Jun Nara

Density functional theory investigation of benzenethiol adsorption on Au(111)

We have studied the adsorption of benzenethiol molecules on the Au(111) surface by using first principles total energy calculations. A single thiolate molecule is adsorbed at the bridge site slightly shifted toward the fcc-hollow site, and is tilted by 61 degrees from the surface normal. As for the self-assembled monolayer (SAM) structures, the (2 square root of 3 x square root of 3)R30 degrees herringbone structure is stabilized against the (square root 3 x square root 3)R30 degrees structure by large steric relaxation. In the most stable (2 square root 3 x square root 3)R30 degrees SAM structure, the molecule is adsorbed at the bridge site with the tilting angle of 21 degrees, which is much smaller compared with the single molecule adsorption. The van der Waals interaction plays an important role in forming the SAM structure. The adsorption of benzenethiolates induces the repulsive interaction between surface Au atoms, which facilitates the formation of surface Au vacancy.

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.

Dependence of the conduction of a single biphenyl dithiol molecule on the dihedral angle between the phenyl rings and its application to a nanorectifier

The transport properties of a biphenyl dithiol (BPD) molecule sandwiched between two gold electrodes are studied using the nonequilibrium Greens function method based on the density functional theory. In particular, their dependence on the dihedral angle (phi=90 degrees -180 degrees ) between two phenyl rings is investigated. While the dihedral-angle dependence of the density of states projected on the BPD molecular orbitals is small, the transport properties change dramatically with phi. The transmission at the Fermi energy exhibits a minimum at phi=90.0 degrees and greatly increases with phi. The ratio of the maximum obtained at phi=180 degrees to the minimum exceeds 100. As an application of this characteristic transport behavior, a BPD molecule functionalized with NH(2) and NO(2) groups is considered. It is found that this molecule works as a nanorectifier.

Electron Transport in a π-Stacking Molecular Chain

We have investigated the electronic structure and transport properties of a pi-stacking molecular chain which is covalently bonded to a H/Si(100) surface, using the first-principles density functional theory approach combined with Greens function method. The highest occupied molecular orbital (HOMO) dispersion is remarkably reduced, but remains noticeable ( approximately 0.1 eV), when a short pi-stacking styrene wire is cut from an infinitely long wire and sandwiched between metal electrodes. We find that the styrene chains HOMO and lowest unoccupied molecular orbital (LUMO) states are not separated from Si, indicating that it does not work as a wire. By substituting -NO2 or -NH2 for the top -H of styrene, we are able to shift the position of the HOMO and LUMO with respect to the Fermi level. More importantly, we find that the HOMO of styrene-NH2 falls into the band gap of the substrate and is localized in the pi-stacking chain, which is what we need for a wire to be electrically separated from the substrate. The conductance of such an assembly is comparable to that of Au/benzene dithiolate/Au wire based on chemical bonding, and its tunability makes it a promising system for a molecular device.

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.

End-Group Dependence of Transport Properties for Biphenyl-Based Molecular Junction System

The transport properties of junction systems that consist of an X–biphenyl–X (X=O, S, Se, and Te) molecule sandwiched between two gold electrodes are studied using the nonequilibrium Greens function method based on the density functional theory. The end-group atom X has an influence on not only the interaction between the molecule and electrodes but also that between the two phenyl rings. Especially, the junction system with X=O exhibits much different properties from the other Xs. The interaction between the molecule and electrodes is weaker and that between π-type orbitals of the two phenyl rings, which mainly contributes to the transmission around the Fermi energy, is stronger. As a result, this system has a larger transmission around the Fermi energy and unusual behaviors, such as a negative differential conductance and a nonlinear potential drop, are observed. We also studied the dependence on dihedral angle between the two phenyl rings.

Tail molecule dependence of thiolate adsorption on Au(111) surface: Theoretical study

The adsorption of thiolates with various tail molecules on the Au(111) surface has been investigated by first-principles calculations. We have considered six typical thiolate molecules, that is, methylthiolate, ethylthiolate, ethylenethiolate, acetylenethiolate, benzenethiolate, and thiophenethiolate. It is found that these thiolates exhibit little difference in their stable adsorption geometries. They are adsorbed at the bridge site with being significantly tilted from the surface normal. The adsorption energy of thiolate on Au, on the other hand, largely varies depending on the type of tail molecule, and is linearly proportional to the binding energy of thiolate with H. We discuss the tail molecule dependence in terms of the bonding environment around the C atom connected to the head S atom.

A New Insight into the Polaron–Li Complex Diffusion in Cathode Material LiFe1-yMnyPO4 for Li Ion Batteries

Based on the Heyd–Scuseria–Ernzerhof hybrid density functionals study, we proposed a new insight into the diffusion of polaron–Li vacancy complexes in LiFe1-yMnyPO4 (y=0,1/2,1). It is found that the polaron migrates along a crossing or a parallel path relative to the Li moving direction. In LiFePO4, the complex diffusion along the zigzag pathway is favorable and has a barrier of 600 meV, while the diffusion along the parallel pathway with a barrier of 623 meV is favorable in LiMnPO4. For LiFe1/2Mn1/2PO4, since the polaron is formed within a single Fe layer, the diffusion proceeds along the parallel pathway with a barrier of 635 meV.

Fluorine diffusion assisted by diffusing silicon on the Si(111)-(7×7) surface

The diffusion process of fluorine (F) atoms on the Si(111)-(7x7) surface is investigated using high-temperature scanning tunneling microscopy. The kinetic parameters of F hopping agree well with those of the diffusing silicon (Si) atoms, which implies that of all reaction processes, the Si diffusion serves as the rate-determining one. Deposition of Si on the surface is found to enhance F hopping, which supports the above-mentioned observation. Theory reveals that the replacement of F adsorption sites by diffusing Si atoms is the key process in the diffusion mechanism.

First-principles calculation on diffusion of Si adatoms on H/Si(001)-(2×1) surface

Abstract We report the result of first-principles calculations on the Si adsorption on the monohydride terminated Si(001)-(2×1) surface. It is found that the Si adatom spontaneously segregates one H atom from a surface Si dimer during adsorption, and further captures the remaining H atom of the same Si dimer during surface migration, leading to the most stable adsorption geometry. The Si adatom diffusion process on the hydrogenated Si(001) surface is complicated by the transfer of H atoms between the adatom and the Si dimer atoms. The migration of the Si adatom is extremely reduced compared with that on the bare Si(001) surface.