Recent advances in submolecular resolution with scanning probe microscopy

Supramolecular Assemblies on Surfaces: Nanopatterning, Functionality, and Reactivity

Understanding how molecules interact to form large-scale hierarchical structures on surfaces holds promise for building designer nanoscale constructs with defined chemical and physical properties. Here, we describe early advances in this field and highlight upcoming opportunities and challenges. Both direct intermolecular interactions and those that are mediated by coordinated metal centers or substrates are discussed. These interactions can be additive, but they can also interfere with each other, leading to new assemblies in which electrical potentials vary at distances much larger than those of typical chemical interactions. Earlier spectroscopic and surface measurements have provided partial information on such interfacial effects. In the interim, scanning probe microscopies have assumed defining roles in the field of molecular organization on surfaces, delivering deeper understanding of interactions, structures, and local potentials. Self-assembly is a key strategy to form extended structures on surfaces, advancing nanolithography into the chemical dimension and providing simultaneous control at multiple scales. In parallel, the emergence of graphene and the resulting impetus to explore 2D materials have broadened the field, as surface-confined reactions of molecular building blocks provide access to such materials as 2D polymers and graphene nanoribbons. In this Review, we describe recent advances and point out promising directions that will lead to even greater and more robust capabilities to exploit designer surfaces.

Real-space imaging with pattern recognition of a ligand-protected Ag374 nanocluster at sub-molecular resolution

High-resolution real-space imaging of nanoparticle surfaces is desirable for better understanding of surface composition and morphology, molecular interactions at the surface, and nanoparticle chemical functionality in its environment. However, achieving molecular or sub-molecular resolution has proven to be very challenging, due to highly curved nanoparticle surfaces and often insufficient knowledge of the monolayer composition. Here, we demonstrate sub-molecular resolution in scanning tunneling microscopy imaging of thiol monolayer of a 5 nm nanoparticle Ag₃₇₄ protected by tert-butyl benzene thiol. The experimental data is confirmed by comparisons through a pattern recognition algorithm to simulated topography images from density functional theory using the known total structure of the Ag₃₇₄ nanocluster. Our work demonstrates a working methodology for investigations of structure and composition of organic monolayers on curved nanoparticle surfaces, which helps designing functionalities for nanoparticle-based applications.

Translating high-resolution imaging methods to the curved organic surface of a nanoparticle has been challenging. Here, the authors are able to spatially resolve the sub-molecular surface details of a silver nanocluster by comparing scanning tunneling microscopy images and simulated topography data through a pattern recognition algorithm.

In Situ Electrochemical Tip-Enhanced Raman Spectroscopy with a Chemically Modified Tip

Chemically modified tips in scanning tunneling microscopy (STM) and atomic force microscopy (AFM) have been used to improve the imaging resolution or provide richer chemical information, mostly in ultrahigh vacuum (UHV) environments. Tip-enhanced Raman spectroscopy (TERS) is a nanoscale spectroscopic technique that already provides chemical information and can provide subnanometer spatial resolution. Chemical modification of TERS tips has mainly been focused on increasing their lifetimes for ambient and in situ experiments. Under UHV conditions, chemical functionalization has recently been carried out to increase the amount of chemical information provided by TERS. However, this strategy has not yet been extended to in situ electrochemical (EC)-TERS studies. The independent control of the tip and sample potentials offered by EC-STM allows us to prove the in situ functionalization of a tip in EC-STM-TERS. Additionally, the Raman response of chemically modified TERS tips can be switched on and off at will, which makes EC-STM-TERS an ideal platform for the development of in situ chemical probes on the nanoscale.

(Multi)functional Atomic Force Microscopy Imaging

Incorporating functionality to atomic force microscopy (AFM) to obtain physical and chemical information has always been a strong focus in AFM research. Modifying AFM probes with specific molecules permits accessibility of chemical information via specific reactions and interactions. Fundamental understanding of molecular processes at the solid/liquid interface with high spatial resolution is essential to many emerging research areas. Nanoscale electrochemical imaging has emerged as a complementary technique to advanced AFM techniques, providing information on electrochemical interfacial processes. While this review presents a brief introduction to advanced AFM imaging modes, such as multiparametric AFM and topography recognition imaging, the main focus herein is on electrochemical imaging via hybrid AFM-scanning electrochemical microscopy. Recent applications and the challenges associated with such nanoelectrochemical imaging strategies are presented.

Dense monolayer films of atomically precise graphene nanoribbons on metallic substrates enabled by direct contact transfer of molecular precursors

Atomically precise graphene nanoribbons (GNRs) of two types, chevron GNRs and N = 7 straight armchair GNRs (7-AGNRs), have been synthesized through a direct contact transfer (DCT) of molecular precursors on Au(111) and gradual annealing. This method provides an alternative to the conventional approach for the deposition of molecules on surfaces by sublimation and simplifies preparation of dense monolayer films of GNRs. The DCT method allows deposition of molecules on a surface in their original state and then studying their gradual transformation to polymers to GNRs by scanning tunneling microscopy (STM) upon annealing. We performed STM characterization of the precursors of chevron GNRs and 7-AGNRs, and demonstrate that the assemblies of the intermediates of the GNR synthesis are stabilized by π-π interactions. This conclusion was supported by the density functional theory calculations. The resulting monolayer films of GNRs have sufficient coverage and density of nanoribbons for ex situ characterization by spectroscopic methods, such as Raman spectroscopy, and may prove useful for the future GNR device studies.

Development of ultrasound bioprobe for biological imaging

We report the development of an ultrasound bioprobe for in vitro molecular imaging. In this method, the phase of the scattered ultrasound wave is mapped to provide in vitro and intracellular imaging with nanometer-scale resolution under physiological conditions. We demonstrated the technique by successfully imaging a magnetic core in silica core shells and the stiffness image of intracellular fibers in endothelial cells that were stimulated with thrombin. The findings demonstrate a significant advancement in high-resolution ultrasound imaging of biological systems with acoustics under physiological conditions. These will open up various applications in biomedical and molecular imaging with subsurface resolution down to the nanometer scale.

Minimizing open-loop piezoactuator nonlinearity artifacts in atomic force microscope measurements

Atomic force microscopes (AFMs) are widely used to study molecular interactions with piconewton force sensitivity. In an AFM, interaction forces are measured by reflecting a laser beam off a cantilever onto a position sensitive detector and monitoring cantilever deflection. Precise measurements of interaction forces rely on accurately determining the optical lever sensitivity, i.e., the relationship between cantilever deflection and changes in detector voltage. The optical lever sensitivity is measured by pressing the cantilever against a hard substrate using a piezoactuator and recording the resulting change in detector voltage. However, nonlinearities in the motion of commonly used open-loop piezo actuators introduce significant errors in measured optical lever sensitivities. Here, the authors systematically characterize the effect of piezo actuator hysteresis and creep on errors in optical lever sensitivity and identify measurement conditions that minimize these errors.

High resolution SPM imaging of organic molecules with functionalized tips

One of the most remarkable and exciting achievements in the field of scanning probe microscopy (SPM) in the last years is the unprecedented sub-molecular resolution of both atomic and electronic structures of single molecules deposited on solid state surfaces. Despite its youth, the technique has already brought many new possibilities to perform different kinds of measurements, which cannot be accomplished by other techniques. This opens new perspectives in advanced characterization of physical and chemical processes and properties of molecular structures on surfaces. Here, we discuss the history and recent progress of the high resolution imaging with a functionalized probe by means of atomic force microscopy (AFM), scanning tunnelling microscopy (STM) and inelastic electron tunneling spectroscopy (IETS). We describe the mechanisms responsible for the high-resolution AFM, STM and IETS-STM contrast. The complexity of this technique requires new theoretical approaches, where a relaxation of the functionalized probe is considered. We emphasise the similarities of the mechanism driving high-resolution SPM with other imaging methods. We also summarise briefly significant achievements and progress in different branches. Finally we provide brief perspectives and remaining challenges of the further refinement of these high-resolution methods.

Strain-induced skeletal rearrangement of a polycyclic aromatic hydrocarbon on a copper surface

Controlling the structural deformation of organic molecules can drive unique reactions that cannot be induced only by thermal, optical or electrochemical procedures. However, in conventional organic synthesis, including mechanochemical procedures, it is difficult to control skeletal rearrangement in polycyclic aromatic hydrocarbons (PAHs). Here, we demonstrate a reaction scheme for the skeletal rearrangement of PAHs on a metal surface using high-resolution noncontact atomic force microscopy. By a combination of organic synthesis and on-surface cyclodehydrogenation, we produce a well-designed PAH—diazuleno[1,2,3-cd:1′,2′,3′-fg]pyrene—adsorbed flatly onto Cu(001), in which two azuleno moieties are highly strained by their mutual proximity. This local strain drives the rearrangement of one of the azuleno moieties into a fulvaleno moiety, which has never been reported so far. Our proposed thermally driven, strain-induced synthesis on surfaces will pave the way for the production of a new class of nanocarbon materials that conventional synthetic techniques cannot attain.

Mechanical strains can induce chemical transformations otherwise inaccessible by conventional stimuli. Here, the authors show the unusual strain-induced transformation of a polycyclic aromatic hydrocarbon on a metal surface by means of atomic force microscopy.

Optimizing qPlus sensor assemblies for simultaneous scanning tunneling and noncontact atomic force microscopy operation based on finite element method analysis

Quartz tuning forks that have a probe tip attached to the end of one of its prongs while the other prong is arrested to a holder ("qPlus" configuration) have gained considerable popularity in recent years for high-resolution atomic force microscopy imaging. The small size of the tuning forks and the complexity of the sensor architecture, however, often impede predictions on how variations in the execution of the individual assembly steps affect the performance of the completed sensor. Extending an earlier study that provided numerical analysis of qPlus-style setups without tips, this work quantifies the influence of tip attachment on the operational characteristics of the sensor. The results using finite element modeling show in particular that for setups that include a metallic tip that is connected via a separate wire to enable the simultaneous collection of local forces and tunneling currents, the exact realization of this wire connection has a major effect on sensor properties such as spring constant, quality factor, resonance frequency, and its deviation from an ideal vertical oscillation.

Energy Ordering of Molecular Orbitals

Orbitals are invaluable in providing a model of bonding in molecules or between molecules and surfaces. Most present-day methods in computational chemistry begin by calculating the molecular orbitals of the system. To what extent have these mathematical objects analogues in the real world? To shed light on this intriguing question, we employ a photoemission tomography study on monolayers of 3,4,9,10-perylene-tetracarboxylic acid dianhydride (PTCDA) grown on three Ag surfaces. The characteristic photoelectron angular distribution enables us to assign individual molecular orbitals to the emission features. When comparing the resulting energy positions to density functional calculations, we observe deviations in the energy ordering. By performing complete active space calculations (CASSCF), we can explain the experimentally observed orbital ordering, suggesting the importance of static electron correlation beyond a (semi)local approximation. On the other hand, our results also show reality and robustness of the orbital concept, thereby making molecular orbitals accessible to experimental observations.

Surface point defects on bulk oxides: atomically-resolved scanning probe microscopy

Metal oxides are abundant in nature and they are some of the most versatile materials for applications ranging from catalysis to novel electronics.

Noise in NC-AFM measurements with significant tip-sample interaction

The frequency shift noise in non-contact atomic force microscopy (NC-AFM) imaging and spectroscopy consists of thermal noise and detection system noise with an additional contribution from amplitude noise if there are significant tip-sample interactions. The total noise power spectral density DΔf (fm) is, however, not just the sum of these noise contributions. Instead its magnitude and spectral characteristics are determined by the strongly non-linear tip-sample interaction, by the coupling between the amplitude and tip-sample distance control loops of the NC-AFM system as well as by the characteristics of the phase locked loop (PLL) detector used for frequency demodulation. Here, we measure DΔf (fm) for various NC-AFM parameter settings representing realistic measurement conditions and compare experimental data to simulations based on a model of the NC-AFM system that includes the tip-sample interaction. The good agreement between predicted and measured noise spectra confirms that the model covers the relevant noise contributions and interactions. Results yield a general understanding of noise generation and propagation in the NC-AFM and provide a quantitative prediction of noise for given experimental parameters. We derive strategies for noise-optimised imaging and spectroscopy and outline a full optimisation procedure for the instrumentation and control loops.

Surface and Interface Aspects of Organometal Halide Perovskite Materials and Solar Cells

The current challenges (e.g., stability, hysteresis, etc.) in organometal halide perovskite solar cell research are closely correlated with surfaces and interfaces. For instance, efficient generation of charges, extraction, and transport with minimum recombination through interlayer interfaces is crucial to attain high-efficiency solar cell devices. Furthermore, intralayer interfaces may be present in the form of grain boundaries within a film composed of the same material, for example, a polycrystalline perovskite layer. The adjacent grains may assume different crystal orientations and/or have different chemical compositions, which impacts charge excitation and dynamics and thereby the overall solar cell performance. In this Perspective, we present case studies to demonstrate (1) how surfaces and interfaces can impact material properties and device performance and (2) how these issues can be investigated by surface science techniques, such as scanning probe microscopy, photoelectron spectroscopy, and so forth. We end this Perspective by outlining the future research directions based on the reported results as well as the new trends in the field.

A robust molecular probe for Ångstrom-scale analytics in liquids

Traditionally, nanomaterial profiling using a single-molecule-terminated scanning probe is performed at the vacuum–solid interface often at a few Kelvin, but is not a notion immediately associated with liquid–solid interface at room temperature. Here, using a scanning tunnelling probe functionalized with a single C₆₀ molecule stabilized in a high-density liquid, we resolve low-dimensional surface defects, atomic interfaces and capture Ångstrom-level bond-length variations in single-layer graphene and MoS₂. Atom-by-atom controllable imaging contrast is demonstrated at room temperature and the electronic structure of the C₆₀–metal probe complex within the encompassing liquid molecules is clarified using density functional theory. Our findings demonstrates that operating a robust single-molecular probe is not restricted to ultra-high vacuum and cryogenic settings. Hence the scope of high-precision analytics can be extended towards resolving sub-molecular features of organic elements and gauging ambient compatibility of emerging layered materials with atomic-scale sensitivity under experimentally less stringent conditions.

Single-molecule-terminated scanning probes typically operate under ultra-high vacuum conditions at low temperatures. Here, the authors show that tips functionalized with C₆₀ can image single-layer graphene and MoS₂ with high definition in a liquid environment at room temperature

Mapping the electrostatic force field of single molecules from high-resolution scanning probe images

How electronic charge is distributed over a molecule determines to a large extent its chemical properties. Here, we demonstrate how the electrostatic force field, originating from the inhomogeneous charge distribution in a molecule, can be measured with submolecular resolution. We exploit the fact that distortions typically observed in high-resolution atomic force microscopy images are for a significant part caused by the electrostatic force acting between charges of the tip and the molecule of interest. By finding a geometrical transformation between two high-resolution AFM images acquired with two different tips, the electrostatic force field or potential over individual molecules and self-assemblies thereof can be reconstructed with submolecular resolution.

The chemical properties of molecules are largely determined by the distribution of charge across them. Here, the authors demonstrate how the electrostatic force field, originating from the inhomogeneous charge distribution in a molecule, can be measured with sub-molecular resolution.

In situ fabrication and investigation of nanostructures and nanodevices with a microscope

The widespread availability of nanostructures and nanodevices has placed strict requirements on their comprehensive characterization.

Resolving Intra- and Inter-Molecular Structure with Non-Contact Atomic Force Microscopy

A major challenge in molecular investigations at surfaces has been to image individual molecules, and the assemblies they form, with single-bond resolution. Scanning probe microscopy, with its exceptionally high resolution, is ideally suited to this goal. With the introduction of methods exploiting molecularly-terminated tips, where the apex of the probe is, for example, terminated with a single CO, Xe or H₂ molecule, scanning probe methods can now achieve higher resolution than ever before. In this review, some of the landmark results related to attaining intramolecular resolution with non-contact atomic force microscopy (NC-AFM) are summarised before focussing on recent reports probing molecular assemblies where apparent intermolecular features have been observed. Several groups have now highlighted the critical role that flexure in the tip-sample junction plays in producing the exceptionally sharp images of both intra- and apparent inter-molecular structure. In the latter case, the features have been identified as imaging artefacts, rather than real intermolecular bonds. This review discusses the potential for NC-AFM to provide exceptional resolution of supramolecular assemblies stabilised via a variety of intermolecular forces and highlights the potential challenges and pitfalls involved in interpreting bonding interactions.

Chemical structure imaging of a single molecule by atomic force microscopy at room temperature

Atomic force microscopy is capable of resolving the chemical structure of a single molecule on a surface. In previous research, such high resolution has only been obtained at low temperatures. Here we demonstrate that the chemical structure of a single molecule can be clearly revealed even at room temperature. 3,4,9,10-perylene tetracarboxylic dianhydride, which is strongly adsorbed onto a corner-hole site of a Si(111)-(7 × 7) surface in a bridge-like configuration is used for demonstration. Force spectroscopy combined with first-principle calculations clarifies that chemical structures can be resolved independent of tip reactivity. We show that the submolecular contrast over a central part of the molecule is achieved in the repulsive regime due to differences in the attractive van der Waals interaction and the Pauli repulsive interaction between different sites of the molecule.

The smallest resonator arrays in atmosphere by chip-size-grown nanowires with tunable Q-factor and frequency for subnanometer thickness detection

A chip-size vertically aligned nanowire (NW) resonator arrays (VNRs) device has been fabricated with simple one-step lithography process by using grown self-assembled zinc oxide (ZnO) NW arrays. VNR has cantilever diameter of 50 nm, which breakthroughs smallest resonator record (>100 nm) functioning in atmosphere. A new atomic displacement sensing method by using atomic force microscopy is developed to effectively identify the resonance of NW resonator with diameter 50 nm in atmosphere. Size-effect and half-dimensional properties of the NW resonator have been systematically studied. Additionally, VNR has been demonstrated with the ability of detecting nanofilm thickness with subnanometer (<10(-9)m) resolution.

Nanoelectrical analysis of single molecules and atomic-scale materials at the solid/liquid interface

Evaluating the built-in functionality of nanomaterials under practical conditions is central for their proposed integration as active components in next-generation electronics. Low-dimensional materials from single atoms to molecules have been consistently resolved and manipulated under ultrahigh vacuum at low temperatures. At room temperature, atomic-scale imaging has also been performed by probing materials at the solid/liquid interface. We exploit this electrical interface to develop a robust electronic decoupling platform that provides precise information on molecular energy levels recorded using in situ scanning tunnelling microscopy/spectroscopy with high spatial and energy resolution in a high-density liquid environment. Our experimental findings, supported by ab initio electronic structure calculations and atomic-scale molecular dynamics simulations, reveal direct mapping of single-molecule structure and resonance states at the solid/liquid interface. We further extend this approach to resolve the electronic structure of graphene monolayers at atomic length scales under standard room-temperature operating conditions.

Unconventional molecule-resolved current rectification in diamondoid-fullerene hybrids

The unimolecular rectifier is a fundamental building block of molecular electronics. Rectification in single molecules can arise from electron transfer between molecular orbitals displaying asymmetric spatial charge distributions, akin to p-n junction diodes in semiconductors. Here we report a novel all-hydrocarbon molecular rectifier consisting of a diamantane-C60 conjugate. By linking both sp(3) (diamondoid) and sp(2) (fullerene) carbon allotropes, this hybrid molecule opposingly pairs negative and positive electron affinities. The single-molecule conductances of self-assembled domains on Au(111), probed by low-temperature scanning tunnelling microscopy and spectroscopy, reveal a large rectifying response of the molecular constructs. This specific electronic behaviour is postulated to originate from the electrostatic repulsion of diamantane-C60 molecules due to positively charged terminal hydrogen atoms on the diamondoid interacting with the top electrode (scanning tip) at various bias voltages. Density functional theory computations scrutinize the electronic and vibrational spectroscopic fingerprints of this unique molecular structure and corroborate the unconventional rectification mechanism.

Using metallic noncontact atomic force microscope tips for imaging insulators and polar molecules: tip characterization and imaging mechanisms

We demonstrate that using metallic tips for noncontact atomic force microscopy (NC-AFM) imaging at relatively large (>0.5 nm) tip-surface separations provides a reliable method for studying molecules on insulating surfaces with chemical resolution and greatly reduces the complexity of interpreting experimental data. The experimental NC-AFM imaging and theoretical simulations were carried out for the NiO(001) surface as well as adsorbed CO and Co-Salen molecules using Cr-coated Si tips. The experimental results and density functional theory calculations confirm that metallic tips possess a permanent electric dipole moment with its positive end oriented toward the sample. By analyzing the experimental data, we could directly determine the dipole moment of the Cr-coated tip. A model representing the metallic tip as a point dipole is described and shown to produce NC-AFM images of individual CO molecules adsorbed onto NiO(001) in good quantitative agreement with experimental results. Finally, we discuss methods for characterizing the structure of metal-coated tips and the application of these tips to imaging dipoles of large adsorbed molecules.

Electron and force microscopy characterization of particle size effects and surface phenomena associated with individual natural organic matter fractions

Natural organic matter (NOM) generically refers to organic substances found in soils, waters, and sediments. It is the brown-to-black, heterogeneous organic material produced through the diagenetic alteration of plant tissue and microbial biomass via a myriad of biotic and abiotic reactions. Since NOM is the primary source of organic carbon in the earth's surficial environment, understanding the processes by which NOM is produced is integral to understanding carbon sequestration, contaminant fate and transport, and other earth surface processes. NOM samples (HA0) consist of nonamphiphilic (HA1), lipid-like (L0 and L1), and strongly amphiphilic (HA2) components. Here we present the structure and morphology of self-assembled NOM components based on scanning electron microscopy (SEM), atomic force microscopy (AFM), and electrostatic force microscopy (EFM) characterizations. Effects of surface charge and hydrophobicity/hydrophilicity of the amphiphile on the interaction and resulting structures were investigated using SEM, AFM, and EFM. Data shows that the component's amphiphilic nature plays a key role in the formation of NOM. SEM data show that aggregates form while AFM/EFM analysis verifies the existence of hydrophobic/hydrophilic moieties in different fractions of HA0. Subsequently, the amphiphilic nature of HA2 will have a substantial effect on interfacial interactions and subsequent self-assembly of HA0's components.

Crystallographic order and decomposition of [MnIII6CrIII]3+ single-molecule magnets deposited in submonolayers and monolayers on HOPG studied by means of molecular resolved atomic force microscopy (AFM) and Kelvin probe force microscopy in UHV

Monolayers and submonolayers of [MnIII6CrIII]3+ single-molecule magnets (SMMs) adsorbed on highly oriented pyrolytic graphite (HOPG) using the droplet technique characterized by non-contact atomic force microscopy (nc-AFM) as well as by Kelvin probe force microscopy (KPFM) show island-like structures with heights resembling the height of the molecule. Furthermore, islands were found which revealed ordered 1D as well as 2D structures with periods close to the width of the SMMs. Along this, islands which show half the heights of intact SMMs were observed which are evidences for a decomposing process of the molecules during the preparation. Finally, models for the structure of the ordered SMM adsorbates are proposed to explain the observations.

Boron–boron J coupling constants are unique probes of electronic structure: a solid-state NMR and molecular orbital study

J couplings measured between ¹¹B spin pairs in solid diboron compounds provide insight into electronic structure and crystallographic symmetry.

Unexpected TFA-catalyzed tandem reaction of benzo[d]oxazoles with 2-oxo-2-arylacetic acids: synthesis of 3-aryl-2H-benzo[b][1,4]oxazin-2-ones and cephalandole A

TFA-catalyzed reaction of benzo[d]oxazoles with 2-oxo-2-arylacetic acids: synthesis of 3-aryl-2H-benzo[b][1,4]oxazin-2-ones and the natural product cephalandole A.

Resolving molecular orbitals self-decoupled from semiconductor surfaces

Molecular orbitals of chemisorbed nitrosobenzene are electronically decoupled from a clean semiconductor substrate and resolved by STM.

Imaging the wave functions of adsorbed molecules

The basis for a quantum-mechanical description of matter is electron wave functions. For atoms and molecules, their spatial distributions and phases are known as orbitals. Although orbitals are very powerful concepts, experimentally only the electron densities and -energy levels are directly observable. Regardless whether orbitals are observed in real space with scanning probe experiments, or in reciprocal space by photoemission, the phase information of the orbital is lost. Here, we show that the experimental momentum maps of angle-resolved photoemission from molecular orbitals can be transformed to real-space orbitals via an iterative procedure which also retrieves the lost phase information. This is demonstrated with images obtained of a number of orbitals of the molecules pentacene (C22H14) and perylene-3,4,9,10-tetracarboxylic dianhydride (C24H8O6), adsorbed on silver, which are in excellent agreement with ab initio calculations. The procedure requires no a priori knowledge of the orbitals and is shown to be simple and robust.

Differentiating amino acid residues and side chain orientations in peptides using scanning tunneling microscopy

Single-molecule measurements of complex biological structures such as proteins are an attractive route for determining structures of the large number of important biomolecules that have proved refractory to analysis through standard techniques such as X-ray crystallography and nuclear magnetic resonance. We use a custom-built low-current scanning tunneling microscope to image peptide structures at the single-molecule scale in a model peptide that forms β sheets, a structural motif common in protein misfolding diseases. We successfully differentiate between histidine and alanine amino acid residues, and further differentiate side chain orientations in individual histidine residues, by correlating features in scanning tunneling microscope images with those in energy-optimized models. Beta sheets containing histidine residues are used as a model system due to the role histidine plays in transition metal binding associated with amyloid oligomerization in Alzheimer's and other diseases. Such measurements are a first step toward analyzing peptide and protein structures at the single-molecule level.

Real-space identification of intermolecular bonding with atomic force microscopy

We report a real-space visualization of the formation of hydrogen bonding in 8-hydroxyquinoline (8-hq) molecular assemblies on a Cu(111) substrate, using noncontact atomic force microscopy (NC-AFM). The atomically resolved molecular structures enable a precise determination of the characteristics of hydrogen bonding networks, including the bonding sites, orientations, and lengths. The observation of bond contrast was interpreted by ab initio density functional calculations, which indicated the electron density contribution from the hybridized electronic state of the hydrogen bond. Intermolecular coordination between the dehydrogenated 8-hq and Cu adatoms was also revealed by the submolecular resolution AFM characterization. The direct identification of local bonding configurations by NC-AFM would facilitate detailed investigations of intermolecular interactions in complex molecules with multiple active sites.

Synthesis, properties, and remarkable 2 D Self-Assembly at the Liquid/Solid interface of a series of triskele-shaped 5,11,17-triazatrinaphthylenes (TrisK)

A series of 5,11,17-triazatrinaphthylene (TrisK) derivatives, large disk-like π-conjugated molecules with C3h symmetry, has been synthesised by following an optimised synthetic pathway. The synthesis was performed by a four-step protocol based on the N-arylation of 1,3,5-tribromobenzene with appropriate anthranilate derivatives. This strategy permits the generation of either chlorinated (TrisK-Cl-OCn) or non-chlorinated (TrisK-H-OCn) alkoxy-substituted derivatives (OCn H2n+1 with n=3, 10, 12 and 16), thus providing additional versatility in the control of the structure-property relationships. The electronic properties of the various TrisK compounds have been characterised in solution by absorption and emission spectroscopies as well as cyclic voltammetry. The crystal structure of 2,8,14-propyloxy-5,11,17-triazatrinaphthylene TrisK-H-OC3 has been determined by X-ray diffraction analysis, which revealed the presence of stabilising weak intermolecular H bonds. Scanning tunnelling microscopy (STM) at the liquid/solid interface has revealed the remarkable 2D self-assembling properties of the TrisK compounds. In particular, it has shown that TrisK-H-OC12 forms three concomitant self-organised 2D phases with different row-packing arrangements. This 2D polymorphism arises from slow ordering due to the presence of three long dodecyloxy chains on the molecular backbone. Individual molecules can be imaged with spectacular intramolecular resolution, thus providing the possibility of correlating the STM features with the calculated charge density distribution.

Tuning molecular self-assembly on bulk insulator surfaces by anchoring of the organic building blocks

Molecular self-assembly constitutes a versatile strategy for creating functional structures on surfaces. Tuning the subtle balance between intermolecular and molecule-surface interactions allows structure formation to be tailored at the single-molecule level. While metal surfaces usually exhibit interaction strengths in an energy range that favors molecular self-assembly, dielectric surfaces having low surface energies often lack sufficient interactions with adsorbed molecules. As a consequence, application-relevant, bulk insulating materials pose significant challenges when considering them as supporting substrates for molecular self-assembly. Here, the current status of molecular self-assembly on surfaces of wide-bandgap dielectric crystals, investigated under ultrahigh vacuum conditions at room temperature, is reviewed. To address the major issues currently limiting the applicability of molecular self-assembly principles in the case of dielectric surfaces, a systematic discussion of general strategies is provided for anchoring organic molecules to bulk insulating materials.

Directed rotations of single porphyrin molecules controlled by localized force spectroscopy

Directed molecular repositioning is a key step toward the build up of molecular machines. To artificially generate and control the motion of molecules on a surface, excitations by light, chemical, or electrical energy have been demonstrated. Here, the application of local mechanical forces is implemented to achieve directed rotations of molecules. Three-dimensional force spectroscopy with sub-Ångström precision is used to characterize porphyrin derivatives with peripheral carbonitrile groups. Extremely small areas on these molecules (≈ 100 × 100 pm(2)) are revealed which can be used to control rotations. In response to the local mechanical forces, the molecular structure elastically deforms and then changes its conformation, which leads to its rotation. Depending on the selection of one of four submolecular areas, the molecule is either rotated clockwise or counterclockwise.

Improvement of scanning tunneling microscopy resolution with H-sensitized tips

Recent scanning tunneling hydrogen microscopy (STHM) experiments on PTCDA (perylene-3,4,9,10-tetracarboxylic-3,4,9,10-dianhydride)/Au(111) have shown unprecedented intramolecular and intermolecular spatial resolution. The origin of this resolution is studied using an accurate STHM theoretical simulation technique that includes a detailed description of the electronic structure of both the tip and sample. Our results show that H2 molecules are dissociated on the Au tip; the adsorbed H atoms change the density of states at the Fermi level (E(F)) of the tip, increasing its p-orbital character and reducing the s-orbital contribution. Also, due to the interaction with the H-decorated tip, E(F) is shifted to the middle of the PTCDA lowest unoccupied molecular orbital peak, increasing dramatically the density of states of the sample at E(F). These effects give rise to the enhanced STHM resolution.