Photoswitching Behavior of a Novel Single Molecular Tip for Noncontact Atomic Force Microscopy Designed for Chemical Identification

Atomic force microscopy applied to interrogate nanoscale cellular chemistry and supramolecular bond dynamics for biomedical applications

Understanding biological interactions at a molecular level grants valuable information relevant to improving medical treatments and outcomes. Among the suite of technologies available, Atomic Force Microscopy (AFM) is unique in its ability to quantitatively probe forces and receptor-ligand interactions in real-time. The ability to assess the formation of supramolecular bonds and intermediates in real-time on surfaces and living cells generates important information relevant to understanding biological phenomena. Combining AFM with fluorescence-based techniques allows for an unprecedented level of insight not only concerning the formation and rupture of bonds, but understanding medically relevant interactions at a molecular level. As the ability of AFM to probe cells and more complex models improves, being able to assess binding kinetics, chemical topographies, and garner spectroscopic information will likely become key to developing further improvements in fields such as cancer, nanomaterials, and virology. The rapid response to the COVID-19 crisis, producing information regarding not just receptor affinities, but also strain-dependent efficacy of neutralizing nanobodies, demonstrates just how viable and integral to the pre-clinical development of information AFM techniques are in this era of medicine.

Reactive-Oxygen-Species-Mediated Surface Oxidation of Single-Molecule DNA Origami by an Atomic Force Microscope Tip-Mounted C60 Photocatalyst

A tripod molecule incorporating a C₆₀ photocatalyst into a rigid scaffold with disulfide legs was designed and synthesized for the stable and robust attachment of C₆₀ onto an Au-coated atomic force microscope (AFM) tip. The "tripod-C₆₀" was immobilized onto the tip by forming S-Au bonds in the desired orientation and a dispersed manner, rendering it suitable for the oxidation and scission of single molecules on a countersurface, thereby functioning as "molecular shears". A DNA origami with a well-defined structure was chosen as the substrate for the tip-induced oxidation. The gold-coated, C₆₀-functionalized AFM tip was used for both AFM imaging and oxidation of DNA origami upon visible-light irradiation. The localized and temporally controlled oxidative damage of DNA origami was successfully performed at the single-molecule level via singlet-oxygen (¹O₂) generation from the immobilized C₆₀ on the AFM tip. This oxidative damage to DNA origami can be carried out under ambient conditions in a fluid cell at room temperature, rendering it well-suited for the manipulation of a variety of species on surfaces via a spatially and temporally controlled oxidation reaction triggered by ¹O₂ locally generated from the immobilized C₆₀ on the AFM tip.

Observation of Collective Photoswitching in Free-Standing TATA-Based Azobenzenes on Au(111)

Light-induced transitions between the trans and cis isomer of triazatriangulenium-based azobenzene derivatives on Au(111) surfaces were observed directly by scanning tunneling microscopy, allowing atomic-scale studies of the photoisomerization kinetics. Although the azobenzene units in these adlayers are free-standing and spaced at uniform distances of 1.26 nm, their photoswitching depends on the isomeric state of the surrounding molecules and, specifically, is accelerated by neighboring cis isomers. These collective effects are supported by ab initio calculations indicating that the electronic excitation preferably localizes on the n-π* state of trans isomers with neighboring cis azobenzenes.

Reversible Photoswitching and Isomer-Dependent Diffusion of Single Azobenzene Tetramers on a Metal Surface

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.

Spatial and Lateral Control of Functionality by Rigid Molecular Platforms

Surface mounted molecular devices have received significant attention in the scientific community because of their unique ability to construct functional materials. The key involves the platform on which the molecular device works on solid substrates, such as in solid-liquid or solid-vacuum interfaces. Here, we outline the concept of rigid molecular platforms to immobilize active functionality atop flat surfaces in a controllable manner. Most of these (multipodal) platforms have at least three anchoring groups to control the spatial arrangement of the protruding functional moieties and form mechanically stable and electronically tuned contacts to the underlying substrate. Another approach is based on employing of flat aromatic scaffolds bearing perpendicular functionalities that form stable lateral assemblies on various surfaces. Emphasis is placed on the need for controllable assembly and separation of these tailor-made molecules that expose functionalities at the molecular scale. The discussions are focused on the different molecular designs realizing functional 3D architectures on surfaces, the role of various anchoring strategies to control the spatial arrangement, and structural considerations controlling physical features like the coupling to the surface or the available space for sterically demanding molecular operations.

Identification of the current path for a conductive molecular wire on a tripodal platform

We present the chemical synthesis as well as charge transport measurements and calculations for a new tripodal platform based on a rigid 9,9'-spirobifluorene equipped with a phenylene-ethynylene wire. The transport experiments are performed with the help of the low-temperature mechanically controlled break junction technique with gold electrodes. By combining experimental and theoretical investigations of elastic and inelastic charge transport, we show that the current proceeds through the designated molecular wire and identify a binding geometry that is compatible with the experimental observations. The conductive molecular wire on the platform features a well-defined and relatively high conductance of the order of 10(-3)G0 despite the length of the current path of more than 1.7 nm, demonstrating that this platform is suitable to incorporate functional units like molecular switches or sensors.

Rigid multipodal platforms for metal surfaces

In this review the recent progress in molecular platforms that form rigid and well-defined contact to a metal surface are discussed. Most of the presented examples have at least three anchoring units in order to control the spatial arrangement of the protruding molecular subunit. Another interesting feature is the lateral orientation of these foot structures which, depending on the particular application, is equally important as the spatial arrangement of the molecules. The numerous approaches towards assembling and organizing functional molecules into specific architectures on metal substrates are reviewed here. Particular attention is paid to variations of both, the core structures and the anchoring groups. Furthermore, the analytical methods enabling the investigation of individual molecules as well as monomolecular layers of ordered platform structures are summarized. The presented multipodal platforms bearing several anchoring groups form considerably more stable molecule-metal contacts than corresponding monopodal analogues and exhibit an enlarged separation of the functional molecules due to the increased footprint, as well as restrict tilting of the functional termini with respect to the metal surface. These platforms are thus ideally suited to tune important properties of the molecule-metal interface. On a single-molecule level, several of these platforms enable the control over the arrangement of the protruding rod-type molecular structures (e.g., molecular wires, switches, rotors, sensors) with respect to the surface of the substrate.

Versatile method for AFM-tip functionalization with biomolecules: fishing a ligand by means of an in situ click reaction

A facile and universal method for the functionalization of an AFM tip has been developed for chemical force spectroscopy (CFS) studies of intermolecular interactions of biomolecules. A click reaction between tripod-acetylene and an azide-linker-ligand molecule was successfully carried out on the AFM tip surface and used for the CFS study of ligand-receptor interactions.

Design of novel luminescent porphyrins bearing donor–acceptor groups

In this work, we report the synthesis and characterization of a novel series of porphyrins, some of them bearing donor-acceptor groups. meso-substituted free-base porphyrins:5-(4-amino-phenyl)-10,15,20-triphenylporphyrin (TPPNH2) and 5-(4-acetamidophenyl)-10,15,20-triphenylporphyrin (TPPNHAc), as well as their tribromo (Br3TPPNH2 and Br3TPPNHAc) and trimethylsilyl-substituted homologs (TMS3TPPNH2 and TMS3TPPNHAc were synthesized and characterized. The optical properties of all compounds have been studied by absorption and fluorescence spectroscopy. Theoretical calculations were performed in order to recognize the optimized geometry and the correlation with the optical properties. On the other hand, an azobenzene containing porphyrin (TPPN2PhC14H29) was also prepared to study the influence of the trans-cis photoisomerization on its optical properties. Almost all porphyrin derivatives exhibited a Soret band at ca. λ = 419–422 nm followed by four Q-bands in the range between 500–700 nm. Besides, these porphyrins showed two emission bands located at ca. λ = 654 nm and 714 nm with different intensities, depending on the substituents. The relative quantum yields were calculated for these compounds with respect to the most emissive species.

Theoretical study of novel azo-tetraphenylporphyrins: potential photovoltaic materials

A density functional theory study was performed to analyze the electron donor-acceptor properties of the cis and trans isomers of a novel azobenzene-containing tetraphenylporphyrin (TPPN2PhC14H29) with different substituents (Br or TMS). In general, the trans isomers are better electron acceptors than the correspondent cis homologues. Their UV-vis spectra were also obtained and a comparison with available experimental results is included. According to these results, the azo compounds reported here are promising materials for the elaboration of dye-sensitized solar cells because their HOMO-LUMO gaps are close to 2 eV. Moreover, the energy of the high intensity absorption bands also fulfills the requirements needed for the operation of a solar cell built with TiO2 and the I(-)/I3(-) pair.

A tripodal molecule on a gold surface: orientation-dependent coupling and electronic properties of the molecular legs

The realization of molecular electronics demands a detailed knowledge of the correlation between chemical groups and electronic function. It has become obvious during the last years that the conformation of a molecule and its coupling to the connecting electrodes plays a crucial role in its conductance behavior and its electronic function, e.g., as a switch. Knowledge about these relationships is therefore essential for future design of molecular electronic building blocks. We present a new three-dimensional molecule, consisting of three identical molecular wires connected to a headgroup. Due to the well-defined spatial arrangement of the molecule in a nonplanar geometry, it is possible to investigate the conductance behavior of these wires with respect to their position and coupling to the surface electrode with the submolecular resolution of a scanning tunneling microscope. The experimental findings are supported by calculations of the electronic structure and conformation of the molecule on the surface by density functional theory with dispersion corrections.

Molecular motions in functional self-assembled nanostructures

The construction of "smart" materials able to perform specific functions at the molecular scale through the application of various stimuli is highly attractive but still challenging. The most recent applications indicate that the outstanding flexibility of self-assembled architectures can be employed as a powerful tool for the development of innovative molecular devices, functional surfaces and smart nanomaterials. Structural flexibility of these materials is known to be conferred by weak intermolecular forces involved in self-assembly strategies. However, some fundamental mechanisms responsible for conformational lability remain unexplored. Furthermore, the role played by stronger bonds, such as coordination, ionic and covalent bonding, is sometimes neglected while they can be employed readily to produce mechanically robust but also chemically reversible structures. In this review, recent applications of structural flexibility and molecular motions in self-assembled nanostructures are discussed. Special focus is given to advanced materials exhibiting significant performance changes after an external stimulus is applied, such as light exposure, pH variation, heat treatment or electromagnetic field. The crucial role played by strong intra- and weak intermolecular interactions on structural lability and responsiveness is highlighted.

Optically and thermally induced molecular switching processes at metal surfaces

Using light to control the switching of functional properties of surface-bound species is an attractive strategy for the development of new technologies with possible applications in molecular electronics and functional surfaces and interfaces. Molecular switches are promising systems for such a route, since they possess the ability to undergo reversible changes between different molecular states and accordingly molecular properties by excitation with light or other external stimuli. In this review, recent experiments on photo- and thermally induced molecular switching processes at noble metal surfaces utilizing two-photon photoemission and surface vibrational spectroscopies are reported. The investigated molecular switches can either undergo a trans-cis isomerization or a ring opening-closure reaction. Two approaches concerning the connection of the switches to the surface are applied: physisorbed switches, i.e. molecules in direct contact with the substrate, and surface-decoupled switches incorporated in self-assembled monolayers. Elementary processes in molecular switches at surfaces, such as excitation mechanisms in photoisomerization and kinetic parameters for thermally driven reactions, which are essential for a microscopic understanding of molecular switching at surfaces, are presented. This in turn is needed for designing an appropriate adsorbate-substrate system with the desired switchable functionality controlled by external stimuli.

Effects of peripheral blood mononuclear cells morphology on vascular calcification in uremic patients on maintenance hemodialysis

We used high-resolution atomic force microscopy (AFM) to examine possible changes in the morphology of peripheral blood mononuclear cells (PBMCs), and to investigate their influence on vascular calcification in uremic patients on maintenance hemodialysis (MHD). 36 uremic patients had cardiovascular diseases after MHD (MHD group1) and 30 uremic patients did not (MHD group 2), and 20 healthy volunteers were the control group. The extent of coronary artery calcification was assessed with coronary artery calcification score (CACS). AFM was used to analyze PBMCs nuances. Concentrations of bone morphogenetic protein-2 (BMP-2) in PBMC supernatants were detected by ELISA. Protein expressions of BMP-2 were measured by Western blot. No significant differences in PBMC morphology were observed among groups by light microscopy. AFM images revealed that uremic patients exhibited significant differences of PBMC morphology and vascular calcification when compared with healthy volunteers. The PBMCs in uremic patients were larger in volume, mean height, half-maximum amplitude, average roughness and higher concentrations and expression of BMP-2 and CACS (P < 0.05), with granular processes or caveolae of uneven size distributed over cell surfaces. These differences were also significant between MHD group 1 and group 2 (P < 0.05). PBMC volume, mean height, half-maximum amplitude, and average roughness were positively correlated with BMP-2 and CACS. Moreover, the correlation PBMC with BMP-2 was higher than with CACS. PBMC morphology in MHD patients was related to the degree of vascular calcification. The larger mean height, half-maximum amplitude, average roughness and cell volume were, the higher degree of vascular calcification was.

Recent trends in surface characterization and chemistry with high-resolution scanning force methods

The current status and future prospects of non-contact atomic force microscopy (nc-AFM) and Kelvin probe force microscopy (KPFM) for studying insulating surfaces and thin insulating films in high resolution are discussed. The rapid development of these techniques and their use in combination with other scanning probe microscopy methods over the last few years has made them increasingly relevant for studying, controlling, and functionalizing the surfaces of many key materials. After introducing the instruments and the basic terminology associated with them, state-of-the-art experimental and theoretical studies of insulating surfaces and thin films are discussed, with specific focus on defects, atomic and molecular adsorbates, doping, and metallic nanoclusters. The latest achievements in atomic site-specific force spectroscopy and the identification of defects by crystal doping, work function, and surface charge imaging are reviewed and recent progress being made in high-resolution imaging in air and liquids is detailed. Finally, some of the key challenges for the future development of the considered fields are identified.

Photoswitching tripodal single molecular tip for noncontact AFM measurements: synthesis, immobilization, and reversible configurational change on gold surface

Tripodal molecules consisting of a tetrasubstituted adamantane with three phenylacetylene legs and a reversibly photoswitching apex were designed as "single molecular tips" for both chemical and topographical characterization of the substrate surface. By covalent attachment onto gold-coated AFM tips through three S-Au bonds, these rigid tripodal molecules are expected to act as sharp, robust, and stationary molecular tips whose configuration can be reversibly changed upon irradiation with UV or visible light. In this report, the full account of the syntheses of two photoswitching tripodal molecular tips, their immobilization onto Au(111) surfaces, and the detection of photoinduced configurational change on Au(111) surface by SPM measurements are documented.

A tripod molecular tip for single molecule ligand-receptor force spectroscopy by AFM

Tripod-shaped molecules were designed for chemical modification of the surface of probes used for atomic force microscopy (AFM). These chemically functionalized tips were used for chemical force spectroscopy (CFS) measurements of the ligand-protein receptor interaction in a biotin-NeutrAvidin model system. We demonstrate that by using this unique tripodal system, we can achieve significantly lower density of ligand on the AFM tip apex, which is optimal for true single molecule measurements. Furthermore, the molecular tripods form highly stable bonds to the AFM probes, leading to more robust and reproducible unbinding force data, thereby addressing one of the challenges in CFS studies. Histogram analysis of the hundreds of collected unbinding forces showed a specific distribution with a peak force maximum at approximately 165 pN, in good agreement with the previously reported data of single rupture events of biotin-avidin. We compared these molecular tripod tips with a molecular monopod. The results showed that the molecular tripods are more robust for repeated measurements. The distinct biotin-avidin force maximum was not observed in the control experiments. This indicated that the force distribution observed for molecular tripods corresponds to the specific rupture force between biotin and avidin. The improved robustness of molecular tripods for CFS will provide benefits in other ligand-receptor unbinding studies, including those of transmembrane receptor systems, which require high resolution, sensitivity, and reproducibility in force spectroscopy measurements.

Tripodal Binding Units for Self-Assembled Monolayers on Gold: A Comparison of Thiol and Thioether Headgroups

Whereas thiols and thioethers are frequently used as binding units of oligodentate precursor molecules to fabricate self-assembled monolayers (SAMs) on coinage metal and semiconductor surfaces, their use for tridentate bonding configuration is still questionable. Against this background, novel tridentate thiol ligands, PhSi(CH(2)SH)(3) (PTT) and p-Ph-C(6)H(4)Si(CH(2)SH)(3) (BPTT), were synthesized and used as tripodal adsorbate molecules for the fabrication of SAMs on Au(111). These SAMs were characterized by X-ray photoelectron spectroscopy (XPS) and near edge X-ray absorption fine structure (NEXAFS) spectroscopy. The PTT and BPTT films were compared with the analogous systems comprised of same tripodal ligands with thioether instead of thiol binding units (anchors). XPS and NEXAFS data suggest that the binding uniformity, packing density, and molecular alignment of the thiol-based ligands in the respective SAMs is superior to their thioether counterparts. In addition, the thiol-based films showed significantly lower levels of contamination. Significantly, the quality of the PTT SAMs on Au(111) was found to be even higher than that of the films formed from the respective monodentate counterpart, benzenethiol. The results obtained allow for making some general conclusions on the specific character of molecular self-assembly in the case of tridentate ligands.

Mounting freestanding molecular functions onto surfaces: the platform approach

A modular system has been developed to mount molecules upright onto metal surfaces in a well controlled geometry. The approach is based on a reactive platform (triazatriangulenium salt) with an electrophilic center. Functional molecules are attached via C-C bond formation. The distance from the surface can be varied by a spacer, and the distance of the functional units from each other by the size of the platform. Self-assembly of the parent triazaangulenium salt as well as the functionalized platforms on Au(111) surfaces results in stable, hexagonally ordered adlayers.

Correlation between the molecular structure and photoresponse in aliphatic self-assembled monolayers with azobenzene tailgroups

We have compared the structural and photoisomerization properties of self-assembled monolayers (SAMs) comprising either the trans or cis isomers of azobenzene terminated dithiolane with in-chain amide unit, viz., 4-(phenyldiazenyl)phenyl-4-(1,2-dithiolane-3-yl)-butylcarboxamide ( 1). These films were prepared on Au(111) from solutions of both isomers. Structure and composition of the SAMs were studied by X-ray photoelectron spectroscopy and near-edge X-ray absorption fine structure spectroscopy. The photoresponse of the films was monitored in real time by ellipsometry. SAMs fabricated from the trans isomer were found to be densely packed and highly ordered. These films did not show any discernible photoresponse upon irradiation with UV light, which, under favorable conditions, triggers the trans- cis isomerization. In contrast, films prepared from solutions containing predominantly the cis isomer were loosely packed and mostly disordered but exhibited reversible photoreactivity. The results confirm that steric effects, i.e., available free volume, play a dominant role for the photoresponse of aliphatic SAMs bearing the photoactive azobenzene group. The crystal structure of 1 ( trans isomer) exhibits a row-like aggregation of neighboring molecules by weak hydrogen bonds and can be taken as a model for the arrangement of 1 in the monolayer films. Further, in addition to the surface coordination behavior, we have also mimicked the chemisorption of the 1,2-dithiolane moiety onto the gold substrate in molecular coordination chemistry in oxidative addition reactions with the zero-valent platinum complex [Pt(PPh 3) 4].

Self-assembled two-dimensional ordered arrays of tripod-type molecules on graphite

Tripod-type molecules with long alkyl chains, 1,1,1-tris(4-alkoxyphenyl)ethanes with octadecyloxy or docosyloxy chains, self-assemble into two-dimensional crystallites on drop-casting onto the surface of highly oriented pyrolytic graphite. In the two-dimensional crystalline domain, the molecules are organized in a mortise-and-tenon motif, as revealed by scanning tunneling microscopy. The time evolution of the crystallite formation has been followed by the dynamic force mode atomic force microscopy. The tripods may be used as a basis for the extension of a two-dimensional order into three-dimensional molecular architectures.