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.

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).

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.

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.

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.

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.

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.

Computational investigations of electronic structure modifications of ferrocene-terminated self-assembled monolayers: effects of electron donating/withdrawing functional groups attached on the ferrocene moiety.

The electrochemical properties of chemically modified electrodes have long been a significant focus of research. Although the electronic states are directly related to the electrochemical properties, there have been only limited systematic efforts to reveal the electronic structures of adsorbed redox molecules with respect to the local environment of the redox center. In this study, density functional theory (DFT) calculations were performed for ferrocene-terminated self-assembled monolayers with different electron-donating abilities, which can be regarded as the simplest class of chemically modified electrodes. We revealed that the local electrostatic potentials, which are changed by the electron donating/withdrawing functional groups at the ferrocene moiety and the dipole field of coadsorbed inert molecules, practically determine the density of states derived from the highest occupied molecular orbital (HOMO) and its vicinities (HOMO-1 and HOMO-2) with respect to the electrode Fermi level. Therefore, to design new, sophisticated electrodes with chemical modification, one should consider not only the electronic properties of the constituent molecules, but also the local electrostatic potentials formed by these molecules and coadsorbed inert molecules.

CO2 adsorption on the copper surfaces: van der Waals density functional and TPD studies.

We investigated the adsorption of CO2 on the flat, stepped, and kinked copper surfaces from density functional theory calculations as well as the temperature programmed desorption and X-ray photoelectron spectroscopy. Several exchange-correlation functionals have been considered to characterize CO2 adsorption on the copper surfaces. We used the van der Waals density functionals (vdW-DFs), i.e., the original vdW-DF (vdW-DF1), optB86b-vdW, and rev-vdW-DF2, as well as the Perdew-Burke-Ernzerhof (PBE) with dispersion correction (PBE-D2). We have found that vdW-DF1 and rev-vdW-DF2 functionals slightly underestimate the adsorption energy, while PBE-D2 and optB86b-vdW functionals give better agreement with the experimental estimation for CO2 on Cu(111). The calculated CO2 adsorption energies on the flat, stepped, and kinked Cu surfaces are 20-27 kJ/mol, which are compatible with the general notion of physisorbed species on solid surfaces. Our results provide a useful insight into appropriate vdW functionals for further investigation of related CO2 activation on Cu surfaces such as methanol synthesis and higher alcohol production.

Dissociative adsorption of CO2 on flat, stepped, and kinked Cu surfaces.

We studied the dissociative adsorption of CO2 to CO + O on the Cu(111), Cu(221), Cu(211), and Cu(11 5 9) surfaces by using state-of-the-art density functional theory (DFT) within a generalized gradient approximation (GGA) and van der Waals density functional (vdW-DF) calculations. The activation energy for CO2 dissociation on the flat Cu(111) surface is 1.33 eV. The activation energies on stepped and kinked surfaces are 1.06 eV, 0.67 eV, and 1.02 eV for the Cu(221), Cu(211), and Cu(11 5 9) surfaces, respectively. Even though the activation energy is 0.66 eV lower on the stepped Cu(211) surface than on the flat Cu(111) surface, we conclude that CO2 does not dissociate on "ideal" flat, stepped, or kinked Cu surfaces at low temperature. We attribute the discrepancy between our theoretical results and experimentally observed CO2 dissociation on stepped Cu surfaces below 150 K to other factors such as effects of Cu adatoms, gas phase or condensed CO2 molecules, or interaction with other gas phase molecules.

Intermolecular interaction as the origin of red shifts in absorption spectra of zinc-phthalocyanine from first-principles.

We investigate electronic origins of a redshift in absorption spectra of a dimerized zinc phthalocyanine molecule (ZnPc) by means of hybrid density functional theoretical calculations. In terms of the molecular orbital (MO) picture, the dimerization splits energy levels of frontier MOs such as the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of the constituent molecules. Consequently, the absorption wavelength seems to become longer than the monomer as the overlap between the monomers becomes larger. However, for a ZnPc dimer configuration with its cofacially stacked monomer arrangement, the calculated absorption spectra within the time-dependent density functional theory indicates no redshift but blueshift in the Q-band absorption spectrum, i.e., a typical H-aggregate. The origin of the apparently contradictory result is elucidated by the conventional description of the interaction between monomer transition dipoles in molecular dimers [Kasha, M. Radiat. Res. 1963, 20, 55]. The redshift is caused by an interaction between the two head-to-tail transition dipoles of the monomers, while the side-by-side arranged transition dipoles result in a blueshift. By tuning the dipole-dipole interaction based on the electronic natures of the HOMO and the LUMO, we describe a slipped-stacked ZnPc dimer configuration in which the Q-band absorption wavelength increases by as large as 144 nm relative to the monomer Q-band.

First-principles molecular-dynamics calculations on chemical reactions and atomic structures induced by H radical impinging onto Si(001)2 x 1:H surface.

Chemical reactions between hydrogen terminated Si(001)2 x 1 surface and impinging H radical are investigated by means of first-principles molecular-dynamics simulations. Reaction probabilities of abstraction of surface terminating H atom with H2 formation, adsorption onto Si surface and reflection of impinging H atom are analyzed with respect to the kinetic energy of incident H radical. The probabilities of abstraction and adsorption turn out to be ranging from 0.81 to 0.58 and from 0.19 to 0.42, respectively, while that of reflection almost zero. As initial kinetic energy of the impinging atom increases, the reaction probability of abstraction decreases and that of absorption increases. Metastable H-absorbed atomic configurations are also derived by optimizing the structures obtained in the impinging dynamics calculations. They are candidates of the so-called reservoir site which is a key to understand the unity hydrogen coverage observed after an exposure to gaseous H atom ambient despite existing residual vacant sites due to abstraction.

Multi-scale Simulation of Equilibrium Step Fluctuations on Cu(111) Surfaces.

Understanding the nature of active sites is a non-trivial task, especially when the catalyst is sensitively affected by chemical reactions and environmental conditions. The challenge lies on capturing explicitly the dynamics of catalyst evolution during reactions. Despite the complexity of catalyst reconstruction, we can untangle them into several elementary processes, of which surface diffusion is of prime importance. By applying density functional theory-kinetic Monte Carlo (DFT-KMC) simulation employed with cluster expansion (CE), we investigated the microscopic mechanism of surface diffusion of Cu with defects such as steps and kinks. Based on the result, the energetics obtained from CE have shown good agreement with DFT calculations. Various diffusion events during the step fluctuations are discussed as well. Aside from the adatom attachment, the diffusion along the step edge is found to be the dominant mass transport mechanism, indicated by the lowest activation energy. We also calculated time correlation functions at 300, 400, and 500 K. However, the time exponent in the correlation function does not strictly follow the power law behavior due to the limited step length, which inhibits variation in the kink density.

Vibration-driven reaction of CO2 on Cu surfaces via Eley-Rideal-type mechanism.

Understanding gas-surface reaction dynamics, such as the rupture and formation of bonds in vibrationally and translationally excited ('hot') molecules, is important to provide mechanistic insight into heterogeneous catalytic processes. Although it has been established that such excitation can affect the reactions occurring via dissociative mechanisms, for associative mechanisms-in which the gas-phase reactant collides directly with a surface-adsorbed species-only translational excitation has been observed to affect reactivity. Here we report a bond-formation reaction that is driven by the vibrational energy of reactant molecules and occurs via an (associative) Eley-Rideal-type mechanism, in which the reaction takes place in a single collision. Hot CO2 in a molecular beam is found to react with pre-adsorbed hydrogen atoms directly on cold Cu(111) and Cu(100) surfaces to form formate adspecies. The vibrational energy of CO2 is more effective at promoting the reaction than translational energy, the reaction rate is independent of the surface temperature and the experimental results are consistent with density functional theory calculations.

Pulse-oximetery is useful in determining the indications for adeno-tonsillectomy in pediatric sleep-disordered breathing.

OBJECTIVE: Although first line therapy of sleep-disordered breathing (SDB) in children is adeno-tonsillectomy, the indications for this operation have not yet been clearly established. We investigated whether pulse-oximetry is useful for determining the optional treatment modality for pediatric SDB. METHOD: Two hundred and thirty-two children presenting with snoring and gasping had their oxygen saturation levels examined during sleep. Among them, 86 underwent on adeno-tonsillectomy and were evaluated pre- and post-surgery. We also examined 25 healthy children as controls. RESULTS: Little desaturation was observed in healthy children. The difference in oxygen saturation levels of the patients between pre- and post-surgery was closely correlated with the pre-surgery levels. We examined the reaction operation characteristics and concluded that children with an oxygen desaturation index of 4% or more (ODI4) of more than 1.5 and/or ODI3 of more than 3.5 should undergo surgery. CONCLUSION: Pulse-oximetry is useful in determining the indications for adeno-tonsillectomy.

Desorption dynamics of CO2 from formate decomposition on Cu(111).

We performed ab initio molecular dynamics analysis of formate decomposition to CO2 and H on a Cu(111) surface using van der Waals density functionals. Our analysis shows that the desorbed CO2 has approximately twice larger bending vibrational energy than the translational, rotational, and stretching vibrational energies. Since formate synthesis, the reverse reaction of formate decomposition, has been suggested experimentally to occur via the Eley-Rideal mechanism, our results indicate that the formate synthesis can be enhanced if the bending vibrational mode of CO2 is excited rather than the translational and/or stretching vibrational modes. Detailed information on the energy distribution of desorbed CO2 as a formate decomposition product may provide new insights for improving the catalytic activity of formate synthesis.

First-Principles Molecular Dynamics Analysis of Ligand-Free Suzuki-Miyaura Cross-Coupling in Water Solvent: Oxidative Addition Step.

We investigated the oxidative addition of PhX (X = Cl, Br) to a single Pd(0) atom or a PdX- complex in water using first-principles molecular dynamics simulations, with solvent H2O molecules explicitly included in the calculation models, to clarify the origin of the extremely high reactivity of a ligand-free Pd catalyst in an aqueous solution for the Suzuki-Miyaura reaction. The free-energy profiles are estimated using blue moon ensemble sampling to include the entropy effect in chemical reactions in a water solvent. The free-energy barrier of the oxidative addition step is quite low for PhBr, whereas the barrier for PhCl is sizable, indicating that the reaction can proceed at room temperature with a high rate for PhBr but a rather low rate for PhCl. We also investigated the effect of the additional halogen anion on the Pd catalyst as a "supporting ligand". The activation barrier of the oxidative addition step is not affected by the supporting halogen ligand, but the final state is significantly destabilized, which should be important for the following transmetalation step. The solvent effect has also been investigated and discussed.

First-principles theoretical study of hydrolysis of stepped and kinked Ga-terminated GaN surfaces.

: We have investigated the initial stage of hydrolysis process of Ga-terminated GaN surfaces by using first-principles theoretical calculations. We found that the activation barrier of H2O dissociation at the kinked site of the Ga-terminated GaN surface is about 0.8 eV, which is significantly lower than that at the stepped site of about 1.2 eV. This is consistent with the experimental observation where a step-terrace structure is observed after the etching process of Ga-terminated GaN surfaces with catalyst-referred etching method. Detailed analysis on the nature of the chemical interaction uring the hydrolysis processes will be discussed.