Submolecular Resolution Imaging Research Articles

Imaging the adsorption sites of organic molecules on metallic surfaces by an adaptive tunnelling current feedback.

Atomic force microscopy (AFM) allows submolecular resolution imaging of organic molecules deposited on a surface by using CO-functionalized qPlus sensors under ultrahigh vacuum and low temperature conditions. However, the experimental determination of the adsorption sites of these organic molecules requires the precise identification of the atomic structure of the surface on which they are adsorbed. Here, we develop an automation method for AFM imaging that provides in a single image both, submolecular resolution on organic molecules and atomic resolution on the surrounding metallic surface. The method is based on an adaptive tunnelling current feedback system that is regulated according to the response of the AFM observables, which guarantees that both the molecules and the surface atoms are imaged under optimum conditions. Therewith, the approach is suitable for imaging adsorption sites of several adjacent and highly mobile molecules such as 2-iodotriphenylene on Ag(111) in a single scan. The proposed method with the adaptive feedback system facilitates statistical analysis of molecular adsorption geometries and could in the future contribute to autonomous AFM imaging as it adapts the feedback parameters depending on the sample properties.

Dinuclear complex-induced DNA melting

Dinuclear copper complexes have been designed for molecular recognition in order to selectively bind to two neighboring phosphate moieties in the backbone of double strand DNA. Associated biophysical, biochemical and cytotoxic effects on DNA were investigated in previous works, where atomic force microscopy (AFM) in ambient conditions turned out to be a particular valuable asset, since the complexes influence the macromechanical properties and configurations of the strands. To investigate and scrutinize these effects in more depth from a structural point of view, cutting-edge preparation methods and scanning force microscopy under ultra-high vacuum (UHV) conditions were employed to yield submolecular resolution images. DNA strand mechanics and interactions could be resolved on the single base pair level, including the amplified formation of melting bubbles. Even the interaction of singular complex molecules could be observed. To better assess the results, the appearance of treated DNA is also compared to the behavior of untreated DNA in UHV on different substrates. Finally, we present data from a statistical simulation reasoning about the nanomechanics of strand dissociation. This sort of quantitative experimental insights paralleled by statistical simulations impressively shade light on the rationale for strand dissociations of this novel DNA interaction process, that is an important nanomechanistic key and novel approach for the development of new chemotherapeutic agents.

Submolecular Resolution Imaging of P3HT:PCBM Nanostructured Films by Atomic Force Microscopy: Implications for Organic Solar Cells.

The efficiency of organic bulk-heterojunction (BHJ) solar cells depends greatly on both the bulk and surface structure of the nanostructured bicontinuous interpenetrating network of materials, known as the active layer. The morphology of the top layer of a coated film is often resolved at the scale of a few nanometers, but fine details of the domains and the order within them are more difficult to identify. Here, we report a high-resolution atomic force microscopy (AFM) investigation of various stoichiometries of the well-studied poly(3-hexylthiophene):[6,6]-phenyl C61 butyric acid methyl ester (P3HT:PCBM) active layer mixture. Images of the surface were obtained using AC-mode AFM exciting higher-order resonance frequencies of a standard silicon probe, a promising technique for acquiring real-space images of organic-based thin films with nanoscale and even submolecular resolution. We provide firm evidence of the nanoscale organization of the P3HT polymer and of the P3HT:PCBM stoichiometric mixtures at the surface-air interface of the BHJ architecture. Our study shows the characteristic periodicity of the regioregular P3HT identified in the nanoscale domain areas with submolecular resolution. Such areas are then distorted in place when adding different quantities of PCBM forming stoichiometric mixtures. When the samples were exposed to ambient light, the morphologies were very different, and submolecular resolution was not achieved. This approach is shown to provide a precise view of the active layer's nanostructure and will be useful for studies of other materials as a function of various parameters, with particular attention to the role of the acceptor in tuning morphology for understanding optimum performance in organic photovoltaic devices.

Submolecular-resolution imaging of water clusters on the Cu(110) surface by atomic force microscopy

<p indent="0mm">Water/solid interfaces are important to a wide range of scientific and technological processes such as ice nucleation and growth, corrosion, lubrication, heterogeneous catalysis and electrochemistry. It is a key issue to understand the structure and dynamics of water on solid surfaces. However, the atomic-scale characterization of the weakly bonded water clusters on metal surfaces remains challenging. Here, we report submolecular-resolution imaging of the water clusters on the Cu(110) surface using a qPlus-based noncontact atomic force microscope with a CO tip. The configurations of water clusters, including the detailed OH directionalities, could be identified unambiguously by probing the weak high-order electrostatic force between the CO-tip and polar water molecules, which is further confirmed by theoretical simulations. Water clusters composed of 4, 5, and 6 water molecules are observed on the Cu(110) surface, which are mainly built from cyclic tetramers and pentamers. We notice that water hexamers contain three different types of H-bonding configurations, one cyclic tetramer with two additional water molecules adsorbed at <italic>ortho</italic>- or <italic>para</italic>-sites of the tetramer and one pentagonal ring with one additional water molecule. More interestingly, these structures could be interconverted by the tip manipulation, because of the similar adsorption energies. The isolated pentamer would act as a nucleation core for the growth of 1D pentagonal chains on the Cu(110) surface.

Chemical bond imaging using torsional and flexural higher eigenmodes of qPlus sensors.

Non-contact atomic force microscopy (AFM) with CO-functionalized tips allows visualization of the chemical structure of adsorbed molecules and identify individual inter- and intramolecular bonds. This technique enables in-depth studies of on-surface reactions and self-assembly processes. Herein, we analyze the suitability of qPlus sensors, which are commonly used for such studies, for the application of modern multifrequency AFM techniques. Two different qPlus sensors were tested for submolecular resolution imaging via actuating torsional and flexural higher eigenmodes and via bimodal AFM. The torsional eigenmode of one of our sensors is perfectly suited for performing lateral force microscopy (LFM) with single bond resolution. The obtained LFM images agree well with images from the literature, which were scanned with customized qPlus sensors that were specifically designed for LFM. The advantage of using a torsional eigenmode is that the same molecule can be imaged either with a vertically or laterally oscillating tip without replacing the sensor simply by actuating a different eigenmode. Submolecular resolution is also achieved by actuating the 2nd flexural eigenmode of our second sensor. In this case, we observe particular contrast features that only appear in the AFM images of the 2nd flexural eigenmode but not for the fundamental eigenmode. With complementary laser Doppler vibrometry measurements and AFM simulations we can rationalize that these contrast features are caused by a diagonal (i.e. in-phase vertical and lateral) oscillation of the AFM tip.

Automated tip functionalization via machine learning in scanning probe microscopy

Auto-CO-AFM is an open-source software package for scanning probe microscopes that enables the automatic functionalization of scanning probe tips with carbon monoxide molecules. This enables machine operators to specify the quality of the tip needed utilizing a pre-trained library with off-the-shelf software. From a single image, the software package can determine which molecules on a surface are carbon monoxide, perform the necessary tip functionalization procedures, interface with microscope software to control the tip position, and determines the centeredness of the tip after a successful functionalization. This is of particular interest for atomic force microscopy imaging of molecules on surfaces, where the tip functionalization is a necessary and time consuming step needed for sub-molecular resolution imaging. This package is freely available under the MIT License. Program summaryProgram Title: Auto-CO-AFMCPC Library link to program files:https://doi.org/10.17632/khfvjhx4vb.1Developer's repository link:https://github.com/SINGROUP/Auto-CO-AFMLicensing provisions: MITProgramming language: PythonSupplementary material: Supplementary Information as PDFNature of problem: Scanning probe microscopy experiments are limited by the lack of automated tools in tip preparation, particularly when functionalizing an adatom or molecule on the end of a tip. These tip functionalizations are commonly manually-driven processes that are time-consuming for the operator.Solution method: We have developed an automated solution for tip functionalization for carbon monoxide molecules, which combines machine learning descriptors with automated software control of the tip preparation process. The Python program interfaces with a major vendor's software to scan, functionalize, and verify the tip quality for the operator. The source code, documentation, and basic program are posted online.Additional comments including restrictions and unusual features: Current version of software in publication requires STMAFM software from CreaTec GmbH in physical connection with a CreaTec DSP.

On-Surface Supramolecular Chemistry with Porphyrins and Phthalocyanines: An Architectural Concept Leading to Engineered Quantum-Functional Nanostructures

The availability of porphyrin and phthalocyanine functionalization and synthesis, ‘by design’, at the time when sub-molecular resolution imaging at surfaces came into action boosted the emergence of ‘On-Surface-Supramolecular Chemistry’. [1] It is instructive to compare supra-molecular binding motifs in the fluid phase with the corresponding or modified analogues found after assembly on surfaces. In some similarity to chemistry and coordination chemistry translating into the corresponding ‘on-surface’ sciences, there are many factors complicating the on-surface assembly and architecture. Examples are provided by the modified dimensionality and kinetics, the site-specific conformational flexure and chirality and the close to irreversible adsorption in the strong surface potential in absence of a solvent which may complicate the on-surface assembly and architecture. Further, porphyrins and phthalocyanines interact with the substrate by different, competitive interactions, i.e. via (1) the central metal atom and (2) the porphyrin pi-system in addition to (3) the functional side groups. Binary and ternary assemblies of porphyrins and other functional components make it possible to create a wealth of ‘phases’, i.e. different complex supramolecular architectures with interesting physical properties to explore and exploit.We analyze structure-function correlations for a broad spectrum of functionalized porphyrins and phthalocyanines in their propensity to create structures of increasing complexity and functionality, on surfaces, also for future quantum technology. Notably, the large delocalized electronic system of the porphyrins and their easy-to-replace central atom further extend the achievable range of architectures and functions. Thus, by their dance on the nose of the ‘devil’ [3], porphyrins and phthalocyanines justify the emergence of ‘on-surface supramolecular physics’ as reflected by ongoing and future research work.[1] N. Wintjes et al. Two-dimensional phase behavior of a bimolecular porphyrin system at the solid-vacuum interface, J. Am. Chem. Soc. 2010, 132, 21, 7306-7311; N. Wintjes et al., Supramolecular synthons on surfaces: Controlling dimensionality and periodicity of tetraarylporphyrin assemblies by the interplay of cyano and alkoxy substituents Chem. Eur. J. 2008, 14, 5794.[2] S. Nowakowska et al., Adsorbate-induced modification of the confining barriers in a quantum box array, ACS Nano 2018, 12, 768.[3] W. Pauli “God made the bulk; surfaces were invented by the devil.” Quoted, e.g. in the Preface of A. Zangwill, Physics at Surfaces, Cambridge University Press, 1988. ISBN 978-0-521-34752-5Fig. 1) Adsorbate-induced modification of the confining barriers in a quantum box array formed by a functionalized fluoro-bi-phenyl porphyrin on Ag(111). (Taken from [2]) Figure 1

Richard P. Van Duyne, plasmonics pioneer

Prof. Richard P. Van Duyne (Fig. 1), a National Academy of Sciences member who played a pivotal role in starting the field of plasmonics and promoting nanoscience, died on July 28, 2019, at the age of 73. Rick’s prominence as a great intellect and visionary is apparent by his tremendous academic success, including a host of academic awards, an impressive publication record, and generations of mentees working to live up to the potential he saw in them. While being elected to the National Academy of Sciences was Rick’s most coveted recognition, he was proud of all of the recognition he achieved in his long career, including an h-index of 125 and rising, the Earle K. Plyler Prize in Molecular Spectroscopy from the American Physical Society, the Charles N. Reilly Award from the Society for Electroanalytical Chemistry, and a 2017 Vannevar Bush Faculty Fellowship. Fig. 1. Rick Van Duyne was proud to be elected to the National Academy of Sciences. Image courtesy of Northwestern University. Rick’s primary contributions to science all stem from his interest in molecular plasmonics, which deals with the interactions of molecules with nanomaterials that support a surface plasmon resonance. Rick entered this field in the early 1970s with training in electrochemistry, and proved himself an early adopter in a number of creative endeavors, including applications in glucose sensing, food safety, art conservation, single-molecule detection, and photocatalysis. As a physical and analytical chemist, Rick’s primary contributions include a number of fundamental insights on the mechanism and applications of surface-enhanced Raman spectroscopy (SERS), the development of nanoplasmonic substrates via nanosphere lithography, and extensions of molecular plasmonics into biosensing and submolecular resolution imaging. Rick’s journey with surface-enhanced spectroscopy began pretenure when he read a newly published paper in 1974. In that paper (1), “Raman spectra of pyridine adsorbed at a silver electrode,” … [↵][1]1To whom correspondence may be addressed. Email: chaynes{at}umn.edu. [1]: #xref-corresp-1-1

Probing surface water at submolecular level with scanning probe microscopy

Water-solid interfaces play important roles in a wide range of scientific areas and technique processes such as the dissolution, lubrication, erosion, electrochemistry and heterogeneous catalysis. Many remarkable physical and chemical properties of water are related to the hydrogen-bonding interaction. Thus it is a key issue to understand the hydrogen-bonding network and relevant dynamics of interfacial water at single molecule or even submolecular level. Scanning probe microscope has become a powerful tool to study the water-solid interfaces due to its capability of imaging with atomic resolution. In this feature article we will introduce the recent progress of our group on the development of submolecular-resolution imaging and spectroscopic techniques, and their applications to address the microscopic structure of the hydrogen-bonded network of water, the dynamics of proton transfer, nuclear quantum effect on the strength of hydrogen bond and water-ion interaction. Finally, future directions and challenges about the study of water-solid interface are remarked.

Emergent Properties of the Organic Molecule-Topological Insulator Hybrid Interface: Cu-Phthalocyanine on Bi2Se3

We unravel the bidirectional influence of the adsorbate–substrate hybrid interface in the case of CuPc doping of the topological insulator (TI) surface Bi2Se3. Using ultrahigh vacuum scanning tunneling microscopy at low temperature (77 K), we observe that for a dilute concentration, single CuPc molecules are dispersed on terraces of Bi2Se3 as individual entities or as clusters. The site-dependent submolecular resolution images of CuPc on Bi2Se3 reveal three different sites for CuPc adsorption. Scanning tunneling spectroscopy (STS) measurements show a rigid shift of the Dirac point toward negative voltage by 336 meV upon CuPc deposition. This is a clear signature that the topological surface state experiences a charge transfer because of CuPc. The highest occupied molecular orbital (HOMO)–lowest unoccupied molecular orbital (LUMO) energy gap of CuPc on Bi2Se3 is also measured using STS. It is found to be larger than that on the Au(111) substrate because of the reduced screening offered by the TI Bi2Se3 sur...

Pentacene/TiO2 Anatase Hybrid Interface Study by Scanning Probe Microscopy and First Principles Calculations.

The understanding and control of the buried interface between functional materials in optoelectronic devices is key to improving device performance. We combined atomic resolution scanning probe microscopy with first-principles calculations to characterize the technologically relevant organic/inorganic interface structure between pentacene molecules and the TiO2 anatase (101) surface. A multipass atomic force microscopy imaging technique overcomes the technical challenge of imaging simultaneously the corrugated anatase substrate, molecular adsorbates, monolayers, and bilayers at the same level of detail. Submolecular resolution images revealed the orientation of the adsorbates with respect to the substrate and allowed direct insights into interface formation. Pentacene molecules were found to physisorb parallel to the anatase substrate in the first contact layer, passivating the surface and promoting bulk-like growth in further organic layers. While molecular electronic states were not significantly hybridized by the substrate, simulations predicted localized pathways for molecule-surface charge injection. The localized states were associated with the molecular lowest unoccupied molecular orbital inside the oxide conduction band, pointing to efficient transfer of photo-induced electron charge carriers across this interface in prospective photovoltaic devices. In uncovering the atomic arrangement and favorable electronic properties of the pentacene/anatase interface, our findings testify to the maturity and analytic power of our methodology in further studies of organic/inorganic interfaces.

Site-Specific Adsorption of Aromatic Molecules on a Metal/Metal Oxide Phase Boundary.

Nanostructured surfaces are ideal templates to control the self-assembly of molecular structures toward well-defined functional materials. To understand the initial adsorption process, we have investigated the arrangement and configuration of aromatic hydrocarbon molecules on nanostructured substrates composed of an alternating arrangement of Cu(110) and oxygen-reconstructed stripes. Scanning tunneling microscopy reveals a preferential adsorption of molecules at oxide phase boundaries. Noncontact atomic force microscopy experiments provide a detailed insight into the preferred adsorption site. By combining submolecular resolution imaging with density functional theory calculations, the interaction of the molecule with the phase boundary was elucidated excluding a classical hydrogen bonding. Instead, a complex balance of different interactions is revealed. Our results provide an atomistic picture for the driving forces of the adsorption process. This comprehensive understanding enables developing strategies for the bottom-up growth of functional molecular systems using nanotemplates.

Probing the Structure and Dynamics of Interfacial Water with Scanning Tunneling Microscopy and Spectroscopy.

Water/solid interfaces are ubiquitous and play a key role in many environmental, biophysical, and technological processes. Resolving the internal structure and probing the hydrogen-bond (H-bond) dynamics of the water molecules adsorbed on solid surfaces are fundamental issues of water science, which remains a great challenge owing to the light mass and small size of hydrogen. Scanning tunneling microscopy (STM) is a promising tool for attacking these problems, thanks to its capabilities of sub-Ångström spatial resolution, single-bond vibrational sensitivity, and atomic/molecular manipulation. The designed experimental system consists of a Cl-terminated tip and a sample fabricated by dosing water molecules in situ onto the Au(111)-supported NaCl(001) surfaces. The insulating NaCl films electronically decouple the water from the metal substrates, so the intrinsic frontier orbitals of water molecules are preserved. The Cl-tip facilitates the manipulation of the single water molecules, as well as gating the orbitals of water to the proximity of Fermi level (EF) via tip-water coupling. This paper outlines the detailed methods of submolecular resolution imaging, molecular/atomic manipulation, and single-bond vibrational spectroscopy of interfacial water. These studies open up a new route for investigating the H-bonded systems at the atomic scale.

Weakly perturbative imaging of interfacial water with submolecular resolution by atomic force microscopy.

Scanning probe microscopy has been extensively applied to probe interfacial water in many interdisciplinary fields but the disturbance of the probes on the hydrogen-bonding structure of water has remained an intractable problem. Here, we report submolecular-resolution imaging of the water clusters on a NaCl(001) surface within the nearly noninvasive region by a qPlus-based noncontact atomic force microscopy. Comparison with theoretical simulations reveals that the key lies in probing the weak high-order electrostatic force between the quadrupole-like CO-terminated tip and the polar water molecules at large tip–water distances. This interaction allows the imaging and structural determination of the weakly bonded water clusters and even of their metastable states with negligible disturbance. This work may open an avenue for studying the intrinsic structure and dynamics of ice or water on surfaces, ion hydration, and biological water with atomic precision.

Submolecular Resolution Imaging of Molecules by Atomic Force Microscopy: The Influence of the Electrostatic Force.

The forces governing the contrast in submolecular resolution imaging of molecules with atomic force microscopy (AFM) have recently become a topic of intense debate. Here, we show that the electrostatic force is essential to understand the contrast in atomically resolved AFM images of polar molecules. Specifically, we image strongly polarized molecules with negatively and positively charged tips. A contrast inversion is observed above the polar groups. By taking into account the electrostatic forces between tip and molecule, the observed contrast differences can be reproduced using a molecular mechanics model. In addition, we analyze the height dependence of the various force components contributing to the high-resolution AFM contrast.

STM study of oligo(phenylene-ethynylene)s

A detailed scanning tunneling microscopy (STM) study of two variants of oligo(phenylene ethynylene) (OPE) molecules is presented. These molecules might serve as molecular wires up to ≈ 5 nm in length. Self-assembled arrangements as well as single molecules on a Au(111) surface were analyzed. The molecular orbitals were directly imaged and are compared to density functional theory calculations. Sub-molecular resolution images of both molecules directly display the chemical structure. One of the OPE variants was lifted off the surface by the STM tip to measure the single-molecule conductance in order to explain previously reported low conduction values. Furthermore, we present a detailed analysis of a tip-induced conformational switching of the hexyl side groups from all-trans to a nonlinear conformation, which was observed for both variants.

Interfacial Organic Layers for Chemical Stability and Crystalline Ordering of Thiophene and Carboxyl Films on a Metal Surface

Organic-based devices require multicomponent, multilayer architectures consisting of functional molecules that may be chemically unstable at a metal interface. In this work, we demonstrate that an interfacial organic layer (IOL) provides chemical stability at and above room temperature, while also achieving desired crystalline ordering of the functionalized organic layer. As the IOL decouples organic species from direct interactions with the metal, new structural motifs become available that are not otherwise observed, yielding the first submolecular resolution imaging of phenylthiophene stacking at a surface. We studied self-organized layers comprising two classes of functional groups, carboxylic acids and thiophenes, which have applications in organic electronics but are each chemically unstable and structurally disordered when deposited directly onto the Cu(001) and other metal surfaces. The IOL strategy demonstrated here resolves these issues and broadens opportunities for organic thin films on metal ...

Real-space imaging of interfacial water with submolecular resolution

Water/solid interfaces are vital to our daily lives and are also a central theme across an incredibly wide range of scientific disciplines. Resolving the internal structure, that is, the O-H directionality, of water molecules adsorbed on solid surfaces has been one of the key issues of water science yet it remains challenging. Using a low-temperature scanning tunnelling microscope, we report submolecular-resolution imaging of individual water monomers and tetramers on NaCl(001) films supported by a Au(111) substrate at 5 K. The frontier molecular orbitals of adsorbed water were directly visualized, which allowed discrimination of the orientation of the monomers and the hydrogen-bond directionality of the tetramers in real space. Comparison with ab initio density functional theory calculations reveals that the ability to access the orbital structures of water stems from the electronic decoupling effect provided by the NaCl films and the precisely tunable tip-water coupling.

Toward the Microscopic Identification of Anions and Cations at the Ionic Liquid|Ag(111) Interface: A Combined Experimental and Theoretical Investigation

The interaction between an adsorbed 1-butyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)imide, [BMP][TFSA], ionic liquid (IL) layer and a Ag(111) substrate, under ultrahigh-vacuum conditions, was investigated in a combined experimental and theoretical approach, by high-resolution scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and dispersion-corrected density functional theory calculations (DFT-D). Most importantly, we succeeded in unambiguously identifying cations and anions in the adlayer by comparing experimental images with submolecular resolution and simulated STM images based on DFT calculations, and these findings are in perfect agreement with the 1:1 ratio of anions and cations adsorbed on the metal derived from XPS measurements. Different adlayer phases include a mobile 2D liquid phase at room temperature and two 2D solid phases at around 100 K, i.e., a 2D glass phase with short-range order and some residual, but very limited mobility and a long-range ordered 2D crystalline phase. The mobility in the different adlayer phases, including melting of the 2D crystalline phase, was evaluated by dynamic STM imaging. The DFT-D calculations show that the interaction with the substrate is composed of mainly van der Waals and weak electrostatic (dipole-induced dipole) interactions and that upon adsorption most of the charge remains at the IL, leading to attractive electrostatic interactions between the adsorbed species.

Orientation of molecular interface dipole on metal surface investigated by noncontact atomic force microscopy

We investigated the orientations of interface dipole moments of individual non-planar titanyl phthalocyanine (TiOPc) molecules on Cu(111) and Cu(100) substrates using scanning tunneling microscope (STM) and noncontact atomic force microscope (NC-AFM). The dipole moment orientations corresponding to two different configurations of individual TiOPc molecules were determined unambiguously. The correlation between the actual molecular structures and the corresponding STM topographies is proposed based on the sub-molecular resolution imaging and local contact potential difference (LCPD) measurements. Comparing with the pristine substrate, the LCPD shift due to the adsorption of non-planar molecule is dependent on the permanent molecular dipole, the charge transfer between the surface and the molecule, and the molecular configurations. This work would shed light on tailoring interfacial electronic properties and controlling local physical properties via polar molecule adsorption.