Modelling electron tunnelling in the presence of adsorbed materials

University of Technology, Sydney. Institute for Nanoscale Technology.The transport characteristics of single-molecule Au(lll) junctions are investigated using density functional theory (DFT) together with the non-equilibrium Green’s functions formalism (NEGF). DFT optimisations of the adsorption of various molecules on a Au(lll) surface are used as starting points for the equilibrium junction geometries. Test calculations are performed to find a recommended set of parameters for the final DFT results. The interaction energies of several molecules with the Au(lll) surface obtained within the same level of theory are compared. Amine compounds bind preferentially in an adatom geometry and weakly in the out op site. A Z-matrix optimiser is implemented in the SIESTA code as a useful tool for future surface and molecular junction optimisations. Transport properties are calculated for molecular junctions in their equilibrium geometry. While the conductances are orders of magnitude larger than experimental data, the sizes are in line with expectation. The junction geometries are altered in various ways. Changing the binding site or altering the nature of the sulphur-gold interaction in a phenylenedimethanethiol junction, reduces the conductance by a factor of two. Orders of magnitude reduction of conductance is only observed when increasing the distance between a physisorbed molecule and the surface. Increasing this distance for a chemisorbed molecule, results in a surprising increase in conductance. This is attributed to an interplay between the coupling strength of the molecule with the surface and the location of the molecular energy levels relative to the Fermi level. When the chemical bond is broken, the system is spin-polarised and the conductances for electrons of opposite spin types are different by a factor of 250 - the junction acts as a spin-filter. When stretching a diethynylbenzene junction, the strong gold-carbon bond does not break, but rather extracts a gold atom from the surface. In this case the conductance decreases rapidly with stretching. A WKB tunnel barrier model is used as an alternate much faster method for calculating I(V) characteristics. With the surface work functions acting as barrier heights, the relative junction conductances are in good agreement with the DFT results. However, the direction of asymmetry in the I(V) characteristics predicted by the two levels of theory are opposite. More sophisticated barrier shapes may be needed to correctly predict the asymmetries. The tunnelling model is used in conjunction with the DFT results to quantify the effect a gap between an STM tip and monolayer may have on STS measurements

The effect of reciprocal-space sampling and basis set quality on the calculated conductance of a molecular junction

We perform density functional theory and non-equilibrium Green's function calculations of the conductance of a gold wire and a 1,4-phenylenedimethanethiol (XYL) molecule adsorbed between Au(111) electrodes using the TranSIESTA software package. The effect of varying different computational parameters is investigated. We find that the conductance is more sensitive to the reciprocal-space sampling grid than the quality of the basis set employed. The conductance can vary up to a factor of five as a result of the choice of computational parameters. We report a set of computational parameters that yields a well-converged conductance value

Effect of dipole moment on current-voltage characteristics of single molecules

We perform empirical calculations of the tunneling current through various small organic molecules sandwiched between gold electrodes by using the Wenzel-Kramers-Brillouin (WKB) approximation. The barrier to tunneling is taken to be the work function of gold and calculated from a first principles electronic structure code. The current-voltage characteristics of these molecules are compared in the context of existing first principles and experimental results. In this model the surface dipole moment, induced by the adsorbed molecule, can have a significant effect on the current and hence dipole moments may be an important property for prediction of the conductance characteristics of a molecule. © 2006 IEEE

A new class of self-assembled monolayers on gold using an alkynyl group as a linker

The geometry and energetics for adsorption of ethynylbenzene on Au(111) have been studied using Density Functional Theory. The alkynyl group, following removal of the terminal H atom, adsorbs covalently to the surface in the fcc hollow site with a bond energy of about 70 kcal.mol-1. Intermediate adsorption states are also possible via a hydrogen 1,2 shift to form a surface-bound vinylidene, or through the opening of the C-C triple bond without removing the hydrogen atom. © 2006 IEEE

Adsorption of amine compounds on the Au(111) surface: A density functional study

A Density Functional Theory study of the adsorption energetics of various amine compounds on the gold-(111) surface revealed that preferential binding occurs in under-coordinated sites. The largest binding energy is obtained when a gold adatom is placed in the fee position and the amine positioned with the nitrogen above the adatom. The results are compared with previous calculations for thiols, phosphines, and ethynylbenzene molecules to provide a meaningful comparison within a consistent computational framework. The systematic increase in binding energy with methyl group substitution previously observed for phosphine compounds is not observed for the amine analogues. The binding energy of the amines is considerably lower than that for thiols and binding is indicated for only the adatom geometry-a result consistent with experimental data. © 2007 American Chemical Society

Electron tunneling through alkanedithiol molecules

We report on first principles calculations of the tunneling current across n-alkanedithiol molecules (n = 4,6,8,10,12) sandwiched between two Au {111} electrodes. The conductance drops exponentially with increased chain length with decay parameter βn= 0.9. The results are compared with scanning tunneling microscopy measurements on decanedithiol and with other n-alkanedithiol (n = 6,8,10) results in the literature. The theoretical results are found to be an order of magnitude larger than experimental values but follow the same trend. However, two additional, more realistic, geometries are modeled by changing the bond type and by combining the first-principles results with a Wentzel-Kramer-Brillouin (WKB) expression for tunneling across the air gap that is invariably present during scanning tunneling microscopy (STM) measurements. These results are more compatible with the experimental data

Exploring the performance of molecular rectifiers: Limitations and factors affecting molecular rectification

There has been significant work investigating the use of molecules as nanoscale rectifiers in so-called "molecular electronics". However, less attention has been paid to optimizing the design parameters of molecular rectifiers or to their inherent limitations. Here we use a barrier tunneling model to examine the degree of rectification that can be achieved and to provide insight for the design and development of molecules with optimum rectification responses. © 2007 American Chemical Society

Educational sessions in pharmacovigilance: What do the doctors think?

Background: The aim of this study was to determine physicians"opinion regarding pharmacovigilance feedback sessions. A survey was conducted in a teaching hospital, and the physicians who attended the sessions were invited to participate by filling out a structured questionnaire. All sessions included a review of adverse drug reactions identified at the hospital and information on pharmacovigilance issues (news on warnings released by regulatory agencies or drug toxicity problems identified by recently published studies in medical journals). The survey questions were related to the interest, satisfaction, and belief in the utility of the sessions. A Likert scale (0-10 points) was used to assess physicians" opinions. Findings: A total of 159 physicians attended the sessions and 115 (72.3%) participated in the survey. The mean (SD) age was 38.9 (12.1) years, and 72 (62.6%) were men. The mean (SD) scores of interest, satisfaction with the information provided, and belief in the utility of these sessions were 7.52 (1.61), 7.58 (1.46), and 8.05 (1.38) respectively. Significant differences were observed among physicians according to medical category and speciality in terms of interest, satisfaction, and belief in the utility of those sessions. Conclusions: Educational activities for physicians, such as feedback sessions, can be integrated into the pharmacovigilance activities. Doctors who attend the sessions are interested in and satisfied with the information provided and consider the sessions to be useful. Additional studies on the development and effectiveness of educational activities in pharmacovigilance are necessary

Role of GP82 in the Selective Binding to Gastric Mucin during Oral Infection with Trypanosoma cruzi

Oral infection by Trypanosoma cruzi has been the primary cause of recent outbreaks of acute Chagas' diseases. This route of infection may involve selective binding of the metacyclic trypomastigote surface molecule gp82 to gastric mucin as a first step towards invasion of the gastric mucosal epithelium and subsequent systemic infection. Here we addressed that question by performing in vitro and in vivo experiments. A recombinant protein containing the complete gp82 sequence (J18), a construct lacking the gp82 central domain (J18*), and 20-mer synthetic peptides based on the gp82 central domain, were used for gastric mucin binding and HeLa cell invasion assays, or for in vivo experiments. Metacyclic trypomastigotes and J18 bound to gastric mucin whereas J18* failed to bind. Parasite or J18 binding to submaxillary mucin was negligible. HeLa cell invasion by metacyclic forms was not affected by gastric mucin but was inhibited in the presence of submaxillary mucin. Of peptides tested for inhibition of J18 binding to gastric mucin, the inhibitory peptide p7 markedly reduced parasite invasion of HeLa cells in the presence of gastric mucin. Peptide p7*, with the same composition as p7 but with a scrambled sequence, had no effect. Mice fed with peptide p7 before oral infection with metacyclic forms developed lower parasitemias than mice fed with peptide p7*. Our results indicate that selective binding of gp82 to gastric mucin may direct T. cruzi metacyclic trypomastigotes to stomach mucosal epithelium in oral infection

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. © 2007 Elsevier B.V. All rights reserved