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Anharmonicity plays a crucial role in hydrogen transfer reactions in hydrogen-bonding systems, which leads to a peculiar spectral line shape of the hydrogen stretching mode as well as highly complex intra/intermolecular vibrational energy relaxation. Single-molecule study with a well-defined model is necessary to elucidate a fundamental mechanism. Recent low-temperature scanning tunnelling microscopy (STM) experiments revealed that the cis↑cis tautomerization in a single porphycene molecule on Cu(110) at 5 K can be induced by vibrational excitation via an inelastic electron tunnelling process and the N–H(D) stretching mode couples with the tautomerization coordinate [Kumagai et al. Phys. Rev. Lett. 2013, 111, 246101]. Here we discuss a pronounced anharmonicity of the N–H stretching mode observed in the STM action spectra and the conductance spectra. Density functional theory calculations find a strong intermode coupling of the N–H stretching with an in-plane bending mode within porphycene on Cu(110). [ABSTRACT FROM AUTHOR]

We describe various experimental approaches that have been used to obtain a detailed understanding of double hydrogen transfer in porphycene, a model system for intramolecular hydrogen bonding and tautomerism. The emerging picture is that of a multidimensional tautomerization coordinate, with several vibrational modes acting as reaction-promoters or inhibitors through anharmonic intermode coupling. Tunnelling processes, coherent in the case of isolated molecules and incoherent in condensed phases, are found to play a major role even at elevated temperatures. Single-molecule spectroscopy studies reveal large fluctuations in hydrogen transfer rates observed over time for the same chromophore. Scanning probe microscopy is employed to directly observe the structure and tautomerization dynamics of single molecules adsorbed on metal surfaces and demonstrates how the interactions of the molecules with atoms of the supporting surface affect their static and dynamic properties: different tautomeric forms are stabilized for molecules depending on the surface structure and the reaction mechanism can also change, from a concerted to a stepwise transfer. The scanning probe microscopy studies prove that tautomerization in single molecules can be induced by different stimuli: heat, electron attachment, light, and force exerted by the microscope's tip. Possible applications utilizing tautomerism are discussed in combination with molecular architectures on surfaces, which could pave the way for the development of single-molecule electronics. [ABSTRACT FROM AUTHOR]

A key challenge in the field of nanotechnology, in particular in the design of molecular machines, novel materials or molecular electronics, is the bottom-up construction of covalently bound molecular architectures in a well-defined arrangement. To date, only rather simple structures have been obtained because of the limitation of one-step connection processes. Indeed, for the formation of sophisticated structures, step-by-step connection of molecules is required. Here, we present a strategy for the covalent connection of molecules in a hierarchical manner by the selective and sequential activation of specific sites, thereby generating species with a programmed reactivity. This approach leads to improved network quality and enables the fabrication of heterogeneous architectures with high selectivity. Furthermore, substrate-directed growth and a preferred orientation of the molecular nanostructures are achieved on an anisotropic surface. The demonstrated control over reactivity and diffusion during covalent bond formation constitutes a promising route towards the creation of sophisticated multi-component molecular nanostructures. [ABSTRACT FROM AUTHOR]

The design of a single-molecule machine consisting of functional components requires a detailed understanding of its mechanical motion. The scanning tunnelling microscope (STM) is the only available tool for driving and imaging such a nanoscale machine on a surface. Both lateral hopping motions and conformational changes of single molecules can be induced using the STM tip. However, no rolling of a wheel has been demonstrated so far at the nanoscale, even though this is a very useful motion at the macroscopic scale. Here we show how the rolling of a single molecule equipped with two wheels (0.8 nm in diameter) can be induced by the STM tip. The characteristics of the rolling are recorded in the STM feedback loop manipulation signal and in real time. We capture unambiguous signatures of the conformational change happening during the rolling. Our approach of controlling the intramolecular mechanics provides a path towards the bottom-up assembly of more complex molecular machines. [ABSTRACT FROM AUTHOR]

The photoemission spectra of the Sn 4d electrons from the (3 × 3)-Sn/Ge(111) surface present two components which are attributed to inequivalent Sn atoms in T4 bonding sites. This structure has been explored by photoelectron diffraction experiments performed at the ALOISA beamline of the Elettra storage ring in Trieste (Italy). The modulation of the intensities of the two Sn components, caused by the backscattering of the underneath Ge atoms, has been measured as a function of the emission angle at fixed kinetic energies and vice versa. The bond angle between Sn and its nearest neighbor atoms in the first Ge layer (Sn-Ge[sub 1]) has been measured by taking polar scans along the main symmetry directions and it was found almost equivalent for the two components. The corresponding bond lengths are also quite similar, as obtained by studying the dependence on the photoelectron kinetic energy with the photon polarization and the collection direction parallel to the Sn-Ge[sub 1] bond orientation (bond emission). A clear difference between the two bonding sites is observed when studying the energy dependence at normal emission, where the sensitivity to the Sn height above the Ge atom in the second layer is enhanced. The (3 × 3)-Sn/Ge(111) is thus characterized by a structure where the Sn atom and its three nearest neighbor Ge atoms form a rather rigid unit that presents a strong vertical distortion with respect to the underneath atom of the second Ge layer. [ABSTRACT FROM AUTHOR]

Essential in halting the COVID-19 pandemic caused by SARS-CoV-2, it is crucial to have stable, effective, and easy-to-manufacture vaccines. We developed a potential vaccine using a tobacco mosaic virus (TMV) epitope display model presenting peptides derived from the SARS-CoV-2 spike protein. The TMV-epitope fusions in laboratory tests demonstrated binding to the SARS-CoV-2 polyclonal antibodies. The fusion constructs maintained critical epitopes of the SARS-CoV-2 spike protein, and two in particular spanned regions of the receptor-binding domain that have mutated in the more recent SARS-CoV-2 variants. This would allow for the rapid modification of vaccines in response to changes in circulating variants. The TMV-peptide fusion constructs also remained stable for over 28 days when stored at temperatures between -20 and 37 °C, an ideal property when targeting developing countries. Immunogenicity studies conducted on BALB/c mice elicited robust antibody responses against SARS-CoV-2. A strong IFNγ response was also observed in immunized mice. Three of the six TMV-peptide fusion constructs produced virus-neutralizing titers, as measured with a pseudovirus neutralization assay. These TMV-peptide fusion constructs can be combined to make a multivalent vaccine that could be adapted to meet changing virus variants. These findings demonstrate the development of a stable COVID-19 vaccine candidate by combining SARS-CoV-2 spike protein-derived peptides presented on the surface of a TMV nanoparticle.

Light is a versatile tool to remotely activate molecules adsorbed on a surface, for example, to trigger their polymerization. Here, we explore the spatial distribution of light-induced chemical reactions on a Au(111) surface. Specifically, the covalent on-surface polymerization of an anthracene derivative in the submonolayer coverage range is studied. Using scanning tunneling microscopy and X-ray photoemission spectroscopy, we observe a substantial increase of the local molecular coverage with the sample illumination time at the center of the laser spot. We find that the interplay between thermally induced diffusion and the reduced mobility of reaction products steers the accumulation of material. Moreover, the debromination of the adsorbed species never progresses to completion within the experiment time, despite a long irradiation of many hours., Competing Interests: The authors declare no competing financial interest., (© 2024 The Authors. Published by American Chemical Society.)

Artificial molecular motors are designed to transform external energy into useful work in the form of unidirectional motion 1 . They have been studied mainly in solution 2-4 , but also on solid surfaces 5,6 , which provide fixed reference points, allowing for tracking of their movement. However, these molecules require sophisticated design and synthesis, because the motor function must be imprinted into the chemical structure, and show reduced functionality on surfaces compared with in solution 5-8 . DNA walkers 9,10 , on the other hand, impart high directionality as they include the surface as part of the motor function, but they require chemical surface patterning and sequential solvent modification for motor activation. Here we show how efficient motors can operate at much smaller length scales on a homogeneous metal surface without any liquid. This is realized by combining a surface with a simple molecule, which, by itself, does not contain any motor unit. The motion, which is tracked at the single-molecule level, is triggered by intramolecular proton transfer with a corresponding modulation of the potential energy surface. Each molecule moves with 100 percent unidirectionality along an atomically defined straight line. Proof of the motor performing meaningful work is shown by controlled transport of single carbon monoxide molecules. This simplistic concept could form the basis for the controlled bottom-up assembly of nanostructures at the atomic scale., (© 2023. The Author(s), under exclusive licence to Springer Nature Limited.)

Understanding the directed motion of a single molecule on surfaces is not only important in the well-established field of heterogeneous catalysis but also for the design of artificial nanoarchitectures and molecular machines. Here, we report how the tip of a scanning tunneling microscope (STM) can be used to control the translation direction of a single polar molecule. Through the interaction of the molecular dipole with the electric field of the STM junction, it was found that both translations and rotations of the molecule occur. By considering the location of the tip with respect to the axis of the dipole moment, we can deduce the order in which rotation and translation take place. While the molecule-tip interaction dominates, computational results suggest that the translation is influenced by the surface direction along which the motion takes place.

Two different metal-organic frameworks with either a honeycomb or Kagome structure were grown on Cu(111) using para -aminophenol molecules and native surface adatoms. Although both frameworks are made up from the same chemical species, they are structurally different emphasizing the critical role being played by the reaction conditions during their growth. This work highlights the importance of the balance between thermodynamics and kinetics in the final structure of surface-supported metal-organic networks.

Building nanostructures one-by-one requires precise control of single molecules over many manipulation steps. The ideal scenario for machine learning algorithms is complex, repetitive, and time-consuming. Here, we show a reinforcement learning algorithm that learns how to control a single dipolar molecule in the electric field of a scanning tunneling microscope. Using about 2250 iterations to train, the algorithm learned to manipulate the molecule toward specific positions on the surface. Simultaneously, it generates physical insights into the movement as well as orientation of the molecule, based on the position where the electric field is applied relative to the molecule. This reveals that molecular movement is strongly inhibited in some directions, and the torque is not symmetric around the dipole moment.

Molecular motors have chemical properties that enable unidirectional motion, thus breaking microscopic reversibility. They are well studied in solution, but much less is known regarding their behavior on solid surfaces. Here, single motor molecules adsorbed on a Cu(111) surface are excited by voltages pulses from an STM tip, which leads to their rotation around a fixed pivot point. Comparison with calculations shows that this axis results from a chemical bond of a sulfur atom in the chemical structure and a metal atom of the surface. While statistics show approximately equal rotations in both directions, clockwise and anticlockwise, a detailed study reveals that these motions are enantiomer-specific. Hence, the rotation direction of each individual molecule depends on its chirality, which can be determined from STM images. At first glance, these dynamics could be assigned to the activation of the motor molecule, but our results show that this is unlikely as the molecule remains in the same conformation after rotation. Additionally, a control molecule, although it lacks unidirectional rotation in solution, also shows unidirectional rotation for each enantiomer. Hence, it seems that the unidirectional rotation is not specifically related to the motor property of the molecule. The calculated energy barriers for motion show that the propeller-like motor activity requires higher energy than the simple rotation of the molecule as a rigid object, which is therefore preferred.

We have studied 22-oxahemiporphycene molecules by a combination of scanning tunneling microscopy at low temperatures and density functional theory calculations. In contrast to other molecular switches with typically two switching states, these molecules can in principle exist in three different tautomers, due to their asymmetry and three inequivalent binding positions of a hydrogen atom in their macrocycle. Different tautomers are identified from the typical appearance on the surface and tunneling electrons can be used to tautomerize single molecules in a controllable way with the highest rates if the STM tip is placed close to the hydrogen binding positions in the cavity. Characteristic switching processes are explained by the different energy pathways upon adsorption on the surface. Upon applying higher bias voltages, deprotonation occurs instead of tautomerization, which becomes evident in the molecular appearance.

microRNAs represent promising drugs to treat and prevent several diseases, such as diabetes mellitus. microRNA delivery brings many obstacles to overcome, and one strategy to bypass them is the manufacturing of self-assembled microRNA protein nanoparticles. In this work, a microRNA was combined with the cell-penetrating peptide protamine, forming so-called proticles. Previous studies demonstrated a lack of microRNA dissociation from proticles. Therefore, the goal of this study was to show the success of functionalizing binary proticles with citric acid in order to reduce the binding strength between the microRNA and protamine and further enable sufficient dissociation. Thus, we outline the importance of the present protons provided by the acid in influencing colloidal stability, achieving a constant particle size, and monodispersing the particle size distribution. The use of citric acid also provoked an increase in drug loading. Against all expectations, the AFM investigations demonstrated that our nanoparticles were loose complexes mainly consisting of water, and the addition of citric acid led to a change in shape. Moreover, a successful reduction in binding affinity and nanoparticulate stability are highlighted. Low cellular toxicity and a constant cellular uptake are demonstrated, and as uptake routes, active and passive pathways are discussed., Competing Interests: The authors declare no conflict of interest.

Molecular motors have been intensely studied in solution, but less commonly on solid surfaces that offer fixed points of reference for their motion and allow high-resolution single-molecule imaging by scanning probe microscopy. Surface adsorption of molecules can also alter the potential energy surface and consequently preferred intramolecular conformations, but it is unknown how this affects motor molecules. Here, we show how the different conformations of motor molecules are modified by surface adsorption using a combination of scanning tunneling microscopy and density functional theory. These results demonstrate how the contact of a motor molecule with a solid can affect the energetics of the molecular conformations., Competing Interests: The authors declare no competing financial interest., (© 2022 The Authors. Published by American Chemical Society.)

On-surface polymerization is a powerful bottom-up approach that allows for the growth of covalent architectures with defined properties using the two-dimensional confinement of a highly defined single-crystal surface. Thermal heating is the preferred approach to initiate the reaction, often via cleavage of halogen substituents from the molecular building blocks. Light represents an alternative stimulus but has, thus far, only rarely been used. Here, we present a direct comparison of on-surface polymerization of dibromo-anthracene molecules, induced either thermally or by light, and study the differences between the two approaches. Insight is obtained by a combination of scanning tunneling microscopy, locally studying the polymer shape and size, and X-ray photoelectron spectroscopy, which identifies bond formation by averaging over large surface areas. While the polymer length increases slowly with the sample heating temperature, illumination promotes only the formation of short covalent structures, independent of the duration of light exposure. Moreover, irradiation with UV light at different sample temperatures highlights the important role of molecular diffusion across the surface., Competing Interests: The authors declare no competing financial interest., (© 2021 The Authors. Published by American Chemical Society.)

Spatial control over molecular movement is typically limited because motion at the atomic scale follows stochastic processes. We used scanning tunneling microscopy to bring single molecules into a stable orientation of high translational mobility where they moved along precisely defined tracks. Single dibromoterfluorene molecules moved over large distances of 150 nanometers with extremely high spatial precision of 0.1 angstrom across a silver (111) surface. The electrostatic nature of the effect enabled the selective application of repulsive and attractive forces to send or receive single molecules. The high control allows us to precisely move an individual and specific molecular entity between two separate probes, opening avenues for velocity measurements and thus energy dissipation studies of single molecules in real time during diffusion and collision., (Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

With the rapid development of scanning probe microscopy, it has become possible to study polymerization processes on suitable surfaces at the atomic level and in real space. In the two-dimensional confinement of a surface, polymerization reactions can give rise to the formation of unprecedented polymers with unique structures and properties, not accessible in solution. After a little over one decade since the discovery of covalent on-surface polymerization, we give an overview of the field, analyse the crucial aspects and critically reflect on the status quo. Specifically, we provide some general considerations about fundamental mechanisms as well as kinetics and thermodynamics of on-surface polymerization processes. The important role of the surface is detailed in view of its ability to control polymer formation with regard to structure, dimensionality and composition. Furthermore, examples that allow for locally induced polymerization are highlighted. Finally, we provide an analysis of scientific challenges in the field and outline future prospects.

The orientation of molecules is crucial in many chemical processes. Here, we report how single dipolar molecules can be oriented with maximum precision using the electric field of a scanning tunneling microscope. Rotation is found to occur around a fixed pivot point that is caused by the specific interaction of an oxygen atom in the molecule with the Ag(111) surface. Both directions of rotation are realized at will with 100% directionality. Consequently, the internal dipole moment of an individual molecule can be spatially mapped via its behavior in an applied electric field. The importance of the oxygen-surface interaction is demonstrated by the addition of a silver atom between a single molecule and the surface and the consequent loss of the pivot point.

Azobenzene is a prototypical molecular switch that can be reversibly photoisomerized between the nearly planar and apolar trans form, and the distorted, polar cis form. Most studies related to azobenzene derivatives have focused on planar adsorbed molecules. We present herein the study of a three-dimensional shape-persistent molecular architecture consisting of four tetrahedrally arranged azobenzene units that is adsorbed on a Ag(111) surface. While the azobenzenes of the tripod in contact with the surface lost their switching ability, different isomers of the upright standing arm of the tetramer were obtained reversibly and efficiently by illumination at different wavelengths, revealing time constants of only a few minutes. Diffusion on the surface was dependent on the isomeric state-trans or cis-of the upright oriented azobenzene group. Hence, molecular mobility can be modulated by its isomeric state, which suggests that molecular growth processes could be controlled by external stimuli., (© 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.)

We report how individual defects affect single graphene nanoribbons by scanning tunneling and atomic force microscopy pulling experiments simultaneously accessing their electrical and mechanical properties. The on-surface polymerization of the graphene nanoribbons is controlled by cooperative effects as theoretically suggested. Further, we find, with the help of atomistic simulations, that defects substantially vary the molecule-substrate coupling and drastically increase the flexibility of the graphene nanoribbons while keeping their desirable electronic properties intact.

Tautomerization in single porphycene molecules is investigated on Cu(111), Ag(111), and Au(111) surfaces by a combination of low-temperature scanning tunneling microscopy (STM) experiments and density functional theory (DFT) calculations. It is revealed that the trans configuration is the thermodynamically stable form of porphycene on Cu(111) and Ag(111), whereas the cis configuration occurs as a meta-stable form. The trans → cis or cis → trans conversion on Cu(111) can be induced in an unidirectional fashion by injecting tunneling electrons from the STM tip or heating the surface, respectively. We find that the cis ↔ cis tautomerization on Cu(111) occurs spontaneously via tunneling, verified by the negligible temperature dependence of the tautomerization rate below ∼23 K. Van der Waals corrected DFT calculations are used to characterize the adsorption structures of porphycene and to map the potential energy surface of the tautomerization on Cu(111). The calculated barriers are too high to be thermally overcome at cryogenic temperatures used in the experiment and zero-point energy corrections do not change this picture, leaving tunneling as the most likely mechanism. On Ag(111), the reversible trans ↔ cis conversion occurs spontaneously at 5 K and the cis ↔ cis tautomerization rate is much higher than on Cu(111), indicating a significantly smaller tautomerization barrier on Ag(111) due to the weaker interaction between porphycene and the surface compared to Cu(111). Additionally, the STM experiments and DFT calculations reveal that tautomerization on Cu(111) and Ag(111) occurs with migration of porphycene along the surface; thus, the translational motion couples with the tautomerization coordinate. On the other hand, the trans and cis configurations are not discernible in the STM image and no tautomerization is observed for porphycene on Au(111). The weak interaction of porphycene with Au(111) is closest to the gas-phase limit and therefore the absence of trans and cis configurations in the STM images is explained either by the rapid tautomerization rate or the similar character of the molecular frontier orbitals of the trans and cis configurations.

Prototypical molecular switches such as azobenzenes exhibit two states, i.e., trans and cis, with different characteristic physical properties. In recent years various derivatives were investigated on metallic surfaces. However, bulk insulators as supporting substrate reveal important advantages since they allow electronic decoupling from the environment, which is key to control the switching properties. Here, we report on the light-induced isomerization of an azobenzene derivative on a bulk insulator surface, in this case calcite (101̅4), studied by atomic force microscopy with submolecular resolution. Surprisingly, cis isomers appear on the surface already directly after preparation, indicating kinetic trapping. The photoisomerization process is reversible, as the use of different light sources results in specific molecular assemblies of each isomer. The process turns out to be very efficient and even comparable to molecules in solution, which we assign to the rather weak molecular interaction with the insulator surface, in contrast to metals.

Molecular machines are a key component in the vision of molecular nanotechnology and have the potential to transport molecular species and cargo on surfaces. The motion of such machines should be triggered remotely, ultimately allowing a large number of molecules to be propelled by a single source, with light being an attractive stimulus. Here, we report upon the photoinduced translation of molecular machines across a surface by characterizing single molecules before and after illumination. Illumination of molecules containing a motor unit results in an enhancement in the diffusion of the molecules. The effect vanishes if an incompatible photon energy is used or if the motor unit is removed from the molecule, revealing that the enhanced motion is due to the presence of the wavelength-sensitive motor in each molecule.

The covalent linking of molecular building blocks on surfaces enables the construction of specific molecular nanostructures of well-defined shape. Molecular nodes linked to various entities play a key role in such networks, but represent a particular challenge because they require a well-defined arrangement of different building blocks. Herein, we describe the construction of a chemically and geometrically well defined covalent architecture made of one central node and three molecular wires arranged in a nonsymmetrical way and thus encoding different conjugation pathways. Very different architectures of either very limited or rather extended size were obtained depending on the building blocks used for the covalent linking process on the Au(111) surface. Electrical measurements were carried out by pulling individual molecular nodes with the tip of a scanning tunneling microscope. The results of this challenging procedure indicate subtle differences if the nodes are contacted at inequivalent termini., (© 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Here, we report the study of tautomerization within a single porphycene molecule adsorbed on a Cu(111) surface using low-temperature scanning tunneling microscopy (STM) at 5 K. While molecules are adsorbed on the surface exclusively in the thermodynamically stable trans tautomer after deposition, a voltage pulse from the STM can induce the unidirectional trans → cis and reversible cis ↔ cis tautomerization. From the voltage and current dependence of the tautomerization yield (rate), it is revealed that the process is induced by vibrational excitation via inelastic electron tunneling. However, the metastable cis molecules are thermally switched back to the trans tautomer by heating the surface up to 30 K. Furthermore, we have found that the unidirectional tautomerization can be remotely controlled at a distance from the STM tip. By analyzing the nonlocal process in dependence on various experimental parameters, a hot carrier-mediated mechanism is identified, in which hot electrons (holes) generated by the STM travel along the surface and induce the tautomerization through inelastic scattering with a molecule. The bias voltage and coverage dependent rate of the nonlocal tautomerization clearly show a significant contribution of the Cu(111) surface state to the hot carrier-induced process.

Molecular-scale electronics is mainly concerned by understanding charge transport through individual molecules. A key issue here is the charge transport capability through a single--typically linear--molecule, characterized by the current decay with increasing length. To improve the conductance of individual polymers, molecular design often either involves the use of rigid ribbon/ladder-type structures, thereby sacrificing for flexibility of the molecular wire, or a zero band gap, typically associated with chemical instability. Here we show that a conjugated polymer composed of alternating donor and acceptor repeat units, synthesized directly by an on-surface polymerization, exhibits a very high conductance while maintaining both its flexible structure and a finite band gap. Importantly, electronic delocalization along the wire does not seem to be necessary as proven by spatial mapping of the electronic states along individual molecular wires. Our approach should facilitate the realization of flexible 'soft' molecular-scale circuitry, for example, on bendable substrates.