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Supramolecular organisation, conformation and electronic properties of porphyrin molecules on metal substrates Weber, Alexander 2007

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Supramolecular organisation, conformation and electronic properties of porphyrin molecules on metal substrates by Alexander Weber B.Sc., University of Konstanz, 2001 M.Sc., Portland State University, 2003 M.Sc., University of British Columbia, 2005 A THESIS SUBMITTED IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY in The Faculty of Graduate Studies (Physics) THE UNIVERSITY OF BRITISH COLUMBIA November 28, 2007 c Alexander Weber, 2007  ii  Abstract The investigation and control of molecular properties is currently a dynamic research field. Here I present molecular level studies of porphyrin molecules adsorbed on metal surfaces via Low Temperature Scanning Tunneling Microscopy/Spectroscopy (STM/STS), supported by complementary X-ray absorption experiments. Intermolecular and molecule-surface interactions of tetrapyrdil porphyrin (TPyP) on Ag(111) and Cu(111) were investigated. TPyP self-assembles on Ag(111) over a wide sample temperature range into large, highly-ordered 2D chiral domains. By contrast, adsorption of TPyP on the more reactive Cu(111) leads to temperature dependent assemblies, governed decisively by the strong substrate influence. The increased metalsurface interactions on Cu(111) are accompanied by a conformational distortion of the porphyrin macrocycle. The TPyP’s pyridil groups were coordinated with single iron molecules, forming metal-organic complexes. Furthermore, the porphyrin’s macrocycle was metalated by exposing a layer of well-ordered TPyP to an iron atom beam, demonstrating a novel approach towards the fabrication of metallo-tetraaryl porphyrins performed in two dimensions under ultrahigh vacuum conditions. This method was similarly used to form lanthanide porphyrinates by coordinating tetraphenyl porphyrin (TPP) macrocycles with cerium. The influence of the metal center on the porphyrins’ electronic structure was investigated via STS for TPP, TPyP,  Abstract  iii  Fe−TPyP, Fe−TPP, Ce−TPP, and Co−TPP, whereby the in-homogenous electron density distribution associated with individual frontier orbitals were imaged via dI/dV mapping. The symmetry and form of the molecular orbitals could be directly correlated to the saddle-shaped conformational adaptation for the case of Co−TPP.  iv  Contents Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .  ii  Contents . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .  iv  List of Figures . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . viii Acknowledgements . . . . . . . . . . . . . . . . . . . . . . . . . . .  xi  1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .  1  2 Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 3 Experiment and Theory . . . . . . . . . . . . . . . . . . . . . . 21 3.1  Scanning Tunneling Microscopy . . . . . . . . . . . . . . . . . 21 3.1.1  Operation Mode  . . . . . . . . . . . . . . . . . . . . . 22  3.2  STM Theory  3.3  Scanning Tunnelling Spectroscopy . . . . . . . . . . . . . . . . 33  3.4  Investigating Molecules with STM and STS . . . . . . . . . . 43 3.4.1  . . . . . . . . . . . . . . . . . . . . . . . . . . . 25  Molecular Manipulation . . . . . . . . . . . . . . . . . 51  3.5  Simulating STM Images . . . . . . . . . . . . . . . . . . . . . 54  3.6  Experimental Set-Up . . . . . . . . . . . . . . . . . . . . . . . 57 3.6.1  STM . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57  Contents  3.7  v  3.6.2  UHV System . . . . . . . . . . . . . . . . . . . . . . . 61  3.6.3  Tip and sample preparation . . . . . . . . . . . . . . . 65  X-ray Absorption Techniques . . . . . . . . . . . . . . . . . . 69 3.7.1  X-ray Photoelectron Spectroscopy (XPS) . . . . . . . . 69  3.7.2  Near-Edge X-ray Absorption Fine Structure (NEXAFS) Spectroscopy . . . . . . . . . . . . . . . . . . . . . . . 73  4 TPyP absorbed on Ag(111) . . . . . . . . . . . . . . . . . . . . 78 4.1  Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78 4.1.1  4.2  4.3  Experimental Section . . . . . . . . . . . . . . . . . . . 82  Results and Discussion . . . . . . . . . . . . . . . . . . . . . . 83 4.2.1  Two-Dimensional Self-Assembly . . . . . . . . . . . . . 83  4.2.2  Molecular Imaging and Conformation . . . . . . . . . . 91  Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93  5 TPyP absorbed on Cu(111) . . . . . . . . . . . . . . . . . . . . 96 5.1  Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 97  5.2  Experimental Section . . . . . . . . . . . . . . . . . . . . . . . 100  5.3  Results and Discussion . . . . . . . . . . . . . . . . . . . . . . 102 5.3.1  Temperature-Dependent Molecular Ordering and Appearance . . . . . . . . . . . . . . . . . . . . . . . . . . 102  5.4  5.3.2  Molecular Conformation and Chemical State . . . . . . 105  5.3.3  Role of Adatoms and Metal-Ligand Interactions . . . . 118  Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121  6 Conformational Adaptation of TPyP on Cu(111) . . . . . . 123 6.1  Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 124  Contents  vi  6.2  Experimental Section . . . . . . . . . . . . . . . . . . . . . . . 128  6.3  Results and Discussion . . . . . . . . . . . . . . . . . . . . . . 129  6.4  6.3.1  Molecular Appearance and Adsorption Site . . . . . . . 129  6.3.2  Molecular Conformation . . . . . . . . . . . . . . . . . 132  6.3.3  Reactivity Towards Metal Centers . . . . . . . . . . . . 139  Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140  7 Iron Metallation of TPyP on Ag(111) . . . . . . . . . . . . . . 144 7.1  Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144  7.2  Results and Discussion . . . . . . . . . . . . . . . . . . . . . . 146  7.3  Conclusions . . . . . . . . . . . . . . . . . . . . . . . . . . . . 155  7.4  Experimental Section . . . . . . . . . . . . . . . . . . . . . . . 157  8 TPP Complexation with Cerium . . . . . . . . . . . . . . . . . 159 8.1  Results and Discussion . . . . . . . . . . . . . . . . . . . . . . 160  8.2  Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 165  9 Visualizing Frontier Orbitals . . . . . . . . . . . . . . . . . . . 166 9.1  Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166  9.2  Results and Discussion . . . . . . . . . . . . . . . . . . . . . . 168  9.3  Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180  9.4  Experimental and Theoretical Section . . . . . . . . . . . . . . 180  10 Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182 11 Publication List . . . . . . . . . . . . . . . . . . . . . . . . . . . 186 Bibliography . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 188  vii  List of Figures 1.1  Schematics of Porphyrin Molecules . . . . . . . . . . . . . . . 12  3.1  Electron Tunneling . . . . . . . . . . . . . . . . . . . . . . . . 23  3.2  STM Operation Principle  3.3  Substrate Electronic Structure and Tunneling Current . . . . . 29  3.4  Tunneling into a Hydrogen Molecule . . . . . . . . . . . . . . 32  3.5  Bias−dependent Imaging of TPyP . . . . . . . . . . . . . . . . 46  3.6  High Resolution Imaging with CO Modified Tip . . . . . . . . 48  3.7  CO Molecule on Cu(111) . . . . . . . . . . . . . . . . . . . . . 49  3.8  Manipulation of single CO Molecules on Cu(111) . . . . . . . 53  3.9  Besocke-type STM . . . . . . . . . . . . . . . . . . . . . . . . 58  . . . . . . . . . . . . . . . . . . . . 26  3.10 LT−STM . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60 3.11 He Bath Cryostat . . . . . . . . . . . . . . . . . . . . . . . . . 62 3.12 Experimental Setup . . . . . . . . . . . . . . . . . . . . . . . . 64 3.13 Sample Holder . . . . . . . . . . . . . . . . . . . . . . . . . . . 65 3.14 Tip Etching . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66 3.15 X-ray Photoelectron Spectscopy . . . . . . . . . . . . . . . . . 71 3.16 X-ray Absorption . . . . . . . . . . . . . . . . . . . . . . . . . 75 4.1  Scheme of TPyP . . . . . . . . . . . . . . . . . . . . . . . . . 81  4.2  TPyP Self Assembled Layer on Ag(111 . . . . . . . . . . . . . 85  List of Figures  viii  4.3  Chiral Domains . . . . . . . . . . . . . . . . . . . . . . . . . . 86  4.4  Moir´e Pattern . . . . . . . . . . . . . . . . . . . . . . . . . . . 89  4.5  Molecular Mechanics Simulations . . . . . . . . . . . . . . . . 90  4.6  Bias-Dependent Imaging . . . . . . . . . . . . . . . . . . . . . 94  4.7  Dihedral Angle . . . . . . . . . . . . . . . . . . . . . . . . . . 95  5.1  Scheme of TPyP . . . . . . . . . . . . . . . . . . . . . . . . . 99  5.2  Temperature Dependent Assembly of TPyP on Cu(111) . . . . 104  5.3  NEXAFS Spectra of the N 1s Edge of TPyP . . . . . . . . . . 107  5.4  Spectral Deconvolution of the Leading N 1s Edge . . . . . . . 111  5.5  XPS of the TPyP’s N 1s Region . . . . . . . . . . . . . . . . . 114  5.6  Thermal and Bias-Induced Change of the TPyP Macrocycle . 117  5.7  Model of Cu Adatom Mediated TPyP Assembly . . . . . . . . 120  6.1  Scheme of TPyP . . . . . . . . . . . . . . . . . . . . . . . . . 127  6.2  Single TPyP Molecules Absorbed on Cu(111) . . . . . . . . . 131  6.3  Adsorption Site Determination . . . . . . . . . . . . . . . . . . 133  6.4  NEXAFS Spectra of the N 1s Edge . . . . . . . . . . . . . . . 135  6.5  Simulated STM Images . . . . . . . . . . . . . . . . . . . . . . 136  6.6  Selective Attachment of Fe Adatoms to the Pyridil Groups . . 141  7.1  Fe Atom Reacting with TPyP Macrocycle . . . . . . . . . . . 148  7.2  Full Fe-TPyP Array  7.3  Assembly and Height Profile of Fe-TPP . . . . . . . . . . . . . 151  7.4  Chemical Sensitivity through Bias-Dependent Imaging . . . . 154  7.5  Model of Metalation Reaction . . . . . . . . . . . . . . . . . . 156  . . . . . . . . . . . . . . . . . . . . . . . 150  List of Figures  ix  8.1  Decoration of H2-TPP Macrocycle with Cerium . . . . . . . . 162  8.2  Electronic Structure of H2-TPP, Co-TPP and Ce-TPP . . . . 164  9.1  Scheme of Co-TPP . . . . . . . . . . . . . . . . . . . . . . . . 170  9.2  NEXAFS Spectra of the C1s Edge of Co-TPP . . . . . . . . . 172  9.3  Visualizing Frontier Orbitals of Co-TPP . . . . . . . . . . . . 177  9.4  Electron density from Extended H¨ uckel Theory . . . . . . . . 178  x  Acknowledgements Many people accompanied and influenced me on my way to this point in my life and I am grateful to each of them. Especially for the support to complete this thesis I want to thank a series of persons. My supervisor Dr. J.V. Barth for his support and guidance, allowing me to develop my own ideas and approaches. Dr. G. Sawatzky for being an amazing source of answers to my questions in surface and solid state physics. The members of my PhD committee with Dr. T. Tiedje, Dr. W. Hardy, Dr. J. Folk, Dr. D. Bonn and Dr. G. Sawatzky for taking their time to read in detail about my work and giving me fruitful input, with Dr. T. Tiedje showing me also BCs beautiful peaks and Dr. W. Hardy for making AMPEL with his coffee room a cozy place to work in. Furthermore, I want to thank ”il gruppo sportivo”, the STM group with Dr. A. Riemann, Dr. W. Auw¨arter, A. Schiffrin, Dr. J Reichert, Dr. Y. Pennec, M. Marshall, G. , E, M. Eichberger, G. Jahnz and E.Varene. Special thanks for guidance I owe Dr. A. Riemann and Dr. W. Auw¨arter who built up with me the experiment and taught me systematic scientific working and for an excellent collaboration with the experiments we performed. Dr. F. Klappenberger for the support with the X-ray absorption experiments and long nights at BESSY and Dr. J. Reichert for the fun common work, discussions and reintroducing my passion for reading. Agustin Schiffrin I  Acknowledgements  xi  thank for perfectly mounted sample holders, to bring close the passion for soccer and especially for becoming a friend. The atmosphere in the STM group with the many nights we worked, to achieve some results, but also the many feasts we cooked together and the lab hikes made it a beautiful time for me − thank you. Dr. N. Ingle for his support, whether it was technical, or a piece of equipment was needed and his devotion supporting my independent studies. Dr. P. Wahl for teaching me tunneling spectroscopy in Dr. K. Kerns Nanoscale Science Department, Dr. T. Strunskus for technical support at the BESSY in Berlin and the BC synchrotron light source for trip financing. Dr. S. H¨ ufner for many XPS discussions, Kondo physics support and fun dinners. I thank also the German Academic Exchange Program (DAAD) for financing my entire PhD at UBC. Moreover, I am very grateful to the department of physics of the University of Konstanz, where several professors supported me and gave me opportunities to discover the research world at a very early stage in my studies. Last but certainly not least I want to thank my family Fulvia WeberBargioni, Frank Weber (Ihr seid grossartige Eltern) and Johannes Weber (danke f¨ ur super radausfahrten und Dein offenes Ohr), who were always a great mental support, giving me the confidence to pursue the goals I am dreaming of, (grazie anche per il cervello nonna) and especially Dr. Karen Peters, my future wife and soul mate, who is always there encouraging me. Thank you all!  Acknowledgements  xii  Co-authorship statement This thesis emerged from a research project, were I collaborated closely with two PostDocs Dr. Auw¨arter and Dr. Klappenberger. The experiments conducted within this collaboration and the framework of this thesis generated substantial novel results. Consequently it was decided together with our supervisor Dr. Barth to divide the outcome of certain experiments into several publications. To prepare these papers efficiently, chapters four to nine were written in form of publications in accordance with my PhD committee. The final published versions, which are based on the chapters presented here, carry alternating main authorships among the collaborators. Although chapter 4, 6 and 7 are the base for publications, where I am not the first author, all data acquisition including Scanning Tunneling Microscopy/Spectroscopy, Synchrotron Measurements and simulations (Extended Hu¨ckel Simulations, Molecular Mechanics) presented in this thesis were generated by myself or in direct collaboration. Furthermore, I was directly involved in all data analysis and manuscript generation of the publications presented in this work, therefore they are included in this thesis.  1  Chapter 1 Introduction Historically, the control over matter exerted a fascination on humanity, inter alia due to the correlation between the development of novel materials and technological advancement. A prominent example nowadays is the information technology, demonstrating the success of basic interdisciplinary material research working in strong entanglement with technological development. The urge of this industry to place ever increasing numbers of functional units per unit area, such as transistors or magnetic bits, obeyed surprisingly accurately over decades Moore’s law, formulated in the 60s by G. Moore, cofounder of Intel Corp., causing a persuasive incentive to find novel ways to scale down materials. This miniaturization is bound to extend into the nanometer regime, where the behavior of materials cannot be predicted from bulk characteristics. The properties of condensed matter are irrevocably determined by its electronic structure, since electrons are the ”glue”, holding atoms together to form molecules or condensed phases. In condensed matter the electrons’ boundary conditions influence the physical properties of a material. Upon decreasing the volume of an object towards the nanometer scale, the electron confinement changes and quantum mechanical effects begin to alter the physical properties of a material, which can express new qualities. Novel and intriguing phenomena at the nanometer scale, found in 2D graphene [1],  Chapter 1. Introduction  2  nanothin quantum wells [2] or molecular electronics model devices [3], have attracted a strong interest in research and technology, with the ultimate goal to control matter on the atomic and molecular scale. This development was accompanied by the advancement in experimental and theoretical tools, providing the opportunity to investigate, control and manipulate matter down to the level of single atoms [4]. Within the thermo-dynamical constraints, molecules and atoms can nowadays be arranged to predesigned shapes and chemical composition [5], arranging the electrons’ boundary conditions at the subnanometer scale. In supramolecular chemistry [6], molecules are used as non-covalent interacting building blocks [7, 8, 9, 10, 11]. In this field the specific interaction between two or more molecules through noncovalent bonding is exploited to engineer materials. These specific interaction are also referred to as molecular recognition driven by hydrogen bonding, metal coordination, hydrophilic forces, van der Waals forces, pi-pi interactions, and/or electrostatic effects. However, the concept of employing assemblies of complex molecules with distinct functionalities is not new. Nature has incorporated the use of molecules as building blocks to produce self-assembled nanostructured materials to perfection. Therefore, it is self-evident to start out studying and using nature’s complex molecules as building blocks and investigating their functionalities. The question then arises whether it is possible to steer the attributes of an entire assembly, by going beyond probing the functionality and selectively modifying building blocks, to alter their physical properties and therewith their functionalities. The functionality of a molecule alludes chemically on a specific arrange-  Chapter 1. Introduction  3  ment of atoms within a molecule, called functional group, which may be also used for specific non-covalent interactions. Prominent examples are the mediation of hydrogen [12, 13, 14] or metal ligand bonds [6, 15], leading to molecular recognition and to bond orientation specific interactions, enabling one to tailor exclusive nanostructures. However, the geometric arrangement of atoms within a molecule, called the molecular conformation, can already influence the functionality of a molecule. It determines bond characteristics of functional groups [16] and can be employed in enzymatic reactions, for example in the case of cobalt-porphyrins in Vitamin B12 [17, 18]. Certain groups adopt catalytic properties, mediating for example the bond synthesis of peptides [19]. Nevertheless, the definition of functionalities should be extended not only to its chemical but also physical properties, such as optical [20] or magnetic properties [21, 22], taking over distinct tasks in a biological or artificial system. This immense variety of possible properties led to molecular engineering, the creation of single molecules which may not exist in nature, exhibiting novel functionalities [23]. Another field of interest is conformational design, where the function of a molecule is altered by changing its conformation as is observed in nature [24, 25]. Finally, an ensemble of complex molecules may develop distinct characteristics for a given purpose, with one of the most prominent examples, being DNA, whose double helix is held together by hydrogen bonded nucleic acids, which carries the information for biological systems. The infinite number of molecules, with their large variety of attributes opens up an immense number of ways to engineer assemblies at the atomic  Chapter 1. Introduction  4  and molecular scale with unique, unprecedented properties. Therefore, it is crucial to understand the physical and chemical properties of individual molecules. Techniques to directly investigate single molecules are Scanning Probe Microscopy (SPM) [26, 27, 28], Molecular Conductance [29, 30], Optical Tweezers [31] and Single-Molecule Spectroscopy [32, 33, 34], reviewed by W.Ho [28]. One way to explore single molecules or small assemblies is to fix them on a substrate. Surfaces epitomize a boundary or interface towards another material, entailing a rich variety of physical phenomena due to the altered geometric and electronic structure. This will influence to some extent an adsorbate on a surface, possibly modifying its original properties, yet this interaction can be affected by the choice of substrate. Moreover, surfaces can be considered as additional investigative tools. They can be prepared with any degree of roughness down to atomically flat and atomically clean, and determining a well-defined environment for an adsorbate. Additionally, molecules can functionalize a surface and are therefore highly attractive for basic research on nanostructured surfaces as well as applications. Fields of potential use are molecular (opto-) electronics, chemical sensing, bio-nonbio interfaces as well as heterogeneous catalysis. This requires a meticulous understanding of the adsorbed molecules’ properties, and tools to investigate it. Many surface sensitive techniques have been developed, Scanning Tunneling Microscopy (STM) being amongst the most versatile. The capability of providing real space images of the surface’s atomic landscape as well as single atoms and molecules in their surface environment removes uncertainties of  Chapter 1. Introduction  5  the system under study and allows one to investigate characteristics of single molecules and atoms one by one. Since its invention in 1981 by Binning and Rohrer, STM has experienced a rapid development [35]. Its manipulation capabilities provided the possibility to touch atoms and molecules one at a time [36], control quantum states at the subnanometer scale [37], influencing single molecules [38] and further to form [39, 40] or dissociate [41, 42] distinct covalent bonds [28]. Scanning Tunneling Spectroscopy (STS) allows one to probe the local electronic structure with a spatial resolution on the atomic scale, giving insights into the electronic structure of surfaces [37] or adsorbates [43, 44] ±3 eV around the Fermi level. Inelastic Tunneling Spectroscopy (IETS), which probes the vibrational states of a molecule [45], can be used as an analytical tool to identify the chemical structure within a molecule [28, 46]. Variable temperature and Fast Scanning Tunneling Microscopes allow one to comprehend dynamic processes such as the mobility of single atoms [47] and molecules [48] on surfaces. The STM’s versatility is founded on its probing mechanism, tunneling electrons, one of the most prominent results of quantum theory. The detected data show an image of the surface, resulting from the convolution of the surface and the probing-tip’s electronic states, making the STM sensitive to the Density of States near the Fermi level [49]. However, STM is principally insensitive to the chemical structure of a surface. Like any experimental measurement, the STM requires an interaction of the probe with the sample and it is important to control and minimize the perturbations on the sample under investigation. How this can be addressed for particular cases will be discussed in the experimental section. Altogether  Chapter 1. Introduction  6  the STM is a powerful tool to explore surfaces, probing single molecules and atoms in their local environment and is therefore being widely used among researchers of different disciplines, playing a key role in the pursuit of nanostructuring and functionalized surfaces [50]. Another crucial technical development setting the basis for this surface science investigations, was the ultra high vacuum (UHV). Pressures below 10−10 mbar ensure no contamination of structures on the molecular or even atomic scale over the typical time a sample is studied (several hours) and guarantee a well-defined environment. Moreover, Low−Temperature STMs ensured high stability and access to physics at temperatures below 10 K. Nevertheless, it is possible to do highly interesting STM experiments in air or in electrochemical environments [51, 52]. There are various strategies for the implementation of nanostructured and functionalized surfaces, the classical being the top-down approach, where nano-objects are constructed from larger entities, via for example (Photo) lithography. In this process, light transfers a geometric pattern from a photomask onto a light sensitive material, which coats a surface. A series of chemical processes engraves the exposed pattern into the substrate underneath. However, structures below 50nm are hard to realize, become very costly and still do not achieve atomic-level control. On the other hand, there is the bottom-up approach where nanostructures are built up using atoms and complex molecules as building blocks. This can be achieved in two ways: one via atom by atom manipulation with an STM, a serial procedure, or by molecular self-assembly, a parallel procedure. The former is a very useful tool for basic research purposes on single  Chapter 1. Introduction  7  molecules or structures [53, 54] but it limits the number of structures built per time. While this approach is based on control over each single atom or molecule, an alternative tactic providing ensembles of nano structures is molecular self-assembly. Materials and devices are built from carefully chosen molecules with specific functional groups and characteristics, which spontaneously organize into low dimensional supramolecular structures, using the principles of molecular recognition [55, 56]. These molecules are in the community, researching self-assembled nano-sturctures, referred to as building blocks. Classically, a building block maintains its properties, independent of its environment. In the case of complex molecules used as building blocks, the original characteristics may alter due to their entourage. I will still refer to molecules in self-assembled structures as building blocks throughout my thesis, as it is the use in this community. However, it is important to keep in mind that the original properties of molecules may alter in an ensemble or absorbed on a surface. Molecular self-assembly on surfaces relies on the vast variety of functional groups, balancing inter-molecular and molecule-substrate interaction and leads to extensive two and three-dimensional supramolecular architectures on surfaces, which began to be systematically investigated only in recent years [5, 50]. The spatial arrangements of building blocks are determined by directional and selective intermolecular interactions. These bonds are typically metal-ligand interactions, hydrogen bonds, van der Waals or electrostatic interactions, depending on the nature of the functional groups employed and are weaker than typical covalent bonds [50]. This approach is very promising but still in its infancy. In order to tailor  Chapter 1. Introduction  8  successful and at large self-assembled structures with novel virtues, it is essential to understand specifically how individual molecules interact with their environment after being deposited on a surface. Of particular interest are the properties leading to distinct functionalities of the molecule and the degree of their modification on a surface. Characteristics of individual molecules which need to be investigated are primarily their nature of binding, their conformational adaptation, and their electronic structure. Adsorbate-substrate and inter-adsorbate interactions are the prominent influences. The bond strength to the substrate, whether it is strong, called chemisorption, or weaker, physisorption, determines amongst other things the modification of the molecule’s electronic structure [57, 58]. Also, different crystal orientations of an identical substrate can change the energy level alignments of an adsorbed species [59]. Accordingly, a strong shift of the energy levels can lead to charge transfers [60, 61], substantially altering the electronic structure. Decisive therefore is the work function (Φ) of the surface material (the energy to remove electrons from the surface), and the admolecule’s electron affinity (EA) (energy from the lowest unoccupied molecular orbital to the vacuum level) as well as the ionization potential (IP) (energy to detach a valence electron from the molecule). For organic/metal interfaces there exists the following rule of thumb: EA> Φ results in a charge transfer from the substrate to the adsorbate, IP< Φ charge transfer from adsorbate into the substrate. Nevertheless, this is just a rough estimate and depends on how the vacuum levels of molecule and substrate align, where dipole moments and image potentials can modify IP, EA and the local work function [62]. Furthermore, one needs to keep in mind that experimentally  Chapter 1. Introduction  9  determined IP and EN give out distorted energy values compared to their theoretical values for the molecule in the ground state, since the electronic charge on the molecule differs by 2 electrons between removal and addition of an electron in the experiments. The molecule-substrate interaction is determined by an attractive potential, which adds to the overall potential, steering the electronic structure and leading to electron level alignments. The redistribution of charges within a molecule can lead to conformational adaptation. This can be caused by covalent bonds, static forces due to polarized substrates or dipole-image charge interactions of an adsorbate on a metal substrate. The conformational adaptation is especially relevant for complex molecules with several internal degrees of freedom [63]. Conformational changes can also be reversible [64], or selectively induced with voltage pulses via an STM tip [65, 66, 67]. The structure and functionality of interfaces due to molecular conformation can be decisive for applications, such as opto-electronic devices [68, 69]. Interactions with the substrate can furthermore lead to the deprotonation of organic species [70], or even the dissociation of molecules [71] due to catalytic properties of the surface. These examples demonstrate that moleculesurface interactions can substantially modify the original properties of an adsorbate. But what about the adsorbate-adsorbate interplay? The main driving forces in the molecular self-assembly of biological systems are reversible weak interactions, which are selectively exploited to form surpamolecular architectures on metal surfaces [50]. Hydrogen bonds incorporate great flexibility due to their weak intermolecular interaction and yet have been successful candidates for highly organized networks [72, 73, 74].  Chapter 1. Introduction  10  For instance, one-dimensional molecular chains have been formed on the mesoscopic scale, determined by the chirality of the employed molecules in conjunction with substrate interactions, all mediated by hydrogen bonds [72]. By deprotonating the bond mediating functional groups, structural phase transitions of the assemblies have been observed. In some cases, hydrogen bonds were replaced by metal-ligand bonds, using adatoms from the substrate, which modifies the architectonic and bond strength of the assembly [75, 76]. The ligand bond between a metal and a polarized functional group of an organic molecule is often referred to as metal complex or the complexation of a molecule. These interactions were used to engineer a variety of extraordinary structures, linking two or multiple molecules by a metal adatom on metal surfaces [76, 77, 78]. The control of the complexation between an individual molecule and an adatom provides a highly interesting playground, modifying functionalities beyond the linking of neighboring molecules. The complexation with various metals alters the electronic structure of molecules [79]. Additionally, organic molecules can be imbued with a magnetic moment by choosing an appropriate transition metal or a rare earth [80, 81, 82, 83]. The concerted complexation of molecules could therewith open ways to specifically set the physical properties of individual molecules. Now, if a molecule with multiple functional groups is used, it should be possible to employ it as a building block for a supramolecular structure with one set of groups and additionally specify the network’s physical and chemical properties by the purposeful complexation of the unexploited functional units.  Chapter 1. Introduction  11  Porphyrin molecules are ideal candidates to study many of the possible, often entangled, properties on a surface, which may lead to novel functionalities. They are organic, complex species, featuring the macrocycle shown in Figure 1.1 that plays a key role in biological processes with a metal atom in its center [84]. This class of molecules exhibit three major properties. One is the macrocycle as chemical pocket, second, the possibility to attach various meso substituents to the macrocycle and third, its conformational flexibility to adapt to a local environment. The macrocycle with its nitrogen lone pairs can be regarded as a chemical pocket, in which various transition metal atoms can be incorporated. Iron porphyrin, for instance is the functional group of heme, providing the oxygen and carbon dioxide transport in blood. Cobalt porphyrin is the catalytically active group in Vitamin B12. Magnesium-porphyrin on the other hand, is the key in photosynthesis. These differing functions are also correlated with conformational changes induced by attached proteins, which define the intermediate environment of these porphyrins. Metallo-porphyrins are significant for life and reveal that the coordination with different metal centers alters the porphyrins’ physical and chemical properties. End-groups attached to the macrocycle represent the second basic virtue of these species. There is a vast variety of meso substituents, which can be utilized. Two examples are shown in Figure 1.1b and c, where pyridil groups attached to the macrocycle form Tetrapyrdil porphyrin (TPyP), whereas the use of phenyl groups forms Tetraphenyl porphyrin (TPP). Depending on the end-group attached, it should be possible to evoke different self-assembled structures. Furthermore, these meso substituents can influence the confor-  Chapter 1. Introduction  12  Figure 1.1: Schematics of Porphyrin Molecules  a) Schematics of the porphyrin macrocycle. The arrow indicates the flexibility of this backbone to adjust to its environment. The macrocycle can furthermore act as a chemical pocket, incorporating metal centers. Meso substituents can be attached, complementing the functionalities of porphyrin molecules. As examples Tetrapyridil porphyrin (b) and Tetraphenyl porphyrin (c) are illustrated. Both, pyridil and phenyl group can rotate around the σ-bond, influencing the conformation of the macrocycle. mation of the macrocycle. This conformational adaptation of porphyrins to their environment is considered their third feature and makes them candidates for conformational design [85]. As mentioned before their geometric structure can have direct influence on their functionalities. Several reports studying their conformation in conjunction with their functions in biological systems mentioned a saddleshaped macrocycle. These different attributes make porphyrins molecular multipurpose tools. Such versatile molecules draw a lot of attention to themselves. Dolphin  Chapter 1. Introduction  13  at UBC worked on and characterized a wide variety of porphyrins and established their use in medicine [84]. Three-dimensional supramolecular structures are another prominent area where metallo-porphy-rins were adopted. This is due to the possibility of bonding laterally over the meso substituents and bonding vertically, by coordinating over the metal center [6, 86]. Such supramolecular systems are candidates for artificial photosynthesis [87], solar cells [84, 88], optical switches [89], chemical sensors [90, 91], and catalysis [92]. Recently, the porphyrins’ large variety of properties have been exploited on surfaces. Their self-assembly into low dimensional supramolecular structures on metal surfaces was investigated via STM [63, 93, 94, 95, 96]. Further STM studies revealed the bias dependent appearance of metal-porphyrins on gold substrates [96] as well as tunneling induced light emission [97], indicating discrete energy levels around the Fermi level after adsorption. So far, only a few studies have focused on individual porphyrins and their physical and chemical properties to exploit systematically their rich potential to take over distinct functionalities [98]. Iancu et al. showed a Kondoeffect like signature of Co-Tetrakis-Bromophenyl- porphyrins (Co-TBPP) on Cu(111) in the electronic structure, affected by the number of next neighbor Co-TBPPs, implying single molecular magnetic behavior [99, 100]. Qiu used tunneling electrons to inelastically excite vibrational modes of individual porphyrins on an aluminum film, demonstrating that the vibrational states depend sensitively on the molecule’s conformation [20]. In order to explore functionalities and to manipulate molecules adsorbed on surfaces, STM is a powerful basic tool. However, complementary surface  Chapter 1. Introduction  14  sensitive techniques help to shed more light onto the systems under investigation. Such experimental tools are Near Edge X-ray Absorption Fine Structure (NEXAFS) and X-ray Standing Wave technique (XSW), used to determine the surface structure, including the conformation of adsorbed molecules, X-ray Photoelectron Spectroscopy (XPS) and Auger Electron Spectroscopy for chemical surface analysis, and Photoemission techniques such as Ultraviolet Photoemission Spectroscopy (UPS) to investigate the occupied electronic states below the Fermi level. In this thesis, the properties of individual porphyrins on well-defined metallic substrates were investigated mainly via LT-STM/STS, and some supportive XPS and NEXAFS experiments. Molecule-substrate as well as intermolecular interactions were studied. The individual iron complexation of pyridil meso substituents was demonstrated as well as the controlled in situ complexation of the porphyrin’s chemical pocket with iron and cerium. The electronic structure of individual Co-Tetraphenyl porphyrins (Co-TPP) was determined around the Fermi level via STS. Distinct energetic resonances were spatially mapped, revealing the frontier orbitals of Co-TPP and their observed appearance related to the conformation of the molecule on the substrate. This is a manuscript-based thesis, where each chapter, describing scientific results, represents an accepted or submitted publication to a peer reviewed journal. A brief introduction of the content of the individual chapters is given in the following overview. This is followed by a description of the experimental tools and modes to analyze the data. The consecutive chapters each correspond to a publication. A summary of the results and  Chapter 1. Introduction future perspectives are given in the conclusion.  15  16  Chapter 2 Overview The main experimental tool employed for molecular level investigations was Low-Temperature Scanning Tunneling Microscopy (LT-STM), ca-pable of atomic manipulation and Tunneling Spectroscopy (STS). The expermintal setup as well as a brief introduction into STM theory is presented in chapter 3. This includes a description of the operation mode and the STS data analysis. Additionally, synchrotron measurements, namely X-ray Photoemission (XPS) and Near-Edge-X-ray Adsorption Fine-Structure (NEXAFS) experiments were conducted at the synchrotron radiation source BESSY in Berlin. Chapter 4 presents a LT-STM study on the supramolecular ordering of tetrapyridyl-porphyrin (TPyP) molecules on Ag(111), where the goal was to investigate the intermolecular and substrate-molecular interaction. Thermal vapour deposition in a wide substrate temperature range revealed that TPyP molecules easily diffuse and self-assemble into large, highly ordered chiral domains. Two mirror-symmetric unit cells were identified, each containing two differently oriented molecules. From an analysis of the respective arrangement it is concluded that lateral intermolecular interactions control the packing of the layer, while its orientation is induced by the coupling to the substrate. This finding is corroborated by molecular mechanics calculations. High-resolution STM images recorded at 15 K allow a direct identification of  Chapter 2. Overview  17  intramolecular features. This makes it possible to determine the molecular conformation. The pyridyl groups are alternately rotated out of the porphyrin plane by an angle of 60◦ . This study has been published in the J. Chem. Phys, 124, 194708 (2006). To investigate the TPyP response in a more reactive environment, it was deposited on Cu(111), increasing the molecule-substrate interaction. Chapter 5 presents a combined LT-STM, XPS and NEXAFS study, demonstrating the complex interplay between a strong substrate interaction and the conformation, the chemical modification and the appearance in STM. Vapor−deposited TPyP assembles into temperature dependent intermolecular arrangements. Deposited at room temperature, individual molecules are randomly distributed, but oriented along the substrates high−symmetry directions. After annealing to 390 K linear chain-like and triangular structures form, whereby in both cases high-resolution STM images reveal a two-fold symmetric sandwich-like contrast. Above 450 K a structural phase transition takes place with altered configurations between two adjacent molecules, meanwhile the molecular appearance changed substantially. A comparable contrast modification was achieved via tip induced voltage sweeps. NEXAFS measurements determined a temperature independent saddle-shape of TPyP on Cu(111). XPS measurements suggest a deprotonation of the macrocycle and a potential copper coordination of the pyridil endgroups after the sample was annealed above 450 K. These findings correlate with the altered appearance in STM and could explain the modified local density of states, influencing its chemical properties. This experiment showed how additional interactions add to the complexity of a molecule-surface system and how a  Chapter 2. Overview  18  molecular building block’s properties can be modified by their environment. This manuscript will be submitted to the Journal of Chemical Physics. To elucidate the interaction of individual TPyP molecules with the Cu(111) substrate in more detail and their coordination with single iron adatoms, again a combined approach of LT-STM and NEXAFS was employed, described Chapter 6. A novel approach using complementary experimental data and image simulations allowed the determination of the adsorption geometry of TPyP on Cu(111). The molecules are centered on bridge sites of the substrate lattice and exhibite a strong deformation involving a distinct saddle-shaped macrocycle distortion as well as considerable rotation and tilting of the meso-substituents. A bonding mechanism, based on the pyridylsurface interaction is proposed, which mediates the molecular deformation upon adsorption. Accordingly, a functionalization by pyridyl groups opens up pathways to control the anchoring of large organic molecules on metal surfaces and tune their conformational state. Furthermore, it was demonstrated that the affinity of the terminal pyridil groups for metal centers allows selective capture of individual iron atoms at low temperature. This study illustrated how a surface can influence the conformation of a molecule and how functional end-groups can be selectively coordinated by metal adatoms, which might be used to investigate metal-organic networks. This manuscript is in print at the Journal of the American Chemical Society. The next step was the attempt to directly metalate the porphyrins chemical pocket and investigate the molecular modification, since metal-porphyrins adopt key functions in biological systems. Therefore TPyP was deposited again on Ag(111) where the macrocycle is not deformed considerably. Chap-  Chapter 2. Overview  19  ter 7 reports a novel approach towards the fabrication of metallo-tetraaryl porphyrins performed in two dimensions under ultrahigh vacuum conditions. LT-STM/STS were employed to characterize the interaction of well- ordered tetrapyridylporphyrin layers self-assembled on a Ag(111) surface with iron centers supplied by an atomic beam. The iron is shown to be incorporated selectively in the porphyrin macrocycle whereas the layer structure remains unaffected. Careful comparison with wet−chemistry synthesized Fetetraphenyl porphyrin molecules deposited on the same substrate reveals that both species have similar structural and electronic properties, demonstrating that the tetrapyridil porphyrin complexation occurs in a novel reaction scheme. Because the template layers provide arrays of reaction sites, superlattices of coordinatively unsaturated and magnetically active metal centers can be fabricated. This approach offers novel pathways to realize lowdimensional metallo-porphyrin architectures, which cannot be achieved by conventional means. This study has been published in Chem. Phys. Chem. 8, 250-254 (2007) To demonstrate the ability to fabricate molecules, which cannot be synthesized by conventional means, a rare earth was positioned in the chemical pocket of tetraphenyl porphyrin (H2-TPP). Chapter 8 presents a Low Temperature Scanning Tunneling Microscopy/Spectroscopy study of a wellordered H2-TPP/Co−TPP matrix before and after being exposed to an atomic cerium beam, illustrating the successful positioning of cerium on the H2-TPP macrocycle. The three species were differentiated by STM imaging and STS, revealing a clear shift of the distinct energy levels around the Fermi level. Space-resolved mapping of the electron distribution exposed the  Chapter 2. Overview  20  spatial extend from the frontier orbitals of Co−TPP and Ce−TPP, participating in the metal complexation, revealing a comparable symmetry, which is an indication for the successful Ce coordination. Porphyrin could so far only be coordinated with cerium by means of wet−chemistry synthesis, bonding two macrocycles via the large cerium ion to a double decker-like feature. Thus, it is possible to engineer low-dimensional architectures with porphyrin molecules, which can be bestowed with specific properties by selective metal or rare earth coordination, which might modify the molecular functionality. These results were submitted. To investigate the interplay between the electron density distribution of orbitals and the molecular conformation, Co(II)-tetraphenyl porphyrin was deposited on Cu(111) and its geometric and electronic structure was carefully investigated. This is discussed in chapter 9. Combined LT-STM and NEXAFS observations reveal how the metal substrate induces a conformational adaptation into a distorted saddle-shape geometry. By scanning tunneling spectroscopy the molecules’ discrete energy levels were identified and their spatial electron density distributions mapped. These results, along with a simple theoretical description, provide a direct correlation between the shape of frontier molecular orbitals and intramolecular structural features. This study is in print in Chem. Phys. Chem.. The last Chapter summarizes the presented work and its relevance for the scientific community. Further ideas and future perspectives are discussed.  21  Chapter 3 Experiment and Theory This chapter will give an introduction to the basic principles and theoretical aspects of the experimental methods used in this thesis. The main instrument is a custom designed apparatus comprising a commercial Low-Temperature Scanning Tunneling Microscope (LT-STM). Its mode of operation and theoretical basics are discussed. Furthermore an introduction into Scanning Tunneling Spectroscopy (STS) is presented. The next section alludes to the basic investigation of molecules on surfaces with STM/STS, briefly covering manipulation techniques, and a simple method to simulate STM images is introduced. The STM part is completed by a description of the experimental setup. Moreover, X-ray Photoemission and Near-Edge X-ray Absorption Fine Structure experiments were performed at the synchrotron Bessy II in Berlin. Both techniques are briefly introduced.  3.1  Scanning Tunneling Microscopy  The Scanning Tunneling Microsope (STM) was invented by Binnig and Rohrer in 1982 [101], yielding them the Nobel prize in 1986. Its basic working principle is related to the tunneling experiments performed in the early 60s, where a bias was applied over two electrodes, separated by an insulating oxide layer, resulting in a tunneling current It . This tunneling current is dependent on the applied bias and turns out to be proportional to the electrodes density  Chapter 3. Experiment and Theory  22  of states (DOS). Thus It provides information about the materials electronic structure around the Fermi level. In the case of STM, the two electrodes are a sample surface and an atomically sharp tip that can be positioned in three dimensions over the sample with picometer precision. The potential barrier between tip and sample is established by a vacuum gap or a liquid layer. An introduction and overview of various developments and techniques in STM can be found in reference [49].  3.1.1  Operation Mode  STM exploits the quantum mechanical effect of electrons tunneling through a potential barrier. An atomically fine tip is brought to within 5 to 10 ˚ A of a surface, as shown in Figure 3.2, resulting into a narrow potential barrier between tip and sample. Electron wave functions, penetrating the classically forbidden region, give electrons a finite probability to tunnel through the gap, as long as there is an overlap of the tip and sample wave functions, as schematically shown in Figure 3.1. By applying a bias voltage between tip and sample, electrons from the occupied states of one electrode can tunnel trough the potential barrier to the unoccupied states of the second electrode. Thus a measurable tunneling current (It ) will flow. This current is exponentially dependent on the tipsample distance making it very sensitive to the change of distance: − zz  It = I0 e  0  (3.1)  Here z0 is in units of 1/m and depends on the height of the energy gap, determined by the materials work function, and the energy of the electron which  Chapter 3. Experiment and Theory  23  Figure 3.1: Electron Tunneling  Schematic drawing of an electron wave tunneling from the sample through the potential barrier into the tip. The height of the potential barrier is equivalent to the work function Φ.  Chapter 3. Experiment and Theory  24  is about to tunnel. This term will be discussed in the STM theory section in more detail. The tunneling current is typically between 10−12 - 10−9 A. Changing the sample-tip distance by 1 ˚ A alters the current typically by one order of magnitude. The tip can be moved laterally over the sample with picometer precision, while the tunnelling current is recorded, revealing a convolution of the tip and surface’s electronic structure. In a first approximation the electronic structure detected is the surface’s Density of States (DOS). Since the tunnelling current passes only through a few atoms of the tip apex closest to the substrate (ideally just through one), the DOS located directly at the tip is detected, therefore called the Local Density of States (LDOS). Hence, the STM is very sensitive to any corrugation, resulting in the lateral resolution, down to the atomic scale. Controlling and measuring with an STM is principally not very complicated and illustrated in Figure 3.2. The tip, mounted on a three−dimensional piezo element, is brought into tunnelling contact, where It is amplified and fed into the feedback control that correlates tip height and measured tunnelling current via the z-piezo, whereas the x and y direction are controlled separately. There are two major operation modes, constant current and constant height. The former is most commonly used, whereby the tunnelling current is set to a fixed value. While the tip scans over the desired sample area, the feedback control keeps the current constant by moving the tip accordingly in the z-direction. The obtained image represents the tip movement in the z-direction in relation to the scanned area. The latter method, the constant height mode, keeps the tip at a fixed height during the scan and records the modification of the tunnelling current. Since it is more likely to crash the tip  Chapter 3. Experiment and Theory  25  into the sample, it is used less frequently but allows faster scanning. The STM, due to its highly sensitive junction, is very sensitive to mechanical vibrations. A series of vibrational damping systems is usually employed, where passive and active damping systems reduce vibrations in the lower frequency range (0−100 Hz), and springs combined with eddy-current brakes minimise the influence of vibrations from 100−500 Hz.  3.2  STM Theory  The tunnelling current can be calculated in several ways [102, 103]. Most of these approaches are based on Fermi’s Golden rule, which gives the transition probability from state µ to ν. The states of two electrodes can be represented by Ψµ and Ψν, respectively. It can then be calculated with Fermi’s ansatz:  It =  2πe  [f (Eν ) − f (Eµ )]|Mµ,ν |2 δ(Eν + eV − Eµ )  (3.2)  µ,ν  Here f (E) is the Fermi function, V the applied bias voltage, Mν,µ the tunneling matrix element between the states of the left and right electrode. Eµ and Eν are the energy levels of the states relative to the Fermi level in the left and right electrode. The difficulty at this point is the proper calculation of the transfer matrix elements. Tersoff and Hamann [104, 105] employed Bardeen’s transfer hamiltonian [105], who calculated the matrix elements for the previously mentioned tunneling experiments, with the assumption, that the two electrodes’ wave functions can be calculated for separate systems. The first part of the Tersoff-Hamann model describes in most cases the principle features  Chapter 3. Experiment and Theory  26  Figure 3.2: STM Operation Principle  Schematic drawing of the STM operation mode. The tip is approached to the sample until a tunneling current is measured and then scanned over the sample surface by piezo elements. The measured tunneling current is fed into a feedback control, regulating the height of the tip with the z piezo. The tunneling current or the z-movement, depending on the imaging mode, are recorded in relation to the scanned area and generate the STM image.  Chapter 3. Experiment and Theory  27  in experimental findings and is briefly discussed here. The matrix element, calculating the transition probability from tip to surface states was expressed as the following integral over a separation plane between tip and sample: 2  Mµ,ν =  2m  dS · (Ψ∗µ ∇Ψν − Ψν ∇Ψ∗µ )  (3.3)  Originally the sample wave function Ψµ was represented by a Bloch wave, decaying exponentially along the surface normal away from the substrate and the tip Ψν was modelled as a spherical s-wave. Depending on the nature of the sample or tip, alternative wave functions can be used. As long as it is assumed that there is no interdependency between the wave functions of the sample and the tip, the result of this model will not depend on the single wave functions but on the Local Density of a State of tip and surface. The calculated matrix elements are put back into the expression for the tunnelling current and lead to the following expression for It (V ):  EF +eV  ρS (r0 E)ρt (E − eV )τ (E, V, z)[f (E − eV, T ) − f (E, T )]dE  It (V ) ∝ EF  (3.4) Here, ρs is the local density of a state (LDOS) of the surface at the position of the tip (r0 , ρt the tip density of a state, and τ the tunnelling transition probability. In the literature, the use of the LDOS is often used in a confusing manner. There LDOS is often referred to as the Local Density of States, but this definition has in condensed matter physics the units of density per energy. However, in the STM community ρ is the square of a wave function, therefore being just a density of a state. Hence I define the LDOS as the local  Chapter 3. Experiment and Theory  28  density of a state. That means the tunneling current depends on the LDOS of the two electrodes, the most important result from the Tersoff-Hamann model. The tunneling transition probability depends on several entities, very similar to the text book example of the tunneling probability of a plane function through a potential barrier : 1. The energy E of the electron, which is about to tunnel; 2. The applied bias V , which sets the energy interval of unoccupied states, into which the electrons can tunnel; 3. The work functions of tip and sample, Ws and Wt respectively, which sets the height of the potential barrier; 4. The substrate−tip sample distance z, determining the width of the potential barrier (measured from surface atom core to tip atom core). Finally τ is given by:  τ (E, V, z) = exp(−2z  me 2  Ws + Wt − 2E + eV )  (3.5)  If one assumes operation at low temperatures, the Fermi distribution can be approximated by a step function. Furthermore, the metal tip density of states may be assumed constant in the vicinity of the Fermi level. The result of these assumptions is that the tunnelling current will be proportional to the integral over the LDOS in the interval between the Fermi level EF and the applied sample bias EF + eV . EF +eV  It ∝  ρS (r0 , E)τ (E, V, z)dE  (3.6)  EF  A further assumption was that the integrated energy range is small compared to the sample’s work function, so that one can neglect the integral.  Chapter 3. Experiment and Theory  29  Figure 3.3: Substrate Electronic Structure and Tunneling Current  Schematics of the electronic structure and the tunneling process. After a bias V is applied, the Fermi levels of the electrodes are shifted eV with respect to each other. Electrons from the occupied states of one electrode can tunnel into the unoccupied states of the second electrode. Depending on the bias polarity, the electrons tunnel from the substrate into the tip, or vice versa. In the Tersoff-Hamann model the resulting tunneling current It is proportional to a sum of the LDOS over the interval [EF , EF + eV ] Then the tunnelling current is directly proportional to the LDOS of the substrate. This however is only valid in first approximation if tip and sample are made out of metals with a constant density of states around the Fermi level. For the majority of samples, which are investigated by STM this is one assumption too many. Therefore it is important to stick to the interpretation if one uses Tersoff Hamann, that the imaged tunneling current is proportional to the summation over the surface LDOS in the interval [EF , EF + eV ] as illustrated in Figure 3.3 and used throughout this thesis. The model presented here provides a qualitative understanding of the tunneling current’s nature and operation of the STM. It has helped to interpret a wide range of experimental results and is used as a basic model for  Chapter 3. Experiment and Theory  30  the work presented here. It has to be noted however, that this model is not the final lore. There are some principal problems with the Tersoff Hamann model and its interpretation: 1. The assumption that the wave function of tip and sample do not influence each other. 2. The off-diagonal matrix elements between the surface and tip wave functions are neglected to calculate the tunneling current and only the charge density of the tip and surface wave functions are considered. This leads to the described proportionality of the tunneling current to the LDOS and the transition probability τ , which is only valid if the tip sits directly over the atom which is imaged. Spatially dependent tunneling contributions from neighboring atoms are not included properly in this picture, for example if a molecule is imaged. Hence, the tunneling current is not anymore strictly proportional to the LDOS. Especially the second point is very important to keep in mind when interpreting STM images. This will be illustrated with the simple example of tunneling between a model - hydrogen molecule and an STM tip (compare figure 3.4) . The tip wave-function is labeled φt . The bonding molecular orbital for the hydrogen molecule ΨM can be described as a linear combination of the √ single hydrogens wave functions ΨM = 1/ 2(ΨA +ΨB ), where ΨA is the wave function for atom A and ΨB for atom B, respectively. This bonding orbital is the highest occupied molecular orbital (HOMO). The anti bonding orbital √ (lowest unoccupied molecular orbital (LUMO)) is Ψ∗M = 1/ 2(ΨA − ΨB ), where ΨB has the opposite phase. In the Tersoff Hamann model as introduced, the tunneling current is  Chapter 3. Experiment and Theory  31  proportional to ρM = |ΨM |2 , which is strictly speaking a charge density, or the density of a state. One can assume, that the overlap between ΨA and ΨB is very small. That means ρM will have the same spatial dependence for the HOMO and the LUMO. Hence, the resulting tunneling current would be the same independent whether one tunnels out of the HOMO ΨM or into the LUMO Ψ∗M . Using a basic symmetry argument, which includes the tip-sample matrix elements will draw a different picture. Let’s assume the tip is located over the center of the hydrogen molecule. The tunneling probability between the tip and the atom wave-functions of the molecule can be determined by the matrix elements between tip and atom A < φt |ΨA > and tip and atom B < φt |ΨB >. In the case of tunneling out of the occupied state, where |ΨA > and |ΨB > have the same phase, both matrix elements contribute equally to a tunneling current resulting in the same contribution as predicted by the Tersoff Hamann model. By contrast, in the case of tunneling into the unoccupied state the different phases will lead to an effective matrix element of 0 and hence, no tunneling current will flow, whereas in Tersoff Hamann the contribution to It is still proportional to the LDOS. This illustrates, that the tunneling current’s spatial dependence is not the same for tunneling in or out of the hydrogen molecule’s LUMO or HOMO as described by the Tersoff Hamann model. When interpreting STM images based on the common use of the Tersoff Hamann model, one must keep in mind, that the the image of a molecule will not depend exactly on the LDOS. Nevertheless, as a first approach the Tersoff Hamann model provides a  Chapter 3. Experiment and Theory  32  Figure 3.4: Tunneling into a Hydrogen Molecule  a) Taking the direct matrix elements between tip and sample into account for the tunneling from the bound state of an hydrogen molecule into an unoccupied state of the tip results in the same contribution to the tunneling current than the LDOS calculated with Tersoff Hamann. b) Tunneling by contrast into the anti bound non-symmetric state, the matrix elements predict a resulting tunneling current of 0 due to the phase difference, whereas the LDOS predicted by Tersoff Hamann predicts the same tunneling current as for the bound state. qualitative understanding of the tunneling current and is thus very often used in the interpretation of STM data. For a more detailed analysis it is sometimes important to use a more sophisticated model to simulate the tunneling current as will be illustrated in the section ”Investigating Molecules with STM and STS”. Overviews of more sophisticated approaches are discussed by W.A. Hofer [102], P.Sautet [106] and in volume 3 of the ”Scanning Tunneling Microscopy” series [49].  Chapter 3. Experiment and Theory  3.3  33  Scanning Tunnelling Spectroscopy  Scanning Tunneling Spectroscopy (STS) is in principle a continuation of the previously mentioned first tunneling experiments between two electrodes, with the main difference being that one electrode is atomically sharp and movable and thus detects the LDOS. At a selected position this is used to probe the occupied and unoccupied LDOS in the vicinity of the Fermi level with a spatial resolution on the atomic scale. STS measurements were employed to study different aspects of the surface electronic structure. Surface states for instance were studied in great detail. Bischoff and coworkers examined the sensitive influence of carbon impurities on the surface state of V(001) [107]. Metal surface state electrons and their reflection at step edges were first studied by Crommie et al. [108]. Quantum well states between step edges were investigated by Burgi et al. [109]. Furthermore, surface electrons confined in two-dimensional Fe adatom corals were explored on Cu(111), their distinct resonances determined and imaged via STS [37]. Even one dimensional surface states on a Fe(100) surface alloyed with Si were discovered and investigated in real space via STS. [110] Other studies used STS to determine chemical properties of materials. Differences in the tunneling spectra of metals were used to provide chemical selectivity for one metal on another [111, 112]. Bode et al. determined the topography and chemical surface structure of a submonolayer Fe film on a W (110) substrate by combined STM and STS [111]. A recent important development was spin−polarized STS by Wiesendanger et al., providing the possibility to investigate magnetic properties of ultrathin ferromagnetic and antiferromagnetic layers [113, 114, 115]. Due to  Chapter 3. Experiment and Theory  34  the spatial resolution of STS, it is an ideal method to study the electronic structure of molecules adsorbed on surfaces. Scudiero determined the energetic position of the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) of Tetraphenylporphyrins on a gold surface [94]. Lu et al. investigated the intramolecular electronic structure of C60 by recording the differential conductance of one specific resonance, while scanning over the molecule, determining the spatial extent of a specific state [43]. An additional important progress for tunneling spectroscopy was the development of inelastic tunneling spectroscopy (IETS) to study vibrational properties in molecules. W.Ho[28] and J.I.Pascual [46, 116] have reviewed this technique and the main results. The physical foundation for the use of scanning tunneling spectroscopy to investigate the electronic structure is the proportionality of the differential conductance to the local density of states. It is based on the Tersoff-Hamann ansatz, already introduced:  It =  πe m  EF +eV  ρS (E)ρT (E − eV )τ (E, V, z)dE  (3.7)  EF  Feuchtwang [117], Selloni [118] and Lang [119] developed further the theory for scanning tunneling spectroscopy, assuming a constant tip density of states and that the transmission coefficient is to first order independent of bias. This led to the mentioned proportionality: dI = AρS (E)τ (E, z) dV  (3.8)  Here A is a constant incorporating the factors in front of the integral and the constant tip density of states. To retrieve the LDOS from the dif-  Chapter 3. Experiment and Theory  35  ferential conductance, the dI/dV data need to be divided by the transmission coefficient. Based on the results for the tunneling current between two one−D electrodes by J. Simmons [120]. Stroscio et al. approximated the transmission coefficient for a given energy with the tunneling current I(V ) [121]. This approximation is valid for intermediate biases applied over the electrodes [122]. Consequently, the differential conductance is normalized, by dividing dI/dV by I/V, canceling out tip-sample variations and energy dependent transmission dependencies. dI/dV ∝ ρS (E) I/V  (3.9)  These approximations have proved themselves in practice. Several studies demonstrated that the DOS determined via STS was identical to the DOS established by photoemission experiments [96, 123]. The normalization, often referred to as the deconvolution of the DOS, was further developed for semiconductors. The tunneling current for biases corresponding to the semiconductor gap goes to zero, but the transmission coefficient does not. The I/V division overnormalizes the data in the energy gap. Martensson and Feenstra suggested an empirical approach to broaden the I/V signal by a one-pole Fourier low-pass filter, where the pole frequency is given by 1/∆ V [124]. Choosing ∆V larger then the band gap, results in a broadened tunneling current, which is non zero in the gap and therefore does not over-compensate the normalization. Ukraintsev provided a novel approach to analyze and deconvolve the STS spectra [125], where he refrained from making the approximations of constant tip density of states and bias independent transition coefficient. However, it involves substantial numerical calculations  Chapter 3. Experiment and Theory  36  and is only useful if the resonances under investigation are very sharp and their energetic positions need to be determined precisely. Otherwise it is most convenient to employ the introduced normalization to determine the LDOS, which proved to be very successful in practice. Having considered the basic theoretical aspects of STS some essentials on the practical side will be discussed. To retrieve the differential conductance in practice, there are conventionally two methods adopted. The first, by recording an I/V curve and numerically differentiating it [126, 127] and the second by the direct extraction of the dI/dV signal via lock-in detection [124]. The former method can be used with every standard STM setup, but has a very limited signal to noise ratio. Therefore each data point needs to be integrated over a long time, resulting in data acquisition lasting several hours, where the drift of the tip becomes a significant issue. The latter method uses the lock-in amplifier technique, increasing strongly the signal to noise ratio and allowing much faster data acquisition. Each method can be performed in two different ways. One is to disrupt the feedback loop during the voltage sweep, keeping the tip at a constant height. The second is to move the tip in the z-direction during the voltage sweep, towards the sample for biases approaching zero and away from the surface for increasing biases. The constant height method has the advantage of keeping the tip at the exact same position, allowing lateral-dependent spectroscopy on the atomic scale. The disadvantage is that the constant height method’s signal to noise ratio is smaller, compared to the vertical tip moving method. The controlled movement of the tip along the surface normal can be especially useful, if the  Chapter 3. Experiment and Theory  37  measurement does not depend crucially on the lateral position. A derivative of this STS mode is to keep the bias constant and to measure the tunneling current’s dependence on the tip height, which can be employed to determine the material’s work function [121]. Recently an additional STS mode has been developed, using a double lock-in technique to achieve a higher energy resolution [128]. For this thesis the differential conductance was determined via lock-in amplifier technique, using an open feedback loop with a constant tip height. The lock-in amplifier technique is based on the concept of correlation functions. The time integral over two multiplied, time dependent functions f (T ) and g(T + δ) determines the degree of their correlation at time δ:  R(δ) = lim  T →inf  1 T  T  f (t)g(t + δ)dt  (3.10)  0  If R(δ) is 0, the functions are completely independent from each other at time δ. The lock-in amplifier employs this principle by using a sinusoidal reference function f (t), to modulate a parameter of interest, resulting in a signal g(t). The returning signal g(t) is correlated to the reference function f (t) in the so called demodulator and integrated over time. Due to the fact that the signal is modulated by the reference frequency, both functions are correlated and so amplify the parameter of interest, which would otherwise be buried in noise. In the case of STS, the lock-in amplifier adds to the tunneling bias of the STM an additional AC signal with an amplitude ∆V and frequency ω. In this way the tunneling current is modulated by a sinusoidal oscillation, resulting in g(t) = I(V + ∆V sin(ωt + φ)). The phase φ is a result of the electronic connections and the tunneling junction. The signal is  Chapter 3. Experiment and Theory  38  fed back into the lock-in amplifier and correlated with the reference function f (t) = ∆V sin(ωt). This leads to the following integral, which is integrated by the lock-in amplifier over an adjustable time.  Rlock−in =  I(V + ∆V sin(ωt + φ))∆V sin(ωt)dt  (3.11)  Rlock−in is then the output signal of the lock-in amplifier and to understand its nature this integral needs to be solved. The amplitude of the modulating bias oscillation ∆V is typically one to two orders of magnitude smaller compared to the actual tunneling bias. Therefore the calculation can be simplified by expanding the tunneling current in a Taylor series around ∆V = 0:  I(V +∆V sin(ωt+φ)) = I(V )+  dI dI 2 ∆V sin(ωt+φ)+ 2 (∆V sin(ωt+φ))2 +... dV dV (3.12)  The term, I(V ), does not correlate with the reference function and the integral over time turns out to be 0. However, the first order term comprises the differential conductance times the same sinusoidal function as the reference signal. If we only consider the first order, the integral will have the following form.  Rlock−in =  dI ∆V sin(ωt + φ)∆V sin(ωt)dt dV  (3.13)  After solving the integral, Rlock−in and thus the output of the lock-in amplifier is proportional to the differential conductance, the square of the modulation amplitude, the phase term between the signal and reference function  Chapter 3. Experiment and Theory  39  and the time of integration.  Rlock−in ∝  dI ∆V 2 sin(φ)T dV  (3.14)  This result contains some important facts about using a lock-in amplifier for STS: 1. Most importantly, the lock-in output is proportional to the differential conductance, i.e. exactly what is desired 2. The higher the modulation amplitude, the stronger the signal. On the other hand, a higher modulation amplitude signifies, that each data point is integrated over an energy range e∆V, thereby reducing the energy resolution of the spectra. 3. It is important to optimize the phase between the incoming signal and the reference to Φ =90◦ , to obtain a maximum signal strength and a correct display of the differential conductance. After any major change of the tip apex, for example by tip forming, the phase has to be reoptimized. 4. The longer the integration time, the better the signal to noise ratio, without compromising the energetic resolution. To successfully conduct scanning tunneling spectroscopy, there are three important points to consider. First is the choice of a good modulation frequency, second the condition of the tip, to achieve reproducible spectra and third, the influence of the electric field on the electronic structure that is probed. The oscillation frequency of the modulation is usually taken between 800 Hz and 5000 Hz. To choose the right frequency there are three criteria to consider: a) The frequency needs to be above the bandwidth of the feedback-loop,  Chapter 3. Experiment and Theory  40  so as to exclude any interference. b) The frequency should not be higher then the capability of the preamplifier c) One needs to be aware of the characteristic frequencies in the tunneling current, and to make sure not to set the modulation frequency to the frequency of an interfering signal or multiples of it. The tip influence is another important issue. In the derivation shown, the tip states were approximated as constant. This assumption is not always applicable. Ukraintsev [125] and Griffith [129, 130] calculated the differential conductance without the assumption of a constant tip density of states and showed that tip states would primarily appear in the negative bias range of the spectra (the occupied states of the sample). These tip states can also be observed experimentally and seem, in my experience, to become more evident the sharper the tip is. The tip sharpness is estimated by the degree of lateral resolution. Conditioning the tip, to obtain meaningful and reproducible results, is very simple in cases where adsorbates on well-known substrates like Ag(111) are spectroscopically investigated. The tip apex is conditioned via tip forming, until the spectra of the substrate reproduces distinct features of the electronic structure, agreeing with results from other techniques such as ultraviolet photoemission spectroscopy. Typically, tip states are not a significant issue but need to be mentioned in this chapter for completeness. Last, the effect of high electric fields from the tip on the electronic structure needs to be addressed, since it is important for the data interpretation and is often the cause of vivid discussions amongst researchers. Several attempts have been made to compute the electric field stemming from the tip  Chapter 3. Experiment and Theory  41  apex [131, 132]. With a sharper tip and a smaller tip-substrate distance, the electric field and its influence on the electronic structure of the sample increases. However, in practice, the tip geometry is difficult to access, rendering exact predictions on the magnitude of the electric field strength impossible. On the other hand one can measure the shift of a distinct state due to the influence of the electric field, called the Stark shift. By decreasing the tipsample distance, the electric field on the sample increases, which changes the magnitude of the Stark shift. Limot et al. investigated the influence of the electric field on the Ag(111) surface state [133]. They took five consecutive spectra of the surface state onset. After each spectrum, the tip-sample distance was decreased by roughly one ˚ A, by increasing the tunneling current one order of magnitude. The result was that a Stark shift of only 5 meV was observed over a tunneling current interval of 50 pA to 1 µA, correlating to an overall tip-sample distance change of 5 ˚ A. Nevertheless, spectroscopic studies on non-metallic samples have proved to be more sensitive to the electric field strength, for example superconducting and semiconducting [134] samples. So, it is advisable to follow the example of Limot and vary the electric field strength by changing the tip-sample distance and compare the shape of the spectra as well as the peak positions, to ensure measurements with the smallest possible perturbation of the system. The criteria for conducting successful STS with a lock-in amplifier apply in the same way for spatially mapping the differential conductance of a distinct resonance, called dI/dV mapping. Instead of sweeping the tunneling bias over an interval, it is kept at a constant value corresponding to the energy of a particular state. With the lock-in technique described, the differential  Chapter 3. Experiment and Theory  42  conductance is recorded while scanning over the region of interest, mapping the spatial distribution of the electrons in this state. To ensure a high resolution dI/dV map, each data point taken by the STM needs to have a longer integration time than the integration time set for the lock-in amplifier. Recently, a study divided the dI/dV map by the parallel-recorded topography map to deconvolve the dI/dV signal from the transmission coefficient, in analogy to the earlier discussed normalization [135]. This normalization affects the result noticeably, i.e. only if the investigated resonance has a small intensity. dI/dV mapping is a very powerful tool to investigate distinct molecular states with intramolecular resolution. This spatial resolution makes STS an ideal tool to investigate detailed differences in the local electronic structure on a surface, which could not be resolved otherwise. However, STS does not replace photoemission experiments, especially since the accessible energy interval in STS is usually not wider then ±4eV around the Fermi level, due to stability limitations of the tunneling tip and the increasing influence of the electric field on the local electronic structure. Nevertheless, STS in combination with STM is one of the most versatile tools to study the electronic properties of individual molecules on a surface. It allows locating and identifying species at particular sites. Highly selective space resolved analysis can be performed, even where there are several different components present. STS also allows to map the electron transport through different portions of a particular molecule or nanostructure. These conduction pathways, both in space and in energy can be used in the design of complex molecular electronic devices. Furthermore, both electron affinity levels and ionization states can be located simultaneously without utilizing  Chapter 3. Experiment and Theory  43  energy probes that can decompose the molecule. The accessible energy interval is fully sufficient to investigate functionalities of a molecule and its interaction with the environment, since the valence electrons in the immediate region in the vicinity of the Fermi level determine the physical and chemical properties.  3.4  Investigating Molecules with STM and STS  Depending on the molecular properties of interest one can decide what kind of STM is employed. If the investigation of self-assembled structures is the main purpose, fast scanning, variable temperature STMs, like the Aarhus type [136], are well suited, since they allow quick sample transfers and especially the possibility to study the dynamics of self-assembly. If the research focus on the other hand is laid on properties of individual molecules, like electronic structure or manipulation, a low-temperature STM is the instrument of choice. There the sample and STM are cooled below 15 K, where, when in equilibrium, piezo drift is not anymore an issue of concern, the tip is stable and large molecules do not have enough energy to diffuse thermally. These are ideal conditions to perform spatially resolved spectroscopy experiments. After molecules are deposited on the surface, the next obvious step is to image them. However, imaging molecules can depend on different factors which are important to realise for a correct data interpretation. Such factors are their bias-dependent appearance, the influence of the tip and the limits of the Tersoff-Hamann model to explain their appearance. These points will be briefly discussed.  Chapter 3. Experiment and Theory  44  The STM theory showed that the tunneling current is proportional to the integral over the density of states in the interval [EF , EF + eV ], depending on the magnitude and sign of the applied bias. For large complex molecules, the energetic gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) can be several eV . After adsorption on a surface these states can still be on the order of a few eV away from the Fermi level. What happens if the DOS in the interval [EF , EF + eV ] does not include the molecular states? Are the molecules invisible? In fact, this depends on the coupling of the molecular states to the electronic structure of the sample. In the case of weak coupling, the molecular states are barely broadened and stay fairly sharp. If these states are now far away from the tunneling interval, it is possible to tunnel directly into the substrate and not to detect the molecules. Li showed that the possibilty of imaging C60 adsorbed on Si(111) depends, for certain biases, on the orientation of the C60s [137]. However, in the case of stronger coupling on metal substrates, the frontier molecular states are often broadened Lorentzians, resulting in far reaching resonance tails (up to 1 eV). Lang showed that for single adatoms, a small fraction of the resonance is already sufficient to tunnel into the resonance, allowing imaging of the adatom [119, 138]. Figure 3.5 shows a spectrum of TPyP from −1000 to 2000 meV, with two states at 500 meV and 1800 meV. Although there is no distinct state between the Fermi level, here 0 meV, and −1000 meV, the STM image taken at −900 mV reveals clearly the TPyP. The image of the same molecule, taken at 1500 mV, integrating over the first state, reveals a significant change in appearance, demonstrating the importance to state precisely the tunneling conditions to be able to  Chapter 3. Experiment and Theory  45  reproduce the results. The tunneling resistance, defined by the ratio of detected tunneling current to applied bias, used to be a common parameter to describe the tunneling conditions. However, the contrast or appearance of a sample depends, as demonstrated, on the applied bias, and it is therefore necessary to list both, the applied bias V and the tunneling current It . Another factor influencing the appearance is the the condition of the tip. It is fairly intuitive that a flat tip resolves less detail laterally, than a sharp tip. Nevertheless, some theoretical studies showed that the tip geometry itself defines the nature of the tip state which is tunneled in or out of, influencing the appearance of the imaged object [102, 139, 140]. In practice the condition of the tip appears to influence the image in two ways. One is its sharpness, affecting the intramolecular resolution and secondly, the adsorption of potential admolecules onto the tip apex, which can distort the image or increase the resolution. To influence the sharpness of the tip, it is convenient to have less then a mono-layer of molecules and therefore bare substrate patches. Depending on the nature of the sample substrate, field emission, voltage pulses or controlled dipping of the tip into the substrate can alter the tip apex geometry. It turns out that a tungsten or platinumiridium tip, even after being modified over and over, reproduces properly the molecule’s appearance, as long as the tip is stable. An additional way to ensure a reproducible tip is using Scanning Tunneling Spectroscopy. As already mentioned in the STS part, a spectra of the bare substrate can be made and compared to already existing reference data. Modifying the tip until one obtains exactly the reference spectra, is a very effective way to ensure reproducible tips.  Chapter 3. Experiment and Theory  46  Figure 3.5: Bias−dependent Imaging of TPyP  Bias dependent imaging of TPyP on Ag(111). a) shows a normalized tunneling spectrum of TPyP on Ag(111), taken over the centre of the molecule. At negative biases (occupied states) there is almost no structure in the spectra observable. In the occupied states there is strong evidence of resonance, originating from TPyP. Figure b) shows an STM image of TPyP on Ag(111), taken with a bias of −900 mV. Although one does not integrate over distinctly detectable states, there is clear intermolecular resolution observable. Taking the image at 1500 mV (c) and integrating over 2 distinct resonances, the intermolecular contrast changes significantly.  Chapter 3. Experiment and Theory  47  During the scan, it is possible to pick up a molecule onto the tip apex. Large complex molecules, absorbed on the tip, alter the contrast, leading for example to a clear atomic resolution of the bare surfaces, but to a very distorted appearance of the molecules. Another case is the modification of a tip by a small molecule such as carbon monoxide (CO), increasing the overall resolution, as shown in Figure 3.6. The left image shows Tetrapyridil porphyrin on Cu(111) imaged with a bare tungsten tip. The right image shows exactly the same image after attaching a CO molecule to the tip, exhibiting detailed intramolecular resolution. The tip modification with small molecules can be employed to obtain very detailed images of a molecule or an assembly. However, since the electronic structure is detected the obtained images are a convolution of the surface and molecular tip density of states. Even in the case of tips, modified by well understood molecules such as CO, the deconvolution of tip and substrate states is extremely difficult, making further interpretation of the detected electronic structure infeasible. To illustrate the difficulty of making statements about a measured electronic structure with a CO modified tip, the simpler system, CO on a Cu(111) surface imaged with a tungsten tip will be illustrated. CO adsorbed on Cu(111), imaged by a bare tungsten tip, behaves counter-intuitively, by appearing as a depression instead of a protrusion (compare Figure 3.7), although one tunnels for positive biases into its π orbitals. This example is mentioned to show the limit of the Tershoff-Hamman Model. Alternative models such as the Greens function approach [102, 103, 141, 142] are needed to explain the depression. This model explains the STM image as a result of interfering tunneling channels, one being between the substrate, through the  Chapter 3. Experiment and Theory  48  Figure 3.6: High Resolution Imaging with CO Modified Tip  Imaging with a CO modified tip. a) shows a matrix of TPP/CoTPP molecules on Ag(111). After a CO molecule attached to the tip, the intramolecular resolution increases significantly b). molecule and the tip, and a second channel directly between the substrate and the tip. In the case of CO on Cu(111) the interference is destructive and explains the appearance as a depression. Based on this model one does not detect strictly the LDOS anymore, but it is possible to obtain more detailed information of the sample’s electronic structure. Unfortunately the interpretation requires already a very detailed knowledge of the electronic structure and advanced computational skills. It turned out that especially to explain the appearance of small molecules this Greens function approach is very useful. However, in the case of larger complex molecules, such as the porphyrins used for this thesis, interfering tunnelling channels do not seem to have a detectable influence on their appearance. The reason therefore is probably the porphyrins’ width and height, making the contribution of tunnelling channels directly from the substrate into the tip negligible. Simulations based on the Tersoff-Hamann model reproduced the experimental data satisfactorily.  Chapter 3. Experiment and Theory  49  Figure 3.7: CO Molecule on Cu(111)  Image of a single CO molecule on Cu(111) at 18 K taken with a bias of 0.3 V and a tunneling current of 8 nA. The lattice underneath represents the Cu (111)lattice and the red line shows the direction of the line scan, demonstrating the depression−like appearance  Chapter 3. Experiment and Theory  50  By now, enough explanations and examples have been demonstrated that the visualisation of molecules with an STM is a complex product of the convoluted electronic structure of tip and molecule. To learn more about the electronic structure of molecules, STS is a very powerful tool. To study the position dependent DOS over a molecule requires extremely stable conditions. This implies a lateral drift of not more then an atomic radius, over the duration of the spectral recording. This can be achieved by employing a LT-STM, reducing the drift to a minimum, a lock-in amplifier, decreasing the time per spectra, and measuring in constant height mode, as discussed in the spectroscopy part. Nevertheless, the tip or the molecule can be modified during the spectroscopic measurement, especially if the probed interval extends over a large voltage range. Typically such changes can be seen as steps in the tunneling current but there are exceptions. Therefore it is useful to make a reference spectrum of the substrate, before and after the molecule was investigated. For this thesis, a distinct position of an individual molecule was measured several consecutive times and the spectra were reviewed on their consistency. Subsequently, the same position was measured on other molecules and again the consistency verified. Lastly, the tip was modified via tip forming, and spectra at the same positions were taken again to confirm the correctness of the obtained spectra. Only then the spectra were included in the work presented here.  Chapter 3. Experiment and Theory  3.4.1  51  Molecular Manipulation  The precise manipulation of individual atoms and molecules with an STM demonstrates the control over matter we have today. It is an important tool for nanoscale science, especially for probing individual molecules. It allows not only the assembly and modification of matter on the atomic scale, but also grants access to basic physical properties of such artificial nanostructures: Highlights include the positioning of single adatoms and molecules [36, 143, 144, 145, 146, 147], induced chemical reactions [27], tip-induced field modulation of adsorbed single molecules [148] and conformational changes in large organic molecules [65, 66, 149, 150, 151]. These studies allow the exploration of molecules or atoms and their interaction with the surrounding environment, as demonstrated already in early experiments on the impact of quantum corrals on the surface electronic structure [108] or in more recent experiments focused on the modification of the electronic structure of adsorbates [152], molecule-metal contacts [153, 154, 155] or metal chains [156]. To fulfil the high requirements to conduct controlled manipulation, an exceeding stability of the apparatus, electronics, and software is necessary. The manipulation experiments of carbon monoxide on a Cu(111) surface presented in this section, are used to introduce the capabilities of our lowtemperature STM setup. The CO/Cu(111) system represented an ideal test case to perform the first manipulation experiments in Canada, since for the positioning of small molecules on metal surfaces established procedures exist [144, 145, 146, 157]. In addition, CO on Cu(111) represents a marker to determine adsorption sites of other adsorbates [146]. Figure 3.8 shows the Cu(111) surface after a minute exposure to CO dosed  Chapter 3. Experiment and Theory  52  in-situ at a sample temperature of 18 K. Each depression corresponds to a single CO molecule imaged with a bare metal tip. This inverted contrast was mentioned before and is explained by different tunnelling channels between sample, molecule and tip [142, 158]. In order to assemble artificial CO structures we applied a lateral manipulation procedure, where the molecule is moved by interactions with the STM tip. A typical manipulation includes the following steps: i) the tip is positioned behind the target molecule and approached close to the surface by applying small bias voltages (50 mV) and large tunnelling currents (80 nA). ii) the tip is translated along a line towards the desired final position. Short range forces between the CO and the tip induce sudden hops of the molecule. These jumps from one lattice site to the next can be observed in the tip height. Figure 3.8a) shows the sawtooth trajectory of the vertical tip position while a CO molecule was moved over 27 lattice sites along a close-packed Cu row. iii) at the target position, the tip is again retracted by changing back to the imaging parameters. A subsequent image is taken to check if the manipulation was successful. While in general the manipulation efficiency strongly depends on the STM tip, decent tips yield a success rate of over 90%. The image sequence displayed in Figure 3.8b ) presents some snapshots during the writing procedure of the letters CFI (short for Canada Foundation for Innovation). The high-resolution image in Figure 3.8c) shows the final step of the manipulation process. Every blue spot is a single CO molecule adsorbed on a ”top position” of the underlying Cu substrate lattice. Thus, for example the separation of two CO molecules in the letter I is a mere 5 ˚ A. The same CO/Cu(111) system was used to write the small-  Chapter 3. Experiment and Theory  53  Figure 3.8: Manipulation of single CO Molecules on Cu(111)  a) To move CO molecules on Cu(111), the lateral manipulation mode was employed, where the tip is placed behind the target with a V=50 mV and large tunnelling currents I=80 nA. While the tip is moved along a line, the CO molecule hops from one site to the next site, which can be observed in the tip height. b) shows different CO manipulation steps on Cu(111). Finally one manages to write the letters CFI (c). The First single molecular manipulation done in Canada is depicted in d), ”the smallest UBC ever written”, which was accomplished during my masters thesis  Chapter 3. Experiment and Theory  54  est UBC, exhibited in Figure d, which was accomplished within my Master Thesis.  3.5  Simulating STM Images  Simulating STM images can be useful to understand the molecular appearance and the correlated electronic structure. There are various levels of approximations [106] to calculate the contrast obtained with an STM, which is typically divided into two parts. The first part calculates the electronic structure of the sample under investigation, the second, how the electronic structure is imaged with the STM. The electronic structure of an adsorbed molecule can be calculated with several methods ranging from Extended H¨ uckel Theory (EHT) to ab-initio calculations like Density Functional Theory. These simulations can determine the DOS, its spatial extent as well as the molecular binding energy to the substrate. The STM image, a result of tunneling processes between the sample and the tip electronic structure, can be calculated based on the Tersoff-Hamann model, presented earlier, or more sophisticated methods, which view the tunneling event as a scattering process [159]. For the work presented here, the Extended H¨ uckel Theory (EHT) was used to determine the electronic structure of a molecule and the STM image was then simulated, based on the Tersoff-Hamann model. The H¨ uckel approach is based on calculating a molecular orbital as a linear combination of atomic orbitals [160]. The resulting Hamiltonian matrix is diagonalized, giving the eigenvalues and eigenfunctions. The eigenvalues correspond to the energy levels of the molecular orbitals, whereas the eigenfunctions repre-  Chapter 3. Experiment and Theory  55  sent the orbitals’ spatial distribution. With increasing computational power, Slater orbitals were used as atomic orbitals, resulting in better agreement with experimental findings, which is referred to as Extended H¨ uckel Theory (EHT). Current software uses empirically determined information, such as atomic ionization potentials and electron affinities to evaluate the integrals, increasing the accuracy of the calculation. The Tersoff-Hamann model assumes a constant tip density of states and interprets the STM image as a direct representation of the DOS, summed over the energy interval [EF , EF + eV ]. The spatial contrast of a molecule, imaged in constant height mode, may be calculated by summing over the molecular orbitals, reaching with their resonances in this energy interval. EHT calculations proved to be successful in determining the orbitalsubstrate influence of benzene on Rh(111) [161], which was confirmed by photo emission experiments [162]. Lippel [163] and Smith [164] were the first who related STM images of organic molecules with simulations based on EHT and Tersoff Hamann model. Intramolecular resolution led to a better comparison with simulations and led to further advancement in the EHT computations [165]. A series of other studies proved the successful implementation of EHT combined with the THM to determine specific adsorption sites of molecules or relate their experimentally determined appearance to their electronic structure [166, 167, 168]. Aside from the proven capability to simulate STM images of larger organic molecules, there is an additional incentive to the combination of EHT and THM: It needs relatively small calculation power, compared to ab-initio calculations. Therefore, it is manageable as an additional tool for experimen-  Chapter 3. Experiment and Theory  56  talists; especially with current software. Moreover, the form and symmetry as well as the energy sequence of molecular orbitals computed with EHT compares well to density functional calculations. Our goal was to simulate the topography and dI/dV maps of porphyrin molecules on metal surfaces. The electron densities of the porphyrins were calculated using HYPERCHEMTM [169], after the molecule’s conformation was optimized using Molecular Mechanics routines or based on the findings of Near Edge X-ray Absorption Fine Structure (NEXAFS) experiments. An additional routine added up the appropriate molecular orbitals. It furthermore allowed variation of the density level for which the summed up DOS was plotted to get images representing different tip-sample distances [170]. Although no substrate interactions were considered, the results were surprisingly accurate, as will be demonstrated in the following chapters. The interactions between the porphyrins and the Cu(111) or Ag(111) surfaces manifest in a significant decrease of the energy gap between highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO), as well as a broadening of their distinct states. These energy shifts make the agreement between experiment and simulation at first glance even more staggering. However, it can be understood, if the Cu(111) and Ag(111) substrates are viewed as a homogenous electron gas, in analogy to Lang’s approach to model adatoms on metal substrates [171, 172]. The interaction of the frontier orbitals with the substrate’s constant density of states and the additional formation of an image potential, causes mainly a modification of the orbital energy alignment and broadening of discrete molecular levels into resonances, without changing significantly the shape of the molecular  Chapter 3. Experiment and Theory  57  orbitals [173]. Moreover, it is remarkable that most of the earlier mentioned EHT simulations were also performed on metallic < 111 > crystals. Thus, it is possible to simulate under specific circumstances a complex system with a very simple method sufficiently accurate to describe a system.  3.6  Experimental Set-Up  Investigating individual molecules and their self-assembly with a Scanning Tunneling Microscope requires well defined conditions. This involves, apart from the STM, Ultra High Vacuum (UHV), vibration isolation to reduce external interference to a minimum, and sample preparation devices. This section describes the experimental set-up, as well as the sample preparation.  3.6.1  STM  The beetle−type STM used here is a commercially available low temperature scanning tunneling microscope (LT-STM), produced by (CreaTec) after a home built design developed by G. Meyer at the Freie Universit¨at Berlin [174]. In the following section, the setup, working modes, the electronics and the cooling mechanisms of this STM are briefly introduced. It is a Besocke beetle type STM which consists of three outer and one inner piezo element, shown in Figure 3.9. The piezos are three dimensional tube piezos. The outer piezos’ movements are synchronised and they each have a sapphire sphere mounted on top of them. An approach plate, which holds the central tip piezo sits on the sapphire speres. The approach plate has three built-in ramps, of 2 degrees each, for the coarse approach. The outer piezos can move the approach plate and so the tip, towards or away from  Chapter 3. Experiment and Theory  58  Figure 3.9: Besocke-type STM  Schematic drawing of a Besocke type STM. The three outer piezos rotate the approach ring and the inner piezo holds the tip. The scanning can be done by both the inner or the synchronized outer piezos. The drawing dimensions of the piezos are not in scale for a better overview. the sample via moment of inertia drive. Once in tunneling contact, there are three piezo scan modes: The first uses exclusively the inner piezo for all three directions of the tip movement, the second uses only the three outer piezos and the third employs the inner piezo for the vertical tip movement, while the outer piezos are responsible for the lateral movement. For the work presented here, the latter mode was used. This combined mode has the advantages that it is the most stable and that the lateral scan direction of the tip is always the same compared to the samples’ crystal orientation. The STM is operated via a digital-signal-processor board (DSP), which is controlled by a program on a regular PC. This allows fairly straightforward electronics: a tunneling current preamplifier, a high-voltage amplifier for the piezos and a dividing amplifier for the sample-tip bias. The amplified tunneling current is fed through an analogue-digital (A/D)converter into the DSP and from there to the actual STM-software. In the other direction, the software controls over the DSP several D/A-converter,  Chapter 3. Experiment and Theory  59  which give the tunneling bias to the STM and the bias to the piezo elements through the high-voltage amplifiers. The feedback loop, correlating tunneling current and vertical tip height, can be implemented into the software and modified if necessary. The DSP, which works at 50 kHz, controls a wide range of applications through the PC program. Apart from several scan modes, there are different manipulation, spectroscopy and tip-forming modes. Additional channels of the DSP card are connected with D/A and A/D converters to read out the STM temperature and the lock-in amplifier output to do spectroscopy. The lock-in amplifier is connected to the STM electronics as follows. First, the lock-in amplifier creates an AC signal with which it modulates the tunneling bias and through that the tunneling current. This is done by feeding this AC signal into the electronics, where it is added onto the bias signal. The modulated tunneling current is divided into two branches after passing the preamplifier. One branch goes back to the electronics, and the second branch is fed into the lock-in amplifier. The latter gets convoluted with a reference signal as described in the spectroscopy section and gives out as a signal the differential conductance. The dI/dV signal is then returned to one of the free DSP channels to be read out by the software. Figure 3.10 shows schematically how the STM hangs on steel springs from the bottom of the cryostat to reduce vibrational interference. To further damp vibrational noise, an eddy-current brake is used, sitting with the magnets opposite to the STM’s base plate. The whole STM is cooled by the cryostat it hangs from, as shown in Figure 3.11. This bath cryostat has two reservoirs. The outer reservoir is  Chapter 3. Experiment and Theory  60  Figure 3.10: LT−STM  Overview drawing of the STM inside the radiation shield. The electronic pins are the counterpiece to the electronic contacts on the sample holder to apply the bias between tip and sample. The magnets oriented towards the base plate act as eddy-current brakes to reduce vibrational noise, after[175]  Chapter 3. Experiment and Theory  61  filled with liquid nitrogen, the central one with liquid helium. Radiation shields are attached at the bottom of the cryostat and surround the STM. Shutters in the radiation shields allow the sample transfer into the STM and in situ evaporation. For the sample transfer, and to cool the STM head down to 5 K, it is pulled via a cable onto the base plate of the inner radiation shield. The radiation shields also have two small windows for optical access. During the measurement, the STM hangs free from the springs. The equilibrium temperature in the hanging position after cooling the STM to 5 K is 8−10 K.  3.6.2  UHV System  To work under well defined conditions, a UHV chamber with a base pressure of 10−10 mbar is necessary as well as a set of sample preparation tools. The UHV-chamber is divided into two parts, a preparation chamber and an STM chamber, separated by a built-in VAT gate valve as shown in Figure 3.12. The whole chamber was modified from the original CreaTecTM design to satisfy our specific needs by Agustin Schiffrin, currently doing his PhD in our group. In the first chamber the samples are prepared, and the second chamber contains the LT-STM with the bath cryostat. To achieve the low pressures, a combination of different pump stages is used. Cold cathode gauges from PfeifferTM are used to monitor the status of the pressure. The pump system is divided in several stages, to reduce the pump gradient for each pump, reulting in a better end pressure. The first pump stage is the fore vacuum, where a dry membrane pump from PfeifferTM achieves a pressure of 1mbar, to fore pump the second pump stage. The second pump stage is a 70 l/s turbo pump from PfeifferTM reaching  Chapter 3. Experiment and Theory  62  Figure 3.11: He Bath Cryostat  Drawing of the cryostat. The double walled cryostat cools the STM and a temperature shield, which keeps the STM constant at a low temperature. The STM itself hangs from the bottom of the cryostat on springs to reduce vibrational noise, after[175]  Chapter 3. Experiment and Theory  63  pressures of 10−7 mbar, pumping the load lock and the third pump stage. The third stage is a 300 l/s turbo pump from LeyboldTM , pumping the rotational feed-through of the manipulator, the molecular and metal evaporators and the last pump stage. The fourth stage is again a 300 l/s turbo pump from PfeifferTM which pumps the preparation chamber and reaches pressures in the high 10−10 mbar regime. All turbo pumps have magnetic bearings for vibrational noise reduction. Both chambers are each pumped by an ion pump. These passive pumps decrease the pressure by half an order of magnitude and predominantly ensure a steady low pressure. The preparation chamber has an additional titanium sublimation pump. A titanium film is evaporated on a panel cooled with liquid nitrogen. The titanium binds most of the oncoming particles for the duration of its low temperature or until the film is saturated. It lowers the pressure to 1×10−10 mbar for about 2 hours and binds especially hydrogen. The STM chamber contains the bath cryostat, which acts like a large cryo pump. The cryostat’s inner temperature shields have a temperature of 5 K and condense particles on them. This yields to a lower pressure in the STM than measured by the cold cathode mounted in the bottom of the chamber. The only indication of the pressure inside the radiation shields is the time a sample stays uncontaminated, which is in our case several weeks. The preparation chamber contains all instruments to set up a sample for investigation in the STM: A sample storage for the sample holder, an argon ion sputtering gun to clean the crystal surfaces, a Low-Energy Electron Diffractometer (LEED) to analyze the sample, an Organic Molecular Beam Evaporator (OMBE), a metal evaporator, a load lock and a manipulator  Chapter 3. Experiment and Theory  64  Figure 3.12: Experimental Setup  Overview of the experimental setup. The UHV chamber is divided into two parts separated by a built-in VAT gate valve. The left chamber contains the devices for the sample preparation. The right chamber accommodates the STM and the cryostat.  Chapter 3. Experiment and Theory  65  Figure 3.13: Sample Holder  Schematic drawing of the sample holder[175]. The button heater and a thermocouple (not shown) can be actuated by the electronic contacts. Any of these contacts can be used in the STM to apply the bias voltage between tip and sample. to transfer the sample between the two chambers. The manipulator can be cooled down to 50 K with a helium flow cryostat and provides the connections for the heaters on the sample holders. The single crystals are each mounted on a separate sample holder, comprising a resistive button heater, as shown in Figure 3.13.  3.6.3  Tip and sample preparation  A crucial part of the STM is the tunneling tip. Initially the tip is formed by electro-chemical etching, where a tungsten wire is placed into a 2-molar aqueous sodium hydroxide (NaOH) solution, where the principle of the etching procedure is shown in Figure 3.14. The anode is an aluminum bar and the cathode is the actual tungsten wire. The etching process is strongest at the NaOH meniscus, where the wire penetrates the solution, making it possible to form very sharp tips [176]. The chemical reaction is  Chapter 3. Experiment and Theory  66  Figure 3.14: Tip Etching  Schematic drawing of the tip etching. The tungsten wire is placed into a NaOH solution and the tip is formed by electro-chemical etching. The etching is strongest at the NaOH meniscus forming very sharp tips  W (s) + 8OH − → W O4−2 + 4H2 O + 6e−  (3.15)  After the etching process the remaining oxides are removed with hydrofluoric acid and finally the tip is neutralized with distilled water. In the chamber the tip is sputtered via Argon ion bombardment and transferred into the STM via the manipulator on a special tip sample holder. The tip can be additionally formed in the STM by driving it, controlled by the program, four to five atomic layers into the sample. The controlled dipping for tip forming is a very common procedure with metal substrates. Additional ways to rework the tip in the STM are voltage pulses during scanning, or field  Chapter 3. Experiment and Theory  67  emission. The former is done by ramping the voltage very fast to 5−10 V, preferably over a free patch of the metal sample. The latter method is very effective, if the substrate does not allow tip forming (like semiconductors) or the tip is covered in molecules, which were picked up during the scan. The field emission is done as follows: 1.The tip is approached to the substrate until it is in tunneling contact and then pulled back with the coarse approach, so that the tip cannot be reapproached by the the vertical extent of the piezo itself. 2. The preamplifier is unmounted, as well as the tunneling bias cable from the electronics. 3. A high voltage power-supply (very little current is needed) applies a bias between tip (ground) and the sample (positive bias). Additionally a multimeter and a 1 MΩ resistor is hooked up in series between power-supply and tip. The multimeter allows monitoring of the current between tip and substrate (not higher then a few µA) . The resistor ensures that even if the tip touches the substrate and short-circuits, there is with a maximum bias of 1000 V no more current flowing than the fine cables of the STM can handle. 4. A bias of 500 V is applied between tip and sample (usually sufficient for this STM), and the tip is approached with the coarse approach in very small steps towards the sample, while monitoring carefully the multimeter. 5. As soon as a small current is detected (< 1 µA), the remaining approach should be done by deflection of the z-piezo. Thereby the current should not exceed 10 µA. 6. Initially the current will vary wildly, due to atomic and molecular clusters flying off the tip. As long as the current does not exceed the critical value  Chapter 3. Experiment and Theory  68  one keeps bias and distance until the current is stable. The ’dirtier’ and the more unstable the tip, the stronger the current variations. The current flow is often accompanied with an observable glow at the tip. 7. After the current is stabilised, the applied bias is slowly turned down to 0, the tip retracted and the original cabling reattached.  The tip itself is obviously only useful if there is a sample to investigate. The sample preparation of metal crystals is a standard procedure in surface science. The cleaning process is a combination of bombarding the substrate with argon ions, called sputtering, and annealing. This combination is referred to as one cleaning cycle. The base pressure before the cleaning is ideally in the order of 10−10 mbar. The ion bombardment sweeps away atomic and molecular contamination and the annealing of the substrate evens out the surface. For the sputtering, argon is introduced into the chamber through a leak valve until the pressure in the chamber is constant 2·10−5 mbar. The substrate is placed in front of the ion gun so that the beam of argon ions is normal to the substrate. The ions are typically accelerated with a bias of 1 kV. The current of ions hitting the substrate is approximately 5µA . After the sputtering the leak valve is closed obtaining again a base pressure of 10−10 mbar. The craters in the substrate, caused by the ion bombardment, are smoothed out by annealing the substrate. Cu(111) is annealed at 800 K and Ag(111) at 750 K. Due to the high mobility of the surface atoms the craters are compensated to energetically more favorable smooth surface configurations like flat terrace planes.  Chapter 3. Experiment and Theory  69  After the substrate is cleaned, molecules are evaporated by the OMBE onto the surface. The sample on the manipulator is then cooled with liquid nitrogen or helium to below 100 K before it is transferred into the STM. Cooling the sample further in the STM to 5 K takes typically three to four hours.  3.7  X-ray Absorption Techniques  X-ray absorption techniques are used in a variety of disciplines to probe the electronic structure of a compound. These techniques are, compared to STS, integral techniques, which average over a certain area or volume. The x-ray absorption edge is element specific and allows to investigate the chemical composition of a surface, what makes these techniques complementary to STM/STS. The techniques employed for this thesis, X-ray Photoelectron Spectroscopy (XPS) and Near-Edge X-ray Absorption Fine Structure(NEXAFS) spectroscopy, were carried out at the HE-SGM beamline of the Berlin synchrotron radiation facility BESSY II with the support of Dr. Klappenberger, Dr. Strunskus and Prof. W¨oll. XPS was used to investigate the chemical environment of specific elements in the porphyrin molecules, whereas the orientation of its subgroups was determined via NEXAFS.  3.7.1  X-ray Photoelectron Spectroscopy (XPS)  X-ray photoelectron spectroscopy (XPS) measures distinct core electron states of an element and the chemical state of this element in a material. This technique is sensitive to the first few nanometers of a material and is therefore applied extensively in surface science. The basic working principle is com-  Chapter 3. Experiment and Theory  70  paratively simple: an incoming photon knocks an electron out from an atom via the photoelectric effect. The electron is then detected by an analyzer. Monochromatic photons with energy ν are absorbed by an atom, exciting an electron with the corresponding photon energy, which is then emitted, ionizing the atom. The kinetic energy of these electrons is determined by their binding energy in the atom Eb and the work function φS of the material, compare also Figure 3.15.  Ekin = ν − Eb − ΦS  (3.16)  The particular binding energy of these core electrons is element specific. By recording the kinetic energy distribution of the emitted photoelectrons, the empirical formula of a compound under investigation can be determined. To have a common reference frame for the energy measurement, the sample and the analyzer are electrically connected to equalize the Fermi levels. From the ratio of the different peak intensities in a spectrum, one can determine the stoichiometric ratio of the different chemical species, since the cross section of the photoinization is nearly independent of the valence states of the atom. A further advantage of XPS is its sensitivity to the local charge distribution, which was exploited for the work presented here. The energies of the core levels shift, depending on the chemical environment of the corresponding atom. The effective binding energy measured is a consequence of different contributions: ef f Ebin = Eb + ∆Echem + ∆EM ad + ∆Erint + ∆Erext  (3.17)  Here the chemical shift ∆Echem and the Madelung term ∆EM ad account  Chapter 3. Experiment and Theory  71  Figure 3.15: X-ray Photoelectron Spectscopy  Energy diagram for the emitted photoelectrons in XPS. The kinetic energy of the photoelectron is a result of the photon energy ν minus the electrons binding energy Eb , minus the work function of the sample ΦS . The kinetic energy of the photoelectron is detected by an electron energy analyzer  Chapter 3. Experiment and Theory  72  for static effects influencing the ground state energy, whereas ∆Erint and ∆Erext account for relaxation effects related to core electrons and valence electrons, respectively. The chemical and Madelung shift are determined by the chemical environment of the corresponding atom. The chemical shift ∆Echem describes the effective charge of an atom (oxidation state) and accounts for the influence of a bond to an adjacent atom. The Madelung term ∆EM ad on the other hand contains the influence of the surrounding environment to the effective potential of the ionized atom. An example of these two shifts is a covalent bond between a nitrogen and hydrogen atom. The N1s binding energy for unadulterated nitrogen is 398 eV. Due to the different electronegativities of these two elements, an effective charge transfer will take place when they bond, shifting the binding energy of the N1s state to higher energy, 400 eV (less screening of the Coulomb potential). This is the chemical shift. If this molecule is now part of a larger molecule, the surrounding ions influence the effective potential energy. This is called the Madelung term. If this molecule is brought close to a a metal surface (less then 10 ˚ A away), a shift to lower binding energies is observed. This results from the additional screening of the corresponding Coulomb potential by the electron gas of the metal surface, lowering the ionization potential and therewith the binding energy. Additionally, the molecule can have a dipole moment, polarizing its surroundings and introducing an image potential in the metal influencing the effective Coulomb potential again. The ionization, during the XPS measurement, increases the polarization of the molecules surroundings. In this thesis a typical investigation consists of comparing binding energies and intensities of the different core levels for several samples, in order to understand the  Chapter 3. Experiment and Theory  73  evolution of the molecule’s chemical state adsorbed on a metal surface. X-rays are well known to penetrate deep into the material. How can XPS be surface sensitive? The x-rays may well penetrate the whole sample, however, the generated photoelectrons have only a short mean free path in solids, which depends on their kinetic energy [177]. In the range between 10 and 1000 eV the mean escape depth is 1-3 nm. The photoelectrons detected, originate therefore from close to the surface. This fact is also exploited for angle resolved XPS in order to obtain a depth profile of the chemical composition. To account for inelastically scattered photoelectrons, a retarding voltage is applied, allowing electrons to pass to the analyzer only above a certain kinetic energy. The remaining background correction is usually done by the method established by Shirley [178].  3.7.2  Near-Edge X-ray Absorption Fine Structure (NEXAFS) Spectroscopy  In contrast to the described XPS technique, NEXAFS spectroscopy detects the photon energy-dependent absorption coefficient for the incoming X-rays. NEXAFS detects specific elements in a compound as well, but is in addition highly sensitive to the transition from core electron states into discrete unoccupied molecular states. These transitions epitomize the absorption fine structure and enable bond-specific properties of a molecule to be investigated. NEXAFS usually employs soft X-rays ( ν <1000 eV), distinguishing itself from other absorptive techniques by concentrating on the fine structure within approximately 30 eV of the absorption edge. This region typically shows the largest variation in the X-ray absorption coefficient and is often  Chapter 3. Experiment and Theory  74  dominated by intense and distinct resonances. The underlying principle is the same as in XPS. The incoming X-ray excites a core level electron of the corresponding atom. In contrast to XPS, the photon energy dependent absorption of the X-rays is measured. This can be done by using a very thin sample, where the X-rays penetrate through and the transmitted X-ray intensity is recorded. While the photon energy is scanned through a certain energy interval one can measure absorption peaks at distinct photon energies, which correspond again to specific elements. If the sample is too thick, one can measure the absorption peaks indirectly. Once the core electron is excited by an absorbed X-ray, an electron from a higher state subsequently fills the hole in the core shell, thereby emitting an Auger electron or a fluorescence photon (compare fig 3.16). The intensity of either the fluorescent photons or the Auger electrons depending on the X-ray energy is a direct measure of the absorption. For this thesis, the Auger electrons were recorded by an analyzer. One additional advantage of absorption spectroscopy compared to XPS is that the excitation of the core electron does need not be to a free photoelectron state, ionizing the atom. Instead it can be excited into an unoccupied molecular orbital. As the X-ray energy is scanned, an absorption peak will be observed whenever the core electron can be excited into an unoccupied orbital. These transitions into distinct unoccupied molecular orbitals determine the so-called fine structure and give insight into the local bonding environment. This is also called the ”fingerprint” technique. One important aspect of NEXAFS is the ability to explore the orientation of a directional covalent bond into which the core electron is excited. The  Chapter 3. Experiment and Theory  75  Figure 3.16: X-ray Absorption  X-ray absorption process. The incoming x-ray ionizes the corresponding atom, by exciting a core electron into a free photoelectron state or into a unoccupied molecular bound state. Subsequently an electron from a higher state fills the core hole by emitting an Auger electron or a fluorescence photon. The NEXAFS experiments presented here detect the Auger electrons. While scanning through the photon energies, the absorption intensity will peak whenever a resonance between core electron and unoccupied molecular state is crossed. The absorption correlates directly with the emission of Auger electrons. These resonances determine the so called fine structure, giving insight into the local bonding environment.  Chapter 3. Experiment and Theory  76  excitation of the electron from the initial state into the final state depends on the overlap between the X-ray’s electric field vector and the transition dipole matrix element (TDM), which is ultimately correlated to the absorption intensity. By changing the angle between the E-field vector and the sample, the intensity of a resonance exhibits dichroism if the molecules are sufficiently well ordered. From the angle-dependent absorption one can deduce the bond orientation. Linearly polarized light is best suited to conduct these experiments. In particular, the transition from the 1s state to the unoccupied 2px ,2py or 2pz states, which form the unoccupied π and σ orbitals of aromatic molecules, can be exploited by this technique. Their TDM elements are oriented perpendicular to, or within the ring plane and can be used to determine the alignment of a molecule on a surface. In the case of a chemisorbed molecule, the π orbitals are involved in the bonding to the substrate, leading to a significant broadening. A more detailed description of this technique can be found in reference [179]. The necessity to scan the photon energy requires a tunable light source, which is provided by synchrotron facilities. Synchrotron radiation offers high intensities, brilliance and a wide energy range, allowing the access to core electrons of a large variety of atoms and enables experiments with a sensitivity sufficient for the study of adlayers in the submonolayer range. Different modes are employed to measure NEXAFS spectra. Most common are total and partial electron yield modes, in which a grid with a retarding voltage prevents electrons with an irrelevant kinetic energy from contributing to the signal. By doing so the signal is optimized for its sensitivity  Chapter 3. Experiment and Theory  77  to the molecular adlayer. Both XPS and NEXAFS experiments were performed under UHV conditions at the HE-SGM beamline at BESSY II. The UHV chamber comprised a sample preparation chamber and an analysis chamber, separated by a gate valve. The Cu(111) and Ag(111) crystals were cleaned by repeated sputter and anneal cycles as described before. The OMBE for evaporating the molecules was borrowed from our STM instrument. The XPS and NEXAFS measurements were performed at room temperature.  78  Chapter 4 Self-assembly and conformation of T etra-pyridyl-porphyrin molecules on Ag(111) We present a low-temperature scanning tunneling microscopy (LT-STM) study on the supramolecular ordering of tetra-pyridyl-porphyrin (TPyP) molecules on Ag(111). Vapor deposition in a wide substrate temperature range reveals that TPyP molecules easily diffuse and self-assemble into large, highly ordered chiral domains. We identify two mirror-symmetric unit cells, each containing two differently oriented molecules. From an analysis of the respective arrangement it is concluded that lateral intermolecular interactions control the packing of the layer, while its orientation is induced by the coupling to the substrate. This finding is corroborated by molecular mechanics calculations. High-resolution STM images recorded at 15 K allow a direct identification of intramolecular features. This makes it possible to determine the molecular conformation of TPyP on Ag(111). The pyridyl groups are alternately rotated out of the porphyrin plane by an angle of 60◦ .  4.1  Introduction  The controlled assembly of highly organized architectures on surfaces using functional molecular species is a promising approach to design novel nanos-  Chapter 4. TPyP absorbed on Ag(111)  79  tructured materials. Notably the formation and characterization of porphyrin adlayers on surfaces are of great interest from the fundamental and technological point of view. This class of molecules plays an important role in biological processes such as oxygen transport and photosynthesis. Accordingly, thin films assembled from these versatile molecular building blocks can be applied as optical switches [89], solar cells [84, 88] and sensors [91]. In the last decade two-dimensional assemblies of meso-substituted porphyrins have been investigated on various substrates making use of the excellent real space imaging capabilities of scanning tunneling microscopy (STM). Particular attention was given to two issues that embody the functionality of this class of porphyrins: First, the meso-substituents, often referred to as legs, are able to rotate around the C-C σ-bond connecting each of them to the porphyrin core (cf. Figure 4.1). This allows conformational adaptation of the molecule to its local environment. Accordingly, a wide range of dihedral angles Θ is observed. While large values (60◦ ≤ Θ ≤ 90◦ ) are typical in solid phases [180, 181, 182] smaller angles down to Θ=0◦ are suggested for molecules adsorbed on metal surfaces [63, 183], promoted by the increased coupling of the molecular π-system to the substrate. The rotation of a leg can also be directly induced by a tip of a scanning probe microscope [149], which even allows to determine the energy necessary to operate such a molecular ”switch” [65]. However, dihedral angles below roughly 60◦ result in distortions of the initially planar porphyrin core [184], as steric repulsion between hydrogen atoms of the ring and the hydrogens of the porphyrin core sets in [85, 185]. Second, meso-substituted porphyrins with a wide variety of endgroups can be synthesized. This makes them well-established building  Chapter 4. TPyP absorbed on Ag(111)  80  blocks for metal-organic networks in solid state chemistry [186]. On surfaces the dependence of their adsorption and self-assembly behavior on the chemical characteristics of the substituents is of special interest. It is the subtle balance between adsorbate-adsorbate and adsorbate-substrate interactions that controls the self-assembly of low-dimensional supramolecular nanostructures. For example, porphyrins functionalized by carboxyl groups enabling hydrogen bonding show an intermolecular ordering very different from the close-packed arrangement expected without hydrogen bonds [187]. Alternatively, substituents with an asymmetric charge distribution promoting dipole-dipole interactions between the porphyrins allow assembly of supramolecular aggregates with controlled size and shape, while the original porphyrins form compact islands [185, 188]. The influence of the substrate on the porphyrin adlayer formation process and the resulting structure was studied in solution on graphite and various Au surfaces [189, 190, 191, 192, 193, 194, 195]. Additionally, self-assembly of vapor deposited porphyrins was explored on several Au, Ag and Cu surfaces [94, 98, 196, 197, 198, 199]. Here, we focus for the first time on the supramolecular ordering of a vapor deposited pyridil-terminated porphyrin species in two dimensions. Specifically, we used 5,10,15,20-T etra(4-pyridyl)porphyrin (TPyP) molecules on Ag(111). TPyP as shown in Figure 4.1 consists of a central porphyrin core and four terminal pyridyl rings. The N-termination of the lateral groups, which favors linking to metal centers, makes TPyP a promising building block for supramolecular aggregates [200, 201] and elaborated metal-organic architectures [15, 182, 202, 203, 204].  Chapter 4. TPyP absorbed on Ag(111)  81  Figure 4.1: Scheme of TPyP  Model of the tetra-pyridyl-porphyrin (TPyP) molecule in its ground-state conformation. The top view (upper panel) highlights the central porphyrin core and the four terminal pyridyl groups, the legs. The latter are alternately rotated out of the porphyrin macrocycle plane resulting in two different sidelengths S1 and S2 in the subsequent STM images. In the side view (lower panel) the dihedral angle Θ ∼ 60◦ between the porphyrin plane and the pyridyl rings is indicated.  Chapter 4. TPyP absorbed on Ag(111)  82  Our high-resolution images of TPyP reveal well-ordered two-dimensional layers on Ag(111). From the data we determine the molecular conformation of the adsorbed species on the surface and conclude that the packing of the layer is controlled by intermolecular interactions while the orientation of the layer is induced by the coupling to the Ag(111) substrate.  4.1.1  Experimental Section  All experiments were performed in a custom-designed ultra high vacuum (UHV) apparatus with a base pressure below 2·10−10 mbar, comprising a lowtemperature scanning tunneling microscope (LT-STM). This highly stable instrument [174] capable of atomic manipulation was designed by G. Meyer at FU Berlin and is commercially available through Createc [175]. The Ag(111) single crystal surface was cleaned by repeated cycles of 800 eV Ar+ sputtering followed by annealing to 750 K. Subsequently, TPyP (97+% purity, Frontier Scientific) was deposited by organic molecular beam epitaxy (OMBE) from a quartz crucible held at 525 K. Typical evaporation rates are roughly 0.03 ML/min. The TPyP was thoroughly degassed prior to any experiments resulting in a background pressure in the 10−10 mbar range during deposition. Typically, coverages below full monolayer saturation were employed for the TPyP layers, in order to have bare metal patches available to form the STM tip and to determine the apparent height of the TPyP molecules. After dosing TPyP at substrate temperatures in the range of 100 to 500 K, the sample was cooled down and transferred into the STM, where constant current images were recorded at ∼15 K using electrochemically etched tungsten tips.  Chapter 4. TPyP absorbed on Ag(111)  83  In agreement with earlier STM studies and investigations employing complementary experimental techniques sensitive to the chemical structure of the molecules such as photoemission and x-ray absorbtion we presume that vapor deposited porphyrins adsorb intact on the sample surface [94, 205]. Furthermore, it was shown that tunneling on porphyrin adlayers applying resistances typical for molecular imaging does not distort the molecular electronic structure [206].  4.2 4.2.1  Results and Discussion Two-Dimensional Self-Assembly  Figure 4.2 shows STM images of the highly ordered layer structure resulting from TPyP deposition on Ag(111). The formation of large domains extended over hundreds of nm even at room temperature indicates a low diffusion barrier of TPyP on Ag(111). Accordingly, no single molecules can be immobilized even by lowering the substrate temperature to 100 K during deposition. One observes a staggered arrangement of clearly resolved molecular units. All molecules within a row (I) following a given direction are oriented the same way, while this orientation switches in the neighboring rows (II). Consequently, every second row shows the same molecular orientation. This characteristic pattern evolves in a wide substrate temperature range of 300 to 500 K. Figure 4.2c highlights the intramolecular features already detectable on the rather large scales of Figure 4.2a and b. Besides the core with a depression in the center, one can identify four protrusions forming a rectangle. From the molecular dimensions we assign each protrusion to one of the pyridyl legs. This is in agreement with the generally encountered paral-  Chapter 4. TPyP absorbed on Ag(111)  84  lel adsorption geometry of the porphyrin macrocycle on metal surfaces and indicates that the pyridyl groups are not oriented perpendicular to the molecular core (dihedral angle Θ = 90◦ ). The corresponding models in Figure 4.2c clarify the structure and help to identify molecular features. We describe this TPyP structure by a nearly rectangular unit cell with a molecule in every corner and a central molecule in a different azimuthal orientation. The unit cell parameters are as follows: b1 = 13.9 ± 0.2˚ A, b2 = 27.4 ± 0.2˚ A, β = 93 ± 2◦ . On the Ag(111) surface one can identify two types of domains, labeled Dδ and Dλ respectively. They are drawn schematically in Figure 4.3. The axis of the corner molecules is rotated either clockwise (Dδ ) or counter-clockwise (Dλ ) away from the long side of the unit cell. Thus, the non-chiral TPyP building blocks assemble into chiral domains, i.e. there is enantiomorphic ordering [78, 207, 208]. When checking the azimuthal orientation of the two domains relative to the substrate, we find that the domains are rotated by an angle ±α = 16◦ away from the close-packed substrate rows, one domain clockwise (+), the other one counter-clockwise (−). This means that these two domains are mirror images of each other, with the mirror plane perpendicular to the surface aligned along a substrate high symmetry direction. Consequently, the domains experience the substrate potential and the azimuthal orientation of the molecular layer is given by the interaction with the substrate. In the experimental data, all possible six distinguishable azimuthal domain orientations (-α, -α-60◦ , -α-120◦ ; α, α+60◦ , α+120◦ ) are observed.  Chapter 4. TPyP absorbed on Ag(111)  85  Figure 4.2: TPyP Self Assembled Layer on Ag(111  Characteristic structure of self-assembled TPyP layer on Ag(111). a) The overview STM image shows that all molecules within a row following the direction marked by the arrows are aligned the same way, while there are two distinguishable rows (I, II) exhibiting a different azimuthal orientation of the molecules (Vsample =−0.3 V, I=0.8 nA). b) On an intermediate scale the molecular entities are easily recognizable. c) The high-resolution image allows to identify intramolecular features (Vsample =−1.2 V, I=0.7 nA). Besides the core with a depression in the center, four protrusions corresponding to the legs are clearly discernible. The TPyP models including the unit cell (b1 , b2 ) highlight the structure and facilitate the identification of core and terminal pyridyl groups. (see text for details).  Chapter 4. TPyP absorbed on Ag(111)  86  Figure 4.3: Chiral Domains  Model of the two mirror-symmetric domain types observed for TPyP on Ag(111). The axis of the corner molecules is either rotated clockwise (on the right) or counter-clockwise (on the left) away from the long side of the unit cell. At the same time the domains are rotated by an angle α of 16◦ away from the close-packed substrate rows, one domain clockwise (−), the other counterclockwise (+). Thus, a substrate high-symmetry direction represents a mirror plane for the two domain types, indicating that the azimuthal orientation of the domains is mediated by the interaction with the substrate.  Chapter 4. TPyP absorbed on Ag(111)  87  To check the registry of the TPyP overlayer with the subjacent Ag(111) substrate we evaluate the epitaxy matrix C relating the overlayer unit cell vectors (b1 , b2 ) to primitive basis vectors of the substrate lattice (a1 , a2 ). The latter are extracted from atomic resolution images recorded on bare Ag(111) patches in between TPyP islands.     3.9 1.5 b1 a1  · a1 =C· = b2 a2 a2 −7.5 10.7 As no element of the matrix C is integer [209], we conclude that the TPyP overlayer is not commensurate with the underlying Ag(111) substrate. This notation based on a classification scheme for molecule-metal heteroepitaxy [210, 211] signals that not every equivalent molecule in the adlayer unit cell resides on an equivalent substrate lattice site. Accordingly, variations in the imaging height exist. Figure 4.4 shows a long-range intensity modulation, a quasi-hexagonal Moir´e pattern with a periodicity of roughly 43 ˚ A along the molecular rows. This indicates that the lateral intermolecular interactions dominate over site-specific adsorption on the smooth Ag(111) substrate. The Moir´e pattern is most pronounced in STM images recorded at low bias voltages. As the molecules act as scattering centers for the surface state electrons [212] one observes a standing wave pattern on the bare Ag(111) region in the bottom part of Figure 4.4. The observed molecular packing is in accordance with results from elementary molecular mechanics calculations. We applied the MM+ force field of the Hyperchem 7.5 molecular modeling package to calculate the noncovalent interactions, i.e. electrostatic and van der Waals forces [213] as a function  Chapter 4. TPyP absorbed on Ag(111)  88  of intermolecular distance and orientation. A similar procedure proved to reflect the relative energetics of different supramolecular arrangements formed by organic molecules on noble metal substrates quite accurately [214, 215]. The very low diffusion barrier and Moir´e pattern formation indicate weak site-specific coupling to the Ag(111) lattice. Thus we neglect electronic interactions with the substrate, the only restriction being that an in-plane alignment of the porphyrin cores is enforced. Starting with two molecules, position (x, y) and orientation (φ) of the two rigid entities relative to each other are changed in steps of 0.2˚ A (∆x, ∆y) and 5◦ (∆φ), respectively (cf. Figure 4.5a). During this process the geometry of a single molecule is not altered, we rather use the conformation shown in Figure 4.1 which is fully consistent with the experimental findings presented in the next section. From all the possible configurations the one shown in Figure 4.5a) has the lowest total energy. It is very close to the in-row alignment observed in the STM data (cf. Figure 4.2). This pair formation accounts for an energy gain of about 0.2 eV/molecule. In a next step a third molecule is added to find the best arrangement (Figure 4.5b). It is straightforward to extend this structure to the complete unit cell (Figure 4.5c). The calculated molecular packing scheme closely resembles the experimentally observed one. One obtains the parallel alignment of the corner molecules, while the central molecule has a different azimuthal orientation. Thus, the lateral coupling mediated by the pyridyl groups seems to be decisive for the molecular packing. Accordingly, a phenyl terminated porphyrin species forms a square unit cell on Ag(111) exhibiting a single molecular orientation [216].  Chapter 4. TPyP absorbed on Ag(111)  89  Figure 4.4: Moir´e Pattern  STM image at low sample voltage exhibiting a long-range intensity modulation, a Moir´e pattern. In the top left corner of the image the contrast is increased to emphasize the modulation. The white circles highlight the regions with an increased apparent height. Along the rows these areas are separated by about 43 ˚ A (arrow). In the bottom part of the image the bare Ag(111) surface is exposed exhibiting the well known standing wave pattern generated by surface state electrons scattered at the molecular lattice (Vsample =−50 mV, I=0.65 nA).  Chapter 4. TPyP absorbed on Ag(111)  90  Figure 4.5: Molecular Mechanics Simulations  Lowest energy configurations for a) two and b) three TPyP molecules confined to two dimensions, as calculated by applying the MM+ force field of the Hyperchem 7.5 package [213]. c) shows the complete unit cell structure as extrapolated from b). The resulting molecular packing scheme is very close to the experimentally observed one (cf. Fig. 4.2)  Chapter 4. TPyP absorbed on Ag(111)  4.2.2  91  Molecular Imaging and Conformation  After discussing the ordering of TPyP on Ag(111), we now address the imaging of the molecule’s intramolecular features and its conformation. At negative sample bias voltages where the occupied states of the molecule contribute to the tunneling current, the envelope of the molecules defines a rectangle (cf. Figure 4.2). The reason for this deviation from a square-like geometry is that the pyridyl groups are alternately rotated out of the porphyrin plane, as depicted in Figure 4.1 [63, 185]. This reduces the symmetry from square planar (D4h ) to D2d and results in two different side lengths S1 and S2 . By contrast, when we apply high positive bias voltages exceeding 0.7 V, we probe the unoccupied molecular orbitals and the imaged shape is close to a square. This voltage-dependence is clearly visible comparing the STM images in Figure 4.6a and b displaying the same surface region. A detailed discussion of the electronic structure of TPyP on Ag(111) is beyond the scope of this article and will be addressed elsewhere [217]. However, to interpret the contrast mechanism we simulated STM images based on semi-empirical extended H¨ uckel calculations in the framework of the package [213]. A constant electron density contour is obtained by integrating over the relevant molecular orbitals, which mimics a constant current STM image [170]. The electron density is given by a three dimensional reconstruction of the slaterorbitals on the basis of the eigenvectors calculated by HyperChem. The vertical position of the contour is then displayed in a color-coded image (Figure 4.6c and d). One can vary the density level for which the contour is plotted to get images representing different tip-sample distances and different tunneling currents, respectively. Similar methods relating calculated charge  Chapter 4. TPyP absorbed on Ag(111)  92  density maps of molecular orbitals to experimental STM data proved to be rather successful [106, 163, 165, 168]. Also in our case, the general molecular appearance can be reproduced surprisingly well, despite ignoring the substrate: For the occupied states we get some intensity from the core and the legs have roughly the same apparent height (Figure 4.6c, contributing molecular orbitals: HOMO to HOMO-6). For the unoccupied states the four bright lobes corresponding to the legs dominate the images (Figure 4.6d, contributing molecular orbitals: LUMO to LUMO+4). These findings indicate that the molecular orbitals are not too strongly perturbed by the substrate electrons [217]. Furthermore, the aspect ratio defined as S1 /S2 depends sensitively on the orientation of the pyridyl legs. Consequently, one can employ these simulations in conjunction with the high resolution STM data to determine the molecular conformation. To do so, we calculate images for different dihedral angles Θ, and extract the aspect ratios. They are plotted in Figure 4.7 as a function of Θ for the occupied and unoccupied states and compared to the experimental observations. The best agreement is achieved for a dihedral angle of 60 ± 5◦ . This value relates well to a TPyP dihedral angle Θ of ∼ 62◦ in a solid state phase [181], to Θ of 63◦ determined by ab initio calculations for the ground state of a gas phase TPP molecule [185] or to Θ=59◦ for TPP on a MoS2 surface extracted by X-ray absorption spectroscopy [60]. The similarity of these values for porphyrin molecules in completely different environments might be explained by the onset of energetically unfavorable ruffling of the molecular core due to steric interaction with the rotated meso-substituents around this Θ angle. While a significant distortion of the porphyrin core is not consistent with our experimental data,  Chapter 4. TPyP absorbed on Ag(111)  93  a slight nonplanar deformation can not be ruled out. It is important to note that Θ is directly related to the separation of the molecular core from the Ag(111) substrate (cf. Figure 4.7). Thus it controls for example the coupling of the metal center in metalloporphyrins to the substrate [94]. The assumption of a perpendicular orientation of terminal aromatic ring systems many reports are based on might not be well justified.  4.3  Conclusion  In summary, highly ordered chiral domains have been observed upon deposition of TPyP on Ag(111) in a wide temperature range. The characteristic supramolecular structure is explained in terms of intermolecular interactions mediated by the terminal pyridyl groups. The observation of a Moir´e pattern points to only a faint influence of the Ag(111) substrate on the ordering. A new approach to determine the conformational adaptation of adsorbed species by STM and simple electronic configuration analysis was presented: the dihedral angle Θ is roughly 60◦ . This finding is an important feature as the separation of the molecular board from the substrate plays a major role in the functionality of 2-D porphyrin layers.  Acknowledgements  We acknowledge partial funding by CFI, NSERC and BCKDF programs. WA thanks the swiss national science foundation for financial support, AW appreciates a scholarship from DAAD.  Chapter 4. TPyP absorbed on Ag(111)  94  Figure 4.6: Bias-Dependent Imaging  Voltage-dependent imaging of TPyP on Ag(111). STM images representing a) the occupied (Vsample =−0.9 V, I=0.65 nA) and b) the unoccupied electronic states (Vsample =1.6 V, I=0.65 nA). Both images display the same surface area, the defect on the bottom right can be used as marker. STM image simulations based on the semiempirical extended H¨ uckel method nicely reflect the rectangular shape for the occupied states (c) and the square-like pattern dominated by the pyridyl groups for the unoccupied orbitals (d).  Chapter 4. TPyP absorbed on Ag(111)  95  Figure 4.7: Dihedral Angle  Comparison of the aspect ratio (= S1 /S2 , cf. Fig. 4.1) extracted from the STM data (horizontal bars) to the aspect ratios from calculated images for different dihedral angles Θ (circles). This method provides a self-consistency test, since both the aspect ratios for the occupied (dark gray) and unoccupied states (light gray) are measured and calculated independently. Reducing the integration range (by three molecular orbitals) has a clearly smaller impact on the aspect ratios than changing the angle by a 5◦ step as indicated by the error bars. The comparison yields Θ = 60 ± 5◦ . This angle is directly related to the separation (about 4 ˚ A) of the molecular board from the outermost Ag(111) layer as visualized by the perspective view in (b).  96  Chapter 5 Tetrapyridyl-porphyrin on Cu(111): Chemical, physical and electronic aspects of a complex system We present a combined scanning tunneling microscopy (STM), near-edge X-ray-absorption fine-structure and x-ray photoemission study on the interaction of tetrapyridyl-porphyrin (TPyP) molecules with the Cu(111) surface in the 300−500 K temperature range. Upon deposition on a surface at 300 K molecules undergo a chemisorption process, leading to a pronounced conformational adaptation of the isolated molecules. After annealing molecular lines and networks evolve that are laterally connected by the coordination of pyridyl groups with Cu adatoms. Annealing temperatures higher then 470 K result in a substantial alteration of the intramolecular appearance in STM, that could be related to the deprotonation of the macrocycle without a conformational readaptation. The deprotonation was also induced by the STM tip in a controlled manner. Under appropriate conditions the deprotonation induces a change of the metal-organic structure formation.  Chapter 5. TPyP absorbed on Cu(111)  5.1  97  Introduction  The control of complex functional molecules on metallic substrates is of great interest and plays a central role in various fields of science and technology, ranging from heterogenous catalysis [208, 218] to molecular electronics [219], optoelectronics [88] based on organic thin films [220], or single molecule contacts [153, 154, 221]. The surface chemical bonding steers the mobility of the adsorbed molecular building blocks [222], which is decisive for a controlled self-assembly of functional architectures on the nanoscale [5]. Furthermore, the interaction between the substrate and a complex molecule, which exhibits internal degrees of freedom, frequently induces modifications of the molecular configuration, be it a conformational adaptation, change in the chemical composition due to bond dissociation or electronic structure caused by charge transfer [48, 223]. These interferences can even alter magnetic properties of molecules [99]. Furthermore, supramolecular nanostructures formed by hydrogen bonds often reveal small energy differences between various assembly modes [5, 224, 225]. Structural phase transformations of 2D networks were observed after temperature induced deprotonation of the carboxylic group, responsible for the molecular self-assembly [76, 226]. The presence of metal adatoms can also lead to a deprotonation, forming, instead of hydrogen bonds, metal-organic complexes and changing thereby character and form of the self-assembled structure [227]. A class of molecules with an intriguing variety of functional properties are porphyrins, which are exploited in both biological and artificial systems [228, 229]. Accordingly, these versatile molecules are promising building blocks to assemble functional nanostructures on surfaces. Moreover, porphyrins open up new opportunities to  Chapter 5. TPyP absorbed on Cu(111)  98  build sensors and optical and magnetic materials on the nanoscale [230, 231]. To profit from the variety of possible functionalities at the organic-metal interface, a comprehensive understanding of the complex interplay of physical, chemical and electronic effects at the single molecule level is necessary. Here we present a combined Scanning Tunneling Microscopy/Spectroscopy (STM/STS), Near-Edge X-ray-Adsorption Fine-Structure (NEXAFS) and X-ray Photoemission Spectroscopy (XPS) study of tetrapyridyl porphyrin (TPyP) on a Cu(111) surface in the 300 K to 500 K range. Upon deposition, the molecules bond to the copper substrate and undergo a distinct conformational adaptation. The electronic properties, determining the appearance in the STM images are strongly altered through a deprotonation process that can be excited thermally or in a controlled manner by the tip via voltage sweeps. We propose, that the presence of a Cu adatom gas interacts with the pyridl meso-groups, leading to metal-organic bonds and thereby to distinct structural formations. TPyP, shown in Figure 5.1, consists of a ring-shaped macrocycle, and four pyridyl groups attached at the meso-carbons, i. e., the carbon atoms connecting two pyrrol rings and one pyridyl ring. The macrocycle features two iminic nitrogen atoms (=N-) at the pyrrole rings (defining the main axis) and two pyrrolic nitrogen atoms (-NH-) at the pyrrole rings [232, 233]. The terminal nitrogen lone pair of TPyP is reactive towards metal centers (Cu [204, 234], Fe [182], Pd [235], Pb [236]), forming ordered three dimensional metal-organic networks. Porphyrins are well-known to adopt their conformation, depending on their environment [85, 180, 181, 182, 237]. The conformational adaptation  Chapter 5. TPyP absorbed on Cu(111)  99  Figure 5.1: Scheme of TPyP  Model of an isolated tetrapyridyl-porphyrin (TPyP) molecule in its groundstate conformation. The top view (upper panel) highlights the central, ringshaped porphyrin macrocycle, and the four terminal pyridyl groups, the legs. The side view (lower panel) displays the rotation angle θ and the inclination angle φ, which determine the conformation of the legs. Possible deformation of the macrocycle is described by the angles ρi .  Chapter 5. TPyP absorbed on Cu(111)  100  includes both the deformation of the macrocycle as well as the substituents. These distortions influence the physical and chemical properties, and thus the molecules’ functionality. We classify the conformation of TPyP by several degrees of freedom, namely the dihedral rotation angle θ, the inclination angle φ and the distortion angles ρi , where i indexes the number of a given pyrrole ring in the macrocycle. The angle θ describes the rotation of a pyridyl group around the C-C bond, connecting it to the porphyrin core, while φ indicates a inclination of this C-C bond out of the macrocycle plane [183] towards the surface. A positive angle φ means that the outer part of a pyrrol ring is pointing towards the substrate, thus the nitrogen atom is pointing away from the substrate. The orientation of the meso-substituents influences the shape of the macrocycle [85, 238], for θ less then 60◦ , steric repulsion between hydrogen atoms of the pyridyl ring and the hydrogens of the porphyrin macrocycle lead to a distorted macrocycle (ρi = 0). A prominent example is the saddle shape distortion, where pyrrol rings 1 and 3 are bend up (ρ1,3 > 0◦ ) and rings 2 and 4 are bend down (ρ2,4 < 0◦ ).  5.2  Experimental Section  All scanning tunneling microscope (STM) experiments were performed in a custom-designed ultrahigh vacuum (UHV) apparatus comprising a commercial low-temperature STM [175] based on a design described elsewhere [174]. The system’s base pressure is below 2·10−10 mbar. The Cu(111) single crystal surface was cleaned by repeated cycles of Ar+ sputtering (800 eV) followed by annealing to 780 K. Subsequently, TPyP (97+% purity, Frontier Scientific) was deposited by organic molecular beam epitaxy (OMBE) from  Chapter 5. TPyP absorbed on Cu(111)  101  a quartz crucible held at 525 K. Typical evaporation rates were roughly 0.03 monolayer/min (one monolayer corresponds to a densely packed molecular film). TPyP was thoroughly degassed prior to any experiments resulting in a background pressure in the 10−10 mbar range during deposition. TPyP was dosed at room temperature on the Cu(111) surface, where it was kept for 5 minutes or annealed at the indicated temperatures. Subsequently the sample was cooled down and transferred into the STM, where constant current images were recorded at about 11 K using electrochemically etched tungsten tips. The NEXAFS and XPS data were taken at the HE-SGM beamline at BESSY II in Berlin. For the NEXAFS measurements at the nitrogen K edge the partial electron yield mode (retarding voltage 270 V) was used. The energy resolution was approximately 0.5 eV. All spectra were recorded at room temperature and referenced against a characteristic peak (399 eV) in simultaneously recorded spectra of a carbon contaminated Au grid. Each incidence angle represents an average of four spectra. To concentrate on the information related to the TPyP adsorbate layer, we processed the raw data by subtracting the signal of the bare crystal, then corrected for the transmission through the beamline and finally normalized the edge jump to one (at 430 eV). Due to the consistency of the data throughout an entire series of NEXAFS measurements (approximately 2 h) we concluded that beam damage of the molecules played no role. The XPS data were obtained at room temperature with a photon energy of 500 eV and a pass energy of the analyzer of 50 eV providing a resolution of approximately 0.9 eV. All spectra were referenced against the Cu 3p3/2 line at 75.1 eV. Shirley background was subtracted from the raw data representing an average of more then 100 mea-  Chapter 5. TPyP absorbed on Cu(111)  102  surements. The limited data statistics prevented an analysis of the accurate XPS lineshapes and instead a Gaussian lineshape was used for the fitting.  5.3 5.3.1  Results and Discussion Temperature-Dependent Molecular Ordering and Appearance  Figure 5.2 shows STM images of TPyP on a Cu(111) surface after deposition just below room temperature (273 K, Fig. 5.2a), after annealing to medium temperatures (393 K, Fig. 5.2b) and high temperatures (500 K, Fig. 5.2c) respectively. Different phases of molecular arrangement can be noted, starting from a seemingly random distribution at 273 K, over first formations of triangular and linear segments at 393 K, to longer lines with sometimes hexagonal patterns at 500 K. The statistical distribution of TPyP over the surface at room temperature (RT) is evidence for a strongly suppressed diffusion. By contrast, on the less reactive Ag(111) surface the same molecule forms close-packed islands [239]. Hence, the interaction of TPyP with the more reactive copper indicates a more chemisorptive character. In a detailed analysis of this phase [240] it was found that the macrocycle is centered over a < 111 > −lattice bridge location and that the main axis, defined in Figure 5.1, is oriented along the high−symmetry orientations of Cu(111). In a high-resolution STM image (Fig. 5.2d) molecules appear as protrusions with two bright maxima (apparent height approximately 1.3 ˚ A) surrounded by two overlapping ellipsoids. From now on we will refer to this shape as ”sandwich-like”. The main axis is defined by connecting the two centers of the maxima. The comparison with a model of TPyP (inset) shows  Chapter 5. TPyP absorbed on Cu(111)  103  that the maxima are located over two opposed pyrrole groups and that the pyridyl legs are located at the terminations of the ellipsoids. After annealing the sample to 393 K (Fig. 5.2b), linear chain segments and triangular structures can be observed. Simply overlaying models onto the image suggests that the pyridyl nitrogen atoms of adjacent molecules face each other. The proximity of roughly 3.5 ˚ A, measured from atom center to center, is surprising at first because the polarized character of the pyridil groups should lead to a repulsive force for such an arrangement. We will come back to this point and discuss this in more detail in section C. In the high temperature case, TPyP forms longer linear chain segments and occasionally hexagonal structures (Fig. 5.2c). In the hexagonal configuration the intermolecular ordering differs from the triangular ones observed at 393 K, therein that the pyridyl groups do not face each other anymore, but instead face the pyrrole group of a neighboring molecule’s macrocycle. In the linear chain arrangements the spacing between adjacent nitrogen atoms is approximately 2.5 ˚ A larger (roughly a Cu(111) lattice constant) than in the medium temperature case. Furthermore, linear chains occasionally show small kinks, changing the direction of the linear assembly by a few degrees. These kinks however are situated within a molecule and not between molecules. A drastic change in the appearance of TPyP is evident, when comparing medium (Fig. 5.2e) with high annealing temperatures (Fig. 5.2f), while probing the sample’s occupied states. In the latter case molecules appear four-leaf ”clover” like, represented by four lobes, being located over the pyridyl groups (inset). In the case of hexagonal structures two types of protrusions exist. Those that are situated where three molecules touch each other appear higher  Chapter 5. TPyP absorbed on Cu(111)  104  Figure 5.2: Temperature Dependent Assembly of TPyP on Cu(111)  STM images of TPyP molecules adsorbed on Cu(111) after annealing the sample to 273 K (a and d), 393 K (b and e), and 500 K (c and f). Three phases can be observed. In a) and d) molecules are randomly distributed, with the main axis oriented along the < 111 > high symmetry directions. 393 K annealing b) and e) results in the formation of linear and triangular structures. c) High temperature annealing leads to longer linear and sometimes hexagonal structures. Additionally the appearance of the molecules undergoes a transition to from the ”sandwich” to the ”clover”-type. All images were taken at 11 K with the same applied bias of −0.7 V and tunneling current of 0.14 nA.  Chapter 5. TPyP absorbed on Cu(111)  105  and the remaining emerge identical as is the case of the linear chains, where typically all four protrusions appear with the same height. This appearance change cannot be explained by a bias effect, since both images were obtained with identical tunneling conditions (V= −0.7 V and I = 0.14 nA). A series of experiments with different tip apex showed the same behavior, ruling out a peculiar tip state as the cause for the appearance change. The adsorption sites for all three temperatures were determined, making use of the known registry of CO molecules as described elsewhere [240]. In all three cases the center of the molecule is situated over a bridge site indicating that an adsorption-site dependent contrast of the molecule [241] does not provide a reasonable explanation here. The last three arguments indicate that the different appearances of TPyP are connected to two different species, namely molecules that differ strongly either in their conformation or in their chemical state. Further experiments with changing adlayer coverages exhibited no dependence on the appearance of the molecules or on the ratio between linear and hexagonal configurations.  5.3.2  Molecular Conformation and Chemical State  NEXAFS measurements were performed for a multilayer (approximately 5 ML), a monolayer deposited at RT, and a monolayer annealed at 500 K with the aim was to investigate the molecules’ conformational state and chemical properties. NEXAFS allows one to obtain information on the chemical state and on the adsorption geometry of molecular adsorbates on surfaces [242]. In the case of large molecules composed of several subgroups, according to the building-block principle [242, 243], each subgroup can be analyzed sep-  Chapter 5. TPyP absorbed on Cu(111)  106  arately if their corresponding spectral parts can be sufficiently separated. This differentiated analysis is possible for adsorbed porphyrin molecules [60]. We focus on the nitrogen K-edge as the spectral separation is more apparant than for the carbon K-edge. The spectra of a TPyP multilayer (Fig. 5.3, top panel) shows five peaks in the π ∗ region (below 404 eV) and a broad σ ∗ structure. For our analysis of the molecular conformation we will focus on the π ∗ region, because a spectral separation is not feasable in the σ ∗ region. From earlier reports [60, 233, 244, 245, 246] it is expected, that peaks A, C, and D originate mainly from the macrocycle, whereas peak B is mainly due to the pyridine endgroups. Peak E should contain information on both parts of TPyP. The dependence of the intensity of these peaks on the incident angle α (Fig. 5.3, inset) is related to the angle between the corresponding π ∗ resonance and the surface normal. For a given geometry, the intensity of peak B should vanish for α = 90◦ , if the pyridyl group adsorbs completely planar on the surface. With increasing α, the intensities of peak A, C, and D become smaller, whereas the intensity of peak B stays approximately constant. In the multilayer the overall molecular plane, which is given by the four meso-carbons, can deviate from the surface plane, hence the interpretation of the NEXAFS data in terms of molecular conformation becomes ambiguous. Nevertheless, the data conforms with the assumption of a typical solid state conformation of TPyP [235, 236], i. e., with an almost planar macrocycle (ρi < 10◦ ,φ = 0◦ ) and pyridyl groups oriented with θ > 60◦ . When comparing the multilayer spectra with the spectra for the monolayer adsorbed at RT, two general trends are evident. First, all the peaks are broadened, such that only peaks B and C remain easily discernible. The  Chapter 5. TPyP absorbed on Cu(111)  107  Figure 5.3: NEXAFS Spectra of the N 1s Edge of TPyP  N 1s spectra of TPyP for the case of a multilayer (top panel), a monolayer deposited at 300 K (middle panel), and a monolayer annealed to 500 K. The incidence angle α (inset) denotes the angle between the surface normal and the E-vector of the incident light.  Chapter 5. TPyP absorbed on Cu(111)  108  broadening is attributed to hybridization of the molecular orbitals with the substrate states. Also short lifetimes of the excited states due to fast charge transfer into the substrate could further increase the width of the peaks. Second, the energetic positions of the peaks are shifted to higher energies indicating a change of the chemical state of TPyP. Both effects indicate that the molecule is strongly interacting with the surface. Before we discuss this interaction in more detail it is helpful to understand the conformation of the molecule. The angular dependences of peaks B and C differ remarkably from those of the multilayer case. Now, when α is increasing peak B gets smaller, whereas peak C becomes more pronounced. For a quantitative analysis we applied the following procedure. The three different types of N atoms (the pyridyl legs (Pyr), the pyrrolic in the macrocycle without (Mac N), and the iminic in the macrocycle with a H atom attached (Mac N-H)) produce characteristic resonances with angle dependences according to the orientation of the corresponding group, i. e., the pyridyl, the pyrrol rings on the main axis, and the pyrrol rings perpendicular to the main axis, respectively. Supported by earlier reports [233] we assume that the two macrocycle N atoms produce the same spectral shapes only shifted by the separation of their initial N 1s states. Thus for the spectral shapes we mimicked the N-edge of metal-tetraphenyl porphyrins [60, 244] that have only one type of N atoms in the macrocycle. The pyridine shape has been fitted according to refs. [242, 246]. In both cases several Gaussian curves were used, where the energy and width of the peaks have been defined relative to the first main peak. Then we fixed the relative energy shifts and widths to maintain a fixed shape per spectral part and adjust the position  Chapter 5. TPyP absorbed on Cu(111)  109  and the width of the main peak corresponding to our spectra. Finally we fitted the leading edge of the N 1s spectra with only three fit parameters representing the intensities of the molecular moieties. An example is shown in Figure 5.4a, where the experimental data (symbols) for α = 50◦ is compared to the fit (solid line) and the spectral decomposition in the three parts (Pyr = blue, Mac N = red, Mac N-H = green). The results of the fitting of the whole series are presented in Figure 5.4b, together with theoretical curves for the angles (30◦ - 60◦ ) between a π−type resonance with 3−fold symmetry and the normal on the surface. The values indicate that the pyridyl substituents have a tilt of 30◦ with respect to the surface, and that the on axis and off axis pyrrol rings feature a tilt of 40◦ , and 50◦ -55◦ respectively. We reported earlier [240], that with the help of high-resolution STM images and semi-empirical calculations it is possible to determine the conformation of the molecule using NEXAFS results. It was found, that the conformation must be similar to that depicted in Figure 5.4e (ρ1,3 = −40◦ , ρ2,4 =50◦ , θ < 10◦ , 20 < φ < 30◦ ). This particular conformation features an extremely distorted macrocycle as a result of the meso-substituents pointing down towards the metal substrate. In earlier NEXAFS studies of pyridine physisorbed on the Ag(111) substrate [247] no shift of the main resonance was observed between the multilayer and the monolayer, whereas for chemisorbed pyridine on Pt(111) [245] the shift amounted to 1.2 eV. Based on detailed ab initio analysis H¨ovel et al. [248] concluded that the shift of 0.6 eV of pyridine on a Zn terminated ZnO surface reflects the binding via the N lone pair. Accordingly, in our case the shift of 0.65 eV indicates chemisorption due to the pyridylic nitrogen lone pair pointing towards the substrate. The  Chapter 5. TPyP absorbed on Cu(111)  110  shift is smaller than on Pt(111), which is reasonable because the optimal chemisorption geometry, that is the whole pyridine plane aligned with the surface normal, can not be adopted due to the constraints imposed by the macrocycle. The shifts of the iminic (0.8 eV) and pyrrolic (0.7 eV) blocks are surprisingly stronger than the pyridylic shift, even though they are further away from the surface (Fig. 5.4e). We believe that the strong deformation of the macrocycle is an additional source for these shifts, but it remains unclear to which extent each of the two effects, chemisorption and distortion, are responsible for this behavior. Now we analyze the situation after annealing to 500 K. In the spectra for α = 30◦ (Fig. 5.3, lower panel) peak B is less pronounced than for the previous sample. The data for larger incidence angles reveal a new peak at slightly higher energy (399.5 eV). Apart from that, the positions and widths of the residual peaks remain the same. From the similarity of the shift of B’ with respect to the mutlilayer position of B, we attribute the new resonance to more stronly coordinating pyridyl substituents. Such an increase in coordination could result from Cu adatoms binding to the porphyrin legs. The angular dependences of the different resonances (Fig. 5.4d) provide results similar to the macrocycle distortion at 300 K. The pyridyl groups show a slightly smaller tilt (20◦ ) for the uncoordinated species and a slightly stronger tilt for the coordinated species (Pyr coor, 40◦ ). We conclude that the conformational state of TPyP is not significantly changed during annealing, and thus the change of the appearance in the STM images cannot be caused by a readaptation of the molecule. XPS measurements were performed for the N 1s region of three TPyP  Chapter 5. TPyP absorbed on Cu(111)  111  Figure 5.4: Spectral Deconvolution of the Leading N 1s Edge  Spectral decomposition of the leading edge of the NEXAFS spectra. a) The experimental data (symbols) for adsorption at 300 K and α = 50◦ are well fitted (solid line) with three spectral parts originating from the on-axis pyrrol rings (red line, Mac N), the pyridyl substituents (blue line, Pyr), and the offaxis pyrrol rings (green line, Mac N-H). b) The normalized intensities of the three spectral parts compared to theory. c) After annealing to 500 K the peaks are even broader, the angle dependence of the normalized intensities (d) indicate the same value, i. e. the conformation of TPyP is the same before and after annealing to 500 K.(e) shows a model of TPyP on Cu(111) based on the interpretation of the NEXAFS data.  Chapter 5. TPyP absorbed on Cu(111)  112  samples. A multilayer sample was used as a reference for the plain molecule (with only weak intermolecular interactions). The comparison with a monolayer adsorbed at RT allows to characterize the molecule-substrate interaction. Finally after annealing at 500 K the data reveal thermally induced changes of the chemical state. As already mentioned, TPyP features three chemically different types of nitrogen atoms. The substituents incorporate four pyridylic types and the macrocycle two of pyrrolic (-NH-) nature and two iminic (=N-) ones, respectively. For all the fits we used three peaks attributed to these types with a fixed intensity ratio (2:1:1) and the same width. An additional fourth peak of small intensity was allowed to ease convergence of the fit. It accounts for the difference between our simple physical model the fit is based on and will not be discussed further. In the multilayer spectrum (Figure 5.5, top panel) the peaks at 400.1 eV and 398 eV are attributed to pyrrolic and iminic nitrogens respectively, in accordance with typical values for porphyrin in the solid state [232]. The third feature at 399.1 eV must result from the pyridylic nitrogen atoms due to the intensity ratio argument. The data for the monolayer at RT (center panel) reveal a general tendency towards lower binding energies. In contrast to NEXAFS, the XPS technique is based on an ionizing excitation. Hence, to interpret the shift of binding energies, the polarization of the surrounding environment needs to be taken into account. The pyridylic peak shifts (-0.8 eV) almost twice as much as the two macrocycle components (pyrrolic and iminic, both -0.5 eV) indicating that the strongest interaction is taking place between the meso substituents’ nitrogens and the copper substrate. The corresponding shift  Chapter 5. TPyP absorbed on Cu(111)  113  between a pyridine multilayer [248] and being physisorbed on Cu(111) [249] are significantly smaller [∼0.3 eV] than in our case. For chemisorbed phases the shift is typically between 1 eV and 2 eV for the case of W(110) [250] and Ni(110) [251], respectively. Ni possesses values for its electronegativity and electron affinity which are similar to those for Cu. Thus, we attribute the pyridylic shift to a coordination of the pyridyl substituents with Cu surface atoms. In accordance with the geometry concluded from NEXAFS, the XPS indicates that the coordination is not carried out to its full extent. The macrocycle shift indicates that its adsorption character is between physisorption and chemisorption. After annealing the sample at 500 K (Fig. 5.5, lower panel) the most significant change is the shift of the pyrrolic signal to lower binding energies (−1.2 eV compared to 300 K). The new position (398.4 eV) is consistent with deprotonated polypyrrols [252, 253] and therefore we conclude that the macrocycle has lost its two hydrogen atoms. The second iminic peak remains at 397.5 eV. The pyridylic peak is now placed at 397.8 eV, the further shift to lower binding energies (−0.5 eV) indicates an increased coordination, probably due to Cu atoms. Spectroscopy We carried out STS measurements on both species with the aim to investigate the electronic structure of the TPyP/Cu(111) system. Typically for physisorbed or weakly chemisorbed molecules, peaks in the dI/dV spectra originate from molecular orbitals, broadened by the interaction with the metal substrate [254]. Recently, we investigated by dI/dV mapping the spatial distribution of the molecular orbitals of a similar molecule, namely cobalt-  Chapter 5. TPyP absorbed on Cu(111)  114  Figure 5.5: XPS of the TPyP’s N 1s Region  XP spectra of the N 1s region of TPyP for a multilayer of (top panel), a monolayer at 300 K (center panel) and a monolayer annealed for 10 min at 500 K (bottom panel). The experimental data (symbols) were fitted (red line) with three peaks (blue), namely the pyridylic (dotted line), the pyrrolic (dashed line), and the iminic (dash-dotted), as visualized by the model. The shifts of the peaks (vertical lines) indicate a coordination of the meso-substituents to Cu and a deprotonated macrocycle in the annealed case in which also the coordination is increased.  Chapter 5. TPyP absorbed on Cu(111)  115  tetraphenylporphyrin (Co-TPP), on the same substrate [255]. In contrast to Co-TPP, the STS spectra for TPyP on Cu(111) (not shown) indicate no evidence of resonances for both species in an energy interval of ±2000 meV. Normalizing the dI/dV spectra by dividing by I/V increases the contrast, making wide peaks more evident [256]. By normalization of the spectra of the cloverleaf species, very broad (800-1000 meV) peaks could be observed. This behavior was independent of alternating lock-in amplifier settings, and the status of the tip. The absence of peaks, respectively the large width of them are indications of hybridization of the molecular orbitals with the metal states and thus for chemisorption. We were not able to map the molecular orbitals for either of the species. The results of the NEXAFS and the XPS measurements suggest that the change from the sandwich to the cloverleaf appearance is induced by the deprotonation of the macrocycle. We carried out two additional experiments to test this hypothesis. First, we assume that at temperatures, where the deprotonation is about to start, only a part of the ensemble of molecules should lose their H atoms as reported earlier [76, 227, 257, 258, 259]. Indeed, the STM data (Fig. 5.6a) of a sample annealed to intermediate temperatures (430 K) reveal a mixture of the two species, sandwich and four-leafed clover, consistent with our assumption. Some molecules are marked (yellow frame) to facilitate the identification of single species. In rare cases molecules appear as if they would consist half of the sandwich and half of the four-leafed clover type. This appearance can easily be explained assuming that the macrocycle has lost only one of its two hydrogens, resulting in sandwich appearance for the molecular half with a hydrogen atom attached and in cloverleaf appear-  Chapter 5. TPyP absorbed on Cu(111)  116  ance for the deprotonated half. To make sure that the clover-like molecules at intermediate temperatures not only show the same appearance, but really are the same species as the one appearing for the high annealing temperature, we analyzed the maximum apparent height along the profiles indicated in Figure 5.6a. We found a statistically relevant difference of 0.4 ˚ A ,i.e., the sandwich species (α) are higher than the clover species (β), independent of the bias voltage (inset). After annealing to 520 K (Fig. 5.6b) exclusively cloverleaf-shaped molecules are present. The profiles (β ) yield values for the voltage dependent apparent height (green symbols in the inset) that are identical to the ones for the cloverleaf molecules in Figure 5.6b, demonstrating the existence of identical states. Second, we succeeded in controlled tip-induced switching of sandwich molecules into clover-leaf molecules. We recorded tunneling spectra up to 3 V (stabilizing conditions V=-1 V, I=0,1 nA) over molecules that showed the sandwich appearance for one or both halves (Fig. 5.6c). We observed a kink in the current (inset Fig. 5.6c,d) occurring between 2.3 V and 2.5 V, only when the spectra was taken at a specific place (cross). After a spectrum showed such a kink, the subsequent topographical image revealed a clovertype molecule (Fig. 5.6d). The switching was irreversible, all of our attempts to achieve the converse were unsuccessful. The irreversibility of the process rules out a conformational change as the origin of the switching [67, 183, 260] and points to a tip-induced deprotonation [259].  Chapter 5. TPyP absorbed on Cu(111)  117  Figure 5.6: Thermal and Bias-Induced Change of the TPyP Macrocycle  Thermally and tip induced deprotonation of TPyP leading to a modification of the molecular appearance. a) Intermediate annealing temperatures (430 K) result in a mixture of ”sandwich” type molecules (α) and ”clover” type molecules (β). The profiles (dotted lines, 25 measurements per profile) of the two species exhibit a constant difference of 0.5 ˚ Afor the apparent heights in the whole bias range (inset a,b). b) After annealing to 520 K the uniform appearance and voltage dependent apparent height (β ) are identical to β. c) At imaging temperatures (10 K) a molecule that shows the ”sandwich” appearance for one half (frame) is irreversibly switched to a ”clover” type (d, frame) by taking a tunneling spectrum from 0 to 3 V at the indicated point (cross). The switching process is joined with a kink in the tunneling spectra (inset) that appeared constantly between 2300 and 2500 mV for different molecules.  Chapter 5. TPyP absorbed on Cu(111)  5.3.3  118  Role of Adatoms and Metal-Ligand Interactions  The different information obtained by the four techniques (STM, STS, NEXAFS and XPS) suggest the following overall scenario. Annealing the sample at high temperatures leads to a deprotonation of the pyrrol group. The remaining negative excess charge is likely to transfer into the metal sample, due to the chemisorptive character of the TPyP-Cu interaction, exhibiting no distinct energy gaps that would prevent the additional electron from merging with the metal Fermi sea. This would reduce the LDOS in the center of the macrocycle, leading to the cloverleaf like appearance after annealing at higher temperatures. The presence of a metal adatom gas at elevated temperatures leads furthermore to a Cu complexation with the pyridil end-groups, shown by the core-level shifts of the involved nitrogens to smaller energies. This shift suggests a partial charge redistribution towards the nitrogens, increasing the LDOS over the pyridyl groups. Moreover, such metal-organic complexes would explain the observed formation of linear chains. Although the strong interaction with the Cu(111) substrate can dominate the self-assembly, it is ambiguous, as to why a repulsive force would lead to a lowering of the energy, resulting in oppositely placed pyridylic N atoms. In contrast, this geometry fits well with the assumption of metal-organic bonds between the pyridyl groups and Cu adatoms similar to networks [204, 234] in three dimensions. Even though Cu(111) does not exhibit a concentration of adatoms as high as Cu(110) or Cu(100) [261, 262] for the same temperature, the density at 500 K is sufficient to explain the proposed metal-ligand bonding. The novel formation of assemblies at higher temperatures, where the pyridil groups of the corresponding molecule face  Chapter 5. TPyP absorbed on Cu(111)  119  the pyrrol groups of the adjacent molecule is not clear. Possible explanations might be an additional configuration, which is energetically accessible above 500 K or the correlation of an altered chemical reactivity due to the evidently modified LDOS. This illustrates again clearly how difficult it is to draw conclusions about conformational adaptation from topographic STM images of adsorbates, advocating for the combination of complementary surface sensitive techniques to achieve a clearer picture. Based on this model, a hypothesis on the character of the observed network formation can be formed, illustrated in Figure 5.7. While the formation of linear chain links at 393 K is provided by a linking Cu adatom between two opposing pyridyl groups, the density of adatoms above 500 K is sufficient to supply each pyridyl group with an adatom. The coordination of copper adatoms in reference to the substrate and the molecules, is illustrated by lying an < 111 > −surface lattice over the STM image. Figure 5.7a shows the situation after annealing at 393 K. The indicated adatoms, red and orange circles are speculative since there is no visible evidence. Therefore the possible adatoms were placed in the center of a direct line between two facing pyridilic nitrogens. The distances were established using a HyperchemTM model of the Cu(111) substrate and a TPyP molecule based on the NEXAFS conformation, both matched with the actual images presented in Fig. 5.7. The red circles represent linking Cu atoms between linear chain segments with a center-N to center-Cu distance of 2.5 ˚ A, sitting on a bridge position. The orange circles represent the adatoms linking the triangular structures, with an increased distance (2.9 ˚ A), sitting on a top  Chapter 5. TPyP absorbed on Cu(111)  120  Figure 5.7: Model of Cu Adatom Mediated TPyP Assembly  Model of the TPyP adsorption site at a) 393 K and b) 500 K with underlaid Cu(111) lattice (green) and the presumption of the Cu adatom site (red). At 393 K the distance between linker atoms for linear structures would be 2.5 ˚ A(sitting on < 111 > lattice bridge site), for the triangular ˚ case 2.9 A(sitting on top site) indicated with orange circles. After 500 K annealing each pyridil group possesses a Cu adatom (sitting over hollow site), 2˚ Afrom the N lone pair.  Chapter 5. TPyP absorbed on Cu(111)  121  position. The pyridil-adatom distance for the triangular structures matches with studies on comparable Cu-carboxylate systems [227, 263], where Chen et al. do not resolve the Cu adatoms either [227]. At higher annealing temperatures the formation of linear and hexagonal chains is not that evident (compare figure 5.7b). The distances between linearly assembled molecules is increased by 2.5 ˚ A, which would spread the center to center distance between a linking Cu and a N to approximately 4 ˚ A. Since we have found nowhere evidence for such long-range metal ligand bonds, we presume each pyridil group is provided with an adatom. Due to the same appearance of TPyP in the hexagonal structure we tentatively suggest there the same configuration of adatoms.  5.4  Conclusion  Our experiments demonstrate the complex effects that can appear at the interface of a large functional molecule with a reactive metal substrate in the temperature range from 300 K to 500 K. The complementary information obtained by the different surface sensitive techniques, namely STM/STS, NEXAFS and XPS, fit together to provide one general picture. Annealing the sample from RT to 500 K three different phases are observed, where at 300 K the strongly distorted molecules are anchored individually. Annealed to 393 K metal-organic networks begin to form by linking facing pyridylic N lonepairs via copper adatoms, resulting in linear and triangular structures. The third phase occurred by heating the sample to 500 K and is characterized by a significant change in appearance and a new bonding motif that can lead to hexagonal arrangements under appropriate conditions. Counter  Chapter 5. TPyP absorbed on Cu(111)  122  intuitively, the conformation, as well as the adsorption-site remains constant during annealing and the appearance change and is explained by a change of the electronic structure initiated by the deprotonation of the macrocycle.  Acknowledgements  We acknowledge Ch. W¨oll and Th. Strunskus for providing technical support for the HE-SGM beamline at BESSY-II as well as for contributing scientific experience to the analysis. We thank S. H¨ ufner and G. Sawatzky for fruitful discussions. Work supported by Canada Foundation of Innovation (CFI), National Science and Engineering research Council of Canada (NSERC), British Columbia Knowledge Development Fund (BCKDF). W.A. thanks the Swiss National Science Foundation (SNF) and A.W.-B. the German Academic Exchange Service (DAAD) for a scholarship, respectively. Support of the travel of A. W.-B. to the Berlin synchrotron source by the BCSI is gratefully acknowledged.  123  Chapter 6 Conformational adaptation and selective adatom capturing of tetrapyridyl-porphyrin molecules on a copper (111) surface We present a combined low-temperature scanning tunneling microscopy and near-edge X-ray-adsorption fine-structure study on the interaction of tetrapyridyl porphyrin (TPyP) molecules with a Cu(111) surface. A novel approach using complementary experimental data and image simulations allows a determination of the adsorption geometry of TPyP on Cu(111). The molecules are centered on bridge sites of the substrate lattice and exhibit a strong deformation involving a saddle-shaped macrocycle distortion as well as considerable rotation and tilting of the meso-substituents. We propose a bonding mechanism based on the pyridyl-surface interaction, which mediates the molecular deformation upon adsorption. Accordingly, a functionalization by pyridyl groups opens up pathways to controlling the anchoring of large organic molecules on metal surfaces and tuning of their conformational state. Furthermore, we demonstrate that the affinity of the terminal groups for metal centers allows one to selectively capture individual iron atoms at low  Chapter 6. Conformational Adaptation of TPyP on Cu(111)  124  temperature.  6.1  Introduction  The control of large functional molecules at metallic substrates is of great interest and plays a centrol role in various fields in science and technology, ranging from heterogenous catalysis [208, 218] to molecular electronics [219], optoelectronics [88] based on organic thin films [220], or single molecule contacts [153, 154, 221]. The surface chemical bonding steers the mobility of the adsorbed molecular building blocks [222], which is decisive for a controlled self-assembly of functional architectures on the nanoscale [5]. Furthermore the interaction of complex molecules exhibiting internal degrees of freedom with the substrate frequently induces modifications of the molecular configuration, be it a conformational adaptation or a change in the chemical composition or electronic structure [48, 223]. These effects are reflected in a varied chemical reactivity, induced charge transfer or altered magnetic properties [99]. Thus it is of fundamental interest to determine the adsorption geometry, i.e. the internal conformation as well as the adsorption site of the molecule on the substrate atomic lattice. This set of information allows to categorize adsorbate-substrate interactions and yields a basis for a theoretical discussions of important issues as bonding mechanisms, bond energies, electronic level alignment or functional properties based on conformational or supramolecular design. Because of its excellent real space imaging capabilities Scanning Tunneling Microscopy (STM) is ideally suited to observe, characterize and manipulate individual molecules on conducting substrates. Notably the conforma-  Chapter 6. Conformational Adaptation of TPyP on Cu(111)  125  tion [63, 183, 185], mobility [190, 191, 193, 196, 264, 265] and self-assembly [94, 197, 239] of porphyrin species on metal surfaces attracted considerable interest in recent years. This class of molecules exhibits an intriguing variety of functional properties, which are exploited in both biological and artificial systems [228, 229]. Accordingly, these versatile molecules are promising building blocks to assemble functional nanostructures on surfaces, specifically opening up new opportunities to build sensors and nanoscale optical and magnetic materials [230, 231]. In the context of this article it is relevant to mention two features connected to the functionality of porphyrins. The rotational degrees of freedom of the chosen meso-substituents and the flexibility of the porphyrin macrocycle allow for a conformational adaptation of the molecule to its local environment. Relative to the molecular core, the conformation of the leg is determined by two angles (θ and φ), which are indicated in Figure 6.1. The angle θ describes the rotation of a pyridyl group around the C-C bond connecting it to the porphyrin core, while φ indicates a bending of this C-C bond out of the macrocycle plane [183]. To some extent, the dihedral angle θ and the nonplanar deformation (ρ) of the macrocycle are interconnected through steric repulsion between hydrogen atoms of the ring and the hydrogens of the porphyrin macrocycle. Accordingly, many reports on macrocycle distortions as well as varying dihedral angles are available for solid state phases [85, 180, 181, 182, 237]. On surfaces however, the vast majority of studies focuses solely on the orientation [63, 183, 239] and considerate manipulation [65, 66] of the meso-substituents. Only some recent reports speculate on nonplanar adsorption geometries [67, 99, 185, 239], however by pure STM imaging the question of intramolecular structure cannot  Chapter 6. Conformational Adaptation of TPyP on Cu(111)  126  be quantitatively addressed. Meso-substituted porphyrins with a wide variety of endgroups can be synthesized. This provides a series of building blocks for metal-organic networks in solid state chemistry [15, 186]. Specifically tetraarylporphyrins functionalized by pyridyl substituents interact via the terminal nitrogen lone pair with a wide variety of reactive metal centers (Cu [204, 234], Fe [182], Pd [235], Pb [236]) to form ordered structures. By contrast, on surfaces, the pyridyl mediated interaction of porphyrins with the substrate or coadsorbed atoms was not explored to date. Nevertheless, the considerate choice of substituents with specific chemical or electrostatic characteristics allows to tune the adsorbate-adsorbate interaction [187], and thus to assemble not only supramolecular aggregates with controlled size and shape [185] but also nanoporous host networks [266, 267]. Here, we focus on the detailed understanding and control of adsorbatesubstrate interactions. By employing a nitrogen termination, it is possible to anchor tetrapyridylporphyrin (TPyP) on the smooth Cu(111) surface and to inhibit molecular diffusion even at room temperature. The underlying binding mechanism locks the molecule into specific positions on the substrate lattice and induces a considerable deformation of TPyP. A saddle-shape conformational adaptation is determined by STM in combination with image simulations and near-edge X-ray adsorption fine-structure (NEXAFS) measurements. Additionally, we directly monitor the affinity of metal centers to the pyridyl groups by selectively attaching Fe adatoms to the TPyP moieties.  Chapter 6. Conformational Adaptation of TPyP on Cu(111)  127  Figure 6.1: Scheme of TPyP  Model of an isolated tetrapyridyl-porphyrin (TPyP) molecule in its groundstate conformation. The top view (upper panel) highlights the central porphyrin core and the four terminal pyridyl groups, the legs. In the side view (lower panel) we indicate the two angles (θ and φ), which determine the conformation of the legs relative to the porphyrin macrocycle. A possible nonplanar deformation of the latter is described by the angle ρ.  Chapter 6. Conformational Adaptation of TPyP on Cu(111)  6.2  128  Experimental Section  All scanning tunneling microscope (STM) experiments were performed in a custom-designed ultrahigh vacuum (UHV) apparatus comprising a commercial low-temperature STM [175] based on a design described in ref. [174]. The system base pressure is below 2·10−10 mbar. The Cu(111) single crystal surface was cleaned by repeated cycles of Ar+ sputtering (800 eV) followed by annealing to 780 K. Subsequently, TPyP (97+% purity, Frontier Scientific) was deposited by organic molecular beam epitaxy (OMBE) from a quartz crucible held at 525 K. Typical evaporation rates are roughly 0.03 monolayer/min (one monolayer corresponds a densely packed molecular film). TPyP was thoroughly degassed prior to any experiments resulting in a background pressure in the 10−10 mbar range during deposition. After dosing TPyP at room temperature, the sample was cooled down and transferred into the STM, where constant current images were recorded at about 11 K using electrochemically etched tungsten tips. In the figure captions V refers to the bias voltage applied to the sample. High-purity carbon monoxide (CO) gas was dosed in-situ at sample temperatures not exceeding 18 K. Fe atoms were evaporated from a home-made water-cooled cell by resistively heating a W filament surrounded by a Fe wire of high purity (99.998%). Our experimental setup allows direct access of the atomic beam to the sample placed in the STM. The NEXAFS data were taken at the HE-SGM beamline at BESSY II in Berlin. For the measurements at the N K edge the partial electron yield mode (retarding voltage 270 V) was used. The energy resolution was approximately 0.5 eV. All spectra have been referenced against a characteristic peak  Chapter 6. Conformational Adaptation of TPyP on Cu(111)  129  (399 eV) in simultaneously recorded spectra of a contaminated Au grid. For each incidence angle an average of four spectra is presented. To concentrate on the information related to the TPyP adsorbate layer, we processed the raw data by substracting the signal of the bare crystal, then corrected for the transmission through the beamline and finally normalized the edge jump to one. As a basis to corroborate and analyze the experimental structural data, we applied basic molecular mechanics calculations to optimize the geometry of TPyP moieties. Specifically, the MM+ force field of the HyperchemTM 7.5 molecular modeling package [213] was used to calculate and minimize the total energy of the system. The STM image simulations are based on semiempirical extended H¨ uckel calculations [213]. A constant electron density contour is obtained by integrating over the relevant molecular orbitals, which mimics a constant current STM image [170]. This procedure proved to reliably reproduce the appearance of adsorbed molecules [168, 215], including TPyP on the Ag(111) surface [239].  6.3 6.3.1  Results and Discussion Molecular Appearance and Adsorption Site  Figure 6.2a shows a large scale STM image of two Cu(111) terraces after submonolayer deposition of TPyP at 300 K. Isolated bright spots, which are randomly distributed on the surface, are clearly discernible. High-resolution data as displayed in Figure 6.2b reveal that each of these protrusions corresponds to a single TPyP molecule, whereby only one species is observed. The  Chapter 6. Conformational Adaptation of TPyP on Cu(111)  130  findings that TPyP neither self assembles into highly ordered agglomerates nor considerably decorates the step edges, signals appreciable interaction between the molecule and the Cu(111) surface. This restricts the mobility of TPyP on Cu(111), in marked contrast to the adsorption of the very same molecule on the less reactive Ag(111) surface, where extended islands are formed even well below room temperature [239]. Nevertheless, the individual TPyP molecules align along the close-packed < 111 > high-symmetry directions of the Cu(111) substrate, as inferred by imaging the atomic lattice (see Figure 6.2c. Thus, three possible azimuthal orientations of TPyP on Cu(111) exist, which are all observed in the experimental data. Discussing the rotational ordering of molecules on surfaces implies that the adsorbates reveal an apparent symmetry break. Indeed STM images with intramolecular resolution (cf. Fig. 6.2b) allow defining a symmetry axis running through the two bright protrusions close to the center of the molecule. Besides these two prominent maxima, one can identify four broad lobes. From the molecular dimensions (side length ∼12 ˚ A), we assign each lobe to one of the pyridyl legs. The overall appearance of TPyP on Cu(111) thus strongly deviates from the one observed on Ag(111), which is imaged with a rectangular envelope and a depression in the center [239]. Since in the latter case the molecule proved to be very close to its natural gas phase configuration (compare Fig. 6.1), the topographic appearance on Cu(111) points to a strong distortion of TPyP and thus to an adsorption induced modification of the molecular conformation. Before addressing this issue in more detail, we discuss the adsorption site of TPyP on Cu(111). The observation of individual molecules azimuthally  Chapter 6. Conformational Adaptation of TPyP on Cu(111)  131  Figure 6.2: Single TPyP Molecules Absorbed on Cu(111)  TPyP adsorption on Cu(111) at room temperature: a) large scale STM topograph depicting a random distribution of TPyP molecules on the Cu terraces (V=-1.1 V, I=0.17 nA). b) high resolution STM image revealing intramolecular features (V=-0.5 V, I=0.35 nA). c) the Cu(111) atomic lattice. High symmetry adsorption sites are marked. (V=27 mV, I=0.65 nA). oriented along substrate high-symmetry directions indicates that TPyP is located at specific sites of the underlying Cu(111) lattice. However, since the positioning can have a drastic impact on STM images of molecules on surfaces [241], it is important to verify this assumption and to determine the adsorption site, prior to any further discussion of the molecular conformation. Due to incompatible imaging parameters, it is not possible to simultaneously resolve the substrate lattice and the adsorbed TPyP molecule. As an al-  Chapter 6. Conformational Adaptation of TPyP on Cu(111)  132  ternative solution, we applied co-adsorbed CO molecules as markers to determine the adsorption site of TPyP. Related approaches were successfully used to obtain the adsorption site of adatoms and molecules [174, 268, 269, 270]. It is well known that at low coverage CO molecules stand upright and occupy exclusively on top positions on the Cu(111) lattice [271, 272]. Additionally, TPyP and CO molecules can easily be imaged simultaneously by STM. This is illustrated in Figure 6.3a: after one minute exposure to CO, dosed in-situ at a sample temperature of 18 K, dim sombrero shaped protrusions representing single CO molecules are visible in between the TPyP molecules. By matching a hexagonal grid representing the Cu(111) lattice (compare Fig. 6.2d) with the positions of the CO molecules, one can conclude that the TPyP molecules are centered on bridge sites, irrespective of which of the three azimuthal orientations they follow (cf. Figure 6.3). The dissimilar appearance of the legs is tentatively explained by partial CO attachment and height modulations due to surface state scattering.  6.3.2  Molecular Conformation  We have succeeded in determining the molecular conformation of TPyP on Cu(111) by the use of a novel procedure based on two steps. First we apply NEXAFS measurements, which yield information on the dihedral angles between the molecular systems and the surface plane. Subsequently we refine the NEXAFS results by comparing simulated STM images with the experimental high-resolution data. The nitrogen K edge of a monolayer of TPyP on Cu(111) (Fig. 6.4) exhibits a pronounced dichroism which differs remarkably from that of a multilayer of the same molecule (not shown) indicating a strong  Chapter 6. Conformational Adaptation of TPyP on Cu(111)  133  Figure 6.3: Adsorption Site Determination  Adsorption site determination of TPyP on Cu(111) by using CO molecules as markers. The top left panel demonstrates the simultaneous imaging of CO and TPyP. The three color-coded plots show that TPyP is centered on bridge site of the underlying Cu(111) lattice (compare Figure 6.2c), irrespective of the azimuthal orientation (V=250 mV, I=0.2 nA).  Chapter 6. Conformational Adaptation of TPyP on Cu(111)  134  conformational adaptation. The spectra are dominated by 2 peaks in the π ∗ region (399.4 eV and 400.9 eV) and a broad σ ∗ structure. For the analysis we need to decompose the spectra into parts stemming from the different types of N. To this end we focus on the π ∗ range, as the broad σ ∗ features prohibit a reliable analysis. Based on earlier reports [60, 244, 246, 248] we expect several overlapping resonances in the π ∗ range (397 eV 405 eV), namely two from the pyridil legs and three from each of the two macrocycle nitrogens. Fitting this range with Gaussian-shaped peaks combined into three sets, where each set was optimized to reproduce published reference spectra, yields a reasonable agreement with the experimental data and allows the determination of the angular dependence of each of the resonances. It becomes evident that the first peak at 399.4 eV and the second at 400.9 eV are mainly due to the pyridilic N and the macrocycle N absorption, respectively. Clearly the two peaks behave differently when changing the photon beam incidence from grazing (30◦ , dotted curve) to normal (90◦ , solid curve), signifying different orientation of the according molecular moieties (Figure 6.4, inset). It follows that the average of the normals on the pyridil endgroups has an angle of 30◦ (inset, solid line) with the substrate. For the average of the normals on the pyrrol groups of the macrocycle a value of 50◦ is found. These findings indicate marked distortions of TPyP upon adsorption, in line with the STM observations (cf. Figure 6.2b). However it is important to realize that the two values determined by NEXAFS do not allow for an unequivocal determination of all three important intramolecular angles, and thus the geometry of the molecule. This is easily recognized by discussing the conformation of the pyridyl legs relative to the porphyrin macrocycle  Chapter 6. Conformational Adaptation of TPyP on Cu(111)  135  Figure 6.4: NEXAFS Spectra of the N 1s Edge  Nitrogen K edge spectra (NEXAFS) of one monolayer TPyP on Cu(111) exhibiting strong dichroism. Two main peaks related to different molecular moieties are marked by vertical lines. Their angular dependence (see inset) yields a nonplanar macrocycle (50◦ ) and inclined pyridyl groups (30◦ ). [273], which is defined by the two angles θ and φ introduced before (cf. Fig. 6.1). NEXAFS however only yields the inclination angle between the pyridyl group and the surface. Thus, there are many possible combinations of θ and φ angles, which are consistent with the single value given by NEXAFS. To resolve the molecular conformation despite this limitation, we simulated STM images for a set of geometries (c.f. Fig. 6.5a-c), which are compatible with the NEXAFS data, and compared them to a typical experimental image (see Fig. 6.5d). This scan was recorded at a low negative sample bias voltage, thus representing occupied electronic states. Accordingly, all the simulated STM images presented below are based on the density of states of the highest occupied molecular orbitals (HOMO and HOMO-1) [274]. Figure 6.5a shows a simulated STM image of TPyP. It represents a geometry, which was obtained by reducing the dihedral angle θ to 30◦ while keeping the C-C  Chapter 6. Conformational Adaptation of TPyP on Cu(111)  136  Figure 6.5: Simulated STM Images  Comparison of simulated STM images based on molecular geometries compatible with the NEXAFS results (a-c) with an experimental STM topograph (d) (V= −0.5 V, I=0.15 nA). e) Adsorption geometry of TPyP on Cu(111). Top view (top) and side view (bottom) clearly reveal the molecular distortion, i.e. a saddle-shaped macrocycle deformation as well as flexure of the pyridyl moieties, upon adsorption. bond parallel to the surface (φ =0). This pyridyl conformation goes hand in hand with a saddle-shaped distortion of the molecular core [85]: the pyrrole rings are fixed at a tilt angle ρ of 45◦ . The simulated image is dominated by two longish protrusions, which extend to the far ends of the molecule. Obviously, this contour bears no close resemblance to the experimental STM image presented in Figure 6.5d. The poor agreement between calculated and simulated STM topographs allows one to discard this molecular conformation and compels us to consider a bending of the C-C bond out of the macrocycle plane. Accordingly, we freeze the pyridyl conformation by setting the angles to θ =20◦ and φ =10◦ and apply a macrocycle distortion ρ of 35◦ . The resulting simulated image (Figure 6.3b) is in good agreement with the experimental data. Both the two central maxima and the appearance of the legs are reproduced. Furthermore, one can distinguish two different types of indentations along and perpendicular to the molecular axis, respectively.  Chapter 6. Conformational Adaptation of TPyP on Cu(111)  137  Finally, Figure 6.5c shows the simulated STM image for a slightly varied geometry (θ =0◦ , φ =30◦ , ρ =45◦ ). Considering the simplicity of the applied procedure, the agreement between experiment and calculations is striking. Not only is the molecular outline nicely reproduced, but also the positions of the two central maxima improved in comparison to Figure 6.5b. In addition, the macrocycle distortion ρ resulting from this optimized geometry is in good agreement with the value of 50◦ determined by NEXAFS (the saddle-shape and in particular the angle ρ Figure 6.5b and c are based on, are obtained by optimizing the geometry of the porphyrin macrocycle by the MM+ procedure complying with the constraints given by the pyridyl conformation). In summary, a molecular conformation characterized by pyridyl rings, which are heavily rotated around the C-C bond (θ ally bent towards the substrate (20◦ macrocycle distortion (40◦  ρ  φ  10◦ ) and addition-  30◦ ) inducing a saddle-shaped  50◦ ), describes the experimental results  best. Already knowing the adsorption site, we thus can establish a complete model for the adsorption geometry of TPyP on Cu(111), which is depicted in Figure 6.5e. To our knowledge, this is one of very few examples where STM and complementary techniques allowed one the full determination of the adsorption geometry of a large functional molecule, i.e. its conformation and the adsorption site. Furthermore, total energy calculations in the MM+ framework indicate that the pyridyl nitrogens are separated by about 2.5˚ A(∆z) from the surface plane defined by the atomic centers. The distance of the pyrrole nitrogens from the substrate is considerably larger. Now we briefly address the possible reasons for the strong deformation of TPyP upon adsorption on Cu(111). An inspection of Figure 6.5e reveals that  Chapter 6. Conformational Adaptation of TPyP on Cu(111)  138  there are two groups of atoms closest to the surface: the pyridyl nitrogens and the outer pyrrolic hydrogens. Judging from the high affinity of the nitrogen to metals discussed in the introduction, the attractive N-Cu interaction is most likely the trigger for the deformation. A close distance between pyridilic N and the Cu surface atoms can only be achieved for small dihedral angles θ and a tilt of the pyridyl leg towards the substrate. As a result, the marked distortion of the porphyrin macrocycle is induced by steric constraints as a consequence of the bending of the legs. At this point it is instructive to further discuss two issues. We already mentioned the strikingly different adsorption behaviour of TPyP on Ag(111) and Cu(111). These differences can be rationalized by comparing the interactions between pyridyl molecules and Ag or Cu surfaces, respectively. Indeed the bonding of pyridyl to Cu via the N lone pair proved to be very important, while in the case of Ag(111) the interaction with the π electrons of the aromatic ring is dominant [275]. At low coverage, this difference results in pyridyl standing upright on Cu(110) with the N pointing towards the surface [276, 277], while it prefers a rather planar adsorption geometry on Ag(111) [247, 278]. A second comparison also corroborates the importance of the nitrogen for the reported adsorption behaviour. Co-Tetraphenylporphyrin (Co-TPP) is a molecule closely related to TPyP. However, it is terminated by phenyl rings and the macrocycle hosts a Co ion bonded to the four pyrrolic nitrogens. After room temperature deposition of Co-TPP on Cu(111) we observe highly ordered compact islands of Co-TPP. Evidencing that the room temperature mobility of Co-TPP is higher than for TPyP, despite the additional interaction of the Co center with the metal substrate. Consequently, also  Chapter 6. Conformational Adaptation of TPyP on Cu(111)  139  this observation points to the decisive role the nitrogen lone pairs play for the mobility and conformation of TPyP on Cu(111).  6.3.3  Reactivity Towards Metal Centers  A second type of bonding mechanism between the terminal pyridyl groups and metal atoms is revealed by the experiment presented in Figure 6.6. Single Fe atoms were added in-situ at 8 K, where thermal diffusion is frozen in. Figure 6.6a accordingly shows randomly distributed Fe monomers appearing as round protrusions coexisting with TPyP molecules. In a next step the sample temperature was slightly increased to about 15 K, which allows the Fe adatoms to freely migrate on the surface, while the TPyP is immobile. Subsequently, the sample was cooled down again to freeze the adatom motion. As a result Fe is selectively captured by the pyridyl groups (Figure 6.6b). Once attached the adatoms stick and do not diffuse. The modified imaging characteristics of both Fe and TPyP-endgroups indicate marked chemical interaction, and differ in this respect from the previously reported STM data of 2D Cu- and Fe-carboxylate mononuclear compounds [207, 263] or dinuclear nanogrids [279, 280]. Judging from the unchanged appearance of the molecular core, a relaxation of the TPyP is rather unlikely. Analogously to the determination of the TPyP adsorption site, we address in Figure 6.6c and d the Fe positions by overlaying an atomic lattice. We find that the bridge adsorption site of TPyP is consistent with isolated Fe adatoms occupying hollow sites of the underlying substrate atomic lattice (Figure 6.6c), an adsorption site suggested in previous reports [37]. The convolution of the molecular and atomic signatures hampers a precise and  Chapter 6. Conformational Adaptation of TPyP on Cu(111)  140  reliable determination of the positions of the Fe centers in the TPyP-Fe complexes. Nevertheless, the STM image in Figure 6.6d demonstrates the highly symmetric appearance and directionality of the pyridyl-Fe complex and suggests a lateral Fe-N distance of about 2.4±0.5 ˚ A. This value compares well with a Fe-pyridyl bond length of 2.2 ˚ A reported for a three dimensional Fe-porphyrin complex [204] and the positioning of diiron units simultanesouly coordinated by carboxylate and pyridil ligands on Cu(100) [281]. These findings confirm that the N containing ligands retain their affinity towards metal centers despite the conformational adaptation implying a non-planar orientation of pyridil groups, and directly visualize the impact of metal-ligand interactions on a metallosupramolecular self-assembly process in two dimensions where the ligands are spatially anchored. Furthermore additional incoming Fe monomers can be trapped by the metal-ligand complex, resulting in small metal clusters pinned to the pyridyl groups of the TPyP. This approach allows in principle the self-assembly of large quantities of metal-molecule-metal bridges [282] which might prove very interesting in the study of metal-molecule contacts as these junctions are defined on an atomic level [153].  6.4  Conclusions  The experiments presented here indicate that the attractive interactions between the functional pyridyl moieties and the Cu substrate, presumably mediated by the lone pair electrons of nitrogen, not only immobilize the TPyP molecule up to room temperature, but also promote a strong deformation of the molecular geometry. Furthermore the functional pyridyl legs are strong  Chapter 6. Conformational Adaptation of TPyP on Cu(111)  141  Figure 6.6: Selective Attachment of Fe Adatoms to the Pyridil Groups  Selective attachment of Fe adatoms to the pyridyl groups of TPyP (a,b, a: V=30 mV, I=0.2 nA, b: V=20 mV, I=0.2 nA). See text for discussion. To main steps of this experiment are schematically illustrated in the column on the right. c) a detailed view of a) which indicates that the reported TPyP adsorption site is consistent with single Fe atoms centered on hollow sites. d) the overlaid substrate lattice grid exemplifies the highly symmetric appearance of the TPyP(Fe)n complexes.  Chapter 6. Conformational Adaptation of TPyP on Cu(111)  142  attractors for Fe atoms. This permitted the presentation of snapshots of the self-assembly process of a metal-organic complex in two dimensions. Our findings allow the selective attachments of metal centers to pyridyl moieties, and open up pathways to steer the mobility of large organic molecules. Especially the possibility to immobilize functional species on surfaces even at elevated temperature should facilitate the controlled construction of complex molecular architectures on surfaces. In addition we presented a novel approach to determine the geometry of adsorbed molecules. Combining the well established NEXAFS method with a procedure relating STM simulations to high-resolution data, presents a useful tool to study conformations of large molecular adsorbates, which should be applicable for a wide variety of systems. We quantified for the first time the saddle-shaped geometry of an adsorbed free-base porphyrin molecule. Such structural information provides a prerequisite to control functional properties of adsorbed complex molecules and the conformational design of flexible species embedded in molecular nanoarchitectures at surfaces.  Acknowledgements  Work supported by Canada Foundation of Innovation (CFI), National Science and Engineering research Council of Canada (NSERC), British Columbia Knowledge Development Fund (BCKDF) and the European Union BIOMACH project. W.A. thanks the Swiss National Science Foundation (SNF) and A.W.-B. the German Academic Exchange Service (DAAD) for financial support. Support of the travel of T.S. to the Berlin synchrotron source by the  Chapter 6. Conformational Adaptation of TPyP on Cu(111) BMBF through project # 05 ES3XBA/5 is gratefully acknowledged.  143  144  Chapter 7 Controlled metalation of self-assembled porphyrin nanoarrays in two dimensions We report a bottom-up approach for the fabrication of metallo-porphyrin compounds and nanoarchitectures in two dimensions. Scanning tunneling microscopy and tunneling spectroscopy observations elucidate the interaction of highly regular porphyrin layers self-assembled on a Ag(111) surface with iron monomers supplied by an atomic beam. The Fe is shown to be incorporated selectively in the porphyrin macrocycle whereby the template structure is strictly preserved. The immobilization of the molecular reactants allows to identify single metalation events in a novel reaction scheme. Because the template layers provide extended arrays of reaction sites, superlattices of coordinatively unsaturated and magnetically active metal centers are obtained. This approach offers novel pathways to realize metallo-porphyrin compounds, low-dimensional metal-organic architectures and patterned surfaces which cannot be achieved by conventional means.  7.1  Introduction  The control of matter at the molecular level is of paramount importance for the development of novel materials and functional device architectures  Chapter 7. Iron Metallation of TPyP on Ag(111)  145  [5, 283]. Well-defined surfaces are particularly useful in this respect, because they represent versatile platforms to engineer molecular architectures with exquisite feature control, which can be examined and manipulated at the nanoscale by scanning tunneling microscopy (STM). Thus a variety of molecular building blocks have been successfully employed to assemble functional layers and nanostructures on surfaces, notably exploiting complex molecular species. Here we focus on the synthesis and organization of novel porphyrin nanoarchitectures in two dimensions. Porphyrins exhibit an intriguing variety of functional properties, which are exploited in both biological and artificial systems [228]. Particularly interesting are the Fe-porphyrins, which play (as hemes) a central role in life processes encompassing transport of respiratory gases and catalytic functions [229, 284]. Accordingly, these versatile molecules are promising building blocks to assemble functional layers and nanostructures on surfaces, specifically opening up new opportunities to build sensors, and nanoscale optical and magnetic materials [230, 231]. The functionality and self-assembly of porphyrins is based on three main features: (i) the porphyrin core macrocycle can host a wide range of metals, which present active sites to reversibly form porphyrin-ligand complexes [285, 286]. (ii) Porphyrins with a wide variety of meso-substituents can be synthesized. They determine the molecules functional properties and render building blocks for metal-organic networks in solid state chemistry [186] and 2-D molecular engineering [5, 95, 185, 189, 199, 287, 288]. (iii) The flexibility of the porphyrin core and the rotational degrees of freedom of the mesogroups allow for a conformational adaptation of the molecule to its local environment [63, 185] and their considerate manipulation [65, 67, 99]. Here we  Chapter 7. Iron Metallation of TPyP on Ag(111)  146  present a molecular-level investigation on a novel scheme for the fabrication of metallo-tetraarylporphyrins in two dimensions (2-D) employing STM and scanning tunneling spectroscopy (STS). The starting point are terapyridylporphyrin (TPyP) layers self-assembled on the Ag(111) surface, which are shown to be highly reactive towards Fe centers provided by an atomic beam. The resulting compounds exhibit structural and electronic characteristics strongly indicating complexation at very unusual reaction conditions. This interpretation is corroborated by a careful comparison with the structural and electronic properties of the related species FeII-tetraphenylporphyrin (Fe-TPP) deposited on the same substrate.  7.2  Results and Discussion  The individual steps in the formation of metallo-porphyrin compounds and highly organized nanoarrays in two dimensions are demonstrated using welldefined tetrapyridylporphyrin (H2-TPyP) template layers. Figure 7.1a shows a structural model of the free base H2-TPyP molecule, our starting material, which consists of the central porphyrin macrocycle and four terminal pyridyl rings. Upon adsorption on Ag(111) the porphyrin board is oriented parallel to the surface, while the pyridyl rings alternately rotate out of the porphyrin plane by a dihedral angle of about 60◦ , resulting in a rectangular envelope of the molecules in the STM topography [239] (cf. Figure 7.1b). Moreover, the surface mobility and lateral interactions enable the self-assembly of well-ordered two-dimensional molecular domains extending over hundreds of nanometers even at room temperature. The high-resolution STM image depicted in Figure 7.1b reveals the molecular packing and intramolecular fea-  Chapter 7. Iron Metallation of TPyP on Ag(111)  147  tures. The H2-TPyP molecules order in a staggered arrangement. Besides the porphyrin core with a depression in the center, four protrusions corresponding to the pyridyl rings are clearly discernible. Two different molecular orientations (labeled I and II, respectively) are observed in the imaged domain. Accordingly, this packing scheme can be described by a nearly rectangular unit cell with a molecule in every corner and a central molecule in a different azimuthal orientation [239]. The models in Figure 7.1b illustrate the structural arrangement and assignment of intramolecular features. In the next step, we examine the reactivity of the well defined H2-TPyP precursor layer toward Fe atoms provided by an atomic beam (cf. Figure 7.1c-e). Upon exposure to minute amounts of Fe at 320 K the appearance of isolated molecules changes drastically: STM images recorded at negative sample voltages show that a unique new species evolves, which is imaged brighter, with an increased apparent height of ≈ 0.7 ˚ A compared to the H2TPyP precursor layer. Instead of the depression in the center, this species exhibits a central rod-like protrusion (≈12 ˚ A long) which is always oriented along the molecular symmetry axis (here defined parallel to the short side of the rectangular envelope) and comprises two or three corrugation maxima. The number of modified molecules directly correlates with the Fe dose, as demonstrated by the image sequence in Figure1. Our data clearly reveal a preserved 2D TPyP layer structure, where exclusively the central porphyrin moieties undergo drastic changes. We observed a spatially inhomogeneous distribution of Fe-TPyP for intermediate Fe doses, reflecting appreciable Fe mass transport on the H2-TPyP layer, cooperative effects and an activation barrier relevant for this reaction. From now on we tentatively refer to the  Chapter 7. Iron Metallation of TPyP on Ag(111)  148  Figure 7.1: Fe Atom Reacting with TPyP Macrocycle  a) Structure model of H2-TPyP (top view) highlighting the central porphyrin core consisting of four pyrrole rings and four terminal pyridyl groups. The latter are alternately rotated out of the porphyrin macrocycle plane resulting in a rectangular envelope of the molecule in the STM topography. The dashed line indicates the molecular symmetry axis we will refer to in the text. b) Self-assembled H2-TPyP layer on Ag(111). The domain comprises two distinguishable types of rows (I, II) with a different azimuthal orientation of the molecules, which are marked by arrows. For negative bias voltages the core is imaged a depression in the center in high-resolution data, and the peripheral four protrusions correspond to the pyridyl groups (VSample = −1.2 V, I=0.7 nA). The H2-TPyP models including the unit cell (b1=13.9 ˚ A, ˚ b2= 27.4 A) highlight the structure and facilitate the identification of the molecular moieties. c)-e) Reaction of a H2-TPyP precursor layer with Fe: Exposing the H2-TPyP precursor layer at 320 K to a beam of Fe atoms drastically alters the shape of individual molecules. The apparent height of the modified species increases, resulting in a brighter appearance in the STM images. By increasing the Fe dose, their number can be tuned from zero to full saturation. As indicated by the unit cell, the molecular packing scheme remains unaffected by the reaction. (c: VSample = −1.2 V, I=0.7 nA, d-e: VSample = −0.3 V, I=0.85 nA).  Chapter 7. Iron Metallation of TPyP on Ag(111)  149  modified molecular species as Fe-TPyP. Higher Fe doses allow the formation of regular Fe-TPyP arrays, where the alternating orientation of the Fe-induced features nicely reflects the orientation of the H2-TPyP template layer (cf. Figure 7.2). The apparent height of the Fe-TPyP molecules as well as the corrugation within the layer depends on the sample bias voltage. Under typical imaging conditions (VSample = −1V) we measure an apparent heigth of 1.9 ˚ A and a corrugation of 0.7 ˚ A, respectively. Figure 7.2b shows height profiles along the molecular axis of two Fe-TPyP molecules in the same row. As mentioned before, between two and three protrusions are observed. This variation in the topographic appearance, observed in both types of molecular rows, is induced by inequivalent adsorption sites of the molecules on the underlying substrate lattice: The TPyP overlayer is not commensurate with the Ag(111) surface, resulting in a Moir pattern with subtle long-range height modulations [239]. In order to investigate the nature of the Fe-TPyP molecules and to rationalize the origin of their drastically modified appearance in the STM topography we performed comparative experiments with FeII-tetraphenylporphyrin (Fe-TPP) layers self-assembled on Ag(111). TPP consists of a central porphyrin macrocycle and four terminal phenyl rings, and thus closely resembles TPyP. Each Fe-TPP comprises a FeII center in the porphyrin plane (cf. inset Figure 7.3) [289]. The self-assembly of this species on Ag(111) can be conducted with similar procedures as those employed for H2-TPyP. An example for a highly regular Fe-TPP layer on Ag(111) is reproduced in the STM image in Figure 7.3. These data expose a striking similarity of the intramolecular features dominated by the porphyrin cores comprising the iron with the Fe-  Chapter 7. Iron Metallation of TPyP on Ag(111)  150  Figure 7.2: Full Fe-TPyP Array  a) STM image showing the regular ordering of a fully developed Fe-TPyP array, representing the completion of the image series in Fig. 7.1 c-e (VSample = −0.4 V, I=0.65 nA). The dashed lines represent two height profiles as displayed in b). Because of the noncommensurate nature of the H2-TPyP template layer, a long-range height modulation of the molecular appearance is induced. As a consequence of the respective different substrate registries the porphyrin cores are imaged with two to three maxima along the molecular axis. TPyP species shown in Figure 7.2. Again, the topographic appearance is dominated by two or three protrusion along the molecular axis. The height profiles in Figure 7.3b accentuate this close resemblance. The data in Figure 7.3a reveal that regular Fe-TPP layers on Ag(111) exhibit a packing scheme with a correlated single azimuthal orientation of the molecules with respect to substrate high-symmetry directions. This distinction to the TPyP case arises from different lateral interactions due to a changed reactivity of the phenyl endgroups in comparison to the pyridyl substituents. The square unit cell (side length b=b2=14.3±0.1 ˚ A) we observe agrees with observations of related metal-TPP molecules on close-packed noble metal surfaces [94, 194]. The isostructural intramolecular features in the Fe-TPyP- and Fe-TPP-  Chapter 7. Iron Metallation of TPyP on Ag(111)  151  Figure 7.3: Assembly and Height Profile of Fe-TPP  STM image of an Fe-TPP island exhibiting a molecular packing scheme described by a square unit cell with side lengths b1=b2=14.3±0.1 ˚ A (VSample = −0.8 V, I=0.65 nA). The inset shows a model of a Fe-TPP molecule placed in the same azimuthal orientation as the Fe-TPPs in the STM image. b) Two height profiles along the molecular axis of the Fe-TPP molecules highlighted by the dashed line in a). Note the close resemblance to the topography of Fe-TPyP shown in Fig. 7.2b. layers are a strong indication that in both cases genuine FeII-porphyrin species are present. The appearance of the Fe-porphyrins revealing an apparent symmetry break characterized by the pronounced protrusions along the molecular axis is associated with a nonplanar geometry of the porphyrin macrocycle. While undistorted porphyrin species feature a four-fold symmetric core appearance (cf. Figure 7.1), nonplanar deformations result in pronounced protrusions establishing a two-fold symmetry of the porphyrin macrocycle [67, 99, 185]. Fe-tetraarylporphyrin species with a saddle shape are well-known and can serve as a tentative explanation of the observed features [85, 237]. In this nonplanar deformation one opposing pair of pyrrole rings tilts up, while the other pair tilts down. Judging from the molecular dimensions the two outer protrusions originate from the upwards bent pyr-  Chapter 7. Iron Metallation of TPyP on Ag(111)  152  role pair, while the central protrusion relates to the Fe ion. The fact that the terminal groups are alternately rotated out of the porphyrin plane allows only one pyrrole pair to tilt up, while the other pair is hindered by steric repulsion between hydrogen atoms of the ring and the terminal groups. Thus, we observe the protrusion exclusively along a specific symmetry axis in the 2-D porphyrin layers. In most cases described so far the nonplanar molecules are FeIII species where the axial ligands induce molecular flexure [290, 291]. The coupling of the present Fe-porphyrins to the Ag(111) substrate seems to induce similar structural distortions. We expect that the molecular conformation can be influenced by the choice of the employed substrate and by reacting the metallo-porphyrin layers with appropriate axial ligands. Because the electronic and magnetic, but also catalytic, properties of the complexes depend sensitively on these parameters, Fe-porphyrin layers represent an interesting playground to investigate the magnetic and biological properties of metalated porphyrin compounds on surfaces. The conclusions drawn from the structural analysis are substantiated by STS observations which elucidate the electronic properties of the different (metallo-)porphyrin species. The data in Figure 7.4d reveal that the step-like increase in the STS spectra resulting from the onset of the Ag(111) surface state at an energy of −65 meV [292, 293] disappears upon the formation of the pure H2-TPyP layers. The latter exhibit rather a pronounced feature at +740 meV associated with the TPyPs two lowest unoccupied molecular orbitals (LUMOs), which are energetically very close in the isolated porphyrin molecule [79, 294]. By contrast, the Fe-TPyP and Fe-TPP LUMO levels  Chapter 7. Iron Metallation of TPyP on Ag(111)  153  shown in Figure 7.4e are shifted towards higher energies and are found at 990 and 1020 meV, respectively. This upward shift is in agreement with spectroscopic observations [295] and theoretical calculations [79]. It arises from the interactions between the LUMOs and the filled dπ metal orbitals and has a direct impact on the topographic imaging of H2-TPyP and Fe-TPyP in constant current STM images (cf. Figure 7.4 a-c). At negative sample voltages the Fe-TPyP molecules appear brighter than the H2-TPyP species (cf. Figure 7.1 c-e and Figure 7.4a), while tuning the sample voltage to a positive value between the H2-TPyP and Fe-TPyP LUMO energies results in a contrast inversion (Figure 7.4b), as the Fe-TPyP LUMO does not mediate electron tunneling. At voltages well above the upshifted Fe-TPyP LUMO levels (Figure 7.4c) the two porphyrin species are essentially indistinguishable, in full agreement with the spectroscopic data. The voltage-dependent topography of Fe-TPP is very similar to that of Fe-TPyP [296]. The almost identical LUMO shift for both Fe-TPyP and Fe-TPP (cf. Figure 7.4e) is ascribed to the fact that these molecular orbitals have major electron densities only at the porphyrin core, whence there energetics is hardly affected by the different meso substituents [79, 95]. Thus both the structural analysis and the electronic structure characteristics of the three porphyrin species evidence a metalation reaction upon exposing adsorbed H2-TPyP to Fe atoms. This implies that the metalloporphyrin formation readily occurs in situ on the surface. The corresponding reaction is schematically illustrated in Figure 7.5. It is formally described by the equation :  Chapter 7. Iron Metallation of TPyP on Ag(111)  154  Figure 7.4: Chemical Sensitivity through Bias-Dependent Imaging  a)-c): Chemical sensitivity through bias-dependent imaging of H2-TPyP and Fe-TPyP. The relative apparent height and appearance of H2-TPyP and FeTPyP is strongly bias voltage dependent due to metalation induced modifications of the molecular electronic structure, as outlined in d and e. While the Fe-TPyP species appears brighter than H2-TPyP at negative sample voltages (cf. Fig. 7.1c-e), an inverted or vanishing contrast can be established by tuning the tunneling voltage to specific positive values. The green circle highlights the position of one specific Fe-TPyP molecule (see text for full discussion). All three images are taken at a set point current of 0.71 nA. d)-e): Unoccupied electronic states of H2-TPyP, Fe-TPyP and Fe-TPP: d) Tunneling spectra taken on bare Ag(111) patches show the pronounced step-like onset of the density of states at ∼ −65 meV associated with the surface state of the pristine substrate. The surface state is quenched upon H2-TPyP adsorption, whereas a peak associated with the lowest lying unoccupied molecular orbitals (LUMOs) appears. The two spectra are shifted by a vertical offset for clarity. e) The comparison of the H2-TPyP with the Fe-TPyP and Fe-TPP tunneling spectra reveals an energetic upward shift of the LUMOs which appear for both Fe-porphyrins at an energy of roughly 1000 meV. The plotted spectra represent a sum over several identical molecules as well as a spacial average over different spots on a molecule. The yellow arrows indicate the bias voltages used to acquire the images a), b) and c), respectively.  Chapter 7. Iron Metallation of TPyP on Ag(111)  H2 − T P yP + F e ⇒ F e − T P yP + H2 ⇑  155  (7.1)  In this process, schematically, the two pyrrolic protons will be reduced to molecular hydrogen (H2) by the simultaneous oxidation of the incoming Fe0 center to FeII. Due to the affinity of Fe for axial ligands [79], intermediate product H atoms might be transiently attached to the Fe centers before recombining to H2 which is thermally desorbed. This drives the redox reaction to completion and establishes local electroneutrality between the metallic FeII centre and the organic tetrapyridylporphyrinato dianion. Thus, we expect the Fe ion to be in the FeII oxidation state, analogously to the Fe-TPP molecules used as a reference in these experiments. The mechanism described here provides a simple and general picture which does not take into account explicitly the influence of the substrate. The latter acts as an anchoring surface with a periodic potential which influences the relative geometry of the reactants, as well as an electron source which can screen the electrical charges held by the adsorbates. The indirect participation of the substrate in the chemical reaction is therefore an important factor, and was similarly encountered in the complexation of metal centers by carboxylate species on surfaces [263, 280, 297].  7.3  Conclusions  In conclusion we demonstrated the formation of a Fe-tetrapyridyl porphyrin on a Ag(111) surface based on a novel reaction scheme. This new approach opens up some appealing opportunities, especially as it seems easily applicable to a large variety of porphyrin species on surfaces which can be met-  Chapter 7. Iron Metallation of TPyP on Ag(111)  156  Figure 7.5: Model of Metalation Reaction  The three main processes during the formation of a metallo-porphyrin on a surface are schematically illustrated in a)-c). a) A pure H2-TPyP layer is exposed to Fe atoms from an atomic beam. b) The pyrrolic protons are reduced to molecular hydrogen which desorbs while the Fe is oxidized and incorporated into the dianionic porphyrinato core. c) This process presumably induces a nonplanar deformation of the porphyrin macrocycle on Ag(111). The saddle shaped geometry is indicated by the arrows and can explain the protrusions along one molecular axis observed in the STM data. alated by Fe and presumably other metal centers. Specifically, it allows the formation of low-dimensional metallo-porphyrin architectures by using preorganized porphyrin arrangements which are subsequentually functionalized by metal centers. Moreover novel porphyrin compounds can be created, because procedures are implementable where the addition of the metal center appears as a final step. In short, the methodology presented here is expected to provide a basis for the synthesis of high-purity metalloporphyrin nanostructures on surfaces, which could not be obtained by conventional methods as organic molecular beam epitaxy or deposition in solution, due to a limited thermal stability and/or high reactivity of the metalloporphyrins. Especially, the availability of the axial position of the metal centers for further reaction with biological relevant ligands (O2, CO, etc.) opens the possibility to carry out biological relevant reaction schemes. Note added: After the completion  Chapter 7. Iron Metallation of TPyP on Ag(111)  157  of this manuscript we noticed that a preliminary presentation of our approach [216], inspired a study using a space averaging method (XPS) that confirms the finding of porphyrin metalation on surfaces [298].  7.4  Experimental Section  All experiments were performed with a custom-designed ultrahigh vacuum (UHV) apparatus comprising a commercial low-temperature scanning tunneling microscope ( based on the design described in ref. [174]. The STM was operated typically at 15 K to obtain high-resolution topographic and spectroscopic data. The STM tip is made out of an etched W wire (Dia. 0.3 mm) and was prepared by Ar-bombardment in UHV. Topographic data were acquired in the constant current mode, with typical tunneling resistances in the range of 10-104 MΩ. In the figure captions V refers to the bias voltage applied to the sample. Tunneling spectroscopy data were recorded with a lock-in technique (typical modulation amplitude and frequency 20 mV and 1 kHz, respectively). The system base pressure was below 2 ·10−10 mbar. The Ag(111) surface was prepared by repeated cycles of argon sputtering (800 eV, 8 µA/cm2 ) followed by annealing at 750 K. TPyP was obtained from Frontier Scientific (97+ % purity). The FeTPP molecules were synthesized following an adapted procedure described in literature using hydrazine as reduction medium [289]. Care was taken not to expose the FeTPP to air in view of their well-known reactivity towards oxygen [299]. Accordingly the molecules were always transferred to UHV under inert gas atmosphere. The porphyrins were first outgassed in vacuum for several hours and then evaporated from a OMBE cell at 525 K onto the substrate kept at  Chapter 7. Iron Metallation of TPyP on Ag(111)  158  330 K. This provided a deposition rate of about 0.05 monolayers (ML) per minute. Fe atoms were evaporated from a home-made water-cooled cell by resistively heating a W filament surrounded by an Fe wire of high purity (99.998 %). During Fe deposition the substrate was held at 320 K.  Acknowledgement  Work supported by the Swiss National Science Foundation through a postdoctoral scholarship for W. A., and by DAAD through a PhD stipendiate for A.W., CFI and BCKDF, NSERC, ESF-SONS-FunSMARTs. We thank A.P. Seitsonen for helpful discussions.  159  Chapter 8 Interaction of cerium atoms with surface-anchored porphyrin molecules Cerium and other lanthanide porphyrinates have been synthesized and investigated for more than three decades in regard to their functional properties and potential for molecular architecture [300, 301, 302]. In contrast to the abundant metalloporphyrins with 3d centers, the large, generally highly coordinated lanthanides cannot be accommodated in the macrocyle plane. Thus sandwich-type complexes could be realized [303, 304], enabling the design of systems with rotating porphyrin rings [305, 306], whose control on surfaces is a topic of current interest [307, 308]. Here we present a combined scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS) study on the interaction of single cerium atoms with free base tetraphenyl-porphyrin (H2-TPP) molecules anchored on a Ag(111) surface. The topographic images reveal that cerium centers are selectively captured by the H2-TPP macrocyle. Tunneling spectroscopy data provide clear evidence for the formation of a novel Ce-porphyrinato complex, whose electronic structure is related to the simultaneously characterized Co-TPP species.  Chapter 8. TPP Complexation with Cerium  8.1  160  Results and Discussion  STM experiments were performed in a custom-designed ultrahigh vacuum apparatus housing a commercial low-temperature STM [239]. The Ag(111) preparation followed procedures outlined earlier [239]. In order to have a metalated reference species, a mix of Co-TPP and H2-TPP was thermally evaporated by organic molecular beam epitaxy at 470 K (flux 0.01ML/min), while keeping the substrate at room temperature. The Ce was evaporated thermally, following literature recipes [309]. The source was degassed close to the Ce melting point for more then 24h. The H2-TPP/CoTPP matrix was held at 300 K and exposed to short periods of the Ce beam with a 0.001 ML/min flux. Subsequently, all samples were cooled down in the LT-STM to 10 K, where the measurements were performed in a shielded environment. The indicated bias voltages were applied to the sample with topographic imaging in the constant current mode. STS data were obtained via lock in amplifier technique, using a 10 mV RMS modulation amplitude at a frequency of 4.3 kHz. The feedback loop was open for point spectroscopy and closed for STS mapping at constant bias. The scheme of both H2-TPP and Co-TPP are depicted in Figure 8.1a. Figure 8.1b shows an STM image of the adsorbed porphyrins, revealing a staggered packing scheme analogous to Fe-TPP/Ag(111) islands [240]. The two different species are marked α (H2-TPP) and β (Co-TPP), respectively. When the occupied states are imaged, the H2-TPP molecules exhibit a central ring, reflecting the porphyrin macrocycle, while the four smaller peripheral protrusions emanate from the phenyl meso substituents. The metalated species (β) exhibits an increased apparent height, dominated by an oval protrusion at the center because of the  Chapter 8. TPP Complexation with Cerium  161  additional density of states with Co d character [79], similar to the imaging of Fe-TPP [240]. A new species with different intramolecular features, labeled γ, appears in the H2-TPP/Co-TPP matrix following Ce exposure. It has a comparable apparent height to Co-TPP, yet is marked by a round central protrusion. The formation of the γ species is associated with the selective interaction of the Ce atoms with the H2-TPP macrocycle. This finding resembles previously observed metalation phenomena of porphyrins with Fe or Co under vacuum conditions [216, 240, 298], and hence the γ species is the designated CeTPP. However, no three-dimensional analogue of the presently encountered compound is known from the literature, because it has been obtained under special reaction conditions on a metal substrate [50] with the Ag substrate spatially confining the molecular reactants, thus preventing from further coordination. In order to explore the nature of the Ce-TPP complex and to compare its electronic structure with conventional (metallo)porphyrins, STS experiments were carried out. Figure 8.2a represents the tunneling spectra of H2-TPP (red), Co-TPP (green) and Ce-TPP (blue) obtained reproducibly with the tip at the center of the molecule. The peaks in the spectra reflect major contributions to the tunneling current, mediated by molecular orbitals, whereby the negative (positive) bias range represents the occupied (unoccupied) states. While the H2-TPP spectrum is flat in the range of −1000 mV to the Fermi level (zero bias), Co-TPP shows a strong resonance at −600 mV, originating from additional states with strong Co d-character [79]. Also the new Ce-TPP species reveals a pronounced occupied resonance,  Chapter 8. TPP Complexation with Cerium  162  Figure 8.1: Decoration of H2-TPP Macrocycle with Cerium  (a) Structure formulae of H2-TPP and Co-TPP. (b) STM image of the Co-TPP and H2-TPP mixture on Ag(111) forming a close-packed matrix. Molecules with an oval central protrusion are Co-TPP (β), the remaining ones are H2-TPP (α). Following exposure to a beam of Ce atoms a third species evolves with a round central protrusion (γ). Both topography images were taken at I=0.1 nA, V= −800 mV.  Chapter 8. TPP Complexation with Cerium  163  which is shifted towards lower voltages (−950 mV). This is a clear indication that a Ce-porphyrinato complex has formed. Regarding the unoccupied states in the positive bias regime, less differences are found: they are comparable in intensity and merely shifted with respect to each other (H2-TPP at 800 mV, Co-TPP at 950 mV and Ce-TPP at 600 mV). In order to characterize the spatial extent of the dominant occupied states, tunneling spectroscopy (dI/dV) mapping at the peak energies was carried out [43]. As a reference, Figure 8.2b shows a topographic image with all three species. The dI/dV map at −600 mV in Figure 8.2c shows pronounced features of a specific molecular orbital, characterized by two protrusions over the macrocycle, which arise from Co-TPP, deduced from comparison with the topographic image. Their anisotropy is associated with a conformational adaptation of the porphyrin leading to a symmetry break [240]. Both CeTPP and H2-TPP show no distinct contributions in the dI/dV map and appear thus transparent. The situation is reversed at −950 mV, i.e., for the Ce-TPP resonance, where exclusively the Ce-related contributions appear (Figure 8.2d). The spatial charge distribution of the Ce-TPP’s occupied state has the same symmetry and shape as that of Co-TPP, apart from a slight asymmetry, implying the presence of an additional ligand (presumably a hydrogen atom) attached to the cerium. The similarity between the CoTPP and Ce-TPP electronic structure is remarkable, indicating that the porphyrin macrocycle response to lanthanides and 3d metal centers is closely related.  Chapter 8. TPP Complexation with Cerium  164  Figure 8.2: Electronic Structure of H2-TPP, Co-TPP and Ce-TPP  Differentiation of the three species electronic structure. (a) STS performed at the center of each species, showing for H2-TPP no feature in the probed negative bias range (occupied states). Co-TPP has a resonance at −600 mV, whereas that of Ce-TPP is shifted to −950 mV. In the un occupied states H2TPP has a state at 800 mV, which is shifted to 950 (600) mV for Co-TPP (Ce-TPP). (b) Topography of the domain used for dI/dV mapping. (c,d) dI/dV map of the electron distribution of Co-TPP (Ce-TPP) resonance at −600 (−950) mV.  Chapter 8. TPP Complexation with Cerium  8.2  165  Conclusion  In conclusion, we presented an atomic-scale investigation of the interaction of single cerium atoms with surface-anchored porphyrin macrocycles. This work demonstrated the first in vacuo synthesis of a coordinatively unsaturated lanthanide-porphyrin compound. The electronic structure of the CeTPP species was determined and its relation to 3d analogues demonstrated. It is suggested that this approach can be applied in general to realize novel rare-earth porphyrinates or phthalocyanides on surfaces, which can be used as scaffolds to design supramolecular architectures, notably including multidecker superstructures.  Acknowledgment  Work supported by Canada Foundation of Innovation, National Science and Engineering research Council of Canada, and British Columbia Knowledge Development Fund. A.W.-B. and J.R. thank the German Academic Exchange Service and the Deutsche Forschungsgesellschaft for scholarships, respectively. We are particularly grateful to F. Patthey for providing the Ce and W.-D. Schneider for a helpful comment.  166  Chapter 9 Visualizing the Frontier Orbitals of a Conformationally Adapted Metalloporphyrin We present a study of the geometric and electronic properties of Co(II)tetraphenyl-porphyrin molecules adsorbed on the Cu(111) surface. Combined low-temperature scanning tunneling microscopy and near-edge X-rayabsorption fine structure observations reveal how the metal substrate induces a conformational adaptation into a distorted saddle-shape geometry. By scanning tunneling spectroscopy we identify the molecules discrete energy levels and map their spatial electron density distributions. These results, along with a simple theoretical description, provide a direct correlation between the shape of frontier molecular orbitals and intramolecular structural features.  9.1  Introduction  The conformation of functional molecules frequently determines their physicochemical properties and their interaction with the local environment. Notably metal-containing species in biological systems show a high degree of flexibility, whereby shape and functionality are intimately related [310]. A prominent class is given by the metallo-porphyrins, which play a central  Chapter 9. Visualizing Frontier Orbitals  167  role in life processes encompassing transport of respiratory gases, photosynthesis and catalytic functions [284, 311]. Nonplanar distortions of the porphyrin macrocycle are key to their photophysical, chemical or magnetic properties [85], and can be exploited for conformational design and development of novel biomimetic systems [238]. For the nanoscale control of such qualities an understanding of the interplay between electronic properties and molecular conformation needs to be developed at the single molecule level. Herein we present a study of the geometric and electronic properties of Co(II)tetraphenyl-porphyrin molecules adsorbed on a well-defined Cu(111) surface. Combined low-temperature scanning tunneling microscopy and near-edge Xray-absorption fine structure observations reveal how the metal substrate induces a conformational adaptation into a distorted saddle-shape geometry. By scanning tunneling spectroscopy we assess the molecule’s internal electronic structure, identify its discrete energy levels and map the corresponding spatial electron density distributions. These results, along with a simple theoretical description, provide a direct correlation between the shape of frontier molecular orbitals and intramolecular structural features. The charge densities from frontier molecular orbitals (MOs) of adsorbed molecules with π-conjugated electron systems can be related to their topographic appearance in scanning tunneling microscopy (STM) observations [165, 254, 270]. Moreover the spectral density of complex adsorbed species, such as C60 was investigated by scanning tunneling spectroscopy (STS) studies demonstrating the energy-selective mapping of individual MOs [43, 312]. However, the rigid carbon backbone of C60 remains essentially preserved upon adsorption [72, 313]. By contrast, STM topographic features of  Chapter 9. Visualizing Frontier Orbitals  168  adsorbed porphyrins signal intramolecular distortions of varying extent on metal substrates [63, 185, 239, 240], and STM manipulation experiments have provided indirect evidence for switching between different conformers [66, 67]. Thus there is a need to quantify the conformation of adsorbed flexible species and correlate it with their electronic structure. Firstly, this is decisive for a comprehensive understanding of adsorption phenomena and conformational adaptation at the single molecule level. Secondly, such knowledge is a mandatory prerequisite to advance the engineering of molecular nanoarchitectures [5], and to develop a rationale for conformational control of flexible species and supramolecular assemblies thereof. While metallo-porphyrins on surfaces have been the subject of intensive research [63, 67, 96, 99, 240, 314], the details of their electronic structure and the spatial characteristics of their individual MOs have been hitherto elusive to STS observations. Our highresolution STM images reveal bias-dependent intramolecular features. With the help of NEXAFS experiments the observed two-fold symmetry is related to a molecular adsorption geometry with a saddle-shaped macrocycle. Using STS we are able to distinguish the energy levels of individual molecular orbitals and selectively map the shape of the pertaining electron density distributions. Simulations based on semi-empirical Extended H¨ uckel Theory (EHT) calculations confirm the link between the measured MO appearance and the molecular conformation.  9.2  Results and Discussion  A structural model of Co-TPP is reproduced in Figure 9.1a showing the central porphyrin macrocycle with the four-fold coordinated Co(II) center.  Chapter 9. Visualizing Frontier Orbitals  169  The phenyl moieties are free to rotate about the σ-bond axis connecting them to the pyrrole units and can therefore adapt to the local environment. For free or weakly adsorbed molecules the corresponding dihedral angles θ exceed values of 60◦ [85, 239]. However, steric constraints interfere for dihedral angles falling below 60◦ , whereby the repulsive interactions between hydrogens at phenyl ortho positions and adjacent pyrrole moieties induce marked macrocycle distortions [85, 238]. Upon depositing small amounts of Co-TPP on Cu(111) regular islands form displaying a nearly square unit cell, whose extent reflects the size of the molecules (b1=14.1˚ A; b2=14.2˚ A; see Figure 9.1b). This packing scheme was similarly identified in metal-TPP assemblies on close-packed noble metal surfaces [96, 240]. The high-resolution STM image depicted in Figure 9.1c, obtained under conditions where a wide spectrum of occupied sample states contributes to the tunneling current, reveals distinct intramolecular features. We use the cigar-shaped protrusion over the macrocycle to define the main axis and associate the four smaller lateral protrusions with the meso-groups [239, 240]. The two-fold symmetric appearance signals that following adsorption the molecule’s conformation differs from that of the free species (where the macrocycle has a four-fold symmetry), and signals nonplanar macrocycle deformations. In order to clarify the connection between STM topographic appearance and molecular conformation NEXAFS experiments were carried out. With this technique the orientation of functional moieties with respect to the substrate plane can be assessed [242]. The spectra of the C1s edge (Figure 9.2a) consist of 3 peaks (285 eV, 286.5 eV, 288 eV) in the π ∗ region and 2 peaks (293 eV, 300 eV) in the σ ∗ region. We concentrated our analysis on  Chapter 9. Visualizing Frontier Orbitals  170  Figure 9.1: Scheme of Co-TPP  Model of an isolated Co-TPP molecule defining the main axis and the dihedral angle θ. A saddle-shape distortion bends down (up) pyrrole rings 1 and 3 (2 and 4). b Co-TPP islands on Cu(111) display a nearly square unit cell (b1=14. ˚ Aand b2=14.2 ˚ A). c High-resolution image with intramolecular features revealing a two-fold symmetry (Vt = −2.1 V, I=0.1 nA).  Chapter 9. Visualizing Frontier Orbitals  171  the leading edge around 285 eV where the deconvolution is straightforward. Following the argumentation in Ref. [60, 315], where closely related systems were studied, we decomposed the spectra into two parts, one originating from the macrocycle and one from the phenyl rings. For fitting we used three Gaussian peaks (dotted lines, inset of Figure 9.2a) with fixed intensity ratios and widths to approximate the macrocycle part as found in Ref. [60, 315]. The same way two Gaussians served for the phenyl related part (dash-dotted lines) according to Ref. [60, 315]. Thus, for the fitting procedure only two free parameters were used, i. e., the intensities of the molecular subunits. The analysis of the angular dependence yields a value of ∼35◦ (phenyl) and ∼20◦ (macrocycle) for the angle between the corresponding π ∗ dipole moment and the surface normal. The nonzero macrocycle angle indicates a distortion of the molecular backbone and is consistent with previously conjectured prominent saddle-shape deformations for metal-TPPs on surfaces. This porphyrin conformation implies that one pair of opposite pyrrole rings tilts upwards, while the other pair bends down (see Figure 9.1a) [85, 238]. Interpreting the NEXAFS data in terms of the saddle-shape model, we find for Co-TPP a dihedral angle θ of approximately 35◦ and estimate the bending of the pyrrole rings to ±20◦ . The resulting two-fold macrocycle symmetry is consistent with both the STM observations and the geometry derived from basic semi-empirical calculations as shown in Figure 9.2b (the saddle-shape deformation was obtained by optimizing the geometry of the macrocycle with the semi-empirical PM3 method complying with the constraints given by the phenyl orientation). Having confirmed with this experiment the conformational surface adap-  Chapter 9. Visualizing Frontier Orbitals  172  Figure 9.2: NEXAFS Spectra of the C1s Edge of Co-TPP  NEXAFS spectra of the C1s edge of a Co-TPP monolayer on Cu(111) for different incidence angles (θ =30◦ −90◦ ) between the E-vector of the synchrotron beam and the surface normal. Symbols do not represent data points but serve to differentiate angles. Inset: Exemplary zoom of the leading edge of the 70◦ spectra with fit components. Symbols represent data points, the solid line indicates the fit. Resonances associated with the macrocycle (phenyl groups) are shown with dotted (dash-dotted) lines. b Structural model for the conformational adaptation of Co-TPP on Cu(111) with a saddle-shaped distortion of the macrocycle and a dihedral angle of 35◦ .  Chapter 9. Visualizing Frontier Orbitals  173  tation of the molecules, we now adress their electronic properties. A comparison of the STM topographs reproduced in Figure 9.3a,d and Figure 9.1 reveals a strong bias dependent appearance of intramolecular features. There are marked differences between images reflecting occupied and unoccupied electronic states obtained at negative and positive bias voltages, respectively. For instance, the dominant cigar-shaped protrusion resolved at Vt = −2.1 V (Figure 9.1c) transforms to an oval bright core at Vt = −400 mV (Figure 9.3d). Upon tunneling into the unoccupied states (Vt = 800 mV, cf. Figure 9.3a), we resolve bright lobes localized over the four mesa-bridge carbons and a local central depression. This changing appearance indicates contributions of different electronic channels to the tunneling current arising from the local density of states (LDOS) associated with MOs [239]. We thus explored the electronic properties by STS. Spectra averaging over several molecules are shown in Figure 9.3b. The orange curve represents the raw dI/dV data whereas the green curve was obtained by normalization, i.e., dividing by I/V. The latter reveals more detailed features, i.e., local maxima, that do not exist for the pristine copper surface. We identify the adsorbed Co-TPPs highest occupied molecular orbital (HOMO) at −350 mV (blue dashed line) and the lowest unoccupied molecular orbital (LUMO) at 420 mV (red dashed line; referenced to the Fermi level (Vt =0), we define the first state at positive (negative) bias voltages in the tunneling spectrum as LUMO (HOMO), the second as LUMO-1 (HOMO+1) and so on, which notation does not discriminate between molecular orbitals solely related to the organic moieties and states with strong metal center d character and thus deviates from alternative definitions). This indicates a marked reduction of the HOMO-LUMO  Chapter 9. Visualizing Frontier Orbitals  174  gap to 770 mV, significantly smaller than the 1.4 eV gap for planar conformers suggested from optical absorption spectra [316] (for comparison, density functional theory (DFT) calculations indicated 2.5 eV [79]). Similar reductions were reported for simpler systems [270] and can be ascribed to surface polarization effects [173, 317]. The interaction with the surface also accounts for the broadening of the isolated molecules discrete levels into the observed resonances displaying 100-400 mV energy widths. In order to identify the Co-TPPs frontier orbitals and discriminate the position-dependence of tunneling current contributions from different conduction channels, we recorded tunneling spectra at selected sites over the molecule. They are reproduced in Figure 9.3c showing a sequence of local maxima reflecting the LDOS at the molecule. There are occupied states close to the Fermi level, at an energy of −350 and −600 meV, and unoccupied states at +420 and +800 meV, respectively. Furthermore the STS measurements reflect marked intramolecular spatial variations: the spectra 1 and 2 taken on dissimilar pyrrole groups (marked in Figure 9.3c) do not match and are very different from spectrum 3 (green) taken on a phenyl endgroup (cf. Figure 9.3d). The data also reveal that the occupied states at negative bias appear with different weight. This explains the macrocycles electronic asymmetry reflected in the two-fold symmetric topography and substantiates the NEXAFS interpretation of a conformational adaptation. The spatial characteristics of the frontier MOs were probed by dI/dV mapping. The data reproduced in Figure 9.3e-i were recorded at bias voltages where STS identified discrete energy levels (dashed lines in Fig. 9.3c; because we achieved at −400 mV the clearest contrast for the first molecular level be-  Chapter 9. Visualizing Frontier Orbitals  175  low the Fermi energy we use this dI/dV map as representation of the HOMO. Note that the intrinsic energy spread and applied bias modulation accounts for frontier MO maps of similar shape over an energy width of typically ∼100 mV. We also took reference maps to probe the possible interference of the Cu(111) surface state 2D electron gas, which due to the associated characteristic standing wave patterns in the vicinity of the Co-TPP islands could be clearly differentiated from the MO contributions). The occupied HOMO-1 state at −600 mV features a protrusions at each pyrrole group on the main axis (see overlaid model in Figure 9.3e). The HOMO in Figure 9.3f similarly displays a distinct two-fold symmetry, however now with an intensity maximum at the Co-TPP center. Hence the occupied states account for the cigar-shaped protrusion along the main axis resolved in topographic data (see Fig. 9.1c, 9.3d). In Figure. 9.3g-i maps of the unoccupied states are reproduced. A toroidal shape is dominant for both +400 and +800 mV, whereby the first dI/dV map represents the LDOS associated with the LUMO and the +800 mV LUMO+1 resonance features a double-lip shape. This data sequence strongly suggests that the observed contours reflect the electron densities associated with individual frontier MOs. For higher unoccupied (and lower occupied) levels there is a substantial peak broadening that renders a distinction of the respective MO contribution more difficult. However, with higher voltages (Vt > 1 V) there is a further clear change in symmetry and shape, whereby the weight is shifted to the location of the phenyl substituents. An exemplary map is reproduced in Figure 9.3i. The spectroscopic signature and selective mapping of the Co-TPP frontier orbitals strongly suggests that the molecular electron system is largely decoupled from that of the  Chapter 9. Visualizing Frontier Orbitals  176  metal substrate [173, 270, 317]. In agreement, a recent DFT investigation reported a non-covalent bonding of transition metal porphines on Au(111) [314]. However, the size of the present system prevents from first-principle analysis. For a first-order approximation we thus calculated MO maps for isolated Co-TPP in the framework of extended-H¨ uckel theory (EHT). EHT is known to reproduce the shape of molecular orbitals quite accurately, and electron density contours derived thereof proved useful for the interpretation of STM topographic data of weakly bound complex adsorbates [168, 170, 239]. These simulations tacitly assume that the Cu(111) substrate mainly modifies the alignment of frontier orbital energies and broadens discrete molecular levels into resonances [173]. We considered distorted vs. planar macrocycle conformers in order to assess their role in the observed asymmetry. The saddle-shape molecular structure was modeled using the NEXAFS parameter set with the phenyl rings fixed at a dihedral angle θ =35◦ and subsequent macrocycle relaxation yielding pyrrole moiety tilts of ±20◦ (cf. Figure 9.2b). The mimicked dI/dV maps reflect charge densities obtained by summing up over nearly degenerate states. The comparison between the planar (Fig. 9.4a-e) and saddle-shaped conformer (Figs 9.4f-j) reveals a similar MO sequence in both cases that reproduces the gross characteristics of the changing LDOS in the experimental findings (Fig. 9.4k-o). However, the distinct symmetry break in the maps can be exclusively explained by the distorted molecular geometry. It is most pronounced for the electron density distribution of the mapped occupied states (Fig. 9.4 i,n and j,o). Moreover, the differences in electron density at the Co(II) center hint a sequence reversal  Chapter 9. Visualizing Frontier Orbitals  177  Figure 9.3: Visualizing Frontier Orbitals of Co-TPP  a,d Contrast change in STM topographs for tunneling into occupied and unoccupied states, respectively (both I=0.25 nA). b Tunneling spectrum averaged over several molecules, where the orange curve represents raw data and the green curve is normalized (dI/dV divided by I/V) (initial conditions Vt = −2.1 V, I=0.2 nA). c Normalized spectra at the three positions over the molecule indicated in d, whereby 1 and 2 are different locations at the macrocycle and 3 right at the phenyl group. Frontier molecular orbital energy levels are marked by dashed lines. e-i Visualization of the spectral density of molecular orbitals by dI/dV mapping. The maps confirm the laterally varying signature of the line spectra.  Chapter 9. Visualizing Frontier Orbitals  178  Figure 9.4: Electron density from Extended H¨ uckel Theory  Comparison of EHT calculations of molecular orbitals for Co-TPP with ae planar macrocycle, f-j the saddle-shaped conformer and k-o STS dI/dV maps. Shape and symmetry of experimental MOs are nicely reproduced by the calculations for the surface-adapted conformation, while the match with orbitals from undistorted molecules is less satisfactory.  Chapter 9. Visualizing Frontier Orbitals  179  of the HOMO and HOMO-1 orbitals. On the one hand side this might be related to limitations of EHT in the description of metal-ligand interactions. DFT calculations of isolated Co-TPP indeed show that HOMO and HOMO1 orbitals bear strong Co d-electron character [79] On the other hand, the nature of d-like orbitals is affected by axial ligands [79], and to some extent by the presence of a metal substrate [96, 314]. These subtle effects are similarly understood as a possible reason for the presently remarkable absence of an STS signature right at the Fermi level that could be associated with a Kondo resonance and thus a magnetic moment of the Co center, and that conversely was observed for a bromophenyl substituted Co-porphyrin on the same substrate [99] Also the unoccupied MOs located at the phenyl substituents (Fig. 9.4f, k) clearly reveal the symmetry break and reproduce the envelope of the corresponding STS map, although the experimentally observed electron density at the center of the adsorbed molecule does not exist for free Co-TPP. Overall, the simple EHT description and STS mapping results can be reconciled and help to rationalize the observed spectral electron density distributions with distinct symmetry. However, a more sophisticated theoretical analysis is clearly required for a comprehensive description of the system. Thereby it would be desirable to address concurrently the electronic structure of the entire molecule-substrate complex and the interactions and energetics driving the Co-TPP conformational adaptation, which implies an orientation of the phenyl -electron systems and a lowering of the macrocycle plane towards the surface.  Chapter 9. Visualizing Frontier Orbitals  9.3  180  Conclusion  In conclusion, the interplay between molecular flexibility and electronic characteristics was investigated by STM and NEXAFS experiments in combination with extended-H¨ uckel theory calculations for Co-TPP molecules adsorbed on Cu(111). The visualization of frontier molecular orbitals with distinct symmetry by tunneling spectroscopy mapping reflects a saddle-shape deformation, which is in agreement with the analysis of NEXAFS data. Our combination of techniques demonstrates the potential to provide deeper insight into conformational adaptation and its effect on electronic structure. This knowledge contributes to an improved understanding and control of flexible functional molecular species anchored on surfaces. It also opens up new vistas to tune the functional properties of active metal centers in adaptive coordination units and to achieve conformational design of molecular nanosystems and biomimetic materials.  9.4  Experimental and Theoretical Section  STM and STS experiments were performed with a custom-designed ultrahigh vacuum apparatus (pressure below 2·10−10 mbar), comprising a commercial low-temperature scanning tunneling microscope ( typically operated at 10 K. The Cu(111) single crystal was prepared by repeated Ar+ sputter-anneal cycles. Subsequently, Co-TPP was deposited from a Knudsen cell, while the sample was held at 270 K. The indicated imaging bias voltages were applied to the sample. Differential conductance (dI/dV) data were obtainedvia lock-in amplifying technique, using a modu-  Chapter 9. Visualizing Frontier Orbitals  181  lation amplitude of 10 mV RMS and a frequency of 1.3 kHz. The feedback loop was open for spectroscopy and closed for the dI/dV mapping. The employed electrochemically etched W-tip was shaped by controlled dipping into the substrate until intramolecular features were clearly resolved and reference spectra of the metal substrate yielded the Cu(111) electronic structure. The presented STS data could thus be obtained reproducibly. Varying the stabilizing tunneling current over two orders of magnitude probed the influence of the tip-sample distance on the dI/dV data, whereby no significant change could be observed. NEXAFS measurements were performed at the HE-SGM beamline at BESSY II using monolayer Co-TPP films deposited on Cu(111) after checking surface cleanliness by photoelectron spectrosopy. Data recording and processing followed procedures outlined elsewhere [257] For the MO calculations within the semiempirical extended Hckel method a commercial software package was employed (HYPERCHEM; Hypercube Inc.: 1115 NW 4th street, Gainesville, Florida 32601). For the molecular relaxation we applied basic molecular mechanics calculations (MM+ force field of the Hyperchem 7.5 molecular modeling package) to optimize the geometry of CoTPP moieties.  182  Chapter 10 Conclusion The work presented here demonstrated the versatile ability of a complex molecule to adopt and interact with its specific environment, modifying therewith its chemical and physical properties. To employ molecules, which inhibit distinct functionalities in nature, as building blocks for nano-structured materials, nano-electronics or even nano-robotics, it is crucial to understand, to control and to modify their physical and chemical properties in a specific environment. A surface represents a well accessible environment, for the purpose of basic research and for applications. The advancements in various surface sensitive techniques, especially Scanning Tunneling Microscopy and Spectroscopy, provided the opportunity to investigate, control and manipulate matter down to the level of single atoms. Hence, these techniques were used to functionalize surfaces with molecules, atoms and combinations of both, to form, for instance, regular nano-structured 2D networks. Fields of potential use are molecular (opto-) electronics, chemical sensing as well as heterogeneous catalysis. However, this requires a meticulous understanding on the individual base of the molecule’s versatile interactions and properties adsorbed on a surface, such as binding characteristics, the conformational adaptation and the electronic structure. In this work, porphyrin molecules and their intermolecular, moleculesurface and metal adatom-molecule interactions, absorbed on silver and cop-  Chapter 10. Conclusion  183  per substrates were investigated. Porphyrins represent a class of molecules, which play a key role in biological systems exhibiting a range of functionalities. Tetrapyridil porphyrin, with its reactive pyridil endgroups was vapor deposited under UHV conditions on Ag(111) and Cu(111). The diverse reactivity of these two surfaces evokes a substantial difference in the molecules’ behaviour on the surface. While the assembly of TPyP on Ag(111) is mainly governed by intermolecular interactions, the same molecule’s response on Cu(111) is mainly determined by the strong substrate influence. On Ag(111) TPyP forms large, highly-ordered chiral domains over a wide sample temperature range. By contrast, TPyP on Cu(111) leads to temperature-dependent assemblies of linear chain segments and triangular structures, accompanied by a significant conformational distortion of the porphyrin macrocycle. The attractive interactions between the functional pyridyl moieties and the Cu substrate were explored in more detail, determining the TPyP’s adsoption site mediated presumably by the lone pair electrons of the pyridil nitrogens.  Furthermore, the functional pyridyl legs’ attraction to metal  adatoms was demonstrated with in-situ evaporated Fe atoms, presenting snapshots of the self-assembly process of a metal-organic complex in two dimensions. In addition, the geometry of adsorbed molecules was determined by NEXAFS, quantifying for the first time the saddle-shaped geometry of an adsorbed free-base porphyrin molecule. This distortion defeated any attempts to study the interaction of iron adatoms with the TPyP’s macrocycle. For this purpose we went back to the Ag(111) substrate, where a well ordered layer of TPyP was exposed  Chapter 10. Conclusion  184  to a beam of iron atoms. The successful metalation of an adsorbed TPyP nanoarray was demonstrated, presenting a novel reaction scheme. It allows the formation of low-dimensional metallo-porphyrin architectures by using preorganized porphyrin arrangements, which are subsequently functionalized by metal centers. Moreover, we showed that novel lanthanide porphyrinate compounds can be created by implementing this procedure to create coordinatively unsaturated Cerium-Tetraphenyl porphyrin species, which could not be obtained by conventional methods and for which no 3D analogues exist. The influence of the metal center on the porphyrins’ electronic structure was investigated by Scanning Tunneling Spectrosopy. Metal specific shifts of the metalloporphyrins’ frontier orbitals were observed. Furthermore, the spatially inhomogenous electron density distribution associated with these frontier orbitals was visualized by mapping the differential conductance of a specific resonance. In the case of cobalt tetraphenyl porphyrin. the symmetry and shape of these frontier orbitals could be related to the saddle-shaped conformation of Co-TPP. These results demonstrate the variety of interactions of complex molecules with their environment and how significant this influence affects the molecule’s properties. This modification of a molecular building blocks depending on their interactions, is especially important to keep in mind when supramolecular nano-structures are developed. In addition, it was illustrated how important the combination of complementary surface sensitive techniques is, to form a well-lid picture of a system under investigation. The presented results encourage future investigations, for example the further investigation of the local influence on the conformation of the molecule.  Chapter 10. Conclusion  185  The choice of substrate, meso substituents or the element placed in the macrocycle’s center might be used for conformational design of molecular systems. Moreover, this work prepares the ground for 3-D nano-structures, arrays with specifically chosen reactive metal centers, where appropriate building blocks can be attached as axial linkers. Systems, like Fe-TPyP could be exploited to form new materials for heterogeneous analysis or spintronics. Ce-TPPs might be used to from double deckers, presenting molecular rotors. By choosing the according element to place in the macrocycle it is conceivable to create Single Molecular Magnets (SMMs), anchored to a metal surface. Magnetic properties of large, well-ordered ensembles of such SMMs could be explored via Spin Polarized Low Energy Electron Microscopy. Furthermore, the availability of the axial positioned metal centers invites to study further reactions with biological relevant ligands (O2 , CO, etc.) and facilitates the possibility to carry out biological relevant reaction schemes. Additional techniques, such as optical spectroscopy represent a complementary approach to STS, which could be employed to investigate the optical properties of these systems, in particular the influence of different metal centers to create photo-active systems. The control over matter on the atomic and molecular scale opens unknown ways to engineer materials with unique unprecedented properties. I want to close this thesis with a quote and a remark. In 1959 at the annual meeting of the American Physical Society, Richard Feynman held an astounding prescient speech over the miniaturization of matter. Its title was ”There’s plenty of room at the bottom”. Today, we might just begin to recognize the bottom.  186  Chapter 11 Publication List 1. L.A. Zotti, G. Teobaldi, W.A. Hofer, W. Auw¨arter, A. Weber-Bargioni, and J.V. Barth. Ab-initio calculations and STM observations on tetrapyridyl and Fe(II)-tetrapyridyl-porphyrin molecules on Ag(111),Surface Science, 601:24092414, 2007  2. A. Schiffrin, A. Riemann, W. Auw¨arter, Y. Pennec, A. Weber-Bargioni, D Cvetko, A. Cossaro, A. Morgante, and J.V. Barth. Zwitterionic self-assembly of L-methionine nanogratings on the Ag(111) surface, PNAS, 104: 5279-5284 (2007)  3.Y. Pennec, W. Auw¨arter, A. Schiffrin, A. Weber-Bargioni, A. Riemann, and J. V. Barth. Supramolecular gratings for tunable confinement of electrons on metal surfaces, Nature Nanotechnology 2:99-103, 2007  4. W. Auw¨arter, A. Weber-Bargioni, S. Brink, A. Riemann, A. Schiffrin, M. Ruben, and J.V. Barth. Controlled metalation of self-assembled porphyrin nanoarrrays in two dimensions,Chem. Phys. Chem. 8:250-254, 2007  5. W. Auw¨arter, A. Weber-Bargioni, A. Riemann, A. Schiffrin, R. Fasel, O. Grning and J.V. Barth. Self-assembly and conformation of tetrapyridil-  Chapter 11. Publication List  187  porphyrin on the Ag(111) surface,J. Chem. Phys. 124:194708, 2006  6. W. Auw¨arter, F. Kappenberger, A. Weber-Bargioni, , A.Schiffrin, A.Riemann, Y.Pennec and J.V. Barth. Conformational adaptation and selective adatom capturing of tetrapyridil-porphyrin molecules on a copper (111) surface, in print JACS  7. A. Weber-Bargioni, W. Auw¨arter, F. Klappenberger, A. Riemann, A. Schiffrin, and J.V. Barth. Visualizing the Frontier Orbitals of a Conformationally Adapted Metalloporphyrin, in print J.Phys.Chem  8. A. Weber-Bargioni, J.Reichert, W. Auw¨arter, A. Schiffrin and J.V. Barth. Interaction of cerium atoms with surface-anchored porphyrin molecules , submitted  9. A. Weber-Bargioni, W. Auw¨arter, F. Klappenberger, A. Riemann, A. Schiffrin, and J.V. Barth. Temperature induced conformational change of Tetrapyridylporphyrin on Cu(111), to be published  10. A. Weber-Bargioni, J. Reichert, W. Auw¨arter, and J. 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