11. Scanning Tunneling Microscopy of Physisorbed Monolayers:
From Self-Assembly to Molecular Devices
Thomas Müller ............................................ 1
11.1. Introduction .......................................... 1
11.2. Source of Image Contrast: Geometric and
Electronic Factors .................................... 2
11.3. Two-Dimensional Self-Assembly: Chemisorbed
and Physisorbed Systems ............................... 4
11.4. Self-Assembly on Graphite ............................. 6
11.4.1. Alkane Functionalization and Driving Forces
for Self-Assembly ............................. 6
11.4.2. Expression of Chirality ...................... 11
11.5. Beyond Self-Assembly ................................. 14
11.5.1. Postassembly Modification .................... 14
11.5.2. Templates for Bottom-Up Assembly ............. 21
11.6. Toward Molecular Devices ............................. 23
11.6.1. Ring Systems and Electronic Structure ........ 23
11.6.2. Model Systems for Molecular Electronics ...... 25
11.7. Summary and Conclusions .............................. 28
References ................................................. 28
12. Tunneling Electron Spectroscopy Towards Chemical
Analysis of Single Molecules
Tadahiro Komeda ......................................... 31
12.1. Introduction ......................................... 31
12.2. Vibrational Excitation Through Tunneling Electron
Injection ............................................ 32
12.2.1. Characteristic Features of the Scanning
Tunneling Microscope as an Electron Source ... 32
12.2.2. Electron-Induced Vibrational Excitation
Mechanism .................................... 33
12.3. IET Process of Vibrational Excitation ................ 36
12.3.1. Basic Mechanism of Vibrational Excitation
in the IET Process ........................... 37
12.3.2. IETS with the Setup of STM ................... 39
12.3.3. Instrumentation of IETS with the Use
of STM ....................................... 40
12.3.4. Examples of STM-IET3 Measurements ............ 41
12.3.5. Theoretical Treatment of STM-IETS Results .... 44
12.3.6. IETS Mapping ................................. 48
12.4. Manipulation of Single Molecule Through
Vibrational Excitation ............................... 49
12.4.1. Desorption via Vibrational Excitation ........ 49
12.4.2. Vibration-Induced Hopping .................... 51
12.4.3. Vibration-Induced Chemical Reaction .......... 54
12.5. Action Spectroscopy .................................. 55
12.5.1. Rotation of cis-2-Butene Molecules ........... 56
12.5.2. Complimentary Information of Action
Spectroscopy and IETS ........................ 57
12.6. Conclusions .......................................... 60
References ................................................. 61
13. STM Studies on Molecular Assembly at Solid/Liquid
Interfaces
Ryo Yamada, Kohei Uosaki ................................ 65
13.1. Introduction ......................................... 65
13.2. STM Operations in Liquids ............................ 66
13.2.1. Instruments .................................. 66
13.2.2. Preparation of Substrates .................... 67
13.3. Surface Structures of Substrates ..................... 68
13.3.1. Introduction ................................. 68
13.3.2. Structures of Au(111) ........................ 68
13.3.3. Structures of Au( 100) ....................... 68
13.4. SA of Organic Molecules .............................. 69
13.4.1. Introduction ................................. 69
13.4.2. Assembly of Chemisorbed Molecules:
Alkanethiols ................................. 70
13.4.3. Assembly of Physisorbed Molecules:
n-Alkanes .................................... 80
13.5. SA of Inorganic Complexes ............................ 84
13.5.1. Introduction ................................. 84
13.5.2. Assembly of Metal Complexes .................. 85
13.5.3. Assembly of Metal Oxide Clusters:
Polyoxometalates ............................. 92
13.6. Conclusions .......................................... 96
References ................................................. 96
14. Single-Molecule Studies on Ceils and Membranes
Using the Atomic Force Microscope
Ferry Kienberger, Lilifl A. Chtcheglova, Andreas
Ebner, Theeraporn Puntheeranurak, Hermann J. Gruber,
Peter Hinterdorfer ..................................... 101
14.1. Abstract ............................................ 101
14.2. Introduction ........................................ 102
14.3. Principles of Atomic Force Microscopy ............... 103
14.4. Imaging of Membrane-Protein Complexes ............... 104
14.4.1. Membranes of Photosynthetic Bacteria and
Bacterial S-Layers .......................... 104
14.4.2. Nuclear Pore Complexes ...................... 106
14.4.3. Cell Membranes with Attached Viral
Particles ................................... 106
14.5. Single-Molecule Recognition on Cells and
Membranes ........................................... 110
14.5.1. Principles of Recognition Force
Measurements ................................ 110
14.5.2. Force-Spectroscopy Measurements on Living
Cells ....................................... 113
14.6. Unfolding and Refolding of Single-Membrane
Proteins ............................................ 117
14.7. Simultaneous Topography and Recognition Imaging
on Cells (TREC) ..................................... 119
14.8. Concluding Remarks .................................. 122
References ................................................ 123
15. Atomic Force Microscopy of DNA Structure and
Interactions
Neil H. Thomson ........................................ 127
15.1. Introduction: The Single-Molecule, Bottom-Up
Approach ............................................ 127
15.2. DNA Structure and Function .......................... 129
15.3. The Atomic Force Microscope ......................... 131
15.4. Binding of DNA to Support Surfaces .................. 137
15.4.1. Properties of Support Surfaces for
Biological AFM .............................. 137
15.4.2. DNA Binding to Surfaces ..................... 138
15.4.3. DNA Transport to Surfaces ................... 142
15.5. AFM of DNA Systems .................................. 143
15.5.1. Static Imaging versus Dynamic Studies ....... 143
15.5.2. The Race for Reproducible Imaging of
Static DNA .................................. 144
15.5.3. Applications of Tapping-Mode AFM to
DNA Systems ................................. 146
15.6. Outlook ............................................. 157
References ................................................ 159
16. Direct Detection of Ligand-Protein Interaction
Using AFM
Malgorzata Lekka, Piotr Laidler, Andrzej J. Kulik ...... 165
16.1. Cell Structures and Functions ....................... 166
16.1.1. Membranes and their Components: Lipids
and Proteins ................................ 166
16.1.2. Glycoproteins ............................... 167
16.1.3. Immunoglobulins ............................. 169
16.1.4. Adhesion Molecules .......................... 170
16.1.5. Plant Lectins ............................... 173
16.2. Forces Acting Between Molecules ..................... 175
16.2.1. Repulsive Forces ............................ 177
16.2.2. Attractive Forces ........................... 179
16.3. Force Spectroscopy .................................. 181
16.3.1. Atomic Force Microscope ..................... 182
16.3.2. Force Curves Calibration .................... 187
16.3.3. Determination of the Unbinding Force ........ 188
16.3.4. Data Analysis ............................... 189
16.4. Detection of the Specific Interactions on
Cell Surface ........................................ 193
16.4.1. Isolated Proteins ........................... 194
16.4.2. Receptors in Plasma Membrane of
Living Cells ................................ 196
16.5. Summary ............................................. 201
References ................................................ 202
17. Dynamic Force Microscopy for Molecular-Scale
Investigations of Organic Materials in
Various Environments
Hirofiimi Yamada, Kei Kobayashi ........................ 205
17.1. Brief Overview ...................................... 205
17.2. Principles and Instrumentation of Frequency
Modulation Detection Mode Dynamic Force
Microscopy .......................................... 206
17.2.1. Transfer Function of the Cantilever as
a Force Sensor .............................. 206
17.2.2. Detection Methods of Resonance Frequency
Shift of the Cantilever ..................... 208
17.2.3. Instrumentation of the Frequency
Modulation Detection Mode ................... 210
17.2.4. Frequency Modulation Detector ............... 212
17.2.5. Phase-Locked-Loop Frequency Modulation
Detector .................................... 212
17.2.6. Relationship Between Frequency Shift and
Interaction Force ........................... 214
17.2.7. Inversion of Measured Frequency Shift to
Interaction Force ........................... 216
17.3. Noise in Frequency Modulation Atomic Force
Microscopy .......................................... 217
17.3.1. Thermal Noise Drive ......................... 217
17.3.2. Minimum Detectable Force in Static Mode ..... 218
17.3.3. Minimum Detectable Force Using the
Amplitude Modulation Detection Method ....... 218
17.3.4. Minimum Detectable Force Using the
Frequency Modulation Detection Method ....... 219
17.3.5. Effect of Displacement-Sensing Noise
on Minimum Detectable Force ................. 220
17.3.6. Comparison of Minimum Detectable Force
for Static Mode and Dynamic Modes ........... 223
17.4. High-Resolution Imaging of Organic Molecules
in Various Environments ............................. 225
17.4.1. Alkanethiol Self-Assembled Monolayers ....... 225
17.4.2. Submolecular-Scale Contrast in Copper
Phthalocyanines ............................. 228
17.4.3. Atomic Force Microscopy Imaging
in Liquids .................................. 230
17.5. Investigations of Molecular Properties .............. 233
17.5.1. Surface Potential Measurements .............. 233
17.5.2. Energy Dissipation Measurements ............. 241
17.6. Summary and Outlook ................................. 243
References ................................................ 244
18. Noncontact Atomic Force Microscopy
Yasuhiro Sugawara ...................................... 247
18.1. Introduction ........................................ 247
18.2. NC-AFM System the Using FM Detection Method ......... 247
18.3. Identification of Subsurface Atom Species ........... 249
18.4. Tip-Induced Structural Change on a Si(001)
Surface at 5 К ...................................... 251
18.5. Influence of Surface Stress on Phase Change
in the Si(001) Step at 5 К .......................... 252
18.6. Origin of Anomalous Dissipation Contrast on
a Si(001) Surface at 5 К ............................ 253
18.7. Summary ............................................. 254
References ................................................ 255
19. Tip-Enhanced Spectroscopy for Nano Investigation
of Molecular Vibrations
Norihiko Hayazawa, Yuika Saito ......................... 257
19.1. Introduction ........................................ 257
19.2. TERS (Reflection and Transmission Modes) ............ 258
19.2.1. Experimental Configuration of TERS .......... 258
19.2.2. Transmission Mode ........................... 259
19.2.3. Reflection Mode ............................. 260
19.3. How to Fabricate the Tips? .......................... 261
19.3.1. Vacuum Evaporation and Sputtering
Technique ................................... 261
19.3.2. Electroless Plating ......................... 261
19.3.3. Etching of Metal Wires Followed by
Focused Ion Beam Milling .................... 262
19.3.4. Other Methods ............................... 263
19.4. Tip-Enhanced Raman Imaging .......................... 263
19.4.1. Selective Detection of Different Organic
Molecules ................................... 264
19.4.2. Observation of Single-Walled
Carbon Nanotubes ............................ 265
19.5. Polarization-Controlled TERS ........................ 268
19.5.1. Polarization Measurement by Using a
High NA Objective Lens ...................... 268
19.5.2. Metallized Tips and Polarizations ........... 269
19.5.3. Example of p- and s-Polarization
Measurements in TERS ........................ 271
19.6. Reflection Mode for Opaque Samples .................. 272
19.6.1. TERS Spectra of Strained Silicon ............ 272
19.6.2. Nanoscale Characterization of
Strained Silicon ............................ 274
19.7. For Higher Spatial Resolution ....................... 275
19.7.1. Tip-Pressurized Effect ...................... 275
19.7.2. Nonlinear Effect ............................ 278
19.8. Conclusion .......................................... 282
References ................................................ 283
20. Investigating Individual Carbon Nanotube/Polymer
Interfaces with Scanning Probe Microscopy
Asa H. Barber, H. Daniel Wagner, Sidney R. Cohen ....... 287
20.1. Mechanical Properties of Carbon-Nanotube
Composites .......................................... 288
20.1.1. Introduction ................................ 288
20.1.2. Mechanical Properties of Carbon
Nanotubes ................................... 288
20.1.3. Carbon-Nanotube Composites .................. 290
20.2. Interfacial Adhesion Testing ........................ 292
20.2.1. Historical Background ....................... 292
20.2.2. Shear-Lag Theory ............................ 293
20.2.3. Kelly-Tyson Approach ........................ 294
20.2.4. Single-Fiber Tests .......................... 294
20.3. Single Nanotube Experiments ......................... 296
20.3.1. Rationale and Motivation .................... 296
20.3.2. Drag-out Testing (Ex Situ Technique) ........ 297
20.3.3. Pull-out Testing (In Situ) .................. 298
20.3.4. Comparison of In Situ and Ex Situ
Experiments ................................. 304
20.3.5. Wetting Experiments ......................... 306
20.4. Implication of Results and Comparison with
Theory .............................................. 311
20.4.1. Interfaces in Engineering Composites ........ 311
20.4.2. Simulation of Carbon-Nanotube/Polymer
Interfacial Adhesion Mechanisms ............. 312
20.4.3. Discussion of Potential Bonding
Mechanisms at the Interface ................. 314
20.5. Complementary Techniques ............................ 314
20.5.1. Raman Spectroscopy .......................... 314
20.5.2. Scanning Electron Microscopy ................ 316
20.5.3. Overall Conclusions ......................... 320
References ................................................ 320
Subject Index ................................................. 325
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