Effect of coverage and defects on the adsorption of propanethiol on Au(111) surface: a theoretical study

Periodic density functional calculations have been carried out to investigate both the thiol adsorption on Au(111) surface and the reaction mechanism for the formation of the self-assembled monolayers, taking propanethiol as a representative example. The effect of coverage and surface defects (adatoms and vacancies) has been analyzed. It is found that the most stable physisorption (undissociated) site is an adatom site, whereas the chemisorption site for the thiol is a vacancy site or protrusion consisting of a pair of adatoms, followed by one adatom site. The results point out that the thiolate self-assembled monolayer adsorption process occurs preferentially on step edges.     

Metals on graphene: correlation between adatom adsorption behavior and growth morphology

We present a systematic study of metal adatom adsorption on graphene by ab initio calculations. The calculations cover alkali metals, sp-simple metals, 3d and group 10 transition metals, noble metals, as well as rare earth metals. The correlation between the adatom adsorption properties and the growth morphology of the metals on graphene is also investigated. We show that the growth morphology is related to the ratio of the metal adsorption energy to its bulk cohesive energy (E(a)/E(c)) and the diffusion barrier (ΔE) of the metal adatom on graphene. Charge transfer, electric dipole and magnetic moments, and graphene lattice distortion induced by metal adsorption would also affect the growth morphologies of the metal islands. We also show that most of the metal nanostructures on graphene would be thermally stable against coarsening.     

A DFT study on the possibility of using a single Cu atom incorporated nitrogen-doped graphene as a promising and highly active catalyst for oxidation of CO

Using dispersion-corrected density functional theory (DFT) calculations, a single Cu adatom incorporated nitrogen-doped graphene (CuN₃-Gr) is proposed as a new and highly active noble-metal-free catalyst for carbon monoxide (CO) oxidation reaction. According to our results, the Cu adatom can be stably anchored onto the monovavancy site of the nitrogen-doped graphene, and the resulting large diffusion barrier suggests that the metal clustering is avoided in CuN₃-Gr. Three possible reaction mechanisms for CO oxidation (ie, Eley–Rideal, Langmuir–Hinshelwood, and termolecular Eley–Rideal) are systematically studied. It is found that the activation energy for the rate-determining step of the termolecular Eley–Rideal mechanism is only 0.13 eV, which is much smaller than those of others. The results of this study may provide a useful guideline for the design of highly active and promising single-metal catalysts for the CO oxidation reaction based on graphene.     

Density Functional Theory Study of Pd Aggregation on a Pyridine-Terminated Self-Assembled Monolayer

By using density functional theory calculations, the initial steps towards Pd metal cluster formation on a pyridine-terminated self-assembled monolayer (SAM) consisting of 3-(4-(pyridine-4-yl)phenyl)propane-1-thiol on an Au(1 1 1) surface are investigated. Theoretical modelling allows the investigation of structural details of the SAM surface and the metal/SAM interface at the atomic level, which is essential for elucidating the nature of Pd–SAM and Pd–Pd interactions at the liquid/solid interface and gaining insight into the mechanism of metal nucleation in the initial stage of electrodeposition. The structural flexibility of SAM molecules was studied first and the most stable conformation was identified, planar molecules in a herringbone packing, as the model for Pd adsorption. Two binding sites are found for Pd atoms on the pyridine end group of the SAM. The strong interaction between Pd atoms and pyridines illustrates the importance of SAM functionalisation in the metal nucleation process. Consistent with an energetic driving force of approximately −0.3 eV per Pd atom towards Pd aggregation suggested by static calculations, a spontaneous Pd dimerisation is observed in ab initio molecular dynamic studies of the system. Nudged elastic band calculations suggest a potential route with a low energy barrier of 0.10 eV for the Pd atom diffusion and then dimerisation on top of the SAM layer.     

Atomic‐Level Elucidation of the Initial Stages of Self‐Assembled Monolayer Metallization and Nanoparticle Formation

The development of high‐performance molecular electronics and nanotech applications requires deep understanding of atomic level structural, electronic, and magnetic properties of electrode/molecular interfaces. Recent electrochemical experiments on self‐assembled monolayers (SAMs) have identified highly practical means to generate nanoparticles and metal monolayers suspended above substrate surfaces through SAM metallizations. A rational basis why this process is even possible is not yet well‐understood. To clarify the initial stages of interface formation during SAM metallization, we used first‐principles spin‐polarized density functional theory (DFT) calculations to study Pd diffusion on top of 4‐mercaptopyridine (4MP) SAMs on Au(111). After distinguishing potential‐energy surfaces (PESs) for different spin configurations for transition metal atoms on the SAM, we find adatom diffusion is not possible over the clean 4MP–SAM surface. Pre‐adsorption of transition‐metal atoms, however, facilitates atomic diffusion that appears to explain multiple reports on experimentally observed island and monolayer formation on top of SAMs. Furthermore, these diffusions most likely occur by moving across low‐lying and intersecting PESs of different spin states, opening the possibility of magnetic control over these systems. Vertical diffusion processes were also investigated, and the electrolyte was found to play a key role in preventing metal permeation through the SAM to the substrate.     

A Surface Coordination Network Based on Copper Adatom Trimers

Surface coordination networks formed by co‐adsorption of metal atoms and organic ligands have interesting properties, for example regarding catalysis and data storage. Surface coordination networks studied to date have typically been based on single metal atom centers. The formation of a novel surface coordination network is now demonstrated that is based on network nodes in the form of clusters consisting of three Cu adatoms. The network forms by deposition of tetrahydroxybenzene (THB) on Cu(111) under UHV conditions. As shown from a combination of scanning tunneling microscopy, X‐ray photoelectron spectroscopy, and density functional theory calculations, all four hydroxy groups of THB dehydrogenate upon thermal activation at 440 K. This highly reactive ligand binds to Cu adatom trimers, which are resolved by high‐resolution STM. The network creates an ordered array of mono‐dispersed metal clusters constituting a two‐dimensional analogue of metal–organic frameworks.     

Two‐Dimensional Ketone‐Driven Metal–Organic Coordination on Cu(111)

Two‐dimensional metal–organic nanostructures based on the binding of ketone groups and metal atoms were fabricated by depositing pyrene‐4,5,9,10‐tetraone (PTO) molecules on a Cu(111) surface. The strongly electronegative ketone moieties bind to either copper adatoms from the substrate or codeposited iron atoms. In the former case, scanning tunnelling microscopy images reveal the development of an extended metal–organic supramolecular structure. Each copper adatom coordinates to two ketone ligands of two neighbouring PTO molecules, forming chains that are linked together into large islands through secondary van der Waals interactions. Deposition of iron atoms leads to a transformation of this assembly resulting from the substitution of the metal centres. Density functional theory calculations reveal that the driving force for the metal substitution is primarily determined by the strength of the ketone–metal bond, which is higher for Fe than for Cu. This second class of nanostructures displays a structural dependence on the rate of iron deposition.     

Atomistic mechanisms for the (1 x 1) <==> hex surface phase transformations of Pt(100)

The atomistic mechanisms and dynamics of the (1 x 1) --> hex surface reconstruction of the clean Pt(100) and its lifting upon CO adsorption have been studied by means of both density functional theory and molecular dynamics simulations based on the modified embedded-atom method. It was found that during the surface reconstruction from the square (1 x 1) to the approximately 20% more dense (quasi)hexagonal phase, the required extra atoms are extracted from the second layer, leaving highly mobile subsurface vacancies, even in the presence of adatom islands or steps. These vacancies will, by surface diffusion, coalesce to form steps. In contrast, during the reverse process--where the hex surface reconstruction is lifted upon adsorption of CO--the roughly 20% excess surface atoms are in a collective manner ejected to form chains of adatoms. In turn, these adatoms coalesce into islands and steps by surface diffusion. A result of the two totally different mechanisms is that the reconstruction process can be concluded not to be the reverse of the deconstruction process.     

贵金属原子与点缺陷石墨烯的键增强作用

通过密度泛函理论研究了Ag、Au、Pt原子在完美和点缺陷(包括N掺杂、B掺杂、空位点缺陷)石墨烯上的吸附以及这些体系的界面性质.研究表明Ag、Au不能在完美的石墨烯上吸附,N、B掺杂增强了三种金属与石墨烯之间的相互作用.而空位点缺陷诱发三种金属在石墨烯上具有强化学吸附作用.通过电子结构分析发现,N掺杂增强了Au、Pt与C形成的共价键,而Au、Ag与B形成了化学键.空位点缺陷不仅是金属原子的几何固定点,同时也增加了金属原子和碳原子之间的成键.增强贵金属原子和石墨烯相互作用的顺序是:空位点缺陷>>B掺杂>N掺杂.     

Phosphorene Supported Single-Atom Catalysts for CO Oxidation: A Computational Study

Single-atom catalysts (SACs) have attracted extensive attention owing to their high catalytic activity. The development of efficient SACs is crucial for applications in heterogeneous catalysis. In this article, the geometric configuration, electronic structure, stabilitiy and catalytic performance of phosphorene (Pn) supported single metal atoms (M=Ru, Rh, Pd, Ir, Pt, and Au) have been systematically investigated using density functional theory calculations and ab initio molecular dynamics simulations. The single atoms are found to occupy the hollow site of phosphorene. Among the catalysts studied, Ru-decorated phosphorene is determined to be a potential catalyst by evaluating adsorption energies of gaseous molecules. Various mechanisms including the Eley-Rideal (ER), Langmuir-Hinshelwood (LH) and trimolecular Eley-Rideal (TER) mechanisms are considered to validate the most favourable reaction pathway. Our results reveal that Ru−Pn exhibits outstanding catalytic activity toward CO oxidation reaction via TER mechanism with the corresponding rate-determining energy barrier of 0.44 eV, making it a very promising SAC for CO oxidation under mild conditions. Overall, this work may provide a new avenue for the design and fabrication of two-dimensional materials supported SACs for low-temperature CO oxidation.     

First-principles studies on doped graphene as anode materials in lithium-ion batteries

Using density functional theory computations, we investigated Li adsorption, diffusion, and desorption in pristine, B- or N-doped graphene. Compared with pristine graphene, B-doping significantly enhances Li adsorption, whereas Li adsorption is slightly weakened on N-doped graphene, which should be attributed to the different electronic structures due to doping. Li diffusion on various graphene systems was also computed through nudged elastic band method, and the results revealed that Li diffusion on N-doped graphene is faster than on pristine and B-doped graphene. Moreover, for Li desorption from the graphene substrate, N-doped graphene showed the lowest desorption barrier. Our results are in agreement with recent experimental reports and also demonstrate that N-doped graphene is a promising anode material with high-rate charge/discharge ability for Li-ion batteries.     

Bidentate Surface Structures of Glycylglycine on Si(111)7×7 by High-Resolution Scanning Tunneling Microscopy: Site-Specific Adsorption via N-H and O-H or Double N-H Dissociation

The early adsorption stage of glycylglycine on Si(111)7×7 surface has been studied by scanning tunneling microscopy (STM). Filled-state imaging shows that glycylglycine adsorbs dissociatively in a bidentate fashion on two adjacent Si adatoms across a dimer wall or an adatom-restatom pair, with the dissociated H atoms on neighboring restatoms. The present STM result validates our hypothesis that both bidentate configurations involving N-H and O-H dissociation and double N-H dissociation are equally probable. Our STM results further show that the relative surface concentrations of the five bidentate configurations follow a specific ordering. This suggests that N-H dissociation at a center adatom site would likely be followed by N-H dissociation at an adjacent restatom, while N-H dissociation at a corner adatom site would be succeeded by O-H dissociation at an adatom across the dimer wall. Evidently, the strong bidentate interactions also inhibit surface diffusion of the adsorbed glycylglycine fragment, and the adsorption apparently follows random sequential adsorption statistics. The random nature of adsorption is also supported by the similar relative occupancies of the center adatom and corner adatom sites, indicating that the relative reactivities of these adatom sites do not play a significant role. Our DFT computational study shows that all three bidentate (Si-)NHCH(2)CONHCH(2)COO(-Si) adatom-adatom configurations (center-center, corner-corner, center-corner) have similar adsorption energies for a double adatom-adatom pair across the dimer wall, while the (Si-)NHCH(2)CON(-Si)CH(2)COOH bidentate adatom-restatom configuration is energetically favorable. The free -CONH- and -COOH groups remaining on the respective bidentate adstructures could facilitate adsorption of the second adlayer through the formation of hydrogen bonding.     

Adatom doping-enriched geometric and electronic properties of pristine graphene: a method to modify the band gap

We have investigated the way in which the concentration and distribution of adatoms affect the geometric and electronic properties of graphene. Our calculations were based on the use of first principle under the density functional theory which reveal various types of π-bonding. The energy band structure of this doped graphene material may be explored experimentally by employing angle-resolved photo-emission spectroscopy (ARPES) for electronic band structure measurements and scanning tunneling spectroscopy (STS) for the density-of-states (DOS) both of which have been calculated and reported in this paper. Our calculations show that such adatom doping is responsible for the destruction or appearance of the Dirac-cone structure.     

Effect of Hydrogen on O2 Adsorption and Dissociation on a TiO2 Anatase (001) Surface

The effect of hydrogen on the adsorption and dissociation of the oxygen molecule on a TiO₂ anatase (001) surface is studied by first‐principles calculations coupled with the nudged elastic band (NEB) method. Hydrogen adatoms on the surface can increase the absolute value of the adsorption energy of the oxygen molecule. A single H adatom on an anatase (001) surface can lower dramatically the dissociation barrier of the oxygen molecule. The adsorption energy of an O₂ molecule is high enough to break the O?O bond. The system energy is lowered after dissociation. If two H adatoms are together on the surface, an oxygen molecule can be also strongly adsorbed, and the adsorption energy is high enough to break the O?O bond. However, the system energy increases after dissociation. Because dissociation of the oxygen molecule on a hydrogenated anatase (001) surface is more efficient, and the oxygen adatoms on the anatase surface can be used to oxidize other adsorbed toxic small gas molecules, hydrogenated anatase is a promising catalyst candidate.     

Reaction of hydrogen with Ag(111): binding states, minimum energy paths, and kinetics

The interaction of atomic and molecular hydrogen with the Ag(111) surface is studied using periodic density functional total-energy calculations. This paper focuses on the site preference for adsorption, ordered structures, and energy barriers for H diffusion and H recombination. Chemisorbed H atoms are unstable with respect to the H(2) molecule in all adsorption sites below monolayer coverage. The three-hollow sites are energetically the most favorable for H chemisorption. The binding energy of H to the surface decreases slightly up to one monolayer, suggesting a small repulsive H-H interaction on nonadjacent sites. Subsurface and vacancy sites are energetically less favorable for H adsorption than on-top sites. Recombination of chemisorbed H atoms leads to the formation of gas-phase H(2) with no molecular chemisorbed state. Recombination is an exothermic process and occurs on the bridge site with a pronounced energy barrier. This energy barrier is significantly higher than that inferred from experimental temperature-programmed desorption (TPD) studies. However, there is significant permeability of H atoms through the recombination energy barrier at low temperatures, thus increasing the rate constant for H(2) desorption due to quantum tunneling effects, and improving the agreement between experiment and theory.     

Surface diffusion and incorporation of adatom in Co/Al (0 0 1) system

The surface diffusion and the incorporation of an adatom on early stage of Co/Al (001) interface formation was investigated using the density functional theory (DFT). The energy barrier for the surface diffusion (migration of Co adatom to an adjacent hollow site passing the bridge site) was calculated as 1.01 eV. Large displacement of neighboring Al atoms was accompanied by the surface diffusion of Co adatom. For incorporation process, the energy barrier was 0.39 eV, only 38.6% of the barrier for surface diffusion and the energy gain of the system was 0.43 eV. After the incorporation process was completed, the Co adatom and Al atoms formed seven Co-Al bonds of highly coordinated B2-like configuration.     

Creation,electronic properties,disorder, and melting of two-dimensional surface-state-mediated adatom superlattices

Surface-state-mediated interactions influence the spatial distribution of adatoms at surfaces. These indirect interactions are the driving force for the creation of superlattices of individual adsorbed atoms when the adatom concentration, the sample temperature, and the adatom diffusion barrier are in a subtle balance, as it has been first reported for Ce adatoms on Ag(1 1 1). The conditions for the formation of such superlattices are discussed. Specifically, the adatom concentration is shown to modify considerably the electronic structure of the Ag(1 1 1) surface. With increasing temperature the superlattice undergoes a direct transition from a two-dimensional solid to a two-dimensional liquid. Such superlattices, consisting of magnetic adatoms, may be interesting as model systems for the study of direct and indirect magnetic interactions in two dimensions.     

Density functional study of hydrogen adsorption and diffusion on Ni‐loaded graphene and graphene oxide

In this work, we performed density functional calculations to investigate the adsorption and diffusion of hydrogen on Ni‐loaded graphene and single layer graphene oxide (SLGO). We evaluated the feasibility of hydrogen spillover in the presence of Ni₄ cluster and the role of oxygen‐containing groups. Our calculations indicate that the hydrogen diffusion is difficult to take place on the Ni/graphene interface due to the stronger Ni? H bond strength. Further, the chemisorbed H atoms are also hard to diffuse freely on the graphene surface. For the SLGO surface, both hydroxyl and epoxide groups may not facilitate the hydrogen diffusion. Instead, they are readily attracted by the nearby Ni catalyst and hydrogenated to water molecules. © 2014 Wiley Periodicals, Inc.     

Adsorption and diffusion of Mg, O, and O2 on the MgO(001) flat surface

A thorough investigation of the adsorption and diffusion of Mg, O, and O(2) on MgO(001) terraces is performed by first-principles calculations. The single Mg adatom weakly binds to surface oxygens, diffuses, and evaporates easily at room temperatures. Atomic O strongly binds to surface oxygens, forming peroxide groups. The diffusion of the O adatom is strongly influenced by the spin polarization, since energy barriers are significantly different for the singlet and triplet states. The crossing of the two Born-Oppenheimer surfaces corresponding to the distinct spin states is also analyzed. Although the O(2) molecule does not stick to the perfect surface, it chemisorbs on surface nonstoichiometric point defects such as O vacancies or Mg adatoms, forming in the latter case new chemical species on the surface. We show that the oxidation rate limiting factor in an O(2) atmosphere is the concentration of point defects (O vacancies and Mg adatoms) in the growing surface. The simulated O core-level shifts for the various adsorption configurations enable a meaningful comparison with the measured values, suggesting the presence of peroxide ions on growing surfaces. Finally, the computed energy barriers are used to estimate the Mg and O surface lifetimes and diffusion lengths, and some implications for the homoepitaxial growth of MgO are discussed.     

The electric field as a novel switch for uptake/release of hydrogen for storage in nitrogen doped graphene

Nitrogen-doped graphene was recently synthesized and was reported to be a catalyst for hydrogen dissociative adsorption under a perpendicular applied electric field (F). In this work, the diffusion of H atoms on N-doped graphene, in the presence and absence of an applied perpendicular electric field, is studied using density functional theory. We demonstrate that the applied field can significantly facilitate the binding of hydrogen molecules on N-doped graphene through dissociative adsorption and diffusion on the surface. By removing the applied field the absorbed H atoms can be released efficiently. Our theoretical calculation indicates that N-doped graphene is a promising hydrogen storage material with reversible hydrogen adsorption/desorption where the applied electric field can act as a switch for the uptake/release processes.