Benzenedithiol Research Articles

Electron tunneling in the presence of adsorbed molecules

We perform ab initio density functional theory calculations of the tunneling current through an electrode–molecule–electrode system with four different small organic molecules, benzenedithiol (BDT), benzenedimethanethiol (XYL), diethynylbenzene (DEB) and dodecanethiol (C12), sandwiched between two gold (1 1 1) electrodes. For the XYL molecule, we test the effect of alternate bonding types and sites. Although this reduces the current considerably, it does not account for the orders of magnitude differences between experimental and theoretical results in the literature. We also model a typical STM experimental setup with a gold nanoparticle absorbed on a self-assembled monolayer (SAM) of the molecule with a gap between the nanoparticle and probing tip and show that such a gap could account for these differences. Finally, we describe the effect that the gap has on the ability of STS measurements to distinguish between the i( V) characteristics and thicknesses of self-assembled monolayers of different molecules.

Study of the transport properties of a molecular junction as a function of the distance between the leads

AbstractWe consider a model of a molecular junction made of BDT (benzene dithiol) molecule trapped between two Au(100) leads. Using the ab initio approach implemented in the SIESTA package we look for the optimal configurations of the molecule as a function of the distance between the leads. We find that for distances long enough the energy of the system is minimized when the molecule is bonded asymmetrically, i.e. chemisorbed to one of the leads, whereas for distances shorter than 12 Å the energy is minimized when the molecule sits in the middle between the leads. We discuss possible consequences of the above findings for the transport properties of the junction. (© 2007 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Mechanically Controlled Quantum Contact With On-Chip MEMS Actuator

We report fabrication and characterization of a mechanically controlled quantum point contact with on-chip electrostatic actuators. Two metallic tips separated with a nano gap are integrated with a micro mechanism, which can be actuated by applied voltage. The electrostatic actuation of the micro mechanism allows the control of separation gap at nanometer level. The gap variation at nanometer level is calibrated with the devices operated in transmission electron microscope. Furthermore, performance of the device is demonstrated by measuring conductance quantization while separating the tips in contact as well as electrical measurements by using tips coated with self assembled monolayers (1-4 benzene dithiol) and conjugated Ru complex

Effects of energetic stability in transport measurements of single benzene-dithiolate by the STM break junction technique

The conductance behavior of the stretching processes in the STM break junction experiments was studied taking account of the effects of the energetic stability of the junction composed of benzene-dithiolate (BDT) and two Au(1 1 1) surfaces using the first principles calculations. The expected value of conductance computed with the three kinds of processes, including the one where only one junction is extended with tilted BDT, shows a flat plateau of conductance similar to the one observed by Xiao et al. [X. Xaio, B. Xu, N.J. Tao, Nano Lett. 4 (2003) 267] just before the break of the junctions.

Adsorption of Benzene-1,4-dithiol on the Au(111) Surface and Its Possible Role in Molecular Conductance

It is a consensus in the field of molecular electronics that the transport of charge across a single molecule depends sensitively on the details of the interaction between the molecule and the metallic leads, such as the molecular orientation. To advance the design of complex molecular devices, it is crucial to have a detailed understanding of these many aspects that influence the electron transport. A simple system that has been used as a paradigm of the class of conjugated aryl molecules is the benzene-1,4-dithiol (BDT). However, we still do not have a full understanding of the BDT transport experiments. Usually the geometries considered in transport calculations assumed that the BDT was connected to the two Au leads via the S atoms, and that the molecule was either perpendicular or close to a perpendicular configuration relative to the Au surfaces. Using ab initio calculations, we show that, for an isolated molecule, the configuration with largest adsorption energy has the BDT phenyl ring closer to being parallel to the surface, and we then argue, based on nonequilibrium Green's function-density functional theory calculations, that, depending on the experimental procedure, this may be the relevant configuration to be used in the transport calculations.

Contact-structure dependence of transport properties of a single organic molecule between Au electrodes

The contact-structure dependence of the transport properties are studied for the junction systems of a benzene dithiolate (BDT) molecule sandwiched between Au(111) atomic electrodes using the nonequilibrium Green's function method based on the density functional theory. The transport properties for the hollow, bridge, and on-top contact structures are calculated. We show clearly that molecular orbitals of the isolated BDT molecule are responsible for the transmission peaks near the Fermi level. The contribution of these molecular orbitals, observed as broadened and shifted peaks in the projected density of states, is determined by the strength of their interaction with the Au electrodes, and the strength of the molecule-electrode interaction is clearly dependent on the contact structures. In the case of hollow contact, which has the strongest molecule-electrode interaction, we observe a linear potential drop across the junction for the various bias voltages. In the on-top contact structure that has the weakest interaction, on the other hand, the nonlinear potential drop and a weak negative differential conductance are observed. We obtain the largest current for the bridge contact structure, which has a moderate interaction. In this way, the transport properties strongly depend on the strength of the molecule-electrode interaction caused by a change of the contact structure and the unusual behavior is obtained for the contact structure that has the weakest interaction.

First-Principles Calculations of Quantum Transport in Single Molecule

We present first-principles calculations of ballistic electron transport in a single molecule between electrodes. The electronic states are calculated using a numerical pseudo atomic orbital basis set in the framework of the density functional theory, and the transport properties are calculated using the Green's function method. We show the conductance of a benzene dithiolate molecule and a fullerene between electrodes, and reveal the transport properties of the systems.

Correlated Ab initio electron propagators in the study of molecular wires

AbstractCorrelated ab initio electron propagators provide a systematic approach to treating correlation effects in the study of molecular wires. Some preliminary formal and computational steps toward the application of such methods to electron transport problems in nanoscience are presented. Retarded and advanced Green functions are expressed in terms of a general electron propagator for a bridge molecule. Terminal and Green function matrices of any rank may be employed. An analytical expression for the current depends on correlated electron binding energies, pole strengths, and Dyson orbitals that may be produced with readily available software. Calculations on benzene dithiolate between gold atoms illustrate the capabilities of this approach. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006

First-principles calculation of the transport properties of molecular wires between Au clusters under equilibrium

Based on the matrix Green's function method combined with hybrid tight-binding / density functional theory, we calculate the conductances of a series of gold-dithiol molecule-gold junctions including benzenedithiol (BDT), benzenedimethanethiol (BDMT), hexanedithiol (HDT), octanedithiol (ODT) and decanedithiol (DDT). An atomically-contacted extended molecule model is used in our calculation. As an important procedure, we determine the position of the Fermi level by the energy reference according to the results from ultraviolet photoelectron spectroscopy (UPS) experiments. After considering the experimental uncertainty in UPS measurement, the calculated results of molecular conductances near the Fermi level qualitatively agree with the experimental values measured by Tao et. al. [{\it Science} 301, 1221 (2003); {\it J. Am. Chem. Soc.} 125, 16164 (2003); {\it Nano. Lett.} 4, 267 (2004).]

Effect of alkali-metal adsorption on the conductance of a molecular device

We show by first-principles density functional calculations that the adsorption of potassium on the platinum electrodes of a benzene dithiolate molecular wire junction will modify the energy-level alignments of the device. But near the Fermi energy, the energy levels, which correspond to sulfur orbitals, are quite inert to the work function change of the electrode due to a strong terminal atom/metal bonding. Our results demonstrate unambiguously that while the coadsorption of potassium on the electrodes may influence the conductance of a molecular device, it cannot change the conductance in a drastic way as the transmission peak near the Fermi level shifts only slightly with the introduction of potassium atoms.

Quantum Collision Current in Electronic Circuits

Some more power is needed to maintain a stationary charge distribution for circulating a current in a quantum device. This effect is a result of the quantum collision current originating from inelastic scattering, which contributes to the observable current density. The picture shows a molecular circuit consisting of a self-assembled monolayer of benzene dithiolate molecules in contact with two gold electrodes.

Transport studies of isolated molecular wires in self-assembled monolayer devices

We have fabricated a variety of isolated molecule diodes based on self-assembled monolayers (SAMs) of solid-state mixture (SSM) of molecular wires [1,4-methane benzene dithiol (Me-BDT)], and molecular insulator spacers [penthane 1-thiol (PT)] with different concentration ratios r of wires∕spacers, which were sandwiched between two gold (Au) electrodes. We introduce two specialized methods borrowed from surface science to (i) confirm the connectivity between the Me-BDT molecules with the upper Au electrode, and (ii) count the number of isolated molecular wires in the devices. The electrical transport properties of the SSM SAM diodes were studied at different temperatures via the conductance and differential conductance spectra. We found that a potential barrier caused by the spatial connectivity gap between the PT molecules and the upper Au electrode dominates the transport properties of the pure PT SAM diode (r=0). The transport properties of SSM diodes with r values in the range 10−8<r<10−4 are dominated by the conductance of the isolated Me-BDT molecules in the device. We found that the temperature dependence of the SSM diodes is much weaker than that of the pure PT device, indicating the importance of the Me-BDT simultaneous bonding to the two Au electrodes that facilitates electrical transport. From the differential conductance spectra we also found that the energy difference between the Au electrode Fermi level and the Me-BDT highest occupied molecular-orbital (or lowest unoccupied molecular-orbital) level is ∼1.5eV; where it is ∼2.5eV for the PT molecule. The weak temperature-dependent transport that we obtained for the SSM diodes reflects the weak temperature dependence of Δ. In addition, our measurements reveal that the conductance of SSM diodes scales linearly with r, showing that the charge transport in these devices is dominated by the sum of the isolated Me-BDT molecular conductance in the device. Based on this finding, and the measured number of the Me-BDT molecules in the device we obtained the “single molecule resistance,” RM. We measured RM=6×109Ω for isolated Me-BDT molecules, which is consistent with previous measurements using other transport measuring techniques. A simple model for calculating RM, where the transport is governed by electron tunneling through the Me-BDT molecule using the WKB approximation, is in good agreement with the experimental data, thus validating the procedures used for our measurements.

Molecular transport calculations with Wannier functions

We present a scheme for calculating coherent electron transport in atomic-scale contacts. The method combines a formally exact Green’s function formalism with a mean-field description of the electronic structure based on the Kohn-Sham scheme of density functional theory. We use an accurate plane-wave electronic structure method to calculate the eigenstates which are subsequently transformed into a set of localized Wannier functions (WFs). The WFs provide a highly efficient basis set which at the same time is well suited for analysis due to the chemical information contained in the WFs. The method is applied to a hydrogen molecule in an infinite Pt wire and a benzene-dithiol (BDT) molecule between Au(1 1 1) surfaces. We show that the transmission function of BDT in a wide energy window around the Fermi level can be completely accounted for by only two molecular orbitals.

Ab initiotight-binding LMTO method for nonequilibrium electron transport in nanosystems

We present an ab initio method for calculation of the electronic structure and electronic transport of nanoscale systems coupled to electrodes with applied voltage bias. The method is based on the local density approximation of density functional theory and implemented in the framework of the tight-binding linear muffin-tin orbital approach in its atomic sphere approximation. A fully atomistic description of the electrodes and the nanosystem is used, and the self-consistent charge and electrostatic potential for the system under applied bias is calculated using the nonequilibrium Green's function (NEGF) approach. General expressions for the lesser Green's function and transmission coefficient obtained within NEGF theory are rewritten using auxiliary Green's functions that are defined by the inverse of the short-ranged structural constants. This reformulation of the theory with auxiliary Green's functions allows the use of very effective and well-developed tight-binding techniques. The method is applied to three systems: a single benzene di-thiol molecule coupled to (111) gold electrodes, a single gold atom coupled to (100) gold electrodes, and a single platinum atom coupled to (100) platinum electrodes.

Impacts of metal electrode and molecule orientation on the conductance of a single molecule

We present first-principles investigation of electrical conductance of a benzene-1,4-dithiolate (SC6H4S) molecule bridging the (111) surfact of Pt and Au carried out using the Lippmann–Schwinger scattering method combined with the density functional theory. We show that Pt makes better electrodes than noble metals, due to a closer positioning of the transmission resonance to the Fermi level. Interestingly, we find that the peak transmission corresponding to the highest occupied molecular orbital decreases with the increasing of the tilting angle of the benzene dithiolate. Moreover, the flattening comes together with a widening of the peak, and consequently, the transmission at the Fermi level is enhanced.

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.

Adsorption of benzene thiolate on the (111) surface of M ( M=Pt, Ag, Cu) and the conductance of M/benzene dithiolate/ M molecular junctions: a first-principles study

To seek more conductive and robust molecular wire junction than that based on Au electrodes, we studied the adsorption of a benzene thiolate (–S–C 6H 5) on the (111) surface of Pt, Ag, and Cu, and the zero-bias conductance of a benzene dithiolate (–S–C 6H 4–S–) between Pt, Ag, or Cu electrodes by density functional theory. For Pt, the fcc–hollow site is found to be the most stable adsorption site, different from noble metal cases where the fcc–bridge site has the largest adsorption energy. The binding energy of a benzene thiolate on Pt(111) is larger than on noble metal surfaces. We evaluated the transmission coefficients by solving the Lippmann–Schwinger equation and determined the conductance of the molecular wire junction with the Landauer formula. At zero bias, the conductance for a molecular wire supported on Pt contact is higher than those supported on noble metals.

Structure and Dynamics of a Benzenedithiol Monolayer on a Au(111) Surface

We use the universal force field (UFF) developed by Rappe et al. (Rappe, A. K.; Casewit, C. J.; Colwell, K. S.; Goddard, W. A.; Skiff, W. M. J. Am. Chem. Soc. 1992, 114, 10024) and the specific classical potentials developed from ab initio calculations for Au−benzenedithiol (BDT) molecule interaction to perform molecular dynamics (MD) simulations of a BDT monolayer on an extended Au(111) surface. The simulation system consists of 100 BDT molecules and three rigid Au layers in a simulation box that is rhombic in the plane of the Au surface. A multiple time scale algorithm, the double-reversible reference system propagator algorithm (double RESPA) based on the Nose−Hoover dynamics scheme, and the Ewald summation with a boundary correction term for the treatment of long-range electrostatic interactions in a 2-D slab have been incorporated into the simulation technique. We investigate the local bonding properties of Au−BDT contacts and molecular orientation distributions of BDT molecules. These results show t...

Models of electron transport through organic molecular monolayers self-assembled on nanoscale metallic contacts

We propose a model of electrical conduction through self-assembled monolayers (SAM's) of organic molecules that bridge the gap between a pair of nanoscale metallic contacts. In this model each molecule bonds chemically to only one of the contacts. For dense SAM's the dominant electric current path is through two overlapping molecules each bonded to a different metal contact whereas for dilute SAM's the current flows through a single molecule. The model accounts quantitatively for the experimental data of M. A. Reed et al. [Science 278, 252 (1997)] on gold break junctions containing benzene-dithiol (BDT) SAM's, including the magnitude of the measured differential conductance. It also accounts for the striking differences between the data on the Au/BDT system and the recent measurements of J. Reichert et al. [cond-mat/0106219, 2001 (unpublished)] on a somewhat different system, namely, the strong asymmetry of the current-voltage characteristic and the larger size of the differential conductance found in latter experiments. We also present calculations of electron transport through dense and dilute SAM's of ${\mathrm{SC}}_{6}{\mathrm{H}}_{4}\mathrm{S}\ensuremath{-}{\mathrm{CH}}_{3}$ molecules. Experiments on these systems should test the validity of the proposed model.

ChemInform Abstract: Synthesis and Reactivity Studies of Model Complexes for Molybdopterin-dependent Enzymes

The molybdenum cofactor (Moco)-containing enzymes are divided into three classes that are named after prototypical members of each family, viz. sulfite oxidase, DMSO reductase and xanthine oxidase. Functional or structural models have been prepared for these three prototypical enzymes: (i) The complex [MoO2(mnt)2]2− (mnt2−=1,2-dicyanoethylenedithiolate) has been found to be able to oxidize hydrogen sulfite to HSO4− and is thus a functional model of sulfite oxidase. Kinetic and computational studies indicate that the reaction proceeds via attack of the substrate at one of the oxo ligands of the complex, rather than at the metal. (ii) The coordination geometries of the mono-oxo [Mo(VI)(O-Ser)(S2)2] entity (S2=dithiolene moiety of molybdopterin) found in the crystal structure of R. sphaeroides DMSO reductase and the corresponding des-oxo Mo(IV) unit have been reproduced in the complexes [M(VI)O(OSiR3)(bdt)2] and [M(VI)O(OSiR3)(bdt)2] (M=Mo,W; bdt=benzene dithiolate). (iii) A facile route has been developed for the preparation of complexes containing a cis-Mo(VI)OS molybdenum oxo, sulfido moiety similar to that detected in the oxidized form of xanthine oxidase.