Towards molecular electronics with large-area molecular junctions

Electronic transport through single molecules has been studied extensively by academic and industrial research groups. Discrete tunnel junctions, or molecular diodes, have been reported using scanning probes, break junctions, metallic crossbars and nanopores. For technological applications, molecular tunnel junctions must be reliable, stable and reproducible. The conductance per molecule, however, typically varies by many orders of magnitude. Self-assembled monolayers (SAMs) may offer a promising route to the fabrication of reliable devices, and charge transport through SAMs of alkanethiols within nanopores is well understood, with non-resonant tunnelling dominating the transport mechanism. Unfortunately, electrical shorts in SAMs are often formed upon vapour deposition of the top electrode, which limits the diameter of the nanopore diodes to about 45 nm. Here we demonstrate a method to manufacture molecular junctions with diameters up to 100 microm with high yields (> 95 per cent). The junctions show excellent stability and reproducibility, and the conductance per unit area is similar to that obtained for benchmark nanopore diodes. Our technique involves processing the molecular junctions in the holes of a lithographically patterned photoresist, and then inserting a conducting polymer interlayer between the SAM and the metal top electrode. This simple approach is potentially low-cost and could pave the way for practical molecular electronics.     

Measurement of the conductance of a hydrogen molecule

Recent years have shown steady progress towards molecular electronics, in which molecules form basic components such as switches, diodes and electronic mixers. Often, a scanning tunnelling microscope is used to address an individual molecule, although this arrangement does not provide long-term stability. Therefore, metal-molecule-metal links using break-junction devices have also been explored; however, it is difficult to establish unambiguously that a single molecule forms the contact. Here we show that a single hydrogen molecule can form a stable bridge between platinum electrodes. In contrast to results for organic molecules, the bridge has a nearly perfect conductance of one quantum unit, carried by a single channel. The hydrogen bridge represents a simple test system in which to understand fundamental transport properties of single-molecule devices.     

Single-electron transistor of a single organic molecule with access to several redox states

A combination of classical Coulomb charging, electronic level spacings, spin, and vibrational modes determines the single-electron transfer reactions through nanoscale systems connected to external electrodes by tunnelling barriers. Coulomb charging effects have been shown to dominate such transport in semiconductor quantum dots, metallic and semiconducting nanoparticles, carbon nanotubes, and single molecules. Recently, transport has been shown to be also influenced by spin--through the Kondo effect--for both nanotubes and single molecules, as well as by vibrational fine structure. Here we describe a single-electron transistor where the electronic levels of a single pi-conjugated molecule in several distinct charged states control the transport properties. The molecular electronic levels extracted from the single-electron-transistor measurements are strongly perturbed compared to those of the molecule in solution, leading to a very significant reduction of the gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital. We suggest, and verify by simple model calculations, that this surprising effect could be caused by image charges generated in the source and drain electrodes resulting in a strong localization of the charges on the molecule.     

A nanometre-scale electronic switch consisting of a metal cluster and redox-addressable groups

So-called bottom-up fabrication methods aim to assemble and integrate molecular components exhibiting specific functions into electronic devices that are orders of magnitude smaller than can be fabricated by lithographic techniques. Fundamental to the success of the bottom-up approach is the ability to control electron transport across molecular components. Organic molecules containing redox centres-chemical species whose oxidation number, and hence electronic structure, can be changed reversibly-support resonant tunnelling and display promising functional behaviour when sandwiched as molecular layers between electrical contacts, but their integration into more complex assemblies remains challenging. For this reason, functionalized metal nanoparticles have attracted much interest: they exhibit single-electron characteristics (such as quantized capacitance charging) and can be organized through simple self-assembly methods into well ordered structures, with the nanoparticles at controlled locations. Here we report scanning tunnelling microscopy measurements showing that organic molecules containing redox centres can be used to attach metal nanoparticles to electrode surfaces and so control the electron transport between them. Our system consists of gold nanoclusters a few nanometres across and functionalized with polymethylene chains that carry a central, reversibly reducible bipyridinium moiety. We expect that the ability to electronically contact metal nanoparticles via redox-active molecules, and to alter profoundly their tunnelling properties by charge injection into these molecules, can form the basis for a range of nanoscale electronic switches.     

分子链长对分子结电输运性质的影响

利用杂化密度泛函理论,研究了烷烃硫醇分子与金电极形成分子结的电子结构,利用弹性散射格林函数方法研究了烷烃硫醇分子的电输运性质,并同实验结果进行了比较。研究结果表明,在低的外加偏压下,烷烃硫醇分子电流值随着分子链长度的增加而指数减小。     

Field regulation of single-molecule conductivity by a charged surface atom

Electrical transport through molecules has been much studied since it was proposed that individual molecules might behave like basic electronic devices, and intriguing single-molecule electronic effects have been demonstrated. But because transport properties are sensitive to structural variations on the atomic scale, further progress calls for detailed knowledge of how the functional properties of molecules depend on structural features. The characterization of two-terminal structures has become increasingly robust and reproducible, and for some systems detailed structural characterization of molecules on electrodes or insulators is available. Here we present scanning tunnelling microscopy observations and classical electrostatic and quantum mechanical modelling results that show that the electrostatic field emanating from a fixed point charge regulates the conductivity of nearby substrate-bound molecules. We find that the onset of molecular conduction is shifted by changing the charge state of a silicon surface atom, or by varying the spatial relationship between the molecule and that charged centre. Because the shifting results in conductivity changes of substantial magnitude, these effects are easily observed at room temperature.     

Evidence for fixed charge in the nexus

The nexus or gap junction has been characterized as a low-resistance junction as well as a highly permeable junctional membrane to many molecules. The transfer of electrical current from one cell interior to another, the aqueous solubility of dyes used to trace cell to cell communication and the fact that these molecules move across the nexus more rapidly than the plasma membrane have led to the hypothesis of an aqueous channel in the junction. Both Ca2+ (ref.11) and H+ (ref. 12) are thought to alter nexal membrane conductance, and a voltage-sensitive gate has been demonstrated within the junction. Recently, Flagg-Newton et al. have concluded that mammalian junctions may contain fixed charge or be of smaller diameter than arthropod junctions. Here we have investigated these alternatives by examining the permeability of nexuses of septa of the median giant axon of Lumbricus terrestris with various derivatives of fluorescein. Both carboxyfluorescein and aminofluorescein were found to have depressed permeabilities relative to their predicted permeabilities based on molecular size and weight (MW). Flourescein diffusion was significantly suppressed in axons pre-injected with aminofluorescein but carboxyfluorescein had no such effect (Table 1). These data suggest the existence of fixed anionic charge within the nexal channel which may have affinity for amino groups.     

Electrically driven directional motion of a four-wheeled molecule on a metal surface

Propelling single molecules in a controlled manner along an unmodified surface remains extremely challenging because it requires molecules that can use light, chemical or electrical energy to modulate their interaction with the surface in a way that generates motion. Nature's motor proteins have mastered the art of converting conformational changes into directed motion, and have inspired the design of artificial systems such as DNA walkers and light- and redox-driven molecular motors. But although controlled movement of single molecules along a surface has been reported, the molecules in these examples act as passive elements that either diffuse along a preferential direction with equal probability for forward and backward movement or are dragged by an STM tip. Here we present a molecule with four functional units--our previously reported rotary motors--that undergo continuous and defined conformational changes upon sequential electronic and vibrational excitation. Scanning tunnelling microscopy confirms that activation of the conformational changes of the rotors through inelastic electron tunnelling propels the molecule unidirectionally across a Cu(111) surface. The system can be adapted to follow either linear or random surface trajectories or to remain stationary, by tuning the chirality of the individual motor units. Our design provides a starting point for the exploration of more sophisticated molecular mechanical systems with directionally controlled motion.     

Self-assembled monolayer organic field-effect transistors

The use of individual molecules as functional electronic devices was proposed in 1974 (ref. 1). Since then, advances in the field of nanotechnology have led to the fabrication of various molecule devices and devices based on monolayer arrays of molecules. Single molecule devices are expected to have interesting electronic properties, but devices based on an array of molecules are easier to fabricate and could potentially be more reliable. However, most of the previous work on array-based devices focused on two-terminal structures: demonstrating, for example, negative differential resistance, rectifiers, and re-configurable switching. It has also been proposed that diode switches containing only a few two-terminal molecules could be used to implement simple molecular electronic computer logic circuits. However, three-terminal devices, that is, transistors, could offer several advantages for logic operations compared to two-terminal switches, the most important of which is 'gain'-the ability to modulate the conductance. Here, we demonstrate gain for electronic transport perpendicular to a single molecular layer ( approximately 10-20 A) by using a third gate electrode. Our experiments with field-effect transistors based on self-assembled monolayers demonstrate conductance modulation of more than five orders of magnitude. In addition, inverter circuits have been prepared that show a gain as high as six. The fabrication of monolayer transistors and inverters might represent an important step towards molecular-scale electronics.     

Molecular control over Au/GaAs diodes

The use of molecules to control electron transport is an interesting possibility, not least because of the anticipated role of molecules in future electronic devices. But physical implementations using discrete molecules are neither conceptually simple nor technically straightforward (difficulties arise in connecting the molecules to the macroscopic environment). But the use of molecules in electronic devices is not limited to single molecules, molecular wires or bulk material. Here we demonstrate that molecules can control the electrical characteristics of conventional metal-semiconductor junctions, apparently without the need for electrons to be transferred onto and through the molecules. We modify diodes by adsorbing small molecules onto single crystals of n-type GaAs semiconductor. Gold contacts were deposited onto the modified surface, using a 'soft' method to avoid damaging the molecules. By using a series of multifunctional molecules whose dipole is varied systematically, we produce diodes with an effective barrier height that is tuned by the molecule's dipole moment. These barrier heights correlate well with the change in work function of the GaAs surface after molecular modification. This behaviour is consistent with that of unmodified metal-semiconductor diodes, in which the barrier height can depend on the metal's work function.     

Molecular manipulation using a tunnelling microscope

In a very short time the scanning tunnelling microscope has become an important tool in surface science, and physics in general. Its primary use has been to obtain atomic-resolution images of surfaces, but recently, efforts have been made to use it to manipulate materials as well as image them. One may now reasonably ask if it is possible to move and alter matter predictably on an atomic scale. Here we report the accomplishment of the smallest yet, purposeful, spatially localized changes in matter, effected on a graphite surface. We believe that the changes result from the pinning of individual organic molecules to the graphite. The reverse manipulation, the removal of pinned molecules, has also been demonstrated. Finally, we have evidence that we can remove a portion of a pinned molecule, effectively performing transformations on single molecules using the tunnelling microscope.     

Aquaporin-0 membrane junctions reveal the structure of a closed water pore

The lens-specific water pore aquaporin-0 (AQP0) is the only aquaporin known to form membrane junctions in vivo. We show here that AQP0 from the lens core, containing some carboxy-terminally cleaved AQP0, forms double-layered crystals that recapitulate in vivo junctions. We present the structure of the AQP0 membrane junction as determined by electron crystallography. The junction is formed by three localized interactions between AQP0 molecules in adjoining membranes, mainly mediated by proline residues conserved in AQP0s from different species but not present in most other aquaporins. Whereas all previously determined aquaporin structures show the pore in an open conformation, the water pore is closed in AQP0 junctions. The water pathway in AQP0 also contains an additional pore constriction, not seen in other known aquaporin structures, which may be responsible for pore gating.     

单分子二极管整流特性的第一性原理计算

在分子电子学领域中, 设计分子的结构可以实现特定的功能. 单分子二极管的整流行为是极具吸引力的器件功能之一. 研究了对称分子和非对称分子结的电子输运, 分别对应为四苯基和二嘧啶基二苯基单分子结, 二者均是共价结合到两金属电极. 与其同源对称嵌段相比, 非对称二嵌段分子表现出明显的整流行为, 且电子输运方向是从二苯基流向二嘧啶基. 利用密度泛函理论(density functional theory, DFT)和非平衡格林函数(non-equilibrium Green's function, NEGF)结合的第一性原理方法研究了单分子结的电子结构及其量子输运. 电流-电压 ($I$-$V$)曲线的非对称性可以用非对称分子二嵌段在偏压下由于电子态的局域性带来的非平衡效应进行解释. 本理论计算定性上符合其他小组的实验结果, 且尝试了不同的末端接触. 结果发现, 实验中的扫描隧道显微镜(scanning tunneling microscope, STM)针尖接触结构会一定程度地抵消非对称分子的整流效应, 而 STM 针尖接触结构的结果分析也符合之前的理论预测.     

Radio-frequency scanning tunnelling microscopy

The scanning tunnelling microscope (STM) relies on localized electron tunnelling between a sharp probe tip and a conducting sample to attain atomic-scale spatial resolution. In the 25-year period since its invention, the STM has helped uncover a wealth of phenomena in diverse physical systems--ranging from semiconductors to superconductors to atomic and molecular nanosystems. A severe limitation in scanning tunnelling microscopy is the low temporal resolution, originating from the diminished high-frequency response of the tunnel current readout circuitry. Here we overcome this limitation by measuring the reflection from a resonant inductor-capacitor circuit in which the tunnel junction is embedded, and demonstrate electronic bandwidths as high as 10 MHz. This approximately 100-fold bandwidth improvement on the state of the art translates into fast surface topography as well as delicate measurements in mesoscopic electronics and mechanics. Broadband noise measurements across the tunnel junction using this radio-frequency STM have allowed us to perform thermometry at the nanometre scale. Furthermore, we have detected high-frequency mechanical motion with a sensitivity approaching approximately 15 fm Hz(-1/2). This sensitivity is on par with the highest available from nanoscale optical and electrical displacement detection techniques, and the radio-frequency STM is expected to be capable of quantum-limited position measurements.     

Molecular structure of r(GCG)d(TATACGC): a DNA--RNA hybrid helix joined to double helical DNA

The molecule r(GCG)d(TATACGC) is self-complementary and forms two DNA--RNA hybrid segments surrounding a central region of double helical DNA; its molecular structure has been solved by X-ray analysis. All three parts of the molecule adopt a conformation which is close to that seen in the 11-fold RNA double helix. The conformation of the ribonucleotides is partly determined by water molecules bridging between the ribose O2' hydroxyl group and cytosine O2. The hybrid-DNA duplex junction contains no structural discontinuities. However, the central DNA TATA sequence has some structural irregularities.     

DNA bending induced by cruciform formation

Cruciform structures in DNA are of considerable interest, both as extreme examples of sequence-dependent structural heterogeneity and as models for four-way junctions such as the Holliday junction of homologous genetic recombination. Cruciforms are of lower thermodynamic stability than regular duplex DNA, and have been observed only in negatively supercoiled molecules, where the unfavourable free energy of formation is offset by the topological relaxation of the torsionally stressed molecule. From an experimental viewpoint this can be a disadvantage, as cruciform structures can be studied only in relatively large supercoiled DNA circles, and are destabilized when a break is introduced at any point. We therefore set out to construct a pseudo-cruciform junction--by generating hereroduplex formation between two inverted repeat sequences. Stereochemically, this should closely resemble a true cruciform but remain stable in a linear DNA fragment. We have now created such a junction and find that it has the expected sensitivities to endonucleases. These DNA fragments exhibit extremely anomalous gel electrophoretic mobility, the extent of which depends on the relative position of the pseudo-cruciform along the length of the molecule. Our results are very similar to those obtained by Wu and Crothers using kinetoplast DNA, and we conclude that the pseudo-cruciform junction introduces a bend in the linear DNA molecule.     

Direct measurement of electrical transport through DNA molecules

Attempts to infer DNA electron transfer from fluorescence quenching measurements on DNA strands doped with donor and acceptor molecules have spurred intense debate over the question of whether or not this important biomolecule is able to conduct electrical charges. More recently, first electrical transport measurements on micrometre-long DNA 'ropes', and also on large numbers of DNA molecules in films, have indicated that DNA behaves as a good linear conductor. Here we present measurements of electrical transport through individual 10.4-nm-long, double-stranded poly(G)-poly(C) DNA molecules connected to two metal nanoelectrodes, that indicate, by contrast, large-bandgap semiconducting behaviour. We obtain nonlinear current-voltage curves that exhibit a voltage gap at low applied bias. This is observed in air as well as in vacuum down to cryogenic temperatures. The voltage dependence of the differential conductance exhibits a peak structure, which is suggestive of the charge carrier transport being mediated by the molecular energy bands of DNA.     

Nanomechanical oscillations in a single-C60 transistor

The motion of electrons through quantum dots is strongly modified by single-electron charging and the quantization of energy levels. Much effort has been directed towards extending studies of electron transport to chemical nanostructures, including molecules, nanocrystals and nanotubes. Here we report the fabrication of single-molecule transistors based on individual C60 molecules connected to gold electrodes. We perform transport measurements that provide evidence for a coupling between the centre-of-mass motion of the C60 molecules and single-electron hopping--a conduction mechanism that has not been observed previously in quantum dot studies. The coupling is manifest as quantized nano-mechanical oscillations of the C60 molecule against the gold surface, with a frequency of about 1.2 THz. This value is in good agreement with a simple theoretical estimate based on van der Waals and electrostatic interactions between C60 molecules and gold electrodes.     

Crystal structure of T4 endonuclease VII resolving a Holliday junction

Holliday proposed a four-way DNA junction as an intermediate in homologous recombination, and such Holliday junctions have since been identified as a central component in DNA recombination and repair. Phage T4 endonuclease VII (endo VII) was the first enzyme shown to resolve Holliday junctions into duplex DNAs by introducing symmetrical nicks in equivalent strands. Several Holliday junction resolvases have since been characterized, but an atomic structure of a resolvase complex with a Holliday junction remained elusive. Here we report the crystal structure of an inactive T4 endo VII(N62D) complexed with an immobile four-way junction with alternating arm lengths of 10 and 14 base pairs. The junction is a hybrid of the conventional square-planar and stacked-X conformation. Endo VII protrudes into the junction point from the minor groove side, opening it to a 14 A x 32 A parallelogram. This interaction interrupts the coaxial stacking, yet every base pair surrounding the junction remains intact. Additional interactions involve the positively charged protein and DNA phosphate backbones. Each scissile phosphate that is two base pairs from the crossover interacts with a Mg2+ ion in the active site. The similar overall shape and surface charge potential of the Holliday junction resolvases endo VII, RuvC, Ydc2, Hjc and RecU, despite having different folds, active site composition and DNA sequence preference, suggest a conserved binding mode for Holliday junctions.     

Electrical generation and absorption of phonons in carbon nanotubes

The interplay between discrete vibrational and electronic degrees of freedom directly influences the chemical and physical properties of molecular systems. This coupling is typically studied through optical methods such as fluorescence, absorption and Raman spectroscopy. Molecular electronic devices provide new opportunities for exploring vibration-electronic interactions at the single molecule level. For example, electrons injected from a scanning tunnelling microscope tip into a metal can excite vibrational excitations of a molecule situated in the gap between tip and metal. Here we show how current directly injected into a freely suspended individual single-wall carbon nanotube can be used to excite, detect and control a specific vibrational mode of the molecule. Electrons tunnelling inelastically into the nanotube cause a non-equilibrium occupation of the radial breathing mode, leading to both stimulated emission and absorption of phonons by successive electron tunnelling events. We exploit this effect to measure a phonon lifetime of the order of 10 ns, corresponding to a quality factor of well over 10,000 for this nanomechanical oscillator.