Density functional theory study of water adsorption at reduced and stoichiometric ceria (111) surfaces

We study the structure and energetics of water molecules adsorbed at ceria (111) surfaces for 0.5 and 1.0 ML coverages using density functional theory. The results of this study provide a theoretical framework for interpreting recent experimental results on the redox properties of water at ceria (111) surfaces. In particular, we have computed the structure and energetics of various absorption geometries at the stoichiometric ceria (111) surface. We find that single hydrogen bonds between the water and the oxide surface are favored in all cases. At stoichiometric surfaces, the water adsorption energy depends rather weakly on coverage. We predict that the observed coverage dependence of the water adsorption energy at stoichiometric surfaces is likely the result of dipole-dipole interactions between adsorbed water molecules. When oxygen vacancies are introduced in various surface layers, water molecules are attracted more strongly to the surface. We find that it is very slightly energetically favorable for adsorbed water to oxidized the reduced (111) surface with the evolution of H(2). In the event that water does not oxidize the surface, we predict that the effective attractive water-vacancy interaction will result in a significant enhancement of the vacancy concentration at the surface in agreement with experimental observations. Finally, we present our results in the context of recent experimental and theoretical studies of vacancy clustering at the (111) ceria surface.     

Slab model studies of water adsorption and decomposition on clean and X- (X = C, N and O) contaminated Pd(111) surfaces

To explore the effect of surface contaminants on water chemistry at metallic surfaces, adsorption and decomposition of water monomers on clean and X/Pd(111)(X = C, N and O) surfaces are investigated based on density functional theory calculations. It is revealed that H(2)O binds to Pd(111) surface primarily through the mixing of its 1b(1) with the Pd 4d(z(2)) state. A charge accumulation between the oxygen atom of water and the bound Pd atom is calculated, which is found to be relevant to the H(2)O-Pd interaction. Water adsorption results in a reduction of surface work function and the polarization of the X 2p states. The O-H bond scission of H(2)O on the clean Pd(111) is an energy unfavorable process. In the case of X-assisted O-H bond breaking on X/Pd(111) surfaces, however, the reaction barrier tends to be lower than that on the clean surface and decreases from C/Pd(111) to O/Pd(111). In particular, water decomposition is found to become feasible on O/Pd(111), in agreement with the experimental observations. The calculated barrier is demonstrated to be correlated linearly with the density of X 2p states at the Fermi level. A thorough energy analysis demonstrates that the following geometrical and electronic factors favor the barrier reduction on X/Pd(111) with respect to water decomposition on clean Pd(111): (i) the less deformed structure of water in TS; (ii) the decreased bonding competition between the fragments OH and H. The remarkable decrease of the barrier on O/Pd(111) is revealed to be due to the largest stabilization of the split H atom and the least deformation of water in the TS.     

The direct observation of 2H‐DPP metalation on Pd(111) and Cu/Pd(111) surface

The metalation behaviors of 5,15‐diphenylporphyrin (2H‐DPP) on Pd(111) and Cu/Pd(111) have been investigated using scanning tunneling microscopy and density functional calculations. We show that 2H‐DPP molecules deposited on Pd(111) surface form Pd‐DPP with a proportion of about 75% already at room temperature (RT). This is in contrast to non‐metalation adsorption of 2H‐DPP on Cu–Pd alloy at RT. Annealing to 323 K facilitates the metalation of 2H‐DPP on Cu–Pd alloy island. The comparison of the results indicates that the metalation of 2H‐DPP calls for both enough surface free energy of approaching N? H bond and enough reactivity of breaking N? H bond. Copyright © 2016 John Wiley & Sons, Ltd.     

甲烷在清洁 Pd(111) 及氧改性的 Pd(111) 表面解离的密度泛函理论研究

 采用广义梯度近似 (GGA) 的密度泛函理论 (DFT) 并结合平板模型, 研究了 CH4 在清洁 Pd(111) 及 O 改性的 Pd(111) 表面发生 C朒 键断裂的反应历程. 优化了裂解过程中反应物、过渡态和产物的几何构型, 获得了反应路径上各物种的吸附能及反应的活化能. 结果表明, CH4 采用一个 H 原子指向表面的构型在 Pd(111) 表面的顶位吸附, CH3 的最稳定的吸附位置为顶位, OH, O 和 H 的最稳定吸附位置均为面心立方. CH4 在清洁 Pd(111) 表面裂解的活化能为 0.97 eV, 低于它在 O 原子改性 (O 没有参与反应) 的 Pd(111) 表面的活化能 1.42 eV, 说明表面氧原子抑制了 CH4 中 C朒 键的断裂. 当亚表面 O 原子和表面 O 原子 (O 参与反应) 共同存在时, C朒 键断裂的活化能为 0.72 eV, 低于只有表层氧存在时的活化能 (1.43 eV), 说明亚表面的 O 原子对 CH4 分子的活化具有促进作用. CH4 在 O 原子改性的 Pd(111) 表面裂解生成 CH3 和 H, 以及生成 CH3 和 OH 的反应活化能分别为 1.42 和 1.43 eV, 说明 CH4 在 O 原子改性的 Pd(111) 表面发生这两种反应的难易程度相当.     

Ab initio studies of a water layer at transition metal surfaces

This paper presents a detailed study of a water adlayer adsorbed on Pt(111) and Rh(111) surfaces using periodic density functional theory methods. The interaction between the metal surface and the water molecules is assessed from molecular dynamics simulation data and single point electronic structure calculations of selected configurations. It is argued that the electron bands around the Fermi level of the metal substrate extend over the water adlayer. As a consequence in the presence of the water layer the surface as a whole still maintains its metallic conductivity-a result of a crucial importance for understanding the process of electron transfer through the water/metal interface and electrochemical reactions in particular. Our results also indicate that there exists a weak bond between the hydrogen of the water and the Rh metal atoms as opposed to the widespread (classical) models based on purely repulsive interaction. This suggests that the commonly used classical interactions potentials adopted for large scale molecular dynamics simulations of water/metal interfaces may need revision. Two adsorption models of water on transition metals with the OH bonds pointing towards or away of the surface are also examined. It is shown that due to the very close values of their adsorption energies one should consider the real structure of water on the surface as a mixture of these simple "up" and "down" models. A model for the structure of the adsorbed water layer on Rh(111) is proposed in terms of statistical averages from molecular dynamics simulations.     

The explicit interactions of five-membered saturated heterocyclics containing one and two heteroatoms with single water molecule

In this article, the hydrogen bonding interaction between saturated five-membered heterocyclic molecules and water has been investigated. Molecular orbital and density functional theory methods have been used to evaluate the stabilization energies associated with the adduct formation between heterocyclic molecules and water. The hydrogen bond acceptor ability of O, S, Se, and N as members of five-membered ring has been analyzed. The effect of the presence of second heteroatom N in the ring on the hydrogen bond interaction has also been evaluated. Atoms in molecules theory calculations were carried out to characterize the hydrogen bond through the changes in electron density and Laplacian of electron density. A natural energy decomposition analysis and natural bond orbital analysis is also performed to understand the nature of hydrogen bonding interaction in monohydrated five-membered heterocyclic adducts.     

Water monomer interaction with gold nanoclusters from van der Waals density functional theory

We investigate the interaction between water molecules and gold nanoclusters Au(n) through a systematic density functional theory study within both the generalized gradient approximation and the nonlocal van der Waals (vdW) density functional theory. Both planar (n = 6-12) and three-dimensional (3D) clusters (n = 17-20) are studied. We find that applying vdW density functional theory leads to an increase in the Au-Au bond length and a decrease in the cohesive energy for all clusters studied. We classify water adsorption on nanoclusters according to the corner, edge, and surface adsorption geometries. In both corner and edge adsorptions, water molecule approaches the cluster through the O atom. For planar clusters, surface adsorption occurs in a O-up/H-down geometry with water plane oriented nearly perpendicular to the cluster. For 3D clusters, water instead favors a near-flat surface adsorption geometry with the water O atom sitting nearly atop a surface Au atom, in agreement with previous study on bulk surfaces. Including vdW interaction increases the adsorption energy for the weak surface adsorption but reduces the adsorption energy for the strong corner adsorption due to increased water-cluster bond length. By analyzing the adsorption induced charge rearrangement through Bader's charge partitioning and electron density difference and the orbital interaction through the projected density of states, we conclude that the bonding between water and gold nanocluster is determined by an interplay between electrostatic interaction and covalent interaction involving both the water lone-pair and in-plane orbitals and the gold 5d and 6s orbitals. Including vdW interaction does not change qualitatively the physical picture but does change quantitatively the adsorption structure due to the fluxionality of gold nanoclusters.     

A density-functional theory study of water on clean and hydrogen preadsorbed Rh(111) surfaces

We study the water bilayer on clean and hydrogen preadsorbed Rh(111) surfaces by means of density-functional theory with the generalized gradient approximation and the van der Waals density functional, to investigate the influence of adsorbed hydrogen on the adsorption state of water. We found that adsorbed hydrogen interacts repulsively with water through its 1b(1) and 4a(1) orbitals. The repulsion dominates at high hydrogen coverage, resulting in a hydrophobic Rh(111)-H surface.     

Pd(111), Pd(100)及Pd(110)表面H2和O2直接合成H2O2的密度泛函理论研究

采用周期性密度泛函理论研究了H₂和O₂在Pd(111),Pd(100)及Pd(110)表面上直接合成H₂O₂的反应机理,对反应的主要基元步骤进行了计算和分析.结果表明,Pd(111)表面对H₂O₂直接合成的催化选择性最好,表面原子密度较低的Pd(100)表面和Pd(110)表面上含有O-O键的表面物种解离严重,不利于H₂O₂的生成.H₂O₂的选择性与含有O-O键表面物种的O-O键能和表面物种的结合能有关.含有O-O键的表面物种在表面的结合能越大,越容易发生解离,不利于形成H₂O₂.     

Hydration of mineral surfaces probed at the molecular level

By employing the nonlinear optical, interface selective experiment of sum frequency spectroscopy together with independent ab initio and density functional theory calculations, we determine the functional species of a corundum (001) surface: doubly coordinated OH groups which differ in their bond tilt angles. The interaction of the functional species with the adjacent water molecules is also observed. In a large pH range around the point of zero charge, the interaction is not controlled electrostatically but by hydrogen bonding. The functional species' tilt angles are crucial parameters, determining whether the species act as hydrogen bond donors or acceptors.     

An extended hybrid density functional (X3LYP) with improved descriptions of nonbond interactions and thermodynamic properties of molecular systems

We derive here the form for the exact exchange energy density for a density that decays with Gaussian-type behavior at long range. This functional is intermediate between the B88 and the PW91 exchange functionals. Using this modified functional to match the form expected for Gaussian densities, we propose the X3LYP extended functional. We find that X3LYP significantly outperforms Becke three parameter Lee-Yang-Parr (B3LYP) for describing van der Waals and hydrogen bond interactions, while performing slightly better than B3LYP for predicting heats of formation, ionization potentials, electron affinities, proton affinities, and total atomic energies as validated with the extended G2 set of atoms and molecules. Thus X3LYP greatly enlarges the field of applications for density functional theory. In particular the success of X3LYP in describing the water dimer (with R(e) and D(e) within the error bars of the most accurate determinations) makes it an excellent candidate for predicting accurate ligand-protein and ligand-DNA interactions.     

Reduced Pd density of states in Pd/SAM/Au junctions: the role of adsorbed hydrogen atoms

Experiments have shown that a Pd monolayer deposited electrochemically on a Au-supported self-assembled monolayer (SAM) of 4-mercaptopyridine (Mpy) exhibits a strongly reduced Pd local density of states (LDOS) at the Fermi energy (E(f)). Understanding the origin of this modified electronic structure is crucial for the use of the sandwich design as a platform for future nanoelectronics. Here we suggest that hydrogen adsorption might be the origin of the modified electronic properties. We performed periodic density functional theory calculation to explore the influence of hydrogen adsorption on the geometric and electronic structure of a Pd/Mpy/Au(111) complex. Dissociative adsorption of H(2) on a Pd monolayer on top of a Mpy SAM is a strongly exothermic process leading to atomic hydrogen atoms preferentially located at the hollow sites. Due to the formation of a strong Pd-H bond the Pd-SAM interaction realized via one-fold N-Pd bonds is substantially weakened. Upon hydrogen adsorption, the Pd LDOS becomes significantly modified exhibiting a drastic reduction of the density of states at E(f). The calculated spectra are in a good agreement with the experiment for a hydrogen coverage corresponding to two monolayers which is still thermodynamically allowed.     

Filled and empty states of carbon nanotubes in water: Dependence on nanotube diameter, wall thickness and dispersion interactions

We have carried out a series of molecular dynamics simulations of water containing a narrow carbon nanotube as a solute to investigate the filling and emptying of the nanotube and also the modifications of the density and hydrogen bond distributions of water inside and also in the vicinity of the outer surfaces of the nanotube. Our primary goal is to look at the effects of varying nanotube diameter, wall thickness and also solute-solvent interactions on the solvent structure in the confined region also near the outer surfaces of the solute. The thickness of the walls is varied by considering single and multi-walled nanotubes and the interaction potential is varied by tuning the attractive strength of the 12–6 pair interaction potential between a carbon atom of the nanotubes and a water molecule. The calculations are done for many different values of the tuning parameter ranging from fully Lennard-Jones to pure repulsive pair interactions. It is found that both the solvation characteristics and hydrogen bond distributions can depend rather strongly on the strength of the attractive part of the solute-water interaction potential. The thickness of the nanotube wall, however, is found to have only minor effects on the density profiles, hydrogen bond network and the wetting characteristics. This indicates that the long range electrostatic interactions between water molecules inside and on the outer side of the nanotube do not make any significant contribution to the overall solvation structure of these hydrophobic solutes. The solvation characteristics are primarily determined by the balance between the loss of energy due to hydrogen bond network disruption, cavity repulsion potential and offset of the same by attractive component of the solute-water interactions. Our studies with different system sizes show that the essential features of wetting and dewetting characteristics of narrow nanotubes for different diameter and interaction potentials are also present in relatively smaller systems consisting of about five hundred molecules. We dedicate this work to Professor Debashis Mukherjee on his 60th Birthday.     

Theoretical study of binding interactions and vibrational Raman spectra of water in hydrogen-bonded anionic complexes: (H2O)n- (n = 2 and 3), H2O...X- (X = F, Cl, Br, and I), and H2O...M- (M = Cu, Ag, and Au)

Binding interactions and Raman spectra of water in hydrogen-bonded anionic complexes have been studied by using the hybrid density functional theory method (B3LYP) and ab initio (MP2) method. In order to explore the influence of hydrogen bond interactions and the anionic effect on the Raman intensities of water, model complexes, such as the negatively charged water clusters ((H2O)n-, n = 2 and 3), the water...halide anions (H2O...X-, X = F, Cl, Br, and I), and the water-metal atom anionic complexes (H2O...M-, M = Cu, Ag, and Au), have been employed in the present calculations. These model complexes contained different types of hydrogen bonds, such as O-H...X-, O-H...M-, O-H...O, and O-H...e-. In particular, the last one is a dipole-bound electron involved in the anionic water clusters. Our results showed that there exists a large enhancement in the off-resonance Raman intensities of both the H-O-H bending mode and the hydrogen-bonded O-H stretching mode, and the enhancement factor is more significant for the former than for the latter. The reasons for these spectral properties can be attributed to the strong polarization effect of the proton acceptors (X-, M-, O, and e-) in these hydrogen-bonded complexes. We proposed that the strong Raman signal of the H-O-H bending mode may be used as a fingerprint to address the local microstructures of water molecules in the chemical and biological systems.     

One-dimensional molecular zippers

We synthesized an azobenzene derivative to demonstrate a one-dimensional molecular zipper. The formation and underlying mechanism of the molecular zipper formed by combined hydrogen-bonding and van der Waals interactions between adjacent molecules were investigated on a Au(111) surface using scanning tunneling microscopy and density functional theory calculations.     

Ru修饰前后Pd(111)面的性质及对糠醛吸附的比较研究

采用密度泛函理论研究了Pd(111)面和Ru-Pd(111)面的性质及对糠醛的吸附.原子尺寸因素、相对键长、形成能及d带中心等计算结果表明,Ru-Pd(111)面比Pd(111)面稳定且活性强,Ru的修饰优化了Pd(111)面的几何构型.糠醛在Pd(111)面及Ru-Pd(111)面的初始吸附位分别为P(top-bridge)位及P(Pd-fcc-Ru-fcc)位时,吸附能最大,吸附构型最稳定.由电荷布局和差分电荷密度可得,糠醛在Ru-Pd(111)面上电荷转移数更多,相互作用更强烈,因此吸附能更大.分析态密度可知,产生吸附的主要原因是位于-7.34 eV处至费米能级处的p,d轨道杂化.吸附于Ru-Pd(111)面后糠醛分子的p轨道向低能级偏移程度更明显,使Ru改性后的Pd催化剂具有更好的催化活性.     

An interaction model for OH + H2O-mixed and pure H2O overlayers adsorbed on Pt(111)

A model potential for the adsorbate-adsorbate interaction among OH and H2O molecules adsorbed on a Pt(111) surface has been developed solely based on first-principle calculations. By combining this directional-dependent model potential for the lateral interaction with a lattice model of Ising type, large length scale structure calculations can be made. The strength of different hydrogen bonds can be analyzed in detail from this model potential. It is found that the hydrogen bond between OH and H2O molecules is stronger than that between two H2O molecules (0.4 eV per pair as compared to 0.2 eV per pair, respectively). Via the computed chemical potential for water in mixed OH + H2O overlayers the water uptake as a function of oxygen precoverage on Pt(111) has been determined. The results compare very well with recent experiments.     

Analysis of the structures,energetics, and vibrational frequencies for the hydrogen-bonded interaction of nucleic acid bases with Carmustine pharmaceutical agent: a detailed computational approach

In the present study, it is attempted to scrutinize the hydrogen bonding interaction between Carmustine drug and DNA pyrimidine bases by means of density functional theory calculations regarding their geometries, binding energies, vibrational frequencies, and topological features of the electron density in the gas phase and the water solution. Based on the density functional theory results, it is found that the process of intermolecular interaction between Carmustine drug and nucleobases is exothermic and all of the optimized configurations are stable. Furthermore, the negative stability energy represented by a polarizable continuum model shows the significant increase in the solubility of the nucleobase after hydrogen bonding intermolecular interaction in the presence of water solvent. It is also found that the intermolecular hydrogen bonds between drug and the nucleobases play the significant role in the stability of the physisorption configurations. Hydrogen bond energies for hydrogen-bonded complexes are obtained from Espinosa method and the atoms-in-molecules theory are also applied to get a more precise insight into the nature of the intermolecular hydrogen bond interactions.     

MP2 study on adsorption of hydrated Na+ and Au+ cations on the Au(111) surface

The interactions of Na+ and Au+ cations with an Au(111) surface in the presence and absence of water molecules were investigated using Au18 and Au22 cluster models and the MP2 method with a triple-zeta valence basis set. The interactions between Na+ ions and the Au(111) surface were found to be primarily electrostatic, contrary to the much stronger Au+-Au(111) interactions that were dominated by orbital contributions. The largest CP-corrected MP2 adsorption energies were -156.9 kJ/mol for Na+ and -478.7 kJ/mol for Au+. When hydrated, Na+ prefers to be completely surrounded by water molecules rather than adsorbed to the surface, whereas Au+ remains adsorbed to the surface as water molecules bond with each other and with the Au surface. CP correction did not change the relative adsorption energy trends of Na+ or Au+ ions, but it had an effect on the interaction energy trends of the hydrated cations because of the weak water-surface and water-water interactions.