Organic Sulfenyl Chlorides As Precursors for the Modification of Gold Surfaces

Organic Sulfenyl Chlorides as Precursors for the Modification of Gold Surfaces

Hamida Sultan Muhammad

A Thesis presented to The University of Guelph

In partial fulfilment of requirements for the degree of Doctor of Philosophy in Chemistry

Guelph, Ontario, Canada

ABSTRACT

ORGANIC SULFENYL CHLORIDES AS PRECURSORS FOR THE MODIFICATION OF GOLD SURFACES

Hamida Sultan Muhammad Advisor: University of Guelph, 2013 Professor A. Houmam

Self-assembled monolayers (SAMs) of organosulfur precursors on gold have been extensively used since they offer a wide range of technological applications such as corrosion inhibition, lubrication, adhesion promotion/inhibition, nanofabrication, chemical and biosensors, catalysis, and molecular electronics. Furthermore, the electronic and optical properties of aromatic SAMs make them a potential candidate for molecular electronics. However, these practical applications are limited by the short-range ordering, low packing density, irreproducibility, and inferior quality of SAMs, which are more critical for aromatic SAMs.

Therefore, the discovery of alternative precursors is essential.

This thesis reports for the first time, the use of organic sulfenyl chlorides as precursors for the modification of gold surfaces. These precursors may help to overcome some practical limitations of the traditional organosulfur precursors. The modification is done in a non-aqueous medium. Characterization of the modified surfaces is performed by X-ray photoelectron spectroscopy (XPS), cyclic voltammetry (CV), polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS), and scanning tunnelling microscopy (STM).

Through the use of 4-nitrophenyl sulfenyl chloride, evidence for the formation of well-ordered aromatic SAMs formation on gold is provided. XPS data shows that the modification involves the scission of the S-Cl bond. PM-IRRAS studies further indicate that the adsorbed molecules are nearly vertically oriented on the surface. Both short and long-range well- ordered aromatic SAMs (a 4 x √3 rectangular and √3 x √3 hexagonal unit cells) are obtained from

the STM images using two different modification conditions. This molecular density is usually only observed for aliphatic SAMs using the traditional precursors. Along with the main hexagonal lattice, the reversible distinct superstructures including hexagons, partial hexagons, parallelograms, and zigzags resulting from specific arrangements of adsorbed molecules provide submolecular details. This is the first direct experimental example, where the STM has shown its effectiveness to provide physical structure information of standing-up aromatic SAMs at room temperature. This work also provides some insight into a heavily debated issue regarding the origin of the various features and contrasts obtained in STM images of SAMs.

The use of 2-nitrophenyl sulfenyl chloride and 2,4-dinitrophenyl sulfenyl chloride for the formation of aromatic SAMs on Au provides some insight regarding the modification extent and the effect of a nitro substituent (at ortho position ) on the quality of nitrophenyl thiolate SAMs on gold. XPS, PM-IRRAS, electrochemistry and STM provide evidence for the formation of less ordered, low density and less stable SAMs that may decompose to sulfur at longer modification times.

The efficient deposition of sulfur on gold is observed using a series of substituted methane sulfenyl chlorides (triphenylmethane sulfenyl chloride, trichloromethane sulfenyl chloride and chlorocarbonyl sulfenyl chloride). The XPS, STM and electrochemical data show the formation of high density sulfur phases. These include rhombus, rectangular, and zig-zag sulfur structures. A mechanism is suggested involving the cleavage of the S-Cl bond and the ejection of the molecular backbone. This study also suggests that substituted methane sulfenyl chlorides do not form long-range ordered SAMs.

Acknowledgements

First off all, I would like to thank my supervisor, Dr. Abdelaziz Houmam for accepting me into his research group and for all his help and guidance while pursuing my PhD degree. His ideas and patience made the experience an enjoyable one. Also I would like to thank my advisory committee members, Dr. Daniel F. Thomas and Dr. Wojciech Gabryelski for their helpful suggestions, and my examination committee members Dr. Tong Leung, Dr. Paul Rowntree and

Dr. Peter Kruse. I would also like to thank Dr. Mario Monteiro for agreeing to chair my thesis defense.

Lab members, former and current, I would like to thank, Dr. Emad Hamed, Dr. Md. Golam

Moula, Dr. Kallum M. Koczkur, Nusrat Serhat Un, Yimeng He and Goli Pourmand, all of who made my time in the Houmam lab a lot of fun.

A special thank you goes to Dr. Daniel F. Thomas, Dr. Kallum M. Koczkur and Ryan Seenath for helping me editing my PhD thesis. I would also like to appreciate Dr. Kallum M. Koczkur for conducting XPS experiments and his help during other lab work. I would like to thank Dr.

Grzegorz Szymanski for his help and assistance in working on Raman spectrometer and ellipsometer and Dr. Md.Golam Moula for his advices on the use of STM, vapour deposition system and electrochemical etching of STM tips. I am also grateful to Dr. Paul Rowntree, Stuart

Read and Ann Vandergust for their help in keeping Midas operational. Also, to Dr. Md. Golam

Moula, Ann Vandergust, Dr. Annia H. Kycia and Jay Leitch for their help in performing surface

IR experiments and all of my neighbours in the MacNaughton building and Science Complex.

Finally, I would like to thank my parents and siblings for their continuous support and encouragement.

Dedicated to

My Parents and Siblings

Table of Contents Page no. i) Acknowledgements iv ii) Dedication v iii) List of Tables x iv) List of Schemes x v) List of Charts xi vi) List of Figures xii vii) List of Abbreviations xxiv viii) List of Symbols xxviii

Preamble 1

Chapter I: Introduction and Background Information

I-1 General Background 3

I-2 Common Methodologies used for Surface Modification 5

I-3 Self-Assembled Monolayers (SAMs) 7

I-4 Organosulfur SAMs on Au 11

I-4a Building Blocks of Organosulfur SAMs on Au 11

I-4b Significance of Organosulfur SAMs on Au 14

I-4c Thermodynamics and Kinetics of Formation of Organosulfur 16

SAMs on Au

I-4d Mechanism of Formation of Organosulfur SAMs on Au 20

I-4e Modification Conditions for Organosulfur SAMs on Au 24

I-4f Structures of Organosulfur SAMs on Au 27

I-4g Debated Au-S Interface 30

I-4h The Quality of Organosulfur SAMs 45

I-4i Aromatic Organosulfur SAMs on Au 49

I-4j Interpretation of STM Images of Organosulfur SAMs 54

I-5 Motivation of the Research 59

I-6 Scope of Thesis 62

Chapter II: Experimental Part

II-1 Chemicals 65

II-2 Preparation of Au(111) Substrates 65

II-3 Modification of the Gold Surfaces 66

II-4 Characterization of the Modified Surfaces 67

II-4a Scanning Tunnelling Microscopy 67

II-4b X-ray Photoelectron Spectroscopy 73

II-4c Polarization Modulation Infrared Reflection Absorption 78

Spectroscopy

II-4d Cyclic Voltammetry 85

Chapter III. 4-Nitrophenyl Sulfenyl Chloride as a New Precursor for

the Formation of Aromatic SAMs on Gold Sulfaces

III-1 Introduction 91

III-2 Modification under Condition 1 93

III-2a Modification Procedure 93

III-2b Results and Discussion 94

III-3 Modification under Condition 2 105

vii

III-3a Modification Procedure 105

III-3b Results and Discussion 106

III-4 Proposed Mechanism of SAM Formation 125

III-5 Summary and Conclusions 126

Chapter IV. The Effect of Substituent(s) Position(s) on SAMs of Nitro

Aromatic Sulfenyl Chlorides on Gold Surfaces

IV-1 Introduction 128

IV-2 Modification using Compound 2 130

IV-2a Modification Procedure 130

IV-2b Results and Discussion 130

IV-3 Modification using Compound 3 140

IV-3a Modification Procedure 140

IV-3b Results and Discussion 140

IV-4 Comparison of Compounds 1-3 149

IV-5 Proposed Adsorption Mechanism for Compounds 2 and 3 153

IV-6 Summary and Conclusions 153

Chapter V. Substituted Methane Sulfenyl Chlorides as Precursors for

the Modification of Gold Surfaces

V-1 Introduction 155

V-2 Modification Procedure 156

V-3 Results and Discussion 156

V-3a XPS Characterization 156

viii

V-3b Stripping Voltammetry 160

V-3c STM imaging 170

V-4 Proposed Mechanism of Sulfur Deposition for Compounds 4-6 on Au 178

V-5 Summary and Conclusions 180

Chapter VI: Summary and Future Work

VI-1 Summary 182

VI-2 Future Work 186

Chapter VII: References 190

Appendix A: Copyright Permissions 227

List of Tables

Chapter I:

Table 1-1. Energies of adsorption (kcal/mol) for methanethiol SAM on Au(111) at different adsorption sites.

Table 1-2. Bond dissociation energies (S-Y bonds) and reduction potentials of compounds 4-

RPhSY.

List of Schemes

Chapter III:

Scheme 3-1. Global reduction reaction of arene sulfenyl chlorides and arene thiocyanates.

Scheme 3-2. Proposed deposition mechanism.

Chapter IV:

Scheme 4-1. Proposed deposition mechanism.

Chapter V:

Scheme 5-1. Proposed deposition mechanism for compound 4-6 on Au.

Chapter VI:

Scheme 6-1. Proposed reactions of the terminal nitro group of the 4-nitrophenyl thiolate SAM on Au in an electrochemical environment.

Scheme 6-2. Proposed reactions of the terminal group of the 4- phenyl thiolate SAM on Au in an electrochemical environment using SECM tip.

Scheme 6-3. Scheme for the synthesis of mixed-ligand CdS nanoclusters containing 1 mol % of 4-(4-Nitrophenylazo) thiophenol ligand.

List of Charts

Chapter III:

Chart 3-1. Structure of 4-nitrophenyl sulfenyl chloride (1).

Chapter IV:

Chart 4-1. Structures of 2-nitrophenyl sulfenyl chloride (2) and 2,4-dinitrophenyl sulfenyl chloride (3).

Chapter V:

Chart 5-1. Structures of compounds 4-6.

List of Figures

Chapter I:

Figure 1-1. Illustrations of Langmuir, Langmuir-Blodgett and Langmuir-Schaefer films deposition methods.

Figure 1-2. Schematics showing (a) a trichlorosilane SAM on SiO2, (b) an alkanethiol SAM on Au, (c) a fatty acid SAM on Al2O3, and (d) a fatty acid SAM on Ag2O.

Figure 1-3. Scheme of an alkanethiol molecule adsorbed on a gold surface. The angles used to describe the molecular orientation are θ, β and χ.

Figure 1-4. Structure and characteristics of an ideal alkanethiol SAM on Au(111).

Figure 1-5. An illustration of the simplified sequences of a SAM growth.

Figure 1-6. Summary of the STM contrasts reported previously for alkanethiol SAMs.

Contrast α (a) represents the (3 x 3)R30° structure and contrasts β-ζ (c-f respectively) have the c(43 x 23) periodicity. For the clarity of the illustration, the STM spots corresponding to alkanethiol molecules are represented as located on equivalent hollow adsorption sites (i.e. assuming zero tilt and rotation angles).

Figure 1-7. The proposed structural models for (b x 3) striped phases of alkanethiol SAMs on Au(111). (a) Head to head arrangement, and (b) head to tail arrangement. The alkyl chain is represented by zig-zag lines. The lateral registry of the molecules and the substrate is assigned arbitrarily with the head group placed on hollow sites of Au(111).

Figure 1-8. Structural models for the adsorption of alkanethiol on Au(111) at different adsorption sites. (a) fcc hollow sites, (b) hcp hollow sites, (c) bridge sites, and (d) on top sites.

Figure 1-9. The proposed structural model for the c(4 x 2) lattice of an alkanethiol on

Au(111) with alternating rows of S head at hollow and bridge sites. The distance between

xii alternating rows is 10 Å and between adjcant rows is 4.5 Å.

Figure 1-10. The proposed dynamic models for the adsorption of alkanthiol on Au(111). (a)

Au-adatom dithiolate model, (b) Au-adatom thiolate model, and (c) a polymeric model, where thiol molecule is bonded to two Au-adatoms.

Figure 1-11. Proposed structural models for the chemisorption of sulfur on Au(111) at low coverage. The sulfur atoms are placed on hollow sites arbitrarily. (a) A (5 x 5) phase (~0.25

ML), (b) a (√3 x √3)R30o phase (~0.33 ML), and (c) a quasi linear phase. The large circles in

Figure 1-11a highlight the ordering of the seven sulfur atoms.

Figure 1-12. Proposed structural models for the chemisorption of sulfur on Au(111) at high coverage. Rectangular/quasirectangular structures (a) a complex AuS phase (~0.5 ML), and

(b) a polysulfide S8 phase (~0.6 ML).

Figure 1-13. XPS spectra in the Au 4f and S 2p regions of the nanoscale AuS formed with

Na2S to HAuCl4 ratios of (1,2) 0.65, (3) 1.2, (4) 2, (5) 3, and (6,7) 5 (bulky amorphous precipitates).

Figure 1-14. Schematic models showing different types of surface defects. (a) A vacancy island, (b) a step edge, (c) missing rows, (d) domain boundries, and (e) molecular defects (pin holes).

Figure 1-15. Schematic representation of a (a) BPT SAM, (b) e-beam induced cross-linking, and (c and d) temperature-induced changes in pristine and e-beam cross-linked BPT SAMs.

Figure 1-16. STM images of heptanethiol SAMs with the c(4 x 2) superlattice: (a) Sample bias (Vs) = +0.5 V, (b) Vs = +2.0 V, and (c) Vs = -1.5 V. The dependencies of the intramolecular patterns on Vs are indicated.

Figure 1-17. Simulated STM images of a single heptanethiol molecule on the Au(111) surface

3 with the sp model (a1) Vs = +0.5 V, (a2) Vs = +2.0 V, (a3) Vs = -1.5 V; and with sp model

xiii

(b1) Vs = +0.5 V, (b2) Vs = +2.0 V, (b3) Vs = -1.5 V. (a) and (b) are the side views of a heptanethiol adsorbed on Au(111) surface with the sp and sp3 mode, respectively.

Figure 1-18. Linear sweep voltammetry (LSV) in 0.1 M NBu4PF6/MeCN at a glassy carbon electrode. 4-MePhSCN (3.26 mM) and 4-MePhSCl (2.65 mM). Scan rates 200 mV/s.

Chapter II:

Figure 2-1. Topographic images of thin gold films on mica prepared by PVD. (a) 500 x 500 nm2, (b) 200 x 200 nm2 and (c) 5 x 5 nm2. Tunnelling conditions: Tip bias = +0.1 V, tunnelling current = 0.8 nA, and scan rate 4.1 lines/s.

Figure 2-2. An illustration of the quantum mechanical tunnelling with respect to distance between two conductors.

Figure 2-3. A scheme of electron tunnelling with respect to the LDOS after applying negative or positive bias to the sample.

Figure 2-4. Schematic view of STM.

Figure 2-5. An illustration of the photoemission principle.

Figure 2-6. Scheme for a monochromatic X-ray photoelectron spectrometer.

Figure 2-7. Directions of electric field vectors (Ep) of incident (subscript i, dashed arrows) and reflected (subscript r, solid arrows) IR beam at air/Au interface (a) p-polarized (b) s- polarized.

-1 Figure 2-8. Angular dependence of phase shift for air/Au interface at 1600 cm .

Figure 2-9. Representation of the image effect for the metal surface.

Figure 2-10. Block diagram of PM-IRRAS spectrometer.

Figure 2-11. A CV for a reversible redox active species.

xiv

Chapter III:

Figure 3-1. XPS signals for compound 1 SAM on Au(111). The modification is done in a 1 mM solution of compound 1 in DMF:EtOH (9:1) for 24 hours.

Figure 3-2. Representation of atomic displacements (black arrows) and IR vectors (red arrows), of the main vibrational modes of compound 1 observed for a SAM on Au(111). The

+ - represented vibrational modes are the symmetric (r NO2) and asymmetric (r NO2) stretch modes of the NO2 group, the superposition of CC stretching and CH in plane bending of the phenyl ring (rCC-δCH) and the CH in plane bending of the phenyl ring (δCH).

Figure 3-3. IR spectra of compound 1 in ~11 mM solution (CCl4) and SAM on Au(111). The modification is performed using a 1 mM solution of compound 1 in an EtOH:DMF (9:1) mixture for 24 hours.

Figure 3-4. Time dependent cyclic voltammetry of bare and previously modified polycrystalline solid gold electrodes in a 0.5 M aqueous KOH solution at 25 oC. Scan rate v =

200 mV/s. The electrodes are modified using a 1 mM solution of compound 1 in an

EtOH:DMF (9:1) mixture.

Figure 3-5. Time dependent coverage of the monolayer deposition calculated from the reductive stripping voltammetry of previously modified polycrystalline solid gold electrodes in a 0.5 M aqueous KOH solution at 25 oC. The modification is performed using a 1 mM solution of compound 1 in an EtOH:DMF (9:1) mixture.

Figure 3-6. (a) 45 x 45 nm2, (b) 15 x 15 nm2, and (c) 5 x 5 nm2 STM images of compound 1

SAMs (obtained using a 1 mM solution of compound 1 in EtOH:DMF (9:1) for 24 hours) on

Au(111). (d) Proposed model with 4 x √3 rect unit cell shown (a = 4.8 ± 0.2 Å and b = 11.7 ±

0.4 Å). (e-g) Line profiles along lines A to C respectively as shown in c. Tunnelling conditions: Tip bias = +0.1 V, tunnelling current = 0.80 nA and scan rate = 4.1 lines/s.

Figure 3-7. IR spectra of compound 1 in ~11 mM solution (CCl4) and SAM on Au(111). The modification is performed using a 10 mM solution of compound 1 in a MeOH:THF (1:1) mixture for 48 hours.

Figure 3-8. IR spectra of compound 1 SAM on Au(111) formed at two different modification conditions.

Figure 3-9. Cyclic voltammetry, in a 0.5 M aqueous KOH solution at 25 oC, of a 2 mm diameter bare and previously modified polycrystalline solid gold electrodes. The electrodes are modified using a 10 mM solution of compound 1 in a MeOH:THF (1:1) mixture. Scan rate v = 200 mV/s.

Figure 3-10. Time dependent coverage of the monolayer deposition calculated from the reductive stripping voltammetry of previously modified polycrystalline solid gold electrodes in a 0.5 M aqueous KOH solution at 25 oC. The modification is performed using a 10 mM solution of compound 1 in a THF:MeOH (1:1) mixture.

Figure 3-11. Unfiltered STM images in air of a Au(111) surface on mica modified using 4- nitrophenyl sulfenyl chloride (10 mM in MeOH:THF (1:1)) for 48 hours. Scan sizes (a) 60 x

60 nm2, (b) 20 x 20 nm2, (c) 10 x 10 nm2, and (d) 5 x 5 nm2. (e and f) Height profiles along line A and line B, respectively. Tunnelling conditions: Tip bias = +2 V, tunnelling current =

0.3-1.0 nA and scan rate = 4.1 lines/s.

Figure 3-12. (a) Unfiltered STM image of a Au(111) surface modified using compound 1, 8.4 x 8.4 nm2. Tunnelling conditions: Tip bias = +2 V, tunnelling current = 0.30 nA and scan rate

= 4.1 lines/s. (b) and (c) Line profiles along lines A and B going through a brighter spot from two different directions.

Figure 3-13. (a-j) Sequential STM imaging of a SAM of compound 1 on Au(111). Scan size:

8.2 x 8.2 nm2. Images (unfiltered) are recorded in the sequence. Tunnelling conditions: Tip

xvi bias = +2 V, tunnelling current = 0.30 nA and scan rate = 4.1 lines/s.

Figure 3-14. Sequential STM imaging of a SAM of compound 1 on Au (111). Scan size: 8.4 x

8.4 nm2. Images (unfiltered) are recorded in the sequence (a to d). Tunnelling conditions: Tip bias = +2 V, tunnelling current = 0.30 nA and scan rate = 4.1 lines/s.

Figure 3-15. (a) Unfiltered STM image of a SAM of compound 1 on Au (111). Scan size: 10 x 10 nm2. Tunnelling conditions: Tip bias = +2 V, tunnelling current = 0.30 nA and scan rate

= 4.1 lines/s. (b and c) Height profiles along line A and B respectively. (d) Profile and top views of an optimized 4-nitrophenyl thiolate structure titled to align one of the oxygen atoms with the S atom (tilt angle 9.35o). (e) Molecular rearrangement providing the hexagonal structure. (f) Slightly filtered STM image showing a hexagon (scan size 2.3 x 2.3 nm2). (g)

Schematic model of image f showing molecular placement of 4-nitrophenyl thiolate molecules on the Au (111) surface.

Figure 3-16. (a) An unfiltered STM image (5 x 5 nm2) of a Au(111) surface modified using compound 1 showing a hexagon structure. (b) to (g) Line profiles along six edges of the hexagon as marked in h.

Figure 3-17. (a) Filtered, (b) unfiltered STM images of a Au(111) surface modified using compound 1 showing a parallelogram structure, and (c-f) line profiles along the parallelogram edges. Tunnelling conditions: Tip bias = +2 V, tunnelling current = 0.30 nA and scan rate =

4.1 lines/s. (g) Schematic representation of the parallelogram structure observed by STM on a

Au(111) surface modified using 4-nitrophenyl sulfenyl chloride.

Figure 3-18. (a) Filtered, (b) unfiltered STM images of a Au(111) surface modified using compound 1 showing a zig-zag structure, and (c and d) line profiles along two zig-zag edges.

Tunnelling conditions: Tip bias = +2 V, tunnelling current = 0.30 nA and scan rate = 4.1 lines/s. (e) Schematic representation of the zig-zag structure observed by STM on a Au(111)

xvii surface modified using compound 1.

Figure 3-19. (a) Filtered, (b) unfiltered STM images of a Au(111) surface modified using compound 1 showing a partial hexagon structure, and (c-g) line profiles along the partial hexagon edges. Tunnelling conditions: Tip bias = +2 V, tunnelling current = 0.30 nA and scan rate = 4.1 lines/s. (h) Schematic representation of the partial hexagon structure observed by

STM on a Au(111) surface modified using compound 1.

Chapter IV:

Figure 4-1. X-ray photoelectron spectra of Au(111) on mica modified using a 1 mM solution of compound 2 in an EtOH:DMF (9:1) mixture for 24 hours.

Figure 4-2. Representation of atomic displacements (black arrows) and IR vectors (red arrows), for the main vibrational modes of compound 2 observed for a SAM on Au(111). The

+ - represented vibrational modes are the symmetric (r NO2) and asymmetric (r NO2) stretch modes of the NO2 group, the CH in plane bending of phenyl ring (δCH) and the superposition of the CC stretching and the CH in plane bending of phenyl ring (rCC-δCH).

Figure 4-3. IR spectra for compound 2 in a ~17 mM solution (CCl4) and SAM on Au(111).

The modification is performed using a 1 mM solution of compound 2 in an EtOH:DMF (9:1) mixture for 24 hours.

Figure 4-4. Time dependent cyclic voltammetry of bare and previously polycrystalline solid gold electrodes in a 0.5 M aqueous KOH solution at 25 oC. The electrodes are modified using a 1 mM concentration of compound 2 in a EtOH:DMF (9:1) mixture. Scan rates 200 mV/s.

Figure 4-5. Time dependent coverage of the monolayer deposition calculated from the reductive stripping voltammetry of previously modified polycrystalline solid gold electrodes in a 0.5 M aqueous KOH solutions at 25 oC. The electrodes are modified using a 1 mM

xviii solution of compound 2 in a EtOH:DMF (9:1) mixture.

Figure 4-6. Unfiltered STM images, in air, of a Au(111) surface on mica modified using compound 2 (10 mM in MeOH:THF (1:1)) for 48 hours. Scan sizes (a) 48 x 48 nm2, (b) 28 x

28 nm2, (c) 10 x 10 nm2, and (d) 5 x 5 nm2. Tunnelling conditions: Tip bias = +0.1 V, tunnelling current = 0.80 nA and scan rate = 4.1 lines/s. (e) Proposed model for the SAM of compound 2 on Au(111).

Figure 4-7. X-ray photoelectron spectra of Au(111) on mica modified using a 1 mM solution of compound 3 in an EtOH:DMF (1:1) mixture for 24 hours.

Figure 4-8. Representation of atomic displacements (black arrows) and IR vectors (red arrows), of the main vibrational modes of compound 3 observed for a SAM on Au(111). The

+ + - represented vibrational modes are the symmetric (r 2-NO2 and r 4-NO2) and asymmetric (r 2-

- NO2 and r 4-NO2) stretch modes of the NO2 group, the superposition of the CC stretching and the CH in plane bending of phenyl ring (rCC-δCH) and the CH in plane bending of phenyl ring (δCH).

Figure 4-9. IR spectra for compound 3 in a ~14 mM solution (CCl4) and SAM on Au(111).

The modification is performed using a 1 mM solution of compound 3 in an EtOH:DMF (1:1) mixture for 24 hours.

Figure 4-10. Time dependent cyclic voltammetry of bare and previously modified polycrystalline solid gold electrodes in a 0.5 M aqueous KOH solution at 25 oC. The electrodes are modified using a 1 mM concentration of compound 3 in an EtOH:DMF (1:1) mixture. Scan rates 200 mV/s.

Figure 4-11. Time dependent coverage of the monolayer deposition calculated from the reductive stripping voltammetry of previously modified polycrystalline solid gold electrodes

xix in a 0.5 M aqueous KOH solution at 25 oC. The electrodes are modified using a 1 mM solution of compound 3 in an EtOH:DMF (1:1) mixture.

Figure 4-12. Unfiltered STM images in air of a Au(111) surface on mica modified using compound 3 (10 mM in MeOH:THF (1:1)) for 48 hours. Scan sizes (a) 23 x 23 nm2, (b) 18 x

18 nm2, (c) 10 x 10 nm2, and (d) 5 x 5 nm2. Tunnelling conditions: Tip bias = +0.1 V, tunnelling current = 0.80 nA and scan rate = 4.1 lines/s.

Figure 4-13. Cyclic voltammetry of previously modified polycrystalline solid gold electrodes in 0.5 M aqueous KOH solutions at 25 oC. The modification is performed using 1 mM concentrations of the investigated compounds (1-3) in EtOH:DMF (9:1 for compounds 1 and

2, and 1:1 for compound 3) mixtures for 30 minutes. Scan rates 200 mV/s.

Figure 4-14. Cyclic voltammetry of previously modified polycrystalline solid gold electrodes in 0.5 M aqueous KOH solutions at 25 oC. The modification is performed using 1 mM concentrations of the investigated compounds (1-3) in EtOH:DMF (9:1 for compounds 1 and

2, and 1:1 for compound 3) mixtures for 18 hours. Scan rates 200 mV/s.

Chapter V:

Figure 5-1. X-ray photoelectron spectra of Au(111) on mica, modified using a 1 mM solution of compound 4 in THF for 48 hours.

Figure 5-2. X-ray photoelectron spectra of Au(111) on mica, modified using a 2 mM solution of compound 5 in THF for 24 hours.

Figure 5-3. Oxidative stripping voltammetry of bare and previously modified polycrystalline solid gold electrodes in a 0.5 M aqueous KOH solution at 25 oC. Scan rates 200 mV/s. The modification is performed in a 1 mM solution of compound 4 in THF at different modification times.

Figure 5-4. Time dependent coverage of sulfur deposition calculated from the oxidative stripping voltammetry of previously modified polycrystalline solid gold electrodes in a 0.5 M aqueous KOH solution at 25 oC. The electrodes are modified using a 1 mM solution of compound 4 in THF.

Figure 5-5. Reductive stripping voltammetry of bare and previously modified polycrystalline solid gold electrodes in a 0.5 M aqueous KOH solution at 25 oC. Scan rates 200 mV/s. The modification is performed in a 1 mM solution of compound 4 in THF at different modification times.

Figure 5-6. Successive reductive stripping voltammetry of previously modified polycrystalline solid gold electrode in a 0.5 M aqueous KOH solution at 25 oC. Scan rates 200 mV/s. The modification is performed in a 1 mM solution of compound 4 in THF for 3 hours.

Figure 5-7. Time dependent coverage of sulfur deposition calculated from the reductive stripping voltammetry of previously modified polycrystalline solid gold electrodes in a 0.5 M aqueous KOH solution at 25 oC, modified using a 1 mM solution of compound 4 in THF.

Figure 5-8. Oxidative stripping voltammetry of bare and previously modified polycrystalline solid gold electrodes in a 0.5 M aqueous KOH solution at 25 oC. Scan rates 200 mV/s. The modification is performed in a 2 mM solution of compound 5 in THF at different modification times.

Figure 5-9. Time dependent coverage of sulfur deposition calculated from the oxidative stripping voltammetry of previously modified polycrystalline solid gold electrodes in a 0.5 M aqueous KOH solution at 25 oC. The electrodes are modified using a 2 mM solution of compound 5 in THF.

Figure 5-10. Oxidative stripping voltammetry of bare and previously modified polycrystalline solid gold electrodes in a 0.5 M aqueous KOH at 25 oC. Scan rates 200 mV/s. The

xxi modification is performed in a 3 mM solution of compound 6 in THF at different modification times.

Figure 5-11. Time dependent coverage of the sulfur deposition calculated from the oxidative stripping voltammetry of previously modified polycrystalline solid gold electrodes in a 0.5 M aqueous KOH solution at 25 oC. The modification is performed using a 3 mM solution of compound 6 in THF.

Figure 5-12. Unfiltered STM images in air of a Au(111) surface on mica modified using a 1 mM solution of compound 4 in THF for 48 h. Scan sizes are (a) 270 x 270 nm2, (b) 25 x 25 nm2, (c) 15 x 15 nm2, (d) 10 x 10 nm2, and (e) 5 x 5 nm2. Tunnelling conditions: Tip bias =

+0.1 V, tunnelling current = 0.55 nA and scan rate = 4.1 lines/s. (f-g) Height profiles along line A and B respectively as shown in Figure 5-12e.

Figure 5-13. (a-f) Proposed structural models for Figure 5-12d showing sulfur deposition on

Au(111) surfaces.

Figure 5-14. Unfiltered STM images in air of a Au(111) surface on mica modified using a 2 mM solution of compound 5 in THF for 24 h. Scan sizes are (a) 500 x 500 nm2, (b) 120 x 120 nm2, (c) 50 x 50 nm2, (d) 10 x 10 nm2 and (e) 5 x 5 nm2 (slightly filtered). Tunnelling conditions: Tip bias = +0.1 V, tunnelling current = 0.525 nA and scan rate = 3.3 lines/s. (f)

Height profiles along line A as shown in Figure 5-14e, showing the step heights. (g-j) Height profiles along line B to E respectively as shown in Figure 5-14e in different directions of a zig-zag structure. (k) Proposed structural models for Figure 5-14d showing sulfur deposition on the Au(111).

Figure 5-15. (a-c) Sequential unfiltered STM images (10 x 10 nm2) in air of a Au(111) surface on mica modified using a 2 mM solution of compound 5 in THF for 24 h. Tunnelling conditions: Tip bias = +0.1 V, tunnelling current = 0.65 nA and scan rate = 3.3 lines/s.

xxii

Figure 5-16. Unfiltered STM images in air of a Au(111) surface on mica modified using a 3 mM solution of compound 6 in THF for 2 h. Scan sizes are (a) 200 x 200 nm2, (b) 70 x 70 nm2, (c) 32 x 32 nm2, (d) 20 x 20 nm2 and (e) 15 x 15 nm2. Tunnelling conditions: Tip bias =

0.1 V, tunnelling current = 0.65 nA and scan rate = 3.3 lines/s.

xxiii

List of Abbreviations

BPT 1,1’-Biphenyl-4-thiol

1-UT 1-undecanethiol

2-NT 2-Naphthaleinthiol

4-AA 4-Acetamidothiophenol

ACS American Chemical Society

AIP American Institute of Physics

ACS Analytical Chemistry Standards

AFM Atomic Force Microscopy

B3LYP Becke, three-parameter, Lee-Yang-Parr

BT Benzenethiol

CCl4 Carbon tetrachloride

CMOS Complementary Metal Oxide Semiconductor

CV Cyclic Voltammetry

DFT Density Functional Theory

DNA Deoxyribonucleic Acid

DMF Dimethylformamide

EAL Effective Attenuation Length

EC Electrochemical

EMR Electromagnetic Radiation

ESCA Electron Spectroscopy for Chemical Analysis fcc Face-centred cubic

FT Fourier Transform

xxiv

FTIR Fourier Transform Infrared Spectroscopy

FT-MS Fourier Transform Mass Spectroscopy

GIXD Grazing Incidence X-ray Diffraction

HP Hewlett-Packard hcp Hexagonal closed packed

HPLC High pressure liquid chromatography

HREELS High Resolution Electron Energy Loss Spectroscopy

IR Infrared

LB Langmuir-Blodgett

LS Langmuir-Schaefer

LZT Lead Zirconium Titanate

LBH Local Barrier Height

LDOS Local Density of States

LEED Low Energy Electron Diffraction

MCT Mercury Cadmium Telluride

ML Monolayer

NEXAFS Near Edge X-ray Absorption Fine Structures

NDR Negative Differential Resistance

NIXSW Normal Incidence X-ray Standing Wave

OCT Octanethiol

OPE Oligo(Phenylene Ethynylene)

OPV Oligo(Phenylene Vinylene)

OCP Open Circuit Potential

PEM Photoelastic Modulator

xxv

PED Photoelectron Diffraction

PVD Physical Vapour Deposition

PM Polarization Modulation

PM-IRRAS Polarization Modulation Infrared Spectroscopy

QCM Quartz Crystal Microbalance

RSF Relative Sensitivity Factor

RSC Royal Society of Chemistry

SCE Saturated Calomel Electrode

SECM Scanning Electrochemical Microscopy

SPM Scanning Probe Microscopy

STM Scanning Tunnelling Microscopy

SHG Second Harmonic Generation

SAMs Self-Assembled Monolayers

SFG Sum Frequency Generation

SERS Surface Enhanced Raman Spectroscopy

SPR Surface Plasmon Resonance

SPRS Surface Plasmon Resonance Spectroscopy

TPD Temperature Programmed Desorption

THF Tetrahydrofuran

TGS Triglycine Sulfate

UHV Ultra High Vacuum

UV Ultraviolet

XAS X-ray Absorption Spectroscopy

XRD X-ray Diffraction

xxvi

XPD X-ray Photoelectron Diffraction

XPS X-ray Photoelectron Spectroscopy

xxvii

List of Symbols

2D 2-Dimensional

A Absorption factor

AlKα Aluminum Kα

Å Angstrom

Ipa Anodic peak current

Epa Anodic peak potential

Rav Average of the reflectance for p and s polarized lights

χ Azimuthal angle

δ Bending vibrations

Vb Bias voltage

EB Binding energy

Ipc Cathodic peak current

Epc Cathodic peak potential cm Centimeter

C Concentration

ΔHAu-S Contribution of the heat of formation towards the total heat of formation due to

the Au-S bond

ΔHbackbone Contribution of the heat of formation towards the total heat of formation due to

the interactions between the molecular backbones

ΔHtail Contribution of the heat of formation towards the total heat of formation due to

the interactions between the tail groups

xxviii

I Current oC Degree Celsius

ΔEp Difference between anodic and cathodic peak potentials

ΔS Differential reflectance

D Diffusion constant d Distance

Ae Effective area

λAu Effective attenuation length (EAL) of photoelectrons of kinetic energy EAu

through organic monolayer for the gold substrate

Ep Electric field vector eV Electron Volt

Ef Energy at Fermi level

F Faraday’s constant

Vf Final potential

ʋ Frequency

R General gas constant

ΔHdiss Heat of dissolution of the adsorbate

ΔHimm Heat of immersion of the substrate.

Vi Initial potential b Interger/half integer

κ Inverse decay length of an electron wave function

K Kelvin kcal Kilocalorie

EAu Kinetic energy of photoelectrons emitted from the gold susbtrate

xxix

Ek Kinetic Energy of the ejected electrons

Φ Local barrier height/work function of a material

ρsa (d, Ef) Local density of state at Fermi level

MgKα Magnesium Kα me mass of an electron

MΩ Megaohm

μC Microcoulomb

μm Micrometer mm Millimeter mM Millimolar mV Millivolt

M Molar nA Nanoampere nm Nanometer pH Negative log of hydrogen ion concentration (molar) nC Number of carbons ne Number of electrons transferred per molecule n Number of moles

Ox Oxidized species p Parallel ppt Parts per thousand s Perpendicular

π Pi h Planck’s constant

xxx

E1/2 Potential at the half wave

ћ Reduced Planck’s constant

Re Reduced species

Rp Reflectance for p-polarized light

Rs Reflectance for s-polarized light

R0 Reflectivity of a bare metal

RA Reflectivity of a metal with an adsorbed layer sp s and p orbital hybridization sp3 s and three p orbitals hybridization

Vs Sample bias

θs Saturation coverage v Scan rate s Second

E0 Standard electrode potential r Stretching vibrations

Vs Switching potential

θA Take off angle with respect to the surface normal

T Temperature tA Thickness of an organic monolayer

ʋ0 Threshold frequency

θ Tilt angle

ΔHad Total heat of formation for the adsorption process

ΔHtotal Total heat of formation of the SAM in a solution

β Twist angle

xxxi

V Volt

Φs Work function of the spectrometer

Is XPS signals for a bare gold substrate

IA XPS signals for the modified gold substrate

xxxii

Preamble

The ever growing interest in self-assembled monolayers (SAMs) of aromatic thiolate on solid surfaces stems from their remarkable electronic and optical properties, and the flexibility to tune their surface properties by an appropriate choice of the precursors. These characteristics of aromatic SAMs offer a manifold of potential applications in lithography, nanomaterials, and optical and electronic devices. The main important obstacles that have been encountered for the successful use of aromatic SAMs include the presence of high density of surface defects, their chemical and thermal instability, short-range ordering, and the availability of only a limited number of precursors. An extensive research has been put forward to find new and more efficient ways to improve the quality of aromatic SAMs including the use of alkyl spacer, the use of fused ring aromatic thiols, postdeposition annealing, the displacement of another adsorbate, and the use of selenium as a head group. The purpose of this study is to introduce organic sulfenyl chlorides as alternative precursors to obtain high quality aromatic SAMs on gold. Gold is chosen as a substrate due to its inert nature towards oxidation and to its specific affinity for sulfur. Molecules with a variety of molecular backbones are investigated (ranging from aliphatic, aromatic and aliphatic-aromatic).

This thesis has four goals. The first goal is to develop a new methodology for the efficient modification of gold using organic sulfenyl chlorides as new precursors. The second goal is to understand the effects of change in the molecular backbone of precursor molecules on the structural quality and ordering of the obtained SAMs. The third goal is to provide fundamental insight regarding a highly debated issue about the origin of the observed features and contrasts in

STM images of thiol SAMs. It is not known with certainity whether the STM tip images the tail group, the head group, the molecular unit adjacent to the tail group, or a combination of the tail group and the adjacent molecular unit. The fourth goal is to study the nature of the Au-S interactions in organosulfur SAMs and sulfur deposition on gold. 1

All XPS spectra and their deconvolutions in Chapters III-V were obtained by one of our previous group members, Dr. Kallum M. Koczkur. Also, the results from Chapter III have been published in the following articles.

1. Abdelaziz Houmam, Hamida Muhammad, M’hamed Chahma, Kallum M. Koczkur and Daniel

F. Thomas Chemical Communication, 2011, 47, 7095. http://pubs.rsc.org/en/Content/ArticleLanding/2011/CC/c1cc11451d

2. Abdelaziz Houmam, Hamida Muhammad and Kallum M. Koczkur Langmuir, 2011, 27,

13544. http://pubs.acs.org/doi/abs/10.1021/la202928z

The results from Chapter IV have been published in the following article.

3. Hamida Muhammad, Kallum M. Koczkur, Annia H. Kycia and Abdelaziz Houmam Langmuir,

2012, 28, 15853. http://pubs.acs.org/doi/abs/10.1021/la303395e

Portions of the results from Chapter V have been published in the following article.

4. Abdelaziz Houmam, Hamida Muhammad, and Kallum M. Koczkur Langmuir, 2012, 28,

16881.

http://pubs.acs.org/doi/abs/10.1021/la3032607

Chapter I. Introduction and Background Information

I-1 General Background

The modification of solid surfaces by organic and/or inorganic molecules has been an important part of the field of surface science for almost a century. Extensive studies have been performed in order to understand the fundamental, theoretical, and practical aspects of the modification process. These studies have led to advances for technological applications in physics, chemistry, biology, and engineering. New insights are being brought into this field by the continuing development of surface characterization techniques like scanning tunnelling microscopy (STM) and atomic force microscopy (AFM).

Surface modification is often performed to change the physical, chemical, biological, electrical, electronic, magnetic, thermal or mechanical characteristics of a solid surface, formed from materials such as metals, metal oxides, insulators and semiconductors. Surface science began with a need to understand the organic surface chemistry of oxide-supported metal catalysts and polymers.1,2 In order to study these materials, researchers faced many difficulties such as control over crystallographic orientation, cleanliness, porosity of metal catalysts,3 and various possible orientations of a specific functional group for a polymer surface.4,5 These issues lead to the development of new routes for studying organic surface chemistry with improved control over many parameters such as the order, orientation, spacing, and nature of the organic functional group.3 One well-known example in the exploration of these routes is the formation of an ordered and thermally stable organic layer on a metal surface in vacuum using volatile organic molecules e.g. ethylene on Pt(111).1 This simple method is limited by the availability of a few highly volatile organic molecules, loss of order with an increase in chain length, little control over terminal functionality and the penetration of secondary adsorbates to the substrate due to the limited thickness of the organic layer.6,7 Langmuir,8 Langmuir-Blodgett (LB)9,10 and Langmuir- 3

Schaefer (LS)11 films of surfactant molecules on liquid and solid substrates were introduced in contrast to the above mentioned procedure. However, these films require special equipment for their preparation, and are only suitable for the formation of organic films of amphiphilic molecules. LB and LS films are thermally unstable12,13 since they involve physisorption (a weak interactions between organic molecules and the substrate). Alternatively, a synthetic method for the formation of well-ordered self-assembled monolayers (SAMs) on solid surfaces was developed.14 SAMs combine the advantages of the formation of organic films in vacuum and LB films at the air/water interface. The procedure used for SAM formation is simple and spontaneous, which involves a chemical bond between the adsorbate and the substrate and intermolecular interactions.

SAMs allow a higher flexibility in designing molecular surfaces with a greater control over surface properties. Unlike LB films, a number of organic precursors can be used with incorporation of various terminal functionalities. Modification can be performed in an ambient environment in a variety of polar and non-polar solvents as well as inside a UHV chamber. In addition, a surface modified using self-assembly of organic molecules is usually considered homogenous, well-ordered, robust and stable (under certain conditions). These characteristics make SAMs attractive for controlling surface properties such as wetting, lubrication, adhesion, passivation, chemical resistance, corrosion, biocompability, chemical and bio-sensing and biomimetics.

Despite the great wealth of research performed and the progress made on organosulfur

SAMs on Au, there are many controversial issues as well as practical limitations which need to be addressed and require furher investigations. The challenges include the availability of limited numbers of organosulfur precursors for surface modification, the chemical and thermal instability of precursor molecules during and after modification, lower quality and packing density of SAMs

(more important for aromatic SAMs), the mechanism of adsorption, the chemistry of the Au-S 4 interface, the adsorption site determination, the formation of etch pits and the origin of the contrast in the STM images of alkanethiol SAMs. In the following sections, an overview will be provided for the common modification techniques and SAMs in general with more emphasis on organosulfur SAMs on Au and related details.

I-2 Common Methodologies used for Surface Modification

The modification concept of solid and liquid surfaces with organic molecules has its origin in Langmuir films in the late 18th century. A Langmuir film is a molecular film at the liquid-gas or liquid-liquid interface. It is commonly obtained by the self-orientation of amphiphilic molecules in an expected manner on an air-water interface. Benjamin Franklin reported the formation of a molecular scale film of oil on water in 1774.8 After Franklin, further work on these films on an air-water interface was conducted by Agnes Pockels.15 Eventually,

Langmuir-Blodgett (LB) films were introduced9,10 for the formation of organized molecular assemblies on solid surfaces. LB films are homogenous, physisorbed monolayers or multilayers obtained by vertical immersion/emersion of a solid surface at a liquid-gas interface.9,10 The transfer of a surfactant to a solid surface in LB films is performed in a controlled environment

(usually under controlled pressure) using a LB trough (first designed by Pockels).15 The stability as well as the efficient packing of the LB films depend on strong intermolecular interactions between neighboring molecules and are increased with increasing the alkyl chain length.16 A related method to the LB procedure is the Langmuir-Schaefer (LS) technique, where the deposition is performed by horizontal lifting.11 Figure 1-1 shows the experimental set up for the deposition of Langmuir, LB and LS films.

Figure 1-1. Illustrations of Langmuir, Langmuir-Blodgett and Langmuir-Schaefer films deposition methods.

The interfacial properties of substrates can be altered through modification using self- assembly. The principle of the formation of self-assembled monolayers (SAMs) involves the spontaneous adsorption of surfactant molecules from a liquid or a gas phase on a solid substrate to form organized monomolecular layers which result in crystalline or semi-crystalline structures.

SAMs are considered organized, densely packed and ordered two-dimensional assemblies, in which a chemical bond is formed between an adsorbate and a substrate surface.

This chemisorption not only helps to remove any physically adsorbed species present on the surface but also results in a covalently bonded surfactant that is difficult to remove. These

6 properties make SAMs more attractive over LB films, which are difficult to organize, as they are formed by physisorption, a process which does not encourage the removal of impurities from the solid surface.17 SAMs do not require any special experimental conditions for their preparation, like ultra-high vacuum (UHV), nor special equipment (LB trough).18

I-3 Self-Assembled Monolayers (SAMs)

SAMs have been extensively used as a model system in bioanalytical, organometallic, physical organic, bio-organic and electrochemistry17-25 due to their self-association and ease in functionalization. In 1946, Zisman and co-workers reported the monolayer formation of long chain alcohols in hexadecane on a glass substrate having wetting properties similar to LB films.26-

28 Gradually the group extended their work by using different substrates (metal and metal oxides) and adsorbates (amines, primary amides and carboxylic acids).26-28 The concept of SAMs, however, first came into common scientific discussions only in the early 1980’s. Sagiv introduced irreversible covalent bonding of silane molecules to the glass surface.29 Taniguchi reported self-assembly of pyridine disulfide on gold surfaces.30 Nuzzo and Allara demonstrated the formation of thiolate SAMs on gold using di-n-alkyl disulfides.14 Maoz & Sagiv also reported assemblies of trichlorosilanes on silicon oxide.31 Presently, alkanethiols on gold and trichlorosilanes on silicon oxide are two well accepted systems for self assemblies. Organic assemblies of sulfur containing compounds such as thiols,32 disulfides,14 sulfides,33 thiosulfates,34,35 thioacetates,36-38 and thiocyanates39,40 on noble (Pt and Pd) and coinage (Au, Ag and Cu) metals, particularly on gold, have been widely studied as a standard system for almost three decades in surface coatings. There has been an exponential increase in the number of papers published annually in this field since the discovery of these monolayers. Advancement in surface science techniques has also enhanced awareness about SAMs.

Planar (thin metal films, metal single crystals, metal foils and metal beads) as well as curved nanostructured surfaces have been used successfully as substrates for SAM formation.

Planar substrates are extensively used owing to their ease of preparation and the ability to be characterized by many surface science techniques. The choice of the type of the substrate depends highly on the applications of the SAMs and on the techniques used to characterize the modified surface. Unlike single crystal metals, thin metal films (pseudo-single crystal) can be prepared in vacuum and do not require polishing. Thin metal film preparation is also cost effective.41-43 Fused silica glass, quartz and silicon wafers have been used as substrates for depositing polycrystalline thin metal films with grain sizes of ~10-1000 nm by physical vapour deposition (PVD). Thin metal film deposition on glass and silicon wafers requires adhesion promoters/primers (chromium, nickel and titanium) to produce mechanically stable films.

However, the primers can diffuse over the metal surface44-46 and can be toxic (chromium and nickel) to biologically active SAMs. Mica (sheet silicate, having a layered structure) is a suitable substrate for thin metal films for scanning probe microscopy (SPM) studies of SAMs. Atomically flat surfaces are obtained after cleaving mica sheets. Cleaving in air results in physically and chemically adsorbed water on the surface which can be removed either by the use of adhesion promoters or heating in vacuum.47,48 Epitaxially grown thin metal films on freshly cleaved mica are “pseudo-single crystal” with grain sizes of ~1000 nm.

Gold is the preferred metal for studies of SAMs as it can be obtained with high purity.

Gold films can be prepared easily by PVD, sputtering and electrodeposition, which give a clean, flat and stable surface. It is reasonably inert, resistant to oxide formation and does not require any special chemical environment for handling. After gold, silver and copper are the most studied metals for SAMs. However, both metals are prone to oxidation49 and silver is bio-incompatible too.50-52 Compared to the coinage metals, palladium is the least studied metal for SAMs, despite some important properties. Palladium is well known for its catalytic properties such as in Suzuki 8 cross coupling reactions.53 It is less susceptible towards oxidation in ambient conditions than silver and copper. It has lower toxicity than gold for living cells,54 is more adaptable to complementary metal oxide semiconductor (CMOS)55 and has a similar price to gold. Thin metal films of palladium are also more appropriate for micro and nanofabrication due to their smaller grain sizes.56,57

Several types of anchoring molecules are used to form organic thin films on solid substrates. These include mainly organosilicon compounds on silicon dioxide (SiO2) (Figure 1-

31,29,58-61 62,63 61 64-66 2a), aluminium oxide (Al2O3), glass, and mica (oxidized or hydroxylated surfaces); and organosulfur compounds on clean metals (Figure 1-2b) and semiconductors.14,32-

40,67-75 76 77,78 Beside these, alcohols and amines on Pt, hydrocarbons on Si, and fatty acids on Al2O3

79-81 82 (Figure 1-2c) and silver oxide (Ag2O) (Figure 1-2d) are also used. Figure 1-2 shows (a) a trichlorosilane SAM on SiO2, (b) an alkanethiol SAM on Au, (c) a fatty acid SAM on Al2O3, and

(d) a fatty acid SAM on Ag2O.

Figure 1-2. Schematics showing (a) a trichlorosilane SAM on SiO2, (b) an alkanethiol SAM on

Historically, a wide variety of organosulfur compounds have been used for the formation of SAMs on different substrates. They can be classified based on their skeleton (aliphatic, aromatic and hybrid), the types of substituents (small, bulky, electroactive, electron donating, electron withdrawing etc.) and the nature of the leaving group (in precursors such as thiols,32 disulfides,14 sulfides,33 thiosulfates,34,35 thioacetates,36-38 and thiocyanates39,40). The most applicable organosulfurs are alkanethiols on coinage metals (Au, Ag and Cu) and to a certain

67 68,69 70 71 extent on Ni, Pt, Pd, and semiconductors (GaAs and SiO2 ). Self-assembly on Cu and Ag metals require the reduction of the metal oxides to the metals. This process causes oxidation of a certain amount of the alkanethiols to the corresponding sulfonates, which diffuse away from the 10 surface while alkanethiol molecules from the bulk solution form self-assembly on the reduced metal. Therefore, either the reduction of the metal oxide is performed prior to the modification or during modification using the precursor molecules. Benzene, toluene and hexane are commonly

70 used solvents for alkanethiols assembly on Cu. Etching with ammonia (NH3) is used to remove the oxide layer from the surface for self-assembly on GaAs.67 Stable nickel oxide (NiO) cannot be reduced by reaction with alkanethiols, hence an electrochemical method is used and the alkanethiol molecules react with the clean surface of Ni after reduction of NiO.72-74

I-4 Organosulfur SAMs on Au

I-4a Building Blocks of Organosulfur SAMs on Au

Molecules used for the modification of solid surfaces can be considered as building blocks with three distinct parts: the head group by which the adsorbate is linked to the surface, the backbone or main chain (chain in between head and terminal groups), and the tail or surface- active group (Figure 1-3). In the case of alkanethiol SAMs, sulfur is the head group, the hydrocarbon chain is the backbone and the terminal methyl group is the surface-active group.

Figure 1-3. Scheme showing the molecular orientation (the angles are θ, β and χ) of an adsorbed alkanethiol molecule on a gold surface.21

On the basis of these units, organic self assemblies have three distinct regions of interactions; the chemisorption involving the substrate and the head group of the adsorbate, the intermolecular interactions between the backbone chains, and the interactions of the tail groups.

The structure and the physio-chemical properties of the SAM greatly depend on these interactions. Figure 1-4 shows an ideal alkanethiol SAM with two interfaces and one interphase formed as a result of the three types of interactions. The stability of SAMs increases with longer alkyl chains resulting from an increase in the van der Waals interactions between neighboring chains.20

Generally, three angles are used to describe the orientation of adsorbed molecules on the substrate (Figure 1-3); the tilt angle (θ) is the angle between the molecular backbone and the surface normal, the twist angle (β) tells about the C-C-C plane rotation with respect to the molecular plane, and azimuthal angle (χ) is the angle between the projection of the molecule on the surface and the next-neighboring molecule.83,84 The distance between two adjacent sulfur atoms (4.97 Å)85-87 is nearly three times greater than the van der Waals distance between two sulfur atoms (1.85 Å)88 and larger than the distance between two interacting adjacent alkyl chains

(4.2-4.4 Å)3 in alkanethiol SAMs. Hence, it is assumed that the S-S interactions are minimum and that the alkyl chain is tilted to maximize van der Waals interactions.83,89 A tilt angle of ~30o is reported for alkanethiol SAMs on gold surfaces.90-92 However, the tilt angle can be larger/smaller, if aromatic groups are linked directly to the head group or linked through oxygen.17

I-4b Significance of Organosulfur SAMs on Au

The wide spread interest in organosulfur assemblies on metal surfaces is related to their potential applications in corrosion inhibition,93 surface passivation,94 chemical and biosensors,95-

98 nanopatterning,99-101 and molecular electronics.102,103 The physical and chemical properties of

SAMs can be altered by a slight variation in the terminal group.16,104,105 Proper choice of the tail group can make surfaces hydrophilic (polar group), hydrophobic (non-polar group), and

106 chemically/biologically reactive/inert (complex groups). The tail groups such as –CH3 and –

107 CF3 groups make SAMs repellent to water, metals and other substances while –NH2, –OH and

-COOH groups make them hydrophilic and attractive for metal ions and proteins.108 The –SH group has a great binding ability for metal ions and metal nanoparticles.109 The wetting properties of SAMs can be altered reversibly through irradiation110 and chemical treatment. The stability of

SAMs allowed the study of chemical reactions at modified surfaces. Monolayers with terminal –

OH, –COOH, -NO2 and –NH2 groups can be chemically/electrochemically transformed to other surface active groups. For example, the –COOH group can be transformed chemically to a H- bonded bilayer, an acid chloride, an amide, an ester, or a thioester by reaction with an alkanoic

111 112 113 acid, SOCl2, an amine, an alcohol, or a thiol, respectively. The introduction of sulfone and amide114 groups within alkyl chains may result in better packing between molecules and improved surface stability due to dipole-dipole and hydrogen bonding interactions, respectively.

Thiol derivatives of biologically active compounds have been used in the formation of

SAMs having applications in bioanalysis/biosensors. However, the synthesis of functionalized thiols linked to complex biomolecules (peptides, proteins, carbohydrate, deoxyribonucleic acid

(DNA), etc.) for applications in biology and biochemistry is quite challenging. Even, after synthesizing such complex molecules, direct anchoring of those molecules on the surface and obtaining good quality SAMs is also difficult. Consequently, SAMs are immobilized after formation to incorporate specific functionalities. Immobilization of biomolecules on SAMs can 14 be done by covalent and non-covalent bonding.106 In covalent coupling, the direct exchange of the complex ligands in a solution takes place with the terminal groups of SAMs.115-118 The direct exchange is more favorable than the displacement of thiols from the surface. For example, the acetyl terminal groups of SAMs can be converted to azide groups which can undergo ‘click’ chemistry to form biologically active surfaces.119 SAMs can be used as biocompatible materials having resistance to protein and biomolecules when exposed to biological environments and consequently reduce chances of infection by bacteria.106

Thiol assemblies containing a tail group which undergoes ionization with a change in pH can be used as pH sensing devices. A simple example is an electron transfer between a metal electrode containing a thiol SAM with –COOH terminal group and a redox couple in a solution

3-/4- 120 (e.g. potassium ferri/ferro cyanide ([Fe(CN)6] ) ions). The first pH sensing electrode was developed by Hickman et al., in which quinone (a pH sensitive species) and ferrocene (a pH insensitive species) were co-immobilized on a SAM.121 Following that, azobenzene,122 nitrobenzoic acid122 and bifunctional carboxylic acids-ferrocene sulfide have been successfully used as pH sensing molecules.123 SAMs with special tail groups can also be used for selective detection of other ions.95.98

SAMs are also now being used as electronic devices. For example, SAMs of octadecanethiol and 11-mercapto-1-undecanol have been used to fabricate memory devices.125

Modified Au-thiol surfaces can act as insulators, resistors, and capacitors.21 This is usually achieved by choosing a suitable organic molecule for SAM formation that can change the electronic properties of metal electrodes. Metal(1)-SAM-Metal(1)/(2)126-128 or Metal(1)-SAM(1)-

SAM(2)-Metal(1)/Metal(2) junctions129-131 are also being used to fabricate electronic devices with certain electronic properties by a careful choice of the metal and SAM.

I-4c Thermodynamics and Kinetics of Formation of Organosulfur SAMs on Au

The heat of formation for an alkanethiol SAM on Au (including the RS-Au bond, intermolecular interactions between the molecular backbones, and tail groups) has been reported in a range of 10-38 kcal/mol.17 Studies of van der Waals interactions between the backbone chains indicated contributions of 1-2 kcal/mol per methylene group for hydrocarbons3,132 and a few kcal/mol19 for interactions between tail groups towards the total heat of formation for the adsorption process (Equation 1-1).

ΔHad = ΔHAu-S + ΔHbackbone + ΔHtail (1-1)

where ΔHad is the total heat of formation for the adsorption process, ΔHAu-S, ΔHbackbone and ΔHtail are the contributions towards the total heat of formation due to the Au-S bond, interactions between the molecular backbones, and the tail groups, respectively.

The strength of the gold-thiolate bond was first determined by Nuzzo et al. using temperature programmed desorption (TPD).133 They found an energy barrier of ~30 kcal/mol for the reversible desorption and recombination of dimethyl disulfide on Au(111).133 Solution phase studies reported lower values i.e. ~20-25 kcal/mol from thermal desorption,105,134 and ~15 kcal/mol from electrochemical measurements.135 The lower values for the formation of SAMs in solution are expected, since the heat of dissolution of the adsorbate and the heat of immersion of the substrate also add in the overall reaction (the SAM formation in a solution, Equation 1-2).

ΔHtotal = ΔHad + ΔHdiss + ΔHimm (1-2)

16 where ΔHtotal is the total heat of formation of the SAM in a solution, ΔHad is the total heat of formation for the adsorption process, ΔHdiss is the heat of dissolution of the adsorbate and ΔHimm is the heat of immersion of the substrate.

It has been demonstrated that adsorbed alkanethiol molecules have the ability to move on the gold surface. The dynamic nature of the gold-sulfur interface can be appreciated from the fact that alkanethiol molecules preadsorbed on the metal surface undergo a displacement reaction at grain boundries when placed in a solution of a different alkanethiol.22 Moreover, it has been observed that alkanethiol molecules adsorbed on a gold surface diffuse over several hours to uncover gold surface.136

The SAM growth requires the transport of the adsorbate to the solid substrate followed by the adsorption (initial physisorption and then chemisorption). The process may be controlled by diffusion,137-141 adsorption142-148 or may involve intermediate kinetics (both diffusion and adsorption in different extent). The initial reports on STM,149 X-ray diffraction (XRD),24 atom diffraction24 and XPS24 studies of decanethiol adsorption on Au(111) from the vapour phase suggested three distinct steps for SAM growth: i) a low density ‘vapour’ phase with randomly oriented molecules, ii) an intermediate density phase with disordered (liquid or condensed phase) or lying down molecules (striped phase), and iii) a high density ‘solid’ phase with ordered and standing up molecules. However, an intermediate density phase may involve few more phases due to varying degrees of freedom of SAM molecules.

Bain et al. first studied the kinetics of the formation of organosulfur SAMs in solution on

Au using contact angle and ellipsometry.105 They have reported that for relatively dilute solutions

(1 mM) the adsorption is a two-step process.105 This is further confirmed by quartz crystal microbalance (QCM),150-153 STM,151 surface plasmon resonance (SPR),138,154 in situ electrochemical,155 XPS (1 μM solution),156 and near edge X-ray absorption fine structures

(NEXAFS)157 studies. In their study, they proposed that the first step is relatively fast, completed 17 within a few minutes, and gives 80-90% surface coverage.105 The second step requires several hours for its completion until saturation is reached.105 They found that the rate of the first step is strongly dependent on the thiol’s concentration and requires an increase in modification time from ~1 minute to over 100 minutes after a change in concentration from 1 mM to 1 μM.105 The second step is called the surface crystallization process, forming two dimensional crystals by the organization of alkyl chains.105 Therefore, they concluded that the kinetics of the first step is dependent on the surface-head group reaction and the second step on the chain organization.105 In contrast, in situ second harmonic generation (SHG),143,158 in situ QCM,159,160 and XPS (0.01 and

0.1 mM solutions)156 studies from solution phase reported a single step growth process.

Furthermore, in situ STM161,162 and AFM163 studies of alkanethiol adsorption from solution on

Au(111) observed three stages of SAM growth similar to the vapour phase deposition. In Figure

1-5, different steps of the SAM growth are shown.

Figure 1-5. An illustration of the simplified sequences of a SAM growth.20

It has been reported that long chain thiol monolayers are reproducible while short chain thiol monolayers are qualitatively different having greater disorder.164 For the two steps adsorption kinetics, it is suggested that the initial adsorption step is fast and the rate decreased with increasing chain length in ethanolic solutions whereas the opposite trend are observed in the second step.138,143,165 The presence of long chains or bulky groups results in the masking of adsorption sites in the first step113 while increasing van der Waals interactions in the second step.19 Nevertheless, the literature on the effects of chain length on the SAM growth is conflicting. Bain, Xu, Jung and co-workers have reported a faster SAM growth for long chain alkanethiols in ethanolic/butanolic solutions.105,139,140,163 On the other hand, DeBono and 19

Karpovich et al. have reported no significant change in the rate of SAM growth after increasing the chain length from C6 to C12 (ethanolic solution) and C8 to C18 (hexane solution), respectively.154,159 For long chain alkanethiols, stronger interactions between the head group and the substrate (stronger S-H bond) and a slower mobility of the molecules (larger size) during the diffusion of the molecules to the substrate are expected.

Ulman and co-workers have conducted a systematic study on SAMs of 4- mercaptobiphenyl thiolate on gold and reported some key differences between alkanethiol and biphenyl thiolate SAMs.166 They found that the rigid conjugated system of biphenyl thiol molecules provide more stable SAMs than alkanethiols. The effect of the substituent at the 4’- position of the biphenyl ring was suggested to be more significant than the ω-substituent of alkanethiol for SAMs formation.166 They suggested that the adsorption kinetics for the derivatives of 4-mercaptobiphenyl thiolate SAMs do not follow Langmuir isotherms (which do not consider intermolecular interactions).167 A new chemisorption lattice gas model has been proposed for the initial step of adsorption based on QCM studies.167 The model considers the interacting chemisorbed layer as lattice gas particles in which molecules are interacting with next nearest neighbour and behaving as a pair.167

I-4d Mechanism of Formation of Organosulfur SAMs on Au

There are still many uncertainties about the actual mechanism of formation of thiol SAMs on Au and various schemes have been proposed. The most accepted mechanism for the formation of alkanethiol SAMs on gold involves the formation of thiolate (R-S-) species as suggested by X- ray photoelectron spectroscopy (XPS),32,168-170 Fourier transform infrared spectroscopy (FTIR),133

FT mass spectroscopy (FT-MS),90 electrochemistry171 and Raman spectroscopy.172-174 The reaction can be written as (Equation 1-3)

- + R-S-H + Aun R-S- Au . Aun-1 + ½ H2 (1-3)

There is also a great ambiguity about the possible outcome of the hydrogen of the thiol group after adsorption.171,175-178 The elimination of hydrogen as molecular hydrogen179-181 and as water133 have been proposed in vacuum and in solution (in the presence of oxygen), respectively.

The origin of this uncertainty resides in the difficulty in the detection of hydrogen during/after

SAM formation. However, the formation of a monolayer in an oxygen free environment in the gas phase further supports the above described mechanism (Equation 1-3).179-181 In addition, the vibrational band for the S-H stretching mode (~2600 cm-1) is also not observed in IR and Raman spectra of an alkanethiol SAM.90,173,174 A recent comparative XPS study on the adsorption of 4- nitrophenyl thiol and bis-(4,4’-nitrophenyl)-disulfide has suggested the release of hydrogen as a result of dissociative adsorption of 4-nitrophenyl thiol in vacuum.182 The authors reported the partial reduction of the nitro groups to amino groups for thiols in gas phase but not for disulfides.

An example of the diversity of adsorption schemes for thiol SAMs is given by the widely investigated methanethiolate SAM, which is commonly performed using dimethyldisulfide vapours in UHV.133,183 An experimental study on the adsorption of methanethiol and dimethyldisulfide on Au(111) below 220 K supports a non-dissociative adsorption of these molecules.184 Density functional theory (DFT) calculations on adsorption of methanethiol on

Au(111) also provide evidence for chemisorption at face-centred cubic (fcc) sites without the cleavage of the S-H bond.185 On the other hand, a few studies have suggested a dissociative adsorption of dimethyldisulfide vapours at room temperature,186 and after annealing at 320 K.187

Monolayers obtained by using di-n-alkyl disulfides are similar to those obtained using alkanethiols forming Au(I) and thiolate (R-S-) species.32,36,49,85,133,170,188-190 A proposed

21 mechanism is the oxidative addition of the S-S bond to the gold surface as shown in Equation 1-

4.36,188,189

- + 1/2R-S-S-R + Aun R-S- Au . Aun-1 (1-4)

Few studies have reported that the rate of desorption is faster for thiol SAMs as compared to the disulfides SAMs.36,188,189 On the other hand, a slower adsorption kinetics is observed for disulfides than corresponding thiols.191 These studies have suggested that disulfides SAMs are difficult to form but are stable than corresponding thiols.

STM190,192 and spectroscopic193 studies have suggested that SAMs obtained from dialkyl- sulfides are less ordered and less stable than those obtained from the corresponding thiols and disulfides. The initial work on dialkyl-sulfide SAMs suggested that the adsorption leads to a cleavage of one of the C-S bonds.33 On the other hand, electrochemistry,194,195 XPS,191,193 high resolution electron energy loss spectroscopy (HREELS)196 and mass spectrometry197 have suggested a non-dissociative adsorption of dialkyl-sulfides.

Organic thiosulfates (Bunte salts) form a Au-thiolate bond similar to thiols in anaerobic aqueous medium.34 Bunte salts can be readily synthesized using known procedures and the thiosulfate group can be conveniently introduced into a variety of redox active and functionalized molecules.34 A general reaction for the synthesis of organic thiosulfates is given in Equation 1-5.

R-X RS-SO3M + MX (1-5)

where M- is a monovalent cation and X- is a halide anion.

A lower coverage and a slower rate of reaction are observed using aliphatic and aromatic thiosulfates as compared to the corresponding thiols.34 The authors suggested that the presence of the bulky thiosulfate group is responsible for the inferior quality of the SAMs and the slower

- adsorption kinetics. The adsorption of organic thiosulfates results in the cleavage of S-SO3 bond with the release of metal sulfite species.34 Equation 1-6 shows the proposed mechanism for the formation of thiolate-SAM from thiosulfate.

- + - RS-SO3M + Aun R-S- Au . Aun-1 + [SO3M] (1-6)

Protected thiols/thioacetates are used as an alternative to chemically unstable thiols.

Thioacetates can be deprotected in situ using acid/base catalyzed hydrolysis to form SAMs similar to thiols. The oxidation of thiols accompanied with 30% reduction of nitro groups to amino groups are reported for the hydrolysis of thioacetate derivatives of nitro-substituted oligo(phenylene-ethynylene) (OPE) in a basic medium.37,38 In situ deprotection also adds extra organic material (reagents used for deprotection and side products formed) on the surface during modification and can complicate the process of SAM formation. Equation 1-7 shows the deprotection step. + H2O/H - or OH - RS-Ac RSH + Ac (1-7)

Thiolate SAMs are also prepared using organic thiocyanates as precursors. The quality of the resulting films is lower than those obtained from thiols.39,40,198,199 They also greatly depend upon the purity of the compounds used199 and the preparation method.198 Nevertheless, thiocyanates are chemically more stable to moisture and light than the corresponding thiols. They do not require special handling conditions and harsh chemicals for the cleavage of the S-CN bond during modification.39,40 On the other hand, it has been suggested that the intrinsic limitation in obtaining good quality thiocyanates SAMs lies in the strength of S-CN bond (~100 kcal/mol for p-substituted phenyl thiocyanate),200 which is reasonably strong.199 Ciszek et al. proposed a surface mediated reduction of thiocyanates as a mechanism for their adsorption along with the

- 39 scission of the S-CN bond, the formation of Au-thiolate bond and the removal of [Au(CN)2] .

The proposed mechanism for the adsorption of thiocyanate SAM is shown in Equation 1-8.

- + - RS-CN + Aun R-S- Au . Au(n-3/2) + 1/2 [Au(CN)2] (1-8)

In short, the overall reaction for the formation of organosulfur SAMs on Au using various organosulfur compounds involves the formation of a Au-thiolate bond. The quality of the obtained SAMs however, depends on the strength of the S-Y bond (Y = leaving group, e.g. H, S-

R, C-R, SO3M, CN etc.), the experimental conditions used for the modification, the purity of the compounds, and the molecular backbone.

I-4e Modification Conditions for Organosulfur SAMs on Au

The modification of metal surfaces can be performed by solution and vapour deposition methods. Solution deposition is more convenient, reproducible, widely accepted, and cost effective method for the formation of organic assemblies on metal substrates. It is commonly performed by the immersion of a freshly prepared and clean substrate into a dilute (~1-10 mM) ethanolic solution of a thiol for ~12-18 hours at room temperature.105 Solution phase deposition is highly advantageous where further immobilization/characterization has to be performed in a liquid phase. Gas phase deposition provides an excellent opportunity to prepare a clean substrate

(ion-sputtering and annealing), to do surface modification and in situ characterization of a modified surface in a clean and controlled environment within UHV chambers. One can also study the early stages of SAMs growth by using the vapour deposition method.3,83 However, in the gas phase, the dense coverage comparable to the solution phase is generally limited by the kinetics of formation (e.g. limited flux, shorter surface residence time). Another drawback of vapour deposition is that the adsorbate should be volatile and have an adequate vapour pressure

24 and only a limited number of precursors fulfill these criteria. It has been reported recently for thiocyanates SAMs that the quality (long-range ordered domains) of the organic thin films can be improved by using a vapour deposition method.198

Eventhough, the solution deposition is the favorable method for the formation of SAMs, an electrochemical or a combination of solution and electrochemical methods can also be used.

The first reported modification using an electrochemical method is performed by Tender et al. for the formation of a mixed SAM.201 They performed selective desorption of an interdigitated electrode previously modified with HO(CH2CH2O)6(CH2)11SH under potential control. A mixed

SAM is obtained after imersing the microelectrode, containing a low density SAM of

HO(CH2CH2O)6(CH2)11SH, into a 6-mercaptohexadecane solution. Another approach is the formation of an array of SAMs by applying a negative potential to the electrode to increase the rate of the adsorption from the alkanethiol solution.202 An electrochemical oxidation/reduction of the organosulfur precursor to form a Au-thiolate bond is another possibility for the formation of a

SAM under potential control. For example, Hsueh et al. have reported the formation of a thiolate

SAM from an electrochemical oxidation of alkylthiosulfate (Bunte salt) after generating a disulfide.203

The solvent effects on the mechanism and the kinetics of the adsorption are not well known. It is considered that the solvent-substrate and solvent-adsorbate interactions result in complications in the thermodynamics and kinetics of formation. The solvent interactions are important, as the adsorbate has to displace the solvent from the surface for adsorption. Ethanol is preferred as a solvent for organic self assemblies on metal surfaces as it can be obtained in high purity, has low toxicity, is inexpensive and has the ability to solvate a large number of compounds. Solvents other than ethanol like methanol, acetonitrile, dimethylformamide, tetrahydrofuran, cyclooctane and toluene have been successively used for SAM formation.105 A few studies suggested that the use of heptane and hexane (non-polar solvents) increase the rate of 25 formation of alkanethiol SAMs138,143,204 while the use of dodecane and hexadecane decrease it.138,143,204 In certain cases, solution phase self-assemblies of alkanethiols formed from non-polar organic solvents are less organized,105,205 while those formed from polar organic solvents are densely packed with fewer defects.151,205,206 The choice of a proper solvent for self-assembly from solution is crucial due to the complex and dynamic nature of interactions between the solvent, the substrate and the adsorbate.

It is well established that temperature has an important effect on both the adsorption and desorption of molecules on and from solid surfaces.83 The rise in temperature above 25 oC aids in the desorption of impurities and physically adsorbed solvent molecules and thermodynamically supports the organization of the adsorbate. The influence of the temperature is more prominent in the first step of adsorption.207 It is suggested that annealing at moderate temperatures also helps to reduce surface defects.83,207-209 For example, octylthiocyanate SAMs formed in solution at temperatures of 75 oC and 50 oC showed well-ordered SAMs with a lower degree of defects as compared to SAMs formed at room temperature.198 Moreover, a recent STM study on the adsorption of benzenethiol (BT) from a 1 mM ethanolic solution on Au(111) at 50 oC have provided evidence for the formation of well-ordered and large domains (~40 nm) of paired molecular rows with a (2 x 32)R23o unit cell.210 The long range ordered structures are not obtained for the BT SAM formed at room temperature. Thermal annealing is suggested to induce structural changes due to the lateral movement of molecules on the surface. For example, for 1- octanethiol (OCT) SAMs on Au, different superstructures are obtained after thermal annealing of a (3 x 3)R30o pre-covered SAM obtained at room temperature or increasing the solution temperature during modification.211-214

High quality modified surfaces can be obtained by using μM to mM adsorbate concentrations and adsorption times from a few hours to a few days. Low coverages are reported

26 for the use of concentrations in the nM range and adsorption time in seconds.215 Self assemblies obtained by immersion in an adsorbate at concentrations less than or equal to 1 μM for a week have been found to possess different physical properties than those obtained from high concentrations of the adsorbates.105 The minimum concentration for dense surface coverage has therefore been suggested to be 1 μM (~6 x 1014 molecules/cm3).3 The effect of impurities is also higher in low concentration solutions. The increase in immersion time decreases the number of defects in self assemblies and the suitable time is recommended from 12 to 18 hours.216

I-4f Structures of Organosulfur SAMs on Au

Various surface structures have been reported depending upon different stages of the

SAMs growth, the surface coverage, the modification conditions and the nature of the head group, leaving group and the molecular backbone. Here, only the most commonly observed structures are discussed.

Saturation Coverage

o At saturation coverage (θs = 1/3) of alkanethiol SAMs on Au (111), stable (3 x 3)R30 lattices85-87, 217,218 regardless of the chain length or terminal groups219,220 are formed along with c(4 x 2) super lattices.91,221 For (3 x 3)R30o lattices, electron diffraction studies of alkanethiol on

Au(111) show that sulfur atoms are arranged in a hexagonal shape (next nearest distance of ~5

Å).85-87 The hexagonal structure is commensurate with the underlying gold lattice.86,222 An area of

21.4 Å2 per molecule is reported for (3 x 3)R30o lattices.85-87

The c(4 x 2) super lattice can be described as a (3 x 23) rectangular lattice. This lattice contains four molecules per unit cell with distinct adsorption geometries and has unit cell dimensions four times greater than the (3 x 3)R30o lattice. This superstructure is first identified from low temperature infrared (IR)223 study of hexagonal lattices and is later confirmed by low

27 energy electron diffraction (LEED)221 and grazing incidence X-ray diffraction (GIXD),91 where the splitting of the CH2 IR band in the former case and extra diffraction peaks in the later case, could not be explained based on (3 x 3)R30o lattices. This c(4 x 2) superstructure was also observed by STM imaging of alkanethiolate SAMs having different terminal groups (-CH3 and –

COOH)219 and for aromatic thiolate SAMs.224 It is suggested that the relative amount of the c(4 x

o 2) super lattice is small compared to the (3 x 3)R30 lattice for long chain (nC > 11)

225,226 alkanethiols SAMs and it is dominant for intermediate chain (nC = 6) alkanethiols SAMs.

Figure 1-6 shows the proposed structural model for (3 x 3)R30° and c(43 x 23) phases of alkanethiol SAMs on Au(111) based on the contrast in STM images.227

Figure 1-6. Summary of the STM contrasts reported previously for alkanethiol SAMs. Contrast α

(a) represents the (3 x 3)R30° structure and contrasts β-ζ (c-f respectively) have the c(43 x

23) periodicity. For the clarity of the illustration, the STM spots corresponding to alkanethiol molecules are represented as located on equivalent hollow adsorption sites (i.e. assuming zero tilt and rotation angles).227 (Adapted with permission from reference 227, Copyright © 2006, ACS).

Non-Saturation Coverage

For non-saturation coverages, striped phases are usually formed.22 In the striped phase, molecules are usually arranged in a lying down phase or having larger tilt angles. The unit cell is described as (b x 3), where b is the integer/half-integer multiple of the distance between two gold atoms (2.88 Å).23,25 The value of b is usually in the order of once/twice the length of the molecular chain of the bulk molecule for a head to head/head to tail configuration.228 Figure 1-7

29 shows the proposed models for (b x 3) striped phases with molecules arranged in head to head and head to tail configurations. Striped phases are also observed at early stages of SAMs growth both from solution228 and gas phase149 depositions. From real time STM imaging of butanethiol lattices, (6 x 3) striped phases along with (3 x 3)R30o lattices are observed, which are later transformed into (3 x 3)R30o lattices.229 The pinstripe structures having (3 x 3)R30o lattices with standing up molecules and periodic missing rows are observed for short chain alkaenthiols due to weak intermolecular interactions.

Figure 1-7. The proposed structural models for (b x 3) striped phases of alkanethiol SAMs on

Au(111). (a) Head to head arrangement,18 and (b) head to tail arrangement. The alkyl chain is represented by zig-zag lines. The lateral registry of the molecules and the substrate is assigned arbitrarily with the head group placed on hollow sites of Au(111).18 (Adapted with permission from reference 18, Copyright © 2005, ACS).

I-4g Debated Au-S Interface

Understanding the true nature of the Au-S interface is relevant from both a fundamental and a practical point of view. In recent years, a new dynamic model for the Au-S interface231,232

30 has been proposed in contrast with the old model of a static Au-S interface22 with adsorption of the deposited molecules on specific sites of the unreconstructed Au(111) surface.233

The Classical Model of the Au-S Interface

The debate about the adsorption sites of alkanethiols on Au (111) is not yet resolved. The determination of the adsorption sites even for the well-known (3 x 3)R30o lattices and c(4 x 2) super lattices is an issue which has many practical implications in the areas of molecular electronics, electron transport to/from redox species, biomolecule immobilization and conductance of a single molecule.234 All equivalent adsorption sites for the commonly accepted

(3 x 3)R30o lattices on the Au(111) are not assigned conclusively. X-ray photoelectron diffraction (XPD)186 and normal incidence X-ray standing wave (NIXSW)235 studies of (3 x

3)R30o methanethiolate lattices on Au(111) from gas phase deposition suggest on top adsorption sites while density functional theory (DFT) calculations of the same system suggest on top adsorption sites to be the least favorable.236,237 However, hexagonal closed packed (hcp) hollow, fcc hollow, bridge, hcp bridge and fcc bridge sites are considered preferred adsorption sites on Au(111) by DFT calculations.236,237 Figure 1-8 shows the adsorption of the alkanethiol molecules on hcp hollow, fcc hollow, bridge and on top sites for (√3 x √3)R30o lattices on

Au(111). Table 1-1 shows binding energies for the adsorption of methanethiol at different adsorption sites of the gold surface. On the other hand, from a GIXD study of (3 x 3)R30o lattices of dodecanethiol on Au(111), two incoherent domains containing either on top or fcc hollow sites are observed.225 Those domains are further supported by theoretical calculations based on two step adsorption kinetics i.e. initial physisorption at on top sites and diffusion to favorable fcc hollow sites on chemisorption.225

Figure 1-8. Structural models for the adsorption of an alkanethiol on Au(111) at different adsorption sites. (a) fcc hollow sites, (b) hcp hollow sites, (c) bridge sites, and (d) on top sites.

Table 1-1. Energies of adsorption (kcal/mol) for methanethiol SAM on Au(111) at different adsorption sites.237

Hcp hollow Fcc hollow Bridge On top

-1.6 0.0 3.0 13.7

It has also been suggested that small differences (1-2 kcal/mol) exist between the binding energy of thiol to different adsorption sites of the gold surface (surface corrugation potential).

Therefore, the diffusion of the molecules to different adsorption sites is expected due to thermal fluctuation at room temperature. For example, ab intio calculations for the adsorption of methanethiol on Au(111) clusters have suggested an energy difference of 4.6 kcal/mol between the hcp hollow and bridge sites.237 The authors have also suggested the movement of sulfur head group over different adsorption sites within picoseconds at room temperature for 0.67 ML of dodecanethiol SAM on Au(111).237

Several adsorption models have also been proposed for c(4 x 2) superlattices of alkanethiols on Au(111). Along with many other arrangements as described in Figure 1-6, the

“zig-zag” and the “rectangular” structures are most commonly used to describe the c(4 x 2) unit cell. One model considers two different heights of alkanethiol molecules within/between rows of molecules due to 90o differences in chain twist (β), supported by both LEED221 and STM data.238

According to this model, the rectangular and zig-zag c(4 x 2) superlattices are suggested. For the rectangular c(4 x 2) superlattice, it is proposed that two chains out of four in (√3 x √3)R30o lattice have similar β values and other two chains have 90o difference (Figure 1-6b and c). For the zig- zag c(4 x 2) superlattice, it is proposed that three chains out of four in (√3 x √3)R30o lattice have similar β values and one chain have 90o difference (Figure 1-6d). On the other hand, GIXD91 and

Sum Frequency Generation (SFG)239 studies support the adsorption of molecules at two different adsorption sites i.e. fcc hollow and bridge sites. A similar model has also been proposed based on

STM images, where distances between bright and less bright rows are less than 5 Å (i.e. 4.5

Å).229 Hence, it has been considered that molecules at less brighter and brighter rows are adsorbed at hollow and bridge sites, respectively. In Figure 1-9, the proposed structural model is shown for the above described STM images.

Figure 1-9. The proposed structural model for the c(4 x 2) lattice of an alkanethiol on Au(111) with alternating rows of S head at hollow and bridge sites. The distance between alternating rows is 10 Å and between adjcant rows is 4.5 Å.229 (Adapted with permission from reference 229,

Photoelectron diffraction (PED) and NIXSW studies235,240,241 on long chain alkanethiols at low coverages (lying down striped phases) suggest on top adsorption sites. Nevertheless, NIXSW

242 studies on C6 and C10 SAMs support adsorption at two different sites.

The Dynamic Models of the Au-S Interface

The work on adsorbate induced surface reconstruction,243,244 the formation of Au vacancy islands243,244 and Au adatoms231,232 was initiated in early 2000. This new concept originated when the adsorption of methanethiolate lattices at on top adsorption sites186,235 and dodecanethiol lattices simultaneously at on top and fcc hollow sites225 on Au(111) are observed experimentally.

The two main configurations that have emerged are Au-adatom thiolate (Figure 1-10a) and Au- adatom dithiolate (Figure 1-10b). The first model considers one fold co-ordination of thiols to the gold adatoms located at fcc sites for (3 x 3)R30o lattices (Figure 1-10a)232,241,243 or a mixture of fcc and hcp hollow sites for c(4 x 2) lattices232,244 in the top most Au layer. The formation of gold

34 vacancies are proposed due to the surface reconstruction. Theoretical,243,244 NIXSW,232 and

XPS241 studies of methanethiolate on Au(111) have supported the Au-adatom thiolate configuration. Alternatively, low temperature STM studies at low coverages,231 DFT calculations based on PED245,246 and GIXD245,246 studies of (3 x 3)R30o and c(4 x 2) lattices for methylthiolate SAMs on Au(111) provided evidence for the second model. In this model, it was considered that the gold adatom lies at a bridge site of the underlying gold layer while two thiolates are bonded to one gold adatom and the sulfur atom of each thiolate is simultaneously bonded to an on top site of the top most gold layer (Figure 1-10b). This means that the sulfur atom of the thiolate is two-fold coordinated. Moreover, Grönbeck et al. has conducted DFT calculations and has proposed a third polymeric model, where adatoms are located at both fcc and hcp hollow sites and thiol molecules are forming a bridge between two gold adatoms (Figure 1-

10c).247 According to this model, Au-adatom dithiolate species are energetically more favorable than Au-adatom thiolate species.247 In addition, this model is also not consistent with the PED and NIXSW results. These three proposed structural models are shown in Figure 1-10. On the basis of the ongoing research about the detailed structure of the Au-S interface in organosulfur

SAMs, no universal model has been identified and this matter still raises many controversies.

However, the notion of the surface induced gold reconstruction and the formation of Au adatoms during adsorption is acknowledged more seriously.

Figure 1-10. The proposed dynamic models for the adsorption of alkanthiol on Au(111). (a) Au- adatom dithiolate model, (b) Au-adatom thiolate model, and (c) a polymeric model, where thiol molecule is bonded to two Au-adatoms.233

Adsorption of Sulfur on Au

The fundamental understanding of the nature of the metal-sulfur interactions is very important due to its wide range of applications in catalysis,248-254 material science (including surface passivation),19,22,221,255-259 electrochemistry,260-264 corrosion prevention,265,266 semiconductor thin films267-272 and nanodevices or molecular electronics.273-279 Sulfur poisoning

(i.e. the adsorption of sulfur on metal catalysts from the decomposition of the sulfur containing compounds present as impurities) has resulted in the loss of useful resources in the chemical and the petrochemical industries.251-254,280-283 Hence, the reactivity of sulfur with metal catalysts is undesirable in certain cases and the knowledge should be acquired to better understand desulfurization reactions.284,285 The Au-S interactions are also the center of the attention in the area of organosulfur SAMs on Au(111).18,83,99

Experimental studies have shown an initial chemisorption of sulfur at step edges.286-289 A study of S on Au(111) from molecular S2 based on LEED and NISXW techniques has revealed 36 three distinct phases of the adsorbed sulfur.290 These include a (5 x 5) phase, a (√3 x √3)R30o phase at room temperature and a “complex” phase after annealing the (√3 x √3)R30o phase to

~450 K. Sulfur coverages of ~0.25, ~0.33 and ~0.5 monolayer (ML), respectively are assigned to these phases. This investigation identified low coverage phases (~0.25 to 0.33 ML) as layers of monoatomic sulfur chemisorbed on hollow sites with sulfur atoms adsorbed at on top sites of the underlying unreconstructed gold surface and a high coverage phase (~0.5 ML) as a AuS monolayer. Figures 1-11a and b show (5 x 5) and (√3 x √3)R30o phases of the adsorbed sulfur on

Au(111).

Figure 1-11. Proposed structural models for the chemisorption of sulfur on Au(111) at low coverage. The sulfur atoms are placed on hollow sites arbitrarily. (a) A (5 x 5) phase (~0.25

ML),290 (b) a (√3 x √3)R30o phase (~0.33 ML), and (c) a quasi linear phase.293 The large circles in Figure 1-11a highlight the ordering of the seven sulfur atoms.290 (Adapted with permission from reference 290, Copyright © 2007, ACS).

Another study involving LEED, high resolution photoemission, thermal desorption and

DFT calculations has shown the adsorption of atomic sulfur at hollow sites at low sulfur

291,292 coverage. The authors have suggested the formation of S2 (S-S bonding) species with a 37 weakening of the Au-S bond when sulfur coverage is equal to or greater than 0.4 ML. This study

291 also indicated the formation of the Sn species at sulfur coverage greater than 1 ML. A recent theoretical study on the adsorption of sulfur on Au(111) at 0.33 ML coverage has shown the co- existence of a (√3 x √3)R30o phase and a new quasi linear chain phase (energies close to the (√3 x √3)R30o phase, S atoms at alternate fcc hollow and hcp hollow sites) at room temperature

(shown in Figure 1-11c).293 Many experimental and theoretical studies on the adsorption of sulfur on Au(111) from liquid and gas phases have suggested the formation of the (√3 x √3)R30o sulfur phase, interatomic distances of ~5 Å, at 0.33 ML.261,287,290,291,293-295 However, this structure is only reported by STM261,294,296 in electrochemical environment and by LEED in the gas phase at room temperature.290,295 Nevertheless, the situation is quite controversial for sulfur coverage equal to or greater than 0.5 ML where rectangular/quasirectangular structures are observed.286,288,289,297 On one side, these structures are assigned to a more “complex” AuS phase.288,290,298 On the other side,

261,286,289,291,294,296,299-302 they are attributed to a polysulfide species having a S8 ring.

XPS analysis of sulfur adlayer modified gold surfaces at high coverages have reported three doublets for the S 2p region with their S 2p3/2 components located at ~161 eV, ~162 eV and

~163 eV. The two doublets at lower binding energies are the dominant contributions while the third doublet at higher binding may be entirely absent (indicating absence of unbound sulfur or sulfur multilayers). The component at lowest binding energy has been assigned to monoatomic sulfur or sulfur adsorbed in the (√3 x √3)R30o phase.260,261,289,291,303 The component at

289,291,303 intermediate binding energy has been attributed to a polysulfide/S8 phase or a “complex”

AuS phase.288,290,295 The component at the highest binding energy has been assigned to elemental sulfur or sulfur multilayers.304-306

Several research groups have suggested the formation of a “complex” AuS phase for the rectangular structures observed in the STM images of the modified gold surface at higher coverage.288,290,295,307 The earliest LEED study combined with a radioactive tracer technique on 38 adsorption of sulfur on Au(111) from H2S gas has also observed a “complex” phase at a coverage of 0.5 ML.308 However, an in situ STM and LEED study in UHV on the deposition of sulfur from

SO2 gas on Au(111) has proposed for the first time a 2D AuS phase for the rectangular features observed at high coverage.288 In other studies, those traditional rectangular structures for sulfur deposition (mostly in electrochemical environment) are assigned to polymeric sulfur species

261,286,289,291,294,296,299-302 having a S8 ring. Friend’s group has shown that 0.05 ML sulfur coverage is enough to modify the herringbone reconstruction of the underlying gold layer and 0.1 ML sulfur coverage results in complete lifting of the gold surface reconstruction.288 At 0.33 ML sulfur coverage, they observed a (√3 x √3)R30o phase on an unreconstructed gold surface.288 The further increase in coverage resulted in “massive mass transport”, the formation of the monoatomic etch pits and a 2D AuS layer with incorporation of gold atoms from terraces to the

AuS phase.288 STM images of this new phase at 0.6 ML coverage have shown “sponge like” morphology. After annealing to 450 K, this new phase is transformed into an ordered 2D AuS having a quasirectangular structure (~8.2 x ~8.8 Å2 and α = ~82o) with 1:1 stoichiometry and 0.5

ML sulfur coverage.288

Friend’s group further extended their work after performing DFT calculations to simulate

STM images observed in their initial work.298,309 Their proposed structural model is shown in

Figure 1-12a. In this model, the unit cell is composed of three types of gold atoms i.e. Au3+ (4- fold co-ordinated), Au2+ (3-fold co-ordinated) and Au+ (2-fold coordinated) and two types of sulfur atoms i.e. 2 and 3-fold co-ordinated.298,309 Another in situ STM study of sulfur coverage using SO2 gas at 420 K has shown a similar behavior to the previous results up to 0.33 ML coverage.295 However, a short range rectangular structure at 0.5 ML coverage is observed at 420

K and a “AuS” phase is assumed. The authors have suggested that the gold atoms are provided from the step edges rather than from terraces for a “complex” AuS phase.295

Figure 1-12. Proposed structural models for the chemisorption of sulfur on Au(111) at high coverage. Rectangular/quasirectangular structures (a) a complex AuS phase (~0.5 ML),298 and (b)

286 a polysulfide S8 phase (~0.6 ML). (Adapted with permission from reference 298 and 286,

A UHV study by LEED, STM, XPS and NIXSW using S2 gas for the sulfur adsorption on

Au(111) has also claimed that the observed rectangular structures in their experiments (at coverage of 0.5 ML, after annealing (√3 x √3)R30o phase at 450 K) are a “complex” AuS phase as reported in earlier studies.290 Based on their NIXSW data, they suggested that even though this complex phase is incommensurate with the underlying gold surface, there is still a local commensuration with most sulfur atoms at on top sites of the underlying gold surface.290

The initial work supporting a “complex” AuS is performed in gas phase under UHV conditions. However, a later in situ electrochemical (EC) STM study has suggested a 2D AuxS phase when an anodic potential is applied to an already modified gold electrode.307 The electrode is modified electrochemically in an aqueous solution containing Na2S and NaOH. For this study, the potential is increased from -0.3 V to of +0.4 V at a fixed sulfur coverage of 0.33 ML containing (√3 x √3)R30o phase in a sulfur free blank solution of NaOH. At +0.4 V, rhombic sulfur structures (lattice constants: a and b = ~8.3 Å and α = ~83o) are observed along with the 40 formation of S vacancies from the (√3 x √3)R30o phase and Au vacancies from smooth terraces.

The authors suggested that the sulfur atoms from the (√3 x √3)R30o phase and Au atoms from smooth terraces are incorporated into the rhombic AuxS phase due to perpendicular mass transport. They also suggested that the formation of AuxS phase is similar to the one observed under UHV conditions after thermal annealing of (√3 x √3)R30o phase at 450 K.288,290 The authors suggested the formation of a AuxS phase in an electrochemical environment under positive potential at room temperature as electrochemical annealing. This concept is based on previous electrochemical studies, where an increase in the mobility of gold surface atoms is suggested under the influence of a specifically adsorbed anion and/or application of a more positive potential. The strength of the two factors (stronger anion-gold interactions or increased positive potential) determines the net effect on the weakening of the Au-Au bond and surface mobility.310,311

In addition to the complex AuS phase explanation, the rectangular structures (unit cell

~6.2 x ~5.8 Å2)286,300 observed in the STM images have been predominantly assigned to polymeric sulfur/S8 rings chemisorbed on the gold surface at high coverage. The polymeric S8

-2 - sulfur structures are observed using S , H2S and HS in aqueous solution at room

289,299 261,286,291,294,296,300 temperature and in an electrochemical environment Although, S3 and S4

286,300 structures are also observed at high coverage. A model has been proposed for the S8 polysulfide ring structure with six sulfur atoms at hollow sites and two sulfur atoms at on top sites (Figure 1-12b).286 XPS studies of these structures have shown signals for elemental sulfur.291,294 Moreover, a XPS study of rectangular structures at ~0.5 ML sulfur coverage obtained from an aqueous Na2S solution have not shown signals for the oxidized gold as expected for a AuS phase.289 However, the authors suggested that a monolayer of AuS could be detected by XPS. Their assumption is based on the observation of an additional peak in the Au 4f and the

O 1s regions for a monolayer of gold oxide deposited electrochemically and a clear distortion in 41

289 the calculated Au 4f spectrum of a monolayer of Au2S and Au2S3. On the other hand, a recent

X-ray absorption spectroscopy (XAS) and XPS study of the nanoscale AuS formed from the reduction of HAuCl4 with Na2S detected signals for metallic gold and polysulfide sulfur species.312 Figure 1-13 shows XPS spectra in the Au 4f and S 2p regions of the nanoscale AuS formed with different ratios of Na2S and HAuCl4.

Figure 1-13. XPS spectra in the Au 4f and S 2p regions of the nanoscale AuS formed with Na2S

312 to HAuCl4 ratios of (1,2) 0.65, (3) 1.2, (4) 2, (5) 3, and (6,7) 5 (bulky amorphous precipitates).

The study on the nanoscale AuxSy have suggested an increase in the Au-S bond length from 2.31 Å to 2.32 Å with an increase in S:Au ratio, which is much longer than the crystalline

AuS (2.17 Å). They have also suggested the decomposition of the AuS into metallic gold and polysulfide species in air and UHV even prior to the X-ray irradiation.312 In addition, XPS study of gold sulfide nanoparticles and bulk Au2S had also not shown any difference in the Au 4f

313 289 signals from elemental gold. The S-S distances observed in a polymeric S8 species (~3 Å) on

286,294,300,314,315 gold surfaces are ~50% larger than the bulk sulfur (S8 ring, ~2.2 Å). It has been suggested that the sulphur/gold interactions are responsible for the elongation of the S-S distance

313 in polymeric S8 species on a gold surface.

Surface enhanced Raman spectroscopy (SERS) of adsorbed sulfur on electrochemically

-1 300 roughened gold obtained from electroxidation of Na2S has shown a Raman band at 270 cm .

This band is asssigned to monoatomic sulfur and is obtained at low sulfur coverage.300 At high sulfur coverage, a broad band is observed at 450 cm-1 for open chain polysulfides; and bands at

-1 -1 -1 300 150 cm , 220 cm and 450 cm are observed for S8 ring sulfur. A few additional SERS studies offered further support for the simultaneous presence of monomeric and polymeric sulfur species.289,291,303 Lustemberg et al. have reported Raman bands at 212, 313 and 453 cm-1 for a nanostructured gold substrate immersed in a 3 mM Na2S and 0.1 M NaOH solution for 10 minutes at open circuit potential (ocp).288 The peak located at 212 cm-1 is assigned to the stretching modes of bulk elemental sulfur, that at 313 cm-1 to the Au-S stretching of the

-1 monoatomic sulfur and that at 450-500 cm to the S-S stretching of the polysulfide Sn species.300,316-319 The authors observed a reduction in the intensities of the bands at 212 cm-1 and

~450 cm-1 with no change in the intensity of the band at 313 cm-1 after shifting the electrode potential from ocp to -0.75 V.288 A previous in situ STM study has indicated that sulfur starts to desorb from rectangular structures at this potential.286 Therefore, the reduction in peak intensities at 212 cm-1 and ~450 cm-1 represents the disappearance of the polysulfide species.288 43

Recent work in our group using several organic compounds as sulfur transfer agents has also supported the formation of S8 polysulfide species for the rectangular structures obtained in the STM images of sulfur adlayer on Au(111) at high coverage.301,302,320 In these studies, sulfur is deposited spontaneously at room temperature using 1-3 mM solutions of hexamethyldisilathiane,

4-substitutedbenzene sulfonyl phthalimides and dithiobisphthalimide in organic solvents e.g. acetonitrile (MeCN), tetrahydrofuran (THF), and Methanol (MeOH).301,302,320,321 Hence, these studies provide a better analogy to study the nature of the Au-S interactions in SAMs on gold since modification conditions are similar. Real time STM imaging has shown that the rectangular structures move as individual units.302 The surface dynamics are supported with the observed reversible association/dissociation of rectangular units in different configurations (parallel, mixed, staggered, random).302 Multilayer formation is also abserved, where a layer of rectangular sulfur units is residing over another with the mobility of rectangular structures as independent units.301 Furthermore, multiple sulfur phases are shown to exist including rectangular structures and new phases (in which rectangles are arranged in a parallel and staggered fashion) as well as the transformation of one phase to the other phase.320 The mobility of the rectangular structures as individual units, phase transformation and multilayer formation are interpreted as meaning that

301,302,320,321 rectangular structures are polysulfide S8 species and not a “complex” AuS phase.

Few previous studies have suggested the mobility of adsorbed sulfur at high temperature

(> 300 K) or in an electrochemical environment.293 DFT calculations on the adsorption of sulfur on Au(111) at various temperatures have shown a thermal energy barrier of 25-30 meV for the mobility of 0.3 ML sulfur to different adsorption sites.293 The higher mobility of sulfur on

Au(111) than other transition metals has been reported by Rodriguez et al. from LEED, thermal desorption and DFT studies.291 Salvarezza et al. have shown the potential dependent reversible transformation of a sulfur adlayer in Na2S and NaOH solution from the rectangular S8 phase to

(√3 x √3)R30o prior to sulfur desorption from terraces by in situ STM studies.286,322 44

I-4h The Quality of Organosulfur SAMs

Surface Defects

The physical properties of SAMs like electron transport, ionic conductivity and redox behavior in electrolyte solutions can be affected by defects in SAMs.23 These defects include missing rows, domain boundaries, vacancies, pinholes and disordered chains. Figure 1-14 shows a schematic representation of different types of surface defects. Molecular defects are found even for the single crystal Au(111) surface and within well ordered, crystalline alkanethiolate SAMs.

Both extrinsic and intrinsic factors are responsible for causing defects in SAMs. The extrinsic factors include the cleanliness of the substrate, the method of preparation of the substrate and the purity of the adsorbate while intrinsic factors are related to the dynamics of SAMs formation.323-

330

Figure 1-14. Schematic models showing different types of surface defects. (a). A vacancy island,

(b) a step edge, (c) missing rows, (d) domain boundries, and (e) molecular defects (pin holes).25

In order to get reproducible SAMs, freshly cleaned substrates should be used. Generally, strong oxidizing chemicals such as piranha solution (sulfuric acid (H2SO4) : hydrogen peroxide

(H2O2) in the ratio of 3:1), chromo-sulfuric acid or oxygen plasma are used for cleaning gold

45 substrates. The choice of a substrate with a lower number of surface irregularities is imperative in order to get defect free SAMs. Even for low index gold surfaces, defects such as step edges are present. There are a few strategies that are commonly used to obtain thin gold film with larger grain sizes and smaller surface roughness. One approach is the annealing of the substrate after deposition of thin films of metals.331-333 Another approach is the change in the angle at which the metal is deposited on the substrate surface.334 Moreover, subsequent treatment with piranha and

335 aqua regia (hydrochloric acid (HCl) : nitric acid (HNO3) in the ratio of 3:1) solutions

(CAUTION: These solutions are extremely corrosive and should be handled with care), chemo- mechanical and electrochemical polishing336-337 are used to increase the grain sizes for thick gold films (~180-200 nm).

The presence of trace amount of impurities such as sulfur and oxidation products of thiols

(disulfides and sulfonates) do not significantly modify the structure of SAMs.105,338 The presence of disulfides as impurities within thiols may affect the physical properties of SAMs because of their lower solubility than thiols which results in physisorption.338 The use of oxygen free solvents and inert environments during modification also support the formation of reproducible

SAMs49,338 and prevent the oxidation of thiols.

STM and AFM images of well-ordered SAMs on Au both from solution and gas phase have shown 2D gold vacancy islands or etch pits of monoatomic or diatomic height (2.4 or 4.8

Å).22,162,339,340 The origin of etch pits is not known completely. It has been considered that the adsorption of alkanethiol molecules may result in the removal of some of the gold atoms from the surface due to the weakening of the Au-Au bond.340-343 A clean Au(111) surface has a (22 x √3) herringbone reconstruction and adsorption of alkanethiol molecules results in lifting of the surface reconstruction. This process is followed by the relaxation of surface atoms and the formation of gold vancancy islands.22,344 The removal of the surface gold atoms during SAM formation is also supported by detection of gold in the solution used for the modification.340 46

However, the amount of gold in solution was less than the total amount of Au atoms removed during SAM formation.

On the other hand, gold surface reconstruction during adsorption of alkanethiol has been also suggested, since etch pit formation is also observed during modification in the gas phase.340-

343 The increased etch pit density is suggested for higher concentration and for short chain alkanethiols.340 A recent adatom model for the adsorption of alkanethiol may help to explain the formation of etch pits or vacancy islands.231,232,243,244

Molecular defects such as missing rows are found for short chain alkanethiol SAMs on

Au.345 It has been suggested that weak intermolecular interactions between short chain alkanethiols and soft annealing of the SAM is responsible for missing rows in SAMs.22,339,346

Molecular vacancies or pin holes are areas where the molecules are not well organized, they have different tilt angles or their hydrocarbon chains are not fully extended. During SAM growth, the commensurate monolayer of the SAM may occupy different symmetries with respect to the underlying gold lattice forming various nucleation centres. A domain boundry is a defective region between two domains of SAMs having different symmetry with respect to underlying gold lattice or two different lattices of the adsorbed molecules on the surface e.g. (√3 x √3)R30o and c(4 x 2) lattices.

Stability of Organosulfur SAMs on Au

Another serious concern for the technological applications of organosulfur SAMs is their chemical and thermal stability. SAMs kept in an ambient environment can degrade over time, through oxidation into disulfides347 or sulfonates,134 (Equations 1-9 and 1-10) which can diffuse away from the surface.25

2 RS-Au RSSR + 2Au (1-9)

RS-Au + H2O + O3 RSO3H + HO-Au (1-10)

It has been suggested that in liquid environments, the degradation rate is faster owing to the formation of both disulfides and sulfonates.25 However, the formation of sulfonates is also possible on the surface in an ambient environment even in the absence of light.134,347 Several factors contribute towards the chemical instability of SAMs. These factors are related to the physiochemical environment of the adsorption reaction i.e. presence of oxygen,348 moisture,349

UV radiation,350,351 the position352 and the nature of the terminal group,353-355 the length of the hydrocarbon chain, the substrate structure356 and the sample storage conditions. It has been found that SAMs formed on gold surfaces with a large number of surface defects (such as gold islands, vacancies, steps and adatoms e.g. nanostructured gold) are chemically more stable347,357 in ambient and aggressive liquid environments (e.g. ethanol) than crystalline Au(111) surfaces.347,357

A desorption temperature in the range of 115-127 oC is reported during the thermal processing of dodecanethiol SAMs on Au by STM238,358 and surface plasmon resonance spectroscopy (SPRS).359 The desorption temperature depends mainly on the chain length,360 roughness183 and the temperature of the substrate during adsorption.361 The possible desorption products are the corresponding thiolates354,360,362,363 and disulfides354,363,364 at low and high SAM coverage, respectively.

Improvement of Organosulfur SAMs Quality

A number of parameters can be controlled to improve the SAM quality and reduce surface defects e.g. the choice of solvent and modification conditions. For dithiol SAMs, it is suggested that the use of an ethanolic solution may result in the formation of multilayers365 and the oxidation of the terminal thiol group to disulfide or sulfonate.366-368 On the other hand, it is

48 suggested that the use of a hexane solution in the absence of light and oxygen results in well- ordered and dense dithiol SAMs.19 Some of the other parameters used to improve the SAMs quality include heating the solution (depending upon the solvent used),369-372 post-deposition soft annealing in air or in UHV,339,346 controlled potential deposition373 and repetitive voltammetry after multiple immersions of the substrate in a precursor solution.374,375 All of the above- described procedures improve the SAMs quality to a certain level.376,377

Additional approaches have been used to obtain thermally stable SAMs. These include the incorporation of polymerizable groups (lateral interaction between neighboring SAM molecules) such as amides,114,378 and acetylene.379,380 Other strategies are electron-irradiation of aromatic

SAMs,381,382 and the use of a gold substrate containing one monolayer of silver.383

I-4i Aromatic Organosulfur SAMs on Au

Awareness of the use of highly conducting aromatic molecules in molecular electronic devices originated in 1974, when a simple rectifier based on a single organic molecule having acceptor/donor pi bonds was constructed.384 Later on, these devices were fabricated using a single molecule274 or a group of molecules as a monolayer.385 The use of SAMs is an effective way to fabricate a wide variety of aromatic molecules on metal electrodes. Thiol derivatives of OPE have been the most studied due to their rigid conjugated system and electrical properties.386 For

OPE SAMs, a range of electronic properties can be introduced. For example, OPE SAMs containing nitro, amino and both nitro and amino functionalities show properties suitable for their applications in the areas of memory devices387 and negative differential resistors (NDR, a decrease in current with an increase in the applied voltage).388 Furthermore, a change in the relative angle between two phenyl rings from 0o to 90o (molecular conformation) determines their conductivity,389 and makes them suitable for use in molecular switches.390 SAMs of

49 unfunctionalized and nitro substituted OPE on Au behaveas a rectifier391 and NDR,392 respectively.

Aromatic SAMs also have useful applications in the area of nanolithography.386 Aromatic structures within a SAM have been successfully cross-linked laterally upon UV irradiation393 or through the use of an electron beam.394 The resulting cross-linked monolayers demonstrated an excellent mechanical stability and were used as nanomembranes after separation from the substrate.395 An e-beam patterned cross-linked pristine SAM of 1,1’-biphenyl-4-thiol (BPT) on polycrystalline gold showed thermal stablity up to 1000 K.381,382 On the other hand, alkanethiol

SAMs and pristine BPT SAMs desorb from the surface at 353 K and 400 K,381 respectively.

Figure 1-15 shows an e-beam and thermally induced changes in a pristine SAM.

Another example is the fabrication of free standing 2D graphene sheets with tunable properties after thermal annealing of cross-linked electron irradiated aromatic SAMs on metal surfaces.396 These nanocrystalline graphene sheets on metal have tremendous applications in the areas of nanobiotechnology and nanoelectronics.396

Figure 1-15. Schematic representation of a (a) BPT SAM, (b) e-beam induced cross-linking, and

(c), and d) temperature induced changes in pristine and e-beam cross-linked BPT SAMs.381

Aromatic (benzenethiol (BT), 2-naphthaleinthiol (2-NT) and 4-acetamidothiophenol (4-

AA) SAMs on polycrystalline copper have shown enhanced chemical stability in sulfuric acid

(0.5 M) solutions after 12 hours of immersion without significant degradation.397 The SAMs of

BT and 2-NT have shown less passivation than SAMs of 4-AA after aging.397 It has also been shown that SAMs of BT,398,399 2-NT399 on Cu are more stable and have a better corrosion prevention in highly acidic solutions than SAMs of 1-undecanethiol (1-UT)398,399 despite having a lower thickness.

Aromatic thiolate SAMs are the least explored yet the most promising class of the organosulfur SAMs. Aromatic SAMs have additional significance over aliphatic SAMs beside 51 their remarkable properties detailed above. The rigid structure of the aromatic ring offers fewer degrees of freedom than an aliphatic chain and also involves stronger intermolecular interactions.

Moreover, different functionalities can be easily introduced by changing the substituents on the phenyl ring. The simplest example of an aromatic thiolate SAM is benzenethiol (BT) adsorbed on gold. The adsorption of BT has been investigated from the gas phase on transition metals400-409 and from solution and gas phases on coinage metals.397,398,410-414 In regards to the molecular orientation of BT, nearly parallel or perpendicular orientation has been proposed. Surface enhanced Raman spectroscopy (SERS),415,416 HREELS411 and XPS (thickness measurement)411studies of BT SAMs on Au(111) have concluded smaller tilt angles which indicates perpendicular orientation. However, other SERS417-419 and ellipsometric16,420 data support larger tilt angles (parallel orientation).

The discrepancy also exists regarding the 2D surface structures of BT SAMs. Molecular dynamics calculations421 and a few experimental studies420,422-424 have suggested that (3 x 3) and (2 x 2) or long range ordered phases of BT SAMs are not possible on Au(111). On the other hand, several experimental studies have reported ordered structures with (m3 x n3)R30o (m and n are integers) symmetries. For example, (3 x 3)R30o phases have been reported for 4- aminothiophenol,425 benzyl marcaptan,420,424 4-biphenylmethane thiol,420 and 4- hydroxythiophenol.426 Moreover, (23 x 3)R30o phases have been reported for oligo(phenylethylnyl)benzene thiol,422 1-phenyl-methane thiol,344 3-phenyl-propane thiol344 and

4-[4’-(phenylethynyl)-phenylethynyl]-benzene thiols.427 Other phases that have been reported are

(5 x 3)R30o phases for 4-mercaptopyridine,423,428,429 and (13 x 13)R13.9o phases for BT.410

DFT calculations of BT adsorption on Au(111) have suggested the adsorption at fcc bridge sites with large tilt angles as the most stable configuration at low coverage.430 At high coverage, (3 x

3) (hexagonal) and (23 x 3) (herringbone) configurations with an upright geometry have been

52 proposed with the latter being more stable.430 Molecular dynamics calculations on (3 x 3)R30o phases of aromatic thiols (BT, 4-methylbenzenethiol and 4-methylbenzylthiol) on Au(111) have suggested fcc hollow sites as the most favorable followed by hcp hollow and bridge sites.431 They also suggested that the system geometry is greatly influenced by the chemical structure of the head and tail groups.431 For aromatic thiols, striped phases with molecules lying parallel to the surface have also been reported.223,344,432

The common obstacle in the practical applications of aromatic SAMs is the high density of surface defects223,344,433-436 due to the lattice mismatch between the aromatic moiety and the gold substrate.433,437Several strategies have been used to overcome this problem including: the use of hybrid aliphatic-aromatic molecules i.e. the insertion of an aliphatic chain between the head group and the aromatic ring(s),424,438-443 the increase in the number of aromatic rings,344,420,422,444,445 the use of aromatic bidentate dithiols,446 post-deposition annealing,440 displacement of a preadsorbed SAM447 increase in the solution temperature to 50 oC,210 and the use of Se as an alternative head group.448,449 The introduction of insulating alkyl spacers may result in long range ordering439,440,450 but also lowers the conductivity of the SAMs.451 The packing density is also affected by the conformational freedom of the terminal aromatic ring(s) for hybrid aliphatic-aromatic molecules.432 Moreover, their ordering also depends on the odd- even effect of the number of carbon atoms in the alkyl spacer.438,439,449 On the other hand, the increase in the number of aromatic rings (acenes) provides a higher conductivity444,445 and a lower solubility of the compounds. Theoretical452-454 and experimental455-457 studies have shown both higher and equivalent conductance of aromatic selenoate SAMs than aromatic thiolate SAMs.

Nevertheless, both lower455,458 and higher459-463 stabilities are reported for Au-Se aromatic SAMs than Au-S aromatic SAMs on Au(111).

I-4j Interpretation of STM Images of Organosulfur SAMs

STM provides molecular scale information of periodic and non-periodic local surface structures and SAM defects in ambient, liquid, electrochemical and UHV environments. Despite the great utility of STM in the development of the field of SAM formation, the origin of different features and the contrast in the STM images of SAMs is still heavily debated. The STM tip images the local density of states (LDOS) at the Fermi level and as such what has been imaged by the STM is not recognized unambiguously. A single spot in the STM images of thiolate SAMs can be assigned to the head group,464,465 the tail group,238,464,465 the molecular backbone or the molecular unit adjacent to the tail group.238,374,375,464,465 Similarly, a protrusion or depression in the STM image can be attributed to the presence or absence of certain group(s)/atom(s) or vice versa and surface features may look entirely/slightly different for a particular surface after varying the tunnelling conditions. The sources of difficulty in obtaining the real information from the STM are the perturbation of the SAM by the STM tip342,466-469 and the convolution of the topographic and the electronic effects of the STM images.467-469 However, scanning with low tunnelling currents may minimize these effects to some extent.342

It has been widely accepted for c(4 x 2) superlattices of alkanethiol SAMs that the STM images are comprised of spots with two distinct intensities and/or shapes.155,238,229,261,470-473

However, contradictory opinions have been given regarding the contrast in the STM images.155,238,261,229,345,470,472 It has been argued that the contrast in the c(4 x 2) lattice can only be explained if the STM tip sees the tail groups155,238,371,472 and not the head groups.229,261,345,474 In this case, a minor variation in the heights of the molecules can be brought after a slight change in the chain twist angle. On the other hand, this interpretation cannot justify the electron tunnelling through the insulating alkanethiol SAMs.345 In addition, the orbitals from the S head groups participate mainly towards the total density of the state after chemisorption475 and a large distance exists between the tail groups and the Au substrate due to nearly vertically oriented molecules.464 54

However, this condition can be much simpler for aromatic SAMs, where electron tunnelling through the aromatic moieties is also possible along with the S-Au bonds. Moreover, orbitals from aromatic rings in principle have a greater contribution to the total density of states after chemisorption.

Zeng et al. have conducted systematic high impedence, low temperature (78 K) and constant height STM studies of heptanethiol and dodecanethiol SAMs on Au(111) in UHV at

464 varied sample bias voltages (Vs). They found a strong dependence of the intramolecular patterns on the applied voltage.464 In the voltage range of +0.5 to +1.5 V, spots with different intensities (bright and gray) as known for c(4 x 2) superlattices are seen.238,261,473 The gray spots are changed to stripe and dumbbell shapes at high positive (+2 V) and negative voltages (-1.5 V), respectively.464 However, there is no change in the shape of the bright spots after varying the sample bias voltage.464 The authors assumed that the molecules for which the C-C plane of the terminal methyl and the adjacent methylene lies perpendicular or parallel to the surface, the terminal methyl groups will appear as the bright spots at all voltages.464 For molecules having the

C-C plane not vertical or horizontal to the surface, the mixture of the terminal methyl and methylene groups will appear as stripes and dumbbells at high positive and negative sample bias voltages, respectively.464 The STM images for heptanethiol SAMs on Au(111) at different sample bias voltages are shown in Figure 1-16.

Figure 1-16. STM images of heptanethiol SAMs with the c(4 x 2) superlattice: (a) Sample bias

(Vs) = +0.5 V, (b) Vs = +2.0 V, and (c) Vs = -1.5 V. The dependencies of the intramolecular

2002, AIP).

On the basis of the voltage and the site dependent ab initio calculations for c(4 x 2) superlattices of heptanethiol SAMs on Au(111), Zeng and co-workers have proposed the variation in intramolecular patterns with voltage only for sp3 hybridization of the S of thiolate on chemisorption.464 Figure 1-17 show the changes in intermolecular patterns with voltage for sp3 and sp hybridizations of an adsorbed hepatanethiol on Au(111).464

Figure 1-17. Simulated STM images of a single heptanethiol molecule on the Au(111) surface

3 with the sp model (a1) Vs = +0.5 V, (a2) Vs = +2.0 V, (a3) Vs = -1.5 V; and with sp model (b1)

Vs = +0.5 V, (b2) Vs = +2.0 V, (b3) Vs = -1.5 V. (a) and (b) are the side views of a heptanethiol adsorbed on Au(111) surface with the sp and sp3 mode, respectively.464 (Reprinted with permission from reference 464, Copyright © 2002, AIP).

The group further extended their work by performing a systematic simulation of the STM images for a single molecule of different alkanethiols SAMs on Au(111). Their study is performed by varying the chain lengths and twist angles under three sample bias voltages.465 The authors have shown that the simulated images for alkanethiols SAMs on Au(111) with an odd number of carbon atoms are independent of the bias voltage for the chain twist angle of ±45o, but appear as round, elliptical or dumbbell shapes at +1, +2 and -1 V, respectively for the chain twist angle of ±135o.465 On the other hand, the opposite trend is observed for alkanethiols SAMs on

465 Au(111) with an even number of carbon atoms. Furthermore, alkanethiols SAMs with nC > 11 do not show the dependence of the intramolecular patterns on the bias voltage, the chain length being even or odd and the chain twist angles.465 The studies conducted by Zeng, Li and coworkers 57 have suggested that the topographic effect dominates in the STM images of alkanethiol SAMs on

Au(111).

Several researchers have observed reversible transitions between (3 x 3) and c(4 x 2) phases470 or two different phases of c(4 x 2)104 SAMs after varying the tunnelling condition or the bias voltage. STM tip induced modifications in the contrast of STM images have also been reported due to the alteration in the molecular orientation (the tilt, twist, and azimuthal angles).229,261,476 A recent systematic STM and scanning tunnelling spectroscopic (STS) study has shown reversible, reproducible contrast transitions in the two coexisting phases of the c(4 x 2) superlattices of annealed undecanethiol SAMs on Au(111) after varying the tunnelling conditions and the distance between the tip and the terminal groups of the SAM molecules.226 The authors concluded that the reorientation of the molecules was not responsible for the variation in the contrast of the STM images after changing the tunnelling conditions.226 According to their results, the LDOS (electronic effect) plays an important role in controlling the contrast in the

STM images and can also be changed after changing the distance between the tip and the terminal group of the SAMs.226

477 A recent in situ STM study of C8 and C10 alkanethiols SAMs on Au(111) at low temperature (4K) and dual imaging modes (constant current and local barrier height (LBH)) has revealed that one can simultaneously image the terminal groups372 (in constant current mode) and the head groups478 (in LBH mode)479 The authors suggested that the dual imaging mode can also help to solve the issue of the true nature of the Au-S interface in organosulfur SAMs on Au due to the sensitivity of the LBH mode to the Au-adatoms.479

In short, special precautions should be taken in getting information from the STM images of organosulfur SAMs on Au(111). The correct interpretation of the STM images can be influenced by the tunnelling conditions used (the bias voltage, the tunnelling current, the tip to the sample distance), the nature and the length of the molecular backbone (aliphatic or aromatic, 58 long or short), and the odd or even number of carbon atoms on the aliphatic chain. Other factors that have to be considered are the molecular orientation of the SAM, the binding sites on the Au surface, the hybridization of the sulfur head group, the mobility of the molecules on the surface, the changes induced by the STM tip (SAM perturbation, change in the adsorption sites or the molecular conformation etc.), and the changes associated with the substrate surface (surface reconstruction or stress).

I-5 Motivation of the Research

Organosulfur SAMs have been extensively studied and are significant in terms of their applicability but they still have many inherent limitations. These limitations include short range

SAMs with inferior quality, low packing densities and irreproducibility. This is especially critical for aromatic SAMs. Another concern is the chemical stability of the available precursors in an ambient environment, before, during and after modification. Specifically, aromatic thiols undergo oxidation to disulfides and sulfonates in solution and to sulfonate on a surface, while dithiols form multilayers as a result of polymerization.36 Hence, there is a need to have alternative precursors, which are chemically stable and more specifically can form long-range, high quality aromatic SAMs. In order to overcome these limitations, the use of protected thiols or organic thiosulfates has been proposed. However, extraneous material used for the deprotection step may cause many problems.37 On the other hand, chemically stable organic thiosulfates SAMs have many defects. They also have low surface coverage and their formation kinetics and structure are not identical to thiol monolayers.34,35 Ciszek et al. proposed use of thiocyanates as alternative precursors for the formation of thiolate assemblies. They chose thiocyanate assemblies because they are chemically stable and can be formed without the use of any deprotecting reagents and special environments.39,40 Most recently, molecular scale information of thiocyanate assemblies is provided by STM,198,199 XPS,198,199 reflection absorption Infrared spectroscopy (RAIRS)199 and 59

NEXAFS.199 It should however, be noted that while the first report on the use of thiocyanate

SAM was published in 2004, STM images for aliphatic thiocyanate SAMs were only reported in

2008. It has been reported that the structural quality was dependent on the purity of the compounds and the modification conditions as well. More importantly, the strength of the S-CN bond was also mentioned as a drawback in obtaining good quality SAMs.

In this thesis, the use of organic sulfenyl chlorides has been proposed for the first time for the modification of gold. Organic sulfenyl chlorides as precursors offer two main advantages over thiocyanates due to their structural similarity. Organic sulfenyl chlorides can be easily reduced (Equation 1-11 and Figure 1-18) and the S-Cl bond is reasonably weak (see Table 1-1.

For example, the reduction potential for 4-MePhSCN is almost 2 V (vs saturated calomel electrode (SCE)) more negative than that of 4-MePhSCl and the S-CN bond is ~60 kcal/mol stronger than the S-Cl bond. Therefore, it is expected that the Au-thiolate bond would be more readily formed due to the above mentioned factors. These characteristics make organic sulfenyl chlorides attractive candidates for surface modification. They can be good alternatives to thiols and thiocyanates, where the cleavage of the S-H bond in short chain alkanethiols and the S-CN bond in thiocyantes is the practical limitation for their self-assembly.

4-RPhSY + 2e- 4-RPhS- + Y- (1-11)

where Y is Cl or CN and R is H, Me, Cl, NO2 etc..

Table 1-2. Bond dissociation energies (S-Y bonds) and reduction potentials of compounds 4-

RPhSY.200,480

Bond dissociation energies

(kcal/mol)

Compound Y = S-Cl480 Y = S-CN200

PhSY ~41 ~100

4-ClPhY ~40 ~100

4-MePhY ~40 ~101

Reduction potential ~0 ~-2

(V vs SCE)

Figure 1-18. Linear sweep voltammetry (LSV) in 0.1 M NBu4PF6/MeCN at a glassy carbon electrode. 4-MePhSCN (3.26 mM) and 4-MePhSCl (2.65 mM). Scan rates 200 mV/s.200,480

I-6 Scope of Thesis

There are four main objectives of this thesis. The first and the primary objective is the investigation of organic sulfenyl chlorides (R-SCl or Ar-SCl) as new organosulfur precursors for the formation of organic assemblies on gold. The need to propose alternative precursors for modification of the gold arises from the desire to overcome the problems associated with other precursors such as thiols, protected thiols, thiosulfates and thiocyanates.

The second objective is to understand how the structural quality and ordering of the SAM depend on the molecular backbone. The modification of Au surfaces using a series of organic sulfenyl chlorides and the characterization of the modified surfaces allow investigation of the usefulness of the S-Cl functional group as a precursor for the modification of Au and the 62 investigation of the dependence of the obtained self assemblies on the precursor’s backbone. A molecular backbone containing a phenyl ring with a para substituent results in the formation of well-ordered, high density and reproducible aromatic SAMs on gold. Alternatively, a molecular backbone containing a phenyl ring with ortho substituent results in the formation of less ordered, low density aromatic SAMs which may decompose after longer periods of time. Moreover, a molecular backbone with a good/stable leaving group results in the spontaneous adsorption of a sulfur adlayer on the gold surface and the ejection of the rest of the molecule..

The third objective of this thesis is to provide fundamental insight regarding the STM ability to image the head group, the tail group, the molecular backbone or the group adjacent to the tail group and the origin of the contrast in the STM images of alkanethiol SAMs. This question was addressed through STM imaging of the 4-nitrophenyl sulfenyl SAM on Au(111) at high coverage. STM images have shown that we can image the tail group if the molecular backbone is highly conducting, such as a phenyl ring, and the formed monolayer is thin i.e. ~10

Å.

The fourth objective of this thesis is to investigate the nature of the Au-S bond in organosulfur SAMs and sulfur adlayers on Au(111).

In this thesis, the solution deposition method is used to prepare SAMs of organic sulfenyl chlorides on Au. For surface characterization, STM, XPS, PM-IRRAS and CV are used. In the context of this thesis, a monolayer (ML) is the number of molecules per gold atom or number of sulfur atoms per gold atom. XPS is performed by one of our previous group members Kallum M.

Koczkur. In chapter II, the method, chemicals, and experimental techniques used for the surface modification, and characterization are detailed. Chapter III will present the findings for the formation of the aromatic SAM using 4-nitrophenyl sulfenyl chloride on Au(111). This chapter will also provide some insights regarding the nature of the features imaged by STM for aromatic molecules. Chapter IV will present a more thorough understanding regarding the use of the 63 proposed precursors for the formation of the aromatic SAMs and will provide insight about the effect of phenyl ring substituent. Chapter V will present the findings for the use of some aliphatic sulfenyl chlorides for SAM formation on Au. Chapter VI will present a summary and furture directions of the present work.

Chapter II. Experimental Part

II-1 Chemicals

4-Nitrophenyl sulfenyl chloride (95% from Sigma Aldrich), 2-nitrophenyl sulfenyl chloride (98% from Lancaster), 2,4-dinitrophenyl sulfenyl chloride (95% from Lancaster), triphenylmethane sulfenyl chloride (99% from Aldrich), trichloromethane sulfenyl chloride (

95% from Aldrich), and chlorocarbonyl sulfenyl chloride (96% from Sigma Aldrich) are used without further purification. N,N-Dimethyl formamide (DMF, certified ACS from Fisher

Scientific), anhydrous ethanol (EtOH, absolute from Commercial Alcohols), and methanol

(MeOH, high pressure liquid chromatography (HPLC) grade from Caledon) are used as received.

Tetrahydrofuran (THF, HPLC grade from Caledon) is dried over sodium metal and distilled under argon, just prior to use. Potassium hydroxide (KOH, 99.99% semiconductor grade from

Sigma Aldrich), sodium hydroxide (NaOH, 99.99% semiconductor grade from Sigma Aldrich), and potassium bromide (KBr, > 99 % FT-IR grade from Sigma Aldrich) are used as received.

Carbon tetrachloride (CCl4, certified ACS grade from Fisher Scientific, dried over molecular sieves), and ultra-pure water (Millipore, 18.2 MΩ) are used for condensed phase IR, and electrochemistry in aqueous medium, respectively. A gold wire (0.762 mm diameter, Premion ®,

99.999% from Alfa Aesar) and freshly cleaved mica sheets (V1 Grade, Ted Pella) are used to deposit thin films of Au(111). Chromo-sulfuric acid (2 mL of chromium trioxide, Cr2O3 from

Chromerge ®, Bel-Art, and 200 mL of sulfuric acid, H2SO4, 95-97%, semiconductor grade from

Riedel-de Haën) is used to clean Au(111) substrates.

II-2 Preparation of Au(111) Substrates

A custom built evaporation system is used to evaporate gold on a freshly cleaved mica sheets. The system operates at a pressure of 1 x 10-7 Torr. It consists of a bell jar (Kurt J. Lesker) 65 and a turbo pump (Varian). In order to obtain high quality Au(111) surfaces, the mica sheets are heated at 600 K for 12 hours before and for an additional 3 hours after the deposition of the gold.

Chromo-sulfuric acid, anhydrous EtOH, and ultra-pure water, are used to clean Au(111) samples after removal from the evaporation chamber. Cleaned gold samples are dried under a gentle stream of nitrogen, and are stored in a desiccator prior to their use. The method is adapted from

Derose et al.48 Scanning tunnelling microscopy (STM) is used routinely to assess the quality of

Au(111) substrates before modification.. Figure 2-1, shows typical wide and small range images of Au(111) substrates.

Figure 2-1. Topographic images of thin gold films on mica prepared by PVD. (a) 500 x 500 nm2,

(b) 200 x 200 nm2 and (c) 5 x 5 nm2. Tunnelling conditions: Tip bias = +0.1 V, tunnelling current

= 0.8 nA, and scan rate 4.1 lines/s.481,482 (Reprinted with permissions from references 481 and

II-3 Modification of the Gold Surfaces

A Au(111) substrate is immersed in a 1 to 10 mM solution of the respective compound for times ranging from a few minutes to 48 hours. Either a pure solvent or a binary solvent mixture are used for the modification depending upon the solubility of the compound and the

66 concentration used e.g. EtOH:DMF (9:1 or 1:1), THF:MeOH (1:1), THF, and EtOH. After thorough rinsing with the binary solvent mixture/pure solvent, the modified substrate is dried under a gentle stream of nitrogen. Electrochemical studies are performed using a polycrystalline solid gold electrode, which is first polished and then cleaned electrochemically after cycling in a

0.5 M aqueous KOH solution. After cleaning, the electrode is thoroughly rinsed with EtOH and dried under gentle stream of nitrogen.

II-4 Characterization of the Modified Surfaces

For surface characterization, analytical techniques such as STM, XPS, PM-IRRAS and

CV are used. STM is used as an important technique for the structural characterization of

Au(111) surfaces modified with organic sulfenyl chlorides. STM uses a probe to obtain information about the structure of the modified gold surface with atomic and molecular resolution. STM, however, does not provide chemical information about species adsorbed at the surface. Therefore, surface spectroscopic techniques such as XPS and PM-IRRAS are also used.

XPS is used to determine the elemental composition, chemical state of each element and any contaminant present on the modified gold surface. RAIRS is used to probe the functional groups of the adsorbed organic molecules and to determine the molecular tilt. CV is used to study the electrochemical stripping of adsorbed species on polycrystalline solid gold electrodes.

II-4a Scanning Tunnelling Microscopy

Scanning tunnelling microscopy (STM) is a powerful surface characterization technique capable of providing structural information about surfaces at the atomic and molecular levels. It was developed in 1981 by Gerd Binnig and Heinrich Rohrer, who earned the Nobel Prize in

Physics in 1986 for their invention.483 STM has the ability to provide 0.1 nm lateral and 0.01 nm depth resolution.484 STM provides images of surfaces in ambient, liquid, gaseous,

67 electrochemical and ultra-high vacuum (UHV, ~10-10 torr) as well as at a wide range of temperatures (few Kelvin (K) to few hundred K).484,485

The operating principle of STM is based on the concept of quantum mechanical tunnelling, which considers the wave like nature of electrons. According to the classical approach, the probability of finding an electron across a vacuum barrier (with its potential energy larger than the kinetic energy of electron) is negligible i.e. the wave function of electrons decays exponentially outside of the conductor. According to quantum mechanics, when two materials

(conductors or semiconductors) are brought in close proximity to one another (within few Å apart) then their wave functions may overlap. The probability of finding electrons beyond a barrier with this mechanism is called quantum tunnelling. In Figure 2-2, an illustration of the quantum mechanical tunnelling is shown with respect to the distance between two conductors.

Figure 2-2. An illustration of the quantum mechanical tunnelling with respect to distance between two conductors.

In the context of STM, a small bias voltage (Vb) is applied in between a sharp conducting

STM tip (commonly called probe) and the sample surface (conducting or semiconducting material). The outcome of which is the tunnelling of electrons from the tip to the sample surface or vice versa depending on the bias voltage and the closeness of the tip to the sample surface

(about few Å). The flow of electrons results in a tunnelling current (few nA) without any physical contact with the surface.

Mathematically, the inverse decay length (κ) of an electron wave function at the Fermi level can be expressed per Equation 2-1

κ = √ (2 m (Φ – eV)) / ћ (2-1)

where me is the mass of an electron, Φ is the LBH or the average wave function of two conductors and ћ = h /2π is the reduced Planck’s constant. At low temperature and a small bias voltage (Vb, Φ >> eV), the tunnelling current (I), Equation 2-2, varies exponentially with respect to the distance between the tip and the sample.

I α Vb ρsa (d, Ef) exp(-2 κ d) (2-2)

where d is the distance between the tip and the sample, and ρsa (d, Ef) is the LDOS (the number of available or empty states across the barrier) at the Fermi level of the sample/tip surface. The electron tunnelling depends upon the number of available electrons at the Fermi level, the number of available or empty states across the barrier (i.e. LDOS at the Fermi level), the LBH, and the distance between the tip and the sample.485 The information about the LDOS of the sample surface can be obtained by keeping d constant and measuring I with respect to Vb. Similarly, the occupied and the unoccupied states of the sample can be probed by applying a negative or positive bias voltage to the sample surface, as shown in Figure 2-3.

Figure 2-3. A scheme of electron tunnelling with respect to the LDOS after applying negative or positive bias to the sample.

The essential elements of STM instruments are a STM probe/tip, a piezoelectric controlled height and a x, y scanner, a coarse sample to tip control, a vibration isolation system and a computer. These components are shown in Figure 2-4.486,487

Figure 2-4. Schematic view of STM.

The use of a clean and stable surface and imaging in a controlled environment are very important in obtaining high quality STM images. An atomically sharp tip having a small radius of curvature is also very important.484 Therefore, great care should be taken in preparing a good quality STM tip. Tungsten, platinum-iridium and gold tips are usually used. They are formed by electrochemical etching or mechanical cutting.484 The tunnelling current is highly sensitive to the separation between the tip and the sample (Equation 2-2). Therefore, a fine positioning of the tip over the sample surface is necessary to improve sensitivity. For this purpose, both coarse and fine positioners are used. The fine positioning is done by using a piezocrystal or piezoceramic

71 material (e.g. quartz, barium titanante or lead zirconium titanante (LZT)). Moreover, a vibration isolation system is also required due to the sensitivity of the tunnelling current to external and internal vibrations.485 This is typically achieved by suspension using bungee cords and imaging in a vibration isolation chamber.

STM can be operated in three modes depending upon the feedback applied to control the z axis (the height) of the scanner/tip. The three modes are the constant height, the constant current and the LBH.488,489 In constant height mode, the applied voltage and the height of the tip is kept constant while the change in the tunnelling current is measured. In constant current mode, the tunnelling current is kept constant and the height of the tip is varied to maintain the required tunnelling current. The tip height at each measurement point is adjusted using feedback loop. The constant height mode is faster as it does not require adjustment of the tip to sample distance but it can be only used for smooth surfaces. The constant current mode is time consuming but it can be used for irregular surfaces.484-487 For heterogeneous samples (having non-uniform surface compositions), the LBH or the work function of the surface varies and virtual holes or adatoms will be observed with constant current/height mode. Hence, the LBH mode is used to directly measure the work function of the surface according to Equation 2-3. In LBH mode, the STM tip vibrates vertically at a single point on the sample surface and a change in tunnelling current is measured as a function of the separation between the tip and the sample surface. A feedback loop is used to control the height of the tip over the sample surface. This mode is less commonly used.

2 [δ (ln I) / δd] α Φ (2-3)

For this thesis, STM (5500 SPM system, Agilent) images are obtained in air using an electrochemically etched (in 3 M NaOH) tungsten tips (0.25 mm diameter, 99.95%, Alfa Aesar).

STM images are obtained in constant current mode with a positive bias voltage applied to the tip with respect to the sample.

II-4b X-ray Photoelectron Spectroscopy

X-ray photoelectron spectroscopy (XPS), also identified as ESCA (electron spectroscopy for chemical analysis), is a quantitative as well as a qualitative spectroscopic technique. XPS provides information about elements present with their chemical and electronic states and the quantity of each element within a sample. In the case of thin films on surfaces, it provides information about the film thickness, its uniformity, its chemical composition, and any element present on the surface as contaminants. XPS can be used for every type of material except hydrogen and helium.490 The first monochromatic XPS instrument was developed by Siegbahn and Hewlett-Packard in 1969.491 Siegbahn received the Nobel Prize in 1981 for his contributions to the technique.492

The operation of XPS is based on the principle of photoelectric effect, which was first discovered by German physicist Heinrich Hertz in 1887.493 The concept was later developed by

Albert Einstein in 1905.494 The phenomenon involves the emission of photoelectrons

(core/valence level) when matter is irradiated with electromagnetic radiation (EMR) of a short wavelength i.e. a few eV to few keV (e.g. ultraviolet (UV) and X-rays). An electron is ejected, if the energy absorbed by the electron within a material exceeds the work function of the material.

The energy of the emitted photoelectrons depends upon the energy of the incident photons and the number of the emitted electrons can be increased by increasing the intensity of incident photons. The maximum kinetic energy (EK) of the emitted electron and the work function (Φ) of the material can be represented by Equations 2-4 and 2-5

EK = hʋ - Φ (2-4)

Φ = hʋ0 (2-5)

where h is Planck’s constant, ʋ is the frequency of the incident photons and ʋ0 is the threshold frequency of the material. The principle of photoemission is illustrated in Figure 2-5.

Figure 2-5. An illustration of the photoemission principle.

A photoelectron spectrum is a plot of electron count versus the binding energy of the emitted electrons. It is obtained by irradiating a sample material with a soft X-ray beam (AlKα and MgKα) and measuring the number of emitted electrons and their kinetic energy from the top

1-12 nm of the surface in UHV. The first photoelectron spectrum was recorded by P. D. Innes in

1907.495

The XPS instrument consists of an X-ray source, a UHV system, an electron energy analyzer, a detection system and a data system as shown in Figure 2-6.

Figure 2-6. Scheme for a monochromatic X-ray photoelectron spectrometer.

The electron spectrometer measures the kinetic energy of the emitted electrons, which is not an intrinsic property of the material. The binding energy relates the electrons to the parent

490 element and the atomic energy level. Hence, the binding energy (EB) is used in the

75 photoelectron spectrum as an essential property of the material. It can be calculated using the relation shown in Equation 2-6.

EB = hυ - EK – Φs (2-6)

490 where Φs is the work function of the spectrometer.

Each element present on the surface has a number of characteristic peaks with a binding energy corresponding to the electronic configuration of electrons within the atom. The binding energy decreases with an increase in the energy levels (1s > 2s) and it increases with an increase in atomic number of elements. A chemical shift in the binding energy of core level electrons for an element is expected by change in the oxidation state or the chemical enevironment. For example, binding energy for a higher oxidation state of an element is higher than a lower oxidation state of an element. Similarly, an element binded to more electronegative atoms has a higher binding energy than an element binded to less electronegative atoms. The binding energy is used as the identification of the element. The ratio of each element present can be obtained by the number of ejected electrons for each characteristic peak within the given volume of the sample surface irradiated. In order to get the amount of each element present on the surface, the raw XPS signal (peak area/intensity) should be corrected for the background and against the corresponding relative sensitivity factor (RSF) and then normalized against all elements detected on the surface. Along with the quantification, depth profiling (<10 nm) and surface mapping are performed by measuring the elemental composition as a function of the depth into the sample or varying the angle of incidence and the lateral position on the sample respectively.

A sample may degrade or certain functional groups on the sample surface may undergo photochemical transformation during XPS analysis. The main source of the degradation/transformation might not be the incident X-rays but it can be the secondary electrons

76 that are produced during the photoemission process. Some of the important reasons that can cause these processes are the sensitive nature of the material analysed; the wavelength and the intensity of the X-rays, the rise in the temperature of the sample surface caused by the X-ray irradiation and the physio-chemical environment of the XPS chamber (e.g. vacuum). Therefore, in interpreting the X-ray photoelectron spectrum, these factors should be considered carefully.

For this thesis, XPS is only used for the identification of chemical species present on the surface, and the measurement of the thickness of the organic thin film on Au. An ultrahigh vacuum (UHV, Omicron, operates at a base pressure of 5 x 10-11 Torr) system is used to conduct

XPS studies. An Al Kα source (1486.6 eV) is used to generate X-rays. The system consists of a hemispherical sector analyzer (operates at a pass energy of 20 eV) along with a multichannel electron detector. All XPS spectra presented in this thesis are measured at a takeoff angle of 75° and are referenced against the Au 4f7/2 peak at 84.0 eV. The XPSPEAK 4.1 software is used to fit all XPS spectra.

The thickness of the monolayer (tA) is calculated from the slope of the plot between log natural of a ratio of the XPS signals for the modified and bare gold substrates to 1/cos (θA), according to Equation 2-7.

ln Is/IA = - tA/{λAu (EAu) . Cos θA} (2-7)

where IA is the XPS signals for the modified gold substrate, Is is the XPS signals for a bare gold substrate, λAu (EAu) is the effective attenuation length (EAL) of gold electrons of kinetic energy

EAu through organic monolayer (a value of 33 Å is used), θA is the takeoff angle with respect to the surface normal (varied at an interval of 10o, from 15o to 75o.)

II-4c Polarization Modulation Infrared Reflection Absorption Spectroscopy

Infrared (IR) spectroscopy is a widely used technique for obtaining information about the structure and specifically the functional groups of molecules on surfaces. The absorption of IR radiation by a molecule brings a change in the vibrational and rotational modes of chemical bonds within a molecule. Each chemical entity within a molecule gives a characteristic peak in an infrared spectrum. IR spectroscopy follows a selection rule, where only vibrational/rotational transitions associated with a change in the dipole moment give rise to a peak in the IR spectrum.

Fourier transform infrared (FTIR) spectroscopy is a highly sensitive technique used to obtain structural information of organic and inorganic samples even at the interface (e.g. gas/solid, liquid /solid and gas/liquid). Sampling techniques used for analysing solids/supported solids can be divided into two categories according to the type of sample used: finely divided or flat sample surfaces. The transmittance or reflectance is measured for species adsorbed on a surface of a transparent material, while reflectance is measured for non-transparent materials

(metals). The molecular orientation of the adsorbed molecules with respect to surface can be determined by using polarized light.496

Prior to the 1960s, it was difficult to obtain a meaningful IR spectrum of thin films of adsorbed molecules on metal surfaces (a few nanometers). This used to result in a poor signal to noise ratios, as the absorption is proportional to the path length.497 In 1966, R. G. Greenler has used the reflection method to study thin samples on solid surfaces. He demonstrated that IR absorption can be increased 5000 times by using IR radiation polarized parallel to the plane of incidence at near grazing incidence.498 For ultra-thin films, the detection of adsorbed molecules by IRRAS suffered from environmental and instrumental instabilities. In the late 1970s, the use of the polarization modulation (PM) in combination with IRRAS helped to enhance signal-to- noise ratio. In 1979, Hipps and Crosby recorded the first PM-IRRAS spectrum in transmission mode499 and the first PM-IRRAS experiment was performed by Golden et al. in 1981.500 PM- 78

IRRAS is used for the characterization of thin films, monolayers or sub-monolayers on metals with high sensitivity. It provides information about the nature and the orientation of the adsorbed species. It has an advantage over conventional IRRAS as the measurement of modulated reflectivity helps to reduce interfering effects of background absorption. Therefore, in-situ PM-

IRRAS can be used to study lipid or protein monolayers at the air-water interface,501-506 reaction mechanisms on catalytic surfaces at high temperatures507,508 and to identity species at electrode/electrolyte interfaces for electrode processes.509

PM-IRRAS employs two different polarizations, the s-polarized and p-polarized lights.

The intensity of the incident electric field of s-polarized light on the metal surface increases with the distance from the metal surface and decreases for the p-polarized light. Hence one can measure all types of absorbing species present on the surface. PM-IRRAS is also suitable for the characterization of adsorbed layers on semiconductor surfaces (e.g. Si and Ge).

To understand the theory of reflectance, one can consider the electric field component of the EMR in the IR range. The electric field can be described in terms of two components; i.e. s- polarized and p-polarized components. p-polarized light has electric field vectors parallel to the plane of incidence while s-polarized light has electric field vectors perpendicular to the plane of incidence (Figure 2-7). For a highly reflective metal surface, the electric wave is formed on the surface of the metal after combination of the incident and reflected lights. If the electric wave has zero amplitude on the metal surface it will not interact with the adsorbed layer (Figure 2-7). For interaction with the adsorbed layer, the electric wave should have acceptable amplitude and must be normal to the metal surface.

Figure 2-7. Directions of electric field vectors (Ep) of incident (subscript i, dashed arrows) and reflected (subscript r, solid arrows) IR beam at an air/Au interface (a) p-polarized (b) s-polarized.

At a non-normal angle of incidence, the phase shift of the reflected wave depends on the angle of incidence and the state of polarization of the light. For perpendicular polarized light i.e. s-polarized, the phase shift is near 180o for all angles of incidence (Figure 2-8). For parallel polarized light i.e. p-polarized, the phase shift of the reflected wave increases with an increase in the angle of incidence of the light while the phase shift for the grazing angle of incidence is 180o

(Figure 2-8).510

KGaA).

After the vector addition of the incident and the reflected vectors, one can find that the resultant vector will be nearly zero for s-polarized light at all angles of incidence, while it will be maximum for p-polarized light at the angle of incidence near grazing angle. Hence the s component of the polarized light will give minimum absorption and only the p component of the polarized light will show some absorption.

Unlike metals, the reflectance for s-polarized light also changes with the angle of incidence for semiconductors.511 Therefore, for an adsorbed layer on semiconductors, the optimum incidence angle would be where the difference between the reflectance of the p- polarized and s-polarized is highest.

The reflectivity of the metal with the adsorbed layer is calculated by the boundary value method.512 The value of the reflectance is <1 even for a sample having no absorption. Therefore, it is better to compare the reflectivity of the metal with the adsorbed layer (RA) to the reflectivity of a bare metal (R0) represented as absorption factor A (Equation 2-8).

A = (R0 – RA) / R0 (2-8)

In the case of metals, the absorption of IR radiation by the adsorbed molecules will result in a change in the dipole. This change in dipole will induce an image dipole into the metal, if the change in the dipole is parallel to the metal surface it will cancel out but if it is perpendicular to the metal surface it will enhance. This generalization gives the surface dipole selection rule i.e. only transitions associated with a transition dipole perpendicular to the metal surface are observed.513 The selection rule is illustrated in Figure 2-9.

Figure 2-9. Representation of the image effect for the metal surface.

For an IR spectrum of an ultra-thin sample, a longer measurement time (a few hours) is required to obtain a better signal-to-noise ratio. A very small change in the instrumental stability or absorption from the surroundings will result in a drastic change in the spectrum during the measurement. In situ analysis is also not possible since only p-polarized incident light will show absorption for the adsorbed layer on the metal surface. Hence, s-polarized light serves as a reference spectrum for p-polarized reflectance spectrum. A photoelastic modulator (PEM) can be used for the PM and the isotropic adsorption from the background can be avoided. For PM, differential reflectance (ΔS, Equation 2-9) is measured.

ΔS = (ΔR / Rav) = 2(Rp – Rs) / (Rp + Rs) (2-9)

where Rp is the reflectance for p-polarized light, Rs is the reflectance for s-polarized light and

Rav is the average of Rp and Rs.

The basic instrumentation consists of a beam from the FTIR spectrometer combined with the polarization modulation system. This is obtained by placing the PEM in the path of the IR beam before or after the sample. The signals are detected after the electronic filtration and the demodulation. An optical layout is shown in Figure 2-10.

Figure 2-10. Block diagram of PM-IRRAS spectrometer.

A commercial FTIR system (Thermo Scientific Nicolet 8700) is used to measure IR spectra of the organic sulfenyl chlorides modified Au(111) surfaces. The system is equipped with an external tabletop optical mount, a PEM (Hinds Instruments PM-90 with a II/ZS50 ZnSe

50 kHz optical head, Hillsboro, OR), a demodulator (GWC Instruments Synchronous Sampling

Demodulator, Madison, WI), and a liquid nitrogen cooled mercury cadmium telluride (MCT-A) detector. All atmospheric regions of the system are purged with dry air (Balston 74-45). All IR spectra are measured at the optimized angle of incidence of the IR beam (~80o with respect to the

-1 surface normal) and at half wave retardation value of the PEM (at 1300 cm for NO2 stretch). For each spectrum 10,000 scans are recorded with a resolution of 4 cm-1. Relative differential reflectivity (Equation 2-9) is used as the output signal. Background correction is performed using the spline interpolation technique after subtracting the sample spectrum from a bare gold spectrum.

ΔS = (ΔR / Rav) = 2(Rp – Rs) / (Rp + Rs) (2-9)

where Rp and Rs are the reflection coefficients for the p and s polarization, respectively.

A commercial FT-IR system (Thermo Instruments NEXUS 870) is used to record transmittance spectra of 4-nitrophenyl sulfenyl chloride (~11 mM), 2-nitrophenyl sulfenyl chloride (~17 mM) and 2,4-dinitrophenyl sulfenyl chloride (~14 mM) in CCl4. The system is coupled with a triglycine sulfate (TGS) detector. The IR spectra are recorded using a flow cell (a home designed) containing two BaF2 windows and a Teflon spacer (~25 μm in thickness). Each spectrum is obtained after measuring 100 scans with a resolution of 2 cm-1. The solvent spectrum

(CCl4) is used to reference the solution spectrum.

II-4d Cyclic Voltammetry

Cyclic voltammetry (CV) is one of the most popular and versatile electroanalytical techniques. It can be used for quantitative and qualitative measurements such as the determination of standard reduction or oxidation potentials, the number of electrons transferred per molecule for a particular system, the diffusion coefficient of an analyte, the reversibility of a

85 system, the mechanism and the reaction intermediates, and the electron transfer kinetics. The electrochemical cell commonly consists of three electrodes i.e. the reference electrode, the working electrode and the counter electrode. The dominant mode of mass transport in the electrochemical cell is the diffusion at the electrode/solution interface. Various working electrodes are used including gold, platinum and glassy carbon. The potential of the working electrode is swept linearly from an initial potential (Vi) to a switching potential (Vs) and then reversed to a final potential Vf (Vf <=> Vi). This process can be reversed many times in either of the directions and the Vi, Vs and Vf values can be changed for one, some or all of the repetitive cycles during a single experiment. The choice of the potential range for the experiment depends upon the electrochemical properties of the electroactive species in a solution/thin organic film on the surface, the electrode material, the solvent and the supporting electrolyte used. Moreover, only those values are chosen for the Vi, Vs and Vf, where no redox reaction(s) occur(s) for the above mentioned species. A cyclic voltammagram is a plot of the working electrode current as a function of the applied potential at a constant scan rate.

In order to understand the working principle of the technique, consider a three electrode electrochemical cell which contains a supporting electrolyte solution and a reversible electroactive species which can undergo a reversible redox reaction with one electron transfer as shown below.

- Ox + e Re (2-10)

In a forward scan, the electrode will behave as a cathode (reduction of Ox) and an increase in the cathodic current will be observed, when the potential will reach to the reduction potential of Ox. The current will reach its maximum value Ipc at the peak potential Epc and then starts to gradually decrease as the concentration of the Ox form decreases beyond a certain value at the

86 electrode. For the backward scan, the electrode will behave as an anode (reoxidation of Re). A response similar to the forward scan will be observed with a peak current Ipa and a peak potential

Epa with reverse polarity. An opposite response can be observed if the electroactive species is present in the Re form and the direction of the scan is reversed too. A reversible electrochemical system in CV will show well defined characteristics such as shown in Equations 2-11 to 2-14

ΔEp = Epc - Epa = 57 mV/ne (2-11)

Ipc/Ipa ~ 1 (2-12)

Ipc or Ipa α √v (2-13)

0 E1/2 = E (2-14)

where ne is the number of electrons transferred per molecule during the redox reaction, v is the

0 scan rate in mV/s, E1/2 is the potential at the half wave and E is the standard potential for the given redox species. The peak position for a reversible system also does not vary with a change in the scan rate. However, the response is completely different for an irreversible redox system. A typical CV scan for a reversible redox species is shown in Figure 2-11.

Figure 2-11. A CV for a reversible redox active species.

Cyclic voltammetry is also used to study the electron transfer of redox active species in a solution, the blocking properties, and the oxidative/reductive stripping of organosulfur/sulfur modified metal electrodes. In this thesis, cyclic voltammetry is used to study the reductive/oxidative desorption of organosulfur monolayers or sulfur adlayers adsorbed on polycrystalline solid gold electrodes.

Previous studies on alkanethiol SAMs on polycrystalline gold electrodes have found that the application of too negative or too positive potentials causes the reductive or the oxidative stripping of the monolayer in acidic, neutral, basic, aqueous or ethanolic solutions.171,377,514-516

The reductive stripping reaction can be represented as per Equation 2-15.171,514

- Au-SR + e- Au0 + RS (2-15)

The desorbed thiolate can readsorb on the surface if the potential is scanned in the reverse direction and if the thiolate species do not diffuse away from the electrode surface.517 The desorption potential depends upon a number of factors such as the degree of ordering, the intermolecular interactions of the film and the crystallinity of the surface.518 A reductive desorption potential above -1.3 V vs Ag/AgCl is reported for long chain alkanethiol SAMs on polycrystalline Au electrodes with a transition region of -0.9 to -1.3 V.516 It has been suggested that sharp desorption peaks are not observed for polycrystalline Au electrodes.519-521 An explanation that has been given to support this observations is that the desorption process takes place over a wide potential range for a polycrystalline Au electrode as the desorption first starts at the defects sites and the grain boundaries and later from the well-organized regions.522

Oxidative stripping voltammetry of organosulfur modified gold electrode has been less

523,524 - - commonly studied. Porter et al. has proposed three electrons oxidation of RS to RSO2 for the first time as a possible oxidative desorption mechanism (Equation 2-15).171 There is however, no general agreement on the exact mechanism for the oxidative desorption of an organosulfur monolayer.171,523-527

For a gold electrode modified with a sulfur adlayer, the reductive as well as the oxidative voltammetry has been performed. The proposed mechanism for the reductive stripping involves the transfer of two electrons per molecule (Equation 2-16).260,261,286,289,322,528 The oxidative stripping involves the transfer of six electrons per molecule (Equation 2-17) along with the oxidation of gold to gold oxide (Equations 2-18, 2-19).286,529-531

0 2 S + 2e- S- (2-16) 0 - -2 - S + 8OH SO4 + 6e + 4H2O (2-17) - - Au + 2OH AuO + 2e + H2O (2-18) And/or - - 2Au + 6OH Au2O3 + 6e + 3H2O (2-19)

For this thesis, electrochemical measurements are conducted using an Autolab

PGSTAT30 (Eco Chemie) system. A three electrode glass cell (operated under dry nitrogen and thermostated at 25 °C) is used. The working electrode is a solid gold/glassy carbon electrode (Ω

Metrohm, 2 mm diameter). The electrodes are carefully cleaned after polishing and ultrasonic rinsing with ethanol. Polycrystalline solid gold electrodes are also cleaned by electrochemical cycling in a 0.5 M KOH aqueous solution. A saturated calomel electrode (SCE) is used as the reference electrode. A platinum wire is used as the counter electrode.

Chapter III. 4-Nitrophenyl Sulfenyl Chloride as a New Precursor for the Formation of

Aromatic SAMs on Gold Surfaces

III-1 Introduction

The increased interest in aromatic SAMs originates from their remarkable electronic properties.386,388,532-542 They have promising potential applications in many areas of technology particularly in the fields of molecular electronics,543-545 lithography394,546-550 and the synthesis of nanocrystalline materials.396 However, aromatic SAMs prepared using the known precursors are usually of low quality and show low packing densities when compared to aliphatic SAMs. While the importance of the head group-substrate and the intermolecular interactions are known to affect all types of SAMs, it is believed that for aromatic SAMs, the lattice mismatch between the gold surface and the rigid aromatic molecules contributes mainly to the lower degree of molecular ordering on the surface. Several strategies have been used to obtain long-range ordered aromatic SAMs are detailed in Section I-4. Beside those approaches, a number of organosulfur precursors were proposed as alternatives including thiols,32 disulfides,14,19,216,551 sulfides,33 thiosulfates,34,35 thioacetates36-38 and thiocyanates.39,40,199,552 Nevertheless, these traditional precursors are more suitable for aliphatic SAMs.438-440,447 For both aliphatic and aromatic SAMs, the structural quality highly depends on the nature of the precursor molecules employed, the leaving group, the experimental conditions,14,19,32-40,198,199,216,438-440,447,551,552 and the purity of the compounds used.199 On the other hand, aromatic SAMs with relatively dense coverage and better ordering are reported for Se-based aromatic SAMs,448,457,458 which suggests that the above mentioned factors are not completely accountable for the lower quality of aromatic SAMs. Therefore, the discovery of alternative precursors is necessary for the practical applications of SAMs and for the fundamental understanding of the process of SAM formation. 91

In this Chapter, the formation of well-ordered aromatic SAMs on gold surfaces is reported using 4-nitrophenyl sulfenyl chloride (compound 1, Chart 3-1) as a new precursor.

The use of 4-nitrophenyl sulfenyl chloride as a precursor for the formation of well-ordered aromatic SAMs will also allow new insights into the origin and the nature of the features observed in STM images. This is a heavily debated issue as previously discussed in Section I-

4. Experimental results show that this compound produces both short and long range ordered aromatic SAMs on Au(111) substrates on mica, as well as on solid polycrystalline gold electrodes at different modification conditions. Arene sulfenyl chlorides are structurally similar to the corresponding thiocyanates. On the basis of this structural similarity, one would expect a reductive adsorption mechanism for sulfenyl chloride similar to the one suggested for thiocyanates.39,40,199,552 Sulfenyl chlorides and thiocyanates present however important differences regarding their electrochemical characteristics. These differences lie in the strength of the cleaving bond, which have an evident impact on the obtained aromatic SAMs.

The reduction of the thiocyanates is almost 2 V higher than that of the sulfenyl chlorides

(Scheme 3-1).200,480 In addition, the S-CN bond is about 50 kcal/mol stronger than the S-Cl bond.200,480 It has been reported previously that the strength of the S-CN bond can account for the lower quality of thiocyanate SAMs.199

Chart 3-1. Structure of 4-nitrophenyl sulfenyl chloride (1).

where Y = CN or Cl R = a substituent (NO2, CN, F, Cl, H, etc.).

Scheme 3-1. Global reduction reaction of arene sulfenyl chlorides and arene thiocyanates.482

Two different modification conditions are used for the formation of aromatic SAMs using compound 1 and create differences in the obtained films. Consequently, this chapter includes two parts, each describing the aromatic SAM formation under specific conditions.

Characterization of all obtained SAMs are performed using a series of techniques including

XPS, STM, PM-IRRAS, and CV. In the first part, the modification is performed using a 1 mM solution of compound 1 in an EtOH:DMF (9:1) mixture. In the second part, a 10 mM solution of compound 1 in a MeOH:THF (1:1) mixture is used for the formation of aromatic

SAMs.

III-2 Modification under Condition 1

III-2a Modification Procedure

The Au(111) substrate on mica is modified at a 1 mM concentration of compound 1 in an

EtOH:DMF (9:1) mixture for 24 hours for XPS, PM-IRRAS and STM studies. The solubility of the precursor is low in EtOH, therefore, it is initially dissolved in DMF and then diluted with

EtOH. After modification, the substrate is carefully rinsed with the solvent mixture and then dried under a gentle stream of argon. The characterization of the modified surface is performed

93 directly after modification or after storage in a dessiccator for a few days to a few weeks. For the reductive desorption studies, a 2 mm solid gold electrode is polished and then cleaned first by sonication in ethanol and then electrochemically using several oxidative/reductive cycles in 0.5

M aqueous KOH. After rinsing with an EtOH:DMF (9:1) solvent mixture and drying under a gentle stream of nitrogen, the gold electrode is immersed in a 1 mM solution of compound 1 in an

EtOH:DMF (9:1) mixture for various times ranging from 1 minute to 24 hours to allow the modification of the surface. After modification, the gold electrode is carefully rinsed with the solvent mixture and then with ultra pure water. After drying with a gentle stream of argon, the gold electrode is immersed in an electrochemical cell containing 0.5 M aqueous KOH for reductive stripping voltammetry.

III-2b Results and Discussion

XPS Characterization

Figure 3-1 shows X-ray photoelectron spectra of a compound 1 SAM on Au(111). An unresolved doublet for the S 2p region is observed at binding energies of 162.0 and 163.2 eV

199 for the S 2p3/2 and S 2p1/2 respectively, and is representative of the gold-thiolate bond. The

S 2p peak for unbounded or higher oxidation species of sulfur are not detected. The C 1s signal is fitted considering two types of carbon atoms in the precursor molecule: 285.5 eV for the C-N and C-S carbons and 284.1 eV for the aromatic carbons. The main O 1s signals is observed at 531.7 eV with a small shoulder at 529.5 eV due to chemisorbed oxygen on Au.289

The absence of the Cl 1s signal suggests a cleavage of the S-Cl bond during monolayer formation and also the absence of Cl in any form on the surface. For the nitro group, the N 1s signal is observed at 405.0 eV, sometimes with a partial or a complete loss of this signal along with the appearance of a signal at 399 eV. The peak at 399 eV is usually assigned to the

NH2 group due to the reduction of the NO2 group as reported earlier for nitroaromatic SAMs 94 of thiols182 and thioacetates37,38 by solution/vapour deposition and nitroaromatic SAM moieties by X-ray beam.553-557 In previous studies, only 30% reduction of the nitro groups have been reported.37,38,182 In our case, the complete or partial reduction of the nitro groups during X-ray exposure suggests a different reduction mechanism under the actual experimental conditions. In addition, a SAM thickness of 7 to 9 Å is deduced using the adlayer-induced Au 4f attenuation. This calculated value is nearly proportional to the length of the precursor molecule i.e. 6 Å (from the sulfur to the mid-distance between the oxygen atoms of the nitro group).480 This value also demonstrates the SAM formation in which the molecules are arranged with small tilt angles.

Figure 3-1. XPS signals for compound 1 SAM on Au(111). The modification is done in a 1 mM solution of compound 1 in DMF:EtOH (9:1) for 24 hours.481,565 (Reprinted with permissions from references 481 and 565, Copyright © 2011 and 2012, RSC and ACS, respectively).

PM-IRRAS Study

PM-IRRAS is also used to characterize the produced SAMs and to get insights into the orientation of the adsorbed thiolate on the Au surface.558-560 For a molecule adsorbed on a metal surface only vibrational modes with a component of the IR vector perpendicular to the surface are probed (surface selection rule, Chapter II, Section II-4).558-560 IR measurements are performed for

SAMs of the investigated compound along with measurements of the bulk samples in CCl4.

The structure of the 4-nitrophenyl sulfenyl chloride is first optimized using Gaussian 03 at the becke, three-parameter, lee-Yang-parr (B3LYP) level with the 6-311++G(d,p) basis set.561 The optimized structure shows a planar nitrophenyl moiety with the nitro groups in the plane of the phenyl ring. No imaginary vibrations are observed. The optimized structure and the calculated IR spectrum are used in determining the main vibration modes (Figure 3-2) discussed below. These vibrations modes are in accordance with the previously reported experimental and theoretical studies of nitrophenyl thiol moieties.562-564

Figure 3-2. Representation of atomic displacements (black arrows) and IR vectors (red arrows), of the main vibrational modes of compound 1 observed for a SAM on Au(111). The represented

+ - vibrational modes are the symmetric (r NO2) and asymmetric (r NO2) stretch modes of the NO2 group, the superposition of CC stretching and CH in plane bending of the phenyl ring (rCC-δCH) and the CH in plane bending of the phenyl ring (δCH).565 (Reprinted with permission from reference 565, Copyright © 2012, ACS).

Figure 3-3 shows IR spectra for compound 1, both in solution (CCl4) and as a SAM on

Au(111) after modification using a 1 mM solution of compound 1 in EtOH:DMF (9:1) for 24 hours. The IR bands for the precursor in solution (CCl4) are seen at 1306, 1340, 1390, 1473,

1525, 1577 and 1599 cm-1 for the CH in plane bending of the phenyl ring (δCH(a)), the

+ symmetric stretch of the NO2 group (r NO2), δCH(b), δCH(c), the asymmetric stretch of the NO2

- group (r NO2), the superposition of CC stretching and CH in plane bending (rCC-δCH(a)), and

97 rCC-δCH(b), respectively. A number of clear and non-overlapping signals can readily be assigned for the 4-nitrophenyl thiolate SAM on Au(111). In the IR spectrum of the SAM on the

Au(111) surface, an intense peak at 1340 cm-1 is seen due to the symmetric stretch of the nitro

+ - group (r NO2). A small peak is observed for the asymmetric stretch of the nitro group (r NO2) at

-1 1520 cm . The intensity of the asymmetric NO2 stretch is markedly lower on the surface as compared to its intensity in the solution. The intensity ratio of the symmetric to the asymmetric

NO2 stretch modes is 5 for the 4-nitrophenyl thiolate SAM while it is 1 in the bulk sample. This reduction can be explained on the basis of the transition dipole moment direction of the given mode on the metal susbtrate. If the direction is perpendicular to the 1,4 molecular axis or parallel to the Au surface, it will not respond to IR irradiation.566 The reduction in the intensity of the nitro strectching mode has been previously observed for nitro containing SAMs obtained from corresponding thiols.567

It is also important to note that only those IR bands for the coupling mode (the C-C stretching and the C-H bending (rCC-δCH(a)) and δCH(c) mode are observed (at 1570 and 1470 cm-1 respectively), which have a transition dipole moment direction parallel to the 1,4 molecular axis or perpendicular to the Au surface. This clearly indicates that the 4-nitrophenyl thiolate is not very tilted and is nearly vertically adsorbed on the gold surface. Small tilt angles have also been reported previously for 4’-nitro-4-mercaptobiphenyls SAMs on Au and Ag (14o and 8o

434 + respectively). While the r NO2 is observed at the same position in the bulk and in the SAM, all

- other bands (r NO2, rCC-δCH(a), rCC-δCH(b) and δCH(c)) are slightly shifted to lower wave numbers by about 6-8 cm-1 in the SAM. Closely related IR signals have been observed previously for nitro-aromatic SAMs on Au.38,147

Figure 3-3. IR spectra of compound 1 in ~11 mM solution (CCl4) and SAM on Au(111). The modification is performed using a 1 mM solution of compound 1 in an EtOH:DMF (9:1) mixture for 24 hours.481,565 (Reprinted with permissions from references 481 and 565, Copyright © 2011 and 2012, RSC and ACS, respectively).

Stripping Voltammetry

A further insight regarding the 4-nitrophenyl thiolate SAM on Au is provided using reductive stripping voltammetry of a monolayer. Figure 3-4 shows a time dependent cyclic voltammetry of a 2 mm solid gold electrode in 0.5 M aqueous KOH after modification in a 1 mM concentration of compound 1 in a mixture of EtOH:DMF (9:1) at different modification times. For the 1st scan, a sharp peak at -0.87 V versus SCE is seen with shoulders before and after the peak. No such peak is observed for the 2nd scan (i.e. the response is similar to the bare gold). This behavior confirms that the monolayer is formed during the modification 99 process, which is stripped during the 1st scan. The area under the stripping peak is increased from 1 to 30 minutes of modification and then becomes constant from 30 minutes to 18 hours of modification. This indicates that the adsorption is a fast process and a saturation coverage is obtained within 30 minutes of modification. The rapid adsorption and the stability of the precursor molecules in solution preclude the formation of other side products during the SAM formation.

Figure 3-4. Time dependent cyclic voltammetry of bare and previously modified polycrystalline solid gold electrodes in a 0.5 M aqueous KOH solution at 25 oC. Scan rate v = 200 mV/s. The electrodes are modified using a 1 mM solution of compound 1 in an EtOH:DMF (9:1) mixture.481,565 (Reprinted with permissions from references 481 and 565, Copyright © 2011 and

2012, RSC and ACS, respectively).

100

Moreover, the shoulder prior to the desorption peak is usually only observed at shorter modification times, so it might be related to a phase transition of the monolayer or a reorientation of the monolayer molecules under the influence of an applied potential. On the other hand, the sharp peak at -0.87 V has a very high charge density of ~400 µCcm-2. For a reductive desorption of a thiolate monolayer, a charge density of ~50-80 µCcm-2 (one electron transfer) is expected.

Therefore, this peak can be related to the reduction of the terminal nitro groups to the amino groups as shown in Equation 3-1 along with the simultaneous desorption of the monolayer

(Equation 3-2).

- - Au-S-Ar-NO2 + 6e + 4H2O Au-S-Ar-NH2 + 6OH (3-1)

- Au-S-Ar-NO + e Au + O N-Ar-S- (3-2) 2 2

The previous electrochemical desorption studies of 4-nitrothiophenol (4NTP) SAM on

Au(111)568,569 have indeed shown the reduction of the terminal nitro groups. The area under the reductive cyclic stripping voltammetry peak and the effective area of the polycrystalline solid gold electrode have been used to deduce the monolayer coverage at different modification times.

The cathodic peak corresponds to the reduction of the nitro to the amino group (Equation 3-1, the desorption of the monolayer (Equation 3-2) and the contribution from the non-faradic current.

The effective area of the polycrystalline solid gold electrode is determined from the cyclic voltammetry of a ~1 mM solution of ferrocene in 0.1 M tetrabutylammonium hexafluorophosphate (n-Bu4NPF6) / acetonitrile (MeCN) at different scan rates and using

Equation 3-3 (the Randles–Sevcik equation).

1/2 1/2 1/2 Ae = I /(0.4663 x ne x F x (nF/RT) x D x C) x v (3-3) 101

2 where Ae is the effective area of the gold electrode in cm , I is the anodic/cathodic peak current in

-1 A, ne is the number of electrons transferred per molecule, F is Faraday’s constant in A.s.mol , R is the general gas constant in C.V.mol-1.K-1, T is the temperature in K, D is the diffusion constant in cm2.s-1, C is the concentration in mol.cm-3, and v is the scan rate in V.s-1.

Figure 3-5 shows a time dependent coverage as a function of the modification time. It is important to note that a coverage of ~0.13 ML is obtained within 1 minute of modification indicating that the process is indeed very fast. The monolayer coverage increases rapidly with time and reaches a maximum value of ~0.23 ML (~28 Å2 per molecule) after modification for 30 minutes. All these values show that very high coverage values are obtained using 4-nitrophenyl sulfenyl chloride.

STM Imaging

Structure of the SAM on Au(111)

STM is also used to get molecular scale information of the obtained SAM. For the STM analysis, the modification is performed in a way similar to the XPS and PM-IRRAS studies.

Figure 3-6 shows unfiltered STM images of compound 1 SAMs on Au(111). The STM images

(Figure 3-6a and b) show relatively short-range ordered domains of 30 x 30 nm2. High resolutions image in Figure 3-6c shows a densely packed well-ordered row structure. The unit cell is expressed in two directions using lattice vectors a = 4.8 ± 0.2 Å and b = 11.7 ± 0.4 Å.

From the experimentally measured dimensions of the unit cell, a 4 x √3 structure is proposed, shown on Figure 3-6d. For the proposed structure, the aromatic thiolate molecules are positioned on hollow sites arbitrarily. This phase has been previously reported for the Se-based anthracene

SAMs.457 An area per molecule of about 27.8 Å2 is deduced from the measured dimension of the unit cell and considering two molecules within a unit cell. The crystalline structure of benzene within the close packed (001) planes has also shown remarkably comparable molecular area with a molecular tilt of 75o.570 This suggests the dense packing of the molecules through significant lateral interactions. A slightly larger area per molecule (i.e. 28.8 Å2) is also obtained for the closed packed structure of selenol-based benzene/anthracene SAMs.457 Furthermore, the line profiles shown in Figure 3-6e-g in the directions and diagonal of the unit cell indicate a larger corrugation of the molecules at the corners compared to those within the unit cell. It is important to note that the molecule that lies inside the unit cell is not exactly at the centre of the unit cell.

These results suggest that the molecules in two adjacent rows are either siting on different adsorption sites on the surface or they differ in terms of their molecular orientation e.g. tilt angles. Electrochemical STM has been previously used to study 4-nitrophenyl thiolate SAMs on

103

Au. However, smaller domains containing both standing up and lying down molecules has been observed when 4-nitrophenyl thiol was used for SAM generation.568

A mixed SAM structure (in which molecules were bound either through sulfur or NO2 group) has been proposed for vertically oriented molecules containing a terminal nitro group, in the gas phase under low temperature conditions.571-576 It has been suggested that in such an orientation the dipole-dipole lateral repulsions are avoided and the unfavourable net surface dipole moment is minimized.572 Formation of a bilayer structure with an antiparallel arrangement of nitro groups in two monolayers has also been suggested as an option for compensating dipoles.572 Neither of these arrangements are however stable at room temperature. Our XPS data which shows only one type of sulfur (corresponding to the Au-S bond) for the 4-nitrophenyl sulfenyl chloride precursor (1), along with the deduced thickness of the SAM (6 Å) rule out the latter two possibilities.

104

Figure 3-6. (a) 45 x 45 nm2, (b) 15 x 15 nm2, and (c) 5 x 5 nm2 STM images of compound 1

SAMs (obtained using a 1 mM solution of compound 1 in EtOH:DMF (9:1) for 24 hours) on

Au(111). (d) Proposed model with 4 x √3 rect unit cell shown (a = 4.8 ± 0.2 Å and b = 11.7 ± 0.4

Å). (e-g) Line profiles along lines A to C respectively as shown in c. Tunnelling conditions: Tip bias = +0.1 V, tunnelling current = 0.80 nA and scan rate = 4.1 lines/s.481,565 (Reprinted with permissions from references 481 and 565, Copyright © 2011 and 2012, RSC and ACS, respectively).

III-3 Modification under Condition 2

III-3a Modification Procedure

The Au(111) substrate on mica is modified with a 10 mM concentration of compound 1 in a MeOH:THF (1:1) mixture for 48 hours for PM-IRRAS and STM studies. The modification is performed in an inert argon environment and the solvent mixture is degassed prior to the use after several cycles of freeze-pump-thaw. After modification, the substrate is carefully rinsed with a

105 solvent mixture and then dried under a gentle stream of argon. The characterization of the modified surface is performed directly after modification or after storage in a dessiccator for a few days to a few weeks. For the reductive desorption studies, a 2 mm polycrystalline solid gold electrode is polished and then cleaned first by sonication in ethanol and then electrochemically using several oxidative/reductive cycles in 0.5 M aqueous KOH. After rinsing with a MeOH:THF

(1:1) solvent mixture and drying under a gentle stream of nitrogen, the gold electrode is kept for modification in a 10 mM concentration of 4-nitrophenyl sulfenyl chloride in a MeOH:THF (1:1) mixture for times ranging from 1 minute to 18 hours. After modification, the gold electrode is carefully rinsed with the solvent mixture. After drying with a gentle stream of argon, the gold electrode is immersed in an electrochemical cell containing 0.5 M aqueous KOH for reductive stripping voltammetry.

III-3b Results and Discussion

PM-IRRAS Study

Figure 3-7 shows IR spectra for compound 1, both in solution (CCl4) and as a SAM on

Au(111) after modification with a 10 mM solution of compound 1 in MeOH:THF (1:1) for 48 hours. IR signals similar to the ones obtained for the modification under condition 1 are observed with some small changes. An intense peak for the symmetric stretch of the nitro group at 1338 cm-1, and a small peak for the asymmetric stretch of the nitro group at 1512 cm-1 are observed along with other signals at 1568 cm-1 (rCC-δCH(a)), 1379 cm-1 (δCH(b)), and 1460 cm-1 (δCH(c)) for the SAM on Au(111). Similar arguments can be used regarding the nearly vertical alignment of the molecules on the surface as stated for the SAM obtained using condition 1 (Section III-2). The appearance of an additional IR band at 1379 cm-1 for

δCH(b) (having a transition dipole nearly perpendicular to the 1,4 molecular axis) indicates that the deposited molecules are slightly more tilted under modification condition 2. 106

Figure 3-7. IR spectra of compound 1 in ~11 mM solution (CCl4) and SAM on Au(111). The modification is perfiomed using a 10 mM solution of compound 1 in a MeOH:THF (1:1)

ACS).

107

2011 and 2011, RSC and ACS, respectively).

Stripping Voltammetry

A further insight regarding the 4-nitrophenyl sulfenyl chloride SAM on Au is provided using reductive stripping voltammetry of the solid gold electrode modified under condition 2.

Figure 3-9 shows cyclic voltammograms of the modified electrode at different modification times. A response similar to the one observed under modification condition 1 is also observed

(Section III-2). A sharp reductive stripping peak is observed for the 1st reductive scan and a response similar to the bare gold is observed for the 2nd reductive scan after modifying the polycrystalline gold electrode for 1 minute. This indicates that a monolayer is formed during modification which is stripped in the 1st cathodic scan. An increase in the reductive stripping peak area is observed with an increase in the modification time from 1 minute to 10 minutes 108 indicating a maximum coverage. At longer modification times (up to 18 hours), there is no increase in the coverage value and a constant coverage is obtained.

Figure 3-10 shows a time dependent coverage calculated using the method described in

Section III-2. A constant coverage of ~0.30 ML (~20 Å2 per molecule) is obtained from 1 to 10 minutes of the modification. This suggests that a high coverage close to the densely packed aliphatic thiol SAMs is obtained within very short modification times. The deduced coverage is indeed higher than the coverage obtained under modification condition 1. 109

STM Imaging

Structure of the SAM on Au(111)

Figure 3-11 shows STM images of a modified Au(111) surface on mica with a 10 mM compound 1 in MeOH:THF (1:1) for 48 hours at different resolutions.

110

Figure 3-11. Unfiltered STM images in air of a Au(111) surface on mica modified using 4- nitrophenyl sulfenyl chloride (10 mM in MeOH:THF (1:1)) for 48 hours. Scan sizes (a) 60 x 60 nm2, (b) 20 x 20 nm2, (c) 10 x 10 nm2, and (d) 5 x 5 nm2. (e and f) Height profiles along line A and line B, respectively. Tunnelling conditions: Tip bias = +2 V, tunnelling current = 0.3-1.0 nA and scan rate = 4.1 lines/s.482 (Reprinted with permission from reference 482, Copyright © 2011,

ACS).

The large scale images provide evidence for the efficiency of modification method and the extent of the modification over wide areas. Moreover, long-range ordered domains are observed over many Au layers (Figure 3-11a) and the small scale images (Figure 3-11b-d) also provide a submolecular detail of the observed surface structures. A well-ordered hexagonal surface structure is observed in the small scale images (Figure 3-11b-d). The origin of the different superstructures on the surface will be discussed below. The two lattice vectors used to 111 describe the unit cell shown in Figure 3-11d are a = 5.0 ± 0.2 Å and b = 4.9 ± 0.2 Å and with an angle between them of α = 61 ± 2o. These dimensions are similar to a √3 x √3 hexagonal structure commonly known for the high density aliphatic SAMs. An area per molecule of about 21.4 Å2 is deduced using the experimentally measured dimensions and considering 1 molecule per unit cell.

This molecular area is closely related to the crystalline structure of benzene570 and suggests excellent molecular packing between aromatic moieties. However, a larger area per molecule of

27.8 Å2 or smaller coverage is observed using the same precursor under modification condition

1.481 Furthermore, this area per molecule is lower compared to the highest density aromatic

(benzene/anthracene) SAMs (28.8 Å2) obtained using Se as a head group.457 More importantly, the STM images of the SAMs obtained using 4-nitrophenyl sulfenyl chloride precursor are very reproducible and are obtained over a wide range of tunnelling conditions. No significant modification of the observed superstructures is seen upon changing the tunnelling current in the range of 0.3 to 1.0 nA and the tip bias values between +0.1 to +2 V. The modified samples are also very stable and a sample provided similar images just after modification as well as after being kept in an ambient environment for 3 weeks.

Particular Superstructures and their Dynamics

A further insight regarding the nature of the brighter spots and the surrounding clear hexagons is provided using high resolution STM. The line profiles going through a brighter spot

(in any direction) show that the brighter spots are the molecules with greater height (Figure 3-12a and b). The difference in the heights of two spots or different contrast in STM images of SAMs usually represent a difference in the orientation or adsorption sites of two molecules within a given SAM structure. The later concept is only valid when the Au surface is unreconstructed.

However, it is not known with certainity if the STM images the terminal or the head groups of the

SAM. Therefore, it is difficult to assign the difference in the brightness of the surface feature in

112 the STM images of the SAM to either of the above mentioned factors without ambiguity. The line profiles in Figure 3-12b and c show that the distance between two adjacents spots is exactly 5 Å

(despite having different contrasts). This means that the main SAM structure does not deviate from the hexagonal lattice and each spot in the STM image of the obtained SAM represents a single molecule on the surface. The data provided below shows that the difference in the brightness of the molecules can be attributed to a difference in the tilt angles of the molecules.

The brighter spots correspond to nearly vertically oriented molecules.

Figure 3-12. (a) Unfiltered STM image of a Au(111) surface modified using compound 1, 8.4 x

8.4 nm2. Tunnelling conditions: Tip bias = +2 V, tunnelling current = 0.30 nA and scan rate = 4.1 lines/s. (b) and (c) Line profiles along lines A and B going through a brighter spot from two different directions.482 (Reprinted with permission from reference 482, Copyright © 2011, ACS).

Sequential STM imaging shows the dynamics of the particular molecular structures.

Figure 3-13 shows consecutive STM images taken after a time interval of 52 seconds of the same area of the SAM. In these images, a solid white rectangle represents a hexagon structure that just appeared in the following image. These newly formed hexagons around brighter spots are 113 represented in Figure 3-13b, c, and f-h. The hexagon that is present in an image but will disappear in the following image is represented as a dashed white rectangle, as observed on going from Figure 3-13a to b, d to e, and i to j. The hexagon whose position is changed from one place to another in the following image is represented as dashed circles. A shift in the position of the hexagon is shown on going from Figure 3-13f to g, where a hexagon has moved one row to the right and two rows down. Its brighter central spot is now located in the middle row of the three rows between the two upper hexagons, whereas it was initially in the left side row. A similar shift in the position of a hexagon is also observed when going from Figure 3-13h to i. In this case, the hexagon shifts one position down and is three rows away from the closest one (Figure 3-13i), but they were only two rows apart in the previous image (Figure 3-13h). A similar shift is observed for the hexagon located at the lower right side corner on going from Figure 3-13a to b. On going from Figure 3-13i to j, a hexagon has moved three positions to the left. These changes suggest that all the spots, dark and bright correspond to the same adsorbed molecule. This also indicates that the difference in the brightness of the spots and surface features are related to different arrangements of the molecules on the surface.

114

Figure 3-13. (a-j) Sequential STM imaging of a SAM of compound 1 on Au(111). Scan size: 8.2 x 8.2 nm2. Images (unfiltered) are recorded in the sequence. Tunnelling conditions: Tip bias = +2

115

Beside the predominantly observed hexagons, other structures such as parallelograms, zig-zags and partial hexagons are also formed on the surface. In Figure 3-13h, the formation of a parallelogram structure is marked using a yellow rectangle. It is important to note that these structures may change from one shape to the other or to the regular √3 x √3 structure for certain areas from one image to the other. This supports that these structures originate from a specific arrangement of these molecules and this arrangement can rearrange the parent hexagonal structure. Therefore, the adsorption of the molecules at different sites cannot be used as an explanation for the formation of these structures. An important characteristic of the observed hexagon structure is that it is formed from a certain specific arrangement of six adsorbed molecules on the surface. In Figure 3-13b, the newly formed hexagon represented as the upper solid white rectangle is composed of six clearly separated spots in the same area in the previous image (Figure 3-13a).

In some areas, other changes involving not only hexagons are also observed, such as the formation of a hexagon from the other structure, the change of the other structure to the parent hexagonal structure and/or vice versa. These changes are shown in consecutive STM images obtained after time intervals of 52 seconds in Figure 3-14. To better observe these changes, the hexagon within the yellow circle is used as a reference while other structural changes are marked using dashed rectangles. A parallelogram seen in image 3-14a is transformed into the parent hexagonal structure in the following image (3-14b). A hexagon seen in Figure 3-14b is converted into a zig-zag structure in the following image. In Figure 3-14c, two new partial hexagons are formed at the top right corner of the image, which were not present in the previous image. One of those two partial hexagons appeared as a half-hexagon composed of only three molecules, and the other three molecules at the top right corner are seen as brighter spots. In the other partial hexagon the molecule at the top corner appeared as a brighter spot and is excluded from the rest of the molecules in the hexagon structure. Moreover, the rest of the five molecules in the hexagon 116 and the middle spot are arranged in a specific manner. In Figure 3-14d, a parallelogram is formed from a hexagon in the previous image.

Figure 3-14. Sequential STM imaging of a SAM of compound 1 on Au (111). Scan size: 8.4 x

8.4 nm2. Images (unfiltered) are recorded in the sequence (a to d). Tunnelling conditions: Tip bias

Origin of the Superstructures

A closer look at these superstructures provides interesting findings regarding their origin.

The length of any edge of a hexagon is around 5 Å as expected for the hexagonal structure. This is shown in the line profiles along all edges of a hexagon in Figure 3-15a-c. More interestingly, in the line profiles along any edge of a hexagon, three peaks are clearly visible. Two of the peaks

117 are closer to each other (~2.2-2.4 Å) and the third peak is at a slightly larger distance (~2.6-2.8

Å). This is observed on the line profiles in Figure 3-15b and c. A line profile along line B

(Figure 3-15c) shows a similar behaviour i.e. three peaks with similar distances. However, in this case, the peak which is at a slightly larger distance in the previous edge is now closer to the middle peak and the third peak is at a slightly larger distance. This indicates that all edges of the hexagon are nearly identical. This is indicated using line profiles along the six edges of a hexagon

(Figure 3-15a) in Figure 3-16b to g. Therefore, it is concluded that two peaks in a line profile indicate a single molecule as known from previous results that a hexagon is composed of six individual molecules with an extra molecule in the middle. After slight filtration (levelling and smoothing) of a STM image shown in Figure 3-15f, it is indeed clear that a hexagon actually contains six dark spots, which is further proved using the line profiles.

On the basis of these results, a special arrangement of the adsorbed molecules is suggested, where the 12 observed dark spots in a hexagon represent the O atoms of the NO2 groups within the six molecules. From an optimized structure of the parent molecule at the

B3LYP level, a distance of 2.19 Å is obtained between the two oxygen atoms of the terminal nitro group in a molecule.561 This value is close to the one obtained from the line profile for each edge of the hexagon in the STM images. A structure is proposed in which six molecules are rearranged in a manner to form a hexagon. A top view of this structure is shown in Figure 3-15g.

In order to locate two spots representing two oxygen atoms of the terminal nitro group along the edge of the hexagon rather than at the corner, the molecule should be tilted in a way that one of the oxygen atoms aligns with the S atom in the same molecule (Figure 3-15d). A tilt of about

9.35o is deduced from the length of the molecule obtained from its optimized structure. For thiophenol SAMs, a tilt angle of 11.6o has been previously reported.431

118

Figure 3-15. (a) Unfiltered STM image of a SAM of compound 1 on Au (111). Scan size: 10 x

10 nm2. Tunnelling conditions: Tip bias = +2 V, tunnelling current = 0.30 nA and scan rate = 4.1 lines/s. (b and c) Height profiles along line A and B respectively. (d) Profile and top views of an optimized 4-nitrophenyl thiolate structure titled to align one of the oxygen atoms with the S atom

(tilt angle 9.35o). (e) Molecular rearrangement providing the hexagonal structure. (f) Slightly filtered STM image showing a hexagon (scan size 2.3 x 2.3 nm2). (g) Schematic model of image f showing molecular placement of 4-nitrophenyl thiolate molecules on the Au (111) surface.482

119

Different arrangements are suggested based on different tilt angles of the molecules and any edge of the observed structure is comprised of three distinct spots with two spots representing one molecule or two oxygen atoms in the terminal nitro group. In Figure 3-17a and b, STM images for a parallelogram structure are shown. Line profiles along four edges of the parallelogram (Figure 3-17c-f) are showing three distinct spots with two being closer than the third. These line profiles also show that the bright spots surrounding the parallelogram are molecules with height slightly greater than the molecules forming parallelograms. On the basis of similar arguments given for the hexagon, a model for the formation of the parallelogram is suggested in Figure 3-17g.

120

STM images for a zig-zag structure are shown in Figure 3-18a and b. Also for this structure, line profiles along two edges of the zig-zag (Figure 3-18c and d) show three peaks with similar distances observed for the hexagon structure. Therefore, a structure is proposed in Figure

3-18e. In this model, each side of the zig-zag is composed of a single molecule tilted in a way so that the two oxygen atoms of the molecules are positioned along the edge.

121

Figure 3-18. (a) Filtered, (b) unfiltered STM images of a Au(111) surface modified using compound 1 showing a zig-zag structure, and (c and d) line profiles along two zig-zag edges.

Tunnelling conditions: Tip bias = +2 V, tunnelling current = 0.30 nA and scan rate = 4.1 lines/s.

2011, ACS).

Figure 3-19a and b show STM images for a partial hexagon structure. Similar to the other structures, line profiles along the four edges and one diagonal of the partial hexagon (Figure 3-

19c-g) also show three peaks with peak separations similar to the hexagon structure. For this partial hexagon, the molecule sitting at the top appears as a single spot, while the molecule in the middle and at the top left side edge appeares as two spots. A model for this structure is proposed in Figure 3-19h using the same analysis used for the hexagon structure.

122

Au(111) surface modified using compound 1.482 (Reprinted with permission from reference 482,

In Figure 3-12, the height profiles going through the brighter spots show that these molecules are slightly higher than the rest of the molecules. On the basis of the structure proposed for the hexagon, it is clear that the central brighter spot is the molecule which interacts equally with all the six molecules in the hexagon. Therefore, it can be reasonably suggested that the central brighter spot is a molecule which is vertically oriented while the rest of the molecules are slightly tilted. Considering that the brighter spots represent vertically oriented molecules, 123 approximate tilt angles for the rest of the molecules can be suggested. A height difference of about 0.35 Å between the brighter spot in the middle of the hexagon and the molecules representing the parent hexagonal structure is obtained. The height of the molecules forming the hexagon is similar to that of the rest of the molecules on the surface. Considering the length of the vertically oriented molecule to be 6.74 Å (the distance from the middle of the two oxygen atoms and the sulfur atom in the optimized structure), a tilt angle of 16o is estimated for the rest of the molecules on the surface which are not vertically oriented. Even though, this is an estimated value, it still shows that the molecules are oriented on the surface with small tilt angles.

This is supported by the IR data that show that the molecules are nearly vertically oriented on the surface, as confirmed by the small anti-symmetric NO2 stretch. A complete model suggested for the SAM on the gold surface is shown in Figure 3-15g, where a hexagon is surrounded with molecules showing a hexagonal structure along with a √3 x √3 phase.

It is still not well understood why certain molecules appear as brighter spots in the STM images. However, it is suggested that the molecules which are forming particular superstructures

(hexagons, parallelograms, and zig-zags), are in a "frozen" state, where submolecular details are also observed. The rest of the molecules not forming these structures may have a certain degree of freedom (slight twisting around the molecular axis) under given tunnelling conditions.

The observed molecular rearrangement on the surface of the aromatic SAM is most likely induced from the SAM stress. The lattice mismatch between an adsorbate layer (aromatic moiety) and the substrate results in the SAM stress (an adsorbate favors commensurate (a perfect registry) structure with the substrate, atleast in one direction). This stress is released by increasing or decreasing the distance between adsorbate molecules. The overall characteristics of the obtained aromatic SAM are summerized in the following main points: (i) A domino like effect is observed due to the disappearance of one hexagon and the appearance of another hexagon in its surroundings. (ii) These superstructures with their surface dynamics is only observed under 124 modification condition 2 of the precursor molecules. Aromatic SAMs formed using traditional precursors, to our knowledge, have not shown these particular features. (iii) The hexagonal structures obtained under modification condition 2 are of higher density than the double row structures obtained under modification condition 1.481 Such high density aromatic SAMs have never been reported previously. The density of the long range and well ordered Se-based aromatic SAMs448,457,458 is also lower than that of the present SAMs. (iv) A close packing of the molecules is suggested from the observed area per molecule. The deduced molecular area is even smaller than the one reported for the crystalline structure of benzene.570 (v) From the STM images, it is apparent that the areas where these superstructures (hexagons, parallelograms, and zig-zags) are seen are much more ordered than the areas where the parent hexagonal structure is observed. The reversible appearance and disappearance of these superstructures also support better molecular packing inside these superstructures.

III-4 Proposed Mechanism of SAM Formation

The S 2p signal in the XPS spectrum of the 4-nitrophenyl sulfenyl chloride SAM on

Au(111) provides evidence for the formation of a Au-S bond.481 An electrochemical response similar to the one reported for thiol based SAMs568 is also observed using this new precursor.

In addition, STM images also support the efficient modification of the Au surface using the proposed precursor. An adsorption mechanism involving physisorption of the precursor molecules on the Au surface with an electron transfer from the Au surface to the precursor molecule is proposed (Scheme 3-2). This results in the cleavage of the S-Cl bond and the formation of the Au-thiolate bond along with the ejection of Cl- ion. A similar mechanism was also suggested for the formation of thiocyanate SAMs.

125

Scheme 3-2. Proposed deposition mechanism.482 (Adapted with permission from reference 482,

III-5 Summary and Conclusions

Evidence for the formation of well-ordered aromatic thiolate SAMs on gold substrates through use of 4-nitrophenyl sulfenyl chloride as a precursor is provided using different techniques including XPS, STM, PM-IRRAS and CV. XPS data shows that the modification occurs through the scission of the S-Cl bond. Occasional reduction of the terminal nitro groups to the amino groups is observed. XPS data also shows that the leaving group (Cl) is not present on the surface. PM-IRRAS studies provide further evidence for the nearly vertical orientation of the precursor molecules on the surface. This is further supported using reductive stripping voltammetry, where the reduction of the nitro group is observed along with the desorption of the monolayer. Electrochemical and STM data suggest high surface coverage. STM shows the formation of closely packed and highly ordered aromatic SAMs, usually not reported using the traditional precursors for aromatic SAMs.

Under condition 1, a realtively short-range, well-ordered aromatic SAM with a 4 x √3 rectangular unit cell with paired molecular rows is formed. An area per molecule of 27.8 Å2 is deduced from the STM images. Under condition 2, the formation of a long-range, well- ordered aromatic SAM with a √3 x √3 hexagonal unit cell and an area per molecule of 21.4 126

Å2 is deduced from the STM images. This molecular density is usually only observed for aliphatic SAMs using the traditional precursors. Along with the main hexagonal lattice, distinct superstructures are observed. These structures can dissociate and reform at different locations on the surface during the sequential STM imaging of various areas. Hexagons, parallelograms, and zig-zags are obtained from specific arrangements of the adsorbed molecules. The areas where these particular structures are formed are more ordered and the molecules are frozen in these structures. In these ordered areas, the molecules are leaning towards each other having tilt angles slightly higher than the rest of the molecules in the surrounding √3 x √3 phase. The areas where no ordered structures are present have molecules, which are mobile under the given tunnelling conditions and provide lower- resolution images. The molecules located in the centre of the hexagon structure appearing as brighter spots are vertically oriented or have the smallest tilt angles. The observation of an intense IR band for the symmetric stretch for the nitro group also supports this data. A fascinating feature of these structures is the STM’s capability to provide submolecular details of the molecules at room temperature, independent of the tunnelling conditions. This is the first direct experimental evidence, where STM has shown its effectiveness in providing the physical structure information of standing-up aromatic SAMs. This is especially important considering the heavily debated issue regarding the origin of different features and contrast obtained in STM imaging of SAMs.

The formation of well-ordered nitro and amino terminated aromatic SAMs has a great significance for obtaining functionalized/complex 3D structures. The sensitivity of the nitro group towards different irradiation sources and the reactivity of the amino group are well acknowledged.37,38,147,182,554,555,557,577 On the other hand, long-range ordered aromatic SAMs not only have potential applications in the area of molecular electronics but they are also good templates for lithography purposes. 127

Chapter IV. The Effect of Substituent(s) Position(s) on SAMs of Nitro Aromatic

Sulfenyl Chlorides on Gold Surfaces

IV-1 Introduction

The structure and physio-chemical properties of SAMs are well known to depend on the precursor molecules (i.e. head group, spacers and tail group) used for self-assembly.25

Alkanethiol SAMs have been extensively investigated and the key parameters affecting the quality of the SAMs have been systematically studied. Attention has been given to both the head group-substrate bonding, alkyl chain orientation and conformation.578 These latter parameters have been shown to depend mainly on the adsorption time, chain length, temperature, substrate quality and the nature of the terminal group.25 A lower quality of alkanethiol SAMs is reported when the –CH3 group is replaced by the introduction of hydrophilic/metalophilic groups (such as

219 –SH, -COOH, -OH, -NH2).

Aromatic SAMs are attracting increasing attention. This is due to their high conductivity, nonlinear optical properties and potential applications in molecular electronic devices.38,147,391,411,568,579,580 These properties greatly depend on the quality of the aromatic SAMs.

Various approaches have been used to improve the quality of the aromatic SAMs as detailed in

Chapter I. It has also been suggested that the rigid conjugated system of an aromatic ring, compared to the conformational freedom of an alkyl chain in alkenethiol, may help to overcome the lack of long term stability.166 For example, the quality of biphenyl SAMs (packing, ordering, and binding of the head group) has been shown to depend on the presence of substituents at the 4’ position of the biphenyl ring.166

The present chapter reports an investigation of the SAM formation using two other nitro- substituted phenyl sulfenyl chlorides (Chart 4-1, 2-nitrophenyl sulfenyl chloride (2) and 2,4- dinitrophenyl sulfenyl chloride (3)). Characterization of the modified surfaces using XPS, STM, 128

PM-IRRAS and CV will provide more insights into the dependence of the quality of the organic

SAMs on the position of the NO2 group on the phenyl ring. This dependence is due to the

3 581 presence of the bulky nitro group (the van der Waals dimensions of NO2 are 23.5 Å ) at the ortho position (the van der Waals dimensions of S are 24.4 Å3),582 that hinders the adsorption to the Au surface. It would also be interesting to see if the previously reported interactions of the nitro group with the gold surface571-576 and through space S---O interactions of the ortho nitro substituted phenyl sulfenyl chlorides583 will affect the quality of the SAM. Moreover, the ortho substituent on the phenyl ring may also lower the SAM’s packing density on the surface. This is apparent from the fact that the molecular width of the 2-nitrophenyl sulfenyl chloride is larger than the 4-nitrophenyl sulfenyl chloride as calculated from the optimized geometries of these molecules.561 The molecular width of the 2-nitrophenyl sulfenyl chloride molecule is ~5.7 Å (a horizontal distance from one hydrogen at 2 position of the phenyl ring to the one oxygen of the nitro group at ortho position), while that of the 4-nitrophenyl sulfenyl chloride molecule is ~4.3

Å (a horizontal distance from one hydrogen at 2/3 position of the phenyl ring to the other hydrogen at 6/5 position of the phenyl ring).561

Chart 4-1. Structures of 2-nitrophenyl sulfenyl chloride (2) and 2,4-dinitrophenyl sulfenyl chloride (3).

129

IV-2 Modification using Compound 2

IV-2a Modification Procedure

The present investigation is performed under similar experimental conditions used for 4- nitrophenyl sulfenyl chloride (1, Chapter III), since a high density aromatic SAM is obtained under these conditions. A Au(111) substrate or a polycrystalline solid gold electrode is immersed in a 1 mM solution of compound 2 in EtOH:DMF (9:1) for times ranging from a few minutes to

24 hours. After thorough rinsing with the binary solvent mixture, the modified substrate is dried under a gentle stream of nitrogen. For STM imaging, the Au(111) substrate is also modified in a

10 mM solution of compound 2 in THF:MeOH (1:1) for 48 hours.

IV-2b Results and Discussion

XPS Characterization

Figure 4-1 shows X-ray photoelectron results for Au(111) surfaces modified using a 1 mM solution of compound 2 in EtOH:DMF (9:1) for 24 hours. Signals corresponding to the main elements S, C, N and O are clearly observed, while no peak is observed for Cl. This is an initial indication of the deposition of these aromatic sulfenyl chlorides through dissociation of the S-Cl bond as has been shown previously.481,482 The S 2p signal can be fitted by 3 doublets with their S

2p3/2 components located at 161.2, 162.2, and 163.2 eV. By comparison with previous data, the S

261,289- 2p3/2 component located at 161.2 eV could be assigned to chemisorbed monoatomic sulfur.

291 The component located at 162.2 eV is usually assigned to Au-thiolate species,199 polymeric sulfur261,289 or complex AuS phases.288,290 The component located at 163.2 eV is attributed to weakly bound or unbound sulfur,261,289 or sulfur multilayers.261,289 This is a first indication of the potential presence of non-adsorbed precursor molecules or sulfur on the surface. Two C 1s

130 signals are observed at 285.5 and 284.1 eV, corresponding to the C-N and the C-S carbons, and to the other aromatic carbons, respectively.

In the N 1s region a signal is observed at 399.2 eV in addition to the signal observed at

405.0 eV. The signals are less intense than the ones observed with the 4-nitrophenyl sulfenyl chloride precursor. As discussed earlier (Chapter III, Section III-2), the signal at 399.2 eV is

37,38,182,553-557 assigned to the nitrogen of the NH2 obtained by reduction of the NO2 group. This signal (399.2 eV) may also result from an interaction between the NO2 group (located at the ortho position) and the substrate. Such interaction has been studied before using nitrobenzene and it has been shown that on Ni,584 Fe584 and Cu(100)585 the initial precursor partially decomposes to nitrosobenzene and shows N 1s signals similar to the ones observed in this study. The main O 1s signal is observed at 531.8 eV in addition to a more pronounced shoulder at 529.8 eV, assigned to the chemisorbed oxygen resulting from the decomposition of the nitro group.289,584,585 The O 1s signal (Figure 4-1) located at 529.8 eV shows indeed a larger contribution as compared to the substrate modified with the 4-nitrophenyl sulfenyl chloride (Chapter III, Section III-2, Figure 3-

1).

131

Figure 4-1. X-ray photoelectron spectra of Au(111) on mica modified using a 1 mM solution of compound 2 in an EtOH:DMF (9:1) mixture for 24 hours.565 (Reprinted with permission from reference 565, Copyright © 2012, ACS).

PM-IRRAS Study

PM-IRRAS is also used to characterize the produced SAMs and to get insights into the orientation of the adsorbed thiolates on the Au surface. For a molecule adsorbed on a metal surface only vibrational modes with a component of the IR vector perpendicular to the surface are probed (surface selection rule, Chapter II, Section II-4).558-560 IR measurements are performed for a SAM of compound 2 along with measurements of the bulk sample in CCl4.

The structure of compound 2 is first optimized using Gaussian 03 at the B3LYP level with the 6-311++G(d,p) basis set.561 The optimized structure shows a planar nitrophenyl moiety with the nitro group in the plane of the phenyl ring. No imaginary vibrations are observed. The optimized structure and the calculated IR spectra are used to determine the main vibration modes

(Figure 4-2) discussed below. These vibration modes are in accordance with the previously

132 reported experimental and theoretical studies of molecules with similar nitrophenyl moieties.562-

564

Figure 4-2. Representation of atomic displacements (black arrows) and IR vectors (red arrows), for the main vibrational modes of compound 2 observed for a SAM on Au(111). The represented

+ - vibrational modes are the symmetric (r NO2) and asymmetric (r NO2) stretch modes of the NO2 group, the CH in plane bending of phenyl ring (δCH) and the superposition of the CC stretching and the CH in plane bending of phenyl ring (rCC-δCH).565 (Reprinted with permission from reference 565, Copyright © 2012, ACS).

133

IR spectra recorded for compound 2, both in solution (CCl4) and after deposition on

Au(111) surfaces are shown in Figure 4-3. In solution, IR bands for the CH in plane bending of phenyl ring are observed at 1246, 1304, 1444 and 1479 cm-1 for the δCH(a’-d’), respectively. The

+ - symmetric (r NO2) and asymmetric (r NO2) stretch modes of the NO2 group are seen at 1329 and

1520 cm-1, respectively. The superposition of the CC stretching and the CH in plane bending of phenyl ring are observed at 1389 cm-1 for the rCC-δCH(a’), 1566 cm-1 for the rCC-δCH(b’), and

1593 cm-1 for the rCC-δCH(c’). For the SAM only 3 main signals are observed including the r-

-1 -1 -1 NO2 signal at 1524 cm , the rCC-δCH(b’) at 1564 cm and the rCC-δCH(c’) at 1581 cm . The

+ suppression of the r NO2 is an indication that the vector associated with this mode (Figure 4-2) is parallel to the Au surface. This suggests that the 2-nitrophenyl thiolate adsorbate is more tilted than the 4-nitrophenyl thiolate (Chapter III, Sections III-2 and III-3). This is further supported by the disappearance of the IR band for the rCC-δCH(a’) and the appearance of a weak band for the rCC-δCH(b’) having transition dipole vectors perpendicular and parallel (Figure 4-2) to the Au surface, respectively.

- -1 The IR signal for the r NO2 is shifted to a slightly higher wavenumber (~4 cm ) while the rCC-δCH(b’) and the rCC-δCH(c’) are shifted to a slightly lower wavenumbers (~2-12 cm-1) for the SAM than in the bulk. Both XPS and IR suggest the adsorption of compound 2 as thiolate.

The IR data also suggest that the 2-nitrophenyl sulfenyl chloride molecules have a well-defined orientation on the gold surface after adsorption.

134

Figure 4-3. IR spectra for compound 2 in a ~17 mM solution (CCl4) and SAM on Au(111). The modification is performed using a 1 mM solution of compound 2 in an EtOH:DMF (9:1) mixture for 24 hours.565 (Reprinted with permission from reference 565, Copyright © 2012, ACS).

Stripping Voltammetry

Stripping cyclic voltammetry is used to assess the modification of a polycrystalline gold surface using compound 2. Figure 4-4 shows the stripping voltammograms, in a 0.5 M KOH aqueous solution, of bare and modified solid gold electrodes using compound 2, at various modification times. After only 1 minute modification time, a sharp reductive stripping peak is observed at -0.83 V versus SCE. When a second scan is run with the same electrode, a cyclic voltammogram similar to the one observed for the bare gold electrode is seen and no reductive striping peak is observed. The disappearance of the reduction peak in the 2nd scan indicates that the deposited layer on the gold surface during the initial modification was stripped during the 1st 135 scan. Increasing the modification time to 10 minutes shows an important increase of the stripping peak area. This is a good indication that the modification process is very fast. The peak area increases again when a longer modification time of 30 minutes is used but does not increase much for modification times longer than 30 minutes. This indicates that a maximum coverage is reached and confirms the rapidity of the process.

A surface coverage is deduced for each cyclic voltammogram considering the reduction of the nitro group to the amino group, the simultaneous desorption of the monolayer, the 136 contribution from the non-faradaic current and the effective area of the gold electrode (as detailed in Chapter III, Section III-2). Figure 4-5 shows a time dependent coverage. An increase in surface coverage from 1 minute to 30 minutes of the modification is obtained (~0.10-0.17 ML). There is no change in the coverage value from 30 minutes to 3 hours of the modification. A maximum coverage of around 0.17 ML (~40 Å2 per molecule) is reached within 30 minutes of the modification.

For short modification times (up to 3 hours) a reductive stripping peak is observed, similar to the one seen for compound 1 (Chapter III, Sections III-2 and III-3). For longer modification times (greater than 3 hours) a dramatic change of the reductive stripping peak is observed. An important decrease of the initial reduction peak (which appears now as a shoulder) 137 is observed along with a new sharp peak at a slightly more negative potential (-0.96 V vs SCE).

Such a change in the CV shape may be interpreted as a change in the structure of the film

(through a change in orientation, density, intermolecular interactions, etc.) or completely a decomposition of the deposited molecule on the surface. The XPS results have shown that it is this second hypothesis that is responsible for the observed CV changes.

Interestingly this new sharp peak is very similar and located at the same position, to that previously reported for the reductive stripping peak of sulfur adsorbed on Au.260,261,286,289,322,528

This data provides further support for the discussed XPS results suggesting the decomposition of the adsorbed 2-nitrophenyl thiolates on the surface. The newly observed sharp reduction peak is more likely due to the adsorbed sulfur resulting from the decomposition of the adsorbate. These results indicate that the presence of the nitro group at the ortho position hinders the molecular packing of the thiolate of compound 2. It is important to note that despite this hindering effect of the NO2 substituent, the deposition is still efficient and fast. This further confirms the efficiency of the sulfenyl chloride functional group as a precursor for thiolate deposition.

STM Imaging

Extensive imaging of Au(111) surfaces modified using 1 mM solutions of compounds 2, in EtOH:DMF (9:1) and (1:1) respectively for various times up to 24 hours, did not allow observation of any well-ordered areas. Various modification conditions (concentration, solvent, and modification time) were used to that end and only at high concentrations (10 mM or higher) and long modification times (48 hours or longer) images showing non uniform areas are obtained.

Figure 4-6 shows images obtained for a Au (111) surface, modified using compound 2 (10 mM in

MeOH:THF (1:1)) for 48 hours. The large scan image shows various areas where bright spots are clearly observed. Zooming into these areas shows non-ordered structures with no well-defined phase. Approximate measurements provide periodicities of the bright spots within rows of about

138

8.8 Å, between 1st and 2nd rows of about 5 Å and between 1st and 3rd rows of about 12.9 Å indicating again a much lower film density than that obtained with the 4-nitrophenyl thiolate

SAM. These measurements correspond to a 3 x √20 phase. The proposed structural model containing a 3 x √20 unit cell is shown in Figure 4-6e. This phase is associated with a coverage value of 38 Å2 per molecule (~0.17 ML) which is very close to the value determined by electrochemistry. The nitro group at the ortho position does not allow good and well-ordered packing on the surface as it is the case for compound 1 (Chapter III, Sections III-2 and III-3).

This was also suggested by the XPS, PM-IRRAS and electrochemical data.

Figure 4-6. Unfiltered STM images, in air, of a Au(111) surface on mica modified using compound 2 (10 mM in MeOH:THF (1:1)) for 48 hours. Scan sizes (a) 48 x 48 nm2, (b) 28 x 28 nm2, (c) 10 x 10 nm2, and (d) 5 x 5 nm2. Tunnelling conditions: Tip bias = +0.1 V, tunnelling current = 0.80 nA and scan rate = 4.1 lines/s. (e) Proposed model for the SAM of compound 2 on

139

IV-3 Modification using Compound 3

IV-3a Modification Procedure

The modification is performed by immersing a Au(111) on mica or a polycrystalline solid gold electrode (cleaned prior to use) in a 1 mM solution of compound 3 in EtOH:DMF (1:1) for durations ranging from a few minutes to 24 hours. The modified gold substrate is thoroughly rinsed with a solvent mixture and then dried under a gentle stream of nitrogen. For STM imaging, the Au(111) substrate is also modified in a 10 mM solution of compound 3 in THF:MeOH (1:1) for 48 hours.

IV-3b Results and Discussion

XPS Characterization

Compound 3 (Figure 4-7) shows signals very similar to those observed for compound 2.

The S 2p, N 1s and O 1s all show multiple contributions. It is important to note the absence of any Cl signal, indicating that the observed signals all result from the nitrosubstitutedphenyl thiolate initially adsorbed through dissociation of the S-Cl bond. In the S 2p region, three unresolved doublets with their S 2p3/2 components located at 161.2, 162.2 and 163.2 eV are observed. The S 2p3/2 component located at 161.2 eV could be assigned to chemisorbed

261,289-291 monoatomic sulfur. The S 2p3/2 component located at 162.2 eV is usually assigned to Au-

261,289 288,290 thiolate species, polymeric sulfur or complex AuS phases. The S 2p3/2 component located at 163.2 eV is attributed to weakly bound or unbound sulfur,261,289 or sulfur multilayers.261,289 Similar to the compound 2, the C 1s peak is fitted for two types of carbons located at 285.5 and 284.1 eV corresponding to the C-N and the C-S carbons, and the other aromatic carbons, respectively. In the N 1s region, two peaks located at 399.2 and 405.0 eV are observed. The N 1s peak at 309.2 eV can be assigned to the NH2 group due to the reduction of

140

37,38,182,553-557 the terminal NO2 group. It may also be attributed to the NO group obtained due to the decomposition of the NO2 group as a result of an interaction between the NO2 group located at the ortho position with the substrate.584,585 The O 1s signals show a main signal at 531.8 eV with a large shoulder at 529.8 eV. The O 1s signal at 529.8 eV is attributed to the chemisorbed oxygen on Au.289,584,585 The nitro substituent at the ortho position seems to still affect the quality of the SAM regardless of the presence or absence of another nitro group at the para position.

Mainly, the presence of different contributions for the S 2p signal suggests potential decomposition of the 2,4-dinitrobenzene thiolate as in the case of compound 2.

Figure 4-7. X-ray photoelectron spectra of Au(111) on mica modified using a 1 mM solution of compound 3 in an EtOH:DMF (1:1) mixture for 24 hours.565 (Reprinted with permission from reference 565, Copyright © 2012, ACS).

141

PM-IRRAS Study

PM-IRRAS is also used to characterize the produced SAMs and to get insights into the orientation of the adsorbed thiolates on the Au surface. For a molecule adsorbed on a metal surface only vibrational modes with a component of the IR vector perpendicular to the surface are probed (surface selection rule, Chapter II, Section II-4).558-560 IR measurements are performed for a SAM of compound 3 along with measurements of the bulk sample in CCl4.

The structure of compound 3 is first optimized using Gaussian 03 at the B3LYP level with the 6-311++G(d,p) basis set.561 The optimized structure shows a planar nitrophenyl moiety with the nitro group in the plane of the phenyl ring. No imaginary vibrations are observed. The optimized structure and the calculated IR spectra are used to determine the main vibration modes

(Figures 4-8) discussed below. These vibrations modes are in accordance with the previously reported experimental and theoretical studies of molecules with similar nitrophenyl moieties.562-

564

142

Figure 4-8. Representation of atomic displacements (black arrows) and IR vectors (red arrows), of the main vibrational modes of compound 3 observed for a SAM on Au(111). The represented

+ + - - vibrational modes are the symmetric (r 2-NO2 and r 4-NO2) and asymmetric (r 2-NO2 and r 4-

NO2) stretch modes of the NO2 group, the superposition of the CC stretching and the CH in plane bending of phenyl ring (rCC-δCH) and the CH in plane bending of phenyl ring (δCH).565

Figure 4-9 shows the spectra for the 2,4-dinitrophenyl sulfenyl chloride (compound 3). In solution, IR signals are observed at 1240, 1300, 1344, 1387, 1450, 1531, and 1597 cm-1 for the

143

+ + - - δCH(a’’), r 2-NO2, rCC-δCH(a’’) and r 4-NO2, rCC-δCH(b’’), δCH(b’’), r 2-NO2 and r 4-NO2, and rCC-δCH(c’’) and rCC-δCH(d’’) respectively. IR spectrum for the resulting SAM on

+ Au(111) shows 3 main signals. The signals include a band for the rCC-δCH(a’’) and r 4-NO2 at

-1 - - -1 -1 1346 cm , r 2-NO2 and r 4-NO2 at 1531 cm , and rCC-δCH(c’’) and rCC-δCH(d’’) at 1583 cm .

These signals are similar to to those observed for the 4-nitrophenyl sulfenyl chloride (Chapter III,

Section III-2) and those determined for the 1,3-dinitrobenzene563 and 2,4-dinitroaniline.564 IR

-1 + -1 - signals at 1346 cm (mainly the r 4-NO2) and at 1531 cm (mainly the r 2-NO2) are observed at the same position while the IR signal at 1583 cm-1 (mainly the rCC-δCH(c’’) mode) is shifted to a slightly lower wavenumber (~14 cm-1) in the SAM than in the bulk. IR signals seen at 1531 cm-

1 and at 1583 cm-1 (having similar direction of the transition dipole vector, Figure 4-8) also show an important decrease in the SAM compared to the solution. This indicates that the transition dipole vectors associated with these modes do not lie perpendicular to the Au surface and the 2,4- dinitrophenyl thiolate adsorbed on the gold surface with a slightly tilted orientation. The IR data support then the XPS data and show the deposition of the 2,4-dinitrophenyl thiolate. It also shows that despite the lower quality of the SAM of 2,4-dinitrophenyl thiolate suggested by XPS, the

SAM shows good IR spectra indicating well defined orientation of the adsorbate on the surface.

144

Figure 4-9. IR spectra for compound 3 in a ~14 mM solution (CCl4) and SAM on Au(111). The modification is performed using a 1 mM solution of compound 3 in an EtOH:DMF (1:1) mixture for 24 hours.565 (Reprinted with permission from reference 565, Copyright © 2012, ACS).

Stripping Voltammetry

Similar voltammetric investigations are performed for compound 3 as described for compound 2 in Section IV-2 and the corresponding results are shown in Figure 4-10. These two compounds show very similar results. A reductive stripping peak (-0.80 V vs SCE) is observed at shorter modification times for the 1st scan and a response similar to the bare gold is observed for the 2nd scan of the modified solid polycrystalline gold electrode. An increase in the reductive stripping peak area is observed with an increase in the modification time from 1 minute to 30 minutes, indicating an increase in the surface coverage. At longer modification times, the peak

145 changes into a shoulder with the appearance of another narrow peak at a slightly negative potential (-0.96 V vs SCE). These changes (also detailed in Section IV-2) suggest the decomposition of the chemisorbed molecules on the surface after a long period of a time (more than 3 hours) as supported by XPS results.

A surface coverage is deduced for each cyclic voltammogram considering the reduction of the nitro group to the amino group, the simultaneous desorption of the monolayer and the

146 contribution from the non-faradaic current (as detailed in Chapter III, Section III-2). A surface coverage as a function of the modification time is shown in Figure 4-11. An increase in surface coverage from 1 minute to 30 minutes of modification is obtained (~0.15-0.17 ML). There is no change in the coverage value from 30 minutes to 3 hours of the modification. A maximum coverage of around 0.17 ML (~40 Å2 per molecule) is reached within 30 minutes of the modification.

Figure 4-11. Time dependent coverage of the monolayer deposition calculated from the reductive stripping voltammetry of previously modified polycrystalline solid gold electrodes in a 0.5 M aqueous KOH solution at 25 oC. The electrodes are modified using a 1 mM solution of compound

3 in an EtOH:DMF (1:1) mixture.

STM Imaging

To gain more insights into the quality of the 2,4-dinitrophenyl sulfenyl chloride SAM on

Au(111) at the molecular level, the modified surfaces are studied by STM. For the compound 3

147 modified Au(111) substrates, imaging under various conditions did not show any well-ordered areas. The only structures that are observed are rectangular structures as shown in Figure 4-12.

These are obtained using a 10 mM concentration of compound 3 in a MeOH:THF (1:1) solution and a modification time of 48 hours. Each rectangular structure shows 8 bright spots. The unit cell dimensions of this rectangular structure are a = 8.2 Å and b = 8.2 Å (detailed in Chapter V).

These rectangular features are characteristics of sulfur modified Au(111) surfaces.260,261,288-

290,301,302,320,321 They have been widely investigated in order to understand the S/Au interaction and to answer important fundamental questions in relation to SAM formation such as the adsorption sites and the mobility of the thiolate adsorbates.301,302,320,321 This suggests that, at least in these areas, decomposition of the precursor takes place, ejecting the aromatic moiety and leaving only sulfur on the Au surface. Deposition of sulfur through decomposition of organic self-assembled monolayers (SAMs) is a well-known process.586-589 Studies have been performed to understand the decomposition mechanism that leads to sulfur and its dependence on the experimental conditions. These studies have shown the initial formation of the SAMs which have been characterized using a number of techniques and then its subsequent decomposition to yield

S through dissociation of S-alkyl or S-aryl chemical bonds, similar to the present case.

148

Figure 4-12. Unfiltered STM images in air of a Au(111) surface on mica modified using compound 3 (10 mM in MeOH:THF (1:1)) for 48 hours. Scan sizes (a) 23 x 23 nm2, (b) 18 x 18 nm2, (c) 10 x 10 nm2, and (d) 5 x 5 nm2. Tunnelling conditions: Tip bias = +0.1 V, tunnelling current = 0.80 nA and scan rate = 4.1 lines/s.565 (Reprinted with permission from reference 565,

IV-4 Comparison of Compounds 1-3

An important result is that when comparing the stripping CVs for compounds with compounds 2 and 3 (Figure 4-13), after a similar modification time (30 minutes), compounds 2 and 3 provide a much smaller peak than compound 1. This is an indication that the modification is less efficient with the former compounds than with the latter one. This is confirmed by the coverage deductions using the stripping signals. Compound 2 and 3 provide a maximum coverage of ~0.17 ML (~40 Å2 per molecule) while compounds 1 provides a similar maximum coverage of ~0.23 ML (~28 Å2 per molecule). 149

Figure 4-13. Cyclic voltammetry of previously modified polycrystalline solid gold electrodes in

0.5 M aqueous KOH solutions at 25 oC. The electrodes are modified using 1 mM concentrations of the investigated compounds (1-3) in EtOH:DMF (9:1 for compounds 1 and 2, and 1:1 for compound 3) mixtures for 30 minutes. Scan rates 200 mV/s.

For a thiolate based SAM, the reductive stripping peak is broader and less negative than that for adsorbed sulfur. Figure 4-14 shows the reductive stripping cyclic voltammograms for electrodes modified for 18 hours in solutions containing nitrosubstituted sulfenyl chlorides (1-3).

The cyclic voltammogram for the 4-nitrophenyl sulfenyl chloride modified Au electrode shows only a single peak at -0.87 V versus SCE corresponding to the stripping of the 4-nitrophenyl thiolate SAM. The electrodes modified with the other two compounds (2 and 3) show, in addition to the peak corresponding to the stripping of the corresponding SAM, an additional sharp peak at 150 a more negative potential ( -0.96 V versus SCE). The additional sharp peak is only observed for long modification times using compounds 2 and 3. This sharp peak is very similar to the one observed for the stripping of sulfur from the Au electrode.260,261,286,289,322,528,590 This indicates that with both the 2-nitrophenyl sulfenyl chloride (2) and 2,4-dinitrophenyl sulfenyl chloride (3) the

SAMs decompose with time leaving only sulfur on the Au surface. A similar behavior has been previously observed with a number of precursors.586-589 This electrochemical data is in accordance with the XPS and indicate the efficient formation of 2-nitrosulfenyl thiolate SAMs, using compound 2 and 3, with a lower stability and a lower coverage than that obtained using the

4-nitro-subtituted compound (1).

151

Figure 4-14. Cyclic voltammetry of previously modified polycrystalline solid gold electrodes in

0.5 M aqueous KOH solutions at 25 oC. The modification is performed using 1 mM concentrations of the investigated compounds (1-3) in EtOH:DMF (9:1 for compounds 1 and 2, and 1:1 for compound 3) mixtures for 18 hours. Scan rates 200 mV/s.565 (Reprinted with permission from reference 565, Copyright © 2012, ACS).

The STM data confirm the results of the other characterization techniques used in this investigation. With compounds 2 and 3, adsorption does take place. However, the non-favourable intermolecular as well as adsorbate/substrare interaction as a result of the bulky ortho substituent for compounds 2 and 3 lead to less stable, disordered and lower quality films on Au(111).

Decomposition of the adsorbed molecules leaving only sulfur on the surface was confirmed by

XPS, electrochemistry and STM. These two precursors are allowing investigation of precursors with excellent adsorption ability but with unfavourable intermolecular and adsorbate/substrate interactions for SAM formation. 152

IV-5 Proposed Adsorption Mechanism for Compounds 2 and 3

The XPS and electrochemical results suggest chemisorption of the molecules on the surface and formation of Au-thiolate bonds. Therefore, a mechanism similar to compound 1

(Chapter III, Section III-4, Scheme 3-2) can be proposed for compounds 2 and 3 (Scheme 4-1).

The mechanism involves a one electron reduction of the nitrobenzene sulfenyl chloride with the formation of the Au-S bond and the removal of the Cl- group.

Scheme 4-1. Proposed deposition mechanism.565 (Adapted with permission from reference 565,

IV-6 Summary and Conclusions

In conclusion, the formation of SAMs using two nitro-substituted arene sulfenyl chlorides as precursors is investigated. The modification extent and the quality of the obtained SAMs are monitored using a series of techniques. XPS shows the successful deposition of all compounds and signatures corresponding to all elements are clearly observed. The electrochemical data show the molecular SAMs formation using compounds 2 and 3. The adsorption process is fast and maximum coverages are reached within 30 minutes of modification. The electrochemical characterization also shows that these two precursors lead to a much lower coverage providing hence the initial clues into the effect of the NO2 group at the ortho position. The PM-IRRAS data

153 provid more information as it show that the ortho substituted phenyl thiolates are more tilted.

This indicates that the hindering aspect of this substituent counteracts ability of the S-Cl group to interact with the gold surface yielding a much lower quality SAM. The XPS and the electrochemical results suggest decomposition of the adsorbed films leaving only sulfur on the

Au surface for longer modification times

STM images also provide evidence for the formation of less ordered and low density

SAMs. The 2-nitrophenyl sulfenyl chloride and the 2,4-dinitrophenyl sulfenyl chloride both form lower quality SAMs where the adsorbed nitrophenyl thiolates are more tilted. Despite the lower quality of the SAMs of compounds 2 and 3 their adsorption, as observed by all the techniques used in this study, shows the importance of the SCl functional group for the efficient deposition of organic compounds on to Au surfaces. The presence of a bulky substituent at the ortho position to the sulfur head group, and the substrate-substituent interactions for compounds 2 and

3 lead to low packing and disordered molecular structures on Au. These SAMs are less stable than the ones obtained with the 4-nitrosubsituted precursor and decompose at longer modification times leaving only sulfur on the gold surface.

154

Chapter V. Substituted Methane Sulfenyl Chlorides as Precursors for the Modification

of Gold Surfaces

V-1 Introduction

Despite the great wealth of research performed in the field of thiol SAMs on metals, many challenges remain regarding the surface stability and the complex chemistry involved in the assembly formation.21,25 The long-established model of a static and unreconstructed Au-S interface for Au-thiolate SAMs has been disputed.25 Several new configurations involving a dynamic Au-S interface, adsorbate induced surface reconstruction, and formation of Au vacancies and Au adatoms have been proposed.233 Another issue that requires great attention is related to the lower quality of obtained SAMs which mainly depends on the nature of the Au-S interactions and to factors governing the adsorbate-adsorbate and adsorbate-substrate interactions.

The deposition of sulfur on Au has been extensively studied due to its significance in understanding the Au-S interactions.260,261,286,288,289,291, 299,301,302,320,321 The traditional deposition

-2 - 260,261,286,289,299 method involves the use of aqueous S , SH or SH2 solutions or a gaseous S2 or

288,291 SO2. Previous studies have also reported the deposition of a dilute sulfur layer on Au as a result of the decomposition of thiolate-based SAMs. This has been observed with precursors such as dimethyldisulfide,588 cystamine, cysteamine and 4-aminothiophenol,587 and 4- mercaptopyridine.589 In these studies, it is suggested that the degradation of unstable SAMs at longer modification times (a few hours) results in the formation of a dilute sulfur layer on Au.

This chapter reports the spontaneous deposition of sulfur on Au using three substituted methane sulfenyl chlorides. The investigated compounds are triphenylmethane sulfenyl chloride

(4), trichloromethane sulfenyl chloride (5) and, chlorocarbonyl sulfenyl chloride (6) (Chart 5-1).

155

Chart 5-1. Structures of compounds 4-6.

The purpose of this chapter is to investigate the efficiency of sulfenyl chloride precursors for the modification of Au using compounds having an entirely different molecular backbone

(substituted methane sulfenyl chloride). This study shows that the change in the molecular structure of sulfenyl chloride functional group may result in the deposition of a dense sulfur layer even at a shorter modification time.

V-2 Modification Procedure

The modification of Au(111) on mica and polycrystalline solid gold electrodes are performed by immersing/dipping substrate in a 1-3 mM solution of compound 4-6 in THF (freshly distilled prior to use) for a varying length of time ranging from a few minutes to 48 hours. After modification, the modified surfaces are thoroughly rinsed with freshly distilled THF and dried under a gentle stream of nitrogen.

V-3 Results and Discussion

V-3a XPS Characterization

Figure 5-1 shows XPS signals for a Au(111) surface modified with a 1 mM solution of compound 4 in THF for 48 hours. The S 2p and S 2s regions show clear signals while the C 1s region shows a small amount of signals. The presence of a small peak for the C 1s suggests that

156 the peak does not correspond to carbon atoms of the precursor molecule. An experimental C/S ratio of ~1/2 is obtained using the C 1s and S 2s/S 2p signals. This value is much lower than the theoretical C/S ratio of 19/1 for triphenylmethane thiolate. This suggests that the C 1s signal corresponds to the adventitious carbon. The Cl 2p region does not show any peak. This suggests the cleavage of the S-Cl bond during adsorption.

In the S 2p region, three unresolved doublets with spin-orbit splitting of 1.2 eV and a branching ratio of 2:1 are observed. Their S 2p3/2 components are located at 161.2, 162.2, and

163.2 eV. The minor component located at 161.2 eV is attributed to the monoatomic/chemisorbed sulfur.261,289,290,291 The component located at 162.2 eV is usually attributed to polymeric sulfur,261,289 a complex AuS phase,288,290 or a thiolate SAM.199 The component located at 163.2 eV is attributed to elemental sulfur,261,289 or sulfur multilayers.261,289

Further information about the nature of the sulfur species on the modified surface is obtained from scanning the S 2s region. In this region, three unresolved peaks at 225.4, 226.8, 228.2 eV are seen. The S 2s peak at the lowest binding energy is consistent with a thiolate/chemisorbed sulfur,591 the peak at 226.8 eV with polysulfide species,592,593 and the peak at the highest binding energy to elemental/unbound sulfur.592-595 The observed S signals are similar to those obtained when only sulfur is deposited.260,261,286,288,289,291,299,301,302,320,321

It is important to note that no S 2p3/2 signal at 168 eV for the oxidized sulfur is observed.

This suggests that the adsorbed sulfur is stable under ambient environment. The presence of a very weak signal for O 1s also supports the absence of the oxidized sulfur. The Au 4f region consists of a doublet at 84 and 87.6 eV consistent with a Au(111) surface. From the XPS results, it is apparent that only sulfur is present on the surface in three different forms, while all other parts of the molecule are ejected at some point during modification.

157

Figure 5-1. X-ray photoelectron spectra of Au(111) on mica, modified using a 1 mM solution of compound 4 in THF for 48 hours.590 (Reprinted with permission from reference 590, Copyright

Figure 5-2 shows the XPS spectra for a Au(111) on mica substrate modified using a 2 mM solution of compound 5 in THF for 24 hours. Despite the fact that the molecule contains four

Cl atoms, the Cl 2p signal is very weak. The S 2p region shows three unresolved doublets with their S 2p3/2 component located at 160.8 eV, 162.4 eV and 163.6 eV. No S 2p3/2 component is observed at higher binding energies i.e. near 168 eV. Scanning in the S 2s region further supports the presence of three types of sulfur species on the surface. The S 2s peaks are observed at 225.4 158 eV, 226.8 eV and 229.6 eV. In the O 1s and C 1s regions, the very weak signals are observed which can be attributed to atmospheric contaminants. These XPS results are similar to the one observed for compound 4 deposition on Au. XPS provides evidence for the deposition of compound 5 as sulfur.

Figure 5-2. X-ray photoelectron spectra of Au(111) on mica, modified using a 2 mM solution of compound 5 in THF for 24 hours.

159

V-3b Stripping Voltammetry

Oxidative stripping voltammetry of bare and previously modified solid gold electrodes in a 0.5 M aqueous KOH solution provides additional information about sulfur deposition on gold using compound 4. The modification is performed using a 1 mM solution of Ph3CSCl in THF for different periods of modification times. Figure 5-3 shows these cyclic voltammograms. The first oxidative scan for a modified electrode clearly shows a stripping peak while the second scan shows a behaviour similar to that of bare gold. This indicates the stripping of the deposited film during the first oxidative scan. An oxidative stripping peak is clearly seen even after a modification period of 1 minute. This indicates the effectiveness and the rapidity of the modification process.

160

The coverage as a function of the modification time is deduced by subtracting the area under the cathodic peak from the area under the anodic peak286 and considering the effective area of a polycrystalline solid gold electrode (detailed in Chapter III, Section III-2). The area under the cathodic peak corresponds to the reduction of the gold oxide and the area under the anodic peak corresponds to the oxidation of sulfur to sulfate (Equation 5-1) and gold to gold oxide (Equations

5-2 and 5-3).286

161

- -2 - Au-S + 8OH Au + SO4 + 6e + 4H2O (5-1)

- - Au + 2OH AuO + 2e + H2O (5-2)

- - 2Au + 6OH Au2O3 + 6e + 3H2O (5-3)

Figure 5-4 shows a plot of the sulphur coverage as a function of the modification time. A sulfur coverage of ~0.3 ML within 1 minute of modification indicates the rapidity of the process.

An increase in sulphur coverage is observed with time and a maximum value of ~0.76 ML is obtained within 3 hours of modification.

Figure 5-4. Time dependent coverage of sulfur deposition calculated from the oxidative stripping voltammetry of previously modified polycrystalline solid gold electrodes in a 0.5 M aqueous

KOH solution at 25 oC. The electrodes are modified using a 1 mM solution of compound 4 in

162

In addition to oxidative stripping voltammetry, reductive stripping provides further information about the nature of the deposition process. Figure 5-5 shows reductive stripping cyclic voltammograms of bare and previously modified polycrystalline solid gold electrodes in a

0.5 M aqueous KOH solution. A reductive striping peak is observed near -0.96 V vs SCE. For the reductive stripping of 4-nitrophenyl thiolate SAMs, a peak near -0.80 to -0.87 V vs SCE is observed.481,482 Previous sulphur deposition studies have reported the reductive stripping of adsorbed sulphur at the similar position.260,261,286,289,322,528 Therefore, this sharp peak is assigned to the reductive stripping of adsorbed sulfur (Equation 5-4) since the reductive desorption for a triphenylmethane thiolate SAM is expected at a slightly less negative potential.481,482 These results further support the deposition of compound 4 as sulfur without any indication of a thiolate

SAM formation.

- - - Au-S + 2e + H2O Au + HS + OH (5-4)

163

Figure 5-6 shows successive reductive stripping scans for the modification time of 3 hours. It is important to note that many scans are needed to completely remove adsorbed sulfur from the gold surface. An increase in the modification time results in an increase in the number of scans required to completely remove deposited sulfur. Figure 5-7 shows coverage values estimated from the reductive stripping voltammetry experiments. Lower coverage values are obtained when only first reductive stripping scan is considered. Coverage values similar to the

164 oxidative stripping voltammetry are obtained when the sum of the reductive stripping scans is considered. The reductive stripping voltammetry provides a maximum coverage of ~0.77 ML.

These findings are in accordance to the previous in situ electrochemical STM studies. It has been previously suggested that the reductive stripping voltammetry only removes adsorbed sulfur from terraces and the desorption from step edges requires a potential near to the hydrogen evolution reaction.260,261,289

165

Figure 5-7. Time dependent coverage of sulfur deposition calculated from the reductive stripping voltammetry of previously modified polycrystalline solid gold electrodes in a 0.5 M aqueous

KOH solution at 25 oC. The electrodes are modified using a 1 mM solution of compound 4 in

Figure 5-8 shows oxidative stripping voltammetry of bare and previously modified polycrystalline solid gold electrodes using a 2 mM solution of compound 5 in THF at different modification times. A response similar to compound 4 is observed. For shorter modification times i.e. 1 to 5 minutes, two overlapping peaks are seen for the first anodic scan. The position of the first oxidative peak is similar to the oxidation of a bare gold (Equations 5-2 and/or 5-3) and the second oxidation peak to the oxidation of sulfur to sulphate (Equation 5-1). This can be explained based on two possibilities. Either a small amount of sulfur is deposited therefore, a peak for the oxidation of a gold is also visible (although its current intensity is much higher than

166 a bare gold, indicating a behaviour different than a bare gold) or there are two types of adsorbed species, which desorb at two different potentials.

At shorter modification times, an accurate estimate of the coverage is not possible as two overlapping peaks are observed and the true nature of these peaks is not known with certainty.

Figure 5-9, shows a time dependent coverage deduced using oxidative stripping voltammetry. A constant coverage of ~0.68 ML is obtained from 10 minutes to 24 hours of modification. Cyclic

167 voltammetry analysis supports the spontaneous deposition of sulfur. This also suggests that the process might be slightly different in the first 5 minutes of the deposition in comparison to compound 4, for which only one oxidative peak is seen.

Figure 5-9. Time dependent coverage of sulfur deposition calculated from the oxidative stripping voltammetry of previously modified polycrystalline solid gold electrodes in a 0.5 M aqueous

KOH solution at 25 oC. The electrodes are modified using a 2 mM solution of compound 5 in

THF.

Figure 5-10 shows cyclic voltammograms of bare and previously modified polycrystalline solid gold electrodes in a 3 mM solution of compound 6 in THF for times ranging from a 1 minute to few hours. The sulfur deposition for compound 6 is assumed by comparison with compounds 4 and 5.

168

Figure 5-10. Oxidative stripping voltammetry of bare and previously modified polycrystalline solid gold electrodes in a 0.5 M aqueous KOH at 25 oC. Scan rates 200 mV/s. The modification is performed in a 3 mM solution of compound 6 in THF at different modification times.

Figure 5-11 shows sulfur coverage as a function of a modification time estimated from the oxidative stripping voltammetry experiments. The sulfur coverage obtained after 1 minute of modification is negligible. On the other hand, a sulfur coverage of ~0.7 ML is obtained within 5 minutes of modification which increases to ~1.5 ML within two hours of the modification. It should be noted that unlike compound 5, overlapping peaks are not observed within the first 5 minutes of modification but the stripping peak position and the shape is significantly different than the oxidation of the bare gold indicating an efficient modification of the electrode.

169

V-3c STM Imaging

STM imaging is used to get further insights about the physical nature of the 2D sulphur structures deposited on Au(111) surfaces using a 1 mM solution of compound 4 in THF for 48 hours. Figure 5-12 shows STM images of a modified Au(111) substrate. The modification over wide areas and terraces with many etch pits is observed in the large size image (Figure 5-12a).

The formation of these etch pits have been previously reported for the formation of

SAMs341,426,596 and the deposition of sulfur on Au.288,291 The origin of the etch pits is however, not completely understood.231,232,243-247,594,597-604 High resolution STM images shown in Figures 5-

170

12b-e confirm the modification over long-range. Images of smaller sizes (10 x 10 and 5 x 5 nm2) reveal densely packed quadrilateral sulfur structures. Each structure is composed of eight clearly visible spots. Their shape and dimensions slightly vary from the well-known rectangular structures. For these structures, a rhombus shape (a solid white circle in Figure 5-12d) with average dimensions of 5.1 ± 0.1 Å by 5.1 ± 0.1 Å is observed. Unit cell dimensions of 8.3 ± 0.1

Å x 8.3 ± 0.2 Å (Figures 5-12f and g) are obtained from line profiles along the edges of a rhombus structure. From these dimensions, a polymeric S8 structural model is proposed. This model is closed to the one previously reported for the rectangular structures.260,261,286,289,301,302,320,321 In the proposed model, the sulfur atoms at the corner of the rhombus are placed on atop sites while the other four sulfur atoms are positioned on bridge sites

(Figure 5-13a). Other similar structures where all sulfur atoms are placed on bridge sites (Figure

5-13b) or where the sulfur atoms at the corner of the rhombus are positioned on bridge sites while two of the four sulfur atoms on the edge of the rhombus structures are positioned on bridge sites and two on atop sites (Figure 5-13c) are also possible. From the dimensions of the unit cell measured from the STM images, and considering 8 sulfur atoms inside a unit cell, a coverage of

~0.76 ML is estimated. A value remarkably similar to the one obtained from the stripping voltammetry experiments at longer modification times.

171

Figure 5-12. Unfiltered STM images in air of a Au(111) surface on mica modified using a 1 mM solution of compound 4 in THF for 48 h. Scan sizes are (a) 270 x 270 nm2, (b) 25 x 25 nm2, (c)

15 x 15 nm2, (d) 10 x 10 nm2, and (e) 5 x 5 nm2. Tunnelling conditions: Tip bias = +0.1 V, tunnelling current = 0.55 nA and scan rate = 4.1 lines/s. (f-g) Height profiles along line A and B respectively as shown in Figure 5-12e.590 (Reprinted with permission from reference 590,

172

Figure 5-13. (a-f) Proposed structural models for Figure 5-12d showing sulfur deposition on

Beside the predominant rhombus structures, the disordered areas and polymeric sulphur structures are also observed. These structures show the S-S distances similar to the rhombus or rectangular structures. In these structures, each edge is composed of three sulfur atoms and the angle between two edges is similar to the rectangular or rhombus structures. More importantly,

Figure 5-12d shows area comprises of alternate rows of rectangular and rhombus structures (a dashed white circle). Line profiles along the edges of these quadrilateral structures provide an average unit cell dimensions of 8.3 ± 0.1 Å x 16.8 ± 0.2 Å. Figure 5-13d shows a proposed model for this phase. In this model, the corner atoms of both the rhombus and rectangular structures are placed on atop sites, while the other four sulfur atoms of the rhombus structures are positioned on bridge sites. Two of the sulfur atoms on the edge of the rectangular structures are placed on atop

173 sites and two on bridge sites. Other similar structures, where all the sulfur atoms of both the rhombus and rectangular structures are positioned on bridge sites (Figure 5-13e) or where the corner atoms of both the rhombus and rectangular structures are placed on bridge sites while two of the four sulfur atoms on the edge of both the rhombus and rectangular structures are positioned on bridge sites and two on atop sites (Figure 5-13f) provide the same pattern.

Figure 5-14(a-e) shows low and high resolution STM images of a modified Au(111) surface using a 2 mM solution of compound 5 in THF for 24 hours. The large scan images show the efficient modification over wide areas with many etch pits. The high resolution images in

Figures 5-14d and e show zig-zag sulfur structures on the surface. Different sulfur structures other than the traditional rectangular structures have been previously reported for sulfur deposition on gold.290,301,320,321 These zig-zag sulfur structures are seen over many layers on the gold surface (Figure 5-14d). Line profile (Figure 5-14f) along these layers shows a height difference of ~2.4 Å (monoatomic step height of gold). This indicates the formation of zig-zag sulfur structures over several gold layers. In order to measure an average length of each edge of the zig-zag sulfur structures and the corresponding unit cell dimensions, line profiles are taken along lines B to E (two edges, between two adjacent rows and within a row for the zig-zag sulfur structures, respectively). Figure 5-14(g-j) shows these line profiles, marked in Figure 5-14e.

Several of these profiles provide an average dimension of 5.1 ± 0.3 Å and 5.0 ± 0.2 Å for the two edges of the zig-zag sulfur structures with an angle of 106o ± 1o between two edges. Unit cell dimensions of 4.6 ± 0.2 Å and 7.5 ± 0.4 Å are also obtained from these profiles. On the basis of these measured dimensions, a structural model is proposed in Figure 5-14k, where the length of the each edge of the zig-zag is ~5 Å. In this model, each edge of the zig-zag is comprised of three sulfur atoms. A coverage of ~0.75 ML is calculated from the measured dimensions of the unit cell and considering four sulfur atoms inside a unit cell.

174

Figure 5-14. Unfiltered STM images in air of a Au(111) surface on mica modified using a 2 mM solution of compound 5 in THF for 24 h. Scan sizes are (a) 500 x 500 nm2, (b) 120 x 120 nm2, (c)

50 x 50 nm2, (d) 10 x 10 nm2 and (e) 5 x 5 nm2 (slightly filtered). Tunnelling conditions: Tip bias

= +0.1 V, tunnelling current = 0.525 nA and scan rate = 3.3 lines/s. (f) Height profiles along line

A as shown in Figure 5-14e, showing the step heights. (g-j) Height profiles along line B to E respectively as shown in Figure 5-14e in different directions of a zig-zag structure. (k) Proposed structural models for Figure 5-14d showing sulfur deposition on the Au(111).

175

In addition to the zig-zags, other sulfur structures are also seen. Figure 5-15 shows consecutive real time high resolution STM images of the modified Au(111) surface. These images are obtained after a time interval of 1.3 minutes. In these images, rectangular and parallelogram sulfur structures are observed, which are similar to the ones reported for compound

4. Figures 5-15a and b, show five relatively ordered quadrilateral structures in the lower left side of the images (marked using a solid white rectangle). All of these quadrilateral structures in

Figure 5-15c are now arranged in random order or a shape other than a quadrilateral. On the other hand, the disordered structures in the lower right side of Figures 5-15a and b (marked using a solid white circle) are now arranged into ordered quadrilateral structures in Figure 5-15c. These changes support the dynamic nature of these sulfur structures. Vericat et al. have previously suggested the mobility of sulfur adlayers.286 Our group has also shown that the observed rectangular sulfur structures are mobile as individual units.301,302,320,321 The observed mobility of the rectangular sulfur structures rules out the existence of a AuS phase. It should be noted that the mobile sulfur structures observed for compound 5 do not move as individual units but they form and dissociate completely. These findings suggest that the Au-S interactions result in the weakening of the bond between two sulfur atoms adsorbed on the gold surface. This is apparent from the observed S-S distances of ~2.6 Å, that are larger than elemental sulfur (~2.2 Å). This also suggests that stable sulfur phases are formed when the Au-S and the S-S interactions are at equilibrium. These interactions, however, are not strong enough to hold sulfur atoms at a fixed position on the gold surface and they also weaken the S-S bond. The old S-S bonds, therefore, are broken and new bonds are reformed.

176

Figure 5-15. (a-c) Sequential unfiltered STM images (10 x 10 nm2) in air of a Au(111) surface on mica modified using a 2 mM solution of compound 5 in THF for 24 h. The freshly prepared sample was used. Tunnelling conditions: Tip bias = +0.1 V, tunnelling current = 0.65 nA and scan rate = 3.3 lines/s.

Figure 5-16 shows large and small scan size images of the Au(111) sample modified using a 3 mM solution of compound 6 in THF for 2 hours. The effective surface modification over wide terraces is observed. In small scan images (Figure 5-16c-e), mixed parallelogram and rectangular sulfur structures are observed as reported earlier using compounds 4 and 5.

177

V-4 Proposed Mechanism of Sulfur Deposition for Compounds 4-6

XPS, STM and stripping voltammetric experiments show the fast and efficient deposition of a dense sulfur layer using compounds 4-6. A high coverage values (~0.33 ML or greater) obtained from stripping voltammetry in a very short period of time indicate a rapid decomposition mechanism leading to sulfur deposition. This suggests that the deposition mechanism does not involve the intermediate formation of a thiolate SAMs as seen in certain cases.586-589 Previous studies have shown the deposition of a dilute sulphur layer at longer modification times through decomposition of an initially formed SAM.586-589

178

Scheme 5-1 (route 1) shows a general mechanism proposed for the deposition of sulfur on

Au using compounds 4-6. The mechanism involves the cleavage of both the S-Cl and C-S bonds simultaneously along with the ejection of RCl and the deposition of sulfur. Another route

(Scheme 5-1, route 2) for the decomposition of compound 4 is also possible. This involves a reductive adsorption of compound 4 along with the scission of the S-Cl and the formation of a

Au-thiolate bond. This is followed by the nucleophilic attack of the chloride anion and the rapid dissociation of the C-S bond. Route 2 for compound 4 is proposed based on the chemical and thermal reactivity (Equation 5-5) of compound 4.605-608

Δ Ph3CSCl Ph3CCl + Sx (5-5)

where R = Ph3C, Cl3C and ClCO.

179

V-5 Summary and Conclusions

In this chapter, the modification of gold surfaces using three susbtituted methane sulfenyl chlorides is reported. XPS allows identification of the adsorbed species on the surface. Analysis of the modified gold surfaces using compound 4 and 5 show the absence of chlorine signal, indicating the scission of the S-Cl bond at some point during modification and the ejection of the substituted methane molecular backbone. The presence of three types of sulfur species suggests the formation of sulfur adlayers on the surface. The oxidative stripping voltammetry of the modified gold electrodes further supports the sulfur deposition on the gold electrode. The oxidative stripping peaks are observed as expected for adsorbed sulfur even after a 1 minute modification. A maximum coverage of ~0.7-1.5 ML is estimated for compound 4-6 from the oxidative stripping voltammetry.

STM investigation of the modified gold surfaces shows an efficient surface modification over large areas. For compound 4, alternate rectangular and paralelogram sulfur structures are observed by STM with unit cell dimensions of 8.3 ± 0.1 Å x 16.8 ± 0.2 Å. STM imaging of the gold surfaces modified using compound 5 shows the formation of the zig-zag, and the mixed parallelogram and rectangular sulfur structures. Unit cell dimensions of 4.6 ± 0.2 Å and 7.5 ± 0.4

Å are obtained for the zig-zag sulphur structures. Mixed quadrilateral sulfur structures

(parallelogram and rectangular) are also observed from the STM imaging of the gold surfaces modified using compound 6.

The deposition of a dense sulfur layer using compounds 4-6 is different than previous studies where only a dilute sulfur layer is formed after decomposition of thiolate-based SAMs within a short period of time. The proposed mechanism involves the deposition of sulfur accompanied with the dissociation of both the S-Cl and C-S bonds. The present case is different than the formation of a thiolate SAM, which involves the cleavage of the only one chemical bond. All observed sulfur structures (rhombus, rectangular and zig-zag) show that each sulfur 180 atom is not only interacting with other sulfur atoms but also to the gold surface. The S-S distance in these observed structures (~2.6 Å) is also greater than the S-S distance in elemental sulfur

(~2.2 Å). This indicates the weakening of the S-S bonds for the sulfur deposition on Au as compared to elemental sulfur. This study shows that the substituted methane sulfenyl chlorides do not form long-range ordered SAMs. It also shows that the substituted methane is a good leaving group and the deposition mechanism involves the cleavage of both the S-Cl and C-S bonds.

181

Chapter VI. Summary and Future Work

VI-1 Summary

The main purpose of this thesis was to develop a new methodology for the modification of gold surfaces using organic sulfenyl chlorides as novel precursors. Thus, six sulfenyl chloride compounds having aliphatic, aromatic and hybrid (aliphatic-aromatic) molecular backbones are studied

4-Nitrophenyl sulfenyl chloride (1) leads to the successful formation of well-ordered and densely packed aromatic SAMs on Au(111) on mica and polycrystalline solid gold electrodes under two different modification conditions. Modification in an EtOH:DMF (9:1) mixture for 24 hours (condition 1) leads to an area per molecule of ~27.8 Å2. A value similar to that found for selenol-based aromatic SAMs. XPS analysis of the modified surface indicates the formation of a

Au-thiolate bond and the cleavage of the S-Cl bond. An adsorption mechanism similar to that reported for organic thiocyanates is proposed.39,40,199,552 It involves the reductive dissociation of the S-Cl bond of the precursor molecule. An occasional reduction of the terminal nitro group to an amino group is also observed by XPS. PM-IRRAS data show signals for the preferential orientation of the precursor molecules with smaller tilt angles. STM has shown the formation of a relatively short-range and well-ordered molecular row structures corresponding to a √3 x 4 rectangular phases with an area per molecule of 27.8 Å2 (~0.23 ML). The traditional precursors used for aromatic SAMs (e.g. benzenethiol) have not shown the formation of highly ordered and densely packed structures obtained using 4-nitrophenyl sulfenyl chloride SAM on Au.

Long-range and highly ordered aromatic SAMs on Au corresponding to a √3 x √3 hexagonal phase with an area per molecule of ~21.4 Å2 (~0.33 ML) is obtained using a 10 mM solution of 4-nitrophenyl sulfenyl chloride in a MeOH:THF (1:1) mixture for 48 hours (condition

2). The PM-IRRAS results suggest a nearly vertical orientation of the adsorbed molecules. The 182 presence of an additional IR band, however, at 1379 cm-1 for the CH bending mode (δCH(b)) having a transition dipole moment parallel to the 1,4 molecular axis suggests that the molecules in the SAM obtained under the modification condition 2 are more tilted under 2nd modification condition. The electrochemical data show that the modification process is very fast and efficient.

A saturation coverage close to the one associated with densely packed aliphatic thiol SAMs

(~0.33 ML) is achieved within a modification time of 10 minutes. Sequential STM imaging of the modified surface shows distinct superstructures beside the main hexagonal lattice. These superstructures, including hexagons, parallelograms and zig-zag are formed from specific arrangements of the molecules on the surface. They disappear and/or reappear on the surface. It is suggested that the molecules forming these superstructures have slightly larger tilt angles than the molecules in the surrounding, and are leaning towards each other. The rest of the molecules surrounding these superstructures are nearly vertically oriented.

STM imaging of the 4-nitrophenyl sulfenyl chloride SAM on Au(111) provides submolecular details, where both oxygen atoms of the terminal nitro group of the precursor molecules are identified. This is the first experimental example of the capability of the STM to provide physical structure information of standing-up aromatic SAMs at room temperature. This is a heavily debated issue and this work shows that at least for these aromatic structures, the STM tip is able to provide the structural details of the terminal group.

2-nitrophenyl sulfenyl chloride (2) and 2,4-dinitrophenyl sulfenyl chloride (3) are used to investigate the dependence of the quality of obtained SAMs on the position of the nitro group on the phenyl ring. The XPS results show the formation of thiolate SAMs along with sulfur deposition. The electrochemical data show that a maximum coverage of ~0.17 ML is reached within 30 minutes of modification. It also shows that modification for times longer than 3 hours leads to the decomposition of the SAM, the deposition of sulfur. The PM-IRRAS results suggest a more tilted orientation of the obtained SAMs. STM imaging provides evidence for the lower 183 quality SAMs with compound 2, the SAM shows a molecular row structure corresponding to a 3 x √20 phase and an area per molecule of 38 Å2 (~0.17 ML). With compound 3, the rectangular features known for sulfur deposition are observed. A one electron surface mediated reduction of compounds 2 and 3 is proposed as a possible adsorption mechanism followed by the decomposition of the SAM leading to sulfur deposition at longer modification times. Despite the lower quality of the obtained aromatic SAMs, due likely to the hindering effect of nitro substituent at ortho position, and the ability of ortho nitro group to interact with the gold surface, all techniques supports the efficiency of the sulfenyl chloride functional group for the formation of the SAMs on Au.

Three substituted methane sulfenyl chlorides, triphenylmethane sulfenyl chloride (4), trichloromethane sulfenyl chloride (5), and chlorocarbonyl sulfenyl chloride (6) show the spontaneous formation of ordered/disordered dense sulfur layers within a very short period of modification time. This indicates that the modification process does not involve initial formation of a molecular SAM followed by its degradation. A deposition mechanism involving the cleavage of both the S-Cl and C-S bonds is proposed leading to the deposition of sulfur only. XPS analysis of Au(111) surfaces modified using compounds 4 and 5 show the presence of polymeric sulfur.

The electrochemical data show that a high sulfur coverage is obtained within a few minutes of modification. A saturation coverage of ~0.8 to 1.5 ML is deduced from the reductive stripping voltammetry of the modified gold electrodes. STM imaging of modified Au(111) surface show the formation of polymeric quadrilateral structures having rhombus, zig-zag and rectangular shapes. These polymeric sulfur structures are observed over many gold layers. The dissociation of both sulfur bonds indicates that the Au-S interactions for sulfur deposition are different than the one involved in the formation of thiolate SAMs. The S-S distances in the observed sulfur structures are ~2.6 Å (larger than in elemental sulphur). Compounds 4, 5 and 6 show that the

184 sulfenyl chloride head group is still very efficient for the modification of gold, despite having an entirely different molecular backbone.

The process of the surface modification is known to depend on the structural compositions of the employed precursors.25,597 Several sulfur precursors such as thiols, disulfides, monosulfides, thiosulfates, thioacetates, thiocyanates and sulfenyl chlorides are known to give variable packing, crystallinity and in some cases decomposition products on the surface despite having the same sulfur head group but different leaving groups. In a similar way, varying the nature of the molecular backbone with one sulfur head group as well as leaving group, produces different results on adsorption on the substrate. For example, well ordered and densely packed molecular SAMs are reported for medium and long chain (nC > 6) alkanethiol. On the other hand, low quality SAMs or the deposition of sulfur through the ejection of the alkyl backbone is reported for short chain alkanethiols.586-589 There are many parameters that contribute towards the difference in behaviour between the substituted methane sulfenyl chlorides to the 4-nitrophenyl,

2-nitrophenyl and 2,4-dinitrophenyl sulfenyl chlorides for their interactions with gold surfaces.

These include the strength of the C-S bond, intermolecular interactions and differences in their geometries. 4-Nitrophenyl sulfenyl chloride is a planar molecule that has ability to pack effeciently with better intermolcular interactions, while the presence of the bulky substituent at ortho position and an additional interaction of the ortho nitro group with the gold surface result in the formation of lower packing and unstable SAMs of 2-nitrophenyl and 2,4-dinitrophenyl sulfenyl chlorides. Moreover, substituted methane (which is the molecular backbone) cannot pack efficiently and may act as a good leaving group leading to the dissociation of the C-S bond.

These results show that the the nature of the molecular backbone for organosulfur precursors plays an important in determining the final adsorption product on the gold surface. It is not only involved in intermolecular interactions and in efficient packing but also in its ability to act as a leaving group. 185

VI-2 Future Work

At this stage of the project, only simple and commercially available organic sulfenyl chloride compounds are used for the modification of the gold surfaces. Future work will involve the use of a wider range of organic sulfenyl chloride compounds with various functional groups.

For this purpose, the derivatives of sulfenyl chlorides with desired physical or chemical properties will be synthesized and will be used for the surface modification. For example, thiol derivatives of the OPE609,610 molecules (nitro-terminated OPEs,38,532,610 nitrile-terminated

OPEs,611 biphenyl- and fluorenyl-based OPEs,612 ferrocene terminated OPEs,613 azobenzenes and bipyridines-based OPEs),610 oligo(phenylene vinylene) (OPV) molecules610,614 (ferrocene- terminated OPVs,615 Oligoanilines,616 aryldiazoniums,617 and ladder oligomers39,618) have been used as precursors for SAMs formation due to their potential applications in molecular electronics. Gold nanoparticles functionalized with 4-(7-mercaptoheptanoxy)azobenzene have shown photoisomerization (trans-cis and cis-trans),619 making them suitable to use as molecular switches.620 SAMs of thiol-derivatives of dipyridinium molecules have shown NDR and are used for designing molecular switches and logic devices.621,622 Sulfenyl chloride derivatives of above mentioned compounds may results in a better quality SAMs. Therefore, these compounds will be synthesized and used for the formation of SAMs and to study their properties.

As an extension of this project, other metals such as platinum, silver and copper will also be tested as substrates. Moreover, the chemical and thermal stability of obtained aromatic SAMs of 4-nitrophenyl sulfenyl chlorides will be investigated. Similarly, the physical properties of 4- nitropheyl thiolate SAMs such as wettability, electron transport and electrochemical behaviour will be explored. It has been known for 4-nitrothiophenol SAM on Au(111) that the terminal nitro group (NO2) can be selectively reduced to a hydroxylamine group (NHOH) and then to an

568,569 amino group (NH2) by electrochemical methods. After selective reduction of the terminal nitro group, the electronic properties of the SAM may be varied and the terminal amino group 186 may be further oxidized or polymerized.623 An hydroxylamine terminated monolayer may act as a switch (can be oxidized or reduced). Moreover, specific substituents at the para position of the phenyl ring may undergo nucleophilic substitution reactions with various nucleophiles in the solution. Scheme 6-1 shows proposed reactions of the terminal group of the SAM obtained from aromatic sulfenyl chloride in electrochemical environment. Scanning electrochemical microscopy

(SECM) tip may also be used to induce these changes locally as shown in Scheme 6-2.

Scheme 6-1. Proposed reactions of the terminal nitro group of the 4-nitrophenyl thiolate SAM on

Au in an electrochemical environment.

187

Scheme 6-2. Proposed reactions of the terminal group of the 4-phenyl thiolate SAM on Au in an electrochemical environment using SECM tip.

In the STM images of 4-nitrophenyl sulfenyl chloride SAM on Au(111), it is not clear why certain molecules appear as brighter spots. Moreover, it is not known that the appearance of the particular superstructures (hexagons, parallelograms, and zig-zags), with submolecular details is the result of the modification or tunnelling conditions. This can be explored further through a study of phenyl sulfenyl chloride SAMs with various substituents as well as a similar precursor under different modification and imaging conditions. It can be checked if the STM study of phenyl sulfenyl chloride SAMs on Au(111) with a monoatomic tail group (e.g. Cl, Br etc.) or 4- nitrophenyl SAM on Au(111) with different modification/tunneling conditions will provide details as observed for the present case.

188

Quantum confined (discrete, quantized energy levels) nanoclusters are important for the development of advanced molecular electronics.624-627 For this purpose, functionalized quantum dots (semiconductor clusters having dimension of nanometers, demonstrating quantum confinement) are being used, which show electronic communication between semiconductor core and the covalently bound substituent (para position).628 Farah et al. have shown that CdS quantum dots functionalized with 4-nitrothiophenol and 4-(4-nitrophenylazo) thiophenol (mixed ligands) (Scheme 6-3) can be used as a probe for surface-core electronic communication.629 4-

Substitutedphenyl sulfenyl chlorides and 4-(4-phenylazo) sulfenyl chlorides with electron donating and electron withdrawing substituents may be used to functionalize quantum dots as alternative capping agents. Furthermore, their photodecomposition and electronic communication may be studied for applications in semiconductor based molecular electronics.

Scheme 6-3. Scheme for the synthesis of mixed-ligand CdS nanoclusters containing 1 mol % of

4-(4-Nitrophenylazo) thiophenol ligand.629 (Adapted with permission from reference 629,

189

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