Electrochemistry and bioelectrochemistry towards the single-molecule level: Theoretical notions and systems

Surface structures controlled at the nanometer and single-molecule levels, with functions crucially determined by interfacial electron transfer (ET) are broadly reported in recent years, with different kinds of electrochemically controlled nanoscale/single molecule systems. One is the broad class of metallic and semiconductor-based nanoparticles, nano-arrays, nanotubes, and nanopits. Others are based on self-assembled molecular monolayers. The latter extend to bioelectrochemical systems with redox metalloproteins and DNA-based molecules as targets.We overview here some recent achievements in areas of interfacial electrochemical ET systems, mapped to the nanoscale and single-molecule levels. Focus is on both experimental and theoretical studies in our group. Systems addressed are organized monolayers of redox active transition metal complexes, and metalloproteins and metalloenzymes on single-crystal Au(1 1 1)-electrode surfaces. These systems have been investigated by voltammetry, spectroscopy, microcantilever technology, and scanning probe microscopy. A class of Os-complexes has shown suitable as targets for electrochemical in situ scanning tunnelling microscopy (STM), with close to single-molecule scanning tunnelling spectroscopic (STS) features. Mapping of redox metalloproteins from the three major classes, i.e. blue copper proteins, heme proteins, and iron-sulfur proteins, at the monolayer and single-molecule levels have also been achieved. In situ STM and spectroscopy of redox molecules and biomolecules have been supported by new theoretical frames, which extend established theory of interfacial electrochemical ET.The electrochemical nanoscale and single-molecule systems discussed are compared with other recent nanoscale and single-molecule systems with conspicuous device-like properties, particularly unimolecular rectifiers and single-molecule transistors. Both of these show analogies to electrochemical in situ STM features of redox molecules and biomolecules.     

Potential of Single-Molecule Live-Cell Imaging for Chemical Translational Biology

Single-molecule live-cell imaging is the most direct approach for monitoring the motility of molecules in living cells. Considering the relationship between the motility of molecules and their function, information obtained from single-molecule imaging involves essential clues for understanding the regulatory mechanisms of the processes of target molecules, and translation to applied sciences such as drug discovery. In this Concept, examples of single-molecule imaging studies on G protein-coupled receptors (GPCRs) are mainly introduced, and recent techniques of single-molecule imaging for overcoming the limitation of single-molecule live-cell imaging are discussed. Based on these studies, the prospects of single-molecule imaging will be outlined.     

Photoswitching Emission with Rhodamine Spiroamides for Super-resolution Fluorescence nanoscopies

Spatial resolution in far-field fluorescence microscopy is limited by diffraction to about 200 nm. With the aid of photoswitchable fluorophores, the diffraction barrier has been successfully overcome, allowing unprecedented resolution in the order of single biomolecules. The imaging process demands markers with strict and reliable control of the switching, to keep most of the markers in a non-emissive state most of the time and to bring a tiny number back to an emissive state, and detection at the single-molecule level. Herein, we describe the use of rhodamine spiroamides with unique photophysical properties as molecular probes for super-resolution techniques based on the localization of single emitters. This family of photochromic and fluorescent compounds fulfils the stringent requirements for such imaging methods; these compounds are robust and capable of enduring single-molecule detection in diverse environments. This has allowed meaningful images with resolution down to a few nanometres. Their design, synthesis and implementation is discussed along with imaging applications in material and life sciences.     

Diversity-oriented synthesis of blue emissive nitrogen heterocycles and their conjugation with carbon nano-onions

The search for new fluorescent molecules for possible applications as functional p-electron systems and their conjugation with different nanomaterials is nowadays of paramount importance to broaden the availability of materials with different properties. Herein we present a diversity-oriented approach to heterocyclic luminophores based on a multicomponent Ugi reaction followed by a Pd-mediated cascade sequence. The new molecules are coupled to carbon nano-onions, and hybrid systems represent the first example of blue emitters conjugated with these carbon nanoparticles.     

Single-molecule imaging of cell surfaces using near-field nanoscopy

Living cells use surface molecules such as receptors and sensors to acquire information about and to respond to their environments. The cell surface machinery regulates many essential cellular processes, including cell adhesion, tissue development, cellular communication, inflammation, tumor metastasis, and microbial infection. These events often involve multimolecular interactions occurring on a nanometer scale and at very high molecular concentrations. Therefore, understanding how single-molecules localize, assemble, and interact on the surface of living cells is an important challenge and a difficult one to address because of the lack of high-resolution single-molecule imaging techniques. In this Account, we show that atomic force microscopy (AFM) and near-field scanning optical microscopy (NSOM) provide unprecedented possibilities for mapping the distribution of single molecules on the surfaces of cells with nanometer spatial resolution, thereby shedding new light on their highly sophisticated functions. For single-molecule recognition imaging by AFM, researchers label the tip with specific antibodies or ligands and detect molecular recognition signals on the cell surface using either adhesion force or dynamic recognition force mapping. In single-molecule NSOM, the tip is replaced by an optical fiber with a nanoscale aperture. As a result, topographic and optical images are simultaneously generated, revealing the spatial distribution of fluorescently labeled molecules. Recently, researchers have made remarkable progress in the application of near-field nanoscopy to image the distribution of cell surface molecules. Those results have led to key breakthroughs: deciphering the nanoscale architecture of bacterial cell walls; understanding how cells assemble surface receptors into nanodomains and modulate their functional state; and understanding how different components of the cell membrane (lipids, proteins) assemble and communicate to confer efficient functional responses upon cell activation. We anticipate that the next steps in the evolution of single-molecule near-field nanoscopy will involve combining single-molecule imaging with single-molecule force spectroscopy to simultaneously measure the localization, elasticity, and interactions of cell surface molecules. In addition, progress in high-speed AFM should allow researchers to image single cell surface molecules at unprecedented temporal resolution. In parallel, exciting advances in the fields of photonic antennas and plasmonics may soon find applications in cell biology, enabling true nanoimaging and nanospectroscopy of individual molecules in living cells.     

Single-Molecule Imaging in Living Plant Cells: A Methodological Review

Single-molecule imaging is emerging as a revolutionary approach to studying fundamental questions in plants. However, compared with its use in animals, the application of single-molecule imaging in plants is still underexplored. Here, we review the applications, advantages, and challenges of single-molecule fluorescence imaging in plant systems from the perspective of methodology. Firstly, we provide a general overview of single-molecule imaging methods and their principles. Next, we summarize the unprecedented quantitative details that can be obtained using single-molecule techniques compared to bulk assays. Finally, we discuss the main problems encountered at this stage and provide possible solutions.     

A new generation of sensors based on extraordinary optical transmission

[Reaction: see text]. Plasmonic-based chemical sensing technologies play a key role in chemical, biochemical, and biomedical research, but basic research in this area is still attracting interest. Researchers would like to develop new types of plasmonic nanostructures that can improve the analytical figures of merit, such as detection limits, sensitivity, selectivity, and dynamic range, relative to the commercial systems. They are also tackling issues such as cost, reproducibility, and multiplexing with the goal of providing the best plasmonic-based platform for chemical analysis. In this Account, we will describe recent advances in the optical and spectroscopic properties of nanohole arrays in thin gold films and their applications for chemical sensing. These nanostructures support the unusual phenomenon of "extraordinary optical transmission" (EOT), that is, they are more transparent at certain wavelengths than expected by the classical aperture theory. The EOT is a consequence of surface plasmon (SP) excitations; hence, the resonance should respond to the adsorption of organic molecules. We explored this effect and implemented the integration of the arrays of nanoholes as sensing elements in a microfluidic architecture. We then demonstrated how these devices could be applied in biochemical affinity tests. Arrays of nanoholes offer a small sensing footprint and operate at normal transmission mode, which make them more suitable for miniaturization. This new approach for SPR sensing is more compatible with the lab-on-chip concept and offers the possibility of high-throughput analysis from a single sensing chip. We explored the field localization properties of EOT for surface-enhanced spectroscopy. We could control the enhancement factors for SERS and SEFS by adjusting the geometry of the arrays. The shape of the individual nanoholes offers another handle to tune the enhancement factor for surface-enhanced spectroscopy and SPR sensitivity. Apexes in shaped nanostructures function as optical antennas, focusing the light at extremely small regions at the tips. We observed additional surface enhancement by tuning the apexes' properties. The extra enhancement in these cases originated only from the small number of molecules in the apex regions. The arrays of nanoholes are an exciting new substrate for chemical sensing and enhanced spectroscopy. This class of nanomaterials has the potential to provide a viable alternative to the commercial SPR-based sensors. Further research could exploit this platform to develop nanostructures that support high field localization for single-molecule spectroscopy.     

Collapse and recovery of green fluorescent protein chromophore emission through topological effects

Housed within the 11-stranded β-barrel of the green fluorescent protein (GFP) is the arylideneimidazolidinone (AMI) chromophore, the component responsible for fluorescence. This class of small-molecule chromophore has drawn significant attention for its remarkable photophysical and photochemical properties, both within the intact protein and after its denaturation. All of the proteins so far isolated that have visible light fluorescence have been found to contain an AMI chromophore. These proteins comprise an extensive rainbow, ranging from GFP, which contains the simplest chromophore, p-hydroxybenzylideneimidazolidinone (p-HOBDI), to proteins having molecules with longer conjugation lengths and a variety of intraprotein interactions. The fluorescence invariably almost vanishes upon removal of the protective β-barrel. The role of the barrel in hindering internal conversion has been the subject of numerous studies, especially in our laboratories and those of our collaborators. A better understanding of these chromophores has been facilitated by the development of numerous synthetic protocols. These syntheses, which commonly use the Erlenmeyer azlactone method, have evolved in recent years with the development of a [2 + 3] cycloaddition exploited in our laboratory. The synthetic AMI chromophores have allowed delineation of the complex photophysics of GFP and its derivatives. Upon denaturation, AMI chromophores are marked by 4 orders of magnitude of diminution in emission quantum yield (EQY). This result is attributed to internal conversion resulting from conformational freedom in the released chromophore, which is not allowed within the restrictive β-barrel. To date, the photophysical properties of the AMI chromophore remain elusive and have been attributed to a variety of mechanisms, including cis-trans isomerization, triplet formation, hula twisting, and proton transfer. Advanced studies involving gas-phase behavior, solvent effects, and protonation states have significantly increased our understanding of the chromophore photophysics, but a comprehensive picture is only slowly emerging. Most importantly, mechanisms in structurally defined chromophores may provide clues as to the origin of the "blinking" behavior of the fluorescent proteins themselves. One approach to examining the effect of conformational freedom on rapid internal conversion of the chromophores is to restrict the molecules, both through structural modifications and through adjustments of the supramolecular systems. We thus include here a discussion of studies involving the crystalline state, inclusion within natural protein-binding pockets, complexation with metal ions, and sequestration within synthetic cavities; all of this research affirms the role of restricting conformational freedom in partially restoring the EQY. Additionally, new photochemistry is observed within these restricted systems. Many of the studies carried out in our laboratories show promise for these molecules to be adapted as molecular probes, wherein inclusion turns on the fluorescence and provides a signaling mechanism. In this Account, we present an overview of the AMI chromophores, including synthesis, overall photophysics, and supramolecular behavior. A significant amount of work remains for researchers to fully understand the properties of these chromophores, but important progress achieved thus far in photophysics and photochemistry is underscored here.     

Peptide-PAINT Enables Investigation of Endogenous Talin with Molecular Scale Resolution in Cells and Tissues

Talin is a cell adhesion molecule that is indispensable for the development and function of multicellular organisms. Despite its central role for many cell biological processes, suitable methods to investigate the nanoscale organization of talin in its native environment are missing. Here, we overcome this limitation by combining single-molecule resolved PAINT (points accumulation in nanoscale topography) imaging with the IRIS (image reconstruction by integrating exchangeable single-molecule localization) approach, enabling the quantitative analysis of genetically unmodified talin molecules in cells. We demonstrate that a previously reported peptide can be utilized to specifically label the two major talin isoforms expressed in mammalian tissues with a localization precision of <10 nm. Our experiments show that the methodology performs equally well as state-of-the-art single-molecule localization techniques, and the first applications reveal a thus far undescribed cell adhesion structure in differentiating stem cells. Furthermore, we demonstrate the applicability of this peptide-PAINT technique to mouse tissues paving the way to single-protein imaging of endogenous talin proteins under physiologically relevant conditions.     

Development of new dyeing photoinitiators based on 6H-indolo[2,3-b]quinoxaline skeleton

The series of new dyes, which structures are based on 6H-indolo[2,3-b]quinoxaline skeleton that possess characteristic electronic absorption band at a boundary of UV and visible light were tested as potential light absorbing chromophores for photoinitiated polymerization.The studied dyes can be classified into two different groups. The first is the group, so called ‘the branched dyes’, which structures possess the part of molecule that can rotate without restraints and are characterized by low photoinitiation ability. The second, planar and rigid group of molecules provides another chromophores, which possess quite different properties in comparison to that observed for the branched dyes. Their photoinitiation ability is comparable to that observed for many commercially available photoinitiating systems.The location of electronic absorption spectra at a boundary of UV and visible light makes the tested dyes the good candidates for the photoinitiating system applied in dental restorative materials. Their high molar absorption coefficient allows to decrease the dyes concentration in dental formulation in comparison to commonly used camphorquinone.     

Nanographenes as active components of single-molecule electronics and how a scanning tunneling microscope puts them to work

Single-molecule electronics, that is, realizing novel electronic functionalities from single (or very few) molecules, holds promise for application in various technologies, including signal processing and sensing. Nanographenes, which are extended polycyclic aromatic hydrocarbons (PAHs), are highly attractive subjects for studies of single-molecule electronics because the electronic properties of their flat conjugated systems can be varied dramatically through synthetic modification of their sizes and topologies. Single nanographenes provide high tunneling currents when adsorbed flat onto conducting substrates, such as graphite. Because of their chemical inertness, nanographenes interact only weakly with these substrates, thereby preventing the need for special epitaxial structure matching. Instead, self-assembly at the interface between a conducting solid, such as the basal plane of graphite, and a nanographene solution generally leads to highly ordered monolayers. Scanning tunneling spectroscopy (STS) allows the current-voltage characteristics to be measured through a single molecule positioned between two electrodes; the key to the success of STS is the ability to position the scanning tunneling microscopy (STM) tip freely with respect to the molecule in all dimensions, that is, both parallel and perpendicular to the surface. In this Account, we report the properties of nanographenes having sizes ranging from 0.7 to 3.1 nm and exhibiting various symmetry, periphery, and substitution types. The size of the aromatic system and the nature of its perimeter are two essential features affecting its HOMO-LUMO gap and charge carrier mobility in the condensed phase. Moreover, the extended pi area of larger substituted PAHs improves the degree of self-ordering, another key requirement for high-performance electronic devices. Self-assembly at the interface between an organic solution and the basal plane of graphite allows deposition of single molecules within the well-defined environment of a molecular monolayer. We have used STM and STS to investigate both the structures and electronic properties of these single molecules in situ. Indeed, we have observed key electronic functions, rectification and current control through single molecules, within a prototypical chemical field-effect transistor at ambient temperature. The combination of nanographenes and STM/STS, with the PAHs self-assembled in oriented molecular mono- or bilayers at the interface between an organic solution and the basal plane of graphite and contacted by the STM tip, is a simple, reliable, and versatile system for developing the fundamental concepts of molecular electronics. Our future targets include fast reversible molecular switches and complex molecular electronic devices coupled together from several single-molecule systems.     

Controlled chain polymerisation and chemical soldering for single-molecule electronics

Single functional molecules offer great potential for the development of novel nanoelectronic devices with capabilities beyond today's silicon-based devices. To realise single-molecule electronics, the development of a viable method for connecting functional molecules to each other using single conductive polymer chains is required. The method of initiating chain polymerisation using the tip of a scanning tunnelling microscope (STM) is very useful for fabricating single conductive polymer chains at designated positions and thereby wiring single molecules. In this feature article, developments in the controlled chain polymerisation of diacetylene compounds and the properties of polydiacetylene chains are summarised. Recent studies of "chemical soldering", a technique enabling the covalent connection of single polydiacetylene chains to single functional molecules, are also introduced. This represents a key step in advancing the development of single-molecule electronics.     

Light-induced conductance switching in azobenzene based near-percolated single wall carbon nanotube/polymer composites

Photochromic molecular switches are a class of organic molecules that allow a reversible control over molecular structure, dipole moment, or conductivity with light. Incorporating these chromophores into polymer composites provides the possibility to photoswitch intrinsic properties of these materials. Here we report reversible light-induced conductance switching of near-percolated single wall carbon nanotube/polymethylmethacrylate (SWCNT/PMMA) nanocomposites containing azobenzene derivatives that do not exhibit molecular conductance switching. Stable switching amplitudes up to 28% were achieved near the percolation threshold. The results suggest a Pool–Frenkel type conduction mechanism where the chromophores are an integral part of the conduction path.     

Molecular strategies to read and write at the nanoscale with far-field optics

Diffraction prevents the focusing of ultraviolet and visible radiations within nanoscaled volumes and, as a result, the imaging and patterning of nanostructures with conventional far-field illumination. Specifically, the irradiation of a fluorescent or photosensitive material with focused light results in the simultaneous excitation of multiple chromophores distributed over a large area, relative to the dimensions of single molecules. It follows that the spatial control of fluorescence and photochemical reactions with molecular precision is impossible with conventional illumination configurations. However, the photochemical and photophysical properties of organic chromophores can be engineered to overcome diffraction in combination with patterned or reiterative illumination. These ingenious strategies offer the opportunity to confine excited chromophores within nanoscaled volumes and, therefore, restrict fluorescence or photochemical reactions within subdiffraction areas. Indeed, information can be "read" in the form of fluorescence and "written" in the form of photochemical products with resolution down to the nanometre level on the basis of these innovative approaches. In fact, these promising far-field optical methods permit the convenient imaging of biological samples and fabrication of miniaturized objects with unprecedented resolution and can have long-term and profound implications in biomedical research and information technology.     

Single-molecule optoelectronics

With discrete states, several-atom Ag(n) nanoclusters exhibit molecule-like behavior with strong visible fluorescence and robust optical properties. This new class of single-molecule fluorophores has been created and electrically contacted in thin films to produce the first electroluminescent single molecules. A direct reporter of nanoscale charge injection and transport through discrete energy levels, bright Ag(n) electroluminescence has been harnessed to create single-molecule light-emitting diodes (LEDs) and optoelectronic logic gates and even to demonstrate full addition operations. These experiments utilizing the small size and quantum behavior of individual Ag nanoclusters usher in the new field of single-molecule optoelectronics.     

The effect of light on some commercially important polymers

Most organic polymers are damaged by exposure to terrestrial sunlight and eventually the useful properties are lost. Once absorbed, radiation in the erythmal region of the solar spectrum has sufficient energy to cause the rupture of polymer chain bonds. It can be difficult to identify the important chromophores in a polymer system and even more difficult to determine precisely what happens to them following electronic excitation. The number of chemical events leading to the mechanical failure of a plastic can be remarkably small although the variety of them is potentially large. Polypropylene is discussed as an example of a thermoplastic which invariably contains small amounts of light-absorbing impurities and which, if unprotected, is highly susceptible to photo-oxidation. Polyethylene terephthalate is used to illustrate a class of polymers which is susceptible to actinic deterioration owing to chromophores in the repeating unit. The primary photochemical reactions occurring in these two systems are described, with improved methods for UV stabilization in mind.     

Bichromophoric paracyclophanes: models for interchromophore delocalization

The electronic delocalization between chromophores in the solid is an important parameter to optimize when designing organic materials for optoelectronic applications. The [2.2]paracyclophane framework allows for the synthesis of well-defined, nonfluxional molecules that bring together two chromophores into close proximity. From the photophysical properties of these molecules we can examine how the chromophore conjugation length, their relative orientation, and the regiochemistry of contact affects the electronic delocalization between the two subunits.     

Functioning nanomachines seen in real-time in living bacteria using single-molecule and super-resolution fluorescence imaging

Molecular machines are examples of "pre-established" nanotechnology, driving the basic biochemistry of living cells. They encompass an enormous range of function, including fuel generation for chemical processes, transport of molecular components within the cell, cellular mobility, signal transduction and the replication of the genetic code, amongst many others. Much of our understanding of such nanometer length scale machines has come from in vitro studies performed in isolated, artificial conditions. Researchers are now tackling the challenges of studying nanomachines in their native environments. In this review, we outline recent in vivo investigations on nanomachines in model bacterial systems using state-of-the-art genetics technology combined with cutting-edge single-molecule and super-resolution fluorescence microscopy. We conclude that single-molecule and super-resolution fluorescence imaging provide powerful tools for the biochemical, structural and functional characterization of biological nanomachines. The integrative spatial, temporal, and single-molecule data obtained simultaneously from fluorescence imaging open an avenue for systems-level single-molecule cellular biophysics and in vivo biochemistry.     

Photophysics of individual single-walled carbon nanotubes

Single-walled carbon nanotubes (SWNTs) are cylindrical graphitic molecules that have remained at the forefront of nanomaterials research since 1991, largely due to their exceptional and unusual mechanical, electrical, and optical properties. The motivation for understanding how nanotubes interact with light (i.e., SWNT photophysics) is both fundamental and applied. Individual nanotubes may someday be used as superior near-infrared fluorophores, biological tags and sensors, and components for ultrahigh-speed optical communications systems. Establishing an understanding of basic nanotube photophysics is intrinsically significant and should enable the rapid development of such innovations. Unlike conventional molecules, carbon nanotubes are synthesized as heterogeneous samples, composed of molecules with different diameters, chiralities, and lengths. Because a nanotube can be either metallic or semiconducting depending on its particular molecular structure, SWNT samples are also mixtures of conductors and semiconductors. Early progress in understanding the optical characteristics of SWNTs was limited because nanotubes aggregate when synthesized, causing a mixing of the energy states of different nanotube structures. Recently, significant improvements in sample preparation have made it possible to isolate individual nanotubes, enabling many advances in characterizing their optical properties. In this Account, single-molecule confocal microscopy and spectroscopy were implemented to study the fluorescence from individual nanotubes. Single-molecule measurements naturally circumvent the difficulties associated with SWNT sample inhomogeneities. Intrinsic SWNT photoluminescence has a simple narrow Lorentzian line shape and a polarization dependence, as expected for a one-dimensional system. Although the local environment heavily influences the optical transition wavelength and intensity, single nanotubes are exceptionally photostable. In fact, they have the unique characteristic that their single molecule fluorescence intensity remains constant over time; SWNTs do not "blink" or photobleach under ambient conditions. In addition, transient absorption spectroscopy was used to examine the relaxation dynamics of photoexcited nanotubes and to elucidate the nature of the SWNT excited state. For metallic SWNTs, very fast initial recovery times (300-500 fs) corresponded to excited-state relaxation. For semiconducting SWNTs, an additional slower decay component was observed (50-100 ps) that corresponded to electron-hole recombination. As the excitation intensity was increased, multiple electron-hole pairs were generated in the SWNT; however, these e-h pairs annihilated each other completely in under 3 ps. Studying the dynamics of this annihilation process revealed the lifetimes for one, two, and three e-h pairs, which further confirmed that the photoexcitation of SWNTs produces not free electrons but rather one-dimensional bound electron-hole pairs (i.e., excitons). In summary, nanotube photophysics is a rapidly developing area of nanomaterials research. Individual SWNTs exhibit robust and unexpectedly unwavering single-molecule fluorescence in the near-infrared, show fast relaxation dynamics, and generate excitons as their optical excited states. These fundamental discoveries should enable the development of novel devices based on the impressive photophysical properties of carbon nanotubes, especially in areas like biological imaging. Many facets of nanotube photophysics still need to be better understood, but SWNTs have already proven to be an excellent starting material for future nanophotonics applications.     

Recent advances in small molecule fluorescent probes for simultaneous imaging of two bioactive molecules in live cells and in vivo

The interrelationships and synergistic regulations of bioactive molecules play pivotal roles in physiological and pathological processes involved in the initiation and development of some diseases,such as cancer and neurodegenerative and cardiovascular diseases.Therefore,the simultaneous,accurate and timely detection of two bioactive molecules is crucial to explore their roles and pathological mechanisms in related diseases.Fluorescence imaging associated with small molecular probes has been widely used in the imaging of bioactive molecules in living cells and in vivo due to its excellent performances,including high sensitivity and selectivity,noninvasive properties,real-time and high spatial temporal resolution.Single organic molecule fluorescent probes have been successively developed to simultaneously monitor two biomolecules to uncover their synergistic relationships in living systems.Hence,in this review,we focus on summarizing the design strategies,classifications,and bioimaging applications of dual-response fluorescent probes over the past decade.Furthermore,future research directions in this field are proposed.