [129]. XPS is a surface sensitive method allows to determine the mean free path of electrons in the solid state. This technique was developed in the mid 1960s by K. Siegbhan, which later in 1980 awarded the Nobel Prize for physics. The energy of the incident radiation used in XPS is usually more than 1000 ev. The mostly used sources to obtain the XPS are Al K α ( ev) or Mg K α ( ev) [130]. The electrons from the core levels of the sample are emitted upon the bombardment of x-rays characteristics energy onto the sample surface. The kinetic energy distribution of the emitted photoelectrons (i.e. the number of emitted photoelectrons as a function of their kinetic energy) can be measured using an appropriate electron energy analyzer. Under the UHV condition the sample irradiated with the x-rays of a characteristic energy results in the emission of electron from the core levels of the surface as shown in fig 2.7. Figure 2.7: Schematic diagram of photoelectron spectroscopy 28

38 Chapter Two Experimental Techniques The kinetic energy, KE, of the emitted photoelectrons can then be measured using an electron energy analyzer. The binding energy of the electron, E B, depends on the atomic charge distribution and can be determined using the following equation according to Koopman s approximation [129]: E hν E φ (2.6) B = Kin where, hυ corresponds to the energy of incident x-ray radiation, is the work function of the sample, E B is the binding energy of the core level, and E Kin is the kinetic energy of emitted photoelectrons. The binding energy of the photoelectron is a fingerprint of the each element in the material and their chemical environment, the peaks appear in an XPS spectrum at distinct values of E B. Thus, XPS provides elemental specificity and a measurement of the chemical environment of the elements present at the surface. In this work, XPS measurements were carried out to identify the elemental composition, molecular adsorption and thickness of SAMs. The film thickness (d sample ) can be calculate by the using of the relative intensities of the Au 4f 7/2 and C 1s peaks and by using a thiol with known thickness on Au as a reference system (escape depth of gold: λ Au =36.5 Å at a kinetic photoelectron energy of 1169 ev for MgK α ) and carbon (escape depth: λ c =30 Å at 996 ev for MgK α ). The film thickness can be calculated by using the following equation: I I I I c Au c Au ( sample) ( reference) d sample 1 exp λc ( Ec ) = d sample exp λc ( E Au ) d reference exp λc ( E Au ) d 1 exp λc ( Ec reference ) (2.7) 29

39 Chapter Two Experimental Techniques 2.5 Low-Energy Electron Diffraction (LEED) This section comprises of the short introduction of the low-energy electron diffraction (LEED) as a surface characterization method, which reveals the geometric structure of the surface. In this technique electrons with the de Broglie wavelength in the order of typical interatomic spacing, which corresponds to energy of ev, are elastically back scattered from a surface. The mean free path for electrons in a solid takes a minimum at typical LEED energies and the diffracted electron beam thus yields the structural information only about the first 2-3 monolayers. The elastically backscattered electron are accelerated onto a fluorescent screen, where the two dimensional pattern can be seen representing the Fourier transform of the surface atoms arrangement. Figure 2.8: Low-energy electron diffraction for a perpendicular incident bean with 0 * wave vector k. a 1 and a 1 are the surface lattice vector and reciprocal vector, respectively. The diffracted beam wave vector k lies in thek 0 a 1 plane. The location of the maxima of the diffracted electron beam can be explained by a simple geometrical theory. These maxima occur at the angles determined by the Laue condition as depicted in fig k k = h a + h a (2.8) 0 * *

40 Chapter Two Experimental Techniques where, and 0 k and k are the wave vectors of the incident and scattered electron waves, * a 2 are the reciprocal lattice vectors, h 1 and h 2 are integers. The Laue condition can be demonstrated in reciprocal space by the Ewald sphere as shown in fig. 10. From a * 1 = 2π a1, a = 2π a and k = 2πλ, where are the surface lattice constants, it * 2 2 follows that the Laue condition is equivalent to one-dimensional Bragg relation (cf. fig. 2.8) * a 1 a sinθ = n λ (2.9) 1 The backscattered waves from neighboring (identical) atoms interfere constructively if the path if the path difference is the multiple of wavelength λ. LEED can be used as the qualitative and quantitative measures for the surface structure. Qualitatively such as the diffraction pattern is recorded and analysis of the spot positions yields information on the size, symmetry and rotational alignment of the adsorbate unit cell with respect to the substrate unit cell. Where as quantitatively the intensities of the various diffracted beams are recorded as a function of the incident electron beam energy to generate so-called I-V curves which, by comparison with theoretical curves, may provide accurate information on atomic positions. Figure 2.9: Schematic illustration of LEED optics. 31

41 Chapter Two Experimental Techniques A typical experimental setup used for the LEED measurements depicted in fig The crystallographic surface structure can be determined using bombardment of an electron gun onto the sample with a beam of electrons associated with typical energy range of ev. In the presence of regular arrangement of atoms, electrons are diffracted back in the discrete directions determined by the lateral periodicity. These electrons move away from the sample and pass through a series of retarding grids. The first gird at the sample front and sample itself have the same potential to have a field-free region thus avoiding changes in the angle of the trajectories of the backscattered electrons. Later under the high potential elastically back scattered electrons are post accelerated onto a phosphor screen by a voltage of several kilovolts to cause efficient luminescence. This causes the screen to glow with intensity at each point on the screen proportional to the incident electron flux, which results in the LEED pattern. 32

42 Chapter Two Experimental Techniques 2.6 Near-Edge X-ray Absorption Fine Structure (NEXAFS) Near-edge X-ray photoelectron spectroscopy (NEXAFS) is the widely used technique in surface science. NEXAFS is an element-specific electron spectroscopic technique which is highly sensitive to bond angles, bond lengths and the presence of adsorbates. NEXAFS is synonymous with XANES (X-ray absorption near edge structure) but NEXAFS by convention is usually reserved for soft x-ray. NEXAFS is distinguished from the closely related XANES method in that NEXAFS concentrates on fine structure within about 30 ev of the absorption edge while EXAFS considers the extended spectrum for hard x-ray absorption spectra. The great power of NEXAFS derives from its elemental specificity. Because the various elements have different core level energies, NEXAFS permits extraction of the signal from a surface monolayer or even a single buried layer in the presence of a huge background signal. Figure 2.10 outlines the principles of NEXAFS spectroscopy. Near the K-shell absorption threshold, a series of fine structures are superimposed on the absorption edge. This method uses monochromatic, linear polarized x-rays of a synchrotron, which are absorbed in the material by excitation of core electrons into unoccupied molecular orbitals. Each excited electron leaves a core hole into which another electron relaxes. In organic molecules, these fine structures are dominated by resonances arising from the Figure 2.10: Schematic illustration of a NEXAFS spectroscopy. 33

43 Chapter Two Experimental Techniques transitions of 1s core electrons to unoccupied π* or σ* orbitals, depending on the covalent bonding in the molecule, as well as to Rydberg orbitals (left side of this Figure). The characteristic features of the K-shell spectrum are shown in the right part of this figure. The NEXAFS spectrum is usually dominated by two types of resonances, with the ionization potential (IP) as a boundary. Resonances below the IP correspond to the excitation of a core electron to a bound orbital. These orbitals are usually of π* or Rydberg character and sometimes of σ* character for saturated species, such as n- alkanes. These resonances are usually sharp and well-defined. Resonances above the IP usually correspond to the excitation of a core electron to an unbound orbital of σ* character, as well as double excitation. These resonances are usually broad. The detection of the entire stream of electrons (total electron yield, TEY) contains more frequently diffuse electrons of deeper layers of the sample. It is not very surface sensitive. A reasonable signal/noise relationship and sufficient sensitivity for the monomolecular adsorbate layers can be attained by measuring in the "partial electron yield" mode, whereby only electrons emitted near to the surface can be acquired. All spectra presented in this study were measured with a backlash potential of 150 V in the PEY mode, due to ensure of a good surface sensitivity by the mean of the free path of the electrons of only unit nanometres. Regarding by the measurements of the carbon edge, a gold lattice is used which give rise to π*-resonances [131]. In this work NEXAFS was used to determine the orientation of the molecules within the SAMs shown in the fig Figure 2.11: Definition and orientation of the angles in the surface coordinate system of the NEXAFS experiment. E and E are the p and the s-polarized portions of the incident light, and TDM is the situation of the dipole transition moment of the excited transition. NEXAFS spectra of a particular film are measured for at least two different angles of the incident e-field to the surface normal of the sample, so one can determine the middle orientation of the TDMs from the observed dichroism of the spectra. In the case of triple substrate symmetry (gold substrates) all orientations φ are averaged around the surface 34

44 Chapter Two Experimental Techniques normal, one receives only the middle tilting angle α of the TDM. In the context of this work for the determination of the middle tilt angles, one has to considered the π*- resonances. The incidental angle dependence in the case of two fold substrate symmetry: I P(cos θ cos α + sin α cos φ) + (1 P)(sin α sin ) (2.10) π φ * where, I is the intensity of the NEXAFS resonances depend on the angle of incidence θ, the adsorption angle α of the adsorbed molecules and on the angle φ of the adsorbed molecule for the azimuth direction of the substrate. The angle dependence in the case of three fold substrate symmetry: Iπ * P(cos θ cos α + sin θ sin α) + (1 P) sin α (2.11) 2 The intensity of the NEXAFS resonances depends in the case of three fold substrate symmetry on the angle of incidenceθ, the adsorption angle α of the adsorbed molecules. 35

45 Chapter Three Substrate Preparation and Characterization Chapter Three Substrate, Sample Preparation and Characterization 3.1 Introduction The detailed description about the substrate and sample preparation, which has been used in this study will be focused in this chapter. The Au(111) substrates have been used as a template for the SAM deposition. The gold substrates either on Silicon wafer or mica has been used as substrates for thiolate film deposition. Preparation of SAMs, chemicals, laboratory equipments used in this work will be illustrate in this chapter. Before describing the substrate preparation and its characterization it is necessary to have first hand knowledge about the mica and Au(111). 3.2 Substrates Muscovite Mica ( ) Muscovite mica KAl SiAlO ( OH) turned about ideal match for yielding the large atomically flat surface area. It is reasonable cheap and easy to cleave, obtaining a atomically flat surface. This allows the preparation of well defined samples by deposition of metallic gold in vacuum without too much disturbance from mica itself. Muscovite mica is a sheet silicates (monoclinic lattice, a=5.2å, b=9.0å, c =20.1 Å, γ = 95.80) [132] consisting of octahedral Al-O layers sandwiched between two tetrahedral Si-O layers. One out of four Si atoms in the tetrahedral layers is replaced by an Al atom. The resulting charge due to this substitution is compensated by an intercalation of potassium ions in between two tetrahedral sheets. The cleavage of the substrate occurs along these inter layers and is almost perfect, resulting in large atomically flat areas on the surface. A freshly cleaved mica surface is positively charged and hydrophilic in nature. 36

46 Chapter Three Substrate Preparation and Characterization K + Si/AlO 4 AlO 4 Figure 3.1: Schematic side view of the layered structure muscovite mica Gold Gold is symbolically represented as Au having the atomic number, Z=79. Gold is a good conductor of heat and electricity and is inert to oxidation. Metallic gold arrange itself in a face-centered cubic (fcc) lattice constant of 4.08 Å [133]. The fcc unit cell can be though of as a cube with eight atoms situated at the eight vertices, (0,0,0), (1,0,0), (0,1,0), (0,0,1), (1,1,0), (0,1,1), (1,0,1) and (1,1,1) along with the six more atoms occupying the centers of the six faces, (0,½,½), (½,0,½), (½,½,0), (1,½,½), (½,1,½), and (½,½,1) shown in fig Figure 3.2: a) Unit cell of face-centered cubic (fcc) lattice. b) (111) plane of fcc crystal. 37

47 Chapter Three Substrate Preparation and Characterization When the unit cells are repeated to generate the lattice, each of the eight corner atoms sit partially in eight cells thereby contributing one eighth of an atom to each unit cell. Each of the six face atoms are shared by only two unit cells so they contribute one half of an atom to each unit cell. Analyzing the unit cell in this manner yields four atoms per unit cell. The (111) plane of the crystal passes through the atoms at positions (0,0,1), (1,0,0), (0,1,0), (0,½,½), (½,0,½), and (½,½,0) forming a hexagonal lattice as shown in Figure 3.2b The nearest neighbor spacing in the (111) plane is 2-1/2 times the lattice constant or α = 2.88 Å. Figure 3.3: Possible stacking sites for close packed lattice. The (111) plane can be thought of as a sheet of densely packed hard spheres shown in fig Because the (111) plane is close packed, it is the low energy plane of the crystal. Starting with a single layer of close packed atoms, the second layer can be stacked on top of the first by placing spheres at B sites. The third layer can sit at the unused C sites or revert back to the original A sites. ABC stacking corresponds to fcc crystals while ABA stacking corresponds to hexagonal close packed (hcp) crystals. 38

48 Chapter Three Substrate Preparation and Characterization Herringbone Reconstruction A typical property associated with the crystalline surface to often undergo reconstruction to reduce the energy of the surface. This happens as the atoms in the top most surface layer do not have as many nearest neighbors as those in the bulk crystal. The surface layer of (111) terminated gold crystals reduces its energy by incorporating one extra atom into every ( 23α 3α ) cell, where α is the gold spacing within the (111) plane. This results in a 4.4 % increase in areal density. The reconstruction realizes this excess by periodically changing from ABC staking of fcc crystal to the faulted ABA stacking of hcp crystals as shown in Fig. 3.4 [48]. Surface layer at phase boundaries buckles because the atoms are forced to occupy bridge sites of the second layer due to the transition from C hollow sites to A hollow sites. One thing should be emphasized that the increases areal density is accommodated by the surface buckling and there is no change in the lattice constant of the fcc and hcp regions [134]. Figure 3.4: Schematic top view of ( 23 3 ) unit cell in red of the herringbone reconstruction showing bridge site phase boundaries (white circles) between ABC stacking and faulted ABA stacking. 39

49 Chapter Three Substrate Preparation and Characterization 3.3 Gold Substrates SAMs of thiols can be fabricated on the various substrates such as gold [48,56, ], silver [137, ], glass [ ], mercury [147,148] and copper surfaces [141,149, 150]. Monolayers formed from organic molecules especially thiols have an affinity to bound covalently to the gold surface [61]. Gold substrate has been used in this study for many reasons; these substrate are inert to oxidation, free from contamination and easy to handle with few precautions such as clean atmosphere for storage. For surface chemical sensitive techniques like IRRAS and XPS responsible for chemical identification of organic compounds require the contaminated surface. For microscopic characterization like STM and AFM it is desirable to have the atomically flat substrate as clean as possible to characterize the adsorbates. Gold surface can have atomically flat terraces extending for up to several hundred of nanometer, making them ideal for microscopic investigation. Furthermore, deposition of organic material like thiols are the principal focus of this study require atomically flat and clean surface Preparation and Characterization of Gold Substrates Normally gold substrates can be prepared be the evaporation of gold onto clean and relatively flat substrates. This can be carried out either by evaporating gold onto silicon wafer or on mica. In this work two different types of substrates were used. For the spectroscopic characterization polycrystalline substrate were obtained by the evaporation of gold on silicon wafers. This procedure started by the evaporation of 5-4 nm of titanium (99.8%) which acts as an adhesive layer for the further evaporation, followed by the subsequently 140 nm of gold ( %, chempur) onto polished silicon wafers (Wacker silicone) at room temperature in an evaporation chamber operating at a base pressure about 10-7 mbar. In fig. 3.5 (a) an STM image of gold on Si-wafer shows gold films grown in polycrystalline fashion having the small grains with the diameter of less than 70 nm. The typical peak-to-valley height is of 7 nm between the grains. It is not necessary to have atomically flat substrates for spectroscopic investigation of SAMs, such gold substrates has been used in this work. For STM studies gold films are required to be atomically flat to reduce the drift between 40

50 Chapter Three Substrate Preparation and Characterization Figure 3.5: Summary of constant-current STM micrographs of gold surfaces. (a) Preparation of gold film onto Si(100) at room temperature. (b) Preparation of gold film onto freshly cleaved and heated mica, before annealing. (c & d) Flame annealed gold substrate as prepared in (b). (d) Showing the step height and close packed direction of Au(111). (e) Damaged gold surface during scanning (f) Line scan indicating the step height of atomically flat terraces of gold. Tunneling parameters: (a-d) U t =300 mv, I t = 500 pa. (e) U t = 200 mv, I t = 1 na. 41

51 Chapter Three Substrate Preparation and Characterization the STM tip and the sample and to probe detailed structural issues of adsorbates at molecular scale. Therefore, the substrate prepared by this method is not appropriate for STM studies. Nevertheless, there is another method to obtain the substrate which is suitable for microscopic studies. For microscopic studies, it is essential to have the atomically flat gold substrate. This can be achieved by the evaporation of gold onto freshly cleaved mica. Freshly cleaved sheet mica which has been heated up to 650 K for about 60 h inside the evaporation apparatus to remove residual water contained between the mica sheets. Subsequently, 140 nm of Au were deposited at a substrate temperature of 180 C and a pressure of approximately 10-7 mbar. After deposition the substrates were allowed to cool down. Between substrate preparation and SAM formation the substrates were stored in an argon atmosphere. Figure 3.5 (b) clearly indicates the improvement in the surface morphology along with the little evidence of smoothness and crystallinity in terraces. This surface morphology is better slightly improved than those substrates prepared at room temperature on gold on silicon wafers. In fig. 3.5 (b) it is quite evident that the size of the grains is larger and the surface roughness is less as compared to fig. 3.5 (a). Even though, these films were unsatisfactory for STM studies. In the course of this study one interesting factor has been observed to obtain high quality and well define substrates. It has been observed that temperature of the mica during the deposition of gold or flame annealing [151,152] of the prepared Au on mica films is the key to obtain the atomically flat and well defined terrace exhibiting a (111)-oriented surface as shown in fig. 3.5 (c, d). This can be attributed to the fact that at higher temperature, the evaporated gold atoms are sufficiently mobile and undergoes to the process of diffusion. The flame annealing process was carried out by using the propane/oxygen gas flame. The samples were quickly passed through the flame till the corner of the sample become white. After that samples are allowed to cool down before immersion into the desired solution of adsorbates. The orientation of step edges of Au(111) can be determined as indicated in fig. 3.5 (d). Atomically flat terraces are separated by monoatomic step having the height of 2.4 Å indicated by line scan in figure 3.5 (f). Since the acquisition of the STM data is not straightforward. For comparison fig. 3.5 (e) displays the destruction of gold surface during the STM scanning which arise 42

52 Chapter Three Substrate Preparation and Characterization from the inappropriate tunneling conditions and the shape and sharpness of the tip, capable of damaging the surface. 3.4 Ultra-flat Gold Substrates (UFGS) Introduction The epitaxial growth of fcc metals on mica as a substrate is well known [153], and Au evaporated thin films form with (111) orientation on the (001) cleavage plane of mica, which have been extensively studied for SAMs. [29,33,48,58,59]. Gold on mica were used in these studies are limited to the surface roughness and grain boundaries. Even though the surface of these metals films consists of domains exhibiting the smoothness on the atomic scale, but overall the Au films are quite rough because the individual domains are small. This fact has been documented that the surface roughness influence on the surface morphology on the stability of SAMs. It has been observed that alkanethiol SAMs on surface exhibiting high roughness and area densities of grain boundaries oxidize within hours to days to the corresponding sulfinates and sulfonates, whereas those having lower area densities showed no apparent oxidation after two weeks [154]. Scientific community working in the field of SAMs is especially interested in the characteristic of surface and how they affect their monolayer s structure and resulting chemical and physical characteristics. One such characteristic of interest is the surface roughness of gold surface, which acts as a substrate. Many research groups have tried to minimize the surface roughness of gold with varying degree of success in their preparation either by use of evaporation rate or temperature during evaporation [ ]. Therefore the use of substrate (especially Au and Ag surfaces) with less roughness and smoothness on the atomic scale extending over an area of few micrometers is essential for arranging the molecule into defect free two dimensional crystals. Presumably in the initial stages of evaporation, the gold surface will lie as smooth as possible which is in direct contact to mica surface. To access the gold surface at gold/mica interface, that is, the back side of gold surface the well known technique named as template stripped gold (TSG) is used [161,162]. These types of substrates are firstly reported as template stripped gold (TSG) process is very novel idea, but is complicated and can lead to adsorption of soluble contamination 43

53 Chapter Three Substrate Preparation and Characterization from either the bonding agent or detachment solvent etc. In this technique, gold film is first grown onto mica; the gold layer is then glued onto a Si-wafer or glass and mica is stripped off. Still the template-stripped ultra-flat gold substrates are not easy to make, due to the fact that interface between the glue and gold surface must be stronger than that of Au and mica surface. Several researchers are still exerting their efforts to improve the quality of these TGS ultra flat substrates [ ] Preparation of Ultra-flat Gold Substrates Freshly cleaved sheet mica which has been heated up to 650K for about 60 h inside the evaporation apparatus to remove residual water contained between the mica sheets. Subsequently, 140 nm of Au were deposited at a substrate temperature of 180 C and a pressure of approximately 10-7 mbar. After deposition the substrates were allowed to cool down and later stored in an argon atmosphere. These deposited mica sheets were glued gold face down onto Si-wafer or glass pieces which are pre-covered with the 3-5 µl of Epo-tek 377 (amber color, often used in laser and fiber optics). Epo-tek 377 glue consists of two components (resin and hardener). It is necessary that these two components should be thoroughly mixed in equal parts by weight. The resulting Si-epoxy glue-au-mica sandwich was cured at C for 8-10 hours. The resulting sandwich could be stored as precursor at least up to several weeks without contamination of surface and detachable loss of quality. Before use, these stripping precursors were soaked in ethanol or THF at room temperature. Finally completed detachment of mica carried out by gently peel off with the help of tweezers shown in figure 3.6. Immediately thereafter, stripped gold surface is washed with corresponding solvent, checked for conductivity and used for characterization or monolayers preparation. The capability to prepare and store these ultra flat surfaces in the form of Si-epoxy glue- Au-mica sandwich, uncontaminated metal surface could be generated on demand is a significant extension to those researcher working the field of SAM etc. Finally, our template-stripped ultra flat gold surfaces are well characterized potential alternative substrates for micro-contact printing, nanolithography, interfacial properties and proteins adsorption. 44

54 Chapter Three Substrate Preparation and Characterization Figure 3.6: Schematic diagram of the procedure for template stripping gold surface (TSG). (a) Gold on mica is glued to a glass or silicon wafer by using Epotek 377 glue. (b) Curing of glass-glue-au-mica to reach an adequate hardness at C for 8-10 h. (c) Immersion into ethanol or THF. (d) Detachment of mica with the pair of tweezers. 45

55 Chapter Three Substrate Preparation and Characterization Characterization of Ultra-flat Gold Substrates The freshly detached mica from the Si-epoxy glue-au-mica sandwich were carried out by gently peel off with the help of tweezers or by soaking it into the THF and ethanol. For characterizing the UFGS it is useful to have some information about the surface morphology and surface roughness of these TSG surfaces Surface Morphology of Ultra-flat Gold Substrates Figure 3.7 shows the constant-current STM micrographs which show the high density of defects i.e. step edges. These steps correspond to close packed azimuth direction derived from the orientation of triangular-shaped gold grains. The line scan indicates quite rough surface due to high density of defects. Within the surface of 1µm 2 the surface exhibits the mean roughness of 3.5Å. The presence of high density of steps and mean roughness could arise from mechanical stress upon detachment of mica. Presumably in the initial stage of growth on mica, the gold will lie as smooth as possible next to mica. The first few monolayers grow as an islands in an epitaxial manner on the mica surface [156,157, 168]. Figure 3.7: Constant-current STM micrographs of UFGS. (a) Surface morphology of gold film having the thickness 140 nm. (b) Local flat terraces with high density of steps. Tunneling parameters: (a and b) U t = 500 mv, I t = 200 pa. 46

56 Chapter Three Substrate Preparation and Characterization As the islands diffuse, coalesce the ultimate top growth surface morphology become rough depending upon the apparent thickness of evaporated gold. The surface morphology was found to become smoother while using the gold evaporated thin films than the already used Au/mica substrates having the thickness of 140nm. Interestingly, reduction in the thickness of gold evaporated films, smoother the surface and the surface roughness was found to be decreased. Figure 3.8 shows the surface morphology of UFGS having the thickness of 100nm and 70nm, corresponding roughness of 2.8Å and 2.0Å respectively. Smoother the surface with the absence of defects like step edges but small gold grains were found while decreasing the thickness of gold evaporated film on mica as shown in figure 3.8 (b). The roughness analysis over the area of (1x1µm 2 ) reveals that decrease in the thickness of gold evaporated films results in the reduction of surface roughness. Nevertheless, some more efforts are needed to be done to increase the size of individual gold grains over the surface of several µm 2. Figure 3.8: Constant-current STM micrographs of UFGS. (a) Surface morphology of gold film having the thickness of 100 nm. (b) Thickness of gold film 70 nm. (c and d) corresponding line scans representing the smoother surface on decreasing the thickness of gold evaporated films on mica. Tunneling parameters: (a) U t = 500 mv, I t = 100 pa. (b) U t =450 mv, I t = 150 pa. 47

57 Chapter Three Substrate Preparation and Characterization Characterization of Alkanethiol Monolayer on UFGS To characterize of UFGS, fabrication of the SAMs on the freshly prepared UFGS on Siwafer were carried out by immersing into the 1mM ethanolic solution of alkanethiol (C18 SAM). Figure 3.9 displays the spectra of highly oriented C18-SAM on the routinely used substrate Si-wafer (for comparison) and UFGS on Si-wafer. In the C18-SAM spectra the peaks at 2851, 2878, 2920, 2936, and 2964 cm -1 correspond to the CH 2 symmetric stretching mode, the CH 3 symmetric stretching mode, the CH 2 asymmetric stretching mode, the CH 3 symmetric stretching mode (Fermi resonance FR) and CH 3 asymmetric stretching mode, respectively. For comparing the oxidative stability of these UFGS on Siwafer, the sandwiches were stored in air for the period of month, after that used for SAMs preparation. No pronounced difference has been observed in all three spectra which are in good agreement with those of crystalline SAMs [128,169]. Absorbance C18-SAM on Au/Si-Wafer C18-SAM on Ulta Flat Au/Si-Wafer C18-SAM on Ulta Flat Au/Si-Wafer Sandwich preserved for one month before use Wavenumbers [cm -1 ] Figure 3.9: IR spectra of octadecanthiol SAM on Au on Si wafer (black), UFGS on Si wafer (red) and sandwich preserved in air for one month (green). 48

58 Chapter Three Substrate Preparation and Characterization 3.5 Preparation of Self-Assembled Monolayers (SAMs) Gold substrates which have been obtained from above mentioned procedures were immersed into the solution of thiols under investigation either at room temperature or higher temperature depending upon the goal of study. The concentration of thiol solutions, used in this work, varies from 0.1 µm to1 mm depending upon the solubility of respective thiol under investigation. Surface coverage of thiolate films were dependent on immersion times, it could be varies from 1 minute to 48 hours depending on the goal of study. Normally 24 hours was considered to be sufficient for saturated films. After the allotted immersion time the samples were removed from the solution and rinsed with pure acetone, ethanol, chloroform and finally with the corresponding pure solvent to remove physisorbed material and dried in N 2 stream. 3.6 Preparation of KBr Disk for RAIR Studies For bulk characterization for IR studies the corresponding thiols and KBr powder in the fixed ratio of (1:3) mg respectively were mixed together homogenously in the vibrating mill (Perkin-Elmer) for 30 seconds or by hand grinding to get homogenous powder mixture. Later, all the substance was used to produce a single disk/pellet. 3.7 Cleaning of Glassware and Laboratory Equipment The crucial step was taken in to account in this study about the cleanliness of all equipments which were used in the laboratory. All the necessary items, first immersed in a bath of KOH/H 2 O 2 /2-propanl (15/15/1) followed by the rinsing with deionized water and ethanol, secondly immersed in a bath containing H2O/HCl (50/1). Finally all the equipments were again cleaned with deionized water and ethanol. Later the equipments were stored in an oven at 333 K till use. Immediately before used the bottles were flushed with corresponding solvent used for preparing the solutions. During experiments one has to make sure that clean tweezers and beakers are used. The tweezers should always be rinsed before contact with the solution. The proper way to clean the tweezers is from tip towards the handle, holding the tweezers tip upward. 49

59 Chapter Three Substrate Preparation and Characterization Rinsing like this removes dust from the tip towards the handle and not the other way around. 3.8 Chemical and Reagents All the chemicals and solvents used in this work with their sources and percentage purity are listed in table 1. Table 1: List of chemical and solvent used in this work Chemical Source % Purity Benzenethiol Aldrich 97% Benzeneselenol Aldrich 97% Ethanol J.T.Backer 99.9% Acetone J.T.Backer 99% Dicholomethane Normapur 99.84% Chloroform J.T.Backer 99% KBr Riedel-de Haen 99% Ammonium Hydroxide Aldrich 98% Epo-tek 377 (Polytech) and D263 thin glass (Schott) were purchased commercially. The compounds (thiols) used in this work will be discussed in coming chapters. 50

60 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) Chapter Four Characterization of Terphenylalkanethiol Self-Assembled Monolayers on Au(111) In this chapter, the structural characterization of 4,4 -terphenyl-substituted alkanethiols C 6 H 5 (C 6 H 4 ) 2 (CH 2 ) n -SH (TPn, n = 1-6) on Au(111) will be discussed in detail. To explore the effect of alkyl chain and deposition temperature on the quality and structure of the resulting SAMs, a detailed spectroscopic analysis together with the high resolution scanning tunneling microscopic characterization will be discussed in detail. 4.1 Introduction During the last two decades, self-assembled monolayers (SAMs) of organic molecules on metal surfaces, in particular on Au(111), have attracted significant attention because of their applications in molecular technologies [1,43]. In most cases, the preparation of SAMs leads to the formation of high-quality and well-defined organic surfaces with a homogeneous composition, structure and thickness. Therefore, SAMs can serve as an ideal model system in understanding various interfacial phenomena, such as wetting [170,171], adhesion [172], catalysis [173,174], electron-transfer barrier [22,24,175] and resist of microlithography and nanolithography [176,177]. Alkanethiol SAMs provides an ideal starting point, as well as model system for organic thin films. The structure of alkanethiol SAMs has been studied by using spectroscopy, diffraction and microscopy [43,51,61,98]. In the case of n-alkanethiolate SAMs on Au(111) it was reported that the alkyl chains are tilted by about with respect to the surface normal. The distance between adjacent sulfur atoms was found to be 5 Å. The latter value is larger than the bulk value for the distance between closely packed alkyl chains ( Å). As a result, the alkyl chains tilt away from the surface normal in order to achieve a close-packed structure. There is now a general agreement that n- alkanethiols on Au(111) form a c(4 2) superstructure with regard to a ( 3 3 )R30 basic lattice. 51

61 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) Recently it has been realized that the lateral chain-chain interaction plays an important role in both the process of SAM formation and in the stabilization of the SAMs [49,178]. Alkanethiolate-based SAMs with short alkyl chains, for example, exhibit film properties which are quite different from those found for long alkyl chains. Therefore, it has to be expected that replacing the alkyl molecular backbone within the alkanethiols by chains of different composition will lead to a significant effects on the molecular packing and on the properties of the SAM. The interest has been shifted to organothiols molecules with aromatic backbones and in a number of publications the monolayers of aromatic oligophenyl thiols have been studied [22,31,33,42, ]. In some cases, it has been found that the structural quality of oligophenyl thiols is superior to that of alkane thiolate SAMs. The latter finding is probably due to the presence of fairly strong interactions between the aromatic moieties within the SAM [56-58]. Moreover, the aromatic thiol molecules are more rigid than n-alkanethiols and this property provides a greater stability for the molecules within the SAMs [42,181]. Last but not least, due to their extended π-systems aromatic thiols are very promising with regard to applications in the field of molecular electronics. The oligophenyl based rigid-rod thiols, which were previously studied, include phenyl, [59,183] biphenyl, [52,55-57,184] and terphenyl [31,181,185] as well as oligophenyl systems linked by acetylenic units [50]. In these oligophenyl-based organothiols the sulfur is either connected directly to the aromatic system of the last phenyl unit or linked via an alkyl unit (i.e. Ph-(CH 2 ) n -S). The previous studies revealed that the inclusion of an alkyl chain between the sulfur atom and the first phenyl unit significantly affects the structure and in particular the surface morphology of the SAMs. In the presence of a short alkyl chain spacer, STM investigation have revealed a morphology similar to that obtained for n-alkanethiols on gold formed at room temperature, namely the presence of typically roundish holes in the top-layer of the gold substrate [35]. For oligophenylthiols without an alkane chain spacer, islands instead of the roundish holes were observed. High-resolution STM images obtained for such systems revealed that the islands are also covered with thiolates and exhibit the same ( )R30 molecular arrangement as observed between the islands [29]. In general, the insertion of methylene units into 52

62 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) aromatic thiols between the sulfur head-group and the last phenyl moiety yields films with a morphology and structure comparable to those of n-alkanethiols. Recently, oligophenyl thiols containing a terphenyl backbone together with an alkyl spacer, i.e. the series (C 6 H 5 -(C 6 H 4 ) 2 (CH 2 ) n -SH, TPn, n = 1-6) have been investigated using different spectroscopic techniques on Au and Ag surfaces [185]. These thiols are different from BPn thiols in that they contain an additional benzene ring in the molecular backbone. Since the interaction between the terphenyl units is significantly larger than for the biphenyls (sublimation temperature of 649 K for p-terphenyl vs K for biphenyl) [186] one might expect a significantly smaller influence of the length of the alkyl-spacer. The spectroscopic results of TPn-SAMs revealed, however, an odd-even behavior with regard to the number of methylene chains in the alkyl spacer similar to that observed for the BPn SAMs [185]. TP1 TP2 TP3 TP4 TP5 TP6 SH SH SH SH SH SH Figure 4.1: Molecular structure of TP series used in this chapter 4.2 Objective of Work Presented in this Chapter In the present study, the orientation and structural ordering of the single molecules within the terphenyl SAMs is extended by using spectroscopic and microscopic techniques. In order to support these investigations, a detailed spectroscopic analysis will be discussed by using infrared spectroscopy (RAIR) and scanning tunneling microscopy (STM). The effect of deposition temperature on the structure of the TPn SAMs will be explained in detail. 53

63 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) 4.3 Adsorption Process of TPn SAMs on Au(111) In order to quantify the adsorption process, the importance of solvent temperature used for SAM formation, the fabrication of homologous series of terphenyl-containing organothiols, C 6 H 5 (C 6 H 4 ) 2 (CH 2 )n-sh (TPn, n = 1-6) on Au(111) have been studied using STM and RAIR spectroscopy. The importance of solvent temperature was investigated by using two different preparation temperatures, 298 K and 333 K on the resulting SAMs, yield to different packing densities and molecular arrangements. 4.4 Results Infrared Spectroscopy In fig. 4.2, the low-frequency region of a TP1 SAM fabricated at 298 K is shown together with the corresponding bulk spectrum recorded using KBr pellets. A comparison of the band positions for bulk samples embedded in KBr and SAM spectra are provided in table 2 together with an assignment of the band positions. Three different labels will be used to assign the RAIR bands: op for out-of-plane modes, i.e. where the transition dipole moment (TDM) is orientated perpendicular to both phenyl ring plane and the molecular 5 x 10-3 Absorbance TP1-SAM KBr Wavenumber (cm -1 ) Figure 4.2: Comparison of the IR spectrum of bulk TP1 (KBR pellet) with the spectrum of SAM of TP1 on Au(111) prepared at 298K 54

64 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) axis; ip-par for the case when the TDM is parallel to both the phenyl-ring- plane and the terphenyl chain axis; and ip-perp for the case when the TDM is orientated parallel to the phenyl ring plane but perpendicular to the terphenyl 4,4 -axis. The most intense absorption bands in the KBr spectrum are located at 761, 824, 1002, and 1485 cm -1. The low-frequency vibrations located at 761 and 824 cm -1 are assigned to op ring modes of the mono- and para-substituted phenyl-units, respectively. The bands located at 1002 and 1485 cm -1 are assigned to C-H bending and C-C ip-par ring modes, respectively. Direction of Assignment transition dipole * 4,4 -axis Ring, C-H op, 11, r 1 Band Position of TP1 [cm -1 ] KBr SAM SAM (298 K) (333 K) ,4 -axis Ring, C-H, op, 17b, r // 4,4 -axis Ring, C-H, ip-par, 18a, r 2 and r 3 4,4 -axis Ring,C-H str // 4,4 -axis Ring, C-C ip-par, 19a // 4,4 -axis Ring, C-C str * r 1 : is the top monosubstituted phenyl ring, r 2 : is the middle ring, and r 3 : is the sulfur-substituted ring Table 2: Vibrational mode assignment for TP1 in the solid state (KBr) and for SAM on Au following the notation of Varsanyi [187]. The IRRAS data recorded for TP1 SAMs on Au(111) reveals significant differences relative to the corresponding KBr spectrum. Below 1600 cm -1, only two bands with high intensity can be detected for the SAM located at 1002 and 1487 cm -1. In addition to these bands, a weak band is seen at 814 cm -1. The strong reduction in intensity of some of the bands results from the so-called surface selection rule governing vibrational spectroscopy at metal surfaces, which states that only those vibrations can be seen which have a component of their TDM orientated perpendicular to the surface of the metal substrate [128,188]. The disappearance and reduction of the bands at 761 and 814 cm -1, respectively, explained by their TDM being oriented almost parallel to the surface. From 55

65 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) the large reduction of the relative intensities of the op peaks (761 and 814 cm -1 ) indicate that the average orientation of the TP1 molecular axis is very close to the surface normal. The IRRAS spectra recorded for the complete series of TPn SAMs on gold obtained for samples prepared at 298 K are shown in fig In the odd-numbered case (TPn with n = 1, 3, and 5), the peak at 761 cm -1 is almost completely absent in all the spectra. The peak at 814 cm -1 exhibits a very low intensity only. Since the relative intensity of the op-band to the ip-par bands is very low, it can be concluded that the TPn (n = 1, 3, and 5) molecules adopt a standing-up conformation with their aromatic backbone orientated almost perpendicular to the gold surface. The IR spectra obtained for TP2 are quite similar to those of the odd-numbered SAMs. Based on this observation we conclude that the orientation of the terphenyl backbone must be similar. Compared to TPn with n = 1, 2, 3, and 5, the IRRAS spectra of TP4 and TP6 SAMs on Au(111) collected at 298 K exhibit significant differences. The op-bands at 761 cm -1 and 825 cm -1 appear with high intensity in the TP4 and TP6 spectra respectively. The relative intensities of the op bands to the ip-par bands is significantly increased, which strongly indicates that the molecules are significantly tilted away from the surface normal. From a comparison to previous IR data for terphenyls [181], yield an estimate of this tilt angle of about 40 from the surface normal. 56

66 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) 2 x 10-3 TP6-SAM TP6-KBr TP5-SAM TP5-KBr Absorbance TP4-SAM TP4-KBr TP3-SAM TP3-KBr TP2-SAM TP2-KBr TP1-SAM TP1-KBr Wavenumber (cm -1 ) Figure 4.3: Low frequency region of the IR spectra of bulk TPn s (KBr pellet) as well as that of the corresponding SAMs on Au(111) prepared at 298 K with n ranging from 1 to 6. 57

67 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) 1x10-2 TP6-SAM TP6-KBr TP5-SAM TP5-KBr Absorbance TP4-SAM TP4-KBr TP3-SAM TP3-KBr TP2-SAM TP2-KBr TP1-SAM TP1-KBr Wavenumber (cm -1 ) Figure 4.4: Low frequency region of the IR spectra of bulk TPn s (KBr pellet) as well as that of the corresponding SAMs on Au(111) prepared at 333 K with n ranging from 1 to 6. 58

68 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) Figure 4.4 shows IRRAS spectra recorded for TPn (n=1 to 6) SAMs prepared at 333 K. Close inspection of the data reveals that with the exception of the TP2 spectrum no significant changes are present when compared with the SAMs prepared at room temperature (298 K). Only for TP2 SAMs, the intensity of the op-band located at 761cm -1 is found to be significantly increased. This observation suggests that adsorption of TP2 from hot solution (333 K) results in a molecular orientation in which the aromatic backbone are significantly tilted away from the surface normal. Based on these observations the schematic model presented in fig. 4.5 for the molecular orientation within the homologous series of terphenyl thiolate SAMs. Figure 4.5: Schematic illustration shows the orientation of TPn SAMs on gold. (A) For odd number of methylene group the aromatic units are less tilted (less θ). For even number of methylene group the aromatic units are more tilted (large θ) than for n= odd and the intermolecular distance d is larger due to the influence of the C-S-Au bending potential. 59

69 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) Scanning Tunneling Microscopy To elucidate the molecular arrangements and packing densities made from homologous series of terphenyl thiols, the high-resolution STM data will be discussed in this section Odd-Numbered TPn (TP1, TP2, TP5) Monolayers 1. SAMs of TP1 The summation STM data obtained for TP1 SAM prepared at 298K & 333K depicted in fig Figure 4.6 (a-c) depicts a representative constant-current STM data for an Au substrate, which has been immersed for 24 h in a 2.5 µm solution of TP1 in ethanol at 298 K. An atomically flat terrace with monatomic is step clearly visible in the left lower part in the fig. 6(a). In fig. 4.6 (b) within the terrace, numerous depressions with diameters of 2-7 nm and a depth corresponding to that of monoatomic steps on Au(111) and shorter domains as indicated by arrows were observed. These depressions have been observed in earlier studies on alkanethiolate adlayers on Au(111), identified as regions where gold atoms are missing in the first layer of the gold surface as well as the typical pits of monoatomic depth (2.4 Å, corresponding to the height of a single step on a Au(111) surface) within the terraces [35]. Figure 4.6 (c) shows high-resolution STM image of TP1 SAM. Acquisition of high-resolution STM data for TP1 SAMs, which were prepared at 298 K, was very difficult. Out of the eight samples prepared under the same conditions, the high-resolution data were collected only in one case. Even in this favorable case, the quality of data is rather poor. Figure 4. 6 (d-f) shows the representative constant-current STM data for an Au substrate, which has been immersed for 24 h in a 2.5 µm solution of TP1 in ethanol at 333 K. Compared to the films prepared at 298 K, the size of the depressions within the film is slightly larger with diameter of 5-12 nm, whereas their density is lower. A higher resolution image of a TP1 SAM in fig. 4.6 (e) clearly shows three domains rotated by 120 with respect to each other, reflecting the symmetry of underneath gold Au(111) substrate. Already at this scale, it is clearly visible that the arrangement of the thiol molecules deviates from a purely hexagonal packing. This becomes more obvious in fig. 4.6 (f) where the bright protrusions, which are assigned to individual molecules 60

70 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) forming the regular spaced rows. The protrusions exhibit two different heights, as can be seen from the height profiles in fig. 4.6 (g, h). The dimension of unit cell were determined by taking the line scans along the lines A and B labeled in fig. 4.6 (f) and amount to be a = 4.8 ± 0.2 Å and B = 10 ± 0.4 Å, which corresponds to about 3 and 2 3 times the Au lattice constant. Figure 4.6: (a-c) Constant-current STM images showing the gold surface after immersing into 2.5 µm ethanolic solution of TP1 at 298 K, (d-f) at 333 K for 24h respectively. (g, h) corresponding line scans in (f). Oblique box in (f) marks the (2 3 3) R30º unit cell. Tunneling parameters: (a) U t = 800 mv, I t = 140 pa; (b) U t = 340 mv, I t = 250 pa; and (c) U t = 284 mv, I t = 500 pa; U t = 950 mv, I t = 128 pa; (e) U t = 340 mv, I t = 187 pa; and (f) U t = 244 mv, I t = 554 pa. 61

71 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) 2. SAMs of TP3 In the left panel, fig. 4.7 (a-c) shows a constant-current STM data of TP3 SAMs, which has been immersed into the ethanolic solution of TP3 for 24 h at 298 K. In the right panel, fig. 4.7(d-f) shows the TP3 SAM prepared at the 333 K. Figure 4.7: (a-c) Constant-current STM images showing the gold surface after immersing into 2.5µM ethanolic solution of TP3 at 298 K, (d-f) at 333 K for 24 h respectively. Oblique box in (c and f) marks the (2 3 3) R30º unit cell. Tunneling parameters: (a) U t = 560 mv, I t = 141 pa; (b) U t = 349 mv, I t = 128 pa; and (c) U t = 384 mv, I t = 280 pa. Tunneling parameters: (d) U t = 500 mv, I t = 161 pa; (e) U t = 280 mv, I t = 138 pa; and (f) U t = 510 mv, I t = 180 pa. 62

72 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) Compared to the TP3 SAMs prepared at 298 K, the size of the depression seen within the films prepared at 333 K is slightly larger (5-10 nm), while their density is smaller. The high-resolution STM images displayed in fig. 4.7 (c) and (f) which were acquired for TP3 adlayers prepared at 298 K and 333 K, respectively, reveals no changes in the molecular structure and ordering. A detailed analysis of structures in high-resolution STM micrograph using line profiles reveals that TP3-SAM exhibits a periodic structure forming a (2 3 3) R30 unit cell. The unit cell consists of two protrusions, which were assigned to individual molecules, corresponding to an area of 21.6 Å SAMs of TP5 Figure 4.8 (a) represents a large-scale constant-current STM data recorded for atomically flat terraces of the Au(111) substrate, which has been immersed for 24 h in 2.5 µm solution of TP5 in ethanol at 298 K. Within the terraces several depressions with diameter of 2-8 nm exhibiting the depth (2.4 Å) to that of monoatomic steps on Au(111) are observed. These depressions have already been reported for the alkanethiolate adlayers on Au(111) and have been assigned to the regions where the topmost gold atoms are missing from the gold surface [35]. Figure 4.8 (b) shows a constant-current STM image recorded for Au(111) substrate, which has been immersed for 24 h in 2.5 µm solution of TP5 in ethanol at 298 K. This micrograph shows domains exhibiting a row structure that can adopt several rotational domains (see arrows). In fig. 4.8 (c-e), a large scale constant current data recorded for a TP5 adlayer prepared using an immersion time of 24 h in 2.5 µm solution of TP5 at 333 K is displayed. The size of order domains with the diameters of about 40 nm that have a row structure, can adopt three different orientations as indicated in the fig. 4.8 (b and d). A detailed analysis of the structures in high-resolution STM data using line profiles reveals that TP5 SAMs, as all the other TPn SAMs with odd n, exhibits a periodic structure with a (2 3 3) R30º unit cell. The unit cell contains two inequivalent molecules, corresponding to an area of 21.6 Å 2 per molecule. No significant changes with variation of the solvent temperature were observed. The data is consistent with the sulfur atoms forming a ( 3 3) R30º lattice, as it is the case for the n-alkanethiolate SAMs. 63

73 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) Considering the van der Waals dimensions of the phenyl rings (6.4 Å by 3.3 Å) [181] with a cross-sectional area of 21.1 Å 2 for the phenyl rings and the area per molecule in the (2 3 3) R30 structure (21.6 Å 2 ), we expect a tilt angle of about across (21.1/21.6)= 12.5º with respect to the surface normal. Figure 4.8: (a,b) Constant-current STM images showing the gold surface after immersing into 2.5 µm ethanolic solution of TP5 at 298 K, (c-e) at 333 K for 24 h respectively. The arrows in (b,d) show the directions of the ordered domains. Tunneling parameters: (a) U t = 650 mv, I t = 150pA; (b) U t = 531 mv, I t = 120 pa. In (e), the unit cell of the (2 3 3) R30 structure is marked by the oblique. Tunneling parameters: (c) U t = 531 mv, I t = 153 pa; (d) U t = 392 mv, I t = 150 pa; and (e) U t = 530 mv, I t = 159 pa. 64

74 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) Structural Model for Odd-Numbered TPn SAMs (TP1, TP2, TP5) Based on the above mentioned STM results obtained for odd-numbered TPn SAMs, which indicate the presence of a high degree of lateral order which can be described by an oblique unit cell with dimensions of (10.0Å 5.0Å) corresponding to a commensurate (2 3 3) R30 structure. The unit cell contains two in equivalent terphenyl molecules, with the sulfur atoms being located at a ( 3 3) R30 sub lattice. The area occupied by a single molecule amounts to 21.6 Å 2, which is similar to the packing density within alkanethiols SAMs on Au(111) substrates. The structural model presented in fig. 4.9, which is derived from the terphenyl bulk structure [189], proposes a herringbone like arrangement of the terphenyl backbones in the (2 3 3) R30 unit cell. Figure 4.9: Top view of a (2 3 3) R30 model for odd-numbered TPn (n= 1-6) SAMs on Au(111). 65

75 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) Even-Numbered TPn SAMs (TP2, TP4, TP6) Monolayers 4. SAMs of TP2 Figure 4.10 shows representative STM data recorded for TP2 SAMs prepared at 298 K and 333 K. Constant-current STM data recorded for TP2 SAMs prepared at 298 K, showing the atomically flat terraces which are separated by the monoatomic step of gold substrate shown in fig.10 (a). Paradoxically no etch pits were observed. The high resolution STM image in fig.10 (c) reveals that the TP2 molecules adopt the same molecular arrangement as observed for the odd numbered TPn, i.e. a (2 3 3) R30 structure. In the right panel of fig representative STM data recorded for TP2 SAMs prepared at 333 K is displayed. In fig (d) large-scale constant-current STM image recorded for an Au(111) substrate, which has been immersed into the dilute ethanolic solution of TP2 thiol for 24 h at 333 K is displayed. The image shows atomically flat terraces separated by monoatomic height steps in gold surface. The size of ordered domains with the diameters of about 40 nm that have a row structure, can adopt three different orientations as indicated in fig (e). Figure 4.10 (f) shows a well-defined periodic arrangement of TP2 molecules exhibiting a c (5 3 3) unit cell which is significantly larger than that of the (2 3 3) R30 structure seen for TP2 SAMs prepared at room temperature. At this higher preparation temperature, a quite different structure has seen. The same structure was found in TP4 SAMs, SAMs prepared at either 298 K or 333 K, which will be discussed later. 66

76 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) Figure 4.10: (a, c) Constant-current STM images showing the gold surface after immersing into 2.5 µm ethanolic solution of TP2 at 298 K, (d-f) at 333 K for 24 h respectively. In (g), the unit cells of the TP2-SAM (2 3 3) R30,and the c (5 3 3) structure at 298 K and 333 K are marked respectively. The arrows in (e) show the direction of the c (5 3 3) domains. In (f), the unit cell of is marked by the rectangle. Tunneling parameters: (a) U t = 530 mv, I t = 150 pa; (b) U t = 341 mv, I t = 252 pa; (c) U t = 341 mv, I t = 252 pa. (d) U t = 1000 mv, I t = 360 pa; (e) U t = 520 mv, I t = 158 pa; and (f) U t = 536 mv, I t = 189 pa. 67

77 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) 5. SAMs of TP4 Figure 4.11 (a) represents a large-scale constant STM image recorded for atomically flat terraces of Au(111) substrate, which has been immersed for 24 h in 2.5µM solution of TP4 in ethanol at 298 K. Within the terraces several depressions with the depth of 2.4 Å corresponds to that of mono-atomic steps on Au(111) were observed. The STM data shown in fig (b) reveals that the SAM consists of different domains rotated by 120 with respect to each other. The acquisition of high-resolution STM images for TP4 SAMs prepared at room temperature turned out to be rather difficult. The high-resolution STM data fig (c) show a highly ordered adlayer structure with a characteristic rectangular primitive unit cell with dimensions of 8.65 Å 25 Å. The unit cell consists of eight molecules, corresponding to an area of 27 Å 2 per molecule. The simplest commensurate structure consistent with these lateral dimensions is a c (5 3 3) structure. Figure 4.11: (a-c) Constant-current STM images showing the gold surface after immersing into 2.5µM ethanolic solution of TP4 at 298 K for 24 h. In (c), the unit cell of the (5 3 3) structure is marked by the rectangular box. Tunneling parameters: (a) U t = 570 mv, I t = 151pA; (b) U t = 381 mv, I t = 200 pa; and (c) U t = 530 mv, I t = 150 pa The summary of large-scale constant STM image recorded for atomically flat terraces of Au(111) substrate, which has been immersed for 24 h in 2.5 µm solution of TP4 in ethanol at 333 K is depicted in the fig The STM data shown in the fig (a) clearly demonstrate that the TP4 SAM reveals the typical feature of organothiolate adlayers i.e. etches pits. The STM image presented in the fig (b) clearly demonstrates that the SAMs consist of domains that are typically about the 300 Å in size 68

78 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) and have a row structure that can adopt two different orientation (see arrows). Within each domain, there are paired rows of protrusions that appear systematically brighter and which are separated by darker regions. At the same time, the STM data demonstrate the presence of same lateral packing for samples prepared at 298 K and 333 K, a less densely packed structure was observed. These types of feature has been reported for the organothiols, containing an oligophenyl-backbone [29,124]. These features become more pronounced in the fig (c). These data show that the regions separate the ordered pair rows also contains the protrusions, which are assigned to individual TP4 molecules. Figure 4.12: (a-c) Constant-current STM images showing the gold surface after immersing into 2.5 µm ethanolic solution of TP4 at 333 K for 24 h. In (d), the unit cell of the c (5 3 3) structure is marked by the rectangle. (e): Cross-sectional height profiles along the colored lines labeled in (e), respectively. Tunneling parameters: (a) U t = 575 mv, I t = 150 pa; (b) U t = 581 mv, I t = 200 pa; (c) U t = 541 mv, I t = 158 pa and (d) U t = 528 mv, I t = 115 pa. 69

79 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) There are several distinct protrusions visible in fig (c) and (d) indicating the presence of eight molecules per unit cell. Along the line A in fig (d), which runs along the substrate <110 > direction, every second molecules have the same topographic height. The spacing between the brighter spots amounts to 8.65 Å, which is three times the substrate lattice constant. The length between the brighter protrusion in the first row and the corresponding one in the second row is 25 Å, which is 5 3 times the substrate lattice constant evident from the line scan B shown in fig (e). The precise height value of the protrusion depends on the tunneling parameters and on the tip used for imaging. However, the data demonstrate unambiguously that the unit cell contains several protrusions, which differ in height. Based on the above observations, the adlayer of TP4 exhibits a rectangular primitive unit cell with dimensions of 8.65 Å 25 Å containing of eight molecules, corresponding to an area of 27 Å 2 per molecule. The simplest commensurate structure consistent with these dimensions is amount to be c (5 3 3) structure. A structural model for TP4 SAM prepared at 298 K and 333 K, again derived from the corresponding bulk data and previously published results for the BPn-series [29] is shown in fig Figure 4. 13: Top view of a structural model for the c (5 3 3) rectangular overlayer of TP4 on Au(111). 70

80 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) 6. SAMs of TP6 The summary of constant-current STM data recorded for TP6 SAMs prepared at 298 K and 333 K will be discussed in fig The STM data shown in fig (a-c) for TP6 films prepared at 298 K reveals that high density of defects and small ordered domains. The STM micrograph shown in the fig (b) reveals, as for TP4, well-defined rows of molecules. Again, three different domains can be observed, which are rotated by 120 with respect to each other. The high-resolution STM data shown in fig (c) are similar to that obtained for TP4 and indicate the presence of a c (5 3 3) structure containing eight molecules per unit cell. Figure 4.14 (d-i) shows the constant-current STM data recorded for TP6 SAMs prepared at 333 K. The large-scale STM micrographs reveal significant differences to films prepared at 298 K, the size of vacancy islands is found to be slightly increased at the expense of their density. The small-scale constant-current STM image shown in fig (e) reveals the presence of six different rotational domains with relative orientations of 60. This observation is in contrast to that seen for samples prepared at 298 K, where only three different rotational domains rotated by 120 with respect to each other have been seen as indicated in fig (b) and (e). Close inspection of the high-resolution data in fig. 14 (f) reveals the coexistence of three different phases/structures labeled α, β, and γ. The α structure exhibits a rectangular unit cell with the same dimensions and molecular arrangements of the c (5 3 3) structure as found for TP4 adsorbates. The unit cell of the β-phase was determined from the height profiles along the lines within the single domain displayed in fig (h). The unit cell is oblique and is consistent with the presence of a commensurate ( ) R30 structure containing eight molecules per unit cell. This result yields an area per molecule of 32.4 Å 2 corresponding to a tilt angle of about arcos (21.1/32.4)= 49º with respect to the surface normal. A schematic model for this structure is shown in fig (b). The variation in the topographic heights of the protrusions (TP6 thiolate species) is assumed to arise from the multiple adsorption sites and from the herringbone arrangement of the terphenyl units. 71

81 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) Figure 4.14: Summary of constant-current STM images showing the gold surface after immersing into 2.5 µm ethanolic solution of TP6 at 298 K (a-c) and 333 K (d-i) for 24 h respectively. In (c), the unit cell structure is marked by the rectangular. The arrow in (e) shows the six directions of the ordered domains. (i) represent the height profiles along the colored lines. The rectangular box depicted in (g) shows the c (5 3 3) structure. The oblique box depicted in (h) marks the ( ) R30 oblique unit cell. Tunneling parameters: (a) U t = 550 mv, I t = 150pA; (b) U t = 581 mv, I t = 115 pa; and (c) U t = 531 mv, I t = 150 pa; (d) U t = 510 mv, I t = 361 pa; (e) U t =523 mv, I t =130 pa; (f) U t = 682mV, I t = 132 pa; (g) U t = 530 mv, I t = 170 pa and (h) U t = 580mV, I t = 130 pa. 72

82 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) The γ-phase was commonly found to be located in the areas between the α- and β-phases. All attempts to obtain molecular resolution within areas belonging to the γ-phase were unsuccessful. Based on the STM data acquired for two different α- and β-phases of TP6 adlayers at different preparation temperature (298 K, 333 K), the schematic models are presented in the fig Figure 4.15: (a) Top view of a structural model for the c (5 3 3) rectangular overlayer of TP6 on Au(111) at 298 K. (b) Top view of a ( ) R30 structural model for TP6 SAMs on Au(111) at 333 K. 73

83 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) 4.5 Summary of Structures Adopted by TPn SAMs: Effect of Alkyl Chain and Deposition Temperature The different adlayer structures for the TPn monolayers prepared at 298 K, 333 K summarized in the table 3. Terphenyl molecules with the odd number of alkyl spacer between the terphenyl moiety and head group adopt the same molecular structure which can be best described (2 3 3) R30 by a superlattice of the simple commensurate ( 3 3) R30 lattice. The unit cell consists of two molecules yielding to a molecular packing density of 21.6 Å 2. In the case of even number of alkyl spacer between the terphenyl moiety and head group different structure were observed depending upon the deposition temperature used for the SAM formation. For TP2 two different structures were found. The (2 3 3) R30 structure appeared at 298 K and the c (5 3 3) structure found at 333 K which correspond to the molecular area of 21.6 Å 2 and 27 Å 2 respectively. The TP6 SAM undergoes the phase transition on preparing the SAM at different temperature. In case of TP6, preparation of the SAMs at 298 K the c (5 3 3) adlayer structure was observed, the SAM formation at 333 K, resulted in the formation of a new ( ) R30 structure characterized by an oblique unit cell. Thiols 298 K 333 K TP1 (2 3 3) R30 (2 3 3) R30 TP2 (2 3 3) R30 c (5 3 3) TP3 (2 3 3) R30 (2 3 3) R30 TP4 c (5 3 3) c(5 3 3) TP5 (2 3 3) R30 (2 3 3) R30 TP6 c (5 3 3) c (5 3 3) (α) ( ) R30 (β) amorphous (γ) Table 3: Summary of structures adopted by the TPn-SAMs (n=1-6) as a function of alkyl chain length and deposition temperature. 74

84 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) 4.6 Exchange of TP2 SAM in C10 Matrix Introduction Self-assembled monolayers of thiol-based compounds are an efficient tool to monitor the surface properties of metals [73,98]. The applications of SAMs range from wetting control, [72] corrosion inhibition [190], metallization [191], protein adsorption [16], and lateral structuring [192] to molecular electronics [22]. Mostly for these applications, SAMs that consist of more than one component (mixed SAMs) are used because these SAMs exhibit more degrees of freedom (i.e., the surface properties can be adjusted by the ratio of the different constituents in the film). This approach is especially promising for molecular electronics. Weiss et al. were the first to characterize electronic transport properties of single molecules via an STM by using mixed SAMs [193]. Nanoscale separated SAMs have been employed previously by coadsorption methods, where the difference in intermolecular strength between two molecules results in the phase separation. There are several ways to prepare mixed SAMs. One method is to fabricate the film from a mixture of different substances (coadsorption). Various mixed SAMs have been previously reported by using this approach: alkanethiols with different chain lengths, [67] and different terminal groups [194,195] or decanethiol and an amidecontaining alkanethiol of similar length [196]. Bain et al. [194] showed that the composition of the monolayer does not fully correspond to the composition of the solution and that longer chains are preferentially adsorbed, which indicate the thermodynamic control of the adsorption process, which is in accordance with the later theoretical study [197]. Another method is the adsorption of asymmetric disulfides [195,198]. By this method, different mixed SAMs have been prepared e.g. mixed SAMs of alkanethiols having different tail groups and chain lengths [199] and symmetrical and asymmetrical alkyl [200], and perfluoroalkyl disulfides [198,201]. Terphenylethylthiol (TP2) are the appropriate substance to insert into an alkanethiol host matrix as they keep difference in the physical height and difference in transconductance of molecules, which is different from the previous reported studies [202]. 75

85 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) Molecular Exchange In this section, a two-steps deposition process was used for isolating electrically active molecules in a host matrix, in contrast to the two previous methods, which always consist of a one-step deposition process. For this method, a preassembled, closely packed C10SH SAM (mostly consisting of insulating alkanethiols) was immersed in a second step into a solution of the electronically active TP2 molecules. In this second step, TP2 molecules exchange by the molecules of host matrix. The exchange of conjugated molecules with phenyl rings embedded into alkanethiol SAMs to form a nanoscale structures will be discussed by microscopic and spectroscopic characterization. 4.7 Results STM For the exchange experiments single-component SAMs were prepared by immersing the substrates into 1mM ethanolic solution C10SH for 24 hours. The exchange of TP2 is accomplished by immersing the saturated closely packed SAM of C10SH into 10µM ethanolic solution of TP2 for specified period. The gold substrates were rinsed in pure ethanol and blown dry with nitrogen. Fig (a) shows the representative constantcurrent STM image of pure C10-SAMs, the typical feature of alkanethiolate monolayer, showing the depressions with a depth of 2.4 Å, corresponding to single Au layer. After immersing the preassembled C10-SAMs into the TP2 solution for fifteen minutes, the surface morphology changed, due to the exchange process see in fig (b). On increasing the surface coverage of exchanged TP2 molecules by increasing the immersion time from fifteen to sixty minutes (c) shows the representative constantcurrent STM images of a mixed TP2/C10 monolayers prepared as mentioned above, the surface morphology dramatically changed. The evolution of TP2 domains islands appears brighter which is in contrast to previous reported studies. 76

86 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) Figure 4.16: Summary of constant-current STM images showing the gold surface. (a) C10-SAM as deposited; (b, c) C10-SAM after dipping into 10 µm ethanolic solution of TP2 for specified time (15, 60) mins respectively. In (c, d), the domains of TP2 molecules embedded in C10-SAM forming a row structure as displayed. (e, f) The cross-sectional height profile of TP2 domains embedded in C10 matrix displayed along the line marked in (e). Tunneling parameters: (a) U t = 900 mv, I t = 80pA; (b-e) U t = 500 mv, I t = 180 pa. 77

87 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) It has been well documented that the exchange process takes place at defect and the domain boundaries [203,204], which was found to be different in the case of mixed TP2/C10 SAM. However, an interesting feature of the mixed TP2/C10 SAM reveals that TP2 molecules do not incorporate only into the film defect sites such as domain boundaries and pits in the gold surface but also mostly in the middle of the C10 domain. Exchange process was found to be occurred at the step edges as well as the flat terraces, where the density of TP2 domains is higher than at the step edges. The higher topographic (brighter) regions were assigned to the longer TP2 molecules forming brighter regions as islands. Figure 4.16 (d-e) shows the representative constant-current STM image of TP2 domains forming the equidistance row structures. However due to the different tunneling conditions used, it was not possible to resolve both C10 and TP2 molecules. Topographic cross section analysis extracted by drawing line as indicated in fig (e). The cross section was taken over the decanethiolate SAM and row structure of inserted TP2 molecules in the domain that comprise the islands. The STM topographic height difference between the region of C10 SAM and TP2 SAM was found to be 1.1 Å ± 0.2 Å. The physical/geometric height of C10 and TP2 molecules are found to be Å and 15.3 Å respectively. The height difference between these molecular lengths yields the value of 1.68 Å, which is different from the topographic height of these molecules i.e. 1.1 Å. STM is capable for monitoring the density of states of the molecules, which gives different contrast depending upon the conductivity of the molecules. The difference between the measured topographic height and physical height of C10 and TP2 attributed to the difference in the tunneling conductance of both molecules, where the gap between the STM tip and film was altered to accommodate this difference [175]. The fig depicts the schematic sketch of the molecularly sharp boundary between the C10 SAMs and inserted TP2 molecules. The probe-tip-film distance due to STM feedback control is shown as grey dotted upper line in the schematic drawing, with a geometric height difference between two regions is indicated as a black solid line. 78

88 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) Figure 4.17: Schematic sketch of decanethiolate host SAM and exchanged terphenyl ethylthiolate SAM depicting the geometric and STM height differences of 1.68 Å and 1.1 Å respectively NEXAFS However, the exact information about the molecular orientation of TP2 molecules is limited to the STM studies. In order to obtain the information about the molecular orientation of embedded TP2 molecules, NEXAFS spectra were recorded for the mixed C10/TP2 SAMs and displayed in fig σ Normalized PEY π Photon Energy [ev] Figure 4.18: Series of C1s NEXAFS spectra recorded for TP2 molecules embedded into the matrix of C10 SAM. 79

89 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) A typical signature of carbon edge NEXAFS spectra of mixed C10/TP2 SAMs is a resonance around 285 ev due to excitations of C 1s electrons into unoccupied π* orbitals. At higher energies broad resonance were observed, attributed to excitation into δ* orbitals. The spectra were recorded for three different incident angles θ = 30, 50, 90. In principle, the intensity of π* resonance as a function of incident angle θ allows the determination of angle between the transition dipole moments (TDM) and the surface normal. The anisotropy of these π* resonances was used to determine the tilt angle and molecular orientation. However, the π* resonance shows very small dichroism, which could be due to mixed SAM. 80

90 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) 4.8 Discussion Common Feature For All TPn SAMs A most common feature found for all TPn SAMs, the well-known depressions (or pitholes) have been observed. These depressions were attributed to vacancy islands in the top most Au layer [35]. Their depth amounts to the height of a step on a Au(111) surface, i.e., 2.4 Å. A comparison of SAMs prepared at 298 K with those prepared at 333 K reveals a pronounced increase in the size and a corresponding decrease in the density of the depressions which has been explained by a Ostwald ripening process [205]. Moreover, the size of the ordered domains is found to be increase with preparation temperature. At 298 K, the size of the ordered domains is in the range of 5-30 nm. Depending on the length of the alkane spacer this size increases to nm at 333 K. The clean Au(111) surface exhibits a well-known herringbone reconstruction [134,206] which locally reduces the surface-symmetry from threefold to twofold. It has been observed in may cases that this reconstruction is lifted upon chemisorption of reactive species [207], which was not observed is this work Odd-Numbered TPn Monolayers The STM results revealed that organothiolate adlayers prepared from the TPn (n = 1-6) form high ordered molecular adlayers. The IR data obtained for odd-numbered TPn-SAMs prepared at 298 K and 333 K demonstrate that the molecules are oriented within the SAM with their molecular axis almost perpendicular to the Au surface. The corresponding STM results show the presence of a high degree of lateral order which can be described by an oblique unit cell with dimensions of (10.0Å 5.0Å) corresponding to a herringbone like arrangement of the terphenyl backbones in the (2 3 3) R30 unit cell. The unit cell contains of two inequivalent terphenyl molecules, with the sulfur atoms being located at a ( 3 3) R30 sublattice. The area occupied by a single molecule amounts to 21.6 Å 2, which is similar to the packing density within alkanethiols SAMs on Au substrates. Among the TPn monolayers with odd-numbered n, the TP1 samples prepared at 298 K created the most difficulties with regard to achieving high-resolution STM images. From eight samples prepared under the same conditions, molecular 81

91 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) resolution obtained only in one case. Even in this favorable case, the quality of the STM topography is rather poor, due to the presence of a high density of defects such as the depressions and domain boundaries. The high-resolution STM images were acquired in a much more straightforward fashion when the preparation of SAMs was carried out at 333 K. A detailed analysis of all available data revealed, however, that the only difference was a lower defect density for the SAMs prepared at higher temperature, the molecular arrangement was within the experimental resolution the same. A rough estimate based on the van der Waals dimensions of the terphenyl-backbone yields a tilt angle of 12.5 of the terphenyl-backbone with respect to the surface normal. This value is consistent with the IR data and with the angle determined in a previous NEXAFS investigation, where a tilt angle of 15±8 was reported for TP1 SAMs [181]. In case of the odd-numbered TPn SAMs no significant changes were observed when SAMs were prepared at elevated temperatures (333 K). The structure adopted by the odd-numbered TPn-SAMs is thus analogous to that of the corresponding BPn SAMs studied in previous work [124] Even-Numbered TPn Monolayers The IR data of TP2 SAMs prepared at room temperature (RT) are comparable to those observed for the odd-numbered TPn SAMs, thus also indicating a near-normal orientation of the terphenyl-backbones. The STM data revealed a (2 3 3) R30 structure for RT-samples. The structure is therefore analogous to that found for the odd-numbered case, see above. For TP2 SAMs prepared at higher temperatures (333 K) the intensity ratio in the IR data of the op-bands to the ip-par bands is comparable to that seen in their bulk spectra. These results reveal the presence of a large tilt-angle between the molecular axis and surface normal. At the same time the STM data demonstrate the presence of a different lateral packing, for the higher temperature a less densely packed c (5 3 3) structure is observed. High-resolution STM data for this phase reveal the presence of eight molecules in each unit cell, yielding an area of 27 Å 2 per molecule. Compared to the total area of 21.6 Å 2 for the (2 3 3) R30 phase seen for the odd-numbered TPn SAMs, this corresponds to a 25% lower packing density. 82

92 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) For SAMs made from the even-numbered TP4 and TP6 the IR results collected for samples prepared at 298 K reveal a significant tilt angle of the TP-backbones away from the surface normal, as seen for TP2 prepared at 333K. For both, TP4 and TP6, the STMdata demonstrate the presence of a c (5 3 3) structure with eight molecules per unit cell, as found for the even-numbered TPn s. In case of TP6 preparation of the SAMs at elevated temperatures (333 K) resulted in the formation of a new ( ) R30 structure characterized by an oblique unit cell with dimensions of (29.9 Å 10.0 Å). The size of this unit cell is about 20% larger compared to the unit cell of the c (5 3 3) phase and indicates a smaller packing density with a larger tilt angle of the molecular axis with respect to the surface normal. The area occupied by a single molecule amounts to 32.4 Å 2. The intermolecular spacing of about 7.5 Å is significantly larger that of a ( 3 3) lattice (5 Å). I propose that the c (5 3 3) structure observed for films prepared at lower temperatures transforms to high temperature ( ) R30 structure through a decrease of packing density. It is interesting to note that for biphenyl-based BP6 SAMs containing only 2 phenyl units the temperature had to be raised to 373 K to observe the c (5 3 3) ( ) R30 phase transition. Therefore, increasing the length of molecular structure of the adsorbate by an additional phenyl ring such as in the TP6 molecules apparently leads to a significant reduction of the threshold temperature needed for the formation of the ( ) R30 phase. One may speculate that this effect is due to the larger oligophenyl-oligophenyl interaction in the TP6 SAM, which stabilizes the ( ) R30 phase Effect of Aliphatic Part in Molecular Packing SAM made from an odd number of CH 2 groups in the alkyl chain of TPn a higher density and smaller till angle of the TP units with respect to the surface normal were found. This scenario was found to be reverse in the case of SAM made from an even number of CH 2 groups in the alkyl chain of TPn molecules. These significant difference in the molecular packing are in the close agreement with the previous reported data on a series of 83

93 Chapter Four Characterization of Terphenylalkanethiol SAMs on Au(111) 4,4 -biphenyl-thiol CH 3 -(C 6 H 4 ) 2 (CH 2 ) n SH (BPn, n= 1-6) [184]. It was found that both the orientation and the packing densities of the biphenyl moieties in the TPn films exhibits a pronounced odd-even variation with the length of aliphatic part. These changes in the packing density and molecular orientation in the even and odd numbered TPn adlayers were explained by a pronounced sulfur head group to adopt a SP 3 bonding configuration on Au(111). The SP 3 hybridization corresponding to Au-S-C bond angle of 104. The spatial orientation of the top most CH 2 -CH 2 segment of the aliphatic part undergoes changes by going from odd to even number of the CH 2 units, which results in very large tilt angle for later case resulting in the increase of molecular area Effect of the Solution Temperature All TPn SAMs, showed the well-known depressions (or pit-holes). These depressions were attributed to vacancy-islands in the top Au layer. These depressions are in the size of few nanometers and one monolayer in depth. The origin of these depressions are the result of a chemical erosion process accompanying the self-assembly of organic thin layer [35]. A comparison of SAMs prepared at 298 K with those prepared at 333 K reveals a pronounced increase in the size and a corresponding decrease in the density of the depressions attributed to thermal activation, which results in the molecular diffusion and improve the long range ordering in the SAMs Influence of Aromatic Part in Molecular Packing There are several factors which contribute the packing and stabilization of SAMs on Au(111) such as van der Waals chain-chain interactions, S-Au covalent bonding and end group-end group interactions. For alkanethiol monolayers on Au(111) the typical ( 3 3) structure result due to the S-Au interaction, which is dominant than the other energetics. In the case of TPn monolayers, significant and dominant intermolecular forces arise from the π system of neighbors aromatic molecules. When intermolecular chain interactions are dominant, the different adlayer structures can be formed. In contrast to alkanethiol SAMs, the saturated phase of TPn monolayers exhibits different structures. The formation of these different structures can be attributed to the rigidity within the terphenyl units which are responsible for herringbone motif. 84

94 Chapter Five Characterization of Thioacetate based SAMs on Au(111) Chapter Five Characterization of Dodecyl thioacetate SAMs on Au(111) In this chapter, the formation and structural characterization of dodecyl thioacetate (C12Ac) on Au(111) will be discussed in depth. In this chapter, novel strategy to control the structure of SAMs for the case of thioacetate, where the H atom in the SH unit is replaced by an acetyl group will be demonstrated. To quantify the unexpected effect of modified thiol by the thioacetate, the quality and structure of the resulting C12Ac SAMs, a detailed spectroscopic and microscopic characterization will be discussed in detail. 5.1 Introduction SAMs have generated considerable excitement among the scientists for well over decades. These organic molecular films in general and SAMs in particular have a wide variety of applications in the field of molecular technologies [8,208]. According to the early reports on of Allara and Nuzzo [8] on the adsorption of organic thiols on gold, various aliphatic thiols were studied [12,72,141,169]. Not only thiols but also organic disulfides adsorb on gold and silver surfaces [137,184]. The important aspect of self-assembly is to understand the chemical interactions between the underlying surface atoms and head groups of adsorbent molecules. Most often the monolayer formation are being utilized from organothiols, organodithiols, organothioacetates and organodithioacetates [42,209,210]. It has been reported that SAMs made from alkanethioacetate reveals the similar quality of SAMs as the one obtained from their corresponding thiols, possibly due to hydrolysis of thioacetate molecule in the solution followed by deposition onto gold substrates [42]. Contrary, it is impossible to grow the well defined self-assembled monolayer of biphenyl-based organodithioacetates [182]. 85

95 Chapter Five Characterization of Thioacetate based SAMs on Au(111) 5.2 Objective of Work Presented in this Chapter However, the adsorption mechanism for SAMs made from thioacetate on gold surfaces is still unclear due to some discrepancies in literature. To figure out the adsorption behavior of alkanethioacetate, the modification of the well know and studied model system dodecyl thiol [ ] to dodecyl thioacetate CH 3 (CH 2 ) 11 SCOCH 3 (C 12 SAc) carried out and will be emphasized in this chapter. In order to rule out any effects resulting from small contaminations by free thiols, the high purity thioacetate virtually free of any thiol by several consecutive fractional distillations were prepared. Note that in the past, trace amounts of thiols in the starting materials lead to wrong conclusions about the monolayer forming properties of dialkylsulfides [42, ]. We have found that in contrast to previously reported results the high purity dodecyl thioacetate do not form self-assembled monolayers with the same (2 3 3) structure as obtained from the corresponding thiols. The objective of this work was to understand better why this difference occurs between thioacetate and the corresponding thiol, and to find the explanation for a kinetic stabilization of the flat lying phase of thioacetates, which is formed by the separation of the acetyl group. Chart 1: Molecules used in this chapter C12 thiol C12 thioacetate SH SCOCH Adsorption of Dodecyl thioacetate SAMs on Au(111) In order to rule out the adsorption process of dodecyl thioacetate (C 12 SAc), the Au/mica substrates were immersed into 10-20µM (ethanol or dichloromethane) solution of dodecyl thioacetate at 298 K for 24 h and 48 h. The SAMs made from dodecanethiol (C 12 SH) were used as reference. After the allotted immersion time, the samples were carefully rinsed with the pure solvent used for SAMs formation to remove physisorbed overlayer and dried in the stream of nitrogen. 86

96 Chapter Five Characterization of Thioacetate based SAMs on Au(111) 5.4 Results Infrared Spectroscopy To understand the local molecular orientation and organizational structures present in dodecyl thioacetate (C 12 SAc) films, first the RAIR measurements were carried out on the well known and studied system, dodecanethiol (C 12 SH) as a reference system. Fig. 5.1 shows vibrational spectroscopy data measured in the C-H stretching region for the monolayer of C 12 SH thiol on poly crystalline gold surface. In the C 12 SAM spectra, the peaks at 2850, 2878, 2899, 2918, 2937, and 2964 cm -1 are attributed to the CH 2 symmetric stretching mode, the CH 3 symmetric stretching mode, the CH 2 asymmetric stretching mode, the CH 3 symmetric stretching mode (Fermi resonance), and the CH 3 asymmetric stretching mode, respectively [128] C 12 SH 1x10-3 Absorbance Wavenumber [cm -1 ] Figure 5.1: C-H vibrational region of the RAIR spectrum of the C 12 SH monolayers on gold surface formed from ethanolic solution for 24 h. 87

97 Chapter Five Characterization of Thioacetate based SAMs on Au(111) The table 4 lists the peak frequencies and mode assignments for the spectra shown in the fig Mode Description Measured [cm -1 ] Literature [cm -1 ] CH 2 sym (d + ) CH 3 sym (r + ) CH 2 sym FR (d + FR) CH 2 asym (d - ) CH 3 sym FR (r + FR) CH 3 asym (r - ) Table 4: The assignment of peaks of C-H vibrational regions obtained from C 12 SH monolayers on gold surface. The fabrication of SAMs was carried out by the immersion of gold substrates into the solutions of C 12 SH and C 12 SAc. The fig. 5.2 shows the gracing incidence IR spectra recorded for the monolayers derived from the corresponding thiols by using ethanol as a solvent. The spectra obtained of similarly prepared samples of these two substances are superimposed for comparison. The spectra obtained for C 12 SH SAMs closely resembled to the earlier reports on the same system [217]. The fig. 5.2 (a) displays the spectra recorded for C 12 SAc, significant different from those obtained for the C 12 SH. The pronounced shift and decrease in the intensities of adsorption peaks, indicates that much less material has adsorbed on the gold surface. To justify this observation and to support that this is not an effect for significant slower kinetics for C 12 SAc film formation, the additional experiments were carried out with very long immersion times (120 h), resulting in virtually no change in the resulting spectra for both thiol and thioacetate as shown in figure 5.2 (b). Another set of measurements were carried out, by using different solvent to see whether this is really an intrinsic effect of C 12 SAc film. The fig. 5.2 (c) displays the IR spectra obtained for C 12 SH and C 12 SAc films prepared by using dichloromethane as a solvent. Interestingly, it has been observed that spectra recorded for C 12 SAc are clearly different from those obtained for the C 12 SH, which indicate the less adsorption of C 12 SAc and presence of a saturated hydrocarbon chains oriented parallel to the gold substrate. It was observed that the films deposited from dichloromethane (DCM) consist either of much 88

98 Chapter Five Characterization of Thioacetate based SAMs on Au(111) less adsorbed material (C 12 SAc) or more disordered (C 12 SH) than the ones generated from ethanolic solution. Therefore, further experiments were carried out by using ethanol as a solvent for SAMs formation. According to the surface selection rules on metallic substrates, only those vibrations having a component with a transition dipole moment (TDM) normal to the surface plane absorb the IR radiation and can be seen in the spectra. It has been already documented in detail that the order and if applicable the tilt angle of the molecules in the films can be determined from the relative intensity of the CH 3 and CH 2 bands because of their differently oriented TDMs [126,128]. While a tilt angle determination for the thiolderived films was possible, an obvious change in the TDMs of the vibrations for the thioacetate made this impossible. This kind of changes in the vibrational spectra has been described earlier for molecules lying flat on metal surfaces and is caused by the electronic coupling to the electron gas of the metal [218]. C 12 SAc C 12 SH Figure 5.2: Comparison of the IR spectra of C 12 SH and C 12 SAc monolayers on Au(111). (a,b) SAMs of C12SH and C 12 SAc on gold surfaces from ethanolic solution for allotted immersion time. (c) SAMs of C12SH and C12SAc on Au(111) from dichloromethane for 24 h. 89

99 Chapter Five Characterization of Thioacetate based SAMs on Au(111) STM To figure out the surface morphology and molecular ordering in the monolayer of C 12 SAc additional experiments were carried out by using high-resolution STM. The summary of STM results obtained for C 12 SAc depicted in the fig The large scale constant-current STM micrographs shown in fig. 5.3 (a and b) recorded for Au/mica substrates, which have been immersed into the μm ethanolic solution of C 12 SH and C 12 SAc for 48 hours at 298 K, respectively. At this lengths scale no major differences were observed, the atomically flat terraces of the gold substrate decorated with the small circular depressions (lower in the density for thioacetate derived films), which have been identified as vacancy islands or etch pits [100]. The high-resolution STM micrograph obtained for C 12 SH shows the saturated and densely packed (2 3 3) structure (not shown) commonly found for the upright standing phase found for alkanethiol-based SAMs [212,213]. While the high-resolution constantcurrent STM data obtained for the monolayers derived from those of the thioacetate clearly show the presence of two different phases. The dominant one is a striped phase (observed for first time) in which alkyl chains oriented parallel to gold surface and thus, results in the formation of three different rotational domains as shown in fig. 5.3 (c). The high-resolution constant-current STM micrograph shown in fig. 5.3 (d) clearly demonstrate the presence of a striped phase which is a typical signature of low density, intermediate SAMs phases [49,219,220]. The line scan along the lines A and B shown in fig. 5.3 (e and f) reveals the rectangular unit cell with a length of long sides equal to Å and that of the shorter side amounting to 5 Å. These values are in the close agreement with the length of extended dodecanethiolate molecules, suggesting straight, flat-lying molecules in a parallel order. The distance between the parallel molecules, as shown by the line scan in fig. 5.3 (e), found to be 5 Å, suggesting a rectangular ( (p 2 3) unit cell containing two molecules, with the larger value being predominantly determined by the length of the molecule. It should be mentioned that in case of an orientation of the molecules parallel to the longer vector (thus being oriented perpendicular to the rows of neighboring sulfur atoms) the value of p should be 6, resulting in a calculated unit-cell length of 17.3 Å. 90

100 Chapter Five Characterization of Thioacetate based SAMs on Au(111) Figure 5.3: (a) Constant-current STM micrographs showing the gold substrate after immersion into a µm ethanolic solution of C 12 SH at 298 K for 48 h. (b-d) Constant-current STM micrographs showing the gold substrate after immersion into a µm ethanolic solution of C 12 SAc at 298 K for 48 h. the arrows in (c) shows the direction of flat-lying phase. Line profile along the lines A and B shown in (e, f). Tunneling parameters: (a) U t = 600 mv, I t = 70 pa, (b) U t = 650 mv, I t = 80 pa. (c) U t = 1000 mv, I t = 65 pa. (d) U t = 1000 mv, I t = 65 pa. 91

101 Chapter Five Characterization of Thioacetate based SAMs on Au(111) Figure 5.4 show the constant-current STM data obtained for Au/mica substrates, which have been immersed into the μm ethanolic solution of C12SAc for 48 hours at 298 K. A close inspection of the STM data reveals that smaller and brighter islands with a more densely packed phase exist in between the areas of flat-lying phase. These islands were found to be localized at the domain boundaries of the striped phase or near surface defects (in particular step edges). Figure 5.4 (b) shows the high-resolution constantcurrent STM micrograph, clearly demonstrating the well known densely packed phase of the alkanethiolate monolayers. The dimensions of the unit cell were determined from the height-profiles along the lines A and B labeled in fig 5.4 (b) and amount to a= 8.5±0.2 Å and b= 10±0.4 Å (see figure 5.4 (b-d) corresponding to about 3 and 2 3 times the lattice vectors of the substrate. These line scans verify the intermolecular distances of the typical (2 3 3) saturated phase, shown as an inset in fig. 4 forming rectangular unit cell. Figure 5.4: Constant-current STM data for the upright phase in the monolayer obtained from C 12 SAc solution. The islands of limited size are shown in figure 4 (a). The line scans in (c) and (d) verify the intermolecular distance of the typical (2 3 3) structure as shown in inset of the figure 4 (b). Tunneling parameters: (a) U t = 800 mv, I t =95 pa; (b) U t = 1000 mv, I t = 75 pa. 92

102 Chapter Five Characterization of Thioacetate based SAMs on Au(111) XPS X-ray photoelectron spectroscopy is a capable method to selectively identify atomic species and elemental composition on the surface. In fig 5.5 summary of the XPS data obtained for SAMs made from the C 12 SH and C 12 SAc are presented. The energy scales of all spectra were referenced to the Au 4f 7/2 peak located at a binding energy of 84.0 ev. The certain amount of bean damage has occurred and considered while analyzing the data. The data obtained for Au 4f core-level lines were found to be more intense for the monolayer of C 12 SAc than for C 12 SH. The difference in these peak intensities reveals that the adlayers of C 12 SAc films are considerably thinner. In the case of C 1s spectra obtained for both films the significant change in the peak intensities along with the peak shift has been observed, which demonstrate that the C 1s spectra exhibit much lower signal intensity for the monolayers deposited from the thioacetate. The recorded C 1s binding obtained for thioacetate adlayers is about 0.4 ev, which is lower Figure 5.5: Summary of XP spectra recorded for polycrystalline gold substrates showing the carbon 1s, gold 4f, oxygen 1s region and sulfur 2p region for the monolayer of both thioacetate (C 12 SAc) and thiol (C 12 SH), formed by the immersion for 24 h into ethanol solution. 93

103 Chapter Five Characterization of Thioacetate based SAMs on Au(111) than the thiol-derived monolayers, which has been documented as flat-lying molecules on the surface [218]. The S 2p data show that the only sulfur bound species with a binding energy ev has been observed, which is consistent with the formation of thiolate upon adsorption from solution [221]. In the case of O 1s region which indicate only the trace amount of the oxygen can be seen from the adlayers made from thiol, whereas, the adlayers made from thioacetate contain about one oxygen atom for every three molecules. Since, this rule out to be different from the adsorption of intact thioacetate molecules (for which a ratio of 1:1 would be expected). On the basis of this observation, it can be conclude that the oxygen atoms rather stem from the oxidation of the monolayer after formation during manipulation and transfer into the XPS set-up. It has been reported in the past that the sulfur atoms of flat-lying thiolate molecules are rather prone to oxidation by atmospheric oxygen [49,131] Re-immersion of C12Sac-SAMs into Thiol Solution SAMs of dodecyl thioacetate (C 12 SAc) form the stable flat-lying phase in which molecular axis align parallel to the gold substrates even after the prolonged immersion times for 48 hours. In order to quantify this hypothesis and to understand whether inhibition for the addition of the further adsorbate molecules is a general phenomenon or the intrinsic property associated to thioacetate SAMs, some of the test experiments were carried out. An important test experiment for this hypothesis is the immersion of preassembled C 12 SAc SAMs that exhibit the striped phase into the C 12 SH solution. Surprisingly, it has been observed that slightly increase in the intensities for absorption band of C-H vibrational region occurs when C 12 SAc SAMs were re-immersed into the solution C 12 SH solution for the period of 24 h as shown in fig 5.6. The IR spectra obtained for this two step process of SAMs formation looks almost similar to densely packed saturated C 12 thiolate SAMs. The significantly lower intensity of adsorption band in the C 12 SAc derived monolayers clearly hint for a much lower surface coverage, which indicate the presence of molecular backbone oriented parallel to the gold substrates. The macroscopic properties of these re-immersed SAMs behave similar to those obtained for C 12 SH monolayers; show the contact angle of 102 indicates the formation of well order SAMs (data not shown) with almost upright oriented molecules [131]. 94

104 Chapter Five Characterization of Thioacetate based SAMs on Au(111) Figure 5.6: C-H vibrational region of the IRRA spectra obtained for the monolayers of C 12 SAc (solid green), C 12 SH (solid red), as well as of the C 12 SAc-derived monolayer (solid black) after re-immersion into C 12 SH solution. 95

105 Chapter Five Characterization of Thioacetate based SAMs on Au(111) 5.5 Structural Model On the basis of all the set of experimental data obtained for the SAMs of C12SAc, it can be concluded that in contrast to the C 12 SH SAMs which form upright standing molecules, the C 12 SAc do not form a SAMs which exhibit upright oriented molecular backbone. The clear and conclusive evidence for the presence of such kinetically stable striped phase comes from the STM data, which clearly indicate the stripes with an average distance of Å and the nearest neighbor distance amount to be 5 Å, forming the (p 2 3) structure as shown in fig This value agrees well to the lengths of the aliphatic hydrocarbon chain in the C 12 SAc SAMs and also corresponds very well to the results obtained by Poirier et al. obtained for decanethiol on Au(111) [97]. The densely packed phases (appearing brighter in the STM micrographs) are always localized at the domain-boundaries of the striped phase, or near the surface defects forming the saturated upright (2 3 3) depicted in left side of fig Figure 5.7: Schematic model of the surface adlayer of C12SAc. The coexistence of dominant flat-lying (p 2 3) and standing up (2 3 3) phases (top view). At domain boundaries or defects the (2 3 3) structure with upright oriented molecules together with the kinetically stable flat-lying phase for clarity presented as shown in the inset (side view). 96

106 Chapter Five Characterization of Thioacetate based SAMs on Au(111) 5.6 Discussion In contrast to C 12 SH SAMs which form the saturated, densely packed and upright standing molecular phase, the monolayer of the C 12 SAc do not form an almost upright orientated alkanethiolate monolayers. Instead, the thioacetate SAMs form a highly ordered stripped phase with flat-lying molecules antiparalell to each other, a structure that so far has not been reported. Its has been observed that the surface is covered by the so called flat lying phase which is in close agreement with the fact that in the XPS data the C 1s core-level is shifted by 1.6 ev to lower binding energy, which strongly indicates the presence of alkyl chains adsorbed on the metal surface. In earlier work this effect has been demonstrated in case of mono- and multilayer of alkanes adsorbed on Cu surface and have been explained by final state screening effects, which are stronger for carbon atoms in close proximity to metal surface [218]. Interestingly, the trace amount of the oxygen can be found from the adlayers of thiol, whereas, the adlayers made from thioacetate contain about one oxygen atom for every three molecules. Since, this rule out to be different from the adsorption of intact thioacetate molecules (for which a ratio of 1:1 would be expected). On the basis of this observation, it can be conclude that the oxygen atoms rather stem from the oxidation of the monolayer after formation during manipulation and transfer into the XPS set-up. The IR spectra also reveal significant differences relative to those obtained for densely packed thiolate SAMs, which also indicate the presence of a saturated hydrocarbon chain with its C-C-C backbone oriented parallel to the substrate as presented in fig. 2. It has been observed that IR spectra recorded for C 12 SAc are clearly different from those obtained for the C 12 SH, which indicating towards the less adsorption of and presence of a saturated hydrocarbon chains oriented parallel to the gold substrate. IR data recorded after the re-immersion of pre-assembled SAMs of C 12 SAc into the C 12 SH solution are basically indistinguishable from the corresponding data recorded for based SAMs. Since, for the corresponding alkanethiol much less space is needed for getting the sulfur in contact with the gold. It has been observed that in the case of two step adsorption process, where first a highly disordered film is formed and this is followed by significantly slower second step where the orientational order is introduced; re-immersion into the solutions of alkanethiols generally results in the formation of upright oriented films. 97

107 Chapter Five Characterization of Thioacetate based SAMs on Au(111) The STM data clearly reveals that the stripes with an average distance of Å, forming the (p 2 3) unit cell. This value corresponds very well to the lengths of the hydrocarbon chain in the C 12 SAc molecule, supported by the previously documented results obtained for the monolayer of decanethiol on Au(111). The fact that the (2 3 3) islands (appearing higher in the STM micrographs) are always localized at the domainboundaries of the striped phase or near surface defects (in particular step edges) suggests that the transformation of the striped-phase containing flat-lying molecules into the dense, upright (2 3 3) phase is significantly hindered. It was concluded that the latter phase should be the thermodynamically more stable, exhibiting kinetic limitation hindering the formation of adsorbed thiolates from the thioacetate. When this coverage is reached, molecules interacting with the surface will first have to find small areas of the bare gold surface where the sulfur of the thioacetate group can get closely enough to the gold surface to form a chemical bond to the substrate and to break the chemical bond to the acetate group. We propose that the further adsorption on the surface is strongly hindered by the striped phase. Such a kinetic limitation is strongly supported by a closer investigation of the previously reported STM data [222]. It was observed that prolonged immersions in the C 12 SAc solution, the evolution of small islands developed which can be identified as regions with upright orientated molecules. Although, the area of these islands are very small, limiting the spectroscopic characterization with IR, NEXAFS or XPS. The high resolution STM data clearly allow an assignment to areas with upright ordered molecules. It was very interesting to note that these small patches of upright orientated molecules were only observed at defects, e.g. at domain boundaries between perfect areas of the striped phase as presented in the fig. 4. After the striped phase has formed the solvated C 12 SAc molecules can only react with the gold surface at defects like etch pits, domain boundaries and possibly step edges. This explanation based on a kinetic stabilization of the flat lying phase is strongly supported by the experiments where C 12 SAc based SAMs were immersed in a solution of the corresponding alkanethiol, C 12 SH. 98

108 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) Chapter Six Anchoring and Ordering in Purely Aromatic Self-Assembled Monolayers on Au(111) This chapter comprises of two parts. In the first part, formation and the detailed structural characterization of simplest and differently anchored SAMs of benzenethiol (BT) and benzeneselenol (BSe) on Au(111) will be discussed. The diversity of these differently anchored molecular adlayers will be discussed in term of the substrate interaction. Whereas, the second part will emphasize on the detailed structural characterization of fully conjugated aromatic anthracene-2-selenol (AntSe) on Au(111). The growth, precise identification for the saturated molecular adlayers structures will be emphasized and explained with the body of data obtained by spectroscopic and microscopic techniques. 6.1 Introduction Organic materials have recently gained a huge impact in materials science due to the adjustability of their properties by synthetic means. In the area of interface and surface science covalently bound SAMs became of significant importance [98]. In addition to the importance and their wide potential applications, the conjugated molecules are useful for future molecular electronics applications because they are considered to be electrically conductive [22,31,60,204]. The essential requirement for such application is to precisely control of the molecular arrangement as well as a high degree of the molecular ordering, which is more difficult to achieve for aromatic SAMs compared to the widely used aliphatic organothiol-based SAMs [51,73]. It is therefore important to control the molecular ordering and arrangement during the SAM formation. In past the improvement in the structural ordering of aromatic SAMs have been reported e.g. the introduction of flexible alkyl spacer between the anchoring group and aromatic molecular backbone [29,33], annealing the post deposited SAMs to activate the polymorphism [56,58], or the alternative way to generate the selenols-based SAMs [223,224]. Infact, such spacer groups enhance the flexibility and provide additional degree of freedom to the molecules, which result in the long range ordering, but at the same time additional complexity 99

109 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) observed. Since the molecular arrangement in such SAMs depends sensitively on the number of alkyl units and reveals pronounced odd-even effect [29,57,224]. In the light of results presented in chapter four, it has been observed that for terphenyl-substituted alkanethiols, the surface morphology and adlayer structures of the corresponding SAMs depends upon the length of the alkyl chain as well as the temperature used for their formation. BT BSe SH SeH O Se AntSe Chart 2: Molecular structure of benzenethiol (BT), benzeneselenol (BSe) and anthracene-2-selenolate (AntSe) To explore the anchoring and ordering in depth, this study will be focused on the comparison of the aromatic SAMs of benzenethiol (BT), benzeneselenol (BSe) and anthracene-2-selenolate (AntSe) on Au(111) with a particular emphasize on ordering and microstructure (see chart 1). Although, numerous studies containing controversial results have already been reported on BT, BSe SAMs [225,226]. This controversy demonstrates that even for such putative simple aromatic SAMs the mechanisms of film formation are not well understood. The detailed picture about the film formation and properties of such SAMs is still missing. Theoretically, large conductance expected for selenium based compounds as compared to the sulfur [227], their use as a selenols based SAMs appears to be particular promising in the field of molecular electronics but so far has been barely investigated. 100

110 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) 6.2 Objective of the Work Presented in this Chapter To study the adsorption process of BT, BSe, AntSe. To explore the effect of different anchoring. To examine the influence of different anchoring on the molecular arrangement. The influence of additional phenyl groups in the molecular backbone (BSe and AntSe) To study the monolayer growth of the AntSe. To precisely identify the molecular adlayer structures. 6.3 Results STM of Benzenethiol SAMs Figure 6.1(a) shows a large-scale constant current STM image acquired for an Au(111) substrate, which has been immersed at least for 12 h in 1mM solution of BT in ethanol at 298 K. The STM micrograph reveals the characteristic triangular shaped islands, which reflect the close packed direction <110> of the underneath gold substrates, together with the presence of characteristic vacancy island (also referred to as etch-pits) with a depth of about 2.4 Å and typical diameters of 5-10 nm (indicated by black arrows in fig 6.1 (a). Their depth corresponds to the interlayer spacing of (111) oriented gold planes and thus, indicates formation of mono-atomic substrate island upon the SAMs formation. Such morphology has been observed upon the adsorption of alkanethiols on Au(111) [35,100]. Although the BT SAM reveals only a poor long range ordering with rather small domains exhibiting the lateral dimension of typically less than 15 nm. The acquisition of high resolution data turn out to be difficult. Even then molecular resolution was obtained once out of five samples. A typical high resolution STM image presented in the fig. 6.1(c) which clearly shows the individual molecules forming an oblique unit cell. The dimension of the unit cell were determined from the height profile along lines A and B labeled in fig. 6.1 (c) and amount to a = 1.65 ± 0.07 nm and b = 1.05 ± 0.07 nm and angle between these lines were found to be 84 ± 3. Using the van-der-walls dimension of 101

111 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) 7.95Å 5.98Å 3.25Å derived from the DFT calculation 1 and considering the average tilt angle of 36 obtained for the NEXAFS data (not shown) a projected molecular area of 38.5 Å 2 is calculated. This value agrees well with the experimental data and thus suggests that the BT monolayer form a close packing of highly tilted molecules. Furthermore, a comparison between the characteristic triangular islands presented in the large scale image fig. 6.1 (a), which reflect the close packed <110> direction of the substrate, allow us to assign the shorter vector aligned along the < 112 > azimuth direction. Thus the molecular adlayer can be well described by a ( ) monolayer structure. A close inspection of high resolution STM image reveals the presence of four molecules within the unit cell as indicated in the inset in fig. 6.1 (c). It has been observed that in each unit cell one molecule appears brighter than the remaining three suggesting either different adsorption geometry or the different adsorption sites on the Au(111) substrate. Furthermore, all the attempt to image the diluted phase of BT SAMs were failed and revealed rather ill defined and rough surface (data not shown), which has been recently documented for the case of anthracene-2-thiol SAM on Au(111) [53]. 1 DFT calculations using the Gaussian 98 package with a B3LYP/6-311+G(2d,2p) basis set (by D. Käfer). 102

112 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) Figure 6.1: Summary of constant-current STM data obtained for a BT-SAM. (a) The large scale image shows the atomically flat terraces of gold surface with the close packed step edges. (b) The black arrows indicate the different rotational domain of adlayer. (c) High-resolution STM image reveals the presence of four molecules in the unit cell as indicated in the inset. (d) Cross-sectional height profile along the line A and B labeled in (c), revealing the corrugation periodicity. Tunneling parameters: (a-c) U t = -1.0 V, I t = 0.35 na. 103

113 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) Structural Model of BT SAMs A schematic structural model explaining the ( ) superlattice is presented in fig In this model the protrusions seen in the STM images are assigned to individual BT molecules. According to the van-der-waals dimension of BT molecules the occupation of different adsorption sites is also required for the BT SAM. The variation in the brightness of the protrusions arises from the multiple adsorption sites, such as near top, bridge and hollow sites. The STM data demonstrate that in each unit cell one molecule appears brighter than the remaining three suggesting either different adsorption geometry or the different adsorption sites on the Au(111) substrate which correspond to a molecular packing density of 39.7 Å 2. Figure 6.2: Top view of the structural model for BT SAMs on Au(111). The unit cell of adlayer is marked by the large oblique box. The unit cell of the Au(111) is marked by the small oblique box. 104

114 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) STM of Benzeneselenol SAMs Figure 6.3 (a) shows a large-scale constant current STM image acquired for an Au(111) substrate, which has been immersed at least for 12 h in 1mM solution of BSe in ethanol at 298 K. Interestingly instead of etch pits, the monoatomic islands with typical diameter of nm has been observed which suggests the distinct difference in the surface strain on the gold surface upon the formation of SAMs from different anchoring (selenol) group. A similar surface morphology has also been observed previously for a BSe monolayer as well as for other selenol-based aromatic SAMs [223,228]. It has been observed that in contrary to BT SAMs the significant enhanced long range ordering BSe- SAMs which typical domain size of more than 50 nm, which reveal the distinct stacking faults as indicated in by dashed arrow in fig. 6.3 (b). High resolution STM data as shown in fig. 6.3 (c) clearly reveal adlayer arrangement. The dimension of the unit cell were determined from the height profile along the lines labeled in (c) and amount to a = 1.31 ± 0.07 nm and b = 1.69 ± 0.07 nm which form an angle of 80 ± 3. The close inspection of the high resolution STM data reveal that the long diagonal of the unit cell is aligned along the <1 10 > direction as shown in fig. 6.3 (a) and (c). Thus the saturated BSe SAMs can be well described by a commensurate ( ) structure which contains the eight molecules within the unit cell and area occupied by single molecule corresponds to 28.8 Å 2. In the previous study the adlayer structure has been reported for BSe SAM but no molecular structure within the unit cell could be resolved [228] which is in contrast to the present identified monolayer structure, which was routinely observed. Moreover, corresponding line scans reveals a distinctly smaller corrugation for the molecules within the unit cell thus indicating the presence of different adsorption sites or local arrangements as compared to the molecules at the corners of the unit cell. Furthermore, to image the diluted phase of BSe-SAMs were failed similar to the BT SAMs, demonstrate that diluted phase are prone to oxidation [131]. 105

115 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) Figure 6.3: Summary of constant-current STM data obtained for a BSe SAM. (a) The large scale image shows the atomically flat terraces of gold surface with the close packed step edges. (b) Black arrows indicates the distinct stacking faults in the large-range ordered domains (c) High-resolution STM image indicates the presence of eight molecules in the unit cell as shown in the inset. (d) Cross-sectional height profile along the line 1, 2 and 3 labeled in (c), revealing the corrugation periodicity. Tunneling parameters: (a-c) U t = -1.0 V, I t = 0.67 na. 106

116 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) Structural Model of BSe SAMs On the basis of STM data obtained for the monolayer of BSe, a schematic model explaining the commensurate ( ) structure was proposed. The model is presented in the fig In this model the BSe molecules are adsorbed as selenolate on gold surface. The unit cell consists of eight molecules corresponding to molecular packing density of the 28.8 Å 2. The selenium atoms are proposed to be adsorbed at different adsorption sites of Au(111) substrates. In this model the size of the molecules and the unit cell demonstrate that this packing density is only achieved if the different adsorption sites of the gold substrate are considered as shown in the fig This structural detail is in the close agreement with the TDS data (not shown) which reflect the presence of differently bound selenolate species [59]. Figure 6.4: Top view of the structural model for BT SAMs on Au(111). The unit cell of adlayer is marked by the large oblique box. The unit cell of the Au(111) is marked by the small oblique box. 107

117 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) 6.4 Monolayer of Anthracene-2-Selenoate (AntSe) on Au(111) Fabrication of AntSeSAMs To prevent the formation of the insoluble diselinides R-Se-Se-R, the selenols group was protected by the acetyl protecting group. During the formation of SAMs, some external agent is normally requirement of the cleavage of Se and acetate functional group. The experimental conditions of self-assembly were adjusted to optimize the growth and formation of the ASe SAMs with or without deprotection. The fabrication of the AntSe monolayer followed by the deprotection was carried out by immersing the gold substrates into 0.1 μm/l ethanolic solution of AntSe at 273 K together with 1.0 mm ethanolic solution of ammonium hydroxide. Acetyl protected selenols were deprotected during the formation of the SAMs. After the allotted immersion times, the samples were efficiently rinsed with the corresponding solvent used for deposition and dried in a stream of nitrogen to remove physisorbed overlayer. Self-Assembled Monolayers of AntSe formed on the gold surface in a 0.1μM ethanolic solution without using the deprotection of the acetyl protected group will be later discussed. 6.5 Microscopic Results Growth of AntSe SAMs Figure 6.5 (a-f) shows the summary of the constant-current STM data obtained for the AntSe SAMs on Au(111) substrates by using the different immersion times into the ethanolic solution of AntSe together with the deprotecting agent (NH 4 OH). Even at a very less surface coverage, the growth of needle like islands were observed as indicated by black arrows shown in the fig. 6.5 (a-b), the further increase occurs in their size and density by increasing the immersion time of the substrates into the AntSe and NH 4 OH solution as shown in the fig. 6.5 (c-d). The lateral dimensions of these islands were amount to be nm. The high resolution STM data reveal that these islands exhibit the certain periodicity, consist of paired rows and similar to densely packed monolayer of AntSe (will be disscued later), in contrast to the low surface converge of the 108

118 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) Figure 6.5: Summary of the constant-current STM data obtained for the monolayer of AntSe by using the different immersion times (5 mins, 1hour, 1day) by using the deprotecting agent. The growth of needle like islands was observed which volumize with the immersion time indicated by black arrows in (d). The density of the contamination also increased with immersion times as shown by green arrows. Tunneling parameters: (a-c) U t = -0.2 V, I t = na. 109

119 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) Figure 6.6: (a) Constant-current STM images for a film prepared by the immersion of gold substrate into the ethanolic solution of AntSe, show growth of needle like islands revealing the certain periodicity in equally spaced rows. (b) 3-D view of needle like structures. Tunneling parameters: (a-c) U t = -0.2 V, I t = na. monolayers of alkanethiol and oligophenyle based SAMS [54,97]. The islands exhibit certain periodicity in the regularly spaced periodic rows shown as in fig Surprisingly, the tiny brighter spots appeared as a byproduct due to deprotecting agent and acetate group that seemed to volumize with immersion times indicated by the green arrows. Figure 6.5 (e-f) depicts the high density of contaminations which may arise from the acetate and deprotecting group yielding to the ammonium acetate indicated by green arrows and the small area of AntSe SAMs (black arrows) free from contamination for the samples prepared using an immersion time of 24 h. Since the AntSe molecules are not completely soluble in the ethanol which results in the formation of such a stable contaminants on the surface even under the rigorously rinsing. For further characterization of AntSe SAMs the samples were prepared without using the deprotecting agent to reduce the contamination on the surface. To avoid such problems another strategy was developed which will be disused in the following section. 110

120 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) Growth of AntSe SAMs by Gently Heating To minimize the effect of the strong physisorbed acetate functional group, the direct adsorption of AntSe followed by gently heating in vacuum were employed. In case of the direct adsorption of the acetyl-terminated AntSe monolayers, the STM results confirmed that the SAMs were similar in their composition to those generated by the using the deprotecting group. Only the difference was observed for the reduction in the density of island in the case of former one. Figure 6.6 (a-f) shows the summary of the constant-current STM data obtained for the AntSe SAMs on Au(111) substrates by using the different immersion times into the ethanolic solution of AntSe without using the deprotecting agent. After the allotted immersion times the substrates were efficiently rinsed with the solvent used for deposition and dried in a stream of nitrogen to remove physisorbed overlayers, later followed by gently annealing in the vacuum. Figure 6.6 (a-b) shows the STM images recorded for AntSe SAMs prepared by using an immersion time of 5 minutes in 0.1 µm solution at 273 K followed by gently annealing in vacuum for half an hour. The STM data clearly shows the improvement in the surface morphology by the reduction of the density of brighter spot (contamination) together with the evolution of needle like islands. The growth and size of these islands start to increase for the samples prepared for longer immersion time (1 hour) which later followed by gently annealing as shown in the fig. 6.6 (c-d). A closer inspection of STM data reveals that on the atomically flat terraces of Au(111) surface, the growth of these island exhibit certain direction and rotated by 60 with respect to each other. Figure 6.6 (e) and (f) show a large scale constant-current STM data recorded for AntSe SAMs prepared by using an immersion time of 3 hours in 0.1 µm solution at 273 K followed by gently annealing at 350 K in vacuum for half an hour. The STM data clearly demonstrated that density and size of these island increases. The growth of these islands exhibit the nearest-neighbor < 112 > direction of Au(111) surface, rotated by 60 or 120 with respect to each other as shown in the fig. 6.6 (e). The high resolution STM data shown as an inset reveals that regular array for paired rows. A close inspection of the STM clearly demonstrates the saturated phase of adlayer structure which will be discussed later. 111

121 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) Figure 6.7: Summary of the constant-current STM data obtained for the monolayer of AntSe by using the different immersion times (5 mins, 1hour,3 hours) by using the deprotecting agent. The growth of needle like islands was observed which volumize with the immersion time indicated by black arrows and shown as inset in (d). The density of the contamination also increased with immersion time as shown by green arrows. Tunneling parameters: U t = -0.2 V, I t = na. 112

122 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) Saturated Phase of AntSe SAMs Figure 6.8 (a-d) shows the summary of the STM data recorded for AntSe SAMs prepared by using an immersion time of 24 hours in 0.1 µm solution at 273 K followed by gently annealing in vacuum for half an hour. Figure 6.8 (a) shows the atomically flat terraces of Au(111) substrate which were separated by monoatomic step separated with the height of 2.4 Å. Interestingly, no vacancy depressions or ad-islands at the gold surface (also referred to as etch-pits) are formed in contrast to thiolate SAMs being attributed to a stress release of the gold surface [51]. The STM image reveals characteristic stripes of closely packed molecules along the < 112 > azimuth directions of the Au(111) substrate as shown in fig. 6.8 (b). This arrangement is rather robust and is not disturbed by point defects thus leading to extended domains with lateral dimensions of more than 50 nm. The extraordinary quality of high resolution STM micrograph depicted in fig. 6.8 (c) clearly reveals the characteristic herringbone arrangement of neighboring molecules forming and angle of ϑ = 48 ± 3, which resembles the herringbone packing of anthracene molecules in the (001)-planes of the bulk phase (50 ) [139]. The dimensions of the unit cell marked in fig. 6.8 (c) were determined from the height profile along the lines A and B labeled and amount to a = 4.9 ± 0.25 Å and b = ± 0.25 Å, corresponding to a commensurate ( 3 4)rect structure consisting of two molecules per unit cell, yielding a molecular area of 28.8 Å 2 which is similar to the molecular packing adopted in anthracene crystals (25.6 Å 2 ) [139]. In order to justify this adlayer structure of AntSe SAMs the LEED measurement were carried out. The summary of LEED data presented in fig. 6.8 (f-h) showing that some diffraction spots reveal only low intensities due to out of phase conditions and can be traced by tuning the incident beam energy. Moreover, the sharpness of the diffraction spots reflects a pronounced long range ordering of the SAM. This long range order could be verified using STM measurements as demonstrated in fig. 6.8 (b). From the position of all observed diffraction spots relative to the first order substrate related diffraction (indicated by dashed hexagon in fig. 6.8 (f, g) the present structure can be unambiguously identified as a commensurate ( 3 4)rect structure. 113

123 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) Figure 6.8: Summary of the constant-current STM data obtained under ambient conditions for the saturated AntSe SAMs on Au(111). (a) The large scale atomically flat gold terraces decorated by AntSe SAMs. Pronounced long range ordering depicted in (b). High resolution data reveal the herringbone packing of the molecules shown in (c). Cross-sectional height profile along the line A and B labeled in (c) and presented in (d), revealing the corrugation periodicity. Tunneling parameters: (a-c) U t = -0.2 V, I t = na. The measured LEED patterns (Measured by D. Käfer) (f) (E=75 ev) and (g) (99 ev) are compared with the reciprocal lattice of a ( 3 4) rect structure including rotational domains in (h). The dashed hexagons represent the first order diffraction of a clean Au(111) substrate [264]. 114

124 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) Structural Model Based on the results obtain from the STM, LEED and NEXAFS the rectangular unit cell is projected on the gold surface. Using the precise unit cell dimensions of Å 5.0 Å, the unit cell can be unambiguously identified as a commensurate ( 3 4) rect structure. By considering the two molecules per unit cell as evident from the STM data results in the molecular area of 28.8 Å 2 which is similar to the molecular packing adopted in the (001) planes of anthracene crystal 25.6 Å 2 [139]. Figure 6.9: Top view of the ( 3 4) rect structural model for AntSe on Au(111). The unit cell is marked by the rectangular box. The side view depicted at right panel showing herringbone motive of anthracene in bulk. 115

125 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) 6.6 Spectroscopic Results RAIRS and XPS Since, the STM is limited to qualitative analysis of AntSe SAMs, further characterization were carried out by using the multidimensional spectroscopic techniques; IRRAS, XPS and NEXAFS. Figure 6.10 shows the RAIRS spectrum of freshly prepared and thoroughly well-rinsed AntSe-SAMs on gold reveals a number of distinct peaks in the finger print region between 800 cm -1 and 1600 cm -1. Based on the theoretical analysis (see below) they have been identified as C-C stretching and rocking vibrations (at 1611, 1581, 1512 and 1462 cm -1 ), C-H rocking and scissoring modes (at 1369, 1255, 1183, 1091 and 1038 cm -1 ), and (out-of-plane) C-H wagging modes of the aromatic rings (at 828 and 805 cm -1 ). Moreover, in addition to the C-H stretching vibration region at about 3050 cm -1 two further modes at 2930 cm -1 (CH3 vibration) and other at 1716 cm -1 (C=O vibration) were Figure 6.10: Comparison of a) RAIRS data and b) XPS data recorded for a freshly prepared AntSe-SAM top curve and for the same film after gently annealing at 330 K in vacuum, top blue and bottom black curve, respectively [264]. (Measured by D. Käfer) observed which are associated to an aromatic acetate and thus indicate the presence of remaining acetate protection groups. This assignment is further corroborated by a distinct 116

126 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) oxygen peak observed in the corresponding XPS spectra as shown in the right panel of fig Whereas thorough rinsing does not completely remove this acetate-related signal it disappeared completely upon gently heating the film at 330 K under vacuum conditions as demonstrated by the subsequently recorded RAIRS and XPS data shown in the lower curves in fig On the basis of spectroscopic characterization, which enable to interpret the already observed those additional islands in the STM data (see fig. 6.5) which clearly demonstrate the acetated related species on the surface NEXAFS To elucidate the orientational order, near-edge X-ray absorption (NEXAFS) measurements were carried out for the monolayer of AntSe prepared by using the above described procedure. As shown in fig (a) a typical signature in the corresponding spectra includes distinct resonances at around 285 ev which are assigned to excitation of C1s electrons into closely spaced unoccupied π*-orbitals. The broad resonance around ev is attributed to the excitation into σ*-orbitals [53,223]. The enlarged view of π*-resonances is depicted as inset in fig (b), previously been observed for the other Figure 6.11: A typical NEXAFS spectrum for a AntSe SAM on Au(111) recorded at room temperature is shown in (a) together with the measuring geometry (inset). A magnification of the π*-region along with the molecular tilt angle derived from the dichroism is displayed in panel (b) [264]. (Measured by D. Käfer) 117

127 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) adlayers of aromatic molecules such as pentacene, naphthalene or perylene [229,230]. By analyzing the linear dichroism of the π*-resonances which is a characteristic signature of the aromatic moiety their tilt angle relative to the sample normal can be determined. While this analysis is generally complicated by the presence of differently arranged molecules within the unit cell yielding only average orientations, in case of a herringbone arrangement the individual molecular tilt angle can be determined. Using the herringbone angle ϑ = 48 ± 3, obtained independently from STM data this yields a tilt angle of the aromatic moiety 33 which parallels the situation in anthracene crystals where molecules are tilted by 34.8 relative to the normal of the (001)-planes. 118

128 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) 6.7 Discussion Monolayer of BT The Au(111) surface modified by BT molecules showed the well-known morphology associated with the thiols modified SAMs such as depressions and domains boundaries. These depressions are in size of few nanometers and one monolayer in depth, originating from the chemical erosion processes accompanying the self assembly of the organic layer. The STM results indicate the less ordering of highly tilted molecules exhibiting low packing density. The saturated monolayer of BT molecules form ( ) structure containing four molecules which yield to a molecular packing 39.7 Å 2. Using the vander-waals dimension and keeping in account the average tilt angle of 36 obtained for NEXAFS data (not shown) [59], a projected molecular area of 38.5 Å 2 was calculated. This value agrees well with the experimental data and thus suggests that the saturated monolayer of BT obtained from the close packing of highly tilted molecules. In the previous theoretical investigations on the adsorption of BT molecules on Au(111), the (2 3 3) R30 or ( 3 3) R30 structures were assumed for the saturated monolayer because such motives are commonly reported for the oligophenyle thiol SAMs [231,232]. In the previous STM study a ( 13 13) R13.9 structure was reported with four molecules per unit cell which correspond to molecular area of 23.3 Å 2, resulting a closer packing than in the benzene crystal. The above mentioned different phases do not represent the comprehensive structural picture of BT on Au(111). However, the present study clearly demonstrated that the monolayer of BT molecules exhibits the close packing of highly tilted molecules Monolayer of BSe On the basis of STM results the self assembly process of BSe revealed significant differences between the monolayer of BT on Au(111) surface. Although both molecules only differ in their anchor group (sulfur vs. selenium), the resulting monolayers reveal significant difference in their packing and molecular structure. In contrast to the BT monolayer the well-known depressions have not been observed within the films formed 119

129 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) from BSe molecules. The BSe monolayer exhibits the presence of monoatomic islands with the typical diameter of nm, which suggest the distinct differences in the surface strain of the gold substrates upon the formation of monolayer. The significant long range ordering was observed for BSe-SAMs which exhibit the typical domain sizes of more than 50 nm, which allows the observation of distinct stacking faults. The STM data reveal the presence of upright standing molecules forming the densely packed monolayer with long-range ordering. The saturated monolayer of BSe forms the commensurate ( ) unit cell containing 8 molecules and molecular area amount to 28.8 Å 2. Interestingly, this packing density is rather similar to the crystalline structure of benzene where the individual molecules within the close packed (001) planes are tilted by 75 which suggest the significant contribution between the aromatic backbone resulting long range ordering which was demonstrated in the present STM results. By comparing the size of molecules and the unit cell this packing density can only be achieved if the molecules adsorbed at the different sites on the gold substrates Monolayer of AntSe The results obtained for the film growth and the self assembly process of anthracene-2-selenolate, revealed the significant differences to that of anthracene-2-thiol, in spite of the only differences between the anchor group (Selenium vs Thiol) in the molecular structure of AntSe. A recent study has revealed that SAMs based on the respective sulfur derivative, anthracene-2-thiol; exhibit only a limited structural quality with a short range ordering due to the significant amount of stress. These structural problems result in the misfit between the arrangement of aromatic backbones aiming to form a packing similar to that in the anthracene bulk and the restrictions on intermolecular distances in a SAM imposed by the interaction between the sulfur atoms and the Au(111) lattice. This stress in the SAM causes the appearance of a high density of defects such as domain boundaries, stacking faults, or point defects which hamper a long range ordering [53]. It has already been concluded in the previous sections and that substitution of selenium for sulfur in aromatic systems results in much high order in the respective 120

130 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) monolayers on Au(111). This long range order has been proved with the present STM data. These data reveal characteristic stripes of closely packed molecules along the < 112 > azimuth directions of the Au(111) substrate. This arrangement is rather robust and is not disturbed by point defects thus leading to extended domains with lateral dimensions of more than 50 nm, which is well supported by the sharpness of the diffraction spots obtained from the LEED measurements. Due to their extraordinary quality of the STM micrographs obtained in this study, the characteristic herringbone arrangement were resolved for the first time always assumed in past for monolayers of upright, aromatic molecules. It might be worth mentioning that this feature becomes only visible if the scanning occurs in the < > direction. The angle of ϑ = 48 ± 3 formed between neighboring molecules closely resembles the herringbone packing of anthracene molecules in the (001)-planes of the bulk phase (50 ). The structure found in the STM micrographs fully support the ( 3 4)rect structure deduced from the LEED measurements. Nevertheless, a structural analysis of molecular monolayers solely by STM in the absence of intrinsic markers such as substrate atoms usually does not permit the precise determination of the unit cell of molecular superstructures, due to thermal drift and/or piezo creep which typically limits the absolute accuracy of lateral dimensions to about 5-10%. Therefore, LEED or other suitable diffraction methods are superior tool for the structure determination of monolayers. Moreover, the intermolecular interaction between the aromatic moieties in AntSe and AntS SAMs is identical and the rigidity of both molecules exclude further any conformational changes. The only difference present in the covalent radius of both anchoring groups (Se 1.16 Å, S 1.02 Å) a larger bond length is expected for selenol gold interaction [233], which result in the long range ordering and can be rationalized by difference in the lateral corrugation of the interaction potential depicted in fig

131 Chapter Six Anchoring and Ordering in Purely aromatic SAMs on Au(111) Figure 6.12: Schematic presentation of the lateral corrugation of the substrate potential experienced by the sulfur and selenium anchor groups. Due to a larger bond length and lower interaction strength a smaller corrugation is seen by the selenolate which implies that a (small) lateral displacement of the selenolate from the preferred adsorption site is energetically less expensive than for a thiolate. In that way the AntSe SAMs can easily cope with the misfit to the substrate lattice and avoids a build-up of stress demonstrating that selenolate anchoring provides an interesting route to prepare highly ordered aromatic SAMs. In conclusion by combining a rigid aromatic moiety - the anthracene backbone - with an anchoring atom selenium - that permits some flexibility regarding the exact adsorption site, result in the extraordinarily ordered self-assembled monolayers in which the molecules adopt an orientation very similar to the bulk material. This dense packing permits the determination of the orientation of the molecular planes by STM even under ambient conditions thus providing the twist angle ϑ of the molecules, which is an essential parameter for the spectroscopic determination of the tilt angle as well as for the understanding of electron transport within self-assembled monolayers. 122

132 Chapter Seven Self-Assembly of Discotic Molecules on Au(111) Chapter Seven Self-Assembly of Discotic Molecules The self assembly process of the hexa-peri-hexabenzocoronene (HBC) derivates adsorbed on Au(111) substrates has been investigated by STM, CITS and RAIR. Self-assembled monolayer grown from the large discotic HBC derivatives one with long and soft tether named as monothiol substituted HBC (HBC-C 3 -SAc) and the other with the short and stiffer tether named as HBC-ethynyl-benzyl thiol (P-HBC-SAc) has been studied and the results will be discussed in this chapter. 7.1 Introduction Organic semiconductors have attracted considerable interest over the last decade due to an immense improvement in the performance of electronic devices based on these materials. This attention has mainly been focused on conjugated polymers and oligomers, as well as small molecules which can be used as active layers in devices such as fieldeffect transistors (FETs) [234,235], photovoltaic cells [236], and light emitting diodes [237]. The critical requirement for the performance of electronic and optoelectronic devices is associated with their charge carrier mobilities. Organic molecules as semiconductor components offer the unique advantage that such mobilities can be increased by establishing supramolecular order within the charge transport channels. The well-know examples are the conjugated polymers such as semiconductors, where rigid chains are solubilized by suitable alkyl substituents [238]. However, the structural defects within the chains or failure to form a perfect order will drastically reduce charge carrier mobilities. For device performance an accurate control of the molecular arrangements over a wide range of length scale, spanning from micrometer down to molecular size. Polycyclic aromatic hydrocarbons (PAHs), which can be regarded as two-dimensional subsection of graphite, are well defined nano object with interesting electronic properties [ ]. Hexa-peri-hexabenzocoronene is graphenes of well-defined size and shape, rich in π electrons exhibiting a high degree of overlap between adjacent π orbitals. The reported studies on HBC molecules demonstrate that these molecules tend to be oriented vertically i.e. edge on with respect to the substrate [ ]. These two-dimensional 123

133 Chapter Seven Self-Assembly of Discotic Molecules on Au(111) π-systems are decorated by peripheral alkyl chains, give rise to another combination of a rigid core and a soft, adaptable shell, and can under certain conditions melt into discotic columnar mesophase [246,248], demonstrating the concept of columnar dick-type-system as charge transport channels in electronic devices [249]. The possible advantages of the columnar approach are due to the disks composed of organic molecules, which result in the defect free molecular structures, processing from melt or form solution become easier due to the lower viscosity, which lead to the additional degree of self-healing ability after columnar formation. The high degree of in-plane alignment can be achieved by a novel orientation technique involving the zone-casting of HBC molecules. It was formed by means of a specially constructed device in which adsorbates deposited through a flat nozzle onto a moving substrate [245,250,251]. Disk like conjugated π systems such as triphenylene, phthalocyanine, porphyrin and hexa-peri-hexabenzocoronene have recently emerged as a kind of important semiconductor with the one dimensional charge transport along the self-assembled columns [249,252]. There are numerous studies have been reported on their selfassembling properties ranging from the bulk state to solution and to liquid-solid interfaces [253,254]. STM technique highlighted flat lying and well ordered monolayers and multilayers at the solution/graphite or solution/au(111) interfaces due to the strong interaction of these molecules with the substrates. The strong π-π interactions between the HBC discs result in well ordered supramolecular aggregates, even in the very dilute solution [255]. The overlapping of π orbitals provide efficient pathways for charge carrier which is manifested in the high charge carrier mobility along the stacking axis of the columnar structures formed by the HBC moieties is among the highest reported so far for organic molecules (0.5-1 cm 2 V -1 s -1 ) [240]. Thus the stack can be considered as selfassembling graphitic nano-wires which make them attractive candidate for application in organic electronic devices. The upright oriented molecule with respect to the metal electrode is prerequisite to measure the electron transport through the HBC disc. In past, numerous studies had been reported demonstrating that HBC molecules oriented flat on the metallic surface [256]. In this study, an effort has been made to substitute one of alkyl spacer around the periphery of HBC core with thiol group as shown in the following chart. The short abbreviations of 124

134 Chapter Seven Self-Assembly of Discotic Molecules on Au(111) these compounds (HBC-C 3 -SAc and P-HBC-SAc) are used in this work. However, the complete nomenclature of HBC-C 3 -SAc and P-HBC-SAc are assign as 2-(3'-S- Acetylthiolpropyl)-5,8,11,14,17-penta(3',7'-imethyloctyl)-hexa-/peri-/hexabenzocoronene and 2-[2'-[4''-(/S-/Acetylthiomethyl)phenyl] ethynyl]- 5,8,11,14,17-penta (3',7'- dimethyloctyl)-hexa-/peri-/hexabenzocoronene respectively. R R R R R R R R R R HBC-C 3 -SAc R = P-HBC-SAc S O S O Chart 3: Molecular structure of HBC derivatives used in this study 7.2 Objective of the Work Presented in this chapter The goal of this work is to study the structure, ordering and electron transport across the hexabenzocoronene within the SAMs generated by using these discotic compounds. The structural characterization of discotic films will be carried out by using STM and RAIR. The main focus of this study is to measure the current flowing through the HBC core within the SAMs by CITS. Furthermore, to explore the effect of short and stiffer tether on the surface morphology and lateral ordering within the SAMs. 125

135 Chapter Seven Self-Assembly of Discotic Molecules on Au(111) 7.3 Monolayer of Mono-thiol Substituted Hexabenzocoronene Formation of HBC-C 3 -SAc SAMs HBC-C 3 -thiol adsorbed Au electrodes were prepared either by immersing a Au substrates into 0.1 µm dm -3 ethanolic solution of a thiol or immersing substrates into the mixture of 1mM dm -3 ammonium hydroxide and 0.1 µm dm -3 ethanolic solution for hours. After the allotted immersion time, the samples were removed from solution and rinsed with pure acetone, ethanol and dried in N 2 stream STM The morphology and structural ordering of the SAMs of HBC derivatives are strongly dependent on preparation conditions. Since the HBC-C 3 -SAc were protected by the acetyl group. The adsorption of the substituted HBC-C 3 -thiol layer with deprotection was carried out by immersing the gold substrates into 0.1µM dm -3 solution of the compound in ethanol at room temperature together with 1mM dm -3 ammonium hydroxide. Acetyl protected thiols were deprotected during the formation of the SAMs. Figure 7.1 (a) shows Figure 7.1: (a, b) Constant-current STM images of HBC-C 3 -thiol SAMs by using the deprotecting agent. The equidistance periodic rows structures together with some contamination as indicated by the black arrows shown in (b). Tunneling parameters: U t =600 mv, I t = 130 pa. 126

136 Chapter Seven Self-Assembly of Discotic Molecules on Au(111) a constant-current STM image of atomically flat terraces of gold surface modified by the HBC-C 3 -thiol. Interestingly, neither etch-pits nor the islands were observed for the HBC- C 3 -thiol SAMs which instead reveal significant enhanced long range ordering of the periodic rows structure. The typical STM image depicted in the fig. 7.1 (b) reveals the equidistance periodic rows together with brighter spots as indicated by the black arrows. The origin of these brighter spots may arise from the cleavage of acetate group to form the ammonium acetate (NH 3 COOH) as a contamination, which promote in situ base promoted, the liberation of thiol. In the early report it has been observed that deprotection of thiols moieties by deacylation of thioacetyl group using base allows the formation of SAMs [42], without keeping in account the side product in the form of ammonium acetate after the thiolate formation. This study will be further focused on to generate SAMs, free of contamination, without using the deprotecting agent. Figure 7.2 (a) shows the large scale constant-current STM micrograph of HBC-C 3 -thiol SAMs fabricated at 298 K without using the base. The HBC-C 3 -thiol SAMs form a contaminated free, long range well-ordered periodic row structure similar to those observed by using deprotecting agent. The STM micrograph clearly shows atomically flat terraces of Au(111) which are separated by monoatomic steps with the characteristic height of 2.4 Å. Remarkable is the size of the domains which corresponds to the lateral dimension of nm and are extended over the whole gold terraces and independent to defect like step edges as shown in fig. 7.2 (a). Paradoxically depression or etch pits were not found, which have previously been reported for the SAMs of alkanethiol, organothiol (biphenyl, terphenyl) adlayer on Au(111) [29, 33, 35, 47], possibly due to the less strain experienced by the gold surface after adsorption of these bulky discotic molecules. Furthermore, the growth of domains is independent of steps. Close inspection of STM data revealed that domains of HBC-C 3 -thiol SAMs are clearly rotated by 120 with respect to each other, which reflects the symmetry of underneath gold substrate. No pronounced difference has been observed in the STM images by repeatedly scanning the same sample area. This implies that the monolayer of HBC-C 3 -thiol is rigid, stable and densely packed in saturated phase. A high resolution image of a HBC-thiol SAMs clearly shows the large domain of parallel lamella. Each lamella consists of HBC-C 3 -thiol molecules which are oriented parallel to < 112 > azimuth and perpendicular to the close 127

137 Chapter Seven Self-Assembly of Discotic Molecules on Au(111) packed <1 10 > direction of Au(111). The line scans depicted in the fig. 7.2 (c and d) reveals the periodicity along the rows amounts to a = 5.0 ± 0.5 Å and the distance between the rows amounts to b = 59.5 ± 0.5 Å. The careful analysis of line scans reveals that within the columnar rows, the HBC-C 3 thiol molecules are interdigitize as evident from the line scans presented in fig. 7.2 (d). The height profile along the lines presented in fig. 7.2 (d) displays the registry mismatch within the two consecutive columnar rows. Figure 7.2: Summation of STM data obtained for the saturated HBC-C 3 thiol SAMs on Au(111). Figure (a) depicts large scale STM micrograph showing atomically flat terraces separated by monoatomic steps of gold clearly exhibiting the azimuth directions of Au(111). Molecular structure of HBC-C 3 thiol presented as an inset. In Fig. (b) high resolution STM image of HBC-C 3 -thiol SAM clearly showing the domain of parallel lamella together with corresponding line scans (black, red, blue) having the periodicity of 5.0 ± 0.5 Å and registry mismatch along lamella. The line scan (green) perpendicular to these rows shows the periodicity of 59.5 ± 0.5 Å. Tunneling parameters: U t =500 mv, I t = 100 pa. 128

138 Chapter Seven Self-Assembly of Discotic Molecules on Au(111) RAIR RAIR spectra of HBC-C 3 -thiol have been recorded for the polycrystalline gold substrates prepared by immersion into ethanolic solution at room temperature (298 K). In fig. 7.3, the low and high frequency regions of the RAIR spectra are shown together with the corresponding bulk spectra recorded using KBr pellets. The ab initio calculation to calculate the characteristic vibrations modes present in HBC-C 3 -thiol SAMs was not successful due to multitude of vibrations present in the HBC molecule. For a determination of the molecular orientation of HBC-C 3 -thiol within the SAMs by using so called surface selection rule [128], it is convenient to analyze the out-of-plane bands (having the transition dipole moment almost perpendicular to molecular axis) and inplane bands (having the transition dipole moment parallel to molecular axis). It has been observed that in contrast to high frequency region (>2000 cm -1 ) mainly related to diatomic vibration (such as the C-H stretching mode), the lower frequency region exhibit the rather collective modes because of the strong coupling through the rigid HBC core. Therefore the vibrational mode of HBC-C 3 -thiol typically observed in RAIR spectra complicates a quantitative analysis of the molecular orientation. Nevertheless, the absorption band appeared at low frequency region at 743 cm -1 typically associated to outof-plane mode (having the transition dipole moment almost perpendicular to molecular axis) can be used to derive the qualitative information about the molecular orientation presented as inset in fig For upright oriented HBC-C 3 -thiol with respect to the surface normal, the intensity of the out-of-plane ring mode must vanish because its transition dipole moment oriented parallel to the surface in this case and thus screened by the metal. The presence of the band at 743 cm -1 reveals that the molecules are significant tilted from the surface normal which corroborate well with the present STM data. The alkyl chain around the periphery of HBC reveals significant orientated ordering as evident from the peaks appeared at 2859, 2876, 2928 and 2963 cm -1 correspond to the CH 2 symmetric stretching mode, the CH 3 symmetric stretching mode, the CH 2 asymmetric stretching mode, the and CH 3 asymmetric stretching mode, respectively, presented in fig

139 Chapter Seven Self-Assembly of Discotic Molecules on Au(111) Figure 7.3: RAIR spectra of HBC-C3-thiol in KBr (bulk) and in a film on gold prepared by overnight immersion of the gold substrate into a 1 µm ethanolic solution at 298 K. The band appear at 743 cm -1 correspond to the transition dipole moment (TDM) almost perpendicular to the HBC disc shown by the schematic model as inset. 130

140 Chapter Seven Self-Assembly of Discotic Molecules on Au(111) Structural Model The schematic structural model presented in the fig The STM data reveals that HBC- C3-thiol SAMs form the large domain of paired lamella rows under the guidance of π-π stacking. The periodicity along these rows amount to a = 5.0 ± 0.5 Å, which run along the < 112 > azimuth of the gold. The distance between the first row and corresponding one in the second row amounts to b = 59.5 ± 0.5 Å. The RAIR results indicate that molecules do not posses the flat adsorption geometry rather highly tilted away from the surface normal. Based on these observation the adlayer structure of HBC-C 3 -thiol SAMs exhibits the rectangular unit cell 20 1 with respect to the unit cell of Au(111). The overlayer unit 1 2 vectors obtained from the STM data is indeed consistent with this commensurate structure. The proposed structural model forms the commensurate structure having the dimension of 5.0 Å 59.5 Å containing two molecules per unit cell. Figure 7.4: Top view of the structural model for HBC-C3-thiol SAMs on Au(111). The unit cell is marked by the large rectangular box. The unit cell of Au(111) is marked by the small oblique box. 131

141 Chapter Seven Self-Assembly of Discotic Molecules on Au(111) 7.4 Lateral Transport through Organic Layers Introduction Electronic transport through organic molecules is the foundation of the ever-increasing field of Organic Electronics. Besides the huge interest in transport phenomena in single molecules [60,147,257] also thin films of molecules have been in the center of numerous studies in this field. A point of crucial importance is the question how charge is transported from one organic molecule to another. Different transport mechanisms have been suggested, ranging from band-like transport in well-ordered arrays of molecules to hopping-like transport in more disordered systems. An ideal system to study such effects is self-assembled monolayers (SAMs), where an ordered array of organic molecules is supported on a conducting substrate. These systems can be imaged and analyzed using scanning tunneling microscopy (STM), where not only the structure, but also the electron transport properties of the molecular films can be studied [175]. Going beyond homogenous systems, also studies on single molecules immersed in an alkanethiol matrix and mixed SAMs have already been reported [204]. Especially in the mixed SAMs effects of lateral electronic coupling between neighboring molecules have been observed [31]. In order to examine the lateral electron transport the STM measurement were carried out by inserting the HBC-C 3 -thiol molecules into the matrix of alkanethiol SAMs. This lateral transport takes place in small islands of HBC-C 3 -thiol molecules. These discotic molecules dispersed in a matrix of alkanethiol and are revealed by the dependence of the apparent height on the size of the HBC-C 3 -thiol islands Results HBC-C3-thiol Islands in An Alkanethiol Matrix Pure alkanethiolate SAMs were prepared by an 18 h or longer immersion into a 1 mm dm 3 ethanol solution containing the alkanethiol (C10-SH). The samples were withdrawn, rinsed in acetone, and ethanol, and dried in the stream of N 2. Exchange of the HBC-C 3 -thiol molecules was carried out by immersion of the host matrix C10 SAMs on Au/mica into the 1µM solution of HBC-C 3 -thiol for 25 minutes. STM measurements in 132

142 Chapter Seven Self-Assembly of Discotic Molecules on Au(111) air and in ultra-high vacuum (UHV) were performed using a JEOL JSPM-4210 and JEOL JSPM-4500S instruments, respectively. No difference has been observed between the experiments carried out in air or in vacuum. After the immersion of the samples covered with the C10-SAM in the solution containing the HBC-C3-thiol, bright protrusions were observed in STM topographs. According to the literature [258], these islands can be attributed to the HBC-C3-thiol. These protrusions vary in shape, size, and apparent height as shown in the fig (a) (b) Height [nm] Line A Line B Length [nm] Figure 7.5: (a) Constant-current STM image of C10 SAMs after immersion into 1µM solution of HBC-C 3 -thiol for 25 minutes. (b) The cross-sectional height profiles across HBC-C3-thiol islands embedded in C10 SAMs. Tunneling parameters: U t =500 mv, I t = 100 pa. The cross-sectional profiles across the HBC islands inserted in the C10 SAMs presented in the fig. 7.5 indicate that the apparent height difference of islands is not uniform, rather depend on the size of islands. The size dependence of these conductive molecular islands on height indicates that the vertical conductance of islands increase as the number of molecule in the islands increases. This can be rationalized due to strong intermolecular electronic coupling via π-π stacking that creates the efficient intermolecular conducting path. 133

143 Chapter Seven Self-Assembly of Discotic Molecules on Au(111) Figure 7.6 depicts a plot of the apparent height of these islands versus island size by careful analysis of more than 150 islands. It is clearly visible that apparent height of islands increase with its size. Height data from islands with the same size is plotted as a single data point, the error bar is derived from the standard error of the distribution of the height values for that point. Height (h) [nm] (a) (b) S S S S S S S S S Au(111) Width d [nm] Figure 7.6: (a) The apparent height (h) versus island size (d) for more than 150 islands obtained from the constant-current STM data for the HBC-C3- thiol immersed for 25 minutes into C10 SAMs. (b) Schematic representation of discotic molecules embedded into C10 SAMs. HBC-C3-thiol molecules in this simple schematic are not stacked with their π- system as it was experimentally observed. 134

144 Chapter Seven Self-Assembly of Discotic Molecules on Au(111) 7.5 Monolayer of Hexabenzocoronene-ethynyl-benzyl Thiol Formation of P-HBC-SAc SAMs Firstly the gold on mica substrates were annealed in butane and oxygen flame and immersed in 0.1µM dm -3 ethanolic solution of P-HBC- SAc for hours. After the allotted immersion time the saturated SAMs were rinsed with pure ethanol, acetone and dried in the stream of N STM Within the case of HBC-C 3 -thiol SAMs it has been observed that the deprotecting agent is not capable of generating the contamination free SAMs. Figure 7.7 (a) shows the large scale STM image of Au(111) surface modified by the monolayer of P-HBC-thiol without using deprotecting agent. Interestingly, depression or etch pits were not observed, which have been observed in the early studies of alkanethiol, organothiol (biphenyl, terphenyl) adlayer on Au(111) [29,33,100]. The coexistence of two different phases was observed which are defined as the region A and B as shown in fig. 7.7 (b). Figure 7.7: Constant-current STM data obtained for the P-HBC-thiol SAMs on Au(111) prepared at 273 K. (a) Large scale image show the presence of characteristic close step edges. The coexistence of two different phases labeled as A and B depicted in (b). Tunneling parameters: U t =500 mv, I t = 100 pa. 135

145 Chapter Seven Self-Assembly of Discotic Molecules on Au(111) The phase A reveal the same structure and packing which were observed for the case of HBC-C 3 -thiol SAMs as shown in fig. 7.2 (b). In the case of P-HBC-thiol, the linker between anchor group and HBC core is rigid and short. The mobility of molecule is quite limited. Thus, the molecules exhibit less degree of freedom which results in the formation of new phase B, which is even further densely packed than the corresponding phase A. Together with these two phases some disorder region were found as well. These two phases will be explained separately in the following sections. 1. Phase A The presence of short and rigid tether between the discotic HBC molecule and sulfur results in the formation of same row structure with the parallel lamellar. Figure 7.8 represent the constant current STM data of P-HBC-thiol SAMs recorded for the phase A. It has been observed that contrary to the short and flexible tether (HBC-C 3 -thiol) which exhibits the long range ordering, the monolayer of P-HBC-thiol exhibits rather small domains exhibiting lateral dimensions of nm. The adlayer of P-HBC-thiol is found to be rather rigid and robust; no morphological changes were observed even after repeatedly scanning the same area. This implies that the P-HBC-thiol SAMs is rigid, stable and densely packed in saturated phase. The STM micrograph represented in the fig. 7.8 (a) demonstrate the equidistance row structure which clearly shows the large domain of parallel lamella. In this image the domains boundaries were clearly seen as indicated by the white arrow. The cross-sectional height profile along the lines A and B labeled in (a) and presented in the (b). Along lines A and B the periodicity amount to be 5.0 ± 0.5 Å and 59.5 ± 0.5 Å respectively. Interestingly, with the single domain regular spaced dark features with the different contrast has been observed, which is evident from the line scan A presented in fig. 7.8 (b) could be attributed to herringbone reconstruction. A high-resolution STM image of a HBC-thiol SAMs clearly shows the large domain of parallel lamella shown in fig. 7.8 (c). The measured periodicity obtained by the line scans clearly demonstrate P-HBC-thiol molecules are oriented parallel to < 112 > azimuth and perpendicular to the close packed <110 > direction of the gold substrate. The close inspection of the STM data reveals the presence of well defined substructures between the regular spaced rows labeled by green circles and arrows shown in fig. 7.8 (c). The 136

146 Chapter Seven Self-Assembly of Discotic Molecules on Au(111) lateral dimension of these substructures obtained independently from the height profile along the line c labeled in figure 7.8 (c) amounts to Figure 7.8: Summary of constant-current STM data obtained for the phase A of P-HBC-thiol SAMs on Au(111) prepared at 273 K. (a) Single domain of phase A showing the domain boundaries labeled by white arrow. (b) Cross-sectional height profiles along lines A and B labeled in (a), respectively, revealing corrugation periodicity. (c) High-resolution STM micrograph revealing the substructure labeled by green arrows and crosssectional height profiles along line C depicted in (d). Schematic sketch of substructure found in the lamella shown in (d). The black solid lines indicate the presence of mismatch in the registry of P-HBC-thiol SAMs. Tunneling parameters: U t =500 mv, I t = 100 pa. 137

147 Chapter Seven Self-Assembly of Discotic Molecules on Au(111) lateral dimension of these substructures estimated to be 11 Å, which can roughly be correlated to the length of the alkyl chain attached to the HBC core shown in the schematic sketch in fig. 7.8 (e). The high-resolution STM data clearly demonstrate the mismatch of registry within the columnar rows of P-HBC-thiol SAMs indicated by the dotted lines presented in fig. 7.8 (c). In order to further explore the structural characterization of the adlayer generated by the discotic molecules in depth, another attempt were carried out on ex-situ prepared P-HBCthiol SAMs and measured in ultra-high vacuum (UHV). The large scale constant-current STM image as shown in figure 7.9 (a) demonstrate that the well-known herringbone reconstruction with the characteristic stripes (marked by black arrows) are superimposed on the monolayer structure of P-HBC-thiol. High-resolution STM image, as in Figure 7.9 (b) show that individual discotic HBC core can be imaged as a rod like structure indicated by schematic sketch. From the ultra-high quality of the STM data acquired from the P- HBC-thiol SAMs, it can evidently state that the adlayers of P-HBC-thiol SAMs form the equidistance paired row structure. Parallel lamella rows were found to be aligned perpendicular to these paired row structure clearly demonstrating the registry mismatch along the lamella rows indicated by dotted lines. Although the same feature were observed for the collection of data in air, but the clarity of registry mismatch become more pronounced and superior for the data obtained in vacuum. The origin of contrast variation in the P-HBC-thiol SAMs becomes quite clear due to the herringbone reconstruction of the underlying gold substrates. The periodicity along the brighter paired rows and along the rod like structures of adlayer were amount to be 5.0 ± 0.5 Å and 59.5 ± 0.5 Å respectively clearly demonstrating two molecules per unit cell. 138

148 Chapter Seven Self-Assembly of Discotic Molecules on Au(111) Figure 7.9: Summary of constant-current STM data obtained for the P-HBC-thiol SAMs on Au(111) prepared at 273 K measured in vacuum. (a) Black arrows indicate the characteristic herringbone reconstruction which is superimposed on the adlayer of P-HBC-thiol. (b) The blue dotted lines indicate the presence of registry mismatch in P-HBC-thiol SAMs. Tunneling parameters: U t =500 mv, I t = 100 pa. 139

149 Chapter Seven Self-Assembly of Discotic Molecules on Au(111) Based on the detailed structural characterization of P-HBC-thiol SAMs schematic structural model presented in the fig The adlayer of P-HBC-thiol SAMs form the equidistance paired row structure. The measured distance between the first row and corresponding one in the second row amounts to b = 59.5 ± 0.5 Å. Parallel lamella rows were found to be align perpendicular to these paired row structure clearly demonstrating the registry mismatch along the lamella rows. The periodicity between these lamella rows amount to a = 5.0 ± 0.5 Å, which run along the < 112 > azimuth of the gold. The adlayer structure of P-HBC-thiol SAMs exhibits the rectangular unit cell 20 1 with respect to 1 2 the unit cell of Au(111). The overlayer unit vectors obtained from the STM data is indeed consistent with this commensurate structure. The proposed structural model forms the commensurate structure having the dimension of 5.0 Å 59.5 Å containing two molecules per unit cell. Figure 7. 10: Top view of the structural model for phase A in the P-HBC-thiol SAMs on Au(111). The unit cell is marked by the large rectangular box. The unit cell of Au(111) is marked by the small oblique box. 140

150 Chapter Seven Self-Assembly of Discotic Molecules on Au(111) 2. Phase B Figure 7.11 shows the large-scale constant-current STM image recorded for the phase B in the adlayer of P-HBC-thiol in air. The single domain of this phase is presented in the fig (a) showing the formation of the equidistance rows structure which has previously been observed for the case of phase A. However, high magnification of this domains demonstrate that the distance between these paired row structure were found to be almost half of the already measured distance for the phase A, yielding the further densely packed and more upright oriented adlayer of P-HBC-thiol shown in fig (b). The cross-sectional height profile along the line A labeled in (b) and presented in the (c) reveal the periodicity between these rows amount to be 28.0 ± 0.2 Å. Interestingly, some substructure were obtained from the line scan showing the two maxima separated by 5 Å separation. The attempts to better resolve and improve the quality of the parallel lamella rows structure turn out to difficult possibly due to presence of alkyl chains to the HBC core which possibly hinder to stabilize the STM tip. Figure 7.11: Summary of constant-current STM data obtained for the phase B of P-HBC-thiol SAMs on Au(111) prepared at 273 K. (a) Single domain showing the structure of phase B. (b) The equidistance densely packed rows. The cross-sectional height profiles along line A depicted in (c), revealing the corrugation periodicity of 28 ± 0.2 Å. Tunneling parameters: U t =200 mv, I t = 180 pa. 141

151 Chapter Seven Self-Assembly of Discotic Molecules on Au(111) Based on the STM data which demonstrate that monolayer of P-HBC-thiol in the phase B also form the paired row structure forming the rectangular unit cell is presented in the fig However the phase B comprises of the more standing up molecules which further densely packed under the influence of π-π stacking. This phase also consists of the equidistance paired rows structure and the distance between them found to be amount to be 28.0 ± 0.2 Å. The periodicity between the lamella rows found to be 5.0 ± 0.2 Å. The adlayer structure of P-HBC-thiol SAMs exhibits the more densely packed rectangular unit cell 10 0 with respect to the unit cell of Au(111). 1 2 Figure 7.12: Top view of the structural model for phase B in the P-HBC-thiol SAMs on Au(111). The unit cell is marked by the large rectangular box. The unit cell of Au(111) is marked by the small oblique box. 142

152 Chapter Seven Self-Assembly of Discotic Molecules on Au(111) 7.6 Current Imaging Tunneling Spectroscopy (CITS) To correlate the electronic properties of a single molecule with its immediate environment i.e. neighbor, adsorption site and molecular conformation etc., electron transport measurements are need to be combined with high-resolution spatial imaging which makes combined (STM/CITS) studies the method of choice. In this section the electron transport properties of conjugated discotic molecules (HBC-C 3 -thiol and P-HBCthiol) adsorbed covalently to the metallic surface will be explored by means of STM and CITS measurements. The highly ordered SAMs of HBC-C 3 -thiol and P-HBC-thiol were already been imaged with sub-nanometer resolution in ambient and UHV, which now allow for the recording of I-V curves with similar spatial resolution. Figure 7.13 (a) displays I-V curves recorded for the HBC-C 3 -thiol SAMs which is quite different to those obtained for the aliphatic and aromatic SAMs [71, ]. The I-V curves recorded on the top of brighter rows and parallel lamella rows were found to be identical. Figure 7.13 (b) displays I-V curves recorded for the P-HBC-thiol SAMs which is quite similar to former case. The similarity between these I-V curves can be explained by taking into account the indistinguishable adlayer structures of both molecules on Au(111). I [na] (a) (b) HBC-C thiol U[V] I [na] P-HBC-thiol U[V] Figure 7.13: (a, b) Current-voltage (I-V) curves recorded for the SAMs of HBC-C 3 -thiol and P-HBC-thiol, respectively (average over 35 single I-Vs). The insets in both spectra depict the STM images of adlayer before and after the CITS measurements. 143

153 Chapter Seven Self-Assembly of Discotic Molecules on Au(111) The obtained I-V curves exhibit the strong symmetric and metallic characteristics which arise from the HBC core. The reliability of these I-V curves become evident due to similarity between the data obtained in the air and vacuum. In order to rule out the temperature dependence on the electron transport through the P- HBC-thiol SAMs the I-V curves were also recorded at liquid nitrogen temperature. Figure 7.14 displays the spectra of I-V curves recorded at 298 K and 80 K representing by black and blue curve, respectively. At low temperature the I-V curve shows the pronounced difference revealing the less value of slope exhibiting less metallic character. This can be attributed to the different electron transport mechanism which results in the combination of hoping and tunneling process K 80K 1.0 I [na] U[V] Figure 7.14: Temperature dependence of current-voltage (I-V) curves recorded for the SAMs of P-HBC-thiol at 298 K (black curve) and 80 K (blue curve). 144

154 Chapter Seven Self-Assembly of Discotic Molecules on Au(111) Model for electron Transport The side view of schematic sketch showing the temperature dependence on the resulting charge transport mechanism depict in the fig The change in the I-V curve obtained at low temperature (80 K) attributed to the different tunneling mechanism. This can be explained by considering the different tunneling path of the electron coming from the STM tip. In the first case the electron can tunneling from the tip into the Au electrode via HBC core (path 1) as shown below which result in the symmetric behavior of I-V curves obtained at 298 K. At low temperature (80 K) the electron can either follow the same path or trap by the HBC core and tunneling into the neighbor molecules result in the change of I-V characteristic, can be correlated to the combination of tunneling and hoping mechanism indicated by the solid and dotted lines labeled as path 2. Since the molecules are significant tilted from the surface normal, the tunneling of electron from one molecule to the neighbor molecules seem not to be more expensive due to the presence of the strong intermolecular force and π-π stacking. Figure 7.15: The side view of the schematic model presenting the different electron mechanism. 145