Benchmark density functional theory calculations for nanoscale conductance

Mechanistic Insights into Electronic Current Flow through Quinone Devices

Molecular switches based on functionalized graphene nanoribbons (GNRs) are of great interest in the development of nanoelectronics. In experiment, it was found that a significant difference in the conductance of an anthraquinone derivative can be achieved by altering the pH value of the environment. Building on this, in this work we investigate the underlying mechanism behind this effect and propose a general design principle for a pH based GNR-based switch. The electronic structure of the investigated systems is calculated using density functional theory and the transport properties at the quasi-stationary limit are described using nonequilibrium Green's function and the Landauer formalism. This approach enables the examination of the local and the global transport through the system. The electrons are shown to flow along the edges of the GNRs. The central carbonyl groups allow for tunable transport through control of the oxidation state via the pH environment. Finally, we also test different types of GNRs (zigzag vs. armchair) to determine which platform provides the best transport switchability.

Morphology Determines an Efficient Coherent Electron Transport for Push-Pull Organic Semiconductors Based on Triphenylamine and Dicyanovinyl Groups

The morphology of the active layer in organic solar cells is fundamental for achieving high power conversion efficiency. However, the morphological characteristics for optimal performance are still being investigated. An atomistic computational approach is required to determine the relationship between active layer morphology and performance. Since the organic solar cell has multiple phases and interfaces, the computational modeling of charge generation and transport is challenging. We then used a set of push-pull semiconductors to illustrate how the electronic transmission spectrum, derived from the Landauer-Büttiker formalism, can be used to investigate the efficiency of coherent charge transport across anisotropic organic solids. The electronic transmission spectrum was calculated from the electronic band structure obtained using the density-functional-based tight-binding method. We found that coherent charge transport was more efficient along the direction parallel with the interface between the electron-acceptor and electron-donor moieties for a herringbone morphology.

Edge Effect in Electronic and Transport Properties of 1D Fluorinated Graphene Materials

A systematic examination of the electronic and transport properties of 1D fluorine-saturated zigzag graphene nanoribbons (ZGNRs) is presented in this article. One publication (Withers et al., Nano Lett., 2011, 11, 3912-3916.) reported a controlled synthesis of fluorinated graphene via an electron beam, where the correlation between the conductivity of the resulting materials and the width of the fluorinated area is revealed. In order to understand the detailed transport mechanism, edge-fluorinated ZGNRs with different widths and fluorination degrees are investigated. Periodic density functional theory (DFT) is employed to determine their thermodynamic stabilities and electronic structures. The associated transport models of the selected structures are subsequently constructed. The combination of a non-equilibrium Green's function (NEGF) and a standard Landauer equation is applied to investigate the global transport properties, such as the total current-bias voltage dependence. By projecting the corresponding lesser Green's function on the atomic orbital basis and their spatial derivatives, the local current density maps of the selected systems are calculated. Our results suggest that specific fluorination patterns and fluorination degrees have significant impacts on conductivity. The conjugated π system is the dominate electron flux migration pathway, and the edge effect of the ZGNRs can be well observed in the local transport properties. In addition, with an asymmetric fluorination pattern, one can trigger spin-dependent transport properties, which shows its great potential for spintronics applications.

Local current analysis on defective zigzag graphene nanoribbons devices for biosensor material applications

In this contribution, we aim at investigating the mechanism of biosensing in graphene-based materials from first principles. Inspired by recent experiments, we construct an atomistic model composed of a pyrene molecule serving as a linker fragment, which is used in experiment to attach certain aptamers, and a defective zigzag graphene nanoribbons (ZGNRs). Density functional theory including dispersive interaction is employed to study the energetics of the linker absorption on the defective ZGNRs. Combining non-equilibrium Green's function and the Landauer formalism, the total current-bias voltage dependence through the device is evaluated. Modifying the distance between the linker molecule and the nanojunction plane reveals a quantitative change in the total current-bias voltage dependence, which correlates to the experimental measurements. In order to illuminate the geometric origin of these variation observed in the considered systems, the local currents through the device are investigated using the method originally introduced by Evers and co-workers. In our new implementation, the numerical efficiency is improved by applying sparse matrix storage and spectral filtering techniques, without compromising the resolution of the local currents. Local current density maps qualitatively demonstrate the local variation of the interference between the linker molecule and the nanojunction plane.

Local decomposition of hybridization functions: Chemical insight into correlated molecular adsorbates

Hybridization functions are an established tool for investigating the coupling between a correlated subsystem (often a single transition metal atom) and its uncorrelated environment (the substrate and any ligands present). The hybridization function can provide valuable insight into why and how strong correlation features such as the Kondo effect can be chemically controlled in certain molecular adsorbates. To deepen this insight, we introduce a local decomposition of the hybridization function, based on a truncated cluster approach, enabling us to study individual effects on this function coming from specific parts of the systems (e.g., the surface, ligands, or parts of larger ligands). It is shown that a truncated-cluster approach can reproduce the Co 3d and Mn 3d hybridization functions from periodic boundary conditions in Co(CO)₄/Cu(001) and MnPc/Ag(001) qualitatively well. By locally decomposing the hybridization functions, it is demonstrated at which energies the transition metal atoms are mainly hybridized with the substrate or with the ligand. For the Kondo-active 3d_x²-y² orbital in Co(CO)₄/Cu(001), the hybridization function at the Fermi energy is substrate-dominated, so we can assign its enhancement compared with ligand-free Co to an indirect effect of ligand-substrate interactions. In MnPc/Ag(001), the same is true for the Kondo-active orbital, but for two other orbitals, there are both direct and indirect effects of the ligand, together resulting in such strong screening that their potential Kondo activity is suppressed. A local decomposition of hybridization functions could also be useful in other areas, such as analyzing the electrode self-energies in molecular junctions.

Nonexponential Length Dependence of Molecular Conductance in Acene-Based Molecular Wires

In the nonresonant regime, molecular conductance decays exponentially with distance, limiting the fabrication of efficient molecular semiconductors at the nanoscale. In this work, we calculate the conductance of a series of acene derivatives connected to gold electrodes using density functional theory (DFT) combined with the nonequilibrium Green's function (NEGF) formalism. We show that these systems have near length-independent conductance and can exhibit a conductance increase with molecular length depending on the connection to the electrodes. The analysis of the molecular orbital energies and transmission functions attribute this behavior to the dramatic decrease of the highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gap with length, which shifts the transmission peaks near the Fermi level. These results demonstrate that the anchoring configuration determines the conductance behavior of acene derivatives, which are optimal building blocks to fabricate single-molecule devices with tunable charge transport properties.

Smart local orbitals for efficient calculations within density functional theory and beyond

Localized basis sets in the projector augmented wave formalism allow for computationally efficient calculations within density functional theory (DFT). However, achieving high numerical accuracy requires an extensive basis set, which also poses a fundamental problem for the interpretation of the results. We present a way to obtain a reduced basis set of atomic orbitals through the subdiagonalization of each atomic block of the Hamiltonian. The resulting local orbitals (LOs) inherit the information of the local crystal field. In the LO basis, it becomes apparent that the Hamiltonian is nearly block-diagonal, and we demonstrate that it is possible to keep only a subset of relevant LOs that provide an accurate description of the physics around the Fermi level. This reduces to some extent the redundancy of the original basis set, and at the same time, it allows one to perform post-processing of DFT calculations, ranging from the interpretation of electron transport to extracting effective tight-binding Hamiltonians, very efficiently and without sacrificing the accuracy of the results.

LCAO-TDDFT-k-: spectroscopy in the optical limit

Understanding, optimizing, and controlling the optical absorption process, exciton gemination, and electron-hole separation and conduction in low dimensional systems is a fundamental problem in materials science. However, robust and efficient methods capable of modelling the optical absorbance of low dimensional macromolecular systems and providing physical insight into the processes involved have remained elusive. We employ a highly efficient linear combination of atomic orbitals (LCAOs) representation of the Kohn-Sham (KS) orbitals within time dependent density functional theory (TDDFT) in the reciprocal space (k) and frequency (ω) domains, as implemented within our LCAO-TDDFT-k-ωcode, applying eithera prioriora posteriorithe derivative discontinuity correction of the exchange functional Δxto the KS eigenenergies as a scissors operator. In so doing we are able to provide a semi-quantitative description of the photoabsorption cross section, conductivity, and dielectric function for prototypical 0D, 1D, 2D, and 3D systems within the optical limit (‖q‖ → 0+) as compared to both available measurements and from solving the Bethe-Salpeter equation with quasiparticleG0W0eigenvalues (G0W0-BSE). Specifically, we consider 0D fullerene (C60), 1D metallic (10, 0) and semiconducting (10, 10) single-walled carbon nanotubes, 2D graphene (Gr) and phosphorene (Pn), and 3D rutile (R-TiO2) and anatase (A-TiO2). For each system, we also employ the spatially and energetically resolved electron-hole spectral density to provide direct physical insight into the nature of their optical excitations. These results demonstrate the reliability, applicability, efficiency, and robustness of our LCAO-TDDFT-k-ωcode, and open the pathway to the computational design of macromolecular systems for optoelectronic, photovoltaic, and photocatalytic applicationsin silico.

Conductivity models for electron energy loss spectroscopy of graphene in a scanning transmission electron microscope with high energy resolution

Recent advancements in the energy resolution and probing capabilities of monochromated electron-beam spectroscopy instruments have made this experimental technique increasingly useful for investigating and understanding the plasmonic, photonic, and electronic properties of graphene-enhanced systems. We develop herein an empirical model for the in-plane conductivity of doped monolayer graphene, comparing with ab initio data from the terahertz (THz) to the upper range of frequencies accessible with the valence electron energy loss spectroscopy (VEELS). Along with our ab initio data, this model is employed to calculate the energy loss spectra using a relativistic formulation, allowing us to analyze the effects that different electron beam parameters have on the response of graphene in a monochromated scanning transmission electron microscope setup. In particular, we explore the effects of reducing the collection angle of scattered electrons, thereby deducing a computational procedure for extracting the real and imaginary parts of the optical conductivity of graphene layers from VEELS measurements. Our modeling ultimately provides insight into how the optoelectronic properties of graphene are expected to manifest in the VEELS obtained via monochromated beams, with the effects of graphene doping, the excitation of its plasmon-polaritons, and relativistic contributions included comprehensively.

Optical excitations of chlorophyll a and b monomers and dimers

A necessary first step in the development of technologies such as artificial photosynthesis is understanding the photoexcitation process within the basic building blocks of naturally occurring light harvesting complexes (LHCs). The most important of these building blocks in biological LHCs such as LHC II from green plants are the chlorophyll a (Chl a) and chlorophyll b (Chl b) chromophores dispersed throughout the protein matrix. However, efforts to describe such systems are still hampered by the lack of computationally efficient and accurate methods that are able to describe optical absorption in large biomolecules. In this work, we employ a highly efficient linear combination of atomic orbitals (LCAOs) to represent the Kohn-Sham (KS) wave functions at the density functional theory (DFT) level and perform time-dependent density functional theory (TDDFT) calculations in either the reciprocal space and frequency domain (LCAO-TDDFT-k-ω) or real space and time domain (LCAO-TDDFT-r-t) of the optical absorption spectra of Chl a and b monomers and dimers. We find that our LCAO-TDDFT-k-ω and LCAO-TDDFT-r-t calculations reproduce results obtained with a plane-wave (PW) representation of the KS wave functions (PW-TDDFT-k-ω) but with a significant reduction in computational effort. Moreover, by applying the Gritsenko, van Leeuwen, van Lenthe, and Baerends solid and correlation derivative discontinuity correction Δ_x to the KS eigenenergies, with both LCAO-TDDFT-k-ω and LCAO-TDDFT-r-t methods, we are able to semiquantitatively reproduce the experimentally measured photoinduced dissociation results. This work opens the path to first principles calculations of optical excitations in macromolecular systems.

Simulations of the effect of an oxide on contact area measurements from conductive atomic force microscopy

Nanoscale contact area in conductive atomic force microscopy can be determined by analyzing current flow using electron transport theories. However, it is recognized that native oxides on the conductive tip will reduce current flow, thus degrading the accuracy of the measured contact area. To quantify the adverse effect of an oxide on contact area measurements, we use molecular dynamics simulations of an oxide-coated platinum tip and a crystalline platinum substrate, where both the contact size and conductance can be inferred from the positions of atoms in the interface. We develop a method to approximate conductance based on the distance between atoms in platinum channels across the contact. Then, the contact area calculated from conductance using ballistic transport and tunneling theories is compared to that obtained using the known positions of atoms in the contact. The difference is small for very thin (<0.1 nm) or very thick (>1.0 nm) oxides, where ballistic transport and tunneling theories work well; however, the difference is significant for oxides between these limits, which is expected to be the case for platinum in many practical applications.

Ab initio scrutiny of endohedral C20 fullerenes implanted in between gold electrodes

Using the smallest non-classical fullerene, we investigate the impact of endohedral fullerene molecules on the quantum transport through molecular junctions, and then compared this with the pure C₂₀-based molecular junction. By employing the density functional theory combined with the non-equilibrium Green's function, we contemplated different electronic parameters, namely, density of states, transmission coefficient, energy levels, molecular orbitals, conduction gaps, electron density and their charge transfer. A knowledge of these physical parameters is necessary in order to calculate current and conductance computed using Landauer-Büttiker formalism. The molecule-electrode coupling influenced by endohedral molecules affects junction devices in a unique manner. We observe that the highest quantum transport is possible in an Au-N@C₂₀-Au and Au-O@C₂₀-Au junction device, and is even higher than that of the intrinsic C₂₀ fullerene junction. Another notable observation is that the F@C₂₀ molecule exhibits the least conducting nature, being even lower than that of the endohedral molecule formed by inserting the noble element, neon. Graphical abstract Electrical characteristics of Endohedral fullerene junctions.

Cyanographone and isocyanographone - Two asymmetrically functionalized graphene pseudohalides and their potential use in chemical sensing

Graphene pseudohalides are natural candidates for use in molecular sensing due to their greater chemical activity as compared to both graphene halides and pristine graphene. Though their study is still in its infancy, being hindered until recently by the unavailability of both selective and efficient procedures for their synthesis, they promise to considerably widen the application potential of chemically modified graphenes. Herein, we employ van der Waals density functional theory to study the structural and electronic properties of two selected graphene pseudohalides, namely, cyanographone and isocyanographone and investigate the potential use of the latter as a chemical sensor via electron transport calculations.

The DFT-NEGF scrutiny of doped fullerene junctions

Using the smallest non-classical fullerene, we investigate the impact of doping at the molecule-electrode interface on the electron transport of molecular junctions. This is accomplished by employing the density functional theory combined with the non-equilibrium Green's function. We contemplate different electronic parameters, namely, density of states, transmission coefficient, energy levels, molecular orbitals, conduction gaps, electron density, and their charge transfer. The relevance of these physical parameters is obtained to calculate their electrical parameters, current, and conductance, computed from Landauer-Büttiker formalism. The molecule-electrode coupling is influenced by the nature of doping atoms and affects the junction devices in a unique course. A particular aftermath is noticed in Au-C₁₈O₂-Au device with highest ballistic transport despite the electro-negative nature of oxygen atoms. Moreover, an interesting feature is observed in Au-C₁₈Be₂-Au device with double-barrier transmission resonance and corresponding oscillating conductance. Graphical abstract The doped C₂₀ fullerene in molecular and device mode.

The atomic simulation environment-a Python library for working with atoms

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks. For example, a sequence of calculations may be performed with the use of a simple 'for-loop' construction. Calculations of energy, forces, stresses and other quantities are performed through interfaces to many external electronic structure codes or force fields using a uniform interface. On top of this calculator interface, ASE provides modules for performing many standard simulation tasks such as structure optimization, molecular dynamics, handling of constraints and performing nudged elastic band calculations.

Electron transport in molecular junctions with graphene as protecting layer

We present ab initio transport calculations for molecular junctions that include graphene as a protecting layer between a single molecule and gold electrodes. This vertical setup has recently gained significant interest in experiment for the design of particularly stable and reproducible devices. We observe that the signals from the molecule in the electronic transmission are overlayed by the signatures of the graphene sheet, thus raising the need for a reinterpretation of the transmission. On the other hand, we see that our results are stable with respect to various defects in the graphene. For weakly physiosorbed molecules, no signs of interaction with the graphene are evident, so the transport properties are determined by offresonant tunnelling between the gold leads across an extended structure that includes the molecule itself and the additional graphene layer. Compared with pure gold electrodes, calculated conductances are about one order of magnitude lower due to the increased tunnelling distance. Relative differences upon changing the end group and the length of the molecule on the other hand, are similar.

Simple and efficient way of speeding up transmission calculations with k-point sampling

The transmissions as functions of energy are central for electron or phonon transport in the Landauer transport picture. We suggest a simple and computationally "cheap" post-processing scheme to interpolate transmission functions over k-points to get smooth well-converged average transmission functions. This is relevant for data obtained using typical "expensive" first principles calculations where the leads/electrodes are described by periodic boundary conditions. We show examples of transport in graphene structures where a speed-up of an order of magnitude is easily obtained.

Numerical solver for first-principles transport calculation based on real-space finite-difference method

We propose an efficient procedure to obtain Green's functions by combining the shifted conjugate orthogonal conjugate gradient (shifted COCG) method with the nonequilibrium Green's function (NEGF) method based on a real-space finite-difference (RSFD) approach. The bottleneck of the computation in the NEGF scheme is matrix inversion of the Hamiltonian including the self-energy terms of electrodes to obtain the perturbed Green's function in the transition region. This procedure first computes unperturbed Green's functions and calculates perturbed Green's functions from the unperturbed ones using a mathematically strict relation. Since the matrices to be inverted to obtain the unperturbed Green's functions are sparse, complex-symmetric, and shifted for a given set of sampling energy points, we can use the shifted COCG method, in which once the Green's function for a reference energy point has been calculated the Green's functions for the other energy points can be obtained with a moderate computational cost. We calculate the transport properties of a C(60)@(10,10) carbon nanotube (CNT) peapod suspended by (10,10)CNTs as an example of a large-scale transport calculation. The proposed scheme opens the possibility of performing large-scale RSFD-NEGF transport calculations using massively parallel computers without the loss of accuracy originating from the incompleteness of the localized basis set.

Length dependence of electron transport through molecular wires – a first principles perspective

The length dependence of coherent electron transport through molecular wires is discussed in the context of a survey of state-of-the-art first principles calculation methods.

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.

Origin of the transition voltage in gold-vacuum-gold atomic junctions

The origin and the distance dependence of the transition voltage of gold-vacuum-gold junctions are investigated by employing first-principles quantum transport simulations. Our calculations show that atomic protrusions always exist on the electrode surface of gold-vacuum-gold junctions fabricated using the mechanically controllable break junction (MCBJ) method. The transition voltage of these gold-vacuum-gold junctions with atomically sharp electrodes is determined by the local density of states (LDOS) of the apex gold atom on the electrode surface rather than by the vacuum barrier shape. More specifically, the absolute value of the transition voltage roughly equals the rising edge of the LDOS peak contributed by the 6p atomic orbitals of the gold atoms protruding from the electrode surface, whose local Fermi level is shifted downwards when a bias voltage is applied. Since the LDOS of the apex gold atom depends strongly on the exact shape of the electrode, the transition voltage is sensitive to the variation of the atomic configuration of the junction. For asymmetric junctions, the transition voltage may also change significantly depending on the bias polarity. Considering that the occurrence of the transition voltage requires the electrode distance to be larger than a critical value, the interaction between the two electrodes is actually rather weak. Consequently, the LDOS of the apex gold atom is mainly determined by its local atomic configuration and the transition voltage only depends weakly on the electrode distance as observed in the MCBJ experiments.

Nonequilibrium thermodynamics of interacting tunneling transport: variational grand potential, density functional formulation and nature of steady-state forces

The standard formulation of tunneling transport rests on an open-boundary modeling. There, conserving approximations to nonequilibrium Green function or quantum statistical mechanics provide consistent but computational costly approaches; alternatively, the use of density-dependent ballistic-transport calculations (e.g., Lang 1995 Phys. Rev. B 52 5335), here denoted 'DBT', provides computationally efficient (approximate) atomistic characterizations of the electron behavior but has until now lacked a formal justification. This paper presents an exact, variational nonequilibrium thermodynamic theory for fully interacting tunneling and provides a rigorous foundation for frozen-nuclei DBT calculations as a lowest-order approximation to an exact nonequilibrium thermodynamic density functional evaluation. The theory starts from the complete electron nonequilibrium quantum statistical mechanics and I identify the operator for the nonequilibrium Gibbs free energy which, generally, must be treated as an implicit solution of the fully interacting many-body dynamics. I demonstrate a minimal property of a functional for the nonequilibrium thermodynamic grand potential which thus uniquely identifies the solution as the exact nonequilibrium density matrix. I also show that the uniqueness-of-density proof from a closely related Lippmann-Schwinger collision density functional theory (Hyldgaard 2008 Phys. Rev. B 78 165109) makes it possible to express the variational nonequilibrium thermodynamic description as a single-particle formulation based on universal electron-density functionals; the full nonequilibrium single-particle formulation improves the DBT method, for example, by a more refined account of Gibbs free energy effects. I illustrate a formal evaluation of the zero-temperature thermodynamic grand potential value which I find is closely related to the variation in the scattering phase shifts and hence to Friedel density oscillations. This paper also discusses the difference between the here-presented exact thermodynamic forces and the often-used electrostatic forces. Finally the paper documents an inherent adiabatic nature of the thermodynamic forces and observes that these are suited for a nonequilibrium implementation of the Born-Oppenheimer approximation.

Polarity switching of charge transport and thermoelectricity in self-assembled monolayer devices

Self-assembled monolayer devices can exhibit drastically different charge-transport characteristics and thermoelectric properties despite being composed of isomeric molecules with essentially identical frontier-orbital energies. This is rationalized by the cooperative electrostatic action of local intramolecular dipoles in otherwise nonpolar species, thus revealing new challenges but also new opportunities for the targeted design of functional building blocks in future nanoelectronics.

DNA base-specific modulation of microampere transverse edge currents through a metallic graphene nanoribbon with a nanopore

We study two-terminal devices for DNA sequencing that consist of a metallic graphene nanoribbon with zigzag edges (ZGNR) and a nanopore in its interior through which the DNA molecule is translocated. Using the nonequilibrium Green functions combined with density functional theory, we demonstrate that each of the four DNA nucleobases inserted into the nanopore, whose edge carbon atoms are passivated by either hydrogen or nitrogen, will lead to a unique change in the device conductance. Unlike other recent biosensors based on transverse electronic transport through translocated DNA, which utilize small (of the order of pA) tunneling current across a nanogap or a nanopore yielding a poor signal-to-noise ratio, our device concept relies on the fact that in ZGNRs local current density is peaked around the edges so that drilling a nanopore away from the edges will not diminish the conductance. Inserting a nucleobase into the nanopore affects the charge density in the surrounding area, thereby modulating edge conduction currents whose magnitude is of the order of microampere at bias voltage 0.1 V. The proposed biosensors are not limited to ZGNRs and they could be realized with other nanowires supporting transverse edge currents, such as chiral GNRs or wires made of two-dimensional topological insulators.

Calculation of transmission probability by solving an eigenvalue problem

The electron transmission probability in nanodevices is calculated by solving an eigenvalue problem. The eigenvalues are the transmission probabilities and the number of nonzero eigenvalues is equal to the number of open quantum transmission eigenchannels. The number of open eigenchannels is typically a few dozen at most, thus the computational cost amounts to the calculation of a few outer eigenvalues of a complex Hermitian matrix (the transmission matrix). The method is implemented on a real space grid basis providing an alternative to localized atomic orbital based quantum transport calculations. Numerical examples are presented to illustrate the efficiency of the method.

The relation between structure and quantum interference in single molecule junctions

Quantum interference (QI) of electron pathways has recently attracted increased interest as an enabling tool for single-molecule electronic devices. Although various molecular systems have been shown to exhibit QI effects and a number of methods have been proposed for its analysis, simple guidelines linking the molecular structure to QI effects in the phase-coherent transport regime have until now been lacking. In the present work we demonstrate that QI in aromatic molecules is intimately related to the topology of the molecule's π system and establish a simple graphical scheme to predict the existence of QI-induced transmission antiresonances. The generality of the scheme, which is exact for a certain class of tight-binding models, is proved by a comparison to first-principles transport calculations for 10 different configurations of anthraquinone as well as a set of cross-conjugated molecular wires.

Bending of conjugated molecular wires and its effect on electron conduction properties

The electronic structure and electron transport properties of simple conjugated molecular wires like oligophenylene ethynylene (OPE) and oligophenylene vinylene (OPV) are studied under compression. If artificially confined to a given shorter length, the oligomers tend to bend and bending causes a loss in the overlap of the conjugated molecular orbitals. Theoretical modeling of electronic transport has been carried out for all undistorted and compressed OPE/OPV oligomers. OPV exists in step-like or V-like conformations and they have the same stability with very similar frontier molecular orbitals. The conductances of these molecular wires are calculated when inserted between two gold probes and the conductances for OPV are found to be comparable to OPE when the interfaces are same. The conductance decreases with bending due to the gradual loss in overlap of the molecular orbitals. It is also found that the conductances of the molecular wires decrease very strongly if the terminal sulfur atom is simultaneously bonded to hydrogen and a gold surface, thus reflecting the importance of the interface in determining the conductance in two-probe systems. From the conductance studies it may be concluded that if one or more benzene rings of OPE are rotated from coplanar conditions, the orthogonal molecular orbitals may completely block the electronic transport, rendering the molecule insulating.

Ghost transmission: How large basis sets can make electron transport calculations worse

The Landauer approach has proven to be an invaluable tool for calculating the electron transport properties of single molecules, especially when combined with a nonequilibrium Green's function approach and Kohn-Sham density functional theory. However, when using large nonorthogonal atom-centered basis sets, such as those common in quantum chemistry, one can find erroneous results if the Landauer approach is applied blindly. In fact, basis sets of triple-zeta quality or higher sometimes result in an artificially high transmission and possibly even qualitatively wrong conclusions regarding chemical trends. In these cases, transport persists when molecular atoms are replaced by basis functions alone ("ghost atoms"). The occurrence of such ghost transmission is correlated with low-energy virtual molecular orbitals of the central subsystem and may be interpreted as a biased and thus inaccurate description of vacuum transmission. An approximate practical correction scheme is to calculate the ghost transmission and subtract it from the full transmission. As a further consequence of this study, it is recommended that sensitive molecules be used for parameter studies, in particular those whose transmission functions show antiresonance features such as benzene-based systems connected to the electrodes in meta positions and other low-conducting systems such as alkanes and silanes.

Understanding effects of molecular adsorption at a single-wall boron nitride nanotube interface from density functional theory calculations

In this paper, we explored computationally the feasibility of modulating the bandgap in a single-wall BN nanotube (BNNT) upon noncovalent adsorption of organic molecules, combined with the application of a transverse electric field. Effects of analytes' physisorption on the surface of BNNTs regarding structural and electronic properties were delineated. Relatively large binding energies were calculated, however, with minimal perturbation of the structural framework. Electronic structure calculations indicated that the bandgap of BNNTs can be modified by weak adsorption due to the presence of adsorbate states in the gap of the host system. Furthermore, we have shown that the application of a transverse electric field can tune the bandgap by shifting adsorbate states, consistent with calculated current-voltage characteristics.

Effects of spin-orbit coupling on the conductance of molecules contacted with gold electrodes

The effects of spin-orbit coupling on the conductance of molecular devices made with Au electrodes are investigated using a fully self-consistent ab initio approach, which combines the non-equilibrium Green's function formalism with density functional theory. In general, we find that the extent to which spin-orbit interaction affects the transport depends on the specific materials system investigated and on the dimensionality of the electrodes. For one-dimensional electrodes contacting benzene-dithiol molecules the spin-orbit coupling induces changes in the low-bias conductance up to about 20%. These originate mostly from changes in the electrode band structure. In contrast when three-dimensional electrodes are used, the bands near the Fermi level are only weakly modified by spin-orbit coupling and most of the variations are due to symmetry changes at the molecule-electrode interface. For this reason strongly coupled systems, such as Au atomic nanowires sandwiched between Au (100) surfaces and benzene-dithiol molecules bonded at the Au (111) hollow site, are rather insensitive to spin-orbit effects. In contrast, in junctions where the coupling between the molecule and the electrodes is weaker, as in the case of benzene-dithiol bonded to Au (111) at adatom positions, the transmission coefficient at the Fermi level can be modified by as much as 14%.

Conductance of sidewall-functionalized carbon nanotubes: universal dependence on adsorption sites

We use density functional theory to study the effect of molecular adsorbates on the conductance of metallic carbon nanotubes (CNT). The five molecules considered (NO2, NH2, H, COOH, OH) lead to very similar scattering of the electrons. The adsorption of a single molecule suppresses one of the two available transport channels at the Fermi level while the other is left undisturbed. If more molecules are adsorbed on the same sublattice, the remaining open channel may or may not be blocked, depending on the relative position of the adsorbates. If the relative positions satisfy a simple geometric condition, this channel remains fully open independently of the number of adsorbed molecules.

Anomalous conductance oscillations and half-metallicity in atomic Ag-O chains

Using spin density functional theory, we study the electronic and magnetic properties of atomically thin, suspended chains containing silver and oxygen atoms in an alternating sequence. Chains longer than 4 atoms develop a half-metallic ground state implying fully spin-polarized charge carriers. The conductances of the chains exhibit weak even-odd oscillations around an anomalously low value of 0.1G0 (G0=2e2/h) which coincide with the averaged experimental conductance in the long chain limit. The unusual conductance properties are explained in terms of a resonating-chain model, which takes the reflection probability and phase shift of a single bulk-chain interface as the only input. The model also explains the conductance oscillations for other metallic chains.