Tracing electronic pathways in molecules by using inelastic tunneling spectroscopy

Using inelastic electron tunneling spectroscopy (IETS) to measure the vibronic structure of nonequilibrium molecular transport, aided by a quantitative interpretation scheme based on Green's function-density functional theory methods, we are able to characterize the actual pathways that the electrons traverse when moving through a molecule in a molecular transport junction. We show that the IETS observations directly index electron tunneling pathways along the given normal coordinates of the molecule. One can then interpret the maxima in the IETS spectrum in terms of the specific paths that the electrons follow as they traverse the molecular junction. Therefore, IETS measurements not only prove (by the appearance of molecular vibrational frequencies in the spectrum) that the tunneling charges, in fact, pass through the molecule, but also can be used to determine the transport pathways and how they change with the geometry and placement of molecules in junctions.     

Tunneling rates in electron transport through double-barrier molecular junctions in a scanning tunneling microscope

The scanning tunneling microscope enables atomic-scale measurements of electron transport through individual molecules. Copper phthalocyanine and magnesium porphine molecules adsorbed on a thin oxide film grown on the NiAl(110) surface were probed. The single-molecule junctions contained two tunneling barriers, vacuum gap, and oxide film. Differential conductance spectroscopy shows that electron transport occurs via vibronic states of the molecules. The intensity of spectral peaks corresponding to the individual vibronic states depends on the relative electron tunneling rates through the two barriers of the junction, as found by varying the vacuum gap tunneling rate by changing the height of the scanning tunneling microscope tip above the molecule. A simple, sequential tunneling model explains the observed trends.     

Conductivity of an atomically defined metallic interface

A mechanically formed electrical nanocontact between gold and tungsten is a prototypical junction between metals with dissimilar electronic structure. Through atomically characterized nanoindentation experiments and first-principles quantum transport calculations, we find that the ballistic conduction across this intermetallic interface is drastically reduced because of the fundamental mismatch between s wave-like modes of electron conduction in the gold and d wave-like modes in the tungsten. The mechanical formation of the junction introduces defects and disorder, which act as an additional source of conduction losses and increase junction resistance by up to an order of magnitude. These findings apply to nanoelectronics and semiconductor device design. The technique that we use is very broadly applicable to molecular electronics, nanoscale contact mechanics, and scanning tunneling microscopy.     

In situ superexchange electron transfer through a single molecule: a rectifying effect

An increasingly comprehensive body of literature is being devoted to single-molecule bridge-mediated electronic nanojunctions, prompted by their prospective applications in molecular electronics and single-molecule analysis. These junctions may operate in gas phase or electrolyte solution (in situ). For biomolecules, the latter is much closer to their native environment. Convenient target molecules are aromatic molecules, peptides, oligonucleotides, transition metal complexes, and, broadly, molecules with repetitive units, for which the conducting orbitals are energetically well below electronic levels of the solvent. A key feature for these junctions is rectification in the current-voltage relation. A common view is that asymmetric molecules or asymmetric links to the electrodes are needed to acquire rectification. However, as we show here, this requirement could be different in situ, where a structurally symmetric system can provide rectification because of the Debye screening of the electric field in the nanogap if the screening length is smaller than the bridge length. The Galvani potentials of each electrode can be varied independently and lead to a transistor effect. We explore this behavior for the superexchange mechanism of electron transport, appropriate for a wide class of molecules. We also include the effect of conformational fluctuations on the lowest unoccupied molecular orbital (LUMO) energy levels; that gives rise to non-Arrhenius temperature dependence of the conductance, affected by the molecule length. Our study offers an analytical formula for the current-voltage characteristics that demonstrates all these features. A detailed physical interpretation of the results is given with a discussion of reported experimental data.     

Charge Transport Characteristics of Molecular Electronic Junctions Studied by Transition Voltage Spectroscopy

The field of molecular electronics is prompted by tremendous opportunities for using a single-molecule and molecular monolayers as active components in integrated circuits. Until now, a wide range of molecular devices exhibiting characteristic functions, such as diodes, transistors, switches, and memory, have been demonstrated. However, a full understanding of the crucial factors that affect charge transport through molecular electronic junctions should yet be accomplished. Remarkably, recent advances in transition voltage spectroscopy (TVS) elucidate that it can provide key quantities for probing the transport characteristics of the junctions, including, for example, the position of the frontier molecular orbital energy relative to the electrode Fermi level and the strength of the molecule–electrode interactions. These parameters are known to be highly associated with charge transport behaviors in molecular systems and can then be used in the design of molecule-based devices with rationally tuned electronic properties. This article highlights the fundamental principle of TVS and then demonstrates its major applications to study the charge transport properties of molecular electronic junctions.     

Contactless experiments on individual DNA molecules show no evidence for molecular wire behavior

A fundamental requirement for a molecule to be considered a molecular wire (MW) is the ability to transport electrical charge with a reasonably low resistance. We have carried out two experiments that measure first, the charge transfer from an electrode to the molecule, and second, the dielectric response of the MW. The latter experiment requires no contacts to either end of the molecule. From our experiments we conclude that adsorbed individual DNA molecules have a resistivity similar to mica, glass, and silicon oxide substrates. Therefore adsorbed DNA is not a conductor, and it should not be considered as a viable candidate for MW applications. Parallel studies on other nanowires, including single-walled carbon nanotubes, showed conductivity as expected.     

A single-molecule diode

We have designed and synthesized a molecular rod that consists of two weakly coupled electronic pi -systems with mutually shifted energy levels. The asymmetry thus implied manifests itself in a current-voltage characteristic with pronounced dependence on the sign of the bias voltage, which makes the molecule a prototype for a molecular diode. The individual molecules were immobilized by sulfur-gold bonds between both electrodes of a mechanically controlled break junction, and their electronic transport properties have been investigated. The results indeed show diode-like current-voltage characteristics. In contrast to that, control experiments with symmetric molecular rods consisting of two identical pi-systems did not show significant asymmetries in the transport properties. To investigate the underlying transport mechanism, phenomenological arguments are combined with calculations based on density functional theory. The theoretical analysis suggests that the bias dependence of the polarizability of the molecule feeds back into the current leading to an asymmetric shape of the current-voltage characteristics, similar to the phenomena in a semiconductor diode.     

Constant-speed vibrational signaling along polyethyleneglycol chain up to 60-Å distance

A series of azido-PEG-succinimide ester oligomers with a number of repeating PEG units of 0, 4, 8, and 12 (azPEG0, 4, 8, and 12) was investigated using a relaxation-assisted two-dimensional infrared (RA 2DIR) spectroscopy method. The RA 2DIR method relies on the energy transport in molecules and is capable of correlating the frequencies of vibrational modes separated by large through-bond distances. Excitation of the azido group in the compounds at ca. 2,100 cm^-1 generates an excess energy which propagates in the molecule as well as dissipates into the solvent. We discovered that a part of the excess energy propagates ballistically via the covalent backbone of the molecules with a constant speed of ca. 550 m/s. The transport is described as a propagation of a vibrational wavepacket having a mean-free-path length of 10–15 Å. The discovery has the potential for developing new efficient signal transduction strategies for molecular electronics and biochemistry. It also permits extending the distances accessible in RA 2DIR structural measurements up to ca. 60 Å.     

Long-range charge hopping in DNA

The fundamental mechanisms of charge migration in DNA are pertinent for current developments in molecular electronics and electrochemistry-based chip technology. The energetic control of hole (positive ion) multistep hopping transport in DNA proceeds via the guanine, the nucleobase with the lowest oxidation potential. Chemical yield data for the relative reactivity of the guanine cations and of charge trapping by a triple guanine unit in one of the strands quantify the hopping, trapping, and chemical kinetic parameters. The hole-hopping rate for superexchange-mediated interactions via two intervening AT base pairs is estimated to be 10(9) s(-1) at 300 K. We infer that the maximal distance for hole hopping in the duplex with the guanine separated by a single AT base pair is 300 +/- 70 A. Although we encounter constraints for hole transport in DNA emerging from the number of the mediating AT base pairs, electron transport is expected to be nearly sequence independent because of the similarity of the reduction potentials of the thymine and of the cytosine.     

A fullerene molecular tip can detect localized and rectified electron tunneling within a single fullerene-porphyrin pair

A fullerene molecular tip was used to detect electron tunneling from a single porphyrin molecule. Electron tunneling was found to occur locally from an electron-donating moiety of the porphyrin to the fullerene through charge-transfer interaction between them. In addition, electron tunneling within the single fullerene-porphyrin pair exhibited rectifying behavior in which electrons can be driven only at the direction from the porphyrin to the fullerene. It is demonstrated that localized electron tunneling enables us to spatially visualize the frontier orbital of the porphyrin involved in electron tunneling. In addition, rectification demonstrates that the fullerene-porphyrin pair constitutes a molecular rectifier. We believe that molecular tips bring insight into intermolecular electron transmission toward realization of molecular electronics as shown here.     

Ion-transport chain of cytochrome oxidase: the two chain-direct coupling principle of energy coupling.

Cytochrome oxidase (ferrocytochrome c:oxygen oxidoreductase, EC 1.9.3.1) couples the aerobic oxidation of ferrocytochrome c to the cyclical transport of monovalent cations or to the active transport of monovalent and divalent cations. This transport capability is mediated by an intracomplex ion-transport chain of two protein-bound molecules of cardiolipin per molecule of cytochrome oxidase. Cardiolipin in a two-phase system shows the identical ionophoric pattern as does the cytochrome oxidase coupled system. A molecular model of the cardiolipin chain suggests the possibility of a cage-like structure through which cations can be transferred from phosphate group to phosphate group. The ion-transport chain and the electron-transport chain are anchored to the same set of subunits (I+IV); the close proximity of the two chains argues for the direct coupling of electron and cation flow. The ion-transport chain of cytochrome oxidase provides an introduction to the molecular mechanisms by which ions are moved across membranes in energy-coupling systems.     

Complementary base-pair-facilitated electron tunneling for electrically pinpointing complementary nucleobases

Molecular tips in scanning tunneling microscopy can directly detect intermolecular electron tunneling between sample and tip molecules and reveal the tunneling facilitation through chemical interactions that provide overlap of respective electronic wave functions, that is, hydrogen-bond, metal-coordination-bond, and charge-transfer interactions. Nucleobase molecular tips were prepared by chemical modification of underlying metal tips with thiol derivatives of adenine, guanine, cytosine, and uracil and the outmost single nucleobase adsorbate probes intermolecular electron tunneling to or from a sample nucleobase molecule. We found that the electron tunneling between a sample nucleobase and its complementary nucleobase molecular tip was much facilitated compared with its noncomplementary counterpart. The complementary nucleobase tip was thereby capable of electrically pinpointing each nucleobase. Chemically selective imaging using molecular tips may be coined "intermolecular tunneling microscopy" as its principle goes and is of general significance for novel molecular imaging of chemical identities at the membrane and solid surfaces.     

DNA molecule provides a computing machine with both data and fuel

The unique properties of DNA make it a fundamental building block in the fields of supramolecular chemistry, nanotechnology, nano-circuits, molecular switches, molecular devices, and molecular computing. In our recently introduced autonomous molecular automaton, DNA molecules serve as input, output, and software, and the hardware consists of DNA restriction and ligation enzymes using ATP as fuel. In addition to information, DNA stores energy, available on hybridization of complementary strands or hydrolysis of its phosphodiester backbone. Here we show that a single DNA molecule can provide both the input data and all of the necessary fuel for a molecular automaton. Each computational step of the automaton consists of a reversible software molecule input molecule hybridization followed by an irreversible software-directed cleavage of the input molecule, which drives the computation forward by increasing entropy and releasing heat. The cleavage uses a hitherto unknown capability of the restriction enzyme FokI, which serves as the hardware, to operate on a noncovalent software input hybrid. In the previous automaton, software input ligation consumed one software molecule and two ATP molecules per step. As ligation is not performed in this automaton, a fixed amount of software and hardware molecules can, in principle, process any input molecule of any length without external energy supply. Our experiments demonstrate 3 x 10(12) automata per microl performing 6.6 x 10(10) transitions per second per microl with transition fidelity of 99.9%, dissipating about 5 x 10(-9) W microl as heat at ambient temperature.     

Programmable motion and patterning of molecules on solid surfaces

Adsorbed on a solid surface, a molecule can migrate and carry an electric dipole moment. A nonuniform electric field can direct the motion of the molecule. A collection of the same molecules may aggregate into a monolayer island on the solid surface. Place such molecules on a dielectric substrate surface, beneath which an array of electrodes is buried. By varying the voltages of the electrodes individually, it is possible to program molecular patterning, direct an island to move in a desired trajectory, or merge several islands into a larger one. The dexterity may lead to new technologies, such as reconfigurable molecular patterning and programmable molecular cars. This paper develops a phase field model to simulate the molecular motion and patterning under the combined actions of dipole moments, intermolecular forces, entropy, and electrodes.     

Molecular electronics sensors on a scalable semiconductor chip: A platform for single-molecule measurement of binding kinetics and enzyme activity

For nearly 50 years, the vision of using single molecules in circuits has been seen as providing the ultimate miniaturization of electronic chips. An advanced example of such a molecular electronics chip is presented here, with the important distinction that the molecular circuit elements play the role of general-purpose single-molecule sensors. The device consists of a semiconductor chip with a scalable array architecture. Each array element contains a synthetic molecular wire assembled to span nanoelectrodes in a current monitoring circuit. A central conjugation site is used to attach a single probe molecule that defines the target of the sensor. The chip digitizes the resulting picoamp-scale current-versus-time readout from each sensor element of the array at a rate of 1,000 frames per second. This provides detailed electrical signatures of the single-molecule interactions between the probe and targets present in a solution-phase test sample. This platform is used to measure the interaction kinetics of single molecules, without the use of labels, in a massively parallel fashion. To demonstrate broad applicability, examples are shown for probe molecule binding, including DNA oligos, aptamers, antibodies, and antigens, and the activity of enzymes relevant to diagnostics and sequencing, including a CRISPR/Cas enzyme binding a target DNA, and a DNA polymerase enzyme incorporating nucleotides as it copies a DNA template. All of these applications are accomplished with high sensitivity and resolution, on a manufacturable, scalable, all-electronic semiconductor chip device, thereby bringing the power of modern chips to these diverse areas of biosensing.

Rapid, specific, and sensitive measurements of target analytes are the goals of many methods used in molecular biology and biotechnology. Bulk methods typically use a binding molecule to recognize the target molecule, combined with indirect optical reporter mechanisms, such as fluorescent dye labels or changes in bulk optical properties resulting from target binding. Such classical methods detect an average over many molecular binding events, and over timescales much longer than that of the primary molecular interactions. In contrast, the binding interactions of interest fundamentally occur at the single-molecule level, and are typically dynamic and stochastic in time, and thus contain far more detail than what is reflected in bulk reaction rates. This highlights the potential to access a fundamentally richer and more powerful level of information when measuring molecular interactions.Approaches to observing the details of single-molecule interactions fall into categories based on the detection method (1). Many are fluorescence-based single-molecule optical biosensors (2–5), although other specialized physical techniques have been used, including electrochemical sensors (6, 7), plasmonic sensors (8), surface-enhanced Raman spectroscopy (9), and methods coupled to nanopore detection (3, 10, 11). In addition to complications of labeling procedures needed to add fluorescent reporters to targets of interest, single-molecule optical methods suffer from fundamental limitations in signal and resolution. A major challenge for single-molecule fluorescence methods is obtaining high signal-to-noise ratio, because the rate of photon production from single dye molecules is restricted by illumination intensity limits and photo-bleaching (12), constraining both short-time and long-time measurements. Molecular motion effects and diffraction also limit the ultimate spatial resolution or density of multiplex optical reporters.Moving away from photon-based detection to all-electronic detection can remove these fundamental constraints on signal-to-noise ratio, scaling, and bandwidth, and moreover is maximally compatible with implementation on modern semiconductor chip devices. It would be advantageous to measure molecular interactions on a complementary metal-oxide semiconductor (CMOS) chip to leverage their low-cost mass manufacturing, speed, and miniaturization. These are hallmarks of modern CMOS chip-based devices, such as portable computers and cell phones. Such on-chip devices also enjoy a durable roadmap for future improvements provided by 50 years of Moore’s Law scaling of CMOS chips, and corresponding chip foundry infrastructure and supply chains.However, the full potential of this vision of moving molecular biosensing “on-chip” can only be realized by using a suitably compatible sensor concept. To this end, there are three fundamental sensor design principles to consider: manufacturability, scalability, and universality (see SI Appendix). The field of molecular electronics provides a conceptual solution to all of these challenges, wherein a single-molecule in a circuit would provide the fully scaled sensor to solve the More-than-Moore scaling problem common to sensor devices. Scientific advances on the electrical properties of molecules, as well as bioelectronic inspirations, led to the proposal in the early 1970s that single molecules could be engineered for use as circuit elements (13), to perform circuit functions such as a rectifier or switch. Due to limitations of nanofabrication technology, it was not until the late 1990s that the first single-molecule circuits were demonstrated experimentally (14). Interest in this field of molecular electronics expanded dramatically after that point (15–18), and it was proclaimed the scientific breakthrough of the year by Science in 2000 (19). There it was noted that integrating molecules into chips would be the critical advance needed for this new field to have broad impact.The experimental study of single-molecule electronic sensing was initially based on carbon nanotube (CNT) sensor devices. Their potential as sensors for single-molecule interactions became apparent (20) initially in the context of sensing gas molecules (21) and then chemical reactions (22). Nuckolls, Shepard, and colleagues (23–25) introduced a single-molecule sensor for DNA–DNA binding (hybridization) processes, by functionalizing a CNT with a single DNA oligomer “probe” molecule. Collins, Weiss, and colleagues (26–28) showed that a CNT can be used for real-time monitoring of the activity of a single enzyme molecule attached to nanotube, including DNA polymerase enzymes. Unfortunately, at present there is no way to mass manufacture CNTs having precise structure and functionalizations, and despite decades of attention (20), there is also no established path to integrating them into manufacturable CMOS chip devices (29, 30). Thus, while CNT molecular wire sensors enabled pioneering work on single-molecule sensing, they do not satisfy the design principles for a CMOS chip sensor platform.In contrast, an ideal molecular wire should allow precision engineering to provide a site-specific conjugation moiety for attachment of probe molecules, as well as to provide suitable end groups for self-assembly into the nanoelectrodes on a CMOS chip, and should be readily available through existing manufacturing processes. This limits the candidates to peptides, proteins, or DNA as molecular wires, as these are in fact the only conducting polymers for which there are well-developed precision synthesis capabilities, including extensive means of precision functionalization. Double-stranded DNA (dsDNA) helices (31–35) and protein α-helices (36–45) have both been studied as molecular wires. Examples from direct current measurements through various (short) α-helixes in the literature (42) suggest a (long) 25-nm α-helix could exhibit currents in the broad range of 3 picoamp (pA) to 120 pA at 1 volt bias, depending on the amino acid sequence, buffer conditions, and the nature of the peptide–metal attachment. Detailed tunneling probe methods have also recently been used to study conduction through larger proteins (46–49). While not nearly as conductive as CNTs, these biopolymers have the great advantage for present purposes of allowing precision engineering using existing manufacturing capacity.     

Organic Zeolite Analogues Based on Multi-Component Liquid Crystals: Recognition and Transformation of Molecules within Constrained Environments

In liquid crystals (LCs), molecules are confined in peculiar environments, where ordered alignment and certain mobility are realized at the same time. Considering these characteristics, the idea of “controlling molecular events within LC media” seems reasonable. As a suitable system for investigating this challenge, we have recently developed a new class of ionic LCs; the salts of amphiphilic carboxylic acids with 2-amino alcohols, or those of carboxylic acids with amphiphilic 2-amino alcohols, have a strong tendency to exhibit thermotropic LC phases. Because of the noncovalent nature of the interaction between molecules, one of the two components can easily be exchanged with, or transformed into, another molecule, without distorting the original LC architecture. In addition, both components are common organic molecules, and a variety of compounds are easily available. Taking advantage of these characteristics, we have succeeded in applying two-component LCs as chiral media for molecular recognition and reactions. This review presents an overview of our recent studies, together with notable reports related to this field.     

Computational and Experimental Study of Nonlinear Optical Susceptibilities of Composite Materials Based on PVK Polymer Matrix and Benzonitrile Derivatives

Theoretical and experimental investigations of the linear and nonlinear optical properties of composite materials based on the (Z)-4-(1-cyano-2-(5-methylfuran-2-yl)vinyl)benzonitrile molecule named as A, the (Z)-4-(2-(benzofuran-2-yl)-1-cyanovinyl)benzonitrile named as B and the (Z)-4-(2-(4-(9H-carbazol-9-yl)phenyl)-1-cyanovinyl)benzonitrile molecule named as C embedded into poly(1-vinylcarbazole) (PVK) polymer matrix were performed. The electronic and optical properties of A, B, and C molecules in a vacuum and PVK were calculated. The guest–host polymer structures for A, B, and C molecules in PVK were modeled using molecular dynamics simulations. The spatial distribution of chromophores in the polymer matrix was investigated using the intermolecular radial distribution (RDF) function. The reorientation of A, B, and C molecules under the influence of the external electric field was investigated by measuring the time-dependent arrangement of the angle between the dipole moment of the chromophore and the external electric field. The polarizabilities and hyperpolarizabilities of tested compounds have been calculated applying the DFT/B3LYP functional. The second- and third-order nonlinear optical properties of the molecule/PVK thin film guest–host systems were investigated by the Maker fringes technique in the picosecond regime at the fundamental wavelength of 1064 nm. The experimental results were confirmed and explained with theoretical simulations and were found to be in good agreement. The modeling of the composites in volumetric and thin-film form explains the poling phenomena caused by the external electric field occurring with the confinement effect.     

Effect of Impurity Adsorption on the Electronic and Transport Properties of Graphene Nanogaps

Graphene stands out as a versatile material with several uses in fields that range from electronics to biology. In particular, graphene has been proposed as an electrode in molecular electronics devices that are expected to be more stable and reproducible than typical ones based on metallic electrodes. In this work, we study by means of first principles, simulations and a tight-binding model the electronic and transport properties of graphene nanogaps with straight edges and different passivating atoms: Hydrogen or elements of the second row of the periodic table (boron, carbon, nitrogen, oxygen, and fluoride). We use the tight-binding model to reproduce the main ab-initio results and elucidate the physics behind the transport properties. We observe clear patterns that emerge in the conductance and the current as one moves from boron to fluoride. In particular, we find that the conductance decreases and the tunneling decaying factor increases from the former to the latter. We explain these trends in terms of the size of the atom and its onsite energy. We also find a similar pattern for the current, which is ohmic and smooth in general. However, when the size of the simulation cell is the smallest one along the direction perpendicular to the transport direction, we obtain highly non-linear behavior with negative differential resistance. This interesting and surprising behavior can be explained by taking into account the presence of Fano resonances and other interference effects, which emerge due to couplings to side atoms at the edges and other couplings across the gap. Such features enter the bias window as the bias increases and strongly affect the current, giving rise to the non-linear evolution. As a whole, these results can be used as a template to understand the transport properties of straight graphene nanogaps and similar systems and distinguish the presence of different elements in the junction.