Conductance switching in single molecules through conformational changes

Enhancing Spin-Transport Characteristics, Spin-Filtering Efficiency, and Negative Differential Resistance in Exchange-Coupled Dinuclear Co(II) Complexes for Molecular Spintronics Applications

Single-molecule spintronics, where electron transport occurs via a paramagnetic molecule, has gained wide attention due to its potential applications in the area of memory devices to switches. While numerous organic and some inorganic complexes have been employed over the years, there are only a few attempts to employ exchange coupled dinuclear complexes at the interface, and the advantage of fabricating such a molecular spintronics device in the observation of switchable Kondo resonance was demonstrated recently in the dinuclear [Co2(L)(hfac)4] (1) complex (Wagner et al., Nat. Nanotechnol. 2013, 8, 575-579). In this work, employing an array of theoretical tools such as density functional theory (DFT), the ab initio CASSCF/NEVPT2 method, and DFT combined with nonequilibrium Green Function (NEGF) formalism, we studied in detail the role of magnetic coupling, ligand field, and magnetic anisotropy in the transport characteristics of complex 1. Particularly, our calculations not only reproduce the current-voltage (I-V) characteristics observed in experiments but also unequivocally establish that these arise from an exchange-coupled singlet state that arises due to antiferromagnetic coupling between two high-spin Co(II) centers. Further, the estimated spin Hamiltonian parameters such as J, g values, and D and E/D values are only marginally altered for the molecule at the interface. Further, the exchange-coupled state was found to have very similar transport responses, despite possessing significantly different geometries. Our transport calculations unveil a new feature of the negative differential resistance (NDR) effect on 1 at the bias voltage of 0.9 V, which agrees with the experimental I-V characteristics reported. The spin-filtering efficiency (SFE) computed for the spin-coupled states was found to be only marginal (∼25%); however, if the ligand field is fine-tuned to obtain a low-spin Co(II) center, a substantial SFE of 44% was noted. This spin-coupled state also yields a very strong NDR with a peak-to-valley ratio (PVR) of ∼56 - a record number that has not been witnessed so far in this class of compounds. Additionally, we have established further magnetostructural-transport correlations, providing valuable insights into how microscopic spin Hamiltonian parameters can be associated with SFE. Several design clues to improve the spin-transport characteristics, SFE and NDR in this class of molecule, are offered.

Electrically gated molecular thermal switch

Controlling heat flow is a key challenge for applications ranging from thermal management in electronics to energy systems, industrial processing, and thermal therapy. However, progress has generally been limited by slow response times and low tunability in thermal conductance. In this work, we demonstrate an electronically gated solid-state thermal switch using self-assembled molecular junctions to achieve excellent performance at room temperature. In this three-terminal device, heat flow is continuously and reversibly modulated by an electric field through carefully controlled chemical bonding and charge distributions within the molecular interface. The devices have ultrahigh switching speeds above 1 megahertz, have on/off ratios in thermal conductance greater than 1300%, and can be switched more than 1 million times. We anticipate that these advances will generate opportunities in molecular engineering for thermal management systems and thermal circuit design.

Spin Polarization in Transport Studies of Chirality-Induced Spin Selectivity

Chirality-induced spin selectivity (CISS) is a recently discovered effect in which structural chirality can result in different conductivities for electrons with opposite spins. In the CISS community, the degree of spin polarization is commonly used to describe the efficiency of the spin filtering/polarizing process, as it represents the fraction of spins aligned along the chiral axis of chiral materials originating from non-spin-polarized currents. However, the methods of defining, calculating, and analyzing spin polarization have been inconsistent across various studies, hindering advances in this field. In this Perspective, we connect the relevant background and the definition of spin polarization, discuss its calculation in different contexts in the CISS, and propose a practical and meaningful figure of merit by quantitative analysis of magnetoresistance in CISS transport studies.

Formation of Molecular Junctions by Single-Entity Collision Electrochemistry

Controlling and understanding the chemistry of molecular junctions is one of the major themes in various fields ranging from chemistry and nanotechnology to biotechnology and biology. Stochastic single-entity collision electrochemistry (SECE) provides powerful tools to study a single entity, such as single cells, single particles, and even single molecules, in a nanoconfined space. Molecular junctions formed by SECE collision show various potential applications in monitoring molecular dynamics with high spatial resolution and high temporal resolution and in feasible combination with hybrid techniques. This Perspective highlights the new breakthroughs, seminal studies, and trends in the area that have been most recently reported. In addition, future challenges for the study of molecular junction dynamics with SECE are discussed.

Light-induced Photoswitching of 4-(Phenylazo)benzoic Acid on Au(111)

Photochromic molecules can undergo a reversible conversion between two isomeric forms upon exposure to external stimuli such as electromagnetic radiation. A significant physical transformation accompanying the photoisomerization process defines them as photoswitches, with potential applications in various molecular electronic devices. As such, a detailed understanding of the photoisomerization process on surfaces and the influence of the local chemical environment on switching efficiency is essential. Herein, we use scanning tunneling microscopy to observe the photoisomerization of 4-(phenylazo)benzoic acid (PABA) assembled on Au(111) in kinetically constrained metastable states guided by pulse deposition. Photoswitching is observed at low molecular density and is absent in tight-packed islands. Furthermore, switching events were noted in PABA molecules coadsorbed in a host octanethiol monolayer, suggesting an influence of the surrounding chemical environment on photoswitching efficiency.

Resonant transport in a highly conducting single molecular junction via metal-metal covalent bond

Achieving highly transmitting molecular junctions through resonant transport at low bias is key to the next-generation low-power molecular devices. Although resonant transport in molecular junctions was observed by connecting a molecule between the metal electrodes via chemical anchors by applying a high source-drain bias (>1 V), the conductance was limited to <0.1G0, G0 being the quantum of conductance. Herein, we report electronic transport measurements by directly connecting a ferrocene molecule between Au electrodes under ambient conditions in a mechanically controllable break junction setup (MCBJ), revealing a conductance peak at ∼0.2G0 in the conductance histogram. A similar experiment was repeated for ferrocene terminated with amine (-NH2) and cyano (-CN) anchors, where conductance histograms exhibit an extended low conductance feature, including the sharp high conductance peak, similar to pristine ferrocene. The statistical analysis of the data and density functional theory-based transport calculation suggest a possible molecular conformation with a strong hybridization between the Au electrodes, and that the Fe atom of ferrocene is responsible for a near-perfect transmission in the vicinity of the Fermi energy, leading to the resonant transport at a small applied bias (<0.5 V). Moreover, calculations including van der Waals/dispersion corrections reveal a covalent-like organometallic bonding between Au and the central Fe atom of ferrocene, having bond energies of ∼660 meV. Overall, our study not only demonstrates the realization of an air-stable highly transmitting molecular junction, but also provides important insights about the nature of chemical bonding at the metal/organo-metallic interface.

Understanding the Two-Dimensional Mixing Behavior of 1-Naphthalenethiol and Octanethiol

A two-dimensional (2D) mixture in the form of a self-assembled monolayer composed of two distinct organothiol compounds was created by sequentially depositing 1-naphthalenethiol (1NT) and octanethiol (OT) on a gold surface. By varying the sequence of deposition, two mixed surface systems were created. The surface structure of the resulting mixed monolayer was characterized with Scanning Tunneling Microscopy (STM) and showed surface disorder across all investigated domains. Elemental analysis was carried out with X-ray Photoelectron Spectroscopy (XPS) and indicated that the 1NT monolayer was prone to significant oxidation. Reductive desorption (RD) was used to characterize the binding strength and electrochemical environments of the molecular components in the mixture, and confirmed disordered molecular layers. Due to the presence of oxidized species in the 1NT monolayer, 1NT was displaced by OT resulting in a novel surface structure composed of either OT or 1NT. Monolayers of OT that were exposed to a solution of 1NT resulted in disordered surface structures with a significant amount of gold vacancy islands. To date, there is no experimental phase diagram explaining the chemical behavior of two-dimensional mixtures. This study addresses the need for an experimental understanding of the phase behavior of mixed organothiol self-assembled monolayers (SAMs).

Polymorphism and Building-Block-Resolved STM Imaging of Self-Assembled Monolayers of 4-Fluorobenzenemethanethiol on Au(111)

Self-assembled monolayers (SAMs) of 4-fluorobenzenemethanethiol (p-FBMT) on Au(111), prepared by immersion procedure (1 mM ethanolic solution; 60 °C; 18 h), were characterized by scanning tunneling microscopy (STM). The data suggest the formation of highly ordered monolayer with a commensurate structure, described by the 2 3 × 13 R 13 ∘ unit cell. The STM appearance of this cell occurs, however, in two different forms, with either well-localized individual spots or splitting of these spots in two components. These components are assigned to the tunneling through the entire molecule or sulfur docking group only. The respective spots correspond then to the terminal fluorine atom and sulfur docking group, manifesting, thus, building-block-resolving STM imaging. The accessibility of the docking group for direct tunneling is most likely related to a specific molecular organization for one of the two possible internal structures of the unit cell. The above results represent a showcase for potential of STM for imaging of upright-arranged and densely packed molecular assemblies, such as SAMs.

Self-assembled organic and hybrid materials derived from oligo-(p-phenyleneethynylenes)

Oligo-(p-Phenyleneethynylenes) (OPEs) have garnered widespread interest over the past three decades due to their excellent opto-electronic properties. However, the chief focus has been on the use of mainly small molecules or polymeric systems for the study of their structural diversity in opto-electronic applications. Recently, researchers have started delving deeper into their utility in material applications. Purely organic materials such as supramolecular polymers, self-assembled nanostructures, nanostructured organogels and single-crystalline materials derived from OPEs have already been developed and researched. Chirality has also been introduced into these systems. Additionally, these have shown physical properties such as polymorphism, liquid crystallinity, melt formation, mechanochromism, etc. All these materials have also shown excellent luminescence properties with high quantum yield and some have even shown energy harvesting properties. There have also been sporadic reports on OPE linker based hybrid systems such as metallogels and metal-organic framework (MOF) structures where structural analysis reveals the origin of tunable emission in these materials. Furthermore, by innovative structural design, unexplored properties of OPEs such as water repellency, bioimaging, drug delivery, photocatalysis, energy transfer, nanomorphology control, photoconductivity, and colour tunability could be achieved. This feature article will, therefore, encompass a detailed discussion on the development of this field as well as the analysis of the properties realized in OPE derived self-assembled supramolecular materials. The main focus will be on the following classes of materials: soft supramolecular materials, crystalline supramolecular π-systems, nanoscale metal-organic frameworks (NMOFs) and bulk metal-organic frameworks (MOFs) and how their application horizon has been expanded by integrating OPEs into their structures.

Controlled Hysteresis of Conductance in Molecular Tunneling Junctions

The problem this paper addresses is the origin of the hysteretic behavior in two-terminal molecular junctions made from an EGaIn electrode and self-assembled monolayers of alkanethiolates terminated in chelates (transition metal dichlorides complexed with 2,2'-bipyridine; BIPY-MCl₂). The hysteresis of conductance displayed by these BIPY-MCl₂ junctions changes in magnitude depending on the identity of the metal ion (M) and the window of the applied voltage across the junction. The hysteretic behavior of conductance in these junctions appears only in an incoherent (Fowler-Nordheim) tunneling regime. When the complexed metal ion is Mn(II), Fe(II), Co(II), or Ni(II), both incoherent tunneling and hysteresis are observed for a voltage range between +1.0 V and -1.0 V. When the metal ion is Cr(II) or Cu(II), however, only resonant (one-step) tunneling is observed, and the junctions exhibit no hysteresis and do not enter the incoherent tunneling regime. Using this correlation, the conductance characteristics of BIPY-MCl₂ junctions can be controlled. This voltage-induced change of conductance demonstrates a simple, fast, and reversible way (i.e., by changing the applied voltage) to modulate conductance in molecular tunneling junctions.

Photoswitchable Machine-Engineered Plasmonic Nanosystem with High Optical Response for Ultrasensitive Detection of microRNAs and Proteins Adaptively

Modulating optoelectronic properties of inorganic nanostructures tethered with light-responsive molecular switches by their conformational change in the solid state is fundamentally important for advanced nanoscale-device fabrication, specifically in biosensing applications. Herein, we present an entirely new solid-state design approach employing the light-induced reversible conformational change of spiropyran (SP)-merocyanine (MC) covalently attached to gold triangular nanoprisms (Au TNPs) via alkylthiolate self-assembled monolayers to produce a large localized surface plasmon resonance response (∼24 nm). This shift is consistent with the increase in thickness of the local dielectric shell-surrounded TNPs and perhaps short-range dipole-dipole (permanent and induced) interactions between TNPs and the zwitterionic MC form. Water contact angle measurement and Raman spectroscopy characterization unequivocally prove the formation of a stable TNP-MC structural motif. Utilizing this form, we fabricated the first adaptable nanoplasmonic biosensor, which uses an identical structural motif for ultrasensitive, highly specific, and programmable detection of microRNAs and proteins at attomolar concentrations in standard human plasma and urine samples, and at femtomolar concentrations from bladder cancer patient plasma (n = 10) and urine (n = 10), respectively. Most importantly, the TNP-MC structural motif displays a strong binding affinity with receptor molecules (i.e., single-stranded DNA and antibody) producing a highly stable biosensor. Taken together, the TNP-MC structural motif represents a multifunctional super biosensor with the potential to expand clinical diagnostics through simplifying biosensor design and providing highly accurate disease diagnosis.

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.

In situ solid-state nanopore fabrication

Nanopores in solid-state membranes are promising for a wide range of applications including DNA sequencing, ultra-dilute analyte detection, protein analysis, and polymer data storage. Techniques to fabricate solid-state nanopores have typically been time consuming or lacked the resolution to create pores with diameters down to a few nanometres, as required for the above applications. In recent years, several methods to fabricate nanopores in electrolyte environments have been demonstrated. These in situ methods include controlled breakdown (CBD), electrochemical reactions (ECR), laser etching and laser-assisted controlled breakdown (la-CBD). These techniques are democratising solid-state nanopores by providing the ability to fabricate pores with diameters down to a few nanometres (i.e. comparable to the size of many analytes) in a matter of minutes using relatively simple equipment. Here we review these in situ solid-state nanopore fabrication techniques and highlight the challenges and advantages of each method. Furthermore we compare these techniques by their desired application and provide insights into future research directions for in situ nanopore fabrication methods.

Tuning Single-Molecule Conductance by Controlled Electric Field-Induced trans-to-cis Isomerisation

External electric fields (EEFs) have proven to be very efficient in catalysing chemical reactions, even those inaccessible via wet-chemical synthesis. At the single-molecule level, oriented EEFs have been successfully used to promote in situ single-molecule reactions in the absence of chemical catalysts. Here, we elucidate the effect of an EEFs on the structure and conductance of a molecular junction. Employing scanning tunnelling microscopy break junction (STM-BJ) experiments, we form and electrically characterize single-molecule junctions of two tetramethyl carotene isomers. Two discrete conductance signatures show up more prominently at low and high applied voltages which are univocally ascribed to the trans and cis isomers of the carotenoid, respectively. The difference in conductance between both cis-/trans- isomers is in concordance with previous predictions considering π-quantum interference due to the presence of a single gauche defect in the trans isomer. Electronic structure calculations suggest that the electric field polarizes the molecule and mixes the excited states. The mixed states have a (spectroscopically) allowed transition and, therefore, can both promote the cis-isomerization of the molecule and participate in electron transport. Our work opens new routes for the in situ control of isomerisation reactions in single-molecule contacts.

Single molecule electronic devices with carbon-based materials: status and opportunity

The field of single molecule electronics has progressed remarkably in the past decades by allowing for more versatile molecular functions and improving device fabrication techniques. In particular, electrodes made from carbon-based materials such as graphene and carbon nanotubes (CNTs) may enable parallel fabrication of multiple single molecule devices. In this perspective, we review the recent progress in the field of single molecule electronics, with a focus on devices that utilizes carbon-based electrodes. The paper is structured in three main sections: (i) controlling the molecule/graphene electrode interface using covalent and non-covalent approaches, (ii) using CNTs as electrodes for fabricating single molecule devices, and (iii) a discussion of possible future directions employing new or emerging 2D materials.

Optically Induced Molecular Logic Operations

Molecular electronics is a promising route for down-sizing electronic devices. Tip-enhanced Raman spectroscopy provides us a setup to probe current-driven molecular junctions that are considered as prototypes of molecular electronic devices. In this setup, the plasmonic tip concentrates optical fields to a degree that allows observing optical response of single molecules. Simultaneously, the tip can also induce a localized optical angular momentum, which has been seldomly considered in previous studies. Here, we propose that the induced optical angular momentum can interact with the probed molecule and strongly modify the response signal. Specifically, we demonstrate the ability to control the vibrational resonance of current-driven molecular junctions with the optical angular momentum. This precise control of light-matter interactions at the nanoscale allows us to demonstrate multiple logic operations. These results provide a fundamental understanding of future molecular electronics applications.

Nanofabrication Techniques in Large-Area Molecular Electronic Devices

The societal impact of the electronics industry is enormous—not to mention how this industry impinges on the global economy. The foreseen limits of the current technology—technical, economic, and sustainability issues—open the door to the search for successor technologies. In this context, molecular electronics has emerged as a promising candidate that, at least in the short-term, will not likely replace our silicon-based electronics, but improve its performance through a nascent hybrid technology. Such technology will take advantage of both the small dimensions of the molecules and new functionalities resulting from the quantum effects that govern the properties at the molecular scale. An optimization of interface engineering and integration of molecules to form densely integrated individually addressable arrays of molecules are two crucial aspects in the molecular electronics field. These challenges should be met to establish the bridge between organic functional materials and hard electronics required for the incorporation of such hybrid technology in the market. In this review, the most advanced methods for fabricating large-area molecular electronic devices are presented, highlighting their advantages and limitations. Special emphasis is focused on bottom-up methodologies for the fabrication of well-ordered and tightly-packed monolayers onto the bottom electrode, followed by a description of the top-contact deposition methods so far used.

Electric field stimulates production of highly conductive microbial OmcZ nanowires

Multifunctional living materials are attractive due to their powerful ability to self-repair and replicate. However, most natural materials lack electronic functionality. Here we show that an electric field, applied to electricity-producing Geobacter sulfurreducens biofilms, stimulates production of previously unknown cytochrome OmcZ nanowires with 1,000-fold higher conductivity (30 S/cm), and 3-fold higher stiffness (1.5 GPa), than the cytochrome OmcS nanowires that are important in natural environments. Using chemical imaging-based multimodal nanospectroscopy, we correlate protein structure with function, and observe pH-induced conformational switching to β-sheets in individual nanowires, which increases their stiffness and conductivity by 100-fold due to enhanced π-stacking of heme groups; this was further confirmed by computational modelling and bulk spectroscopic studies. These nanowires can transduce mechanical and chemical stimuli into electrical signals to perform sensing, synthesis and energy production. These findings of biologically-produced, highly-conductive protein nanowires may help to guide the development of seamless, bidirectional interfaces between biological and electronic systems.

Design of a molecular memory element with an alternating circular array of dipolar rotors and rotation suppressors

As a new element for electric-field driven molecular memory, we developed a hexaarylbenzene derivative in which three difluorophenyl groups and three aryl groups as a dipolar rotor and a rotation suppressor, respectively, are alternately positioned on the central benzene core. This molecule has two rotational isomeric forms, both of which preserve their conformational states at room temperature but exhibit interconversion at high temperatures. Amorphous thin films fabricated from the hexaarylbenzene show a reversible change in surface potential by application of electric fields.

A hexaarylbenzene derivative with an alternating circular array of dipolar rotors and rotation suppressors holds promise as a new element for electric-field driven molecular memory.

Mechanism Study of Molecular Deformation of 2,2',5',2″-Tetramethylated p-Terphenyl-4,4″-dithiol Trapped in Gold Junctions

Molecular junctions hold great potential for future microelectronics, while the practical utilization has long been limited by the problem of conformational deformation during charge transport. Here we present a first-principles theoretical study on the surface-enhanced Raman spectroscopy (SERS) characterization of the p-terphenyl-4,4″-dithiol molecule and its 2,2',5',2″-tetramethylated analogue in gold junctions to investigate the molecular deformation mechanism. The effects of charge injection and external electric field were examined, both of which could change π-conjugation by varying the dihedral angle between the central and ending rings (D_IPT). The induced significant structural deformations then change SERS responses. Only the SERS responses under an external electric field can account for the experimentally observed Raman spectra, and those of charge injections cannot. Moreover, applying a strong electric field could enlarge the conductivities of the two molecular junctions, agreeing well with experiments. This information not only elaborates that the electric field effect constitutes one important mechanism for molecular deformation but also provides useful insights for the control of charge transport in molecular junctions.

Temperature dependence of charge transport in solid-state molecular junctions based on oligo(phenylene ethynylene)s

The ultimate goal of molecular electronics is to achieve practical applications. For approaching the target, we have successfully fabricated solid-state junctions based on oligo(phenylene ethynylene)s (OPEs) and cruciform OPEs with extended tetrathiafulvalene (TTF) (OPE3 and OPE3-TTF) self-assembled monolayers (SAMs) with a diamine anchoring group. SAMs were confined in micropores with gold substrates to ensure well-defined device surface areas. The transport properties were conducted on a double-junction layout, which the rGO films used for top contacts and interconnects between adjacent SAMs. The solid-state devices based on OPE3-TTF SAMs showed the expected higher conductance under ambient conditions because of the incorporation of a TTF moiety. The two devices displayed varying degrees of temperature dependence with decreasing temperature, which resulted from the cross-conjugated OPE3-TTF molecule exhibiting quantum interference while the linear-conjugated OPE3 molecule did not. This study shows the temperature dependence of the electrical properties of molecular devices based on cruciform OPEs, further enriching the research results of functional molecular devices.

Fabrication and functions of graphene-molecule-graphene single-molecule junctions

The past two decades have witnessed increasingly rapid advances in the field of single-molecule electronics, which are expected to overcome the limitation of the miniaturization of silicon-based microdevices, thus promoting the development of device manufacturing technologies and characterization means. In addition to this, they can enable us to investigate the intrinsic properties of materials at the atomic- or molecular-length scale and probe new phenomena that are inaccessible in ensemble experiments. In this perspective, we start from a brief introduction on the manufacturing method of graphene-molecule-graphene single-molecule junctions (GMG-SMJs). Then, we make a description on the remarkable functions of GMG-SMJs, especially on the investigation of single-molecule charge transport and dynamics. Finally, we conclude by discussing the main challenges and future research directions of molecular electronics.

Effect of the linkage modes of thiolated ethynyl groups on the spin-dependent electronic transport properties in transition metal porphyrin molecular junctions

Using density functional theory and nonequilibrium Green's function method, the spin-dependent electronic transport properties of six transition metal porphyrin molecules (VP, CrP, MnP, FeP, CoP, and NiP), which are linked to gold electrodes through the thiolated ethynyl groups, are investigated. Two different linkage modes (beta linkage and meso linkage) of the substituted ethynyl groups on the porphyrin macrocycle are considered. The results show that the linkage mode of ethynyl groups plays an important role on the spin transport properties of the molecular junctions and the beta linkage is more favorable for the spin filtering efficiency of current than the meso linkages. The spin-up and spin-down energy levels show the different evolutions which is responsible for the difference of spin filtering efficiency between the two linkage modes. The computational results of total current show that the meso-linked molecular junctions have the better conductive performances than the beta-linked ones which may be caused by the different electronic transport paths.

Annealing effect for self-assembled monolayers formed from terphenylethanethiol on Au(111)

Formation of several different structural phases and desorption took place from a standing-up phase at an annealing temperature of 473 K.

Introducing mesoscopic charge transfer rates into molecular electronics

It has been demonstrated that the concept of mesoscopic rate is able to establish a bridge between electrochemical and molecular electronic concepts.

Tuning of electron tunneling: a case study using BODIPY molecular layers

Using simple surface chemistry, rectification characteristics can be tuned to reproducible negative differential resistance (NDR) with a very high peak-to-valley ratio (PVR) up to 1000 in BODIPY grafted on Si.

Electric-Field-Controllable Conductance Switching of an Overcrowded Ethylene Self-Assembled Monolayer

Molecular isomerism has been discussed from the viewpoint of the tiniest switch and memory elements in electronics. Here, we report an overcrowded ethylene-based molecular conductance switch, which fulfills all the essential requirements for implementation into electronic devices, namely, electric-field-controllable reversible conductance change with a molecular-level spatial resolution, robust conformational bistability under ambient conditions, and ordered monolayer formation on electrode surfaces. The conformational state of this overcrowded ethylene, represented by a folded or twisted conformer, is susceptible to external environments. Nanoscopic measurements using scanning tunneling microscopy techniques, together with theoretical simulations, revealed the electronic properties of each conformer adsorbed on Au(111). While the twisted conformer prevails in the molecularly dispersed state, upon self-assembly into a monolayer, a two-dimensional network structure of the folded conformer is preferentially formed due to particular intermolecular interaction. In the monolayer state, folded-to-twisted and its reverse isomerization can be controlled by the modulation of electric fields.

Correlated impurity complex in the asymmetric tunneling contact: an ideal system to observe negative tunneling conductivity

We studied theoretically electron transport through the impurity complex localized between the tunneling contact leads by means of the generalized Keldysh diagram technique. The formation of multiple well pronounced regions with negative tunneling conductivity in the I-V characteristics was revealed. The appearance of negative tunneling conductivity is caused by the presence of both strong Coulomb correlations and the asymmetry of tunneling rates, which lead to the blockade of the electron transport through the system for a certain values of applied bias. The developed theory and obtained results may be useful for the application of impurity (dopant) atoms as a basic elements in modern nanoelectronic circuits.

In Operando Characterization and Control over Intermittent Light Emission from Molecular Tunnel Junctions via Molecular Backbone Rigidity

In principle, excitation of surface plasmons by molecular tunnel junctions can be controlled at the molecular level. Stable electrical excitation sources of surface plasmons are therefore desirable. Herein, molecular junctions are reported where tunneling charge carriers excite surface plasmons in the gold bottom electrodes via inelastic tunneling and it is shown that the intermittent light emission (blinking) originates from conformational dynamics of the molecules. The blinking rates, in turn, are controlled by changing the rigidity of the molecular backbone. Power spectral density analysis shows that molecular junctions with flexible aliphatic molecules blink, while junctions with rigid aromatic molecules do not.

Porphyrinoid–Fullerene Hybrids as Candidates in Artificial Photosynthetic Schemes

Natural photosynthesis inspired the scientific community to design and synthesize molecular assemblies that possess advanced light-harvesting and electron-transfer features. In this review, we present the preparation and the photophysical investigation of novel porphyrin–fullerene hybrids acting as artificial photosynthetic systems. Porphyrinoids stand as chlorophyll analogues and have emerged as suitable photosensitizers in supramolecular electron donor–acceptor hybrids. Fullerenes (C60) are versatile electron acceptors with small reorganization energy and low reduction potentials. The novel derivatives presented herein mimic the fundamental features of the photosynthetic reaction center, namely, light harvesting, charge separation, and charge transport. To this end, a comprehensive analysis on these key processes that occur in various porphyrin–fullerene entities is illustrated in this work.

Photoinduced Charge Transfer in Single-Molecule p-n Junctions

We measured photoinduced charge separation in isolated individual C₆₀-tethered 2,5-dithienylpyrrole triad (C₆₀ triad) molecules with submolecular resolution using a custom-built laser-assisted scanning tunneling microscope. Laser illumination was introduced evanescently into the tunneling junction through total internal reflection, and the changes in tunneling current and electronic spectra caused by photoexcitation were measured and spatially resolved. Photoinduced charge separation was not detected for all C₆₀ triad molecules, indicating that the conformations of the molecules may affect the excitation probability, lifetime, and/or charge distribution. A photoinduced signal was not observed for dodecanethiol molecules in the surrounding matrix or for control molecules without C₆₀ moieties, as neither absorbs incident photons at this energy. This spectroscopic imaging technique has the potential to elucidate detailed photoinduced carrier dynamics, which are inaccessible via ensemble-scale (i.e., averaging) measurements, which can be used to direct the rational design and optimization of molecular p-n junctions and assemblies for energy harvesting.

Reversible Photoisomerization of Monolayers of π-Expanded Oligothiophene Macrocycles at Solid-Liquid Interfaces

Self‐assembled monolayers of a π‐expanded oligothiophene macrocycle undergo photoisomerization between their Z,Z and E,E diastereomers at the interface between octanoic acid solutions and highly oriented pyrolytic graphite (HOPG). The switching process proceeds in situ at the solid–liquid interface and was followed by scanning tunneling microscopy (STM). Upon illumination with light at 365 nm (546 nm), a monolayer of Z,Z‐8mer (E,E‐8mer) photoisomerizes to the E,E‐8mer (Z,Z‐8mer) form with changes in 2D hexagonal packing. These findings provide insight towards the design of photoresponsive surfaces with desirable optoelectronic and structural (host–guest) properties.

Nucleotide and structural label identification in single RNA molecules with quantum tunneling spectroscopy

Although a number of advances have been made in RNA sequencing and structural characterization, the lack of a method for directly determining the sequence and structure of single RNA molecules has limited our ability to probe heterogeneity in gene expression at the level of single cells. Here we present a method for direct nucleotide identification and structural label mapping of single RNA molecules via Quantum Molecular Sequencing (QMSeq). The method combines non-perturbative quantum tunneling spectroscopy to probe the molecular orbitals of ribonucleotides, new experimental biophysical parameters that fingerprint these molecular orbitals, and a machine learning classification algorithm to distinguish between the ribonucleotides. The algorithm uses tunneling spectroscopy measurements on an unknown ribonucleotide to determine its chemical identity and the presence of local chemical modifications. Combining this with structure-dependent chemical labeling presents the possibility of mapping both the sequence and local structure of individual RNA molecules. By optimizing the base-calling algorithm, we show a high accuracy for both ribonucleotide discrimination (>99.8%) and chemical label identification (>98%) with a relatively modest molecular coverage (35 repeat measurements). This lays the groundwork for simultaneous sequencing and structural mapping of single unknown RNA molecules, and paves the way for probing the sequence-structure-function relationship within the transcriptome at an unprecedented level of detail.

Supramolecular Assemblies on Surfaces: Nanopatterning, Functionality, and Reactivity

Understanding how molecules interact to form large-scale hierarchical structures on surfaces holds promise for building designer nanoscale constructs with defined chemical and physical properties. Here, we describe early advances in this field and highlight upcoming opportunities and challenges. Both direct intermolecular interactions and those that are mediated by coordinated metal centers or substrates are discussed. These interactions can be additive, but they can also interfere with each other, leading to new assemblies in which electrical potentials vary at distances much larger than those of typical chemical interactions. Earlier spectroscopic and surface measurements have provided partial information on such interfacial effects. In the interim, scanning probe microscopies have assumed defining roles in the field of molecular organization on surfaces, delivering deeper understanding of interactions, structures, and local potentials. Self-assembly is a key strategy to form extended structures on surfaces, advancing nanolithography into the chemical dimension and providing simultaneous control at multiple scales. In parallel, the emergence of graphene and the resulting impetus to explore 2D materials have broadened the field, as surface-confined reactions of molecular building blocks provide access to such materials as 2D polymers and graphene nanoribbons. In this Review, we describe recent advances and point out promising directions that will lead to even greater and more robust capabilities to exploit designer surfaces.

Quantum Transport through a Single Conjugated Rigid Molecule, a Mechanical Break Junction Study

This Account provides an overview of our recent efforts to unravel charge transport characteristics of a metal-molecule-metal junction containing an individual π-conjugated molecule. The model system of our choice is an oligo(phenylene-ethynylene) consisting of three rings, in short OPE3, which represents a paradigmatic model system for molecular-scale electronics. Members of the OPE family are among the most studied in the field thanks to their simple and rigid structure, the possibility of chemically functionalizing them, and their clear transport characteristics. When investigating charge transport in molecular systems, two general directions can be distinguished: one in which assemblies composed of many molecules contacted in parallel are studied, while in the other a single molecule is investigated at a time. In the former approach, molecule-molecule interactions and ensemble-averaged quantities may play a role, thereby introducing broadening of spectral features and hindering the study of the behavior of individual molecules making it more difficult to deconvolute local and intrinsic molecular effects from collective ones. In contrast, single-molecule experiments directly probe individual molecular features and, when they are repeated many times, allow build up of a statistical representation of the changes introduced by, e.g., different junction configurations. Especially in recent years, experimental techniques have advanced such that now large sets of individual events can be measured and analyzed with statistical tools. To study individual single-molecule junctions, we use the break junction technique, in which two sharp movable electrodes are formed by breaking a thin metallic wire and used to contact a single or few molecules. By probing thousands of single-molecule junctions in different conditions, we show that their creation involves independent events justifying the statistical tools that are used. By combining room- and low-temperature data, we show that the dominant transport mechanism for electrons through the OPE3 molecule is off-resonant tunneling. The simplest model capturing transport details in this case is a single-level model characterized by three parameters: the level alignment of the frontier orbital with the Fermi energy of the leads and the electronic couplings to the leads. Variations in these parameters give a broad distribution (1 order of magnitude) in the observed conductance values, indicating that at the microscopic level both the hybridization with the metallic electrodes and the molecular electronic configuration can fluctuate. The low-temperature data show that these variations are due to abrupt changes in the configuration of the molecule in the junction leading to changes in either one of these parameters or both at the same time. The complementary information gained from different experiments is needed to build up a consistent and extended picture of the variability of molecular configurations, omnipresent in single-molecule studies. Knowledge of this variability can help one to better understand the behavior of molecules at the atomic level and at the metal-molecule interface in particular.

An Unusual Salt Effect in an Interfacial Nucleophilic Substitution Reaction

This paper reports a kinetic characterization of the interfacial reaction of N-methylpyrrolidine with a self-assembled monolayer presenting an iodoalkyl group. SAMDI (self-assembled monolayers for matrix-assisted laser desorption/ionization) mass spectrometry was used to determine the extent of reaction for monolayers that were treated with a range of concentrations of the nucleophile for a range of times. These data revealed a second-order rate constant for the reaction that was approximately 100-fold greater than that for the analogous solution-phase reaction. However, addition of sodium iodide to the reaction mixture resulted in a 7-fold decrease in the reaction rate. Addition of bromide and chloride salts also gave slower rate constants for the reaction, but only at 100- and 1000-fold higher concentrations than was observed with iodide, respectively. The corresponding solution-phase reactions, by contrast, had rate constants that were unaffected by the concentration of halide salts. This work provides a well-characterized example illustrating the extent to which the kinetics and properties of an interfacial reaction can depart substantially from their better-understood solution-phase counterparts.

Effect of molecular conformations on the electronic transport in oxygen-substituted alkanethiol molecular junctions

The relationship between the molecular structure and the electronic transport properties of molecular junctions based on thiol-terminated oligoethers, which are obtained by replacing every third methylene unit in the corresponding alkanethiols with an oxygen atom, is investigated by employing the non-equilibrium Green's function formalism combined with density functional theory. Our calculations show that the low-bias conductance depends strongly on the conformation of the oligoethers in the junction. Specifically, in the cases of trans-extended conformation, the oxygen-dominated transmission peaks are very sharp and well below the Fermi energy, E_F, thus hardly affect the transmission around E_F; the Au-S interface hybrid states couple with σ-bonds in the molecular backbone forming the conduction channel at E_F, resulting in a conductance decay against the molecular length close to that for alkanethiols. By contrast, for junctions with oligoethers in helical conformations, some π-type oxygen orbitals coupling with the Au-S interface hybrid states contribute to the transmission around E_F. The molecule-electrode electronic coupling is also enhanced at the non-thiol side due to the specific spatial orientation introduced by the twist of the molecular backbone. This leads to a much smaller conductance decay constant. Our findings highlight the important role of the molecular conformation of oligoethers in their electronic transport properties and are also helpful for the design of molecular wires with heteroatom-substituted alkanethiols.

Monitoring the Dynamic Process of Formation of Plasmonic Molecular Junctions during Single Nanoparticle Collisions

The capability to study the dynamic formation of plasmonic molecular junction is of fundamental importance, and it will provide new insights into molecular electronics/plasmonics, single-entity electrochemistry, and nanooptoelectronics. Here, a facile method to form plasmonic molecular junctions is reported by utilizing single gold nanoparticle (NP) collision events at a highly curved gold nanoelectrode modified with a self-assembled monolayer. By using time-resolved electrochemical current measurement and surface-enhanced Raman scattering spectroscopy, the current changes and the evolution of interfacial chemical bonding are successfully observed in the newly formed molecular tunnel junctions during and after the gold NP "hit-n-stay" and "hit-n-run" collision events. The results lead to an in-depth understanding of the single NP motion and the associated molecular level changes during the formation of the plasmonic molecular junctions in a single NP collision event. This method also provides a new platform to study molecular changes at the single molecule level during electron transport in a dynamic molecular tunnel junction.

Acid-Base Control of Valency within Carboranedithiol Self-Assembled Monolayers: Molecules Do the Can-Can

We use simple acid-base chemistry to control the valency in self-assembled monolayers of two different carboranedithiol isomers on Au{111}. Monolayer formation proceeds via Au-S bonding, where manipulation of pH prior to or during deposition enables the assembly of dithiolate species, monothiol/monothiolate species, or combination. Scanning tunneling microscopy (STM) images identify two distinct binding modes in each unmodified monolayer, where simultaneous spectroscopic imaging confirms different dipole offsets for each binding mode. Density functional theory calculations and STM image simulations yield detailed understanding of molecular chemisorption modes and their relation with the STM images, including inverted contrast with respect to the geometric differences found for one isomer. Deposition conditions are modified with controlled equivalents of either acid or base, where the coordination of the molecules in the monolayers is controlled by protonating or deprotonating the second thiol/thiolate on each molecule. This control can be exercised during deposition to change the valency of the molecules in the monolayers, a process that we affectionately refer to as the "can-can." This control enables us to vary the density of molecule-substrate bonds by a factor of 2 without changing the molecular density of the monolayer.

Diacetylene polymerization on a bulk insulator surface

Molecular electronics has great potential to surpass known limitations in conventional silicon-based technologies. The development of molecular electronics devices requires reliable strategies for connecting functional molecules by wire-like structures. To this end, diacetylene polymerization has been discussed as a very promising approach for contacting single molecules with a conductive polymer chain. A major challenge for future device fabrication is transferring this method to bulk insulator surfaces, which are mandatory to decouple the electronic structure of the functional molecules from the support surface. Here, we provide experimental evidence for diacetylene polymerization of 3,3'-(1,3-butadiyne-1,4-diyl)bisbenzoic acid precursors on the (10.4) surface of calcite, a bulk insulator with a band gap of around 6 eV. When deposited on the surface held at room temperature, ordered islands with a (1 × 3) superstructure are observed using dynamic atomic force microscopy. A distinct change is revealed upon heating the substrate to 485 K. After heating, molecular stripes with a characteristic inner structure are formed that excellently match the expected diacetylene polymer chains in appearance and repeat distance. The corresponding density functional theory computations reveal molecular-level bonding patterns of both the (1 × 3) superstructure and the formed striped structure, confirming the assignment of on-surface diacetylene polymerization. Transferring the concept of using diacetylene polymerization for creating conductive connections to bulk insulator surfaces paves the way towards application-relevant systems for future molecular electronic devices.