Electron conduction in molecular wires. II. Application to scanning tunneling microscopy

Theoretical Study on the Open-Shell Electronic Structure and Electron Conductivity of [18]Annulene as a Molecular Parallel Circuit Model

Herein, the electron conductivities of [18]annulene and its derivatives are theoretically examined as a molecular parallel circuit model consisting of two linear polyenes. Their electron conductivities are estimated by elastic scattering Green's function (ESGF) theory and density functional theory (DFT) methods. The calculated conductivity of the [18]annulene does not follow the classical conductivity, i.e., Ohm's law, suggesting the importance of a quantum interference effect in single molecules. By introducing electron-withdrawing groups into the annulene framework, on the other hand, a spin-polarized electronic structure appears, and the quantum interference effect is significantly suppressed. In addition, the total current is affected by the spin polarization because of the asymmetry in the coupling constant between the molecule and electrodes. From these results, it is suggested that the electron conductivity as well as the quantum interference effect of π-conjugated molecular systems can be designed using their open-shell nature, which is chemically controlled by the substituents.

Synthesis of Hidden Subgroup Quantum Algorithms and Quantum Chemical Dynamics

We describe a general formalism for quantum dynamics and show how this formalism subsumes several quantum algorithms, including the Deutsch, Deutsch-Jozsa, Bernstein-Vazirani, Simon, and Shor algorithms as well as the conventional approach to quantum dynamics based on tensor networks. The common framework exposes similarities among quantum algorithms and natural quantum phenomena: we illustrate this connection by showing how the correlated behavior of protons in water wire systems that are common in many biological and materials systems parallels the structure of Shor's algorithm.

Reversed Conductance Decay of 1D Topological Insulators by Tight-Binding Analysis

Reversed conductance decay describes increasing conductance of a molecular chain series with increasing chain length. Realizing reversed conductance decay is an important step toward making long and highly conducting molecular wires. Recent work has shown that one-dimensional topological insulators (1D TIs) can exhibit reversed conductance decay due to their nontrivial edge states. The Su-Schrieffer-Heeger (SSH) model for 1D TIs relates to the electronic structure of these isolated molecules but not their electron transport properties as single-molecule junctions. Herein, we use a tight-binding approach to demonstrate that polyacetylene and other diradicaloid 1D TIs show a reversed conductance decay at the short chain limit. We explain these conductance trends by analyzing the impact of the edge states in these 1D systems on the single-molecule junction transmission. Additionally, we discuss how the self-energy from the electrode-molecule coupling and the on-site energy of the edge sites can be tuned to create longer wires with reversed conductance decays.

Theoretical Study on the Difference in Electron Conductivity of a One-Dimensional Penta-Nickel(II) Complex between Anti-Ferromagnetic and Ferromagnetic States-Possibility of Molecular Switch with Open-Shell Molecules

The electron conductivity of an extended metal atom chain (EMAC) that consisted of penta-nickel(II) ions bridged by oligo-α-pyridylamino ligands was examined by density functional theory (DFT) and elastic scattering Green’s functions (ESGF) calculations. The calculated results revealed that an intramolecular ferromagnetic (FM) coupling state showed a higher conductivity in comparison with an anti-ferromagnetic (AFM) coupling state. The present results suggest the potential of the complex as a molecular switch as well as a molecular wire.

Thermal Decoherence and Disorder Effects on Chiral-Induced Spin Selectivity

We use a nonlinear master equation formalism to account for thermal and disorder effects on spin-dependent electron transport in helical organic molecules coupled to two ideal leads. The inclusion of these two effects has important consequences in understanding the observed length and temperature dependence of spin polarization in experiments, which cannot be accounted for in a purely coherent tunneling model. Our approach considers a tight-binding helical Hamiltonian with disordered onsite energies to describe the resulting electronic states when low-frequency interacting modes break the electron coherence. The high-frequency fluctuating counterpart of these interactions, typical of intramolecular modes, is included by means of temperature-dependent thermally activated transfer probabilities in the master equation, which lead to hopping between localized states. We focus on the spin-dependent conductance and the spin-polarization in the linear regime (low voltage), which are analyzed as a function of the molecular length and the temperature of the system. Our results at room temperature agree well with experiments because our model predicts that the degree of spin-polarization increases for longer molecules. Also, this effect is temperature-dependent because thermal excitation competes with disorder-induced Anderson localization. We conclude that a transport mechanism based on thermally activated hopping in a disordered system can account for the unexpected behavior of the spin polarization.

Single-Molecule Conductance through Hydrogen Bonds: The Role of Resonances

The single-molecule conductance of hydrogen-bonded and alkane systems are compared in this theoretical investigation. The results indicate that for short chains, the H-bonded molecules exhibit larger conductance than the alkanes. Although earlier experimental investigations attributed this observation to a large density of states (DOS) corresponding to an occupied molecular orbital below the Fermi energy, the current work indicates the presence of a Fano resonance in the transmission function in the vicinity of the Fermi energy. The inclusion of this observation is essential in understanding the behavior of these systems. We also address the characteristics of the H-bond for transport and provide an explanation for the presence of a turnover regime wherein the conductance of the alkanes becomes larger than the H-bonded systems. Incidentally, this feature cannot be explained using a simple DOS argument.

Single and double valence configuration interactions for recovering the exponential decay law while tunneling through a molecular wire

The exponential decay of the electronic transmission through a molecular wire with its length is calculated using a configuration interaction elastic scattering quantum chemistry (CI-ESQC) theory [1, 2]. In the HOMO-LUMO gap and in a one-electron approximation, this decay is exponential since the scattering matrix comes from a product of spatial propagators along the wire. In a valence SD-CI (single and double-configurations interaction) description, such a product does not exist. An effective one was numerically obtained from the CI-ESQC scattering matrix. Fluctuations over the effective CI-exponential decay come from the truncation of the full CI basis set and also from many-body exchange-correlation effects along the molecular wire.

Contact effects and quantum interference in engineered dangling bond loops on silicon surfaces

Dangling bond structures created on H-passivated silicon surfaces offer a novel platform for engineering planar nanoscale circuits, compatible with conventional semiconductor technologies. In this investigation we focus on the electronic structure and quantum transport signatures of dangling bond loops built on H-passivated Si(100) surfaces contacted by carbon nanoribbons, thus leading to a two-terminal planar, nanoscale setup. The computational studies were carried out to rationalize the influence of the local atomic-scale contacts of the dangling bond system to the mesoscopic electrodes as well as the possibility of revealing quantum interference effects in the dangling bond loops. Our results reveal a strong sensitivity of the low-energy quantum transmission to the loop topology and to the atomistic details of the electrode-loop contact. Varying the length of the loop or the spatial position of at least one of the electrodes has a drastic impact on the quantum interference pattern; depending on whether constructive or destructive interference within the loop takes place, the conductance of the system can be tuned over several orders of magnitude, thus suggesting the possibility of exploiting such quantum mechanical effects in the design of two-dimensional, atomic-scale electronic devices such as logic gates.

Rethinking first-principles electron transport theories with projection operators: the problems caused by partitioning the basis set

We revisit the derivation of electron transport theories with a focus on the projection operators chosen to partition the system. The prevailing choice of assigning each computational basis function to a region causes two problems. First, this choice generally results in oblique projection operators, which are non-Hermitian and violate implicit assumptions in the derivation. Second, these operators are defined with the physically insignificant basis set and, as such, preclude a well-defined basis set limit. We thus advocate for the selection of physically motivated, orthogonal projection operators (which are Hermitian) and present an operator-based derivation of electron transport theories. Unlike the conventional, matrix-based approaches, this derivation requires no knowledge of the computational basis set. In this process, we also find that common transport formalisms for nonorthogonal basis sets improperly decouple the exterior regions, leading to a short circuit through the system. We finally discuss the implications of these results for first-principles calculations of electron transport.

Electroluminescence of a polythiophene molecular wire suspended between a metallic surface and the tip of a scanning tunneling microscope

The electroluminescence of a polythiophene wire suspended between a metallic surface and the tip of a scanning tunneling microscope is reported. Under positive sample voltage, the spectral and voltage dependencies of the emitted light are consistent with the fluorescence of the wire junction mediated by localized plasmons. This emission is strongly attenuated for the opposite polarity. Both emission mechanism and polarity dependence are similar to what occurs in organic light emitting diodes (OLED) but at the level of a single molecular wire.

Theoretical studies of electronic structures, magnetic properties and electron conductivities of one-dimensional Ni(n) (n = 3, 5, 7) complexes

Electronic structures, magnetic properties and electron conductivities of linearly aligned one-dimensional (1-D) Ni(II)3, Ni(II)5 and Ni(II)7 complexes, i.e. [Ni3(dpa)4NCS2], [Ni5(tpda)4X2] (X = Cl, CN, N3, NCS) and [Ni7(teptra)4Cl2], are systematically investigated by the broken-symmetry B3LYP calculations and simulations based on an elastic scattering Green's function theory. Calculated spin densities appear only at terminal Ni ions, while inner Ni ions are the closed-shell. The calculated effective exchange integrals (J(ab)) values reproduce well the experimental results that indicate anti-ferromagnetic (AF) interactions between two terminal Ni ions. Natural orbitals and their occupation numbers show that a change in the weak AF couplings by axial ligands in penta-nickel complexes originates in σ-type orbitals. Simulated electron conductivities of [Ni3(dpa)4NCS2] and [Ni5(tpda)4NCS2] semi-quantitatively correspond to the experimental results. By the analyses, it is elucidated that electrons are mainly transmitted by σ-type orbitals, but the bonds between Au and axial ligands are also dominant factors for conductivity.

Activationless charge transport across 4.5 to 22 nm in molecular electronic junctions

In this work, we bridge the gap between short-range tunneling in molecular junctions and activated hopping in bulk organic films, and greatly extend the distance range of charge transport in molecular electronic devices. Three distinct transport mechanisms were observed for 4.5-22-nm-thick oligo(thiophene) layers between carbon contacts, with tunneling operative when d < 8 nm, activated hopping when d > 16 nm for high temperatures and low bias, and a third mechanism consistent with field-induced ionization of highest occupied molecular orbitals or interface states to generate charge carriers when d = 8-22 nm. Transport in the 8-22-nm range is weakly temperature dependent, with a field-dependent activation barrier that becomes negligible at moderate bias. We thus report here a unique, activationless transport mechanism, operative over 8-22-nm distances without involving hopping, which severely limits carrier mobility and device lifetime in organic semiconductors. Charge transport in molecular electronic junctions can thus be effective for transport distances significantly greater than the 1-5 nm associated with quantum-mechanical tunneling.

Defect-induced conductance oscillations in short atomic chains

Electronic transport through a junction made of two gold electrodes connected with a gold chain containing a silver impurity is analyzed with a tight binding model and the density-functional theory. It is shown that the conductance depends in a simple way on the position of the impurity in the chain and the parity of the total number of atoms of the chain. For an odd chain the conductance takes on a higher value when the Ag impurity substitutes an even Au atom in the chain, and a lower one for an odd position of the Ag atom. In the case of an even chain the conductance hardly depends on the position of the Ag atom. This new kind of a defect-induced parity oscillation of the conductance is significantly more prominent than the well-known even-odd effect related to the dependence of the conductance on the parity of number of atoms in perfect chains.

Long-range electron transport of ruthenium-centered multilayer films via a stepping-stone mechanism

We studied electron transport of Ru complex multilayer films, whose structure resembles redox-active complex films known in the literature to have long-range electron transport abilities. Hydrogen bond formation in terms of pH control was used to induce spontaneous growth of a Ru complex multilayer. We made a cross-check between electrochemical measurements and I-V measurements using PEDOT:PSS to eliminate the risk of pinhole contributions to the mechanism and have found small β values of 0.012-0.021 Å(-1). Our Ru complex layers exhibit long-range electron transport but with low conductance. On the basis of the results of our theoretical-experimental collaboration, we propose a modified tunneling mechanism named the "stepping-stone mechanism", where the alignment of site potentials forms a narrow band around E(F), making resonant tunneling possible. Our observations may support Tuccito et al.'s proposed mechanism.

EFFECTS OF PHASE-BREAKING ON LONG-RANGE CHARGE TRANSFER IN DNA: PARTIALLY-COHERENT-TUNNELING MODEL STUDY

The mechanism of hole charge transfer in DNA of various lengths and sequences is investigated based on a partially coherent tunneling theory (Zhang et al., J Chem Phys117:4578, 2002), where the effects of phase-breaking in adenine–thymine and guanine–cytosine base pairs are treated on equal foot. This work aims at providing a self-consistent microscopic interpretation for rate experiments on various DNA systems. We will also clarify the condition under which the simple superexchange-mediated-hopping picture is valid, and make some comments on the further development of present theory.

Single molecule logical devices

After almost 40 years of development, molecular electronics has given birth to many exciting ideas that range from molecular wires to molecular qubit-based quantum computers. This chapter reviews our efforts to answer a simple question: how smart can a single molecule be? In our case a molecule able to perform a simple Boolean function is a child prodigy. Following the Aviram and Ratner approach, these molecules are inserted between several conducting electrodes. The electronic conduction of the resulting molecular junction is extremely sensitive to the chemical nature of the molecule. Therefore designing this latter correctly allows the implementation of a given function inside the molecular junction. Throughout the chapter different approaches are reviewed, from hybrid devices to quantum molecular logic gates. We particularly stress that one can implement an entire logic circuit in a single molecule, using either classical-like intramolecular connections, or a deformation of the molecular orbitals induced by a conformational change of the molecule. These approaches are radically different from the hybrid-device approach, where several molecules are connected together to build the circuit.

Dependence of single-molecule conductance on molecule junction symmetry

The symmetry of a molecule junction has been shown to play a significant role in determining the conductance of the molecule, but the details of how conductance changes with symmetry have heretofore been unknown. Herein, we investigate a naphthalenedithiol single-molecule system in which sulfur atoms from the molecule are anchored to two facing gold electrodes. In the studied system, the highest single-molecule conductance, for a molecule junction of 1,4-symmetry, is 110 times larger than the lowest single-molecule conductance, for a molecule junction of 2,7-symmetry. We demonstrate clearly that the measured dependence of molecule junction symmetry for single-molecule junctions agrees with theoretical predictions.

Microfabrication and integration of diazonium-based aromatic molecular junctions

Microfabrication techniques common in commercial semiconductor manufacturing were used to produce carbon/nitroazobenzene/Cu/Au molecular junctions with a range of areas from 3×3 to 400×400 μm, starting with 100-mm-diameter silicon wafers. The approach exhibited high yield (90-100%) and excellent reproducibility of the current density (relative standard deviation of typically 15%) and 32 devices on a chip. Electron-beam-deposited carbon films are introduced as substrates and may be applied at the full wafer level before dicing and electrochemical deposition of the molecular layer. The current scaled with the device area over a factor of >600, and the current density was quantitatively consistent with structurally similar molecular junctions made by other techniques. The current densities were weakly dependent on temperature over the range of 100-390 K, and maximum current densities above 400 A/cm2 were observed without breakdown. To simulate processing and operation conditions, the junction stability was tested at elevated temperatures. The JV curves of microfabricated junctions were unchanged after 22 h at 100 °C. A ∼50% increase in the current density was observed after 20 h at 150 °C but then remained constant for an additional 24 h. Parallel fabrication, thermal stability, and high yield are required for practical applications of molecular electronics, and the reported results provide important steps toward integration of molecular electronic devices with commercial processes and devices.

Interpretation of transition voltage spectroscopy

The promise of transition voltage spectroscopy (TVS) is that molecular level positions can be determined in molecular devices without applying extreme voltages. Here, we consider the physics behind TVS in more detail. Remarkably, we find that the Simmons model employed thus far is inconsistent with experimental data. However, a coherent molecular transport model does justify TVS as a spectroscopic tool. Moreover, TVS may become a critical test to distinguish molecular junctions from vacuum tunnel junctions.

Combined density functional theory and Landauer approach for hole transfer in DNA along classical molecular dynamics trajectories

We investigate in detail the charge transport characteristics of DNA wires with various sequences and lengths in the presence of solvent. Our approach combines large-scale quantum/classical molecular dynamics (MD) simulations with transport calculations based on Landauer theory. The quantum mechanical transmission function of the wire is calculated along MD trajectories and thus encodes the influence of dynamical disorder arising from the environment (water, backbone, counterions) and from the internal base dynamics. We show that the correlated fluctuations of the base pair dynamics are crucial in determining the transport properties of the wire and that the effect of fluctuations can be quite different for sequences with low and high static disorders (differences in base ionization potentials). As a result, in structures with high static disorder as is the case of the studied Dickerson dodecamer, the weight of high-transmissive structures increases due to dynamical fluctuations and so does the calculated average transmission. Our analysis further supports the basic intuition of charge-transfer active conformations as proposed by Barton et al. [J. Am. Chem. Soc. 126, 11471 (2004)]. However, not DNA conformations with good stacking contacts leading to large interbase hopping values are necessarily the most important, but rather those where the average fluctuation of ionization potentials along the base stack is small. The reason behind this is that the ensemble of conformations leads to average electronic couplings, which are large enough for sufficient transmission. On the other hand, the alignment of onsite energies is the critical parameter which gates the charge transport.

Fragment analysis of single-molecule conduction

In the tight-binding source and sink potential model of transmission in single-molecule pi-conjugated conductors, vanishing of the opacity polynomial defines a necessary condition for zero conductance at a given energy. Theorems are given for calculating opacity polynomials of composite devices in terms of opacity and characteristic polynomials of the subunits. These relations rationalize the positions and shapes of zeros in transmission curves for devices consisting of molecules with side chains or of units assembled in series and take an especially simple form for polymeric molecules with identical repeat units.

Transport in state space: voltage-dependent conductance calculations of benzene-1,4-dithiol

We implement a method to study transport in a basis of many-body molecular states using the nonequilibrium Hubbard Green's function technique. A well-studied system, a junction consisting of benzene-dithiol on gold, is the focus of our consideration. Electronic structure calculations are carried out at the Hartree-Fock (HF), density functional theory (DFT), and coupled-cluster singles and doubles (CCSD) levels, and multiple molecular states are included in the transport calculation. The conductance calculation yields new information about the transport mechanism in BDT junctions.

Localization vs conduction: anionic excitations in alkanethiol self-assembled monolayers

Low-energy (6-11 eV) electron injection into Xe-coated self-assembled alkanethiol monolayers (SAMs) is reported. At most energies, the presence of the Xe film has negligible effect on the incident electrons, which penetrate the overlayer and induce significant C--H bond rupture at the terminal methyl sites and the subsurface methylene sites of the organic substrates. However, irradiation at 7.7 +/- 0.2 eV can lead to resonant electronic excitations of the Xe adsorbates to create transient anionic states in the Xe overlayer. Transfer of anionic excitations from the Xe overlayer to the SAM initially prepares excited anionic states at the terminal CH3 groups and leads to highly selective dissociations at the methyl sites, with negligible conduction along the alkane chain which would lead to subsurface C-H bond rupture at the methylene sites. These results demonstrate that the mobility of electronically excited charged states along the alkanethiol chains is significantly less than that of simple excess electrons and that highly site-selective chemical modifications can be induced by low-energy electrons in these highly homogeneous organic films.

Back-electron transfer suppresses the periodic length dependence of DNA-mediated charge transport across adenine tracts

DNA-mediated charge transport (CT) is exquisitely sensitive to the integrity of the bridging pi-stack and is characterized by a shallow distance dependence. These properties are obscured by poor coupling between the donor/acceptor pair and the DNA bridge, or by convolution with other processes. Previously, we found a surprising periodic length dependence for the rate of DNA-mediated CT across adenine tracts monitored by 2-aminopurine fluorescence. Here we report a similar periodicity by monitoring N 2-cyclopropylguanosine decomposition by rhodium and anthraquinone photooxidants. Furthermore, we find that this periodicity is attenuated by consequent back-electron transfer (BET), as observed by direct comparison between sequences that allow and suppress BET. Thus, the periodicity can be controlled by engineering the extent of BET across the bridge. The periodic length dependence is not consistent with a periodicity predicted by molecular wire theory but is consistent with a model where multiples of four to five base pairs form an ideal CT-active length of a bridging adenine domain.

Electron transport in open systems from finite-size calculations: Examination of the principal layer method applied to linear gold chains

We describe the occurrence of computational artifacts when the principal layer method is used in combination with the cluster approximation for the calculation of electronic transport properties of nanostructures. For a one-dimensional gold chain, we observe an unphysical band in the band structure. The artificial band persists for large principal layers and for large buffer sizes. We demonstrate that the assumption of equality between Hamiltonian elements of neighboring layers is no longer valid and that a discontinuity is introduced in the potential at the layer transition. The effect depends on the basis set. When periodic boundary conditions are imposed and the k-space sampling is converged, the discontinuity disappears and the principal layer method can be correctly applied by using a linear combination of atomic orbitals as basis set.

Formation and characterization of organic monolayers on semiconductor surfaces

Organic-semiconductor interfaces are playing increasingly important roles in fields ranging from electronics to nanotechnology to biosensing. The continuing decrease in microelectronic device feature sizes is raising an especially great interest in understanding how to integrate molecular systems with conventional, inorganic microelectronic materials, particularly silicon. The explosion of interest in the biological sciences has provided further impetus for learning how to integrate biological molecules and systems with microelectronics to form true bioelectronic systems. Organic monolayers present an excellent opportunity for surmounting many of the practical barriers that have hindered the full integration of microelectronics technology with organic and biological systems. Of all the semiconductor materials, silicon and diamond stand out as unique. This review focuses upon the preparation and characterization of organic and biomolecular layers on semiconductor surfaces, with special emphasis on monolayers formed on silicon and diamond.