Novel conjugated molecules for molecular electronics

C.: molecular materials for electronics utilizes the properties of the molecules to affect the bulk properties of a material, while molecular scale electronics focuses on single-molecu

Chapter One Introduction

1.1 Molecular Electronics (Moletronics)

Molecular electronics, also called moletronics, is an interdisciplinary

subject that spans chemistry, physics and materials science The unifying feature

of molecular electronics is the use of molecular building blocks to fabricate electronic components, both active (e.g transistors) and passive (e.g resistive wires) The concept of molecular electronics has aroused great excitement, both in science fiction and among scientists This is because of the prospect of size reduction in electronics which is offered by molecular-level control of properties Molecular electronics provides means to extend Moore’s Law1 beyond the foreseen limits of small-scale conventional silicon integrated circuits

“Molecular electronics” is a poorly defined term Some authors refer to it

as any molecular-based system, such as a film2 or a liquid crystalline array.3 Other authors, including Tour J M.,4 prefer to reserve the term “molecular electronics” for single-molecule tasks, such as single molecule-based devices or even single molecular wires Due to the broad use of this term, molecular electronics are split

into two related but separate subdisciplines by Petty M C.: molecular materials

for electronics utilizes the properties of the molecules to affect the bulk properties

of a material, while molecular scale electronics focuses on single-molecule

applications.4, 5

1.2 Background

Study of the charge transfer in molecules was promoted in the late 1940s

by Albert Szent-Gyorgiand and Robert S Mulliken.6 They discussed the so-called

“donor-acceptor” systems and then developed the study of charge transfer and energy transfer in molecules In 1959, Richard P Feynman presented his lecture

“There’s Plenty of Room at the Bottom” This famous call was for chemists,

engineers and physicists to work together and to build structures from bottom up

at the molecular level Feynman’s suggestion spurred serious notion to the possibility of engineering single molecules to function as elements in the information-processing systems This idea was tested by a 1974 paper entitled

“Molecular Rectifiers” by Mark Ratner and Ari Aviram.7 This paper illustrated a theoretical molecular rectifier and generalized molecular conduction in molecular electronics They discussed theoretically the possibility of constructing a “very simple electronic device, a rectifier, based on the use of a single organic molecule” It has turned out in later years that observing true molecular rectification is very difficult Their proposal formed a brave attempt that would strengthen the foundations of the field with hopes of electronic applications truly

at the molecular scale Later, in 1988, Aviram described in detail a theoretical single-molecule field-effect transistor.8 Further concepts were proposed by Forrest Carter5 of the Naval Research Laboratory, including single-molecule logic gates

These were all theoretical constructs and not concrete devices The direct measurement of the electronic characteristics of individual molecules has to wait for the development of new techniques which are capable of making reliable

electrical contacts at the molecular scale This was not an easy task The first experiment measuring the conductance of a single molecule was only reported in

1997 by Mark Reed and co-workers.9 Since then, the development of nano-scale measuring techniques has progressed rapidly and the theoretical predictions of the early workers have mostly been confirmed Rapid progress in molecular electronics has been made in the last three decades owing to advent of new characterization techniques An indicator of the evolution of molecular electronics (Fig 1.1) is provided by the number of citations per year to the seminal Aviram-Ratner study7 during the last three decades It shows that research of molecular electronics is rapidly expanding

Fig 1.1 An indicator of the evolution of molecular electronics is provided by the number

of citations per year to the seminal Aviram-Ratner study 7 during the last three decades Data is taken from the ISI Web of Knowledge

The development of new techniques such as scanning probe microscopy and nano-lithography-patterning has played a vital role in the realization of molecular electronics These sophisticated tools have allowed the current-voltage

characteristics of single or bundle of molecules to be measured Molecular electronics is now driving one of the most exciting interdisciplinary efforts in nanotechnology and nanoscience Molecular electronics embraces many traditional disciplines such as (i) self-assembly and supramolecular chemistry, a domain lying between the chemistry and biology and (ii) electronic device characterization at the nano-scale, a common strength of physical and electrical engineering research

But why do we want to study molecular electronics? In addition to the exponential miniaturization trend of conventional semiconductor-based electronics imposed the technological needs, molecular electronics also flourishes due to the important fundamental issues it poses One example is the manifestations of quantum transport when electrons transverse a single molecule

at a constant rate

1.3 Advantages of Molecular Electronics

Molecular structures are very important in determining the properties of bulk materials, especially for application as electronic devices The intrinsic properties of existing inorganic electronic materials may not be capable of forming a new generation of electronic devices envisioned, in terms of feature sizes, operation speeds and architectures However, electronics based on organic molecules could offer the following advantages:10

Size – Molecules are in the nanometer scale between 1 and 100 nm This

scale permits small devices with more efficient heat dissipation and less overall production cost to be made

Assembly – One can exploit different intermolecular interactions to form

a variety of structures by the array of self-assembly techniques which are reported

in the literature The scope of application of the self-assembly technique is only limited by the researcher’s ability to explore

Stereochemistry – A large number of molecules can be made with

indistinguishable chemical structures and properties.11 On the other hand, many molecules can exist as distinct stable geometric structures or isomers Such geometric isomers exhibit unique electronic properties Moreover, electronic properties of conformers can be affected by pressure and temperature.13 We can therefore make use of stereochemistry to tune properties

Synthetic flexibility – Organic synthesis is extremely versatile It

provides the means to tailor make molecules with the desired physical, chemical, optical and transport properties The multitude of electronic energy levels in molecules can be fine-tuned by simple variations in molecular structure, e.g., by changing substituents on aromatic rings in conjugated compounds Moreover, derivatization of a molecule can lead to improving the processibility of the material without changing the device properties This allows an entirely new dimension in engineering flexibility that does not exist with the typical inorganic electronic materials.12

Organic molecules have disadvantages such as instability at high temperatures and when exposed to oxygen and UV light Atoms at surfaces and edges on substrates are of higher energies, and consequently less stable than atoms in the bulk lattice.12 But overall, the four advantages mentioned above

render organic molecules ideal for electronics applications, as Feynman noted in his 1959 speech.13

1.4 Molecular Electronic Systems

In order to perform as an electronic material, molecules need a set of overlapping electronic states These states should connect two or more distant functional points or groups in the molecule A conjugated π orbital system is required for a typical candidate of molecular electronics This conjugated system needs to extend on an σ-framework with terminal functional groups Molecules for electronic applications generally have 1-, 2-, or 3-dimensional shapes as depicted in Figure 1.2 Alligator clip, which provides stable connection of the material to the metallic electrodes or inorganic substrates, is the caudal functional group of the organic electronic material It is important to note that each part of an organic molecule used as the active component in nano scale electronic device has their own contribution.4 In general, by measuring the conductivity of a series of systematically modified molecules, the contribution of each component can be determined For example, by varying the molecular alligator clip and examining the molecules’ conductivity, the contribution of the alligator clip to the conductivity can be determined

Fig 1.2 Schematic of 1D, 2D and 3D shapes for molecular electronics.12

1.4.1 Electronic Structures

The simplest molecules studied in molecular electronics are the thiols,14, 15 which only have σ-bonds The others are organic molecules represented by alternating double and single bonds or alternating triple and single bonds These are indicative of an σ-bonded C-C backbone with π-electron delocalization.16 The conjugation length is defined as the extent over which the π-electrons are delocalized The double or triple bonds between carbon atoms in the molecules have an electron excess to that normally required for just σ-bonds.17These extra electrons are in the pz orbitals which are mainly perpendicular to the bonding orbitals between adjacent carbon atoms These electrons overlap with adjacent pz orbitals to form a delocalized π-electron cloud This cloud spreads over several units along the backbone When this happens, delocalized π valence (bonding) and π* conduction (anti-bonding) bands with defined bandgap are formed — which meets the requirements for (semi)conducting behavior Normally the electrons reside in the lower energy valence band If given sufficient energy, they can be excited into the normally empty upper conduction band, giving rise to a π–π* transition Intermediate states are forbidden by quantum

alkyl-mechanics The delocalized π-electron system confers the (semi)conducting properties on the molecule and gives it the ability to support charge transport.18 Modifications can be done based on the backbone to improve electron transfer properties Scheme 1.1 shows several popular backbones for a 1D molecular electronic material Backbones for 2D and 3D molecular electronics are similar to 1D’s

SH

SH HS

(a)

(b)

(c)

Scheme 1.1 Representative structures for 1D molecular electronic materials; (a)

alkyl-dithiol; (b) Oligo(p-phenylene)-alkyl-dithiol; (c) (p-phenylene ethynylene)-dithiol

1.4.2 Different Alligator Clips in SAMs

SH HS

SH

S S

Scheme 1.2 Representative alligator clips for forming SAMs 1,2-dioctyldisulfane (a);

bis(4,4’-biphenyl)ditelluride (b); benzenethiol (c); benzene-1,4-dithiol (d); S-phenyl

ethanethioate (e); S,S’-1,4-phenylene diethanethioate (f); 4,4’-biphenyl selenoacetate (g); phenyl isocyanide (h); 1,4-phenylene diisocyanide (i); 2-nitro-1,4-bis(phenylethynyl)

benzene diazonium tetrafluoroboride (j)

Scheme 1.2 shows some common alligator clips used in molecular electronics for forming SAMs The acetyl-protected thiols and dithiols can be deprotected in situ under acid or base conditions19 to form SAMs on gold substrate The diazonium salt20 generates an aryl radical by loss of N2 and ultimately produces an irreversible gold-aryl bond Isocyanide and diisocyanide21 also perform gold-carbon bond Among all the alligator clips, sulfur compounds have a strong affinity to transition metal surfaces.22-26This is probably because of the possibility to form multiple bonds with surface metal clusters.27 The number

of reported surface active organosulfur compounds and their derivatives that form

monolayers on gold has increased and dominated the literature in recent years

These include, di-n-alkyl sulfide,28, 29 di-n-alkyl disulfides,30 thiophenols,31, 32thiophenes,33 mercaptopyridines,32 mercaptoanilines,34 xanthates,35 cysteines,36, 37thiocarbamates,38 thiocarbaminates,39 thioureas,40 mercaptoimidazoles,41-43ditellurides4 and alkaneselenols.44 SAMs of alkanethiolates on Au surfaces are the most studied and well understood

1.4.3 Electrode Effects

There has been great interest in molecular electronics since the observation of electrical conductivity of the molecules from early experiments with the junction formed by sandwiching the molecule between two metal electrodes.45, 46

However, it has been shown that in some systems, it was not the molecules themselves but the metal contacts that mainly contribute to the junction conductivity The misleading observations from early experiments are due to the

so called “metal nanofilaments” effect.47 The “metal nanofilaments” effect is caused by the movements of metal atoms from the contacts to the tiny gap (several nanometers) between the two contacts with a bundle of molecules in between when an electric field is applied The metal atoms in the gap act as a low-resistance bridge between the two contacts (Figure 1.3 (a)) Instead of flowing through the molecule, electrical current tends to pass through the low-resistance

bridge More recently, He et al.48 proposed a metal-free system in which the two sides of a molecular monolayer attached to single-crystal silicon and a mat of single-walled carbon nanotubes, respectively (Figure 1.3 (b)).49 Such a design

eliminated the metal nanofilaments effect and switching property was observed under an applied field

(a) (b)

Fig 1.3 (a) Metal-molecule-metal junction with “metal nanofilaments” effect 49 (b) Carbon nanotube-molecule-silicon junction 49

Molecule-electrode interface is therefore a critically important component

in molecular electronics.10 It may limit the current flow or completely modify the measured electrical response of the junction Most experimental platforms for constructing the molecular-electronic devices are based on the fact that the sulfur-gold bond is an excellent chemical handle for forming self-assembled, robust organic monolayers on metal surfaces Other methods, such as contacting a scanning probe tip with the surface of the molecule, are frequently employed Ideally, the choice of electrode materials should not be based on the ease of fabrication or measurement They must follow the first-principles considerations

of the molecule-electrode interactions

However, the current level of understanding of the molecule-electrode interface is rather poor Very little theory exists that can adequately predict how the energy levels of the molecular orbitals will align with the Fermi energy of the electrode Small changes in energy levels can dramatically affect the junction

conductance Therefore it is critical to understand the correlation of the interface energy levels which demands both theoretical and experimental study A relevant consideration involves how the chemical nature of the molecule-electrode interface affects the rest of the molecule The zero-bias coherent conductance of a molecular junction may be described as a product of functions that describe the molecule’s electronic structure and the molecule-electrode interfaces However, it

is likely that the chemical interaction between the molecule and the electrode will modify the molecule’s electron density in the vicinity of the contacting atoms and,

in turn, modify the molecular energy levels or the barriers within the junction There is little doubt that the molecular and interface functions must be considered

in tandem in theoretical studies

1.5 Applications of Molecular Electronics

Molecular electronics seeks to be the next technology in the electronics industry where molecules assemble themselves into devices using environmentally friendly and low cost fabrication techniques It goes beyond the limitations of rigid silicon-based solutions It implements one or a few molecules

to function as connections, switches, and other logic devices in future computational devices.7 Molecular electronics can be used in emerging technologies ranging from novel optical discs based on bistable biomolecules to conceptual design of the computers based on molecular switches and wires

The processing speed of existing computers is limited by the time it takes for an electron to travel between devices Molecular electronics-based computation addresses the ultimate requirements in a dimensionally scaled system:

ultra dense, ultra fast and molecular-scale.50 By the use of molecular scale

electronic interconnects,5 the transmittance times could be minimized This could

result in novel computational systems operating at far greater speeds than

conventional inorganic electronics.51 Nowadays it is found that the fabrication

costs of electronic devices rise rapidly when their dimensions decrease to the nano

scale.52 Additionally, traditional semiconductor devices start to exhibit

non-optimal behavior in the nano dimensions New technologies need to be developed

for use at the nano dimension.53-59

The design of a molecular CPU can bring great technical renovation in

computer science Table 1.1 shows the main differences between the present bulk

electronic devices and the proposed molecular electronic devices.53

Table 1.1 Main characteristics of bulk and molecular CPU circuits

Electrons needed for bit of information 16,000 electrons Much less than one electron

Power sources to operate Need external power supply Molecules are always ready to operate Integration scale 10 8 gates/cm 2 10 13 gates/cm 2

Novel molecular electronics would approach the density of ~1013 logic

gates/cm2 It offers a 105 decrease in the size dimensions compared to the present

feature of a silicon-based microchip.53 In addition, the present fastest devices can

only operate in nanosecond while the response times of molecular-sized systems

can reach the range of femtoseconds Thus, the speed may be attained to a 106

increase On the basis of these estimates, a 1011 foldincrease in the performance

can be expected with molecular electronics, which offers an exciting impetus for intense research and development though numerous obstacles remain

In this nano size regime, several fundamental properties of quantum systems, such as uncertainty, superposition, entanglement and interference, have

to be considered Therefore, extension of conventional electronics to molecular electronics requires exploration of organic structures which can scale far beyond the present size limits.57, 58, 60-62

Many of the technological applications of molecular electronics, including the computational applications, should be considered and viewed as the drivers for the field Tour’s group has demonstrated the synthetic/computational approach

to digital computing of molecular scale electronics.63 In his paper, the alligator clip –SH acted as the contact to input or output in digital computing of molecular electronics The alkyl groups which broke the conjugation of the wire served as the transport barrier in the integrated circuits The successful development of molecular-electronic integrated circuitry would also benefit nanomechanical devices, ultradense single-molecule sensor arrays, the interfaces to biosystems,64,

65 and the pathways toward molecular mechanical systems

1.6 Future of Molecular Electronics

The drive toward yet further miniaturization of silicon-based electronics has led to a revival of efforts to build devices with molecular-scale organic components However, the fundamental challenges of realizing a true molecular-electronics technology are daunting Controlled fabrication within specified tolerances and its experimental verification are major issues Self-assembly

schemes based on molecular recognition will be crucial for that task Ability to measure electrical properties of organic molecules more accurately and reliably is paramount in future developments Fully reproducible measurements of junction conductance are just beginning to be realized in labs at Purdue, Harvard, Yale, Cornell, Delft, and Karlsruhe Universities and at the Naval Research Laboratory and other centers

Robust modeling methods are also necessary in order to bridge the gap between the synthesis and understanding of molecules in solution and the performance of solid-state molecular devices In addition, the searching of fabrication approaches which can couple the densities achievable through lithography with those achievable through molecular assembly is also a great challenge Controlling the properties of molecule-electrode interfaces and constructing molecular-electronic devices that can exhibit signal gain are also crucial to the development in the field

1.7 Project Objectives

The overall objective of this research work is to investigate pure BPDT (biphenyl-dithiol) and DPA (diphenylanthracene) derivatives as new materials for use in molecular electronics The specific aims of the project are listed as the following:

(i) Synthesis of BPDT and DPA derivatives with dithioacetate alligator clip

(ii) Preparation of ordered self-assembled monolayers of these BPDT and DPA derivatives on gold surfaces

(iii) Fabrication of metal-SAM-metal junctions and study the conductivities of these junctions

It has been shown in the previous paragraphs that the molecule-electrode interface is a critically important component of a molecular junction Among all the alligator clips, sulfur compounds have the strongest affinity to transition metal surfaces We use the same dithioacetate alligator clip but modify the backbone of the compounds By measuring the conductivity of a series of molecules that are systematically altered, the contribution of each component of the backbone will

be studied and discussed in this thesis

CHAPTER TWO General Experimental Section and Characterization Techniques

2.1 General Experimental Section

2.1.1 Chemicals

Ammonium hydroxide (Reagent Chemical PTE LTD); 1,2-dibromoethane (Fluka); dichlorodimethylsilane, dimethylacetamide (Merk); 3,3'-dimethylbiphenyl, 9, 10-dibromoanthracene (TCI); acetyl chloride, 4-methoxyphenylboric acid, tetrakis(triphenylphosphine)palladium(0), diphenylmethane, zinc (Alfa Aesar) Chlorosulfonic acid, dibenzyl, dimethylacetamide (DMA), acetyl chloride, hydrobromic acid, magnesium sulfate,

1, 10-dibromodecane and 1, 6-dibromohexane were purchased from Sigma (Singapore) THF was distilled from sodium/benzophenone ketyl DMF was freshly distilled under reduced pressure Other solvents were used as received without further purification Unless otherwise noted, reactions were magnetically stirred and monitored by thin-layer chromatography (TLC) on silica gel precoated glass plates (0.25 mm thickness, 60F-254, E Merck) Flash column chromatography was performed using pre-coated 0.2 mm silica plates from Selecto Scientific Chemical yields refer to pure isolated substances Compounds were named using the Struct=Name algorithm in ChemDraw 8.0 developed by CambridgeSoft

2.1.2 Characterization Techniques

The nuclear magnetic resonance (NMR) spectra were collected on a

standard 1H NMR data were recorded in the order of chemical shift value, multiplicity (s, singlet; d, doublet; t, triplet; q, quartet; m, multiplet; br, broad), and number of protons that gave rise to the signal Mass spectra (MS) were obtained by using an Agilent 5975C MSD DIP at an ionizing voltage of 70 eV Thermogravimetry (TG) was performed on a 2960 TA Instrument at a heating rate

of 20 ℃/min under N2 Ultraviolet-visible (UV-vis) spectra were recorded on a Shimadzu UK1601 spectrophotometer fitted with a quartz cell Photoluminescence (PL) emission and excitation spectra were carried out on a Perkin–Elmer LS55 luminescence spectrometer with a xenon lamp as a light source Gold substrates were prepared in vacuum using Univex 300 E-Beam Evaporator Fourier transform infrared spectroscopy (FT-IR) was performed on a Bio-Rad Excalibur FTS 3000 FT-IR spectrometer Samples were prepared as KBr pellets.Reflectance Fourier Transform Infrared Spectroscopy (reflectance FT-IR)

of the self-assembled monolayers (SAMs) on gold substrates was collected on a

Shimadzu Reflectance IRPrestige-21 The contact angles were measured on an AST Products Inc., VCA-Optima contact angle goniometer Layer thicknesses of the SAMs on gold substrates were characterized by spectroscopic elipsometry (M-

2000, JA Woollam, Lincoln) Images of the surfaces were performed on Atomic Force Microscopy (AFM) Dimension 3100 (Veeco Metrology Group) using tapping 300 silicon AFM probes (PhotoniTech, Singapore; resonant frequency:

300 kHz; force constant: 40 N/m; tip radius : <10 nm) Images of the current of

SAMs on Au and I-V curves were recorded on Conductive Atomic Force

Microscopy (C-AFM) Dimension 3100 (Veeco Metrology Group) using coating silicon AFM probes (PhotoniTech, Singapore; resonant frequency: 13 kHz; force constant : 0.2 N/m; tip radius : <25 nm)

Pt-2.2 Formation of Self-Assembled Monolayer (SAM)

2.2.1 General Procedure for Si Substrate Pretreatment

The starting material was a 0.5 mm-thick single side polished silicon (100) wafer (N-doped, 2 nm-thick SiO2) The silicon wafer was cleaved into 1 cm × 1

cm squares Pretreatment of the silicon wafers was carried out in piranha solution which typically consists of a 1:3 v/v solution of 30% hydrogen peroxide (H2O2) and concentrated sulfuric acid (H2SO4) Caution! Piranha solution is a very strong oxidant and is extremely dangerous to work with; gloves, goggles and lab coats should be worn The preparation procedure is described in the following

steps

(i) Wafers were immersed in the piranha solution for 5 to 10 mins Piranha solution removed organic contaminants by oxidizing them, and metals by forming soluble complexes Exact time of immersion may vary depending

on the substrate used and the temperature Prolonged exposure to piranha solution can result in sample surface roughening

(ii) Wafers were rinsed with deionized (DI) water (>18 MΩcm) for at least 1 min

(iii) Wafers were immersed in base piranha (a 5:1:1 mixture of DI water, H2O2

and ammonium hydroxide) for 10 mins

(iv) Wafers were rinsed with DI water for at least 1 min

(v) Wafers were finally rinsed with acetone (HPLC grade), IPA (HPLC grade), dried with a flowing ultrahigh purity N2 gas

2.2.2 General Procedure of Gold Substrate Preparation

100 nm of gold (99.99% purity) were evaporated onto freshly cleaned 1

cm × 1 cm silicon wafers at a rate of 1 Å/s with an adhesion layer of titanium (5

nm, 99.9% purity,0.1 Å/s) using a Univex 300 E-Beam Evaporator The chamber pressure during evaporation was about 3×10-6 Torr After preparation the films were kept in the vacuum chamber at 10-6 Torr for about half an hour, subsequently removed from the chamber and was characterized immediately Atomic Force Microscopy (AFM) measurements of the substrate showed root-mean-square

(RMS) roughness factor of 1.039 over a surface of 1 µm2 (See Figure 2.1)

Fig 2.1 AFM image of the gold substrate: Si/Ti (5 nm)/Au (100 nm); pressure:2.75 x 10-6

Torr; rate: 1 Å/sec

2.2.3 Formation of Self-Assembled Monolayer (SAM)

The gold thiolate (R-S-Au) system is the most commonly studied assembled monolayers (SAM).66The assembly takes place within seconds or days, depending on the concentration of the materials and the molecular structure of the monolayers, resulting in crystalline ordering domains ranging from several to hundreds of square nanometers At the same time, the defect density will depend

self-on the quality of the gold surface, the backbself-one structures and the alligator clips

of the monolayer materials used In a well-ordered self-assembled molecular array, the defect density may be 1-5% The gold thiolate bond (R-S) has the strength of

~2 eV or ~50 kcal/mol; hence it is quite robust relative to Cu-S and Ag-S bonds that can be formed at ambient temperatures There are numerous other surfaces that have been employed in SAM construction.67 Despite some problems associated with self-assembly, it promises to be far superior to tedious single-molecule manipulations using, for example, a scanning probe microscopy (SPM) tip

The use of free thiols, rather than thioacetates, proved to be problematic since they were prone to very rapid oxidative disulfide formation Although disulfides can self-assemble on gold surface, the assembly is ~1000 times slower

than that with the thiols Moreover, when using the α,ω-dithiols, oxidative

polymerization ensues, rapidly resulting in insoluble materials In addition, the thioacetate end groups can be selectively deprotected in THF to afford the free thiols during the deposition process.68 Based on these considerations, thioacetates are some of the mostly studied materials for self-assembled monolayers on gold

2.2.3.1 Theory for Self-Assembled Monolayer (SAM) Formation

The formation of self-assembled monolayer of thiol on gold surface can be considered formally as an oxidative addition of the S-H bond to the gold surface, followed by a reductive elimination of the hydrogen When a clean gold surface is used, the proton probably ends as a H2 molecule This can be deduced from the fact that monolayers can be formed in the complete absence of oxygen:

R−S−H +Au 0 n = R−S⎯Au + ·Au 0 n-1 + 1 / 2 H 2

The combination of hydrogen atoms at the metal surface to yield H2molecules may be an important exothermic step in the overall chemisorption

energetics That the adsorbing species is the thiolate (RS⎯) has been shown by

XPS,69-72 electrochemistry,73 Raman spectroscopy,74-76 Fourier transform mass spectrometry,77 and Fourier transform infrared (FT-IR) spectroscopy.78 A number

of papers addressing the thermal stability of thiolate SAMs have also been reported.78, 79 The chemical state of the sulfur head group on Au is not explicitly known Even cleavage of the S-H bond upon the adsorption was questioned recently.80

2.2.3.2 Deprotection Procedure of Thiolacetate to Form Free Thiol

SAMs were prepared by either of two reliable and reproducible methods: base-promoted or acid-promoted adsorption.19

In the base-promoted technique, thioacetate (1 mM) was dissolved in a

suitable solvent, e.g., THF, ethanol, or a mixture of acetone/MeOH, in a 20 mL vial Concentrated NH4OH (28.0-30.0%) was then added to the solution and the mixture was incubated for a few minutes to generate the free thiol group Excess addition of NH4OH would lead to precipitation A clean gold substrate was then immersed into the solution at room temperature for a period of at least 24 h

In the acid-promoted method, concentrated H2SO4 was used instead of

NH4OH and the mixture was incubated for 1-4 h to produce the free thiol A clean gold substrate was then immersed into the solution at room temperature for a period of at least 24 h

2.2.3.3 General Process of Self-Assembled Monolayer (SAM) Formation

The self-assembly of alkanethiols is usually carried out under relatively high concentrations (1-10 mM) Tour and co-workers68 showed that at high concentrations, conjugated dithiols usually form multilayer and precipitation due

to poor solubility In addition, conjugated thiols can easily dimerize due to oxidative disulfide formation It was observed that in situ deprotection of thioacetyl groups by addition of NH4OH appeared to be an excellent method to prevent multilayer formation and get nearly quantitative yield.68 In our case, the self-assembly of conjugated dithioacetates was performed in much more dilute solutions (≤1 mM) to avoid these problems

Prior to immersion into the thiol-containing THF (anhydrous) solution, the gold substrates were cleaned for 30 mins in a mixture of water/NH4OH/H2O2 (5:1:1) held at 75 °C, rinsed with deionized water (3 times), and blown dry with

N2 The acetyl protected molecules were dissolved in THF (1 mM), deprotected

by adding 1 drop (50 µL) of 30% ammonium hydroxide (aq) per 10 ml of THF

solution, purged with N2 for an oxygen-free environment All the solutions were freshly prepared, previously purged with N2 and kept in the dark during immersion The gold substrate was immersed into the solution for at least 24 h with the gold layer facing up After the assembly, the samples were removed from the solutions, thoroughly rinsed three times with freshly distilled THF and iso-propanol (IPA, HPLC grade), dried with a flowing ultrahigh pure N2 gas, and their electrical characteristics measured immediately All preparations were performed

at room temperature, and all samples were used within 1 day after preparation for

Fig 2.2 Side view of the SAM Structure

2.3 Characterization of the Molecules as SAMs

2.3.1 Thickness Measurement by Spectroscopic Ellipsometry (SE)

2.3.1.1 Spectroscopic Ellipsometry (SE) Characteristics

Ellipsometry is a very sensitive measurement technique that uses polarized light to characterize surfaces, thin films, and material microstructures The polarization condition of an electromagnetic wave is altered by reflection from a

surface In general, both the phase and the relative amplitude of the Cartesian

components of light are changed These changes are reflected in the ellipsometric

quantities delta (∆) and psi (Ψ) which can be used to determine the complex

dielectric response (refractive index) and thickness of overlayers on a reflective

surface Delta (∆=δ1-δ2) is defined as the phase difference between the p-wave

and the s-wave before (δ1) and after the reflection (δ2) Ψ (tanΨ=|Rp|/|Rs|), is the

angle whose tangent is the ratio of the magnitudes of the total reflection

coefficients with Rp being the reflection coefficient of the p-wave and Rs the reflection coefficient for the s-wave.81

Fig 2.3 Geometry of an ellipsometric experiment, showing the p- and s- directions.82

Ellipsometric data (∆(λ),ψ(λ)) was collected for each Au substrate before

SAM assembly to allow for optical function variation due to film roughness and

grain effects, and at selected intervals after immersion into thiol solution at room

temperature (22 °C) All layer thicknesses reported were calculated after

averaging over at least five measurements To measure the film thickness, it is essential to first estimate the refractive index function of the films, since the refractive index and thickness parameters of ultrathin films are strongly coupled together and thus cannot be independently determined by ellipsometry

In our case, layer thicknesses were measured on a spectroscopic ellipsometry (M-2000, JA Woollam, Lincoln) equipped with a sodium D line (589 nm) at an incidence angle of 54.9° with respect to the surface normal Reading were taken on the clean gold, to establish the bare substrate optical constants, and after monolayer formation, the thickness were calculated using a parallel, homogeneous three-phase (ambient/organic film/gold substrate) model

To estimate the refractive index function, we referred to the extensive data already known for organic materials For example, in the liquid state, the

refractive index at room temperature at the sodium D line (589 nm) n D is 1.43 for

octane and tetradecane, 1.49 for toluene and 1.62 for cis-stilbene; and in the solid

state, 1.51–1.52 for polyethylene, 1.49–1.50 for polystyrene Therefore we

estimate for the alkyl segment of the SAM molecules n D ≈ 1.45 in agreement with other workers,83, 84 and for phenyl segment n D ≈ 1.50–1.60 For the SAM

monolayer we estimate their effective refractive index n using

d

d n d

d

n

n

2 2 2

1 2

1

2

11

1

⋅+

⋅

of the alkyl and aromatic chains, d 1 and d 2 are their respective thicknesses, and d

is the total thickness This then gives an average n D ≈ 1.48–1.50 for the monolayer film The small anisotropy in these ultrathin films makes little or no difference to the ellipsometry results To include the effects of the weak optical dispersion, we

used the Cauchy function n (λ) = A + B / λ2 + C / λ4 with λ in microns This

function leads to n D = 1.49 From these considerations, the total uncertainty in the refractive index function is thus expected to be ± 0.05 units For this uncertainty, simulation of the ellipsometry data suggests an error of ± 5% in the deduced film thickness, which is acceptable for our purpose

2.3.1.2 Semiempirical Calculations

Semiempirical calculations were performed using the Gauss View 3.07 software The optimization was run from several initial conformations to make sure the global minimum was found The maximal monolayer thickness was estimated as the distance from the Au atom to the farthest hydrogen atom in the

optimized molecule, dAu-S+dS-ω+dvdw,where dAu-S is the distance of S above the Au

surface (≈2.4 Å); dS-ω is the distance of the frontier atom/group above the S plane (AM185); dvdw is the van der Waals radius of that frontier atom/group (e.g., ≈1.20

Å for H).86 The C-S-Au angle was constrained to 180°.20 And the S atoms were assumed to be adsorbed in a hollow site of the gold surface A comparison of experimental and the calculated thicknesses will be given in Chapters 3 and 4

2.3.2 Contact Angle (CA) Measurements of SAMs

Fig 2.4 Representative picture of a drop on the substrate.82

The contact angle (CA) is the angle at which a liquid/vapor interface meets the solid surface; it is equally applicable to the interface of two liquids or two vapors The contact angle is specific for any given system and is determined

by the interactions across the three interfaces Most often the concept is illustrated with a small liquid droplet resting on a flat horizontal solid surface The shape of the droplet is determined by the Young’s Equation:

γsg = γsl + γlg cos θ

γ is the surface tension which can be thought of as the energy required to create a unit area of an interface, θ is the contact angle If the energy required to create the solid-liquid (sl) interface is greater than that required for creation of a solid-gas (sg) interface, then the critical angle will be greater than 90° In other words, the liquid will bead up on the surface to minimize the solid-liquid interfacial area A contact angle less than 90° generally termed hydrophilic, and one greater than 90°

as hydrophobic Contact angle measurement is a simple and useful technique to determine the macroscopic surface properties of thin films.87-90 The wettability of surfaces covered with monolayers can be correlated with the quality and

hydrophilic or hydrophobic nature of the monolayers

The advancing contact angles (CAs) of deionized water (>18 MΩcm)

were measured shortly (<10 mins) after removal of the slides from the adsorption solution using a VCA-Optima contact angle goniometer The advancing CAs were

measured immediately after placing a drop of 2 µL water on the substrate with a

micropipette and determined from the circumference of the drop, which was acquired with a video camera The image was digitized and the circumference was extracted after thresholding the gray level of each pixel The values of the contact angle were averaged for at least triplicate measurements taken at different positions of a substrate All measurements were made at 23 ± 1 °C and ambient humidity

2.3.3 Reflectance Fourier Transform Infrared Spectroscopy (Reflectance

FT-IR)

Fig 2.5 Experimental setup for reflectance FT-IR.82

Reflectance FT-IR is a technique used to probe the vibrations of molecules

at surfaces The theory of reflectance FT-IR is based on the vibrational excitation

of molecules arising from the interaction of the electromagnetic field of reflected

IR light with the dipole moments of adsorbed molecules The process is depicted

in Figure 2.5 A change in the dipole moment of the molecule is induced by the absorption of radiation, causing the molecule to be in an excited vibrational state The IR radiation consists of a p-polarized component (refer to Figure 2.3), which

is perpendicular to the surface plane, and an s-polarized component, which is parallel to plane of the surface As shown by Greenler,91, 92 it is only the p-polarized component of the radiation that can interact with the molecule’s dipole This is because the phase of the s-polarized radiation changes by almost 180° on reflection at all angles of incidence, and as a consequence, the surface field vectors of the incident and reflected radiation cancel each other, yielding a resultant surface field of almost zero However, the phase change which the p-polarized radiation undergoes upon reflection is strongly dependent on the angle

of incidence Therefore, the measured infrared band intensity of a vibrational mode directly depends on the projection of its transition dipole moment onto the surface normal This implies that one can only probe IR modes that have a nonzero component of the transition moment along the surface normal, that is, perpendicular to the gold surface

Reflectance infrared spectroscopy can be used to obtain the orientations of adsorbate molecules, adsorbate-substrate and adsorbate-adsorbate interactions (e.g hydrogen-bonding), adsorption sites and relative coverages It has traditional been used in a wide variety of applications, such as general organic chemistry, polymer science, pharmaceuticals, and food Reflectance FT-IR is now being applied in

industries such as semiconductors, optical components, and electronic devices Very high sensitivity is required to analyze the thin layers or the small impurities that cause concerns in these fields However, obtaining good S/N ratios is a common problem in reflectance FT-IR experiments because the amount of absorbing material is so small – just one molecular layer So the molectron polarizer was placed in front of the detector to increase the S/N ratio by removing s-polarized light

Reflectance FT-IR spectra were collected using an IRPrestige-21 (P/N 206-72010) spectrophotometer, Shimadzu (Asia Pacific) Pte Ltd., with a high sensitivity DLATGS (Deuterated triglycine sulfate doped with L-alanine) detector

at a resolution of 4 cm-1 and an incident angle of 80° to the surface normal The mirrors used in the IRPrestige-21 are gold-coated silicon wafers and have 98% reflectance compared to the 95% reflectance of traditional aluminum mirrors The over 40,000 : 1 S/N ratio of the IRPrestige-21 assists in the high sensitivity analysis

Before measurement of the SAMs on gold-coated silicon wafers, a reference spectrum was recorded on a freshly cleaned gold substrate 500 consecutive scans were averaged before the spectrum was corrected for the gold

substrate by plotting the absorbance as -log(R/R0), where R is the reflectivity of the substrate with the monolayer and R0 is the reflectivity of the reference gold substrate

2.3.4 Surface Imaging by Atomic Force Microscopy (AFM)

In 1981 researchers at IBM were able to utilize the methods first demonstrated by Young to create the scanning tunneling microscope (STM) Although the STM was considered a fundamental advancement for scientific research, it had limited applications, because it worked only on conducting or semiconducting surfaces.93, 94 The Atomic Force Microscope (AFM) was developed in 1986 to overcome this basic drawback with STM.95 The AFM has the advantage of imaging almost any type of surface, including polymers, ceramics, composites, glass, and biological samples

There are three primary modes of AFM: non-contact mode AFM, contact mode AFM and tapping mode AFM For non-contact mode AFM, the cantilever is oscillated at a frequency which is slightly above the cantilever’s resonance frequency typically with an amplitude of a few nanometers (<10 nm), in order to obtain an AC signal from the cantilever Contact mode AFM operates by scanning

a tip attached to the end of a cantilever across the sample surface while monitoring the change in cantilever deflection with a split photodiode detector Tapping mode AFM (Figure 2.6) operates by scanning a tip attached to the end of

an oscillating cantilever across the sample surface Non-contact mode AFM only has the advantage of no force exerted on the sample surface Although Tapping

mode AFM has slightly slower scan speed than contact mode AFM, it has higher

lateral resolution on most samples and lower forces and less damage to soft samples imaged in air In our experiments, images of the SAM surfaces were performed on Atomic Force Microscopy (AFM) Dimension 3100 (Veeco

Metrology Group) using Tapping 300 silicon AFM probes (Resonant frequency:

300 kHz; force constant: 40 N/m)

Fig 2.6 Illustration of Tapping Mode AFM.96

2.3.5 Current and Current-Voltage Characteristics Measured by

Conductive Atomic Force Microscopy (C-AFM)

2.3.5.1 Images of Current

For conductive AFM measurement, it is important to know the topological information of the sample surface, because surface roughness affects contact conditions To perform current image on SAM surface, a selectable bias was applied between the sample and the conductive scanning probe microscopy (SPM) tip, while the C-AFM tip contact with the surface of a SAM on Au We measured the current that flows across a SAM in response to the fixed bias voltage As the tip is scanning the sample in contact mode and imaging the topography, a linear amplifier with a range of 1pA to 1µA senses the current

passing through the sample Thus, the sample’s topography and current image are measured simultaneously, enabling the direct correlation of a sample location with its electrical properties

2.3.5.2 Current-Voltage Characteristics of Metal-SAM junctions

Metal junctions are currently considered as key elements in based electronic devices pursuing so-called “bottom-up” approach in nanotechnology66, 97-99 Characterization of charge transport and conduction mechanism in SAMs has therefore gained particular interest A full understanding

molecule-of the electronic transport characteristics through SAMs is essential for any device applications However such transport measurements are experimentally challenging due to the difficulty of making reliable electrical contacts with the nanometer scale monolayers.Transport studies for these molecular junctions have been performed by various methods such as mechanically controllable break junction technique,9 scanning tunneling microscopy (STM),100 nanopore,101, 102conductive atomic force microscopy (C-AFM),15, 103 electromigration nanogap,104,

105 cross-wire tunnel junction,106 mercury-drop junction,107 nanorod,108 and others C-AFM methods have key advantages for easy accessible junction formation, since no micro- or nanofabrication process is required Unlike STM, the C-AFM probe provides a direct contact on a sample, so that it eliminates vacuum tunneling effect, ensuring that the voltage is applied fully across the molecular layer between C-AFM probe and bottom electrode Additionally, the tip-SAM contact area in these junctions is small, meaning the junction properties reflect transport through a small number of molecules for a <25 nm radius probe

Fig 2.7 A rough schematic of the C-AFM setup 109

In our work, a junction is fabricated by placing a conductive AFM tip in stationary point contact with a metal-supported self-assembled monolayer (SAM)

on Au, as schematically illustrated in Figure 2.7 Current was recorded while voltages were applied to the probe tip and the substrates were grounded Figure 2.8 shows the side view of the Metal–SAM–Metal junction of platinum-BPDT-gold as an example of systems investigated in this thesis

CHAPTER THREE Biphenyl-Dithiol (BPDT) Derivatives for Molecular Electronics

3.1 Introduction

Molecular electronics (moletronics) represent the ultimate challenge in device miniaturization Molecular devices could be systems having one, two or more termini with current-voltage responses that would be expected to be nonlinear due to intermediate barriers or heterofunctionalities in the molecular framework while molecular wires refer to especially tailored molecular nanostructures whose spatial and energetic properties promote a distant electron transfer (ET) between two microelectrodes.110-114 In testing our molecular electronic systems, a wire is defined as a two-terminal entity that possesses a

reasonably I-V curve prior to the breakdown limit

Molecular wires (or sometimes called molecular nanowires) are molecular-scale objects which conduct electrical current They are the fundamental building blocks for molecular electronic devices The term molecular wire also refers to the ability to make connections to other devices Beyond that,

no physical similarity to macroscopic wires is implied

The resistance R of a wire with uniform cross section was calculated by

ℓ is the length of the wire, measured in meters [m];

A is the cross-sectional area of the current flow, measured in square meters [m2];

ρ is the electrical resistivity of the material, measured in ohm-meters (Ω m)

The resistance is proportional to its length, inversely proportional to its sectional area, and proportional to the resistivity of the material

cross-An ideal wire has zero resistance For practical reasons, any connections

to a real wire will almost certainly mean the current density is not totally uniform Practical wires normally have a resistance much smaller than 1 Ω However, the resistance of molecular wires is likely to be considerably larger than the practical wires.9, 115 Their typical diameters are less than three nanometers, while their bulk lengths may be macroscopic, extending to centimeters or more

3.2 Molecular Design

3.2.1 Design of Terminal Groups

The very close contacts of the sulfur atom to the two electrodes, namely the tip of the C-AFM and the gold substrate reflect ideal electronic tunneling through molecules This is different from the electron hopping mechanism found

in STM Chemically bonding each end of a molecule to a metal electrode is very important for making stable contacts for molecular electronics.103

Since aromatic dithiol compounds are usually easily oxidized and likely to polymerize through disulfide formation, they are more difficult to handle To overcome this problem, we used acetyl protection for the thiol functional groups similar to those described by Tour et al.11, 66, 68 Monothiols116 have a substantial dipole moment along the asymmetric phenyl chain, which lowers the packing efficiency when grafted on the gold surface Dithiols, on the other hand, have a

very small dipole which favour interchain interactions to promote packing on the gold surface similar to biphenyl systems with a small molecular dipole moment.117

We have designed dithioacetyl biphenyl derivatives that can be easily deprotected to dithiols which form strong chemically bonding with gold substrates

3.2.2 Design of Synthetic Routes

Scheme 3.1 Different synthetic routes to S-acetyl-4-iodothiophenol

As a candidate of molecular wires, arenethiols and their S-protected derivatives with precise length and backbone structure were prepared by diverse synthetic routes.11, 118 One of the advantages of these synthetic routes lies in that the S-protected group can be deprotected in mild conditions.119 However, as show

in Scheme 3.1, classical routes to prepare S-protected aromatic thiols usually

afford relatively lower yields with impurities In route 1, reduction of pipsyl chloride in zinc-aqueous acid system followed by reacting with acetic anhydride

in basic conditions usually give the desired thiols accompanied by various product such as disulfides,120 which are difficult to purify Route 2 involves a lithium-halogen exchange reaction on the arylhalides followed by treatment with sulfur and then acetyl chloride to afford S-acetyl 4-iodothiophenol with only a moderate yield.121

by-Wang’s group presents a convenient and efficient one-pot reaction (Route 3) to prepare S-acetyl-4-iodothiophenol in high yields This protecting group can stand with basic conditions and is stable at relatively high temperatures; two important conditions for the subsequent aryl coupling reactions Moreover, the protecting groups can be removed under mild conditions to give free thiols.121

3.2.3 Design of Conduction Barriers and Substitution Group

Alkyl units such as methylene and ethylene units pose larger electronic transport barriers (higher resistance to currents) than the π-conjugated moieties in single molecular systems.66, 115 These alkyl conduction barriers are incorporated in the rigid-rod backbone to disrupt the electronic characteristics of the wires It is hoped that the use of these internal methylene and ethylene tunnel barriers in molecular wires may allow the development of molecular devices that show non-linear I-V curve.122

In addition, methyl substituent groups were introduced on phenyl rings with an aim to increase the solubility and investigate effect of the electron-donating group on the packing order of the SAM and the charge transport

R

n SAc AcS

5: n= 2, R= H ( 91%) 6: n= 1, R= H ( 93%) 7: n= 0, R= H ( 89%)

SO2Cl ClO2S

9: n= 2, R= H (90%) 10: n= 1, R= H (88%) 11: n= 0, R= H (89%)

Scheme 3.2 Synthetic routes for compounds 9-12

3.3.1.1 4,4'-(ethane-1,2-diyl)dibenzene-1-sulfonyl chloride (5)

Diphenylethane (1) (1 g, 5.5 mmol) was rapidly added to chlorosulfonic

acid (1.7 ml, 25 mmol) without cooling The mixture turned from colorless to

yellow The suspension was left for 48 h The mixture was poured into crushed

ethanol mixture, filtered and the precipitate was thoroughly washed with

ice-ethanol The crude product was charged on a silica gel column Elution of the

column with DCM-hexane (1:1) mixture gave the white solid (2.02 g, 93%) 1H

NMR (300 MHz, CDCl3): δ (ppm) 8.03, 8.00 (d, 4H), 7.45, 7.42 (d, 4H), 3.14 (s,

4H); 13C NMR (300 MHz, CDCl3): δ (ppm) 146.0, 141.4, 129.0, 128.5, 37.5 ;

EI-MS m/z calcd for C14H12Cl2O4S2 378.0, found 377.9

3.3.1.2 4,4'-methylenedibenzene-1-sulfonyl chloride (6)

Diphenylmethane (2) (1 ml, 6.0 mmol) was rapidly added to

chlorosulfonic acid (2.0 ml, 30 mmol) without cooling The brown solution was