Functional and spectroscopic measurements with scanning tunneling microscopy

Adsorption and reversible conformational change of a thiophene based molecule on Au(111)

We present a low temperature scanning tunneling microscope investigation of a prochiral thiophene-based molecule that self-assembles forming islands with different domains on the Au(111) surface. In the domains, two different conformations of the single molecule are observed, depending on a slight rotation of two adjacent bromothiophene groups. Using voltage pulses from the tip, single molecules can be switched between the two conformations. The electronic states have been measured with scanning tunneling spectroscopy, showing that the electronic resonances are mainly localized at the same positions in both conformations. Density-functional theory calculations support the experimental results. Furthermore, we observe that on Ag(111), only one configuration is present and therefore the switching effect is suppressed.

Low temperature and high magnetic field performance of a commercial piezo-actuator probed via laser interferometry

The advances in the fields of scanning probe microscopy, scanning tunneling spectroscopy, point contact spectroscopy, and point contact Andreev reflection spectroscopy to study the properties of conventional and quantum materials under cryogenic conditions have prompted the development of nanopositioners and nanoscanners with enhanced spatial resolution. Piezoelectric-actuator stacks as nanopositioners with working strokes of 10 μm and positioning resolution ∼(1-10) nm are desirable for both basic research and industrial applications. However, information on the performance of most commercial piezoelectric actuators in cryogenic environment and in the presence of magnetic fields in excess of 5 T is generally not available. In particular, the magnitude, the rate, and the associated hysteresis of the piezo-displacement at cryogenic temperatures are the most relevant parameters that determine whether a particular piezoelectric actuator can be used as a nanopositioner. Here, the design and realization of an experimental setup based on interferometric techniques to characterize a commercial piezoelectric actuator over a temperature range of 2 K ≤ T ≤ 260 K and magnetic fields up to 6 T are presented. The studied piezoelectric actuator has a maximum displacement of 30 μm at room temperature for a maximum driving voltage of 75 V, which reduces to 1.2 μm with an absolute hysteresis of 9.1±3.3nm at T = 2 K. The magnetic field is shown to have no substantial effect on the piezo-properties of the studied piezoelectric-actuator stack.

Melanins as Sustainable Resources for Advanced Biotechnological Applications

Melanins are a class of biopolymers that are widespread in nature and have diverse origins, chemical compositions, and functions. Their chemical, electrical, optical, and paramagnetic properties offer opportunities for applications in materials science, particularly for medical and technical uses. This review focuses on the application of analytical techniques to study melanins in multidisciplinary contexts with a view to their use as sustainable resources for advanced biotechnological applications, and how these may facilitate the achievement of the United Nations Sustainable Development Goals.

Quantifying reversible nitrogenous ligand binding to Co(ii) porphyrin receptors at the solution/solid interface and in solution

We present a quantitative study comparing the binding of 4-methoxypyridine, MeOPy, ligand to Co(ii)octaethylporphyrin, CoOEP, at the phenyloctane/HOPG interface and in toluene solution. Scanning tunneling microscopy (STM) was used to study the ligand binding to the porphyrin receptors adsorbed on graphite. Electronic spectroscopy was employed for examining this process in fluid solution. The on surface coordination reaction was completely reversible and followed a simple Langmuir adsorption isotherm. Ligand affinities (or ΔG) for the binding processes in the two different chemical environments were determined from the respective equilibrium constants. The free energy value of -13.0 ± 0.3 kJ mol^-1 for the ligation reaction of MeOPy to CoOEP at the solution/HOPG interface is less negative than the ΔG for cobalt porphyrin complexed to the ligand in solution, -16.8 ± 0.2 kJ mol^-1. This result indicates that the MeOPy-CoOEP complex is more stable in solution than on the surface. Additional thermodynamic values for the formation of the surface ligated species (ΔH_c = -50 kJ mol^-1 and ΔS_c = -120 J mol^-1) were extracted from temperature dependent STM measurements. Density functional computational methods were also employed to explore the energetics of both the solution and surface reactions. At high concentrations of MeOPy the monolayer was observed to be stripped from the surface. Computational results indicate that this is not because of a reduction in adsorption energy of the MeOPy-CoOEP complex. Nearest neighbor analysis of the MeOPy-CoOEP in the STM images revealed positive cooperative ligand binding behavior. Our studies bring new insights to the general principles of affinity and cooperativity in the ligand-receptor interactions at the solution/solid interface. Future applications of STM will pave the way for new strategies designing highly functional multisite receptor systems for sensing, catalysis, and pharmacological applications.

Single molecule level studies of reversible ligand binding to metal porphyrins at the solution/solid interface

Ligands bind reversibly to metal porphyrins in processes such as molecular recognition, electron transport and catalysis. These chemically relevant processes are ubiquitous in biology and are important in technological applications. In this article, we focus on the current advances in ligand binding to metal porphyrin receptors noncovalently bound at the solution/solid interface. In particular, we restrict ourselves to studies at the single molecule level. Dynamics of the binding/dissociation process can be monitored by scanning tunneling microscopy (STM) and can yield both qualitative and quantitative information about ligand binding affinity and the energetics that define a particular ligation reaction. Molecular and time dependent imaging can establish whether the process under study is at equilibrium. Ligand-concentration-dependent studies have been used to determine adsorption isotherms and thermodynamic data for processes occurring at the solution/solid interface. In several binding reactions, the solid support acted as an electron-donating fifth coordination site, thereby significantly changing the metal porphyrin receptor’s affinity for exogenous ligands. Supporting calculations provide insight into the metalloporphyrin/support and ligand–metalloporphyrin/support interactions and their energetics.

On the Probability Density of the Nuclei in a Vibrationally Excited Molecule

For localized and oriented vibrationally excited molecules, the qualitative features of the one-body probability density of the nuclei (one-nucleus density) are investigated. Like the familiar and widely used one-electron density that represents the probability of finding an electron at a given location in space, the one-nucleus density represents the probability of finding a nucleus at a given position in space independent of the location of the other nuclei and independent of their type. In contrast to the electrons, however, the nuclei are comparably localized. Due to this localization of the individual nuclei, the one-nucleus density provides a quantum-mechanical representation of the "chemical picture" of the molecule as an object that can largely be understood in a three-dimensional space, even though its full nuclear probability density is defined on the high-dimensional configuration space of all the nuclei. We study how the nodal structure of the wavefunctions of vibrationally excited states translates to the one-nucleus density. It is found that nodes do not necessarily lead to visible changes in the one-nucleus density: Already for relatively small molecules, only certain vibrational excitations change the one-nucleus density qualitatively compared to the ground state. It turns out that there are simple rules for predicting the shape of the one-nucleus density from the normal mode coordinates. A Python module for the computation of the one-nucleus density is provided at https://gitlab.com/axelschild/mQNMc.

Photoinduced Charge Transfer in Single-Molecule p-n Junctions

We measured photoinduced charge separation in isolated individual C₆₀-tethered 2,5-dithienylpyrrole triad (C₆₀ triad) molecules with submolecular resolution using a custom-built laser-assisted scanning tunneling microscope. Laser illumination was introduced evanescently into the tunneling junction through total internal reflection, and the changes in tunneling current and electronic spectra caused by photoexcitation were measured and spatially resolved. Photoinduced charge separation was not detected for all C₆₀ triad molecules, indicating that the conformations of the molecules may affect the excitation probability, lifetime, and/or charge distribution. A photoinduced signal was not observed for dodecanethiol molecules in the surrounding matrix or for control molecules without C₆₀ moieties, as neither absorbs incident photons at this energy. This spectroscopic imaging technique has the potential to elucidate detailed photoinduced carrier dynamics, which are inaccessible via ensemble-scale (i.e., averaging) measurements, which can be used to direct the rational design and optimization of molecular p-n junctions and assemblies for energy harvesting.

Deep Learning of Atomically Resolved Scanning Transmission Electron Microscopy Images: Chemical Identification and Tracking Local Transformations

Recent advances in scanning transmission electron and scanning probe microscopies have opened exciting opportunities in probing the materials structural parameters and various functional properties in real space with angstrom-level precision. This progress has been accompanied by an exponential increase in the size and quality of data sets produced by microscopic and spectroscopic experimental techniques. These developments necessitate adequate methods for extracting relevant physical and chemical information from the large data sets, for which a priori information on the structures of various atomic configurations and lattice defects is limited or absent. Here we demonstrate an application of deep neural networks to extract information from atomically resolved images including location of the atomic species and type of defects. We develop a "weakly supervised" approach that uses information on the coordinates of all atomic species in the image, extracted via a deep neural network, to identify a rich variety of defects that are not part of an initial training set. We further apply our approach to interpret complex atomic and defect transformation, including switching between different coordination of silicon dopants in graphene as a function of time, formation of peculiar silicon dimer with mixed 3-fold and 4-fold coordination, and the motion of molecular "rotor". This deep learning-based approach resembles logic of a human operator, but can be scaled leading to significant shift in the way of extracting and analyzing information from raw experimental data.

Stick-Slip Motion of ssDNA over Graphene

We have performed molecular dynamics simulations of nanomanipulation experiments on short single-stranded DNA chains elastically driven on a graphene surface. After a brief transient, reproducible stick-slip cycles are observed on chains made by 10 units of thymine, cytosine, adenine, and guanine. The cycles have the periodicity of the graphene substrate, and take place via an intermediate stage, appearing as a dip in the sawtooth variations of lateral force recorded while the chains are manipulated. Guanine presents remarkable differences from the other bases, since a lower number of nucleotides are prone to stick to the substrate in this case. Nevertheless, the magnitudes of static friction and lateral stiffness are similar for all chains (30 pN and 0.7 N/m per adsorbed nucleotide respectively).

Data mining graphene: correlative analysis of structure and electronic degrees of freedom in graphenic monolayers with defects

The link between changes in the material crystal structure and its mechanical, electronic, magnetic and optical functionalities-known as the structure-property relationship-is the cornerstone of modern materials science research. The recent advances in scanning transmission electron and scanning probe microscopies (STEM and SPM) have opened an unprecedented path towards examining the structure-property relationships of materials at the single-impurity and atomic-configuration levels. However, there are no statistics-based approaches for cross-correlation of structure and property variables obtained from the different information channels of STEM and SPM experiments. Here we have designed an approach based on a combination of sliding window fast Fourier transform, Pearson correlation matrix and linear and kernel canonical correlation methods to study the relationship between lattice distortions and electron scattering from SPM data on graphene with defects. Our analysis revealed that the strength of coupling to strain is altered between different scattering channels, which can explain the coexistence of several quasiparticle interference patterns in nanoscale regions of interest. In addition, the application of kernel functions allowed us to extract a non-linear component of the relationship between the lattice strain and scattering intensity in graphene. The outlined approach can be further used to analyze correlations in various multi-modal imaging techniques where the information of interest is spatially distributed and generally has a complex multi-dimensional nature.

Unconventional Electrochemistry in Micro-/Nanofluidic Systems

Electrochemistry is ideally suited to serve as a detection mechanism in miniaturized analysis systems. A significant hurdle can, however, be the implementation of reliable micrometer-scale reference electrodes. In this tutorial review, we introduce the principal challenges and discuss the approaches that have been employed to build suitable references. We then discuss several alternative strategies aimed at eliminating the reference electrode altogether, in particular two-electrode electrochemical cells, bipolar electrodes and chronopotentiometry.

Confinement properties of 2D porous molecular networks on metal surfaces

Quantum effects that arise from confinement of electronic states have been extensively studied for the surface states of noble metals. Utilizing small artificial structures for confinement allows tailoring of the surface properties and offers unique opportunities for applications. So far, examples of surface state confinement include thin films, artificial nanoscale structures, vacancy and adatom islands, self-assembled 1D chains, vicinal surfaces, quantum dots and quantum corrals. In this review we summarize recent achievements in changing the electronic structure of surfaces by adsorption of nanoporous networks whose design principles are based on the concepts of supramolecular chemistry. Already in 1993, it was shown that quantum corrals made from Fe atoms on a Cu(1 1 1) surface using single atom manipulation with a scanning tunnelling microscope confine the Shockley surface state. However, since the atom manipulation technique for the construction of corral structures is a relatively time consuming process, the fabrication of periodic two-dimensional (2D) corral structures is practically impossible. On the other side, by using molecular self-assembly extended 2D porous structures can be achieved in a parallel process, i.e. all pores are formed at the same time. The molecular building blocks are usually held together by non-covalent interactions like hydrogen bonding, metal coordination or dipolar coupling. Due to the reversibility of the bond formation defect-free and long-range ordered networks can be achieved. However, recently also examples of porous networks formed by covalent coupling on the surface have been reported. By the choice of the molecular building blocks, the dimensions of the network (pore size and pore to pore distance) can be controlled. In this way, the confinement properties of the individual pores can be tuned. In addition, the effect of the confined state on the hosting properties of the pores will be discussed in this review article.

Manipulating interfacial hydrogens at palladium via STM

In this contribution, we provide a quantum dynamical analysis of the interfacial hydrogen migration mediated by scanning tunneling microscopy (STM). It is observed that the hydrogen impurity favors resurfacing over occupation of the bulk and subsurface sites whenever possible. The present simulations give strong indication that the experimentally observed protuberances after STM-excitation are due to H accumulating in the vicinity of the surface.

From the bottom up: dimensional control and characterization in molecular monolayers

Self-assembled monolayers are a unique class of nanostructured materials, with properties determined by their molecular lattice structures, as well as the interfaces with their substrates and environments. As with other nanostructured materials, defects and dimensionality play important roles in the physical, chemical, and biological properties of the monolayers. In this review, we discuss monolayer structures ranging from surfaces (two-dimensional) down to single molecules (zero-dimensional), with a focus on applications of each type of structure, and on techniques that enable characterization of monolayer physical properties down to the single-molecule scale.

Pointed carbon fiber ultramicroelectrodes: a new probe option for electrochemical scanning tunneling microscopy

Carbon tips for in situ scanning tunneling microscopy studies in an electrochemical environment were prepared by electrochemical etching of carbon fibers and subsequent coating with electrodeposition paint and a silicone elastomer. The tips obtained were stable in acidic electrolyte and allowed high-resolution in situ imaging of the bare Au(111) electrode surface and of Au(111) covered by monolayers of the octyl-triazatriangulenium molecule.

STM manipulation of a subphthalocyanine double-wheel molecule on Au(111)

A new class of double-wheel molecules is manipulated on a Au(111) surface by the tip of a scanning tunneling microscope (STM) at low temperature. The double-wheel molecule consists of two subphthalocyanine wheels connected by a central rotation carbon axis. Each of the subphthalocyanine wheels has a nitrogen tag to monitor its intramolecular rolling during an STM manipulation sequence. The position of the tag can be followed by STM, allowing us to distinguish between the different lateral movements of the molecule on the surface when manipulated by the STM tip.

Electron affinity states of metal supported phthalocyanines measured by tunneling spectroscopy

Orbital Mediated Tunneling Spectroscopy OMTS (elastic electron tunneling) was employed in measuring electron affinity levels (EA) of unsubstituted, alkylated, sulfonated, and metalated phthalocyanines (Pc) adsorbed as single molecules or aggregates on metal substrates and imbedded in metal-insulator-metal (M-I-M) devices. MPc complexes were vapor deposited, solution phase doped, or transferred as Langmuir–Blodgett films. It was determined that while the nature of the substituents has a large effect on the gas phase electron affinities, they play a minimal role on the electron affinities of metal supported phthalocyanines. Moreover, the orientation of monolayer films and the method of film deposition (vapor, solution, Langmuir–Blodgett) also appear to play only a minor role in determining the electron affinities. Electrochemical reduction potentials obtained for the solution phase molecular systems are compared to the OMTS data and a strong correlation is observed. In contrast, the predicted EA values for the gas phase molecules show little correspondence with their OMTS equivalents for adsorbed phthalocyanines. Inelastic scattering from phthalocyanine π→π* transitions and metal centered d–d transitions are observed for chromophores imbedded in tunnel diodes. Both the observed lowest spin forbidden transitions and the calculated gas phase HOMO–LUMO gaps are only weakly affected by Pc substitution and surface orientation.

Tunneling spectroscopy of organic monolayers and single molecules

Basic concepts in tunneling spectroscopy applied to molecular systems are presented. Junctions of the form M-A-M, M-I-A-M, and M-I-A-I'-M, where A is an active molecular layer, are considered. Inelastic electron tunneling spectroscopy (IETS) is found to be readily applied to all the above device types. It can provide both vibrational and electron spectroscopic data about the molecules comprising the A layer. In IETS there are no strong selection rules (although there are preferences) so that transitions that are normally IR, Raman, or even photon-forbidden can be observed. In the electronic transition domain, spin and Laporte forbidden transitions may be observed. Both vibrational and electronic IETS can be acquired from single molecules. The negative aspect of this seemingly ideal spectroscopic method is the thermal line width of about 5 k(B)T. This limits the useful measurement of vibrational IETS to temperatures below about 10 K. In the case of most electronic transitions where the intrinsic linewidth is much broader, useful experiments above 100 K are possible. One further limitation of electronic IETS is that it is generally limited to transitions with energy less than about 20,000 cm(-1). IETS can be identified by peaks in d(2) I/dV (2) vs bias voltage plots that occur at the same position (but not necessarily same intensity) in either bias polarity.Elastic tunneling spectroscopy is discussed in the context of processes involving molecular ionization and electron affinity states, a technique we call orbital mediated tunneling spectroscopy, or OMTS. OMTS can be applied readily to M-I-A-M and M-I-A-I'-M systems, but application to M-A-M junctions is problematic. Spectra can be obtained from single molecules. Ionization state results correlate well with UPS spectra obtained from the same systems in the same environment. Both ionization and affinity levels measured by OMTS can usually be correlated with one electron oxidation and reduction potentials for the molecular species in solution. OMTS can be identified by peaks in dI/dV vs bias voltage plots that do not occur at the same position in either bias polarity. Because of the intrinsic width of the ionization and affinity transitions, OMTS can be applied at temperatures above 500 K.This is not a comprehensive review of more than 20 years of research and there are many excellent papers that are not cited here. An absence of a citation is not a reflection on the quality of the work.

Electrons, photons, and force: quantitative single-molecule measurements from physics to biology

Single-molecule measurement techniques have illuminated unprecedented details of chemical behavior, including observations of the motion of a single molecule on a surface, and even the vibration of a single bond within a molecule. Such measurements are critical to our understanding of entities ranging from single atoms to the most complex protein assemblies. We provide an overview of the strikingly diverse classes of measurements that can be used to quantify single-molecule properties, including those of single macromolecules and single molecular assemblies, and discuss the quantitative insights they provide. Examples are drawn from across the single-molecule literature, ranging from ultrahigh vacuum scanning tunneling microscopy studies of adsorbate diffusion on surfaces to fluorescence studies of protein conformational changes in solution.

Analytical chemistry in molecular electronics

This review discusses the analytical characterization of molecular electronic devices and structures relevant thereto. In particular, we outline the methods for probing molecular junctions, which contain an ensemble of molecules between two contacts. We discuss the analytical methods that aid in the fabrication and characterization of molecular junctions, beginning with the confirmation of the placement of a molecular layer on a conductive or semiconductive substrate. We emphasize methods that provide information about the molecular layer in the junction and outline techniques to ensure molecular layer integrity after the complete fabrication of a device. In addition, we discuss the analytical information derived during the actual device operation.

Polarizabilities of adsorbed and assembled molecules: measuring the conductance through buried contacts

We have measured the polarizabilities of four families of molecules adsorbed to Au{111} surfaces, with structures ranging from fully saturated to fully conjugated, including single-molecule switches. Measured polarizabilities increase with increasing length and conjugation in the adsorbed molecules and are consistent with theoretical calculations. For single-molecule switches, the polarizability reflects the difference in substrate-molecule electronic coupling in the ON and OFF conductance states. Calculations suggest that the switch between the two conductance states is correlated with an oxidation state change in a nitro functional group in the switch molecules.

Manipulating double-decker molecules at the liquid-solid interface

We have used a scanning tunneling microscope (STM) to manipulate heteroleptic phthalocyaninato, naphthalocyaninato, and porphyrinato double-decker (DD) molecules at the liquid-solid interface between 1-phenyloctane solvent and graphite. We employed nanografting of phthalocyanines with eight octyl chains to place these molecules into a matrix of heteroleptic DD molecules; the overlayer structure is epitaxial on graphite. We have also used nanografting to place DD molecules in matrices of single-layer phthalocyanines with octyl chains. Rectangular scans with a STM at low bias voltage resulted in the removal of the adsorbed DD molecular layer and substituted the DD molecules with bilayer-stacked phthalocyanines from phenyloctane solution. Single heteroleptic DD molecules with lutetium sandwiched between naphthalocyanine and octaethylporphyrin were decomposed with voltage pulses from the probe tip; the top octaethylporphyrin ligand was removed, and the bottom naphthalocyanine ligand remained on the surface. A domain of decomposed molecules was formed within the DD molecular domain, and the boundary of the decomposed molecular domain self-cured to become rectangular. We demonstrated a molecular "sliding block puzzle" with cascades of DD molecules on the graphite surface.

Bioenergy research: a new paradigm in multidisciplinary research

The field of biology is becoming increasingly interdisciplinary and cross-cutting. This changing research atmosphere is creating the way for a new kind of enquiry that while building upon the traditional research establishment is providing a new multidisciplinary framework to more effectively address scientific grand challenges. Using the US Department of Energy sponsored BioEnergy Science Center as an example, we highlight how impactful breakthroughs in biofuel science can be achieved within a large cross-disciplinary team environment. Such transformational insights are key to furthering our understanding and in generating models, theories and processes that can be used to overcome recalcitrance of biomass for sustainable biofuel production. Multidisciplinary approaches have an increasingly greater role to play in meeting rising demands for food, fibre, energy, clean environment and good health. Discoveries achieved by diverse minds and cross-applications of tools and analytical approaches have tremendous potential to fill existing knowledge gaps, clear roadblocks and facilitate translation of basic sciences discoveries as solutions towards addressing some of the most pressing global issues.

Charge transport through molecular switches

We review the fascinating research on charge transport through switchable molecules. In the past decade, detailed investigations have been performed on a great variety of molecular switches, including mechanically interlocked switches (rotaxanes and catenanes), redox-active molecules and photochromic switches (e.g. azobenzenes and diarylethenes). To probe these molecules, both individually and in self-assembled monolayers (SAMs), a broad set of methods have been developed. These range from low temperature scanning tunneling microscopy (STM) via two-terminal break junctions to larger scale SAM-based devices. It is generally found that the electronic coupling between molecules and electrodes has a profound influence on the properties of such molecular junctions. For example, an intrinsically switchable molecule may lose its functionality after it is contacted. Vice versa, switchable two-terminal devices may be created using passive molecules ('extrinsic switching'). Developing a detailed understanding of the relation between coupling and switchability will be of key importance for both future research and technology.

Functional molecules and assemblies in controlled environments: formation and measurements

The local environment of a functional molecule or nanoscale assembly has tremendous impact on it and thus can be used for functional control. In addition, the local environment is critical in the interface to the physical, chemical, and biological worlds beyond the assemblies that are the most common applications targeted. Functional measurements without local structural information lack key insight into both the details and the roles of the environment. This Account focuses on progress toward and challenges in the controlled assembly and measurements of functional nanostructures in well-defined environments. The study of single precise supramolecular assemblies in well-defined environments offers unique insights into both interactions and function. By designing interactions between molecules and controlling assembly conditions, we can create and place atomically precise nanostructures. The tools to test the structures targeted and to measure the function of these assemblies are just now being developed and becoming available. Advances in this field have depended on gaining access to measurements at this scale. In particular, we recognize but do not yet understand the critical role of the chemical and physical environment of the assemblies. Likewise, we are just now realizing the important role that the substrates to which the assemblies are attached play in these processes. In order to develop a predictive understanding and the ability to design and to optimize functional assemblies, we must elucidate the physical, chemical, and electronic couplings among the molecules in the assemblies and with their substrates. With a suite of atomic- and molecular-resolution analytical tools, we are able both to ascertain whether the targeted structures have been formed and to measure their function. One of the keys to our ability to determine structure and measure function has been the development and application of methods for the automated acquisition, analysis, and associations of thousands or tens of thousands of single-molecule/particle/assembly structural, dynamic, spectroscopic, and functional data points.