Properties of Single Organic Molecules on Crystal Surfaces

The following sections are included:

• Contents

• Preface

• Authors' Biographies

Clean metal surfaces often display an atomic arrangement at the surface that differs from the one in the bulk. Some of these surface reconstructions show mesoscopic order and are very adequate to act as a template for the ordered growth of arrays of atoms, molecules or clusters. The electronic states at some surfaces can be prototypes of highly dense 2D electron gases where a number of fundamental properties can be addressed in detail. Localized surface states, on the other hand, are relevant in chemical processes at surfaces. The recent developments in experimental and theoretical techniques allow the exploration of these issues with unprecedented precision.

This chapter addresses the basic fundamental properties of silicon surfaces, including structural, electronic and chemical properties. An introduction is given to STM topographic imaging and tunneling spectroscopy as applied to semiconductors. The chapter will then give a brief overview of scanning tunneling microscope studies of clean silicon semiconductor surfaces under ultra-high vacuum conditions. Particular emphasis will be placed on the most common low index Si surface and a discussion of typical adsorbates observed on these surfaces. The use of hydrogen lithography to control the atomic placement of adsorbates on silicon is reviewed. Finally the work will be put in context of the fabrication of novel nano and atomic-scale semiconductor devices using scanning tunneling microscopy.

Scanning tunneling microscopy (STM) and atomic force microscopy (AFM) are vital tools for the study of single organic moelcules on surfaces. In particular, a combination of these tools allows to compare images derived by forces to those derived by measuring tunneling currents. Operation at low temperatures enables to measure even the weak forces acting between organic molecules at an excellent signal-to-noise ratio, because the thermal drift that plagues highprecision measurements at room temperatures is essentially absent at liquid helium temperatures (4 K). However, the implementation of combined STM/AFM instruments is challenging. In this article, we describe the essential component parts, the functionality and the limitations of traditional microscopes and compare them to a new design that incorporates the qPlus sensor, a stiff cantilever based on a quartz tuning fork that greatly facilitates combined STM/AFM. First, results of simultaneous STM and AFM measurements on graphite, a material that can be viewed as a prototype of an organic molecule, are presented. The complementary nature of STM and AFM data and the value of access to both data sources is outlined.

This chapter deals with optical detection of single fluorescent molecules inside and close to the boundary of complex media. After discussing the fundamentals of single-emitter detection based on luminescence detection, experimental set-ups and methods are introduced. Advantages and disadvantages of scanning near-field optical microscopy and scanning confocal optical microscopy are discussed in view of applications for single-emitter studies. The remainder of the chapter is devoted to the discussion of selected applications of single-emitter experiments including their use as deterministic single-photon sources, and applications as minimally invasive probes and labels in biology and material science.

In this Chapter, we review a state-of-the-art theoretical formalism for modeling quantum transport properties of molecular scale conductors. The formalism is based on carrying out density functional theory (DFT) analysis within the Keldysh non-equilibrium Green's function (NEGF) framework. It allows predictions of nonlinear and nonequilibrium charge transport through nano-electronic devices without using phenomenological parameters. We present relevant details to the physical, mathematical, and numerical backgrounds of this formalism. An example will be given to illustrate the application of this technique.

With the availability of first principles methods to simulate the operation of a scanning tunneling microscope (STM), theory has moved from the qualitative and topographic to the quantitative and dynamic. Simulations in effect predict the influence of a model-tip or chemical interactions between tip and sample in the actual imaging process. By comparing experiments and simulations, the information about the analyzed system can be substantially extended. We give an overview of recent work, where the combination of first principles simulations with high resolution measurements was decisive in arriving at consistent results.

The fascinating advances in the manipulation of single atoms and molecules with the scanning tunneling microscope tip allow scientists to build atomic scale structures and to probe chemical and physical properties of matters at an atomic level. Due to these advances, the basic steps of a catalyzed chemical reaction such as dissociation, diffusion, adsorption, re-adsorption and bond formation processes can be performed by using the STM-tip. Here a short review of these steps and the techniques involved is presented. The lateral manipulation is used for the controlled positioning of atoms/molecules whereby only the tip– atom/molecule forces are employed. By measuring the tip-height signal during the manipulation, different modes of motion of the adparticle can be distinguished. Lower corrugated surfaces exhibit more complex motions than higher corrugated surfaces where the adparticle movement is confined to one dimension. Molecules have more degrees of freedom which allow a rotational motion or change in configuration. Even internal degrees of freedom can be detected and manipulated. The vertical manipulation not only allows the pick-up of adparticles and the subsequent transfer back to the surface, but also the manipulation of fragments of larger molecules. Effects due to the tunneling curent can be used for a controlled dissociation of chemical bonds as well as for the formation of new bonds. The combination of these manipulation techniques can induce chemical reactions at a single molecule level and construct new molecules. These achievements in STM manipulation of molecules open up new opportunities in nanochemistry and nanochemical technology. In this article, various STM manipulation techniques used for the single molecule reaction process are reviewed, and their impact on the future of nanoscience and nanotechnology is discussed.

The ultimate characterization of a single molecule relies on its chemical identification. Single-molecule vibrational spectroscopy has been a major breakthrough in the development of individual molecule handling. On one hand it provides a tool to characterize local structure and bonding; on the other it provides a methodology to manipulate single molecules by activating specific vibrations. Here we introduce the topic of single molecule vibrational characterization with the scanning tunneling microscope (STM) and its specificities with regards to the excitation and detection of local vibrations. We will expound how inelastic electrons can serve to this end, and how to interpret the results of such a technique. An important consequence of exciting localized modes is the enhanced control that the excitation grants over possible molecular reaction paths.

We describe the state-of-the-art in the creation of ordered superlattices of adsorbed atoms, molecules, semiconductor quantum dots, and metallic islands, by means of self-assembly during atomic-beam growth on single crystal surfaces. These surfaces often have long-period reconstructions or strain relief patterns which are used as template for heterogeneous nucleation. However, repulsive adsorbate-adsorbate interactions may also stabilize ordered superlattices, and vertical correlations of growth sequences of buried islands will be discussed in the case of semiconductor quantum dots. We also present new template surfaces considered as particularly promising for the creation of novel island superlattices.

Concepts, recent developments and achievements in investigations addressing the mobility of complex organic molecules on welldefined metal surfaces are reviewed.

Formation of organic molecular monolayers on silicon surfaces offers the promise of enhancing the functionality of existing silicon-based materials and devices. These monolayers can function as passivating layers, stabilizing the properties of the underlying substrate, or used to tailor its physical, chemical and electronic properties. Monolayers can also impart new functionality to the silicon surface, such as molecular recognition capability. In this chapter we review the methods that have been developed for the formation of molecular monolayers via reactions with hydrogen terminated silicon, and summarize the current understanding regarding the mechanisms behind these reactions. A variety of chemical approaches have been employed to form alkyl monolayers covalently attached to the surface via Si-C, Si-O or Si-N linkages. Multi-step reactions have been developed to build up more complex chemical functionalities as well as for the attachment of biomolecules such as DNA and proteins. The characterization of the resulting monolayers, employing a wide variety of surface science probes, will be discussed. Investigations of the electronic properties of these layers with both electrochemical and solid-state approaches are summarized. Attempts to demonstrate the utility of these monolayers for molecular electronic and chemical/bio sensing applications are critically reviewed.

In the age when the miniaturization trend that has driven the semiconductor industry is reaching its limits, organic modification of semiconductors is emerging as a field that could give much-needed impetus. We review the current state of understanding of the functionalization of C(100), Si(100), and Ge(100) surfaces through chemisorption of alkenes and alkynes, focusing on adsorbate structural control. While reactions on C(100) show most of the properties expected for concerted cycloaddition reactions such as [2+2] and [4+2] (Diels–Alder) processes, reactions on Si(100) present a wide range of variant behavior, including in some cases the prominence of non-cycloaddition products. More general stepwise free-radical addition processes are seen to provide a better description of reactions on Si(100), their prominence being attributed to either the non-existence or ineffectiveness of π bonding within surface silicon dimers. The investigations of these systems provide not only insight into driving mechanisms for chemisorption but also motivation for the development of new techniques of organic functionalization on semiconductors.

Molecular electronics is one of the most promising candidates currently discussed for electronic nanodevices. One big advantage of this field is that organic molecules are well-defined stable structures on an atomic scale, which in principle can be modified atom by atom in large quantities by means of chemical synthesis. This cannot in general be achieved for inorganic or more precisely non-carbon based materials, although Si-nanowires are a special case. Therefore, the use of molecules in electronic circuits might well represent the final frontier in miniaturization. There are, however, different approaches depending on the types and numbers of molecules used in an active device and on the ways they are connected to form a circuit. These approaches vary widely in their near future feasibility, state of development and in their ultimate limits for miniaturization and performance, and are usually difficult to categorize. For this chapter recent research has been divided into (1) theory and experiments on electron transport through single small molecules, (2) design and fabrication of small circuits based on single macromolecules as active transistor elements, and (3) integrated circuits with a few thousand molecules representing one diode in a regular metallic grid structure on the nanoscale.

In this chapter, we recount a recent success story in the quest for a molecular-level view of a large-scale catalytic process, namely ethylene (C₂H₄) partial oxidation to ethylene epoxide (C₂H₄O). This selective oxidation reaction, which is catalyzed uniquely by silver, is more than sixty years old and one of the most widely studied in heterogeneous catalysis. What the microscopic mechanism of this reaction is, however, remains unclear, and why the noble metal Ag is the only metal that catalyses this process is also unknown. Traditionally, studies (and hence debates!) have centered on identifying the nature of the ‘active’ oxygen species, i.e. the one that actuates the catalysis and leads to the desired partial oxidation product. Here, we begin by describing density functional theory (DFT), scanning tunneling microscopy (STM) and STM simulation studies which have characterized the atomic level structures of O on the {111} surface of Ag. These studies have identified two types of stable phase of O on Ag: (i) Low coverage O adatom phases (θ ∼ 0.05 monolayers); and (ii) ultra-thin Ag_xO (x ≠ 2) surface oxides. Following this, the relative stabilities of these overlayers are assessed at finite temperatures and pressures in order to link these ‘surface science’ ultrahigh- vacuum conclusions with the high pressure and high temperature realm of industrial catalysis. This is done through the application of thermodynamics (with a strategy now commonly referred to as “ab initio thermodynamics”) and leads to an ab initio surface phase diagram for O on Ag{111}. Next the reactivity of the phases predicted to be stable at, or close to, industrial epoxidation conditions is examined. This involves (i) a combined STM and DFT study of ethylene adsorption on one of the ultra-thin Ag_xO surface oxides; and (ii) a DFT study in which reaction pathways and transition states for the conversion of ethylene to ethylene epoxide have been determined. One of the key findings of the latter study is that whether on a surface oxide overlayer or on a surface with a low coverage of O adatoms, ethylene epoxidation is not a direct reaction. Instead it is a two-step non-concerted process, which proceeds via an oxametallacycle intermediate.

The following sections are included:

• Index