Molecular Architectonics

The architecture of single-molecule Boolean logic gates can be based on classical, semi-classical, or quantum design rules. The advantages and limitations of each architecture in terms of computing power, clock frequency, and interconnects are discussed together with a complete description of the quantum Hamiltonian computing approach to help for comparison. For all those approaches, the often-mentioned problem of “contact” between a single molecule and a metallic nano-electrode must be re-analyzed in terms of quantum measurements. The metallic nano-electrodes of a tunnel junction is a true measurement apparatus, and its functioning is described by a new transduction function to pass from the intrinsic time-dependent electron transfer to the tunneling current intensity.

This chapter addresses various subjects, including some open questions related to energy dissipation, information, and noise, that are relevant for nano- and molecular electronics. The object is to give a brief and coherent presentation of the results of a number of recent studies of ours.

In recent years, molecular-protected metallic nanoparticles (NPs) have attracted a great deal of attention. Because of their reduced size, they behave like tiny capacitors so that there is an energy penalty when adding an electron to the NP which suppresses the electric current at a potential lower than a threshold value. This phenomenon is known as Coulomb blockade (CB) and allows the transport of electrons to be modulated through an external gate provided that the energy penalty is higher than the thermal energy. Together with the possibility of tailoring their properties, molecular protected NPs are potential candidates as future components of high density, low consumption electronics. However, they face a number of problems before they can be considered as a technological viable option. To be used at room temperatures, NPs radii need to be in the nanometer range, and then fabrication processes lead to significant variability in the NPs physical properties. We use here two systems, a XOR gate and a R-SET model which mimics some characteristics of neurons, to show strategies that may be used to cope with the variability problem so that a robust information processing can be achieved despite using nominally different components.

One of the key components in the single-molecule-based informatics is the interface between the single-molecule and the conventional electronics. This component reads out the very small charge state of the molecule in real time and also controls the charge state. A big challenge here is the precise operation under various fluctuations. In this chapter, we describe our recent results on detection of molecule charge state using a III-V compound semiconductor nanowire field-effect transistor (FET) having a metal gate electrode. It is found that the metal gate enhances the sensitivity to the molecule charge in an electrostatic manner. The dynamics of the molecule charge state is detected in terms of the drain current noise. Our unique technique is applied to single-molecule identification and detection of spatial distribution of charges in a molecular network. Representation of information by controlling the molecule charge state under thermal fluctuation through the nonlinearity under the detailed balance condition is also discussed.

Beyond single molecular transistors, the exploration of device architecture is a central issue in molecular-scale electronics. One of the attractive directions is molecular nanonetwork system, similar to neural networks, by self-assembly. In particular, DNA, which can be regarded as a one-dimensional molecular wire, has attracted much attention as a promising scaffold. The ionic interactions at DNA backbone allow high-density integration of cationic macromolecules. DNA and DNA complexes can be isolated on a solid surface without decomposing and observed in single molecular level by atomic force microscopy. Cytochrome c/DNA complex networks show threshold behavior in current–voltage characteristics that exhibits stochastic resonance as a basis of neural information processing.

In organic materials, peculiar nonlinearity to current voltage appears, thought a general and comprehensive explanation has not been achieved. Generally, organic conductors have disorder structures so charge transfers from one place with high conductivity to another place with high conductivity. Conductive segments in poorly conductive organic materials are expected to have a smaller electrical capacity, leading to a higher critical temperature for the blockade effect. In such occasions, Coulomb blockade of charge transport takes place in organic conductors. In this chapter, experimental evidence to prove Coulomb blockade taking place on two-dimensional organic conducting polymer films and its theoretical evidence through quantum calculations and the verification of conductivity models are described. The significance of the blockade effect, i.e., the difficulty of charge injection from one conducting segment into another should be stressed, since this has not hitherto been taken into account when considering the charge transport mechanism in organic materials. By considering both the charge blockade effect and the influence of structural disorder, it is hoped that a clear understanding of charge transport in organic materials can be achieved.

Novel and functional nonlinear nano-electronic circuits and devices based on “nature-inspired” and “bio-mimetic” techniques are discussed. The targeted nano-electronic devices are single-electron devices, in particular. A significant factor in the production of nature-inspired and bio-mimetic circuits or devices is the accuracy with which the natural world phenomena and the biological behaviors relate to the targeted nanodevices. To construct nature-inspired or bio-mimetic circuits, “perfect mimicking” and “rough mimicking” techniques can be used. Nature-inspired and bio-mimetic single-electron circuits are described as demonstrations. These demonstrations indicate that the circuits based on the proposed approaches are representative of the nature-inspired and bio-mimetic circuits and are useful and functional devices. Although single-electron circuits are targeted here, the concepts introduced, namely, the perfect and rough mimicking techniques, can be applied not only to single-electron circuits but to other devices also.

Finding reliable methods to exploit molecular degrees of freedom represents an intriguing problem involving the control of new mechanisms at the nanoscale and several technological challenges. Here, we report a novel approach to address a single molecular spin embedded in an electronic circuit. Our devices make use of molecules with well-defined magnetic anisotropy (TbPc₂) embedded in nanogapped electrodes obtained by electroburning graphene layers. Such devices work as molecular spin transistors allowing the detection of the Tb spin flip during the sweep of an external magnetic field. The spin readout is made by the molecular quantum dot that, in turns, is driven by an auxiliary gate voltage. In the general context of (spin-)electronics, these results demonstrate that: (1) molecular quantum dots can be used as ultra-sensitive detectors for spin flip detection and (2) the use of graphene electrodes as a platform to contact organometallic molecules is a viable route to design more complex nanoarchitectures.

In the second half of the twentieth century, two new investigation techniques emerged that both revolutionized science and technology in their fields. The first one is (nuclear and electron) magnetic resonance (NMR, ESR), which exhibits superior energy resolution owing to the high precision of frequency measurements at resonant conditions. The second technique is scanning tunneling microscopy (STM) that has quickly established as a major investigation tool with its atomic spatial resolution. In order to benefit from both, the superior spatial resolution of the STM and the exceptional energy resolution of resonance techniques, we developed a radio-frequency (rf) STM based on a commercial low-temperature STM upgraded by a home-built rf-spectroscopic system that can be operated in active and passive modes. Here, we review recent progress in the field of rf-STM, with particular focus on our recent results on the detection and excitation of mechanical vibrations of one-dimensional molecular nanoresonators as well as of nuclear, electron, and mixed nuclear/electron spin transitions in single molecules.

In this article, recent studies of the surface spin of adsorbed molecules by the detection of the Kondo resonance are reviewed. The Kondo resonance is a phenomenon that is caused by an interaction between an isolated spin and conduction electrons. First observed in the 1930s as an anomalous increase in the low-temperature resistance of metals embedded with magnetic atoms, the Kondo physics mainly studied the effects of bulk magnetic impurities in the resistivity. In the last 15 years, it has undergone a revival by scanning tunneling microscope (STM) which enables the measurement of the Kondo resonance at surfaces using an atomic scale point contact. The detection of the Kondo resonance can be a powerful tool to explore surface magnetism. Researches on spin behavior of double-decker and triple-decker phthalocyanine (Pc) molecules adsorbed on surfaces are examined, together with their bonding configuration and electronic structure. These molecules attract attentions as a material for molecule spintronics of special interests, since some of the double-decker Pc molecules show single-molecule magnet (SMM) behavior that exhibits slow relaxation of their magnetization induced by the combined effects of high-spin ground states and the zero-field splitting. The SMM behavior of the molecule is examined in terms of the detection of the Kondo resonance for the molecule.

Nanotechnology developed from a purely theoretical vision pioneered by Feynman (Eng. Sci. 23(5), 22 (1960), [1]) and popularized, for example, by Drexler (Engines of Creation. Anchor Books (1986), [2]) into a large, scientifically and commercially active field.

DNA/functional molecules complexes have attracted much attention for fabricating DNA-based functional nanowires. In this chapter, we describe the DNA-based functional nanowires stretched and immobilized between a pair of electrodes. First, previously reported methods for stretching of DNA as nanowires will be reviewed. Then, we mention the morphology of DNA nanowires on mica substrate without stretching and alignment treatments. Next, in order to stretch the DNA nanowires, dielectrophoretic trapping method was performed. High frequency and high electric field voltage was applied to DNA aqueous solution between a pair of comb-shaped Au electrodes. The structures of the stretched and immobilized DNA nanowires were analyzed with AFM. As the result, huge numbers of DNA nanowires was aligned and immobilized between the electrodes, forming the DNA brush-like structure. Aiming for investigation of optoelectronic properties of single molecular DNA nanowire, we have examined adequate method for obtaining singly immobilized DNA nanowire in terms of DNA concentration, applied voltage, and shape of the electrodes. As a result, we successfully fabricated almost singly stretched and immobilized DNA nanowires. Then, functionalization of the stretched DNA nanowires was subsequently carried out. As the photoelectro-functional molecule, tris(bipyridine)ruthenium(II) complex (Ru(bpy) ₃ ²⁺ ) was associated to the stretched DNA nanowires to introduce photoelectronic functionalities. The height of DNA/Ru(bpy) ₃ ²⁺ nanowires was ranging from 1.5 to 3.5 nm, which was higher than that of the native DNA. This indicated that the Ru(bpy) ₃ ²⁺ was successfully associated to stretched DNA nanowires. Fluorescent microscopy and I–V measurement were also suggested the formation of stretched and immobilized DNA/Ru(bpy) ₃ ²⁺ functional nanowires.

Understanding charge transport mechanism of single-molecule–metal–molecule junctions is important in the field of molecular electronics. Till now, most of the reported works focused on small molecules, where tunneling transport dominates the charge transport. As the length of the molecule increases, the charge transport is expected to show a transition from tunneling to hopping. In this work, we performed a comprehensive investigation on oligothiophene molecules. We have measured the temperature dependence of electrical conductance and thermopower of oligothiophene molecular junctions with molecular lengths ranging from 2.2 nm (5T-di-SCN) to 7 nm (17T-di-SCN) using the homebuilt scanning tunneling microscope. The conductance measurement results reveal that the dominant charge transport for oligothiophene changed from tunneling to hopping transport at molecular length of ca. 5 nm. In addition, the thermopower for all the oligothiophene molecules was found to be positive, indicating the transport of charge carrier through the highest occupied molecular orbital level.

A single-molecule junction (SMJ), a molecule bridging two metal electrodes, is a primitive model of molecular electronic devices and provides a unique platform to resolve fundamental questions how the electrical current flows through a single molecule and what functionality emerges arising from the original characteristics of the molecule. Recently, the conductance values of various molecules have been measured experimentally by using mechanically controllable break junction (MCBJ) and scanning tunneling microscopy (STM) junction. The accumulated database combined with first-principles theoretical calculations enables us to discuss the relation of the transport characteristics with the geometrical configuration of molecule in the junction, the molecule electronic structure and the molecule–electrode coupling. Although the conductance is always analyzed by using Landauer formula, it is still challenging to experimentally partition the conductance to the contributions from multiple transport channels and determine the total number of transport channels and their transmission probabilities. These quantities provide deeper insights on the electron transport through a single molecule and specify the SMJ like a personal identification number (PIN) code. This chapter describes a method to determine the “PIN” code based on multiple Andreev reflections (MARs) and demonstrates the application to a C₆₀-SMJ fabricated with STM technique.

This chapter summarizes research progress in the immobilization of metal nanoparticles, nanosized organic and complex molecules, and biological molecules on electrode surfaces with an emphasis on our recent study. Self-assembled monolayers (SAMs) are an excellent model system to study the binding of molecular-sized objects on surfaces. They are a simple, effective, and highly versatile method for modifying various surfaces with different nanosized molecules at the molecular level with precise control. Detailed structural information about the structure of SAMs has been obtained using UV/vis spectroscopy, ellipsometry, atomic force microscopy (AFM), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and electrochemistry. The use of these modified surfaces in photovoltaic devices and in nanotechnology is also discussed in this chapter. Molecular-level approaches to modifying electrode surfaces are central to molecular nanotechnology, which is likely to become an important field in the near future.

Nonsymmetric electric properties such as rectification, negative differential resistance, threshold gate, hysteresis effect, and integrated threshold gate are essential for realizing molecular brain computers, which are believed to withstand noise and fluctuations. So far, there is no fixed design principle for single-molecule electronic devices, mainly because the current–voltage (I–V) characteristics of such devices differ owing to differing conduction mechanisms. In the tunneling regime of the molecules, the I–V characteristics are essentially dependent on the density of states of the system, whereas in the hopping mechanisms, the molecules can be charged to change their electronic characteristics. To understand this principle, we have synthesized a series of molecules to study the electric properties of single molecules.

Large polycyclic π-system compounds such as higher phenacenes, fused azulenes, and pyrrole-containing compounds such as porphyrinoids and cyclopyrroles were prepared to measure their physical and electric properties by scanning tunneling microscope.

The synthesis of a molecular wire assembly is a key technology to construct molecular architectures toward single-molecular organic electronic devices. Two new methods to fabricate highly organized and assembled molecular wires are described: 1. one-dimensionally assembled polythiophene molecular wires by electrochemical epitaxial polymerization; 2. multilayered graphene nanoribbon assemblies by two-zone chemical vapor deposition.

A new method for the synthesis of an insulated π-conjugated molecule as a powerful building block for the construction of a insulated molecular wire (IMW) was developed via the sequential self-inclusion of π-conjugated guest-branched permethylated α-cyclodextrin followed by the elongation of the π-conjugated unit. Covering a single π-conjugated wire by an α-cyclodextrin derivatives can suppress conductance fluctuation. The insulated π-conjugated molecules were utilized in the synthesis of highly conductive zigzag- and functionalized insulated molecular wires.

Single-molecule electronics have attracted a great deal of attention in terms of the bottom-up construction of electronic circuits and the potential for the ultimate miniaturization of devices. Because of the accumulated understanding of single-molecule electronics, developing new functions by orchestrated molecules, the so-called molecular architectonics, has become a new aspect of device fabrication. To realize these smart molecule devices, development of novel organic components has become an active area of research. We have developed new π-conjugated systems to act as “anchor” and “wire” units because we cannot construct molecule-based electronic devices without using these units. In this Chapter, we focus on tetraphenylmethane-based tripodal structures with anchoring functional groups to act as anchor units. We also focus on structurally well-defined oligothiophenes with encapsulating substituents for preventing intermolecular electronic communications. These oligothiophenes are candidates for “insulated molecular wire” units.