Third Edition Of Introduction To Scanning Tunneling Microscopy

Third Edition of Introduction to Scanning Tunneling MicroscopyThe first edition of Introduction to Scanning Tunneling Microscopy was published in 1993. Itsoon became the standard reference book and graduate-level textbook of the field. The secondedition 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 scanningtunneling microscopy: Using a tip functionalized by a CO molecule to image molecules laid on aNaCl insulated substrate, the details of the molecular wavefunctions, especially the nodalstructures, are directly observed. It provides an intuitive understanding of the basic elements ofthe atomic world: The wavefunctions become an observable objective reality. The discovery wasverified by large number of follow-up publications. A third edition is justified for including therecent 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 EditionTen years have passed since the publication of the second edition of Introduction of ScanningTunneling Microscopy (STM). Significant advances in this research field have been made duringthat decade. One of the most important advances is the direct observation of the nodal structurein 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 thediscovery "will help future generations of chemists in obtaining an intuitive understanding ofmolecular properties that will guide them to novel solutions in all areas of chemistry". Thatadvance came out from two breakthroughs:The first breakthrough took place around 1997, when a group at FU Berlin discovered a reliablemethod 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 metalsurface. The oxygen atom is always pointing outwards. STM images with a CO-functionalizedtip showed dramatic difference to the images obtained with a metal tip. However, the nature ofthe enhanced resolution was not understood at that time.The second breakthrough came about 2005 when a group at IBM Zurich Laboratory discovered amethod to image organic molecules in pristine state using STM by separating the molecule andthe metal substrate with an ultrathin film of insulator, typically NaCl [5]. By using differentbiases, images of highest occupied molecular orbital (HOMO) and lowest unoccupied molecularorbital (LUMO) are clearly observed, which agrees with the overall charge density contours ofthose wavefunctions calculated using density-functional methods.It is natural to try to image pristine organic molecules by a CO-functionalized STM tip. Ithappened in 2011 with a miracle [1, 2]. The STM images did not resemble the charge densitycontour 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 molecularwavefunctions became directly observed by experiments. The discovery was attributed to the pxand py states at the oxygen end of the CO molecule [1, 2]. To verify the imaging mechanism, anumber 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 forcemicrocopy (AFM) and inelastic electron tunneling spectroscopy (IETS) experiments using COfunctionalized tips were conducted. The observed sub-molecular features have been attributed tomechanical effects due to the flexibility of the linear-molecule tip [11-15]. However, the STMimages cannot be solely attributed to the effect of Newtonian mechanics. Quantum-mechanicaleffects, described by the derivative rule, always dominate [16-17].

Recognizing that the observation of details in molecular orbital is one of the most significantadvances 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 andexperimental study of the role of p-waves of CO molecules on the STM tip. Two reports werepublished on Physical Review B in 2016 and 2017. Four cases were studied: a Cu tip and a Cusample, 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 adonut, respectively. The predictions were beautifully confirmed by careful theoreticalcomputations and STM/AFM experiments [18-19].The main purpose of the third edition is to include the above new developments. The mostsignificant 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 TipTreatment chapter to cover References [2] and [3]. A new section Flexing of Linear Molecules isadded to the chapter of Nanomechanical Effects to cover References [11] through [15]. There areother 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, "HighResolution Molecular Orbital Imaging Using a p-wave STM Tip", Phys. Rev. Lett. 107, 086101(2011).[2] L. Bartels, "Viewpoint: Visualizing Quantum Mechanics", Physics 4, 64 (2011).[3] L. Bartels, G. Meyer, K. H. Rieder, "Controlled Vertical Manipulation of Single COMolecules 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 InsulatingFilms: 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 STMTopography 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 MolecularOrientation from Convoluted Orbitals", Phys. Rev. B 88, 035447 (2013).

[8] A. N. Chaika, "Visualization of Electron Orbitals in Scanning Tunneling Microscopy", JETPLetters, 99, 731-741 (2014).[9] G. Mandi, G. Teobaldi, and K. Palotas, "What is the Orientation of a Tip in a ScanningTunneling Microscope?", Progress in Surface Science, 90, 223-228 (2015).[10] G. Mandi and K. Palotas, "Chen's Derivative Rule Revisited: Role of Tip-OrbitalInterference 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 andChemical 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-STMImages 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 IntermolecularBonds", Phys. Rev. Lett., 113, 186102 (2014).[14] P. Hapala, G. Kichin, C. Wagner, F. S. Tautz, R. Temirov, and P. Jelinek, "Mechanism ofHigh-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 theInelastic 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 HighResolution STM Images with a Flexible Tip Apex", Phys. Rev. B 95, 045407 (2017).[17] P. Jelinek, "High-Resolution SPM Imaging of Organic Molecules with FunctionalizedTips", Journal of Physics: Condensed Matter, 29, 343022 (2017).[18] A. Gustafsson and M. Paulsson, " Scanning Tunneling Microscopy Current from LocalizedBasis Orbital Density Functional Theory", Phys. Rev. B 93, 115434 (2016).[19] A. Gustafsson, N. Okabayashi, A. Peronio, F. J. Giessibl, and M. Paulsson, "Analysis ofSTM Images with Pure and CO-Functionalized Tips: A First-Principles and ExperimentalStudy", 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 andConductance", Phys. Rev. Lett., 111, 106803 (2013).

Introduction to Scanning Tunneling MicroscopyThird Edition(Bold-faced items are new)Preface to the Third EditionPreface to the Second EditionPreface to the First EditionGalleryChapter 1: Overview1.1 The scanning tunneling microscope1.2 The concept of tunneling1.2.1 Transmission coefficient1.2.2 Semiclassical approximation1.2.3 The Landauer theory1.2.4 Tunneling conductance1.3 Probing electronic structure at atomic scale1.3.1 Experimental observations1.3.2 Origin of atomic resolution in STM1.3.3 Imaging Molecular Wavefunctions1.4 The atomic force microscope1.4.1 Atomic-scale imaging by AFM1.4.2 Role of covalent bonding in AFM imaging1.5 Illustrative applications1.5.1 Catalysis researchNi-Au catalyst for steam reformingUnderstand and improve the MoS2 catalyst1.5.2 Atomic-scale imaging at the liquid-solid interface1.5.3 Atom manipulation1.5.3 Molecule manipulation1.5. 5 Imaging and manipulating DNA using AFMImmobilization and imagingDNA manipulationDNA surgeryPart I PrinciplesChapter 2: Tunneling Phenomenon2.1 The metal--insulator--metal tunneling junction1

2.2 The Bardeen theory of tunneling2.2.1 One-dimensional case2.2.2 Tunneling spectroscopy2.2.3 Energy dependence of tunneling matrix elements2.2.4 Asymmetry in tunneling spectrum2.2.5 Three-dimensional case2.2.6 Error estimation2.2.7 Wavefunction correction2.2.8 The transfer-Hamiltonian formalism2.2.9 The tunneling matrix2.2.10 Relation to the Landauer theory2.3 Inelastic tunneling2.3.1 Experimental facts2.3.2 Frequency condition2.3.3 Effect of finite temperature2.4 Spin-polarized tunneling2.4.1 General formalism2.4.2 The spin-valve effect2.4.3 Experimental observationsChapter 3: Tunneling Matrix Elements3.1 Introduction3.2 Tip wavefunctions3.2.1 General form3.2.2 Tip wavefunctions as Green's functions3.3 The derivative rule in spherical coordinates3.3.1 s-wave tip state3.3.2 p-wave tip states3.3.3 d-wave tip states3.3.4 Complex tip states3.4 The derivative rule: general case3.4.1 Tunneling problem in general curvilinear coordinates3.4.2 The sum rule and the derivative rule3.4.3 Case of spherical coordinates3.5 Derivative rule in parabolic coordinates3.6 Derivative rule with coordinate transformation (Ref. 10)3.7 Correlation with LCAO representation (Ref. 14)Chapter 4: Atomic Forces4.1 Van der Waals force4.1.1 The van der Waals equation of state4.1.2 The origin of van der Waals force4.1.3 Van der Waals force between a tip and a sample4.2 Hard-core repulsion4.3 The ionic bond4.4 The covalent bond: The concept2