Chirality Detection in Scanning Tunneling Microscopy Data Using Artificial Intelligence.

Enantiospecific effects play an uprising role in chemistry and technical applications. Chiral molecular networks formed by self-assembly processes at surfaces can be imaged by scanning probe microscopy (SPM). Low contrast and high noise in the topography map often interfere with the automatic image analysis using classical methods. The long SPM image acquisition times restrain Artificial Intelligence-based methods requiring large training sets, leaving only tedious manual work, inducing human-dependent errors and biased labeling. By generating realistic looking synthetic images, the acquisition of real datasets is avoided. Two state-of-the-art object detection architectures are trained to localize and classify chiral unit-cells in a regular molecular chiral network formed by self-assembly of linear molecular bricks. The comparison of different architectures and datasets demonstrates that the training on purely synthetic data outperforms models trained using augmented datasets. A Faster R-CNN model trained solely on synthetic data achieved an excellent mean average precision of 99% on real data. Hence this approach and the transfer to real data show high success, also highlighting the high robustness against experimental noise and different zoom levels across the full experimentally reasonable parameter range. The generalizability of this idea is demonstrated by achieving equally high performance on a different structure, too.

Organic Molecular Glues to Design Three-Dimensional Cubic Nano-assemblies of Magnetic Nanoparticles.

Self-assembled magnetic nanoparticles offer next-generation materials that allow harnessing of their physicochemical properties for many applications. However, how three-dimensional nanoassemblies of magnetic nanoparticles can be synthesized in one-pot synthesis without excessive postsynthesis processes is still a bottleneck. Here, we propose a panel of small organic molecules that glue nanoparticle crystallites during the growth of particles to form large nanoassembled nanoparticles (NANs). We find that both carbonyl and carboxyl functional groups, presenting in benzaldehyde and benzoic acid, respectively, are needed to anchor with metal ions, while aromatic rings are needed to create NANs through π-π stacking. When benzyl alcohol, lacking carbonyl and carboxyl groups, is employed, no NANs are formed. NANs formed by benzoic acid reveal a unique combination of high magnetization and coercivity, whereas NANs formed by benzaldehyde show the largest exchange bias reported in nanoparticles. Surprisingly, our NANs show unconventional colloidal stability due to their unique nanoporous architectures.

Controlling Nanoparticle Distance by On-Surface DNA-Origami Folding.

DNA origami is a flexible platform for the precise organization of nano-objects, enabling numerous applications from biomedicine to nano-photonics. Its huge potential stems from its high flexibility that allows customized structures to meet specific requirements. The ability to generate diverse final structures from a common base by folding significantly enhances design variety and is regularly occurring in liquid. This study describes a novel approach that combines top-down lithography with bottom-up DNA origami techniques to control folding of the DNA origami with the adsorption on pre-patterned surfaces. Using this approach, tunable plasmonic dimer nano-arrays are fabricated on a silicon surface. This involves employing electron beam lithography to create adsorption sites on the surface and utilizing self-organized adsorption of DNA origami functionalized with two gold nanoparticles (AuNPs). The desired folding of the DNA origami helices can be controlled by the size and shape of the adsorption sites. This approach can for example be used to tune the center-to-center distance of the AuNPs dimers on the origami template. To demonstrate this technique's efficiency, the Raman signal of dye molecules (carboxy tetramethylrhodamine, TAMRA) coated on the AuNPs surface are investigated. These findings highlight the potential of tunable DNA origami-based plasmonic nanostructures for many applications.

Positional control of DNA origami based gold dimer hybrid nanostructures on pre-structured surfaces.

This study explores important parameters for achieving a high-level positional control of DNA-nanoparticle hybrid structures by drop-casting onto a pre-structured silicon surface, in which the active adsorption sites were defined using electron beam lithography. By confining the adsorption sites to the scale of the DNA origami, we create multi-dimensional patterns and study the effect of diffusion and hybrid nanostructure concentration in the liquid on site occupation. We also propose a physical diffusion model that highlights the importance of surface diffusion in facilitating the adsorption of hybrid nanostructure onto active sites, particularly for two and one-dimensional adsorption sites. Our study shows prominent results of the hybrid nanostructure's selective adsorption, indicating high adsorption efficiency and precise control over the position, as well as the spatial orientation. We anticipate similar results in related systems, both in terms of different surfaces and similar DNA structures. Overall, our findings offer promising prospects for the development of large-scale nanoarrays on micrometer-scale surfaces with nanometer precision and orientation control.

Biosynthesis of bifunctional silver nanoparticles for catalytic reduction of organic pollutants and optical monitoring of mercury (II) ions using their oxidase-mimic activity.

In this study, an aqueous extract of Sclerocarya birrea leaves was used as a reducing agent to synthesize silver nanoparticles (AgNPs). The synthesis was carried out at room temperature and was both rapid and simple. Different characterization techniques such as UV/visible spectroscopy, surface-enhanced Raman spectroscopy, X-ray diffraction, and focused ion beam scanning electron microscopy were used to confirm the formation of AgNPs. The synthesized nanoparticles exhibited catalytic activity for the reduction of 4-nitrophenol, methyl orange, methylene blue, and rhodamine 6G. The catalytic activity was monitored by measuring the UV/visible absorbance spectra of the compounds using sodium borohydride as a reducing agent and found to be high. Additionally, the particles displayed oxidase-like activity. In the presence of AgNPs, 3, 3', 5, 5'-tetramethylbenzidine (TMB) which is colorless was transformed to oxidized TMB, which is blue, using dissolved oxygen as the oxidant. In the presence of Hg2+, the oxidase-like activity was enhanced. On the basis of this observation, an assay for the analysis of Hg2+ was developed. The linear range of the calibration curve is wide (0-600 µM) and the limit of detection (LOD) is low, as small as 34.8 nM. The method is strongly selective towards Hg2+. Tap water obtained from the laboratory where these experiments were carried out was used to study the feasibility of the method in real sample analyses.

Point-of-need detection of pathogen-specific nucleic acid targets using magnetic particle spectroscopy.

The ongoing COVID-19 pandemic stresses the need for widely available diagnostic tests for the presence of SARS-CoV-2 in individuals. Due to the limited availability of vaccines, diagnostic assays which are cheap, easy-to-use at the point-of-need, reliable and fast, are currently the only way to control the pandemic situation. Here we present a diagnostic assay for the detection of pathogen-specific nucleic acids based on changes of the magnetic response of magnetic nanoparticles: The target-mediated hybridization of modified nanoparticles leads to an increase in the hydrodynamic radius. This resulting change in the magnetic behaviour in an ac magnetic field can be measured via magnetic particle spectroscopy (MPS), providing a viable tool for the accurate detection of target nucleic acids. In this work we show that single stranded DNA can be detected in a concentration-dependent manner by these means. In addition to detecting synthetic DNA with an arbitrary sequence in a concentration down to 500 pM, we show that RNA and SARS-CoV-2-specific DNA as well as saliva as a sample medium can be used for an accurate assay. These proof-of-principle experiments show the potential of MPS based assays for the reliable and fast diagnostics of pathogens like SARS-CoV-2 in a point-of-need fashion without the need of complex sample preparation.

Gigahertz Frame Rate Imaging of Charge-Injection Dynamics in a Molecular Light Source.

Light sources on the scale of single molecules can be addressed and characterized at their proper sub-nanometer scale by scanning tunneling microscopy-induced luminescence (STML). Such a source can be driven by defined short charge pulses while the luminescence is detected with sub-nanosecond resolution. We introduce an approach to concurrently image the molecular emitter, which is based on an individual defect, with its local environment along with its luminescence dynamics at a resolution of a billion frames per second. The observed dynamics can be assigned to the single electron capture occurring in the low-nanosecond regime. While the emitter's location on the surface remains fixed, the scanning of the tip modifies the energy landscape for charge injection into the defect. The principle of measurement is extendable to fundamental processes beyond charge transfer, like exciton diffusion.

Dynamical Coulomb Blockade as a Local Probe for Quantum Transport.

Quantum fluctuations are imprinted with valuable information about transport processes. Experimental access to this information is possible, but challenging. We introduce the dynamical Coulomb blockade (DCB) as a local probe for fluctuations in a scanning tunneling microscope (STM) and show that it provides information about the conduction channels. In agreement with theoretical predictions, we find that the DCB disappears in a single-channel junction with increasing transmission following the Fano factor, analogous to what happens with shot noise. Furthermore we demonstrate local differences in the DCB expected from changes in the conduction channel configuration. Our experimental results are complemented by ab initio transport calculations that elucidate the microscopic nature of the conduction channels in our atomic-scale contacts. We conclude that probing the DCB by STM provides a technique complementary to shot noise measurements for locally resolving quantum transport characteristics.

Stability of metallo-porphyrin networks under oxygen reduction and evolution conditions in alkaline media.

Transition metal atoms stabilised by organic ligands or as oxides exhibit promising catalytic activity for the electrocatalytic reduction and evolution of oxygen. Built-up from earth-abundant elements, they offer affordable alternatives to precious-metal based catalysts for application in fuel cells and electrolysers. For the understanding of a catalyst's activity, insight into its structure on the atomic scale is of highest importance, yet commonly challenging to experimentally access. Here, the structural integrity of a bimetallic iron tetrapyridylporphyrin with co-adsorbed cobalt electrocatalyst on Au(111) is investigated using scanning tunneling microscopy and X-ray absorption spectroscopy. Topographic and spectroscopic characterization reveals structural changes of the molecular coordination network after oxygen reduction, and its decomposition and transformation into catalytically active Co/Fe (oxyhydr)oxide during oxygen evolution. The data establishes a structure-property relationship for the catalyst as a function of electrochemical potential and, in addition, highlights how the reaction direction of electrochemical interconversion between molecular oxygen and hydroxyl anions can have very different effects on the catalyst's structure.

On-surface transmetalation of metalloporphyrins.

Increasing the complexity of 2D metal-organic networks has led to the fabrication of structures with interesting magnetic and catalytic properties. However, increasing complexity by providing different coordination environments for different metal types imposes limitations on their synthesis if the controlled placement of one metal type into one coordination environment is desired. Whereas metal insertion into free-base porphyrins at the vacuum/solid interface has been thoroughly studied, providing detailed insight into the mechanisms at play, the chemical interaction of a metal atom with a metallated porphyrin is rarely investigated. Herein, the breadth of metalation reactions is augmented towards the metal exchange of a metalloporphyrin through the deliberate addition of atomic metal centers. The cation of Fe(ii)-tetraphenylporphyrins can be replaced by Co in a redox transmetalation-like reaction on a Au(111) surface. Likewise, Cu can be replaced by Co. The reverse reaction does not occur, i.e. Fe does not replace Co in the porphyrin. This non-reversible exchange is investigated in detail by X-ray absorption spectroscopy complemented by scanning tunneling microscopy. Density functional theory illuminates possible reaction pathways and leads to the conclusion that the transmetalation proceeds through the adsorption of initially metallic (neutral) Co onto the porphyrin and the expulsion of Fe towards the surface accompanied by Co insertion. Our findings have important implications for the fabrication of porphyrin layers on surfaces when subject to the additional deposition of metals. Mixed-metal porphyrin layers can be fabricated by design in a solvent-free process, but conversely care must be taken that the transmetalation does not proceed as an undesired side reaction.

Single Charge and Exciton Dynamics Probed by Molecular-Scale-Induced Electroluminescence.

Excitons and their constituent charge carriers play the central role in electroluminescence mechanisms determining the ultimate performance of organic optoelectronic devices. The involved processes and their dynamics are often studied with time-resolved techniques limited by spatial averaging that obscures the properties of individual electron-hole pairs. Here, we overcome this limit and characterize single charge and exciton dynamics at the nanoscale by using time-resolved scanning tunneling microscopy-induced luminescence (TR-STML) stimulated with nanosecond voltage pulses. We use isolated defects in C60 thin films as a model system into which we inject single charges and investigate the formation dynamics of a single exciton. Tunable hole and electron injection rates are obtained from a kinetic model that reproduces the measured electroluminescent transients. These findings demonstrate that TR-STML can track dynamics at the quantum limit of single charge injection and can be extended to other systems and materials important for nanophotonic devices.

Quantum Brownian Motion at Strong Dissipation Probed by Superconducting Tunnel Junctions.

We have investigated the phase dynamics of a superconducting tunnel junction at ultralow temperatures in the presence of high damping, where the interaction with environmental degrees of freedom represents the leading energy scale. In this regime, theory predicts the dynamics to follow a generalization of the classical Smoluchowski description, the quantum Smoluchowski equation, thus, exhibiting overdamped quantum Brownian motion characteristics. For this purpose, we have performed current-biased measurements on the small-capacitance Josephson junction of a scanning tunneling microscope placed in a low impedance environment at milli-Kelvin temperatures. We can describe our experimental findings with high accuracy by using a quantum phase diffusion model based on the quantum Smoluchowski equation. In this way we experimentally demonstrate that overdamped quantum systems follow quasiclassical dynamics with significant quantum effects as the leading corrections.

Sensing the quantum limit in scanning tunnelling spectroscopy.

The tunnelling current in scanning tunnelling spectroscopy (STS) is typically and often implicitly modelled by a continuous and homogeneous charge flow. If the charging energy of a single-charge quantum sufficiently exceeds the thermal energy, however, the granularity of the current becomes non-negligible. In this quantum limit, the capacitance of the tunnel junction mediates an interaction of the tunnelling electrons with the surrounding electromagnetic environment and becomes a source of noise itself, which cannot be neglected in STS. Using a scanning tunnelling microscope operating at 15 mK, we show that we operate in this quantum limit, which determines the ultimate energy resolution in STS. The P(E)-theory describes the probability for a tunnelling electron to exchange energy with the environment and can be regarded as the energy resolution function. We experimentally demonstrate this effect with a superconducting aluminium tip and a superconducting aluminium sample, where it is most pronounced.

Restoring the Co magnetic moments at interfacial Co-porphyrin arrays by site-selective uptake of iron.

Magnetochemistry recently emerged as a promising approach to control addressable spin arrays on surfaces. Here we report on the binding, spatial ordering, and magnetic properties of Fe on a highly regular Co-tetraphenylporphyrin (Co-TPP) template and highlight how the Fe controls the magnetism of the Co centers. As evidenced by scanning tunneling microscopy (STM) single Fe atoms attach to the saddle-shape conformers site-selectively in a unique coordination environment offered through a heptamer defined by the Co-N-C-C-C-N cyclic subunit. While the magnetic moment of Co is quenched for bare Co-TPP/Ag(111), the Fe presence revives it. Our X-ray magnetic circular dichroism (XMCD) experiments, complemented by density functional theory (DFT) calculations, evidence a ferromagnetic coupling between the Fe and the Co center concomitant with a complex charge redistribution involving the porphyrin ligand. Thus, we demonstrate an unusual metalloporphyrin coordination geometry that opens pathways to spatially order and engineer magnetic moments in surface-based nanostructures.

Probing absolute spin polarization at the nanoscale.

Probing absolute values of spin polarization at the nanoscale offers insight into the fundamental mechanisms of spin-dependent transport. Employing the Zeeman splitting in superconducting tips (Meservey-Tedrow-Fulde effect), we introduce a novel spin-polarized scanning tunneling microscopy that combines the probing capability of the absolute values of spin polarization with precise control at the atomic scale. We utilize our novel approach to measure the locally resolved spin polarization of magnetic Co nanoislands on Cu(111). We find that the spin polarization is enhanced by 65% when increasing the width of the tunnel barrier by only 2.3 Å due to the different decay of the electron orbitals into vacuum.

Dynamic control of plasmon generation by an individual quantum system.

Controlling light on the nanoscale in a similar way as electric currents has the potential to revolutionize the exchange and processing of information. Although light can be guided on this scale by coupling it to plasmons, that is, collective electron oscillations in metals, their local electronic control remains a challenge. Here, we demonstrate that an individual quantum system is able to dynamically gate the electrical plasmon generation. Using a single molecule in a double tunnel barrier between two electrodes we show that this gating can be exploited to monitor fast changes of the quantum system itself and to realize a single-molecule plasmon-generating field-effect transistor operable in the gigahertz range. This opens new avenues toward atomic scale quantum interfaces bridging nanoelectronics and nanophotonics.

Short-term acute hypercapnia affects cellular responses to trace metals in the hard clams Mercenaria mercenaria.

Estuarine and coastal habitats experience large fluctuations of environmental factors such as temperature, salinity, partial pressure of CO2 ( [Formula: see text] ) and pH; they also serve as the natural sinks for trace metals. Benthic filter-feeding organisms such as bivalves are exposed to the elevated concentrations of metals in estuarine water and sediments that can strongly affect their physiology. The effects of metals on estuarine organisms may be exacerbated by other environmental factors. Thus, a decrease in pH caused by high [Formula: see text] (hypercapnia) can modulate the effects of trace metals by affecting metal bioavailability, accumulation or binding. To better understand the cellular mechanisms of interactions between [Formula: see text] and trace metals in marine bivalves, we exposed isolated mantle cells of the hard clams (Mercenaria mercenaria) to different levels of [Formula: see text] (0.05, 1.52 and 3.01 kPa) and two major trace metal pollutants - cadmium (Cd) and copper (Cu). Elevated [Formula: see text] resulted in a decrease in intracellular pH (pHi) of the isolated mantle cells from 7.8 to 7.4. Elevated [Formula: see text] significantly but differently affected the trace metal accumulation by the cells. Cd uptake was suppressed at elevated [Formula: see text] levels while Cu accumulation has greatly accelerated under hypercapnic conditions. Interestingly, at higher extracellular Cd levels, labile intracellular Cd(2+) concentration remained the same, while intracellular levels of free Zn(2+) increased suggesting that Cd(2+) substitutes bound Zn(2+) in these cells. In contrast, Cu exposure did not affect intracellular Zn(2+) but led to a profound increase in the intracellular levels of labile Cu(2+) and Fe(2+). An increase in the extracellular concentrations of Cd and Cu led to the elevated production of reactive oxygen species under the normocapnic conditions (0.05 kPa [Formula: see text] ); surprisingly, this effect was mitigated in hypercapnia (1.52 and 3.01 kPa). Overall, our data reveal complex and metal-specific interactions between the cellular effects of trace metals and [Formula: see text] in clams and indicate that variations in environmental [Formula: see text] may modulate the biological effects of trace metals in marine organisms.

A 10 mK scanning tunneling microscope operating in ultra high vacuum and high magnetic fields.

We present design and performance of a scanning tunneling microscope (STM) that operates at temperatures down to 10 mK providing ultimate energy resolution on the atomic scale. The STM is attached to a dilution refrigerator with direct access to an ultra high vacuum chamber allowing in situ sample preparation. High magnetic fields of up to 14 T perpendicular and up to 0.5 T parallel to the sample surface can be applied. Temperature sensors mounted directly at the tip and sample position verified the base temperature within a small error margin. Using a superconducting Al tip and a metallic Cu(111) sample, we determined an effective temperature of 38 ± 1 mK from the thermal broadening observed in the tunneling spectra. This results in an upper limit for the energy resolution of ΔE = 3.5 kBT = 11.4 ± 0.3 µeV. The stability between tip and sample is 4 pm at a temperature of 15 mK as demonstrated by topography measurements on a Cu(111) surface.

Large band gap opening between graphene Dirac cones induced by Na adsorption onto an Ir superlattice.

We investigate the effects of Na adsorption on the electronic structure of bare and Ir cluster superlattice-covered epitaxial graphene on Ir(111) using angle-resolved photoemission spectroscopy and scanning tunneling microscopy. At Na saturation coverage, a massive charge migration from sodium atoms to graphene raises the graphene Fermi level by ~1.4 eV relative to its neutrality point. We find that Na is adsorbed on top of the graphene layer, and when coadsorbed onto an Ir cluster superlattice, it results in the opening of a large band gap of Δ(Na/Ir/G) = 740 meV, comparable to the one of Ge and with preserved high group velocity of the charge carriers.

Top-down control analysis of the cadmium effects on molluscan mitochondria and the mechanisms of cadmium-induced mitochondrial dysfunction.

Cadmium (Cd) is a toxic metal and an important environmental pollutant that can strongly affect mitochondrial function and bioenergetics in animals. We investigated the mechanisms of Cd action on mitochondrial function of a marine mollusk (the eastern oyster Crassostrea virginica) by performing a top-down control analysis of the three major mitochondrial subsystems (substrate oxidation, proton leak, and phosphorylation). Our results showed that the substrate oxidation and proton leak subsystems are the main targets for Cd toxicity in oyster mitochondria. Exposure to 12.5 µM Cd strongly inhibited the substrate oxidation subsystem and stimulated the proton conductance across the inner mitochondrial membrane. Proton conductance was also elevated and substrate oxidation inhibited by Cd in the presence of a mitochondrially targeted antioxidant, MitoVitE, indicating that Cd effects on these subsystems were to a large extent ROS independent. Cd did not affect the kinetics of the phosphorylation system, indicating that it has negligible effects on F1, F(O) ATP synthase and/or the adenine nucleotide transporter in oyster mitochondria. Cd exposure altered the patterns of control over mitochondrial respiration, increasing the degree of control conferred by the substrate oxidation subsystem, especially in resting (state 4) mitochondria. Taken together, these data suggest that Cd-induced decrease of mitochondrial efficiency and ATP production are predominantly driven by the high sensitivity of substrate oxidation and proton leak subsystems to this metal.