Third Edition of Introduction to Scanning Tunneling Microscopy The first edition of Introduction to Scanning Tunneling Microscopy was published in 1993. It soon became the standard reference book and graduate-level textbook of the field. The second edition was published in 2007. The accumulated citations is 2078, see the figure below. In 2011, a group at IBM Zurich Research Center made a breakthrough discovery in scanning tunneling microscopy: Using a tip functionalized by a CO molecule to image molecules laid on a NaCl insulated substrate, the details of the molecular wavefunctions, especially the nodal structures, are directly observed. It provides an intuitive understanding of the basic elements of the atomic world: The wavefunctions become an observable objective reality. The discovery was verified by large number of follow-up publications. A third edition is justified for including the recent discoveries. A book contract was signed by Oxford University Press on May 8, 2019. Attached are the Preface and the Table of Contents of the third edition.
Transcript
Third Edition of Introduction to Scanning Tunneling Microscopy
The first edition of Introduction to Scanning Tunneling Microscopy was published in 1993. It soon became the standard reference book and graduate-level textbook of the field. The second edition was published in 2007. The accumulated citations is 2078, see the figure below.
In 2011, a group at IBM Zurich Research Center made a breakthrough discovery in scanning tunneling microscopy: Using a tip functionalized by a CO molecule to image molecules laid on a NaCl insulated substrate, the details of the molecular wavefunctions, especially the nodal structures, are directly observed. It provides an intuitive understanding of the basic elements of the atomic world: The wavefunctions become an observable objective reality. The discovery was verified by large number of follow-up publications. A third edition is justified for including the recent discoveries. A book contract was signed by Oxford University Press on May 8, 2019.
Attached are the Preface and the Table of Contents of the third edition.
Preface to the Third Edition
Ten years have passed since the publication of the second edition of Introduction of Scanning Tunneling Microscopy (STM). Significant advances in this research field have been made during that decade. One of the most important advances is the direct observation of the nodal structure in single molecular wave functions in its pristine state using a CO-functionalized STM tip [1]. That publication was reviewed by a Viewpoint article in Physics [2], which commented that the discovery "will help future generations of chemists in obtaining an intuitive understanding of molecular properties that will guide them to novel solutions in all areas of chemistry". That advance came out from two breakthroughs:
The first breakthrough took place around 1997, when a group at FU Berlin discovered a reliable method to transfer CO molecules from a Cu sample surface to a STM tip and vice versa [3, 4]. When a CO molecule is transferred, the carbon atom is always directly attached to the metal surface. The oxygen atom is always pointing outwards. STM images with a CO-functionalized tip showed dramatic difference to the images obtained with a metal tip. However, the nature of the enhanced resolution was not understood at that time.
The second breakthrough came about 2005 when a group at IBM Zurich Laboratory discovered a method to image organic molecules in pristine state using STM by separating the molecule and the metal substrate with an ultrathin film of insulator, typically NaCl [5]. By using different biases, images of highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) are clearly observed, which agrees with the overall charge density contours of those wavefunctions calculated using density-functional methods.
It is natural to try to image pristine organic molecules by a CO-functionalized STM tip. It happened in 2011 with a miracle [1, 2]. The STM images did not resemble the charge density contour at all, but resemble the squares of the lateral derivatives of the molecular wavefunctions, which peak at the nodal planes of the molecular wavefunctions. The nodal structure of molecular wavefunctions became directly observed by experiments. The discovery was attributed to the px and py states at the oxygen end of the CO molecule [1, 2]. To verify the imaging mechanism, a number of theoretical studies on the subject of derivative rule were published [6-10].
Motivated by the success of STM experiments with CO-functionalized tip, many atomic force microcopy (AFM) and inelastic electron tunneling spectroscopy (IETS) experiments using CO-functionalized tips were conducted. The observed sub-molecular features have been attributed to mechanical effects due to the flexibility of the linear-molecule tip [11-15]. However, the STM images cannot be solely attributed to the effect of Newtonian mechanics. Quantum-mechanical effects, described by the derivative rule, always dominate [16-17].
Recognizing that the observation of details in molecular orbital is one of the most significant advances in STM history, and the importance to understand the role of functionalized STM tips, such as a CO molecule, a group at Linnaeus University did a large-scale theoretical and experimental study of the role of p-waves of CO molecules on the STM tip. Two reports were published on Physical Review B in 2016 and 2017. Four cases were studied: a Cu tip and a Cu sample, a CO tip and a Cu sample, a Cu tip and a CO sample, and a CO tip and CO sample. According to the derivative rule in STM imaging, the images should be either like a bun or a donut, respectively. The predictions were beautifully confirmed by careful theoretical computations and STM/AFM experiments [18-19].
The main purpose of the third edition is to include the above new developments. The most significant addition is a new chapter, Imaging Molecular Wavefunctions to cover References [1] through [10], and [16] through [19]. A new section Tip Functionalizing is added to the Tip Treatment chapter to cover References [2] and [3]. A new section Flexing of Linear Molecules is added to the chapter of Nanomechanical Effects to cover References [11] through [15]. There are other minor additions as well. See the attached Table of Contents for details.
News References:
[1] L. Gross, N. Moll, F. Mohn, A. Curioni, G. Meyer, F. Hanke, and M. Person, "High-Resolution Molecular Orbital Imaging Using a p-wave STM Tip", Phys. Rev. Lett. 107, 086101 (2011).
[3] L. Bartels, G. Meyer, K. H. Rieder, "Controlled Vertical Manipulation of Single CO Molecules with the Scanning Tunneling Microscope: A Route to Chemical Contrast", Appl. Phys. Lett. 71, 213 (1997).
[4] L. Bartels, G. Meyer, K. H. Rieder, D. Velic, E. Knoesel, A. Hotzel, M. Wolf, and G. Ertl, "Dynamics of Electron-Induced Manipulation of Individual CO Molecules on Cu(111)", Phys. Rev. Lett. 80 (9), 2004-2007 (1998).
[5] J. Repp, G. Meyer, S. M. Stojkovic, A. Gourdon, and C. Joachim, "Molecules on Insulating Films: Scanning Tunneling Microscopy Imaging of Individual Molecular Orbitals", Phys. Rev. Lett. 94, 026803 (2005).
[6] B. Siegert, A. Donarini, and M. Grifoni, "The Role of Tip Symmetry on the STM Topography of π-Conjugated Molecules", Phys. Status Solidi. B 250, 2444-2451 (2013).
[7] A. J. Lakin, C. Chiutu, A. M. Sweetman, P. Moriaty, and J. L. Dunn, "Recovering Molecular Orientation from Convoluted Orbitals", Phys. Rev. B 88, 035447 (2013).
[8] A. N. Chaika, "Visualization of Electron Orbitals in Scanning Tunneling Microscopy", JETP Letters, 99, 731-741 (2014).
[9] G. Mandi, G. Teobaldi, and K. Palotas, "What is the Orientation of a Tip in a Scanning Tunneling Microscope?", Progress in Surface Science, 90, 223-228 (2015).
[10] G. Mandi and K. Palotas, "Chen's Derivative Rule Revisited: Role of Tip-Orbital Interference is STM", Phys. Rev. B 91, 165406 (2015).
[11] C. I. Chang, C. Xu, Z. Han, and W. Ho, "Real-Space Imaging of Molecular Structure and Chemical Bonding by Single-MoleculeInelastic Tunneling Probe", Science, 344, 885 (2014).
[12] P. Hapala, R. Temirov, F. S. Tautz, and P. Jelinek, "Origin of High-Resolution IETS-STM Images of Organic Molecules with Functionalized Tips", Phys. Rev. Lett., 113, 226101 (2014).
[13] S. K. Hamalainen, N. van der Heijden, J. van der Lit, S. den Hartog, P. Liljeroth, and I. Swart, "Intermolecular Contrast in Atomic Force Microscopy Images without Intermolecular Bonds", Phys. Rev. Lett., 113, 186102 (2014).
[14] P. Hapala, G. Kichin, C. Wagner, F. S. Tautz, R. Temirov, and P. Jelinek, "Mechanism of High-Resolution STM/AFM Imaging with Functionalized Tips", Phys. Rev. B 90, 084521 (2014).
[15] B. de la Torre, M. Svec, G. Foti, O. Krejci, P. Hapala, A. Garcia-Lekue, T. Frederiksan, R. Zhoril, A. Arnau, H. Vazquez, and P. Jelinek, "Submolecular Resolution by Variation of the Inelastic Electron Tunneling Spectroscopy Amplitude and its Relation to the AFM/STM Signal", Phys. Rev. Lett., 119, 166001 (2017).
[16] O. Krejci, P. Hapala, M. Ondracek, and P. Jelinek, "Principles and Simulations of High-Resolution STM Images with a Flexible Tip Apex", Phys. Rev. B 95, 045407 (2017).
[17] P. Jelinek, "High-Resolution SPM Imaging of Organic Molecules with Functionalized Tips", Journal of Physics: Condensed Matter, 29, 343022 (2017).
[18] A. Gustafsson and M. Paulsson, " Scanning Tunneling Microscopy Current from Localized Basis Orbital Density Functional Theory", Phys. Rev. B 93, 115434 (2016).
[19] A. Gustafsson, N. Okabayashi, A. Peronio, F. J. Giessibl, and M. Paulsson, "Analysis of STM Images with Pure and CO-Functionalized Tips: A First-Principles and Experimental Study", Phys. Rev. B 96, 085415 (2017).
[20] Y. Sugimoto, M. Ondracek, M. Abe, P. Pou, S. Morita, R. Perez, F. Flores, and P. Jelinek, "Quantum Degeneracy in Atomic Point Contacts Revealed by Chemical Force and Conductance", Phys. Rev. Lett., 111, 106803 (2013).
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Introduction to Scanning Tunneling Microscopy
Third Edition
(Bold-faced items are new) Preface to the Third Edition Preface to the Second Edition Preface to the First Edition Gallery Chapter 1: Overview 1.1 The scanning tunneling microscope 1.2 The concept of tunneling 1.2.1 Transmission coefficient 1.2.2 Semiclassical approximation 1.2.3 The Landauer theory 1.2.4 Tunneling conductance 1.3 Probing electronic structure at atomic scale 1.3.1 Experimental observations 1.3.2 Origin of atomic resolution in STM 1.3.3 Imaging Molecular Wavefunctions 1.4 The atomic force microscope 1.4.1 Atomic-scale imaging by AFM 1.4.2 Role of covalent bonding in AFM imaging 1.5 Illustrative applications 1.5.1 Catalysis research Ni-Au catalyst for steam reforming Understand and improve the MoS2 catalyst 1.5.2 Atomic-scale imaging at the liquid-solid interface 1.5.3 Atom manipulation 1.5.3 Molecule manipulation 1.5. 5 Imaging and manipulating DNA using AFM Immobilization and imaging DNA manipulation DNA surgery Part I Principles Chapter 2: Tunneling Phenomenon 2.1 The metal--insulator--metal tunneling junction
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2.2 The Bardeen theory of tunneling 2.2.1 One-dimensional case 2.2.2 Tunneling spectroscopy 2.2.3 Energy dependence of tunneling matrix elements 2.2.4 Asymmetry in tunneling spectrum 2.2.5 Three-dimensional case 2.2.6 Error estimation 2.2.7 Wavefunction correction 2.2.8 The transfer-Hamiltonian formalism 2.2.9 The tunneling matrix 2.2.10 Relation to the Landauer theory 2.3 Inelastic tunneling 2.3.1 Experimental facts 2.3.2 Frequency condition 2.3.3 Effect of finite temperature 2.4 Spin-polarized tunneling 2.4.1 General formalism 2.4.2 The spin-valve effect 2.4.3 Experimental observations Chapter 3: Tunneling Matrix Elements 3.1 Introduction 3.2 Tip wavefunctions 3.2.1 General form 3.2.2 Tip wavefunctions as Green's functions 3.3 The derivative rule in spherical coordinates 3.3.1 s-wave tip state 3.3.2 p-wave tip states 3.3.3 d-wave tip states 3.3.4 Complex tip states 3.4 The derivative rule: general case 3.4.1 Tunneling problem in general curvilinear coordinates 3.4.2 The sum rule and the derivative rule 3.4.3 Case of spherical coordinates 3.5 Derivative rule in parabolic coordinates 3.6 Derivative rule with coordinate transformation (Ref. 10) 3.7 Correlation with LCAO representation (Ref. 14) Chapter 4: Atomic Forces 4.1 Van der Waals force 4.1.1 The van der Waals equation of state 4.1.2 The origin of van der Waals force 4.1.3 Van der Waals force between a tip and a sample 4.2 Hard-core repulsion 4.3 The ionic bond 4.4 The covalent bond: The concept
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4.4.1 Heisenberg's model of resonance 4.4.2 The hydrogen molecule-ion 4.4.3 Three regimes of interaction 4.4.4 Van der Waals force 4.4.5 Resonance energy as tunneling matrix element 4.4.6 Evaluation of the modified Bardeen integral 4.4.7 Repulsive force 4.5 The covalent bond: Many-electron atoms 4.5.1 The homonuclear diatomic molecules 4.5.2 The perturbation approach 4.5.3 Evaluation of the Bardeen Integral 4.5.4 Comparison with experimental data Chapter 5: Atomic Forces and Tunneling 5.1 The principle of equivalence 5.2 General theory 5.2.1 The double-well problem 5.2.2 Canonical transformation of the transfer Hamiltonian 5.2.3 Diagonizing the tunneling matrix 5.3 Case of a metal tip and a metal sample 5.3.1 Van der Waals force 5.3.2 Resonance energy between two metal electrodes 5.3.3 A measurable consequence 5.3.4 Repulsive force 5.4 Experimental verifications 5.4.1 An early experiment 5.4.2 Experiments with frequency-modulation AFM 5.4.3 Experiments with static AFM 5.4.4 Non-contact atomic force spectroscopy 5.4.5 The classical case of Si-Si junction (Ref 20) 5.5 Threshold resistance in atom manipulation Chapter 6: Nanometer-Scale Imaging 6.1 Types of STM and AFM images 6.2 The Tersoff--Hamann model 6.2.1 The concept 6.2.2 The original derivation 6.2.3 Profiles of surface reconstructions 6.2.4 Extension to finite bias voltages 6.2.5 Surface states: the concept 6.2.6 Surface states: STM observations 6.2.7 Heterogeneous surfaces 6.3 Limitations of the Tersoff--Hamann model
6.4 Imaging self-assembled films of organic molecules Chapter 7: Atomic-Scale Imaging
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7.1 Experimental facts 7.1.1 Universality of atomic resolution 7.1.2 Corrugation inversion 7.1.3 Tip-state dependence 7.1.4 Distance dependence of corrugation 7.2 Intuitive explanations 7.2.1 Sharpness of tip states 7.2.2 Phase effect 7.2.3 Arguments based on the reciprocity principle 7.3 Analytic treatments 7.3.1 A one-dimensional case 7.3.2 Surfaces with hexagonal symmetry 7.3.3 Corrugation inversion 7.3.4 Profiles of atomic states as seen by STM 7.3.5 Independent-orbital approximation 7.4 First-principles studies: tip electronic states 7.4.1 W clusters as STM tip models 7.4.2 Density-functional study of a W--Cu STM junction 7.4.3 Transition-metal pyramidal tips 7.4.4 Transition-metal atoms adsorbed on W slabs 7.5 First-principles studies: the images 7.5.1 Transition-metal surfaces 7.5.2 Atomic corrugation and surface waves 7.5.3 Atom-resolved AFM images 7.6 Spin-polarized STM 7.7 Chemical identification of surface atoms 7.8 The principle of reciprocity Chapter 8: Imaging Wavefunctions 8.1 Experimental condition to image pristine wavefunctions 8.1.1 Conditions to observe molecules (Ref. 5) 8.1.2 The NaCl buffer layer (Ref. 5) 8.2 Imaging HOMO and LUMO states (Ref 5) 8.3 Imaging using functionalized tips (Ref. 1-10) 8.3.1 CO-functionalized tip 8.3.2 Scanning hydrogen microcopy 8.3.3 Other functionalizing items 8.4 Imaging mechanism studies (Ref. 18,19) 8.4.1 First-principle computations (Ref. 18) 8.4.2 Experimental verifications (Ref. 19) Chapter 9: Nanomechanical Effects 9.1 Mechanical stability of the tip--sample junction 9.1.1 Experimental observations 9.1.2 Condition of mechanical stability 9.1.3 Relaxation and the apparent G~z relation
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9.2 Mechanical effects on observed corrugations 9.2.1 Soft surfaces 9.2.2 Hard surfaces 9.2.3 First-principles simulations 9.2.4 Advanced topics 9.2.5 The Pethica mechanism 9.3 Effects of tip flexibility (Ref. 12-17) 9.3.1 Experimental observations (Ref. 11-13) 9.3.2 The Probe Particle model (Ref. 12) 9.3.3 Compare with AFM and IETS experiments 9.3.4 Effect to STM measurements (Ref. 16) 9.4 Force in tunneling-barrier measurements Part II Instrumentation Chapter 10: Piezoelectric Scanner 10.1 Piezoelectricity 10.1.1 Piezoelectric effect 10.1.2 Inverse piezoelectric effect 10.2 Piezoelectric materials in STM and AFM 10.2.1 Quartz 10.2.2 Lead zirconate titanate ceramics Curie point Temperature dependence of piezoelectric constants Depoling field Mechanical quality number Coupling constants Aging 10.3 Piezoelectric devices in STM and AFM 10.3.1 Tripod scanner 10.3.2 Bimorph 10.4 The tube scanner 10.4.1 Deflection 10.4.2 In situ testing and calibration 10.4.3 Resonant frequencies Stretching mode Bending mode 10.4.4 Tilt compensation: the s-scanner 10.4.5 Repolarizing a depolarized tube piezo 10.5 The shear piezo 265 Chapter 11: Vibration Isolation 11.1 Basic concepts 11.2 Environmental vibration 11.2.1 Measurement method 11.2.2 Vibration isolation of the foundation
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11.3 Vibrational immunity of STM 11.4 Suspension-spring systems 11.4.1 Analysis of two-stage systems 11.4.2 Choice of springs 11.4.3 Eddy-current damper 11.5 Pneumatic systems Chapter 12: Electronics and Control 12.1 Current amplifier 12.1.1 Johnson noise and shot noise 12.1.2 Frequency response 12.1.3 Microphone effect 12.1.4 Logarithmic amplifier 12.2 Feedback circuit 12.2.1 Steady-state response 12.2.2 Transient response 12.3 Computer interface 12.3.1 Automatic approaching Chapter 13: Mechanical design 13.1 The louse 13.2 The pocket-size STM 13.3 The single-tube STM 13.4 The Besocke-type STM: the beetle 13.5 The walker 13.6 The kangaroo 13.7 The Inchworm 13.8 The match Chapter 14: Tip Treatment 14.1 Introduction 14.2 Electrochemical tip etching 14.3 Ex situ tip treatments 14.3.1 Annealing 14.3.2 Field evaporation and controlled deposition 14.3.3 Annealing with a field 14.3.4 Atomic metallic ion emission 14.3.5 Field-assisted reaction with nitrogen 14.4 In situ tip treatments 14.4.1 High-field treatment 14.4.2 Controlled collision 14.5 Tip functionalization (Ref. 3,4) 14.5.1 Attach atoms 14.5.2 Attach molecules 14.6 Tip treatment for spin-polarized STM 14.6.1 Coating the tip with ferromagnetic materials
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14.6.2 Coating the tip with antiferromagnetic materials 14.6.3 Controlled collision with magnetic surfaces 14.7 Tip preparation for electrochemistry STM Part III: Extensions Chapter 15: Scanning Tunneling Spectroscopy 15.1 Electronics for scanning tunneling spectroscopy 15.2 Nature of the observed tunneling spectra 15.3 Tip treatment for spectroscopy studies 15.3.1 Annealing 15.3.2 Controlled collision with a metal surface 15.4 The Feenstra parameter 15.5 Determination of the tip DOS 15.5.1 Ex situ methods 15.5.2 In situ methods 15.6 Inelastic scanning tunneling spectroscopy 15.6.1 Instrumentation 15.6.2 Effect of finite modulation voltage 15.6.3 Experimental observations Chapter 16: Atomic Force Microscopy 16.1 Static mode and dynamic mode 16.2 The cantilever 16.2.1 Basic requirements 16.2.2 Fabrication 16.3 Static force detection 16.3.1 Optical beam deflection 16.3.2 Optical interferometry 16.4 Tapping-mode AFM 16.4.1 Acoustic actuation in liquids 16.4.2 Magnetic actuation in liquids 16.5 Non-contact AFM 16.5.1 Case of small amplitude 16.5.2 Case of finite amplitude 16.5.3 Response function for frequency shift 16.5.4 Second harmonics 16.5.5 Average tunneling current 16.5.6 Implementation Appendix A: Green's Functions Appendix B: Real Spherical Harmonics Appendix C: Spherical Modified Bessel Functions
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Appendix D: Plane Groups and Invariant Functions D.1 A brief summary of plane groups D.2 Invariant functions Plane group pm Plane group p2gm Plane group p2mm Plane group p4mm Plane group p6mm Appendix E: Elementary Elasticity Theory E.1 Stress and strain E.2 Small deflection of beams E.3 Vibration of beams E.4 Torsion E.5 Helical springs E.6 Contact stress: The Hertz formulas
