Interaction between benzenedithiolate and gold: classical force field for chemical bonding

We have constructed a group of classical potentials based on ab initio density-functional theory (DFT) calculations to describe the chemical bonding between benzenedithiolate (BDT) molecule and gold atoms, including bond stretching, bond angle bending, and dihedral angle torsion involved at the interface between the molecule and gold clusters. Three DFT functionals, local-density approximation (LDA), PBE0, and X3LYP, have been implemented to calculate single point energies (SPE) for a large number of molecular configurations of BDT-1, 2 Au complexes. The three DFT methods yield similar bonding curves. The variations of atomic charges from Mulliken population analysis within the molecule/metal complex versus different molecular configurations have been investigated in detail. We found that, except for bonded atoms in BDT-1, 2 Au complexes, the Mulliken partial charges of other atoms in BDT are quite stable, which significantly reduces the uncertainty in partial charge selections in classical molecular simulations. Molecular-dynamics (MD) simulations are performed to investigate the structure of BDT self-assembled monolayer (SAM) and the adsorption geometry of S adatoms on Au (111) surface. We found that the bond-stretching potential is the most dominant part in chemical bonding. Whereas the local bonding geometry of BDT molecular configuration may depend on the DFT functional used, the global packing structure of BDT SAM is quite independent of DFT functional, even though the uncertainty of some force-field parameters for chemical bonding can be as large as approximately 100%. This indicates that the intermolecular interactions play a dominant role in determining the BDT SAMs global packing structure.     

Single molecule electron transport junctions: charging and geometric effects on conductance

A p-benzenedithiolate (BDT) molecule covalently bonded between two gold electrodes has become one of the model systems utilized for investigating molecular transport junctions. The plethora of papers published on the BDT system has led to varying conclusions with respect to both the mechanism and the magnitude of transport. Conductance variations have been attributed to difficulty in calculating charge transfer to the molecule, inability to locate the Fermi energy accurately, geometric dispersion, and stochastic switching. Here we compare results obtained using two transport codes, TRANSIESTA-C and HUCKEL-IV, to show that upon Au-S bond lengthening, the calculated low bias conductance initially increases by up to a factor of 30. This increase in highest occupied molecular orbital (HOMO) mediated conductance is attributed to charging of the terminal sulfur atom and a corresponding decrease in the energy gap between the Fermi level and the HOMO. Addition of a single Au atom to each terminal of the extended BDT molecule is shown to add four molecular states near the Fermi energy, which may explain the varying results reported in the literature.     

Theoretical investigation on electron transport through an organic molecule: effect of the contact structure

Knowing how the contact geometry influences the conductance of a molecular wire junction requires both a precise determination of the molecule/metallic-electrode interface structure and an evaluation of the conductance for different contact geometries with a fair accuracy. With a greatly improved method to solve the Lippmann-Schwinger equation, we are able to include at least one atomic layer of each electrode into the extended molecule. The artificial effect of the jellium model used for the electrodes is therefore significantly reduced. Our first-principles calculations on the transport properties of a single benzene dithiolate molecule sandwiched between Au(111) surfaces show that the transmission of the bridge site contact, which is the most stable adsorption configuration in equilibrium, displays different features from those of other configurations, and that the inclusion of the surface layers of Au electrodes into the extended molecule shifts and broadens the transmission peaks due to a stronger and more realistic S-Au bonding. We discuss the geometry dependence of the transport properties by analyzing the density of states of the molecular orbitals.     

Molecular conductance: chemical trends of anchoring groups

Combining density functional theory calculations for molecular electronic structure with a Green function method for electron transport, we calculate from first principles the molecular conductance of benzene connected to two Au leads through different anchoring atoms-S, Se, and Te. The relaxed atomic structure of the contact, different lead orientations, and different adsorption sites are fully considered. We find that the molecule-lead coupling, electron transfer, and conductance all depend strongly on the adsorption site, lead orientation, and local contact atomic configuration. For flat contacts the conductance decreases as the atomic number of the anchoring atom increases, regardless of the adsorption site, lead orientation, or bias. For small bias this chemical trend is, however, dependent on the contact atomic configuration: an additional Au atom at the contact with the (111) lead changes the best anchoring atom from S to Se, although for large bias the original chemical trend is recovered.     

Models of electrodes and contacts in molecular electronics

Bridging the difference in atomic structure between experiments and theoretical calculations and exploring quantum confinement effects in thin electrodes (leads) are both important issues in molecular electronics. To address these issues, we report here, by using Au-benzenedithiol-Au as a model system, systematic investigations of different models for the leads and the lead-molecule contacts: leads with different cross sections, leads consisting of infinite surfaces, and surface leads with a local nanowire or atomic chain of different lengths. The method adopted is a nonequilibrium Green's-function approach combined with density-functional theory calculations for the electronic structure and transport, in which the leads and molecule are treated on the same footing. It is shown that leads with a small cross section will lead to large oscillations in the transmission function T(E), which depend significantly on the lead structure (orientation) because of quantum waveguide effects. This oscillation slowly decays as the lead width increases, with the average approaching the limit given by infinite surface leads. Local nanowire structures around the contacts induce moderate fluctuations in T(E), while a Au atomic chain (including a single Au apex atom) at each contact leads to a significant conductance resonance.     

电化学门控调节具有平行路径的单分子电路中电子传输

电化学门控已成为一种可行且高效调节单分子电导的方法.在本研究中,我们证实了具有两个平行苯环的单分子电路中电子传输可以通过电化学门控控制.首先,我们利用STM-BJ技术以金为电极构筑了具有两条平行路径的单分子结.与单条路径的单分子结相比,两条路径的分子结由于具有增强性量子干涉效应,具有2.82倍的电导值.进一步地,我们利...     

Nonequilibrium electronic transport of 4,4'-bipyridine molecular junction

The electronic transport properties of a 4,4'-bipyridine molecule sandwiched between two Au(111) surfaces are studied with a fully self-consistent nonequilibrium Green's-function method combined with the density-functional theory. The 4,4'-bipyridine molecule prefers to adsorb near the hollow site of the Au(111) surface and distorts slightly. The modifications on the electronic structure of the molecule due to the presence of the electrodes are described by the renormalized molecular orbitals, which correspond well to the calculated transmission peaks. The average Fermi level lies close to the lowest unoccupied renormalized molecular orbital, which determines the electronic transport property of the molecular junction under a small bias voltage. The total transmission is contributed by a single channel. The transmission peaks shift with the applied bias voltage, and this behavior depends on the spatial distribution of the renormalized molecular orbitals and the voltage drop along the molecular junction. The shape of the calculated conductance curve of the equilibrium geometric configuration reproduces the main feature of the experimental results, but the value is larger than the measured data by about 6 times. Good agreement with the experimental measurements can be obtained by elongating the molecular junction. The electronic transport behaviors depend strongly on the interface configuration.     

Adsorption of 1,3‐Benzenedithiol and 1,3‐Benzenedimethanethiol on Gold Surfaces

The adsorption characteristics of 1,3‐benzenedithiol (1,3‐BDT) and 1,3‐benzenedimethanethiol (1,3‐BDMT) on Au surfaces are investigated by means of surface‐enhanced Raman scattering, UV/Vis absorption spectroscopy, and cyclic voltammetry (CV). 1,3‐BDMT is found to adsorb via two S–Au linkages at concentrations below monolayer coverage, but to have an upright geometry as the concentration increases on Au nanoparticles. On the other hand, 1,3‐BDT is found to adsorb by forming two S–Au linkages, regardless of concentration, based on the disappearance of the ν(SH)_free stretching band. Because of the absence of the methylene unit, 1,3‐BDT appeares not to self‐assemble efficiently on Au surfaces. The UV/Vis absorption spectroscopy and CV techniques are also applied to check the formation of self‐assembled monolayers of 1,3‐BDT and 1,3‐BDMT on Au. Density functional theory calculations based on a simple adsorption model using an Au₈ cluster are performed to better understand the nature of the adsorption characteristics of 1,3‐BDT and 1,3‐BDMT on Au surfaces.     

Using ONIOM calculations to investigate the abilities of simple and nitrogen,boron, sulfur-doped carbon nanotubes in sensing of carbon monoxide

In this work, geometries, stabilities, and electronic properties of the carbon monoxide (CO) molecule as an adsorbent in a simple carbon nanotube (CNT) and nitrogen (N), boron (B), sulfur (S)-doped CNTs (NCNT, BCNT, and SCNT) with parallel and perpendicular configurations are fully considered using ONIOM, natural bond orbital, and quantum theory of atom in molecule (QTAIM) calculations. The adsorption energies (E_ad) demonstrate that a CO molecule could be adsorbed on the surface of the simple CNT with parallel configuration and N-doped CNT with perpendicular configuration in an exothermic process. QTAIM calculations showed the close-shell (noncovalent) interactions between the CO molecule and CNT or N, B, S-doped CNTs. In addition, the energy gap (E_g) values between the highest occupied molecular orbital and the lowest unoccupied molecular orbital are calculated. In accordance with the results of energy gap, simple and N-doped CNTs could be used as CO sensors.     

Geometric Effects on Conductance in Single Molecule Electron Transport Junctions

We studied electron transport properties of a dithiol‐benzene molecule covalently bonded between two gold electrodes by combining ab initio calculations for the central molecule and a green function method to calculate electron transport. Due to the large computational demand, this type of calculations usually involves certain ways of simplification. The simplification commonly used is to fix the contact surface of the electrodes by ignoring the disturbance of the Au contact surface by contacting with the central molecule, i.e. without scattering region relaxation. In this study, we intended to resolve the difference between models with and without the above simplification. The large conductance found in our models without scattering region relaxation is due to the highly symmetric arrangement of the Au contact surface and those layers near the contact. The disturbance of the Au contact surface by the contact of the central molecule is important since the increase of the Au‐S bond and the distortion of the Au atom on the FCC site can lower the transmission coefficient between the two electrodes. In order to obtain better results, the model should include scattering region relaxation. However, when such relaxation is not applicable or demands too much calculation resource, the center molecule of the electronic transport junction should be at least optimized by the calculation level including electronic correlation, i.e. post‐HF methods.     

Ab initio investigation of the switching behavior of the dithiole-benzene nano-molecular wire

We report a first-principle study of electrical transport and switching behavior in a single molecular conductor consisting of a dithiole-benzene (DTB) sandwiched between two Au(100) electrodes. Ab initio total energy calculations reveal DTB molecules on a gold surface, contacted by a monoatomic gold scanning tunneling microscope (STM) tip to have two classes of low energy conformations with differing symmetries. Lateral motion of the tip or excitation of the molecule cause it to change from one conformation class to the other and to switch between a strongly and a weakly conducting state. Thus, surprisingly, despite their apparent simplicity, these Au-DTB-Au nanowires are shown to be electrically bi-stable switches, the smallest two-terminal molecular switches to date. The projected density of states (PDOS) and transmission coefficients are analyzed, and it suggests that the variation of the coupling between the molecule and the electrodes with external bias leads to switching behavior.     

Ab initio derivation of multi-orbital extended Hubbard model for molecular crystals

From configuration interaction (CI) ab initio calculations, we derive an effective two-orbital extended Hubbard model based on the gerade (g) and ungerade (u) molecular orbitals (MOs) of the charge-transfer molecular conductor (TTM-TTP)I(3) and the single-component molecular conductor [Au(tmdt)(2)]. First, by focusing on the isolated molecule, we determine the parameters for the model Hamiltonian so as to reproduce the CI Hamiltonian matrix. Next, we extend the analysis to two neighboring molecule pairs in the crystal and we perform similar calculations to evaluate the inter-molecular interactions. From the resulting tight-binding parameters, we analyze the band structure to confirm that two bands overlap and mix in together, supporting the multi-band feature. Furthermore, using a fragment decomposition, we derive the effective model based on the fragment MOs and show that the staking TTM-TTP molecules can be described by the zig-zag two-leg ladder with the inter-molecular transfer integral being larger than the intra-fragment transfer integral within the molecule. The inter-site interactions between the fragments follow a Coulomb law, supporting the fragment decomposition strategy.     

Investigation of the adsorption of 4-cyanopyridine on Au(111) by in situ visible–infrared sum frequency generation

We have investigated the configuration of 4-cyanopyridine on Au(111) electrodes in perchlorate solution by in situ visible–IR sum frequency generation (SFG). Thanks to the use of two IR tunable lasers (the free electron laser CLIO and a table laser based on an optical parametric oscillator) we have obtained SFG spectra of the system in the spectral range of both the aromatic cycle and the CN stretching modes. We present herein the first SFG spectra ever obtained under electrochemical conditions in the 9–12 μm range. Our results show a potential-dependent orientation of the adsorbed 4-cyanopyridine from a configuration where the molecule is adsorbed perpendicular to the electrode via the nitrogen of the pyridine ring at negative potentials, to a flat adsorption configuration at intermediate potentials, and finally a perpendicular orientation again where the molecule is bound through the nitrogen of the cyanide end.     

Self-assembly of 1,4-benzenedithiolate/tetrahydrofuran on a gold surface: a Monte Carlo simulation study

We report a Monte Carlo simulation study of the self-assembly of 1,4-benzenedithiolate (BDT), tetrahydrofuran (THF), and their mixtures on a Au (111) surface. We use the grand canonical Monte Carlo method to obtain the equilibrium adsorption coverage. Canonical ensemble (NVT) simulation is then used to explore further the structural information of the equilibrated systems. Our results indicate that BDT molecules adsorb onto the Au (111) surface with one of the sulfur atoms bonded to Au atoms. THF molecules form clusters on the surface. For BDT-THF mixtures, BDT can selectively adsorb on Au (111) to form a monolayer, whereas the solvent THF molecules either float above BDT monolayer or occupy vacancies on the surface that are not covered by BDT molecules. BDT molecules adsorb on a Au (111) surface with an average tilt angle of about 18-35 degrees to the surface normal. The tilting angle decreases as the coverage increases. In addition, the BDT monolayer constitutes an ordered herringbone structure on the Au (111) surface, and the ordering pattern is insensitive to the BDT coverage. In comparison, the THF molecules exhibit amorphous structure on the Au surface. Interestingly, simulations indicate that the bonding behavior of BDT molecules on Au (111) is coverage-dependent. BDT bonds preferably on the Au top site when the surface coverage is low. As coverage increases, most BDT molecules bond on the bridge and fcc hollow sites.     

Changes of coupling between the electrodes and the molecule under external bias bring negative differential resistance

We report a first-principles study of electrical transport and negative differential resistance (NDR) in a single molecular conductor consisting of a borazine ring sandwiched between two Au(100) electrodes with a finite cross section. The projected density of states (PDOS) and transmission coefficients under various external voltage biases are analyzed, and it suggests that the variation of the coupling between the molecule and the electrodes with external bias leads to NDR. Therefore, we propose that one origin of NDR in molecular devices is caused by the characteristics of both the molecule and the electrodes as well as their cooperation, not necessarily only by the inherent properties of certain species of molecules themselves. The changes of charge state of the molecule have minor effects on NDR in this device because the Mulliken population analysis shows that electron occupation variation on the molecule is very small when different external biases are applied.     

Electronic structure and electron transport characteristics of a cobalt complex

The molecular and electronic structures and electron transport characteristics of a Co complex are investigated using first principles calculations. The Co complex belongs to the D(2d) point group, and its two ligands are perpendicular to each other. The central atom Co forms a distorted octahedron with six donor N atoms. In a low oxidation state, the bond length between Co and pyrrole nitrogen, 1.849 A, is much shorter than the distance between Co and pyridine nitrogen, 2.168 A, while, in a high oxidation state, the bond length differences between Co and pyrrole nitrogen, 1.814 A, and between Co and pyridine nitrogen, 1.990 A, are not as large as those in the Co2+ complex. The HOMO energy of the low oxidation state is very close to the Fermi level of bulk Au, allowing hole creation in the molecule. On the other hand, the LUMO energy of the high oxidation state is close to the Au Fermi level, allowing a low barrier for electron injection from the Au cathode to the molecule. These structural characteristics make the Co complex a good hole-conduction molecule. The density of states, transmission probability, and I-V characteristics are evaluated using the Green function approach.     

Solvation of Au+ versus Au0 in aqueous solution: electronic structure governs solvation shell patterns

The solvation behavior of Au(+) and Au(0) in liquid water under ambient conditions has been studied using ab initio molecular dynamics. The Au(+) aqua ion forms a rigid and well-defined quasi-linear structure in the sense of ligand field theory, where two water molecules are tightly bound to the gold cation through oxygen atoms ("cationic solvation"). Yet, transient charge accumulation in the direction perpendicular to the O-Au(+)-O linear core structure leads occasionally to the formation of a short Au(+)-H contact within the distance range of the first solvation shell, which is typical of "anionic solvation". Upon adding an electron to Au(+), the resulting solvation pattern of Au(0)(aq) has nothing in common with that of Au(+)(aq). Quite surprisingly we discover that the first solvation shell of Au(0)(aq) consists of a single water molecule and features both "anionic" and "cationic" solvation patterns depending on fluctuation and polarization effects. Thus, charging/decharging of metals dissolved in water, M(0)? M(+) + e(-), as occurring e.g. during elementary electrochemical steps, is expected to change dramatically their solvation behavior in the sense of re-solvation processes.     

Conductivity in alkylamine/gold and alkanethiol/gold molecular junctions measured in molecule/nanoparticle/molecule bridges and conducting probe structures

Charge transport through alkane monolayers on gold is measured as a function of molecule length in a controlled ambient using a metal/molecule/nanoparticle bridge structure and compared for both thiol and amine molecular end groups. The current through molecules with an amine/gold junction is observed to be more than a factor of 10 larger than that measured in similar molecules with thiol/gold linkages. Conducting probe atomic force microscopy is also used to characterize the same monolayer systems, and the results are quantitatively consistent with those found in the nanoparticle bridge geometry. Scaling of the current with contact area is used to estimate that approximately 100 molecules are probed in the nanoparticle bridge geometry. For both molecular end groups, the room-temperature conductivity at low bias as a function of molecule length shows a reasonable fit to models of coherent nonresonant charge tunneling. The different conductivity is ascribed to differences in charge transfer and wave function mixing at the metal/molecule contact, including possible effects of amine group oxidation and molecular conformation. For the amine/Au contact, the nitrogen lone pair interaction with the gold results in a hybrid wave function directed along the molecule bond axis, whereas the thiol/Au contact leads to a more localized wave function.     

A search for a strong physisorption site for H2 in Li-doped porous carbons

The mechanism of hydrogen absorption between two coronene molecules has been studied by first principle calculations. Examination of different sites for H(2) molecule confirmed the classical picture of physisorption. We have also considered molecular hydrogen adsorption in a charged carbon structure achieved by doping with lithium at a density corresponding to the intercalate compound LiC(6). We have performed different types of calculations [Hartree-Fock and density functional theory (DFT)] for various atomic basis sets using CRYSTAL98, GAUSSIAN98, and DMOL3 codes. B3LYP-DFT (B3LYP-three-parameter functional of Backe, Lee, Yang and Parr) energy minimization calculations unravel that there is a stable adsorption site for molecular hydrogen in Li-doped sp(2) carbon structure. These calculations also give an insight into the atomic configurations of interlayer species (H(2) and Li) as the interlayer spacing increases. It can be shown that large changes occur in the positions and electronic properties of interlayer species. Hydrogen molecule does not show any tendency for dissociation and adopts a position in the interlayer void that is deeply related to that of lithium ions. We have evidenced a rather large charge transfer from lithium and capping hydrogen species on neighboring slab carbon atoms that induce the stabilization of molecular hydrogen. We have also found that rotating one carbon layer with respect to the other one (at constant interlayer distance) does not change the adsorption energy to a large extent. The best adsorption site is about five times deeper than the physisorption site found in the undoped case and occurs at an interlayer separation of 5.5+/-0.5 A. The corresponding atomic configuration consists in a hydrogen molecule standing (nearly) perpendicular to the plane surface surrounded by the three lithium ions in a configuration close to that of the LiC(6) intercalation compound.     

Protonation effects on electron transport through diblock molecular junctions:A theoretical study

Diblock oligomers are widely used in molecular electronics. Based on fully self-consistent nonequilib-rium Green's function method and density functional theory, we study the electron transport properties of the molecular junction with a dipyrimidinyl-diphenyl (PMPH) diblock molecule sandwiched between two gold electrodes. Effects of different kinds of molecule-electrode anchoring geometry and protona-tion of the PMPH molecule are studied. Protonation leads to both conductance and rectification en-hancements. However, the experimentally observed rectifying direction inversion is not found in our calculation. The preferential current direction is always from the pyrimidinyl to the phenyl side. Our calculations indicate that the protonation of the molecular wire is not the only reason of the rectification inversion.