Playing catch and release with single molecules: mechanistic insights into plasmon-controlled nanogaps

Single-molecule (SM) detection is essential for investigating processes at the molecular level. Nanogap-based detection approaches have proven to be highly accurate SM capture and detection platforms in the last decade. Unfortunately, these approaches face several inherent drawbacks, such as short detection times and the effects of Brownian motion, that can hinder molecular capture. Nanogap-based SM detection approaches have been successfully coupled to optical-based setups to exploit nearfield-assisted trapping to overcome these drawbacks and thus improve SM capture and detection. Here we present the first mechanistic study of nearfield effects on SM capture and release in nanogaps, using unsupervised machine learning methods based on hidden Markov models. We show that the nearfield strength can manipulate the kinetics of the SM capture and release processes. With increasing field strength, the rate constant of the capture kinetics increase while the release kinetics decrease, favouring the former over the latter. As a result, the SM capture state is more likely and more stable than the release state above a specific threshold nearfild strength. We have also estimated the decrease in the capture free-energy profile and the increase in the release profiles to be around 5 kJ mol^-1 for the laser powers employed, ranging from laser-OFF conditions to 11 mW μm^-2. We envisage that our findings can be combined with the electrocatalytic capabilities of the (nearfield) nanogap to develop next-generation molecular nanoreactors. This approach will open the door to highly efficient SM catalysis with precise extended monitoring timescales facilitated through the longer residence times of the reactant trapped inside the nanogap.

Single-molecule determination of chemical equilibrium of DNA intercalation by electrical conductance

We investigated a single-molecule reaction of DNA intercalation as an example of a bimolecular association reaction. Single-molecule conductance values of the product and reactant molecules adsorbed on an Au surface were measured to identify and quantify these molecules. The binding isotherm was constructed, and the association constant of the reaction was determined on a single-molecule basis.

The Characterization of Electronic Noise in the Charge Transport through Single-Molecule Junctions

With the goal of creating single-molecule devices and integrating them into circuits, the emergence of single-molecule electronics provides various techniques for the fabrication of single-molecule junctions and the investigation of charge transport through such junctions. Among the techniques for characterization of charge transport through molecular junctions, electronic noise characterization is an effective strategy with which issues from molecule-electrode interfaces, mechanisms of charge transport, and changes in junction configurations are studied. Electronic noise analysis in single-molecule junctions can be used to identify molecular conformations and even monitor reaction kinetics. This review summarizes the various types of electronic noise that have been characterized during single-molecule electrical detection, including the functions of random telegraph signal (RTS) noise, flicker noise, shot noise, and their corresponding applications, which provide some guidelines for the future application of these techniques to problems of charge transport through single-molecule junctions.

Elementary processes of DNA surface hybridization resolved by single-molecule kinetics: implication for macroscopic device performance

Direct monitoring of single-molecule reactions has recently become a promising means of mechanistic investigation. However, the resolution of reaction pathways from single-molecule experiments remains elusive, primarily because of interference from extraneous processes such as bulk diffusion. Herein, we report a single-molecule kinetic investigation of DNA hybridization on a metal surface, as an example of a bimolecular association reaction. The tip of the scanning tunneling microscope (STM) was functionalized with single-stranded DNA (ssDNA), and hybridization with its complementary strand on an Au(111) surface was detected by the increase in the electrical conductance associated with the electron transport through the resulting DNA duplex. Kinetic analyses of the conductance changes successfully resolved the elementary processes, which involve not only the ssDNA strands and their duplex but also partially hybridized intermediate strands, and we found an increase in the hybridization efficiency with increasing the concentration of DNA in contrast to the knowledge obtained previously by conventional ensemble measurements. The rate constants derived from our single-molecule studies provide a rational explanation of these findings, such as the suppression of DNA melting on surfaces with higher DNA coverage. The present methodology, which relies on intermolecular conductance measurements, can be extended to a range of single-molecule reactions and to the exploration of novel chemical syntheses.

Hybridization of a single DNA molecule on a surface was investigated by electrical conductance measurements. The hybridization efficiency increases with increasing the DNA concentration, in contrast to preceding studies with ensemble studies.