Atomic Imaging of Interface Defects in an Insulating Film on Diamond.

The insulator/semiconductor interface structure is the key to electric device performance, and much interest has been focused on understanding the origin of interfacial defects. However, with conventional techniques, it is difficult to analyze the interfacial atomic structure buried in the insulating film. Here, we reveal the atomic structure at the interface between an amorphous aluminum oxide and diamond using a developed electron energy analyzer for photoelectron holography. We find that the three-dimensional atomic structure of a C-O-Al-O-C bridge between two dimer rows of the hydrogen-terminated diamond surface. Our results demonstrate that photoelectron holography can be used to reveal the three-dimensional atomic structure of the interface between a crystal and an amorphous film. We also find that the photoelectron intensity originating from the C-O bonds is strongly related to the interfacial defect density. We anticipate significant progress in the study of amorphous/crystalline interfaces based on their three-dimensional atomic structures analysis.

Origin of Unexpected Ir3+ in a Superconducting Candidate Sr2IrO4 System Analyzed by Photoelectron Holography.

The reason for the absence of superconductivity in Sr2IrO4 was estimated by photoelectron spectra and photoelectron holograms. The analysis of the La photoelectron hologram concluded that La atoms are substituted to Sr sites. Two O 1s peaks were observed and were identified as the oxygens in the IrO2 and SrO planes by photoelectron holography and density functional theory (DFT) calculations. In the Ir 4f spectrum of Sr2IrO4, an unexpected Ir3+ peak was observed as much as 50% of all of the Ir. The photoelectron hologram of Ir3+ showed a displacement of about 0.15 Å. This displacement is thought to be due to the oxygen vacancies in the IrO2 plane. These oxygen vacancies and the associated local displacement of the atoms might inhibit superconductivity in spite of sufficient electron doping.

Hydrogenation of Formate Species Using Atomic Hydrogen on a Cu(111) Model Catalyst.

The reaction mechanism of the CH3OH synthesis by the hydrogenation of CO2 on Cu catalysts is unclear because of the challenge in experimentally detecting reaction intermediates formed by the hydrogenation of adsorbed formate (HCOOa). Thus, the objective of this study is to clarify the reaction mechanism of the CH3OH synthesis by establishing the kinetic natures of intermediates formed by the hydrogenation of adsorbed HCOOa on Cu(111). We exposed HCOOa on Cu(111) to atomic hydrogen at low temperatures of 200-250 K and observed the species using infrared reflection absorption (IRA) spectroscopy and temperature-programmed desorption (TPD) studies. In the IRA spectra, a new peak was observed upon the exposure of HCOOa on Cu(111) to atomic hydrogen at 200 K and was assigned to the adsorbed dioxymethylene (H2COOa) species. The intensity of the new peak gradually decreased with heating from 200 to 290 K, whereas the IR peaks representing HCOOa species increased correspondingly. In addition, small amounts of formaldehyde (HCHO), which were formed by the exposure of HCOOa species to atomic hydrogen, were detected in the TPD studies. Therefore, H2COOa is formed via hydrogenation by atomic hydrogen, which thermally decomposes at ∼250 K on Cu(111). We propose a potential diagram of the CH3OH synthesis via H2COOa from CO2 on Cu surfaces, with the aid of density functional theory calculations and literature data, in which the hydrogenation of bidentate HCOOa to H2COOa is potentially the rate-determining step and accounts for the apparent activation energy of the methanol synthesis from CO2 on Cu surfaces.

Role of Intermolecular Interactions in the Catalytic Reaction of Formic Acid on Cu(111).

Formic acid (HCOOH) can be catalytically decomposed into H2 and CO2 and is a promising hydrogen storage material. As H2 production catalysts, Cu surfaces allow selective HCOOH decarboxylation; however, the on-surface HCOOH decomposition reaction pathway remains controversial. In this study, the temperature dependence of the HCOOH/Cu(111) adsorption structures is elucidated by scanning tunneling microscopy and non-contact atomic force microscopy, establishing the adsorbate chemical species using density functional theory. 2D HCOOH islands at 80 K, linear chains of HCOOH and monodentate formate at 150 K, chain-like assemblies of monodentate and bidentate formate at 200 K, and bidentate formate clusters at 300 K are observed. At each temperature, the adsorbates experience attractive interactions among themselves. Such aggregation stabilizes them against desorption and decomposition. Thus, accurate evaluation of intermolecular interactions is essential to understand catalytic reactivity.

Mechanistic insight into oxygen vacancy migration in SrFeO3-δ from DFT+U simulations.

SrFeO3-δ is known to be an effective oxygen ion conductor and oxygen vacancies are central to its performance. SrFeO3-δ displays four crystallographic structural transitions as it undergoes oxygen reduction over a broad range of operating temperatures. In this work, systematic density functional theory calculations using the Hubbard U correction were performed to understand oxygen vacancy interactions and migration as a function of vacancy concentrations in SrFeO3-δ (δ = 0-0.5). We found strong repulsion between oxygen vacancies at close distance while these oxygen vacancies are stabilized at further distance. We also found that the oxygen migration is highly anisotropic and the calculated effective migration energy for the oxygen migration tends to be high and increases from 0.91 eV to 1.30 eV as δ goes from 0.125 (tetragonal phase) to 0.25 (orthorhombic phase). In the ordered brownmillerite SrFeO2.625, the oxygen migration is restricted in the one-dimensional channel because of the highly anisotropic nature of the crystal structure, resulting in the relatively low effective migration energy of 0.49 eV. This explains the experimental activation energy of 0.55 ± 0.05 eV. These results suggest the importance of regulating the oxygen migration path via the crystal structure design toward development of a SrFeO3-δ based fast oxygen conductor.

A flat-lying dimer as a key intermediate in NO reduction on Cu(100).

The reaction of nitric oxide (NO) on Cu(100) is studied by scanning tunneling microscopy, electron energy loss spectroscopy and density functional theory calculations. The NO molecules adsorb mainly as monomers at 64 K, and react and dissociate to yield oxygen atoms on the surface at ∼70 K. The temperature required for the dissociation is significantly low for Cu(100), compared to those for Cu(111) and Cu(110). The minimum energy pathway of the reaction is via (NO)2 formation, which converts into a flat-lying ONNO and then dissociates into N2O and O with a considerably low activation energy. We propose that the formation of (NO)2 and flat-lying ONNO is the key to the exceptionally high reactivity of NO on Cu(100).

Manipulable Metal Catalyst for Nanographene Synthesis.

Performing bottom-up synthesis by using molecules adsorbed on a surface is an effective method to yield functional polycyclic aromatic hydrocarbons (PAHs) and nanocarbon materials. The intramolecular cyclodehydrogenation of hydrocarbons is a critical process in this synthesis; however, thus far, its elementary steps have not been elucidated thoroughly. In this study, we utilize the metal tip of a low-temperature noncontact atomic force microscope as a manipulable metal surface to locally activate dehydrogenation for PAH-forming cyclodehydrogenation. This method leads to the dissociation of a H atom of an intermediate to yield the cyclodehydrogenated product in a target-selective and reproducible manner. We demonstrate the metal-tip-catalyzed dehydrogenation for both benzenoid and nonbenzonoid PAHs, suggesting its universal applicability as a catalyst for nanographene synthesis.

Blue moon ensemble simulation of aquation free energy profiles applied to mono and bifunctional platinum anticancer drugs.

Aquation free energy profiles of neutral cisplatin and cationic monofunctional derivatives, including triaminochloroplatinum(II) and cis-diammine(pyridine)chloroplatinum(II), were computed using state of the art thermodynamic integration, for which temperature and solvent were accounted for explicitly using density functional theory-based canonical molecular dynamics (DFT-MD). For all the systems, the "inverse-hydration" where the metal center acts as an acceptor of hydrogen bond has been observed. This has motivated to consider the inversely bonded solvent molecule in the definition of the reaction coordinate required to initiate the constrained DFT-MD trajectories. We found that there exists little difference in free enthalpies of activation, such that these platinum-based anticancer drugs are likely to behave the same way in aqueous media. Detailed analysis of the microsolvation structure of the square-planar complexes, along with the key steps of the aquation mechanism, is discussed.

Correlation between mobility and the hydrogen bonding network of water at an electrified-graphite electrode using molecular dynamics simulation.

Focusing on the electric double layer formed at aqueous solution/graphite electrode interfaces, we investigated the relationship between the mobility of interfacial water and its hydrogen bonding networks by using molecular dynamics simulations. We focused on the mobility of the first hydration layer constructed nearest to the electrode. The mobility was determined by calculating the diffusion coefficient which showed an opposite trend to that of the applied potential polarity. The mobility decreased upon positive potentials while showing an increase upon negative potentials, which is rationalized by the strength of the interfacial hydrogen bonding networks.

Atomic and molecular adsorption on single platinum atom at the graphene edge: A density functional theory study.

We present a density functional theory study of atomic and molecular adsorption on a single Pt atom deposited at the edges of graphene. We investigate geometric and electronic structures of atoms (H, C, N, and O) and molecules (O2, CO, OH, NO, H2O, and OOH) on a variety of Pt deposited graphene edges and compare the adsorption states with those on a Pt(111) surface and on a Pt single atom. Furthermore, using the calculated adsorption energy and simple kinetic models, the catalytic activities of a Pt single-atom catalyst for the oxygen reduction reaction and CO oxidation are discussed.

Experimental and computational studies on ruthenium(ii) bis-diimine complexes of N,N'-chelate ligands: the origin of changes in absorption spectra upon oxidation and reduction.

This work presents an interpretation of the origin of changes in absorption spectra upon one-electron oxidation and reduction of two ruthenium polypyridyl complexes based on a combination of UV-Vis spectroelectrochemical experiments and theoretical calculations using the Gaussian 09 program. A bis-chelating ligand containing a p-bromobenzoylthiourea unit connected to 1,10-phenanthroline (phen-p-BrBT) has been prepared. Complexation of phen-p-BrBT to ruthenium bis-diimine centres, Ru(N-N)2 [N-N = 2,2'-bipyridine (bpy) or 1,10-phenanthroline (phen)], affords octahedral Ru(ii) tris-diimine complexes that are synthesised and structurally characterised. The two complexes exhibit similar MLCT bands and electronic energy levels owing to the similar electronic structures of the bpy and phen ligands. However, [Ru(phen)2(phen-p-BrBT)]2+ exhibits a slightly broader visible region MLCT (metal-to-ligand-charge transfer) band than [Ru(bpy)2(phen-p-BrBT)]2+ as expected from a slightly more delocalised π-electron system in the phen diimine ligands. In addition, the π→π* absorption in the UV is blue-shifted for [Ru(phen)2(phen-p-BrBT)]2+ relative to that for [Ru(bpy)2(phen-p-BrBT)]2+, because of greater stabilisation of the bpy HOMO relative to that of phen. The extra C-C bond in phen produces greater delocalisation of electron density leading to a blue-shift in the π→π* transition. The MLCT band is blue-shifted and diminished in intensity upon oxidation due to stabilisation of the Ru d-orbitals by removal of one electron. A new broad absorption band appears in the UV region upon reduction. The new transition is attributed to a blue-shift of the first MLCT transition for [Ru(bpy)2(phen-p-BrBT)]2+ and a red-shift of the second MLCT transition for [Ru(phen)2(phen-p-BrBT)]2+. The new transitions originate from destabilisation or stabilisation of the ligand LUMO orbitals relative to the Ru d-orbitals. A red-shift of the UV band in the initial complex also contributes to the new band produced upon reduction of [Ru(bpy)2(phen-p-BrBT)]2+. The new band does not involve an n(C[double bond, length as m-dash]S) →π* transition. Although both complexes show subtle differences in behaviour, their spectral changes are distinct, and the origin of changes in their absorption spectra upon oxidation and reduction is successfully interpreted.

Van der Waals density functional study of formic acid adsorption and decomposition on Cu(111).

We present a density functional theory study on the adsorption and decomposition mechanisms of monomeric formic acid (HCOOH) on a Cu(111) surface. We used Perdew-Burke-Ernzerhof (PBE) functional, PBE with dispersion correction (PBE-D2), and van der Waals density functionals (vdW-DFs). We found that the adsorption energy of HCOOH by using the PBE functional is smaller than the experimental value, while the PBE-D2 and vdW-DFs give better agreement with experimental results. The activation energies of decomposition calculated by using PBE-D2 and vdW-DFs are lower compared with desorption energies, seemingly in contradiction with experimental findings at room temperature, in which no decomposition of HCOOH on Cu(111) is observed when the surface is exposed to the gas phase HCOOH. We performed the reaction rate analysis based on the first-principles calculations for desorption and decomposition processes to clarify this contradiction. We found that the desorption of monomeric HCOOH is faster than that of its decomposition rate at room temperature because of a much larger pre-exponential factor. Thus, no decomposition of monomeric HCOOH should take place at room temperature. Our analysis revealed the competition between desorption and decomposition processes of HCOOH.

Ab initio molecular dynamics of solvation effects on reactivity at electrified interfaces.

Using ab initio molecular dynamics as implemented in periodic, self-consistent (generalized gradient approximation Perdew-Burke-Ernzerhof) density functional theory, we investigated the mechanism of methanol electrooxidation on Pt(111). We investigated the role of water solvation and electrode potential on the energetics of the first proton transfer step, methanol electrooxidation to methoxy (CH3O) or hydroxymethyl (CH2OH). The results show that solvation weakens the adsorption of methoxy to uncharged Pt(111), whereas the binding energies of methanol and hydroxymethyl are not significantly affected. The free energies of activation for breaking the C-H and O-H bonds in methanol were calculated through a Blue Moon Ensemble using constrained ab initio molecular dynamics. Calculated barriers for these elementary steps on unsolvated, uncharged Pt(111) are similar to results for climbing-image nudged elastic band calculations from the literature. Water solvation reduces the barriers for both C-H and O-H bond activation steps with respect to their vapor-phase values, although the effect is more pronounced for C-H bond activation, due to less disruption of the hydrogen bond network. The calculated activation energy barriers show that breaking the C-H bond of methanol is more facile than the O-H bond on solvated negatively biased or uncharged Pt(111). However, with positive bias, O-H bond activation is enhanced, becoming slightly more facile than C-H bond activation.

Potential dependent changes in the structural and dynamical properties of 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide on graphite electrodes revealed by molecular dynamics simulations.

An understanding of the characteristics of ionic liquid/graphite interfaces is highly important for electrochemical devices such as batteries and capacitors. In this paper, we report microscopic studies of 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide (BMIM-TFSI) on charged graphite electrodes using molecular dynamics simulations to reveal the two-dimensional arrangement of the ions and their dynamics at the interfaces. Analyses of surface distribution and mobility of ions revealed that the ion arrangement changes from a bilayer type to a checkerboard type with increasing applied potential. Whereas the bilayer type arrangement increases the ionic mobility parallel to the interfaces with the negative potential, the ions arranged in the checkerboard type tend to localize because of the increased lateral electrostatic interactions. Furthermore, we revealed that the inhomogeneity of ionic distribution at the positive potential propagates up to a few nanometers from the interface.

Structural and dynamic properties of 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide/mica and graphite interfaces revealed by molecular dynamics simulation.

It has been observed that the properties of room temperature ionic liquids near solid substrates are different from those of bulk liquids, and these properties play an important role in the development of catalysts, lubricants, and electrochemical devices. In this paper, we report microscopic studies of ionic liquid/solid interfaces performed using molecular dynamics simulations. The structural and dynamic properties of 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide (BMIM-TFSI) on mica and graphite interfaces were thoroughly investigated to elucidate the microscopic origins of the formation of layered structures at the interfaces. Our investigation included the observation of structural and orientational changes of ions as a function of distance from the surfaces, and contour mappings of ions parallel and perpendicular to the surfaces. By virtue of such detailed analyses, we found that, during the 5 ns simulation, the closest layer of BMIM-TFSI behaves as a two-dimensional ionic crystal on mica and as a liquid or liquid crystal on graphite.

Diffusion mechanism of Na ion-polaron complex in potential cathode materials NaVOPO4 and VOPO4 for rechargeable sodium-ion batteries.

Using the density functional method, we investigated the crystal and electronic structures and the electrochemical properties of NaxVOPO4 (x = 0, 1) and explored the diffusion mechanism of Na ions in these materials. The van der Waals interaction was also taken into account to include the non-local electron correlation in the calculation of structural parameters and voltage. The diffusion of Na ions is treated as a process of the Na vacancy-positive small polaron complex in NaVOPO4 and the Na ion-negative small polaron complex in VOPO4, respectively. During the charging (discharging) process, the removal (insertion) of a Na ion would result in the formation of a positive (negative) small polaron at one of the two first nearest vanadium sites to the Na vacancy. Three elementary diffusion processes, including the single, crossing and parallel diffusion processes, are explored. It is found that the [010] direction is preferable for Na ion diffusion in both the charging and discharging processes. The influence of small polaron migration on Na ion diffusion in the charging state is negligible, whereas such effect is considerably strong in the discharging process. Moreover, while three elementary diffusion processes in NaVOPO4 require the same energy, the parallel diffusion process in VOPO4 is not preferred. The diffusion of Na vacancy accompanied by a positive polaron in the full charging process requires an activation energy of 395 meV, while the diffusion of Na ion accompanied by a negative polaron in the discharging state, VOPO4, has a higher activation energy of 627 meV. With a voltage and activation barrier similar to that of the olivine phosphate LiFePO4, these sodium-based materials are expected to be promising cathode materials for sodium ion batteries.

Microscopic properties of ionic liquid/organic semiconductor interfaces revealed by molecular dynamics simulations.

Electric double-layer transistors based on ionic liquid/organic semiconductor interfaces have been extensively studied during the past decade because of their high carrier densities at low operation voltages. Microscopic structures and the dynamics of ionic liquids likely determine the device performance; however, knowledge of these is limited by a lack of appropriate experimental tools. In this study, we investigated ionic liquid/organic semiconductor interfaces using molecular dynamics to reveal the microscopic properties of ionic liquids. The organic semiconductors include pentacene, rubrene, fullerene, and 7,7,8,8-tetracyanoquinodimethane (TCNQ). While ionic liquids close to the substrate always form the specific layered structures, the surface properties of organic semiconductors drastically alter the ionic dynamics. Ionic liquids at the fullerene interface behave as a two-dimensional ionic crystal because of the energy gain derived from the favorable electrostatic interaction on the corrugated periodic substrate.

Enhancement of CO2 adsorption on oxygen-functionalized epitaxial graphene surface under near-ambient conditions.

The functionalization of graphene is important in practical applications of graphene, such as in catalysts. However, the experimental study of the interactions of adsorbed molecules with functionalized graphene is difficult under ambient conditions at which catalysts are operated. Here, the adsorption of CO2 on an oxygen-functionalized epitaxial graphene surface was studied under near-ambient conditions using ambient-pressure X-ray photoelectron spectroscopy (AP-XPS). The oxygen-functionalization of graphene is achieved in situ by the photo-induced dissociation of CO2 with X-rays on graphene in a CO2 gas atmosphere. The oxygen species on the graphene surface is identified as the epoxy group by XPS binding energies and thermal stability. Under near-ambient conditions of 1.6 mbar CO2 gas pressure and 175 K sample temperature, CO2 molecules are not adsorbed on the pristine graphene, but are adsorbed on the oxygen-functionalized graphene surface. The increase in the adsorption energy of CO2 on the oxygen-functionalized graphene surface is supported by first-principles calculations with the van der Waals density functional (vdW-DF) method. The adsorption of CO2 on the oxygen-functionalized graphene surface is enhanced by both the electrostatic interactions between the CO2 and the epoxy group and the vdW interactions between the CO2 and graphene. The detailed understanding of the interaction between CO2 and the oxygen-functionalized graphene surface obtained in this study may assist in developing guidelines for designing novel graphene-based catalysts.

Individual Atomic Imaging of Multiple Dopant Sites in As-Doped Si Using Spectro-Photoelectron Holography.

The atomic scale characterization of dopant atoms in semiconductor devices to establish correlations with the electrical activation of these atoms is essential to the advancement of contemporary semiconductor process technology. Spectro-photoelectron holography combined with first-principles simulations can determine the local three-dimensional atomic structures of dopant elements, which in turn affect their electronic states. In the work reported herein, this technique was used to examine arsenic (As) atoms doped into a silicon (Si) crystal. As 3d core level photoelectron spectroscopy demonstrated the presence of three types of As atoms at a total concentration of approximately 1020 cm-3, denoted as BEH, BEM, and BEL. On the basis of Hall effect measurements, the BEH atoms corresponded to electrically active As occupying substitutional sites and exhibiting larger thermal fluctuations than the Si atoms, while the BEM atoms corresponded to electrically inactive As embedded in the AsnV (n = 2-4) type clusters. Finally, the BEL atoms were assigned to electrically inactive As in locally disordered structures.

Augmented pH-sensitivity absorbance of a ruthenium(ii) bis(bipyridine) complex with elongation of the conjugated ligands: an experimental and theoretical investigation.

An absorbance-based sensor employing ruthenium bipyridyl with a phenanthroline-fused benzoylthiourea moiety formulated as [Ru(ii)(bpy)2(phen-nBT)](PF6)2 {bpy = 2,2'-bipyridine, phen = 1,10-phenanthroline, nBT = n-benzoylthiourea} has been synthesized and characterized by elemental analyses, mass spectrometry, and infrared, ultraviolet-visible, luminescence and nuclear magnetic resonance spectroscopy. The changes in the intensity of absorption and emission of the complex induced by functionalization of the benzoylthiourea ligands with amino and carbonyl in their protonated and deprotonated forms were studied experimentally. The absorption and emission properties of the complex exhibit a strong dependence on the pH (1-11) of the aqueous medium. This work highlights the pH-sensitivity augmentation of the absorption band by elongating the conjugation length in the structure of the ruthenium bipyridine complex. The principle of this work was to design the title compound to be capable of enhancing the differences in the absorption sensitivity responses towards pH between the protonated and deprotonated complexes in the absorption measurement. Along with significant and noticeable changes in the absorption spectra, subsequent theoretical investigations specifically on the electronic and absorbance properties of the title compound were carried out in this study. Protonation of the molecule significantly stabilized the lowest-unoccupied molecular orbital (LUMO), whereas the highest-occupied molecular orbital (HOMO) is greatly destabilized upon deprotonation. A time-dependent density functional theory (TDDFT) calculation in the linear-response (-LR) regime was performed to clarify the origin of the experimentally observed linear dependence of absorption intensity upon pH (1-11). The MLCT band exhibits hyperchromic shift at low pH as indicated by the large transition dipole moment and a wider distribution of the response charge of the molecule, which is induced by the stabilization of the electrostatic potential at the carbonyl moiety by protonation. This study provides the possibility of employing theoretical information to gain insight into the origin of the optical absorption obtained experimentally. The ruthenium complex was designed with an elongated ligand conjugation length and exhibited a tremendously large change in the absorption intensity of the protonated and deprotonated forms, which therefore demonstrates its feasibility as an indicator molecule especially for absorbance measurements.