Yoshitada Morikawa

Adsorption state of dimethyl disulfide on Au(111): Evidence for adsorption as thiolate at the bridge site

We studied the adsorption state of dimethyl disulfide and methylthiolate on the Au(111) surface by means of the density functional theory (DFT) within a generalized gradient approximation and experimental high-resolution electron energy loss spectroscopy (HREELS) techniques. It turns out that the methylthiolate adsorption is more stable than the dimethyl disulfide adsorption and that the most stable adsorption site for the methylthiolate is the bridge site slightly off-centered towards the fcc-hollow site with its S–C bond tilted from the surface normal by 53°. HREELS results are in excellent agreement with the DFT results, providing very strong support to the depicted adsorption scenario.

State-selective dissociation of a single water molecule on an ultrathin MgO film

The interaction of water with oxide surfaces has drawn considerable interest, owing to its application to problems in diverse scientific fields. Atomic-scale insights into water molecules on the oxide surface have long been recognized as essential for a fundamental understanding of the molecular processes occurring there. Here, we report the dissociation of a single water molecule on an ultrathin MgO film using low-temperature scanning tunnelling microscopy. Two types of dissociation pathway--vibrational excitation and electronic excitation--are selectively achieved by means of injecting tunnelling electrons at the single-molecule level, resulting in different dissociated products according to the reaction paths. Our results reveal the advantage of using a MgO film, rather than bulk MgO, as a substrate in chemical reactions.

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.

Density functional theoretical study of pentacene/noble metal interfaces with van der Waals corrections: Vacuum level shifts and electronic structures

In order to clarify factors determining the interface dipole, we have studied the electronic structures of pentacene adsorbed on Cu(111), Ag(111), and Au(111) by using first-principles density functional theoretical calculations. In the structural optimization, a semiempirical van der Waals (vdW) approach [S. Grimme, J. Comput. Chem. 27, 1787 (2006)] is employed to include long-range vdW interactions and is shown to reproduce pentacene-metal distances quite accurately. The pentacene-metal distances for Cu, Ag, and Au are evaluated to be 0.24, 0.29, and 0.32 nm, respectively, and work function changes calculated by using the theoretically optimized adsorption geometries are in good agreement with the experimental values, indicating the validity of the present approach in the prediction of the interface dipole at metal/organic interfaces. We examined systematically how the geometric factors, especially the pentacene-substrate distance (Z(C)), and the electronic properties of the metal substrates contribute to the interface dipole. We found that at Z(C) > or = 0.35 nm, the work function changes (Delta phis) do not depend on the substrate work function (phi(m)), indicating that the interface level alignment is nearly in the Schottky limit, whereas at Z(C) < or = 0.25 nm, Delta phis vary nearly linearly with phi(m), and the interface level alignment is in the Bardeen limit. Our results indicate the importance of both the geometric and the electronic factors in predicting the interface dipoles. The calculated electronic structure shows that on Au, the long-range vdW interaction dominates the pentacene-substrate interaction, whereas on Cu and Ag, the chemical hybridization contributes to the interaction.

Electrode Dynamics from First Principles

The investigation of electrode dynamics has been a major topic in the field of electrochemistry for a century. Electrode dynamics consist of electron transfer reactions that give rise to, or are caused by, a bias voltage, and are influenced by surface catalysis, electrolyte solution, transport of electrons and ions. The first-principles molecular dynamics simulation of the electrochemical system has been hampered by the difficulty to describe the bias voltage and the complex solution-electrode interface structure. Here we utilize a new algorithm called the effective screening medium to characterize the biased interface between platinum and liquid water, revealing the microscopic details of the first, Volmer, step of the platinum-catalyzed hydrogen evolution reaction. By clarifying the important roles played by both the water and the bias, we show why this reaction occurs so efficiently at the interface. Our simulations make a significant step towards a deeper understanding of electrochemical reactions.

First-principles theoretical study of alkylthiolate adsorption on Au(1 1 1)

We have studied methylthiolate (MeS), ethylthiolate (EtS), and butylthiolate (BuS) adsorption on the Au(111) surface using density functional theory within a generalized gradient approximation (GGA). EtS and BuS are also adsorbed at the bridge site slightly off-centered towards the fee-hollow site and the S-C bond is tilted from the surface normal by 52°. The S 2p core level shift of MeS adsorbed at the bridge site agrees quite well with the experimental results, further supporting the bridge configuration. Finally, we have examined several possible MeS configurations in the c(43 × 23) superstructure. At present, however, we cannot obtain consistent results with the experimental ones, presumably due to the limited accuracy of the present GGA functional and/or substrate reconstructions.

First-principles molecular dynamics study of acetylene adsorption on the Si(001) surface

We present a first-principles molecular dynamics study of acetylene adsorption on the Si(001) surface. Acetylene molecules are di-σ bonded to the first layer Si dimers with the adsorption energy of 64.8 kcal/mol. It is elucidated that the CC bond is essentially double bond and the Si dimer bonds are not cleaved. The normal mode analyses well reproduce the experimental results, giving a strong support to our results.

A Density Functional Theory Study of Self-Regenerating Catalysts LaFe1–xMxO3–y (M = Pd, Rh, Pt)

Periodic density functional theory was used to investigate the stability and electronic structures of precious-metal atoms in the vicinity of LaFe(1-x)M(x)O(3) (M = Pd, Rh, Pt) perovskite catalyst surfaces. It was found that the surface segregation of Pd and Pt is significantly stabilized by the introduction of O vacancies, whereas the solid-solution phase is favorable for Rh, suggesting an important role of O vacancies in the self-regeneration of Pd and Pt. On the basis of the results, we propose a possible scenario for the self-regeneration of the precious metal in the perovskite catalyst.

Ab initio study of surface structural changes during methanol synthesis over Zn/Cu(111)

Abstract We have studied the adsorption state of formate on clean and Zn-deposited Cu(111) surfaces by using a DFT–GGA–pseudopotential method. We show that, although the deposited Zn alone is substitutionally adsorbed on the Cu(111) surface, the formate stabilizes the Zn atom sitting on the Cu surface and forms a tilted bidentate formate bound to the Zn and Cu atoms. Our results suggest that the adsorption state of Zn changes from the substitutional to on-surface adsorption by co-adsorption with the formate.

First-principles theoretical study of Alq3∕Al interfaces: Origin of the interfacial dipole

We have studied the atomic geometries and the electronic properties of the tris-(8-hydroxyquinoline) aluminum (Alq(3))Al interfaces by using density functional theoretical calculations, and clarified the origin of the interfacial dipole moment. We have examined various possible adsorption geometries of Alq(3) on Al surfaces and calculated the work function change induced by adsorption of Alq(3) on Al surfaces. We found that the stability depends crucially on the number of O-Al bonds formed at the interface, and Alq(3) tends to expose its O atoms to the Al substrate side and its N atoms to the vacuum side. Although the binding energies are influenced by the poor description of the van der Waals interaction by the density functionals used, the resulting bonding configurations are found to give correct binding energies when the van der Waals interaction is taken into account based on the recently proposed van der Waals density functional [Dion et al., Phys. Rev. Lett. 92, 246401 (2004)]. This bonding configuration arranges molecular permanent dipoles of Alq(3) directed towards the vacuum, leading to the decrease of the surface work function. The calculated interface dipoles agree reasonably well with the experimental results and the origin of the interface dipole formation mainly comes from the alignment of the permanent dipoles of Alq(3). The HOMO levels of the Alq(3) molecules significantly depend on the orientation of the molecular permanent dipoles and the interfacial gap state observed by experiments is ascribed to the coexistence of the two orientations of the molecular dipole moments.