The injecting energy at molecule/metal interfaces: Implications for conductance of molecular junctions from an ab initio molecular description

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.

Impact of electron-phonon coupling on the quantum yield of photovoltaic devices

In describing the charge carriers' separation mechanism in the organic solar cell, providing a method, which considers the impact of all parameters of interest on the same footing within an inexpensive numerical effort, could play an essential role. We use here a simple tight-binding model to describe the dissociation of the charge carriers and investigate their dependence on the physical parameters of the system. We demonstrate that the quantum yield of the cell is subtly controlled by the collective action of the Coulomb interaction of the electron-hole pair, electron-phonon coupling, and the geminate recombination of the charge carriers. This approach should help us understand the performance of organic solar cells and optimize their efficiency.

A DFT study on surface-enhanced Raman spectroscopy of aromatic dithiol derivatives adsorbed on gold nanojunctions

A computational study on aromatic dithiol derivatives (HS-Ar-X-Ar-SH, X=O, S, Se, NH, CH₂, NN, CHCH, CC) interacting with gold cluster(s) was presented to investigate the chemical enhancement mechanism related to surface-enhanced Raman spectroscopy (SERS) for molecular junctions. Density functional theory (DFT) were performed on derivatives molecules as well as their single-end-linked (SEL) or double-end-linked (DEL) complexes for geometric, spectra, electronic and excitation properties, leading to discussions on dominant factor during SERS process. The resulted enhancement factors of SEL and DEL complexes exhibited specific dependency on linking atom or functional group between two phenyls, which was in accordance with the variation of polarizabilities and molecule-cluster transition energy.

Near omni-conductors and insulators: Alternant hydrocarbons in the SSP model of ballistic conduction

Within the source-and-sink-potential model, a complete characterisation is obtained for the conduction behaviour of alternant π-conjugated hydrocarbons (conjugated hydrocarbons without odd cycles). In this model, an omni-conductor has a molecular graph that conducts at the Fermi level irrespective of the choice of connection vertices. Likewise, an omni-insulator is a molecular graph that fails to conduct for any choice of connections. We give a comprehensive classification of possible combinations of omni-conducting and omni-insulating behaviour for molecular graphs, ranked by nullity (number of non-bonding orbitals). Alternant hydrocarbons are those that have bipartite molecular graphs; they cannot be full omni-conductors or full omni-insulators but may conduct or insulate within well-defined subsets of vertices (unsaturated carbon centres). This leads to the definition of "near omni-conductors" and "near omni-insulators." Of 81 conceivable classes of conduction behaviour for alternants, only 14 are realisable. Of these, nine are realised by more than one chemical graph. For example, conduction of all Kekulean benzenoids (nanographenes) is described by just two classes. In particular, the catafused benzenoids (benzenoids in which no carbon atom belongs to three hexagons) conduct when connected to leads via one starred and one unstarred atom, and otherwise insulate, corresponding to conduction type CII in the near-omni classification scheme.

An approach to the electronic structure of molecular junctions with metal clusters of atomic thickness

TD-DFT calculations predict a linear dependence of the energies of charge transfer states of Ag_n-pyrazine-Ag_n molecular junctions on the inverse of the size (1/n) of the linear metal chains. The density of charge (q_eff = q/n) in the metal-to-metal charge transfer excited states (CT_MM: Ag_n^q-pyrazine-Ag_n^-q) smoothly tunes the electronic structure of the junction, especially the metal-to-molecule charge transfer states (CT₀ and CT₁) and the first excited singlet of pyrazine (S_1,Pz). In enlarged junctions, pyrazine bonds preferably to one of the Ag_n clusters and this weak adsorption produces a significant unexpected asymmetry for forward and reverse charge transfer processes.

Ab initio electron propagator calculations of transverse conduction through DNA nucleotide bases in 1-nm nanopore corroborate third generation sequencing

BACKGROUND

The conduction properties of DNA molecule, particularly its transverse conductance (electron transfer through nucleotide bridges), represent a point of interest for DNA chemistry community, especially for DNA sequencing. However, there is no fully developed first-principles theory for molecular conductance and current that allows one to analyze the transverse flow of electrical charge through a nucleotide base.

METHODS

We theoretically investigate the transverse electron transport through all four DNA nucleotide bases by implementing an unbiased ab initio theoretical approach, namely, the electron propagator theory.

RESULTS

The electrical conductance and current through DNA nucleobases (guanine [G], cytosine [C], adenine [A] and thymine [T]) inserted into a model 1-nm Ag-Ag nanogap are calculated. The magnitudes of the calculated conductance and current are ordered in the following hierarchies: gA>gG>gC>gT and IG>IA>IT>IC correspondingly. The new distinguishing parameter for the nucleobase identification is proposed, namely, the onset bias magnitude. Nucleobases exhibit the following hierarchy with respect to this parameter: Vonset(A)<Vonset(T)<Vonset(G)<Vonset(C).

CONCLUSIONS

The difference in current magnitudes and onset voltages implies the possibility of nucleobases electrical identification by virtue of DNA translocation through an electrode-equipped nanopore.

GENERAL SIGNIFICANCE

The results represent interest for the theorists and practitioners in the field of third generation sequencing techniques as well as in the field of DNA chemistry.

Analyzing the electric response of molecular conductors using "electron deformation" orbitals and occupied-virtual electron transfer

The concept of "electron deformation orbitals" (EDOs) is used to investigate the electric response of conducting metals and oligophenyl chains. These orbitals and their eigenvalues are obtained by diagonalization of the deformation density matrix (difference between the density matrices of the perturbed and unperturbed systems) and can be constructed as linear combinations of the unperturbed molecular orbitals within "frozen geometry" conditions. This form of the EDOs allows calculating the part of the electron deformation density associated to an effective electron transfer from occupied to virtual orbitals (valence to conduction band electron transfer in the band model of conductivity). It is found that the "electron deformation" orbitals pair off, displaying the same eigenvalue but opposite sign. Each pair represents an amount of accumulation/depletion of electron charge at different molecular regions. In the oligophenyl systems investigated only one pair contributes effectively to the charge flow between molecular ends, resulting from the promotion of electrons from occupied orbitals to close in energy virtual orbitals of appropriate symmetry and overlapping. Analysis of this pair along explains the differences in conductance of olygophenyl chains based on phenyl units.

QUANTUM TRANSPORT AND CURRENT-TRIGGERED DYNAMICS IN MOLECULAR TUNNEL JUNCTIONS

The modelling of nanoelectronic systems has been the topic of ever increasing activity for nearly two decades. Yet, new questions, challenges and opportunities continue to emerge. In this article we review theoretical and numerical work on two new developments in the theory of molecular-scale electronics. First we review a density functional theory analysis within the Keldysh non-equilibrium Green function formalism to predict nonlinear charge transport properties of nanoelectronic devices. Next we review a recently developed quantum mechanical formalism of current-triggered nuclear dynamics. Finally we combine these theories to describe from first principles the inelastic current and the consequent molecular dynamics in molecular heterojunctions.

Inelastic electron tunneling spectroscopy of gold-benzenedithiol-gold junctions: accurate determination of molecular conformation

The gold-benzenedithiol-gold junction is the classic prototype of molecular electronics. However, even with the similar experimental setup, it has been difficult to reproduce the measured results because of the lack of basic information about the molecular confirmation inside the junction. We have performed systematic first principles study on the inelastic electron tunneling spectroscopy of this classic junction. By comparing the calculated spectra with four different experimental results, the most possible conformations of the molecule under different experimental conditions have been successfully determined. The relationship between the contact configuration and the resulted spectra is revealed. It demonstrates again that one should always combine the theoretical and experimental inelastic electron tunneling spectra to determine the molecular conformation in a junction. Our simulations have also suggested that in terms of the reproducibility and stability, the electromigrated nanogap technique is much better than the mechanically controllable break junction technique.

Ab initio calculations of structural evolution and conductance of benzene-1,4-dithiol on gold leads

By performing ab initio density functional theory (DFT) calculations and electronic transport simulations based on the DFT nonequilibrium Green's functions method we investigate how the conformational changes of a benzene-1,4-dithiol molecule bonded to gold affect the molecular transport as the electrodes are separated from each other. In particular we consider the full evolution of the stretching process until the junction breaking point and compare results obtained with a standard semilocal exchange and correlation functional to those computed with a self-interaction corrected method. We conclude that the inclusion of self-interaction corrections is fundamental for describing both the molecule conductance and its stability against conformational fluctuations.

Formation and electronic transport properties of bimolecular junctions based on aromatic coupling

A systematic first-principles study on conductance-voltage characteristics of bi-(quasi)oligo(phenylene ethynylene)-monothiol molecular junctions reported by Wu et al (2008 Nat. Nanotechnol. 3 569) is presented. The so-called ortho- and para-conformations of the bimolecular junction are considered. Our calculation indicates that the bimolecular junction prefers to take the ortho-conformation because of its lower energy. The simulation supports the experimental findings that aromatic coupling between two molecules is strong enough to induce the formation of molecular junctions. By comparing with experimental results, structure parameters for a probable bimolecular junction are determined. The underlying mechanism for formation of the bimolecular junction and its electron transport is discussed.

ELECTRON TRANSPORT INVESTIGATION OF METAL–MOLECULE–METAL INTERFACE FOR NANOELECTRONICS

Theoretical understanding of electron transport phenomena through single molecules is of great importance for the design of future devices and materials in molecular electronics. Nonequilibrium Green's function (NEGF) formalism combined with extended Huckel (EHT) theory is used to investigate the electron transport characteristics of Au –benzene– Au , Au –borazine– Au , and Au –BCN– Au systems with selenium (Se) as terminal group. It is observed that the energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of borazine ring is higher than the benzene and BCN does. Our result shows that for the terminal group selenium borazine is the best core molecule than benzene and BCN systems.

Towards an accurate description of the electronic properties of the biphenylthiol/gold interface: the role of exact exchange

We investigate the role of the exact exchange in describing the biphenylthiol/gold interface. The study is performed by simulating the electronic properties of mercaptobiphenylthiol and aminobiphenylthiol molecules adsorbed on a Au(23) cluster, using local, semilocal and hybrid functionals and an effective exact exchange method, namely, the localized Hartree-Fock (LHF). We find that the local/semilocal functionals strongly underestimate the charge transfer and the bond dipole at the interface due to the self-interaction-error (SIE), which alters the correct level alignment. On the other hand the LHF method is SIE free and predicts a larger charge transfer and bond dipole. We also found that LHF results can be reproduced using hybrid functionals and that conventional local/semilocal correlation functionals are unable to improve over the exchange-only description.

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.

ELECTRON TRANSPORT THROUGH MULTILEVEL QUANTUM DOT

Quantum transport properties through some multilevel quantum dots sandwiched between two metallic contacts are investigated by the use of Green's function technique. Here, we do parametric calculations, based on the tight-binding model, to study the transport properties through such bridge systems. The electron transport properties are significantly influenced by (a) the number of quantized energy levels in the dots, (b) the dot-to-electrodes coupling strength, (c) the location of the equilibrium Fermi energy E F , and (d) the surface disorder. In the limit of weak-coupling, the conductance (g) shows sharp resonance peaks associated with the quantized energy levels in the dots, while, they get substantial broadening in the strong-coupling limit. The behavior of the electron transfer through these systems becomes much more clearly visible from our study of the current–voltage (I–V) characteristics. In this context, we also describe the noise power of current fluctuations (S) and determine the Fano factor (F) which provides an important information about the electron correlation among the charge carriers. Finally, we explore a novel transport phenomenon by studying the surface disorder effect in which the current amplitude increases with the increase of the surface disorder strength in the strong disorder regime, while, the amplitude decreases in the limit of weak disorder. Such an anomalous behavior is completely opposite to that of bulk disordered system where the current amplitude always decreases with the disorder strength. It is also observed that the current amplitude strongly depends on the system size which reveals the finite quantum size effect.

QUANTUM TRANSPORT THROUGH SINGLE PHENALENYL MOLECULE: EFFECT OF INTERFACE STRUCTURE

The electronic transport characteristics through a single phenalenyl molecule sandwiched between two metallic electrodes are investigated by using Green's function technique. A parametric approach, based on the tight-binding model, is used to study the transport characteristics through such molecular bridge system. The electronic transport properties are significantly influenced by (a) the molecule-to-electrodes interface structure and (b) the molecule-to-electrodes coupling strength.

Carbonyl mediated conductance through metal bound peptides: a computational study

Large increases in the conductance of peptides upon binding to metal ions have recently been reported experimentally. The mechanism of the conductance switching is examined computationally. It is suggested that oxidation of the metal ion occurs after binding to the peptide. This is caused by the bias potential placed across the metal-peptide complex. A combination of configurational changes, metal ion involvement and interactions between carbonyl group oxygen atoms and the gold leads are all shown to be necessary for the large improvement in the conductance seen experimentally. Differences in the molecular orbitals of the nickel and copper complexes are noted and serve to explain the variation of the improvement in conductance upon binding to either a nickel or copper ion.

The effect of self-assembled monolayers on polarization-dependent two-photon photoemission and on the angular distribution of the photoelectrons

The effect of a self-assembled organized organic monolayer on the two-photon photoemission from semiconductor substrates was investigated. It has been found that the monolayer affects the relative yield of photoelectrons emitted by p-polarized versus s-polarized light. In addition, the monolayer affects the angular distribution of the ejected electrons. The effect on the photoelectron yield is attributed to the monolayer "smoothing" the electronic potential on the surface by eliminating surface states and dangling bonds. The effect on the angular distribution is attributed to a post-ejection interaction between the photoelectrons and the adsorbed molecules.

Configuration-dependent interface charge transfer at a molecule-metal junction

The role of the molecule-metal interface is a key issue in molecular electronics. Interface charge transfer processes for 4-fluorobenzenethiol monolayers with different molecular orientations on Au(111) were studied by resonant photoemission spectroscopy. The electrons excited into the LUMO or LUMO+1 are strongly localized for the molecules standing up on Au(111). In contrast, an ultrafast charge transfer process was observed for the molecules lying down on Au(111). This configuration-dependent ultrafast electron transfer is dominated by an adiabatic mechanism and directly reflects the delocalization of the molecular orbitals for molecules lying down on Au(111). Theoretical calculations confirm that the molecular orbitals indeed experience a localization-delocalization transition resulting from hybridization between the molecular orbitals and metal surface. Such an orientation-dependent transition could be harnessed in molecular devices that switch via charge transfer when the molecular orientation is made to change.

Statistical approach to investigating transport through single molecules

We present a statistical approach that combines comprehensive current-voltage data acquisition during the controlled manipulation of a molecular junction with subsequent statistical analysis. Thereby the most probable transport characteristics can be determined. The excellent sensitivity of this impartial approach to even subnanometer-long molecules is illustrated by benzene-1,4-dithiol and 4,4"-bis(acetylthiol)-2,2',5',2"-tetramethyl-[1,1';4',1"] terphenyl results.

Conformational analysis of diphenylacetylene under the influence of an external electric field

Theoretical investigation of the torsional potentials of a molecular wire, diphenylacetylene, was carried out at the B3LYP/6-311+G** level by considering the influence of the external electric field (EF). It demonstrates that many molecular features are sensitive to the EF applied. In particular, the torsional barrier increases and the LUMO-HOMO gap decreases with the increase of EF. Quantitative correlations between these features and the external EF were revealed. The current-voltage behavior corresponding to different conformers was studied as well by non-equilibrium Green's function method combined with the density functional theory. Further, the evolution of the LUMO-HOMO gap and the spatial distribution of molecular orbital were used to analyze these structure-property relationships.