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Abstract: Using scanning probe microscopy techniques, at low temperatures and in ultrahigh vacuum, individual molecules adsorbed on surfaces can be probed with ultrahigh resolution to determine their structure and details of their conformation, configuration, charge states, aromaticity, and the contributions of resonance structures. Functionalizing the tip of an atomic force microscope with a CO molecule enabled atomic‐resolution imaging of single molecules, and measurement of their adsorption geometry and bond‐order relations. In addition, by using scanning tunneling microscopy and Kelvin probe force microscopy, the density of the molecular frontier orbitals and the electric charge distribution within molecules can be mapped. Combining these techniques yields a high‐resolution tool for the identification and characterization of individual molecules. The single‐molecule sensitivity and the possibility of atom manipulation to induce chemical reactions with the tip of the microscope open up unique applications in chemistry, and differentiate scanning probe microscopy from conventional methods for molecular structure elucidation. Besides being an aid for challenging cases in natural product identification, atomic force microscopy has been shown to be a powerful tool for the investigation of on‐surface reactions and the characterization of radicals and molecular mixtures. Herein we review the progress that high‐resolution scanning probe microscopy with functionalized tips has made for molecular structure identification and characterization, and discuss the challenges it will face in the years to come. [ABSTRACT FROM AUTHOR]

Antiaromatic and open-shell molecules are attractive because of their distinct electronic and magnetic behaviour. However, their increased reactivity creates a challenge for probing their properties. Here, we describe the on-surface and in-solution generation and characterisation of a highly reactive antiaromatic molecule: indeno[1,2-b]fluorene (IF). In solution, we generated IF by KI-induced dehalogenation of a dibromo-substituted precursor molecule and found that IF survives for minutes at ambient conditions. Using atom manipulation at low temperatures we generated IF on Cu(111) and on bilayer NaCl. On these surfaces, we characterised IF by bond-order analysis using non-contact atomic force microscopy with CO-functionalised tips and by orbital imaging using scanning tunnelling microscopy. We found that the closed-shell configuration and antiaromatic character predicted for gas-phase IF are preserved on the NaCl film. On Cu(111), we observed significant bond-order reorganisation within the s-indacene moiety because of chemisorption, highlighting the importance of molecule surface interactions on the π-electron distribution. [ABSTRACT FROM AUTHOR]

Si dangling bonds at the interface of quasi-free-standing monolayer graphene (QFMLG) are known to act as scattering centers that can severely affect carrier mobility. Herein, we investigate the atomic and electronic structure of Si dangling bonds in QFMLG using low-temperature scanning tunneling microscopy/spectroscopy (STM/STS), atomic force microscopy (AFM), and density functional theory (DFT) calculations. Two types of defects with different contrast were observed on a flat graphene terrace by STM and AFM; in particular, their STM contrast varied with the bias voltage. Moreover, these defects showed characteristic STS peaks at different energies, 1.1 and 1.4 eV. The comparison of the experimental data with the DFT calculations indicates that the defects with STS peak energies of 1.1 and 1.4 eV consist of clusters of three and four Si dangling bonds, respectively. The relevance of the present results for the optimization of graphene synthesis is discussed. [ABSTRACT FROM AUTHOR]

Petroleum is one of the most precious and complex molecular mixtures existing. Because of its chemical complexity, the solid component of crude oil, the asphaltenes, poses an exceptional challenge for structure analysis, with tremendous economic relevance. Here, we combine atomicresolution imaging using atomic force microscopy and molecular orbital imaging using scanning tunnelling microscopy to study more than 100 asphaltene molecules. The complexity and range of asphaltene polycyclic aromatic hydrocarbons are established in detail. Identifying molecular structures provides a foundation to understand all aspects of petroleum science from colloidal structure and interfacial interactions to petroleum thermodynamics, enabling a first-principles approach to optimize resource utilization. Particularly, the findings contribute to a long-standing debate about asphaltene molecular architecture. Our technique constitutes a paradigm shift for the analysis of complex molecular mixtures, with possible applications in molecular electronics, organic light emitting diodes, and photovoltaic devices. [ABSTRACT FROM AUTHOR]

We describe a nanostencil lithography tool capable of operating at variable temperatures down to 30 K. The setup is compatible with a combined low-temperature scanning tunneling microscope/atomic force microscope located within the same ultra-high-vacuum apparatus. The lateral movement capability of the mask allows the patterning of complex structures. To demonstrate operational functionality of the tool and estimate temperature drift and blurring, we fabricated LiF and NaCl nanostructures on Cu(111) at 77 K. [ABSTRACT FROM AUTHOR]

Force and conductance were simultaneously measured during the formation of Cu-C60 and C60-C60 contacts using a combined cryogenic scanning tunneling and atomic force microscope. The contact geometry was controlled with submolecular resolution. The maximal attractive forces measured for the two types of junctions were found to differ significantly. We show that the previously reported values of the contact conductance correspond to the junction being under maximal tensile stress. [ABSTRACT FROM AUTHOR]

Scanning tunnelling microscopy and atomic force microscopy can be used to study the electronic and structural properties of surfaces, as well as molecules and nanostructures adsorbed on surfaces, with atomic precision, but they cannot directly probe the distribution of charge in these systems. However, another form of scanning probe microscopy, Kelvin probe force microscopy, can be used to measure the local contact potential difference between the scanning probe tip and the surface, a quantity that is closely related to the charge distribution on the surface. Here, we use a combination of scanning tunnelling microscopy, atomic force microscopy and Kelvin probe force microscopy to examine naphthalocyanine molecules (which have been used as molecular switches) on a thin insulating layer of NaCl on Cu(111). We show that Kelvin probe force microscopy can map the local contact potential difference of this system with submolecular resolution, and we use density functional theory calculations to verify that these maps reflect the intramolecular distribution of charge. This approach could help to provide fundamental insights into single-molecule switching and bond formation, processes that are usually accompanied by the redistribution of charge within or between molecules. [ABSTRACT FROM AUTHOR]

A covalent bond between an individual pentacene molecule and a gold atom was formed by means of single-molecule chemistry inside a scanning tunneling microscope junction. The bond formation is reversible, and different structural isomers can be produced. The single-molecule synthesis was done on ultrathin insulating films that electronically isolated the reactants and products from their environment. Direct imaging of the orbital hybridization upon bond formation provides insight into the energetic shifts and occupation of the molecular resonances. [ABSTRACT FROM AUTHOR]

The nanostencil is a tool for resistless lithography. It allows the direct patterning of complex nanometer-sized structures composed of a wide range of materials in an ultrahigh vacuum environment. This is combined with state-of-the-art scanning probe microscopy techniques (atomic force microscopy, scanning tunneling microscopy) and an electronic four-point probe. Moreover, all these capabilities are in situ and autoaligned in the field of view. The direct patterning is based on the shadow-mask technique and allows multimask processes in a static and dynamic manner. [ABSTRACT FROM AUTHOR]

In this article we present a short review on low temperature scanning tunneling microscopy (LT-STM) investigations of specially designed molecules, performed with the help of manipulation techniques. The possibilities offered by LT-STM to build structures at the atomic scale are here extended to the manipulation of complex molecules. Single porphyrin-based molecules deposited on copper substrates are investigated and manipulated by means of their interaction with the STM tip. In a constant height mode of manipulation, the tunneling current recorded during the process contains detailed information on the internal mechanics of the molecule when guided by the STM tip. Moreover, recording images in constant height mode allows to investigate the interaction between tip and molecule with high spatial resolution. Finally we show that the manipulation of the molecules on Cu(211) offers the possibility to selective modify their internal conformation realizing the principle of a conformational molecular switch. [Copyright &y& Elsevier]

A detailed low temperature scanning tunneling microscope investigation of the intramolecular conformations of individual porphyrin-based molecules adsorbed on different copper surfaces is presented. Depending on the substrate geometry, the molecules show different orientations on the surface and different internal configurations. While on the Cu(1 1 1) surface the molecule lies flat on the surface, on Cu(1 0 0) its legs are oriented nearly perpendicular to the substrate. On Cu(2 1 1) an intermediate situation takes place. The molecule lies flat on (1 1 1) nanofacets, but other configurations are found with one leg rotated out of the substrate plane. Accurate theory–experiment comparisons allow to precisely determine the conformation of the molecule in the different cases. [Copyright &y& Elsevier]

Details the design of a low-temperature scanning tunneling microscope (STM). Main features including a scanner and the provision for extension of the microscope to work as a force microscope using the optical lever detection technique for force measurement.

We present a method that enables atomic-resolution measurements of the short-range force field above a single organic admolecule using noncontact atomic force microscopy. We have extended the standard force-mapping technique to be able to measure at close tip-molecule distances, in regions that cannot be accessed by normal constant-height or constant-frequency-shift imaging. Our technique can be used to study the interaction between a well-defined scanning probe tip and an admolecule on the atomic scale and yields atomic resolution of both molecule and substrate. Furthermore, it enables the measurement of constant-frequency-shift topographies of molecules with nonplanar adsorption geometries. [ABSTRACT FROM AUTHOR]

The nature and control of individual metal atoms on insulators are of great importance in emerging atomic-scale technologies. Individual gold atoms on an ultrathin insulating sodium chloride film supported by a copper surface exhibit two different charge states, which are stabilized by the large ionic polarizability of the film. The charge state and associated physical and chemical properties such as diffusion can be controlled by adding or removing a single electron to or from the adatom with a scanning tunneling microscope tip. The simple physical mechanism behind the charge bistability in this case suggests that this is a common phenomenon for adsorbates on polar insulating films. [ABSTRACT FROM AUTHOR]

The possibility of extending the lateral manipulation process performed with the tip of a scanning tunneling microscope at low temperature to large molecules is demonstrated. Single Cu-TBPP molecules deposited on a Cu substrate were manipulated by means of the interaction between the molecule and the tip. Due to the complicated structure of the molecules and to their high conductance, we have explored the possibilities of performing controlled lateral manipulation at constant height. On Cu(111) this method makes possible translation combined with rotation of the molecules on the surface. © 2001 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We present results of manipulation experiments for single C2H4 molecules and single Pb atoms and buildup of small nanostructures on a Cu(211) substrate employing our temperature-variable scanning tunneling microscope. We further discuss novel ‘‘indirect’’ lateral manipulation experiments with C2H4 chains and Pb dimers. The latter experiments prove the special stability of Pb dimers. Co-adsorption experiments with CO allow determination of the adsorption sites of C2H4 molecules as well as Pb atoms and Pb dimers. © 1996 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Highlights • Damping caused by sequential tunneling through a Cl-vacancy on a NaCl film. • Damping depends on thickness of the NaCl film, tip position and tip-sample bias. • Features of current-induced damping explained by a rate-equation model. • Subfemtoampere tunneling currents are detected by the damping signal. • Maps of the damping signal can be used to inspect the tip shape. Graphical abstract Abstract Sequential tunneling of electrons through a single chlorine vacancy on a multilayer NaCl film on Cu(100) in the junction of a non-contact atomic force microscope with a conductive tip can lead to a negative damping of the cantilever. The characteristic features in the damping signal as a function of NaCl-layer thickness, tip position and tip-sample bias can be explained in a simple rate-equation model for the sequential tunneling process through the double-barrier tunnel junction. The first barrier results from the vacuum gap between tip and vacancy and its tunneling rate is tuned by the tip position and the applied bias. The second barrier results from the NaCl film and its tunneling rate is governed by the film's thickness. The current-induced damping is strongest if the two tunneling rates through each of the barriers individually are both comparable to the cantilever's oscillation frequency. The damping signal can be employed for detecting subfemtoampere tunneling currents and furthermore, maps of the damping signal can be used to inspect the mesoscopic tip shape. The observed and described current-induced damping should be a common phenomenon in non-contact atomic force microscopy for double-barrier tunnel junction geometries. [ABSTRACT FROM AUTHOR]

We explore different tip functionalizations for atomic force microscopy (AFM), scanning tunneling microscopy (STM), and Kelvin probe force microscopy (KPFM) of organic molecules on thin insulating films. We describe in detail how tips terminated with single Br and Xe atoms can be created. The performance of these tips in AFM, STM, and KPFM imaging of single molecules is compared to other tip terminations, and the advantages and disadvantages of the different tips are discussed. The Br tip was found to be particularly useful for AFM and lateral manipulation, whereas the Xe tip excelled in STM and KPFM. [ABSTRACT FROM AUTHOR]

The bistability in the position of the two hydrogen atoms in the inner cavity of single free-base naphthalocyanine molecules constitutes a two-level system that was manipulated and probed by low-temperature scanning tunneling microscopy. When adsorbed on an ultrathin insulating film, the molecules can be switched in a controlled fashion between the two states by excitation induced by the inelastic tunneling current. The tautomerization reaction can be probed by resonant tunneling through the molecule and is expressed as considerable changes in the conductivity of the molecule. We also demonstrated a coupling of the switching process so that the charge injection in one molecule induced tautomerization in an adjacent molecule. [ABSTRACT FROM AUTHOR]

The formation of extended electron states in one-dimensional nanostructures is of key importance for the function of molecular electronic devices. Here, we study the effects of strong electron-phonon interaction on the formation of extended electronic states in intentionally created Cl vacancy pairs and chains in a NaCl bilayer on Cu(111). The interaction between the vacancies was tailored by fabricating vacancy pairs and chains of different orientation and separation with atomic precision using vertical manipulation. Small vacancy separations led to the formation of quantum-well-like vacancy states and localized interface states. By using scanning tunneling spectroscopy, we measured their energy splitting and broadening as a function of the intervacancy separation. Remarkably, the energy splitting between the vacancy states is enlarged by level repulsion resulting from the phonon dressing of the electronic states, as evidenced by theory. [ABSTRACT FROM AUTHOR]

Resolving individual atoms has always been the ultimate goal of surface microscopy. The scanning tunneling microscope images atomic-scale features on surfaces, but resolving single atoms within an adsorbed molecule remains a great challenge because the tunneling current is primarily sensitive to the local electron density of states dose to the Fermi level. We demonstrate imaging of molecules with unprecedented atomic resolution by probing the short-range chemical forces with use of noncontact atomic force microscopy. The key step is functionalizing the microscope's tip apex with suitable, atomically well-defined terminations, such as CO molecules. Our experimental findings are corroborated by ab initio density functional theory calculations. Comparison with theory shows that Pauli repulsion is the source of the atomic resolution, whereas van der Waals and electrostatic forces only add a diffuse attractive background. [ABSTRACT FROM AUTHOR]

Charge states of atoms can be investigated with scanning tunneling microscopy, but this method requires a conducting substrate. We investigated the charge-switching of individual adsorbed gold and silver atoms (adatoms) on ultrathin NaCl films on Cu(111) using a qPlus tuning fork atomic force microscope (AFM) operated at 5 kelvin with oscillation amplitudes in the subangstrom regime. Charging of a gold atom by one electron charge increases the force on the AFM tip by a few piconewtons. Moreover, the local contact potential difference is shifted depending on the sign of the charge and allows the discrimination of positively charged, neutral, and negatively charged atoms. The combination of single-electron charge sensitivity and atomic lateral resolution should foster investigations of molecular electronics, photonics, catalysis, and solar photoconversion. [ABSTRACT FROM AUTHOR]