Machine learning molecular dynamics simulation of CO-driven formation of Cu clusters on the Cu(111) surface.

The behavior of adsorbate-induced surface transformation can be clearly understood given the mechanical aspects of such phenomenon are well described at the atomic level. In this study, we provide the atomic-level description on the formation of Cu clusters on the Cu(111) surface by performing set of molecular dynamics simulations driven by machine-learning force-field. The simulations at 450 K-550 K show clusters are formed within a hundred of ns when the Cu surface is exposed with CO. On the other hand, no cluster is formed within the same time interval on the clean Cu surface even at 550 K, which signifies the importance of CO exposure to the surface transformation. The effect of temperature to the formation of clusters is also investigated. The CO-decorated Cu clusters ranging from dimer to hexamer are detected within a hundred of ns at 450 K. Lowering the temperature to 350 K does not result in the formation of clusters within a hundred ns due to the scarce detachments of adatom, while raising the temperature to 550 K results in the formation of more clusters, ranging from dimer to heptamer, but with shorter lifetimes. The clusters can be formed directly through instantaneous detachment of a group of step-atoms, or indirectly by aggregation of wandering Cu monomers and smaller clusters on the surface terrace. The preference to the indirect mechanism is indicated by the higher frequency of its occurrence. Set of nudged elastic band calculations has been performed to confirm the promotion of CO adsorptions to the detachment of Cu step-atoms by lowering the detachment barrier.

Electronic and optical properties of the hydrogen boride sheet from the many-body perturbation theory.

We study the electronic and optical properties of the hydrogen boride sheet by using the many-body perturbation theory with the perturbativeGW(G0W0) approximation. It was found that the hydrogen boride sheet shows a semimetallic electronic structure, supporting the previous theoretical study based on the semilocal density functional theory calculations. It was also found that the optical spectrum calculated based on the quasiparticle energies agrees well with the experiments. This work suggests thatG0W0approximation may be useful for predicting precise electronic and optical properties of the hydrogen boride sheet and its derivatives.

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.

Polymorphs of Titanium Dioxide: An Assessment of the Variants of Projector Augmented Wave Potential of Titanium on Their Geometric and Dielectric Properties.

Titanium dioxide (TiO2) is one of the important functional materials owing to its diverse applications in many fields of chemistry, physics, nanoscience, and technology. Hundreds of studies on its physicochemical properties, including its various phases, have been reported experimentally and theoretically, but the controversial nature of relative dielectric permittivity of TiO2 is yet to be understood. Toward this end, this study was undertaken to rationalize the effects of three commonly used projector augmented wave (PAW) potentials on the lattice geometries, phonon vibrations, and dielectric constants of rutile (R-)TiO2 and four of its other phases (anatase, brookite, pyrite, and fluorite). Density functional theory calculations within the PBE and PBEsol levels, as well as their reinforced versions PBE+U and PBEsol+U (U = 3.0 eV), were performed. It was found that PBEsol in combination with the standard PAW potential centered on Ti is adequate to reproduce the experimental lattice parameters, optical phonon modes, and the ionic and electronic contributions of the relative dielectric permittivity of R-TiO2 and four other phases. The origin of failure of the two soft potentials, namely, Ti_pv and Ti_sv, in predicting the correct nature of low-frequency optical phonon modes and ion-clamped dielectric constant of R-TiO2 is discussed. It is shown that the hybrid functionals (HSEsol and HSE06) slightly improve the accuracy of the above characteristics at the cost of a significant increase in computation time. Finally, we have highlighted the influence of external hydrostatic pressure on the R-TiO2 lattice, leading to the manifestation of ferroelectric modes that play a role in the determination of large and strongly pressure-dependent dielectric constant.

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.

Formation and growth characteristics of nanostructured carbon films on nascent Ag clusters during room-temperature electrochemical CO2 reduction.

Synthesis of carbon nanostructures at room temperature and under atmospheric pressure is challenging but it can provide significant impact on the development of many future advanced technologies. Here, the formation and growth characteristics of nanostructured carbon films on nascent Ag clusters during room-temperature electrochemical CO2 reduction reactions (CO2RR) are demonstrated. Under a ternary electrolyte system containing [BMIm]+[BF4]-, propylene carbonate, and water, a mixture of sp2/sp3 carbon allotropes were grown on the facets of Ag nanocrystals as building blocks. We show that (i) upon sufficient energy supplied by an electric field, (ii) the presence of negatively charged nascent Ag clusters, and (iii) as a function of how far the C-C coupling reaction of CO2RR (10-390 min) has advanced, the growth of nanostructured carbon can be divided into three stages: Stage 1: sp3-rich carbon and diamond seed formation; stage 2: diamond growth and diamond-graphite transformation; and stage 3: amorphous carbon formation. The conversion of CO2 and high selectivity for the solid carbon products (>95%) were maintained during the full CO2RR reaction length of 390 min. The results enable further design of the room-temperature production of nanostructured carbon allotropes and/or the corresponding metal-composites by a viable negative CO2 emission technology.

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.

Elucidation of Cu-Zn Surface Alloying on Cu(997) by Machine-Learning Molecular Dynamics.

The Cu-Zn surface alloy has been extensively involved in the investigation of the true active site of Cu/ZnO/Al2O3, the industrial catalyst for methanol synthesis which remains under controversy. The challenge lies in capturing the interplay between the surface and reaction under operating conditions, which can be overcome given that the explicit dynamics of the system is known. To provide a better understanding of the dynamic of Cu-Zn surface at the atomic level, the structure and the formation process of the Cu-Zn surface alloy on Cu(997) were investigated by machine-learning molecular dynamics (MD). Gaussian process regression aided with on-the-fly learning was employed to build the force field used in the MD. The simulation reveals atomistic details of the alloying process, that is, the incorporation of deposited Zn adatoms to the Cu substrate. The surface alloying is found to start at upper and lower terraces near the step edge, which emphasize the role of steps and kinks in the alloying. The incorporation of Zn at the middle terrace was found at the later stage of the simulation. The rationalization of alloying behavior was performed based on statistics and barriers of various elementary events that occur during the simulation. It was observed that the alloying scheme at the upper terrace is dominated by the confinement of Zn step adatoms by other adatoms, highlighting the importance of step fluctuations in the alloying process. On the other hand, the alloying scheme at the lower terrace is dominated by direct exchange between the Zn step adatom and the Cu atom underneath. The alloying at the middle terrace is dominated by the wave deposition mechanism and deep confinement of Zn adatoms. The short propagation of alloyed Zn in the middle terrace was observed to proceed by means of indirect exchange instead of local exchange as proposed in the previous scanning tunneling microscopy (STM) observation. The comparison of migration rate and activation energies to the result of STM observation is also made. We have found that at a certain distance from the surface, the STM tip significantly affects the elementary events such as vacancy formation and direct exchange.

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).

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.

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.

Alkaline earth atom doping-induced changes in the electronic and magnetic properties of graphene: a density functional theory study.

Density functional theory was used to investigate the effects of doping alkaline earth metal atoms (beryllium, magnesium, calcium and strontium) on graphene. Electron transfer from the dopant atom to the graphene substrate was observed and was further probed by a combined electron localization function/non-covalent interaction (ELF/NCI) approach. This approach demonstrates that predominantly ionic bonding occurs between the alkaline earth dopants and the substrate, with beryllium doping having a variant characteristic as a consequence of electronegativity equalization attributed to its lower atomic number relative to carbon. The ionic bonding induces spin-polarized electronic structures and lower workfunctions for Mg-, Ca-, and Sr-doped graphene systems as compared to the pristine graphene. However, due to its variant bonding characteristic, Be-doped graphene exhibits non-spin-polarized p-type semiconductor behavior, which is consistent with previous works, and an increase in workfunction relative to pristine graphene. Dirac half-metal-like behavior was predicted for magnesium doped graphene while calcium doped and strontium doped graphene were predicted to have bipolar magnetic semiconductor behavior. These changes in the electronic and magnetic properties of alkaline earth doped graphene may be of importance for spintronic and other electronic device applications.

Adsorption of toxic gases on borophene: surface deformation links to chemisorptions.

ß12 borophene has received great attention because of its intriguing mechanical and electronic properties. One of the possible applications of borophene is gas sensing. However, the interaction between common gases and ß12 borophene remains to be clarified. In this work, we study the interactions of ß12 borophene towards five hazardous gases, namely, CO, NO, NH3, NO2, and CO2 using various non-empirical van der Waals density functionals and provide an insight into the adsorption behavior of borophene. The adsorption mechanism and molecular vibrations are discussed in great detail. Among the gases considered, CO2 is physisorbed while other gases are chemically bonded to ß12 borophene. We also demonstrate that the deformation at the ridge of borophene enables its active p z orbital to strongly hybridize with frontier orbitals of the studied polar gases. Consequently, borophene is predicted to interact strongly with CO, NO, NH3, and especially NO2, making it a sensitive sensing material for toxic gases.

Density functional theory study on a nitrogen-rich carbon nitride material C3N5 as photocatalyst for CO2 reduction to C1 and C2 products.

A new-type nitrogen-rich carbon nitride material C3N5 has been synthesized recently, in which the C:N ratio increases from 3:4 in g-C3N4 to 3:5 due to the introduction of azo linkage (NN) connecting segments in two C6N7 units. Herein, C3N5 as a photocatalyst for CO2 reduction was investigated by density functional theory methods. The electronic and optical properties indicate that C3N5 has a longer visible-light region with 2.0 eV of band gap in comparison with g-C3N4. The spatial distributions of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) show that the π network of C3N5 is extended by introducing -NN- linkage, which results in much higher photocatalytic efficiency than g-C3N4. The Gibbs free energies for possible CO2 reaction paths on C3N5 were computed. The results show that CO2 can be reduced to CH4 with a low limiting potential of -0.54 V and to CH3CH2OH with a low limiting potential of -0.61 V, which all driven by solar energy. The present work is expected to provide useful guide for new-type nitrogen-rich C3N5 as promising photocatalyst for CO2 reduction reaction (CO2RR).

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.

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.

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.

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.