Energy density analysis of cluster size dependence of surface-molecule interactions (II): formate adsorption onto a Cu(111) surface

Adsorption of formate (HCOO) onto a Cu(111) surface has been treated theoretically using 18 kinds of Cu(n) (6 < or = n < or = 56) clusters. The energy density analysis (EDA) proposed by Nakai has been adopted to examine surface-molecule interactions for different cluster sizes. EDA results for the largest model cluster Cu(56) have shown that the adsorption-induced energy density variation in Cu atoms decays with distance from the adsorption site. Analysis of this decay, which can be carried out using the EDA technique, is important because it enables verification of the reliability of the model cluster used. In the case of formate adsorption onto the Cu(111) surface, it is found that at least a four-layer model cluster is necessary to treat the surface-molecule interaction with chemical accuracy.     

Improving the efficiency and convergence of geometry optimization with the polarizable continuum model: new energy gradients and molecular surface tessellation

New equations are derived and implemented for efficient and accurate computation of solvation energy derivatives for the conductor-like polarizable continuum model (C-PCM) and the isotropic integral equation formalism polarizable continuum model (IEF-PCM). Two new molecular surface tessellation procedures GEPOL-RT and GEPOL-AS that generate near continuous potential energy surfaces are proposed for PCM geometry optimization. The combined use of these new techniques leads to efficient and convergent geometry optimizations with the PCMs.     

The linear combination of localized orbitals methods (LCLO) for polymers

The application of the Linear Combination of Localized Orbitals (LCLO) method to the band structure of polyethylene in the T, TG, TGTG' and G conformations is reported. The method uses full ab initio results on molecules to construct Fock matrix elements and deduce the energy bands. The main advantages of the technique are the low cost and the simplicity. Results are compared with those obtained from published ab initio and empirical calculations.Chargé de Recherches of the Fonds National Belge de la Recherche Scientifique.Titulaire d'une bourse de spécialisation I.R.S.I.A.     

Coupled‐cluster reaction barriers of : An application of the coupled‐cluster//Kohn–Sham density functional theory model chemistry

In this work, we report a theoretical investigation concerning the use of the popular coupled‐cluster//Kohn‐Sham density functional theory (CC//KS‐DFT) model chemistry, here applied to study the entrance channel of the reaction, namely by comparing CC//KS‐DFT calculations with KS‐DFT, MRPT2//CASSCF, and CC//CASSCF results from our previous investigations. This was done by performing single point energy calculations employing several coupled cluster methods and using KS‐DFT geometries optimized with six different functionals, while conducting a detailed analysis of the barrier heights and topological features of the curves and surfaces here obtained. The quality of this model chemistry is critically discussed in the context of the title reaction and also in a wider context. © 2013 Wiley Periodicals, Inc.     

Global minimum geometries of acetylene clusters (HCCH)n with n ≤ 55 obtained by a heuristic method combined with geometrical perturbations

Geometry optimization of acetylene clusters (HCCH)_n in the range of n ≤ 55 was carried out with a recently proposed intermolecular potential consisting of Morse potentials, damped dispersion terms, and damped Coulomb terms. The heuristic method developed by the present author was used in the optimization: optimal geometries were searched by using geometry perturbations and subsequent local optimizations. The calculations were repeated until the global minimum was found for each cluster at least three times. The obtained results were analyzed to examine structural evolution of the clusters. The geometries of the clusters with n ≥ 25 were similar to the geometry in the cubic crystal of acetylene whereas smaller clusters take icosahedron‐based geometries. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Method for performing LCAO band structure calculations in crystalline solids: Application to rubidium

In this work we present a method for performing LCAO (linear combination of atomic orbitals) band structure calculations (tight binding) in crystalline solids. In the first part of the article we apply group theoretical methods to the establishment of a least‐squares scheme for the calculation of the matrix of the crystal potential: This scheme is based on a well‐defined choice of independent parameters for the Bloch vector‐dependent matrix elements and on the considerations of the symmetries between these independent parameters and their Fourier coefficients. In the second part of this work we deal with the representation of the matrices of the identity operator and of the operator of the kinetic energy by linear combinations in terms of two center integrals: We express these linear combinations by a closed formula, which can be easily programmed on a computer, and we mention a method by which the two center integrals can be evaluated numerically fast and accurately. Finally we apply our theory to the derivation of numerical results: We determine the electronic states and the high‐momentum components of Compton rates in the alkali metal rubidium and we compare the results obtained with those of augmented plane‐wave (APW) calculations. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 78: 212–225, 2000     

Poly(methyl methacrylate) composites with size‐selected silver nanoparticles fabricated using cluster beam technique

An embedment of metal nanoparticles of well‐defined sizes in thin polymer films is of significant interest for a number of practical applications, in particular, for preparing materials with tunable plasmonic properties. In this article, we present a fabrication route for metal–polymer composites based on cluster beam technique allowing the formation of monocrystalline size‐selected silver nanoparticles with a ±5–7% precision of diameter and controllable embedment into poly (methyl methacrylate). It is shown that the soft‐landed silver clusters preserve almost spherical shape with a slight tendency to flattening upon impact. By controlling the polymer hardness (from viscous to soft state) prior the cluster deposition and annealing conditions after the deposition the degree of immersion of the nanoparticles into polymer can be tuned, thus, making it possible to create composites with either particles partly or fully embedded into the film. Good size selection and rather homogeneous dispersion of nanoparticles in the thin polymer film lead to excellent plasmonic properties characterized by the narrow band and high quality factor of localized surface plasmon resonance. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 1152–1159     

Structure of Ag clusters Grown on Fs-Defect Sites of an MgO(1 0 0) surface

The structure of AgN clusters (N=1-4, 6, 8, 10), both in the gas phase and grown on the MgO(1 0 0) surface containing Fs-defects, has been investigated by a density functional basin-hopping (DF-BH) approach. In analogy with what observed in the case of gold clusters, it is found that the presence of the defect implies a double frustration and a cylindrical invariance of the metal-surface interaction, causing small Ag clusters growing around the Fs defect to be highly fluxional. Nevertheless, two different structural crossovers are found to be induced by the metal-defect interaction for the adsorbed clusters such that: 1) planar structures prevail for Nor=7), prevail for N=6 and N=8; 3) distorted face-centered cubic (fcc) structures grown pseudomorphically on the defected surface prevail for N=10. The transition from fivefold to fcc motifs is rationalized in terms of the double-frustration effect, which increases the bond strain of the noncrystalline structures. Detrapping energies from the defect were also calculated; the lowest energy pathway corresponds to the detachment of a dimer.     

Pd/Cu(111)双金属表面催化糠醛脱碳及加氢的反应机理

采用密度泛函理论(DFT)研究糠醛在最稳定Pd/Cu(111)双金属表面上的吸附构型和糠醛脱碳及加氢的反应机理。结果表明,当糠醛初始吸附于O_3-Pd-top、O_7-Cu-hcp位时,吸附构型最稳定,其吸附能为73.4 kJ/mol。糠醛在Pd/Cu(111)双金属表面上更易发生脱碳反应。对于糠醛脱碳反应,所需活化能较低,各个基元反应均为放热反应,糠醛更易先失去支链上的H形成(C_4H_3O)CO,然后中间体脱碳加氢得到呋喃,其中,C_4H_3O加氢生成呋喃所需活化能(72.6 kJ/mol)最高,是反应的控速步骤。对于加氢反应,糠醛与首个氢原子的反应需要最大的活化能(290.4 kJ/mol),是反应的限速步骤。     

Mechanisms for H2O decomposition on the Si(111)‐7 × 7 surface: A DFT cluster model study

The mechanisms for the complete decomposition of water molecules on the Si (111)‐7 × 7 surface were investigated theoretically. The reaction pathways for dissociation of four water molecules over the adatom and rest atom sites were calculated using the density functional theory (DFT) in conjunction with the B3LYP functional. The calculated results demonstrated that the initial O? H bond dissociation from the first H₂O to form the adsorbed OH species is more preferential on the adatom site (Si_a) than the rest atom site (Si_r) of Si (111)‐7 × 7. Four water molecules dissociate successively over the adatom site, backbonds of adatoms which are saturated by OH species can reasonably be the place of insertion of oxygen atoms, yielding a tetrahedral SiO₄ structure with one on top and three inserted oxygen atoms. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Theoretical prediction for the structures of gas phase lithium oxide clusters: (Li2O)n (n = 1–8)

We apply genetic algorithm combining directly with density functional method to search the potential energy surface of lithium‐oxide clusters (Li₂O)_n up to n = 8. In (Li₂O)_n (n = 1–8) clusters, the planar structures are found to be global minimum up to n = 2, and the global minimum structures are all three‐dimensional at n ≥ 3. At n ≥ 4, the tetrahedral unit (TU) is found in most of the stable structures. In the TU, the central Li is bonded with four O atoms in sp³ interactions, which leads to unusual charge transformation, and the probability of the central Li participating in the bonding is higher by adaptive natural density partitioning analysis, so the central Li is in particularly low positive charge. At large cluster size, distortion of structures is viewed, which breaks the symmetry and may make energy higher. The global minimum structures of (Li₂O)₂, (Li₂O)₆, and (Li₂O)₇ clusters are the most stable magic numbers, where the first one is planar and the later both have stable structural units of tetrahedral and C_4v. © 2012 Wiley Periodicals, Inc.     

Energy gradients in combined fragment molecular orbital and polarizable continuum model (FMO/PCM) calculation

The analytic energy gradients for the combined fragment molecular orbital and polarizable continuum model (FMO/PCM) method are derived and implemented. Applications of FMO/PCM geometry optimization to polyalanine show that the structures obtained with the FMO/PCM method are very close to those obtained with the corresponding full ab initio PCM methods. FMO/PCM (RHF/6‐31G* level) is used to optimize the solution structure of the 304‐atom Trp‐cage miniprotein and the result is in agreement with NMR experiments. The key factors determining the relative stability of the α‐helix, β‐turn and the extended form in solution are elucidated for polyalanine. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Unexpected reaction of the unsaturated cluster host and catalyst [Pd3(mu3-CO)(dppm)3]2+ with the hydroxide ion: spectroscopic and kinetic evidence of an inner-sphere mechanism

The title cluster, [Pd(3)(mu(3)-CO)(dppm)(3)](2+) (dppm=bis(diphenylphosphino)methane), reacts with one equivalent of hydroxide anions (OH(-)), from tetrabutylammonium hydroxide (Bu(4)NOH), to give the paramagnetic [Pd(3)(mu(3)-CO)(dppm)(3)](+) species. Reaction with another equivalent of OH(-) leads to the zero-valent compound [Pd(3)(mu(3)-CO)(dppm)(3)](0). From electron paramagnetic resonance analysis of the reaction medium using the spin-trap agent 5,5-dimethyl-1-pyrroline-N-oxide (DMPO), the 2-tetrahydrofuryl or methyl radicals, deriving from the tetrahydrofuran (THF) or dimethyl sulfoxide (DMSO) solvent, respectively, were detected. For both [Pd(3)(mu(3)-CO)(dppm)(3)](2+) and [Pd(3)(mu(3)-CO)(dppm)(3)](+), the mechanism involves, in a first equilibrated step, the formation of a hydroxide adduct, [Pd(3)(mu(3)-CO)(dppm)(3)(OH)]((n-1)+) (n=1, 2), which reacts irreversibly with the solvent. The kinetics were resolved by means of stopped-flow experiments and are consistent with the proposed mechanism. In the presence of an excess of Bu(4)NOH, an electrocatalytic process was observed with modest turnover numbers (7-8). The hydroxide adducts [Pd(3)(mu(3)-CO)(dppm)(3)(OH)]((n-1)+) (n=1, 2), which bear important similarities to the well-known corresponding halide adducts [Pd(3)(mu(3)-CO)(dppm)(3)(mu(3)-X)](n) (X=Cl, Br, I), have been studied by using density functional theory (DFT). Although the optimised geometry for the cluster in its +2 and 0 oxidation states (i.e., cation and anion clusters, respectively) is the anticipated mu(3)-OH form, the paramagnetic species, [Pd(3)(mu(3)-CO)(dppm)(3)(OH)](0), shows a mu(2)-OH form; this suggests an important difference in electronic structure between these three species.     

First principle and ReaxFF molecular dynamics investigations of formaldehyde dissociation on Fe(100) surface

Detailed formaldehyde adsorption and dissociation reactions on Fe(100) surface were studied using first principle calculations and molecular dynamics (MD) simulations, and results were compared with available experimental data. The study includes formaldehyde, formyl radical (HCO), and CO adsorption and dissociation energy calculations on the surface, adsorbate vibrational frequency calculations, density of states analysis of clean and adsorbed surfaces, complete potential energy diagram construction from formaldehyde to atomic carbon (C), hydrogen (H), and oxygen (O), simulation of formaldehyde adsorption and dissociation reaction on the surface using reactive force field, ReaxFF MD, and reaction rate calculations of adsorbates using transition state theory (TST). Formaldehyde and HCO were adsorbed most strongly at the hollow (fourfold) site. Adsorption energies ranged from ?22.9 to ?33.9 kcal/mol for formaldehyde, and from ?44.3 to ?66.3 kcal/mol for HCO, depending on adsorption sites and molecular direction. The dissociation energies were investigated for the dissociation paths: formaldehyde → HCO + H, HCO → H + CO, and CO → C + O, and the calculated energies were 11.0, 4.1, and 26.3 kcal/mol, respectively. ReaxFF MD simulation results were compared with experimental surface analysis using high resolution electron energy loss spectrometry (HREELS) and TST based reaction rates. ReaxFF simulation showed less reactivity than HREELS observation at 310 and 523 K. ReaxFF simulation showed more reactivity than the TST based rate for formaldehyde dissociation and less reactivity than TST based rate for HCO dissociation at 523 K. TST‐based rates are consistent with HREELS observation. © 2013 Wiley Periodicals, Inc.     

Reaction model for methane oxidation on reduced SnO2 (110) surface

A reaction model for methane oxidation on a reduced SnO₂ (110) crystal surface has been proposed theoretically using a point‐charge model. The geometric and electronic structures for all the molecules along the four reaction channels have been calculated by means of the MP2/6‐311++G(2d, p) level of theory. On the basis of the optimized geometries in the gas phase, the single‐point calculations of the energies on the point‐charge model are carried out. The results indicate that the energetically favorable reaction paths to yield methanol and formaldehyde on the reduced SnO₂ surface are via the reactant complex CH₃O H₂O and via the secondary production of methanol oxidation, respectively. It is also found that CH₃O⁻ is a stable anion on the surface due to having the high barriers of about 70 kcal/mol in both hydrogen abstraction with O⁻ and thermal decomposition, which is favorable to yield methanol and also is consistent with X‐ray photoelectron spectroscopy (XPS) experiments. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 74: 423–433, 1999     

On the ion‐pair dissociation mechanisms in the small NaCl·(H2O)6 cluster: A perspective from reaction path search calculations

We performed reaction path search calculations for the NaCl·(H₂O)₆ cluster using the global reaction route mapping (GRRM) code to understand the atomic‐level mechanisms of the NaCl → Na⁺ + Cl⁻ ionic dissociation induced by water solvents. Low‐lying minima, transition states connecting two local minima and corresponding intrinsic reaction coordinates on the potential energy surface are explored. We found that the Na Cl distances at the transitions states for the dissociation pathways were distributed in a relatively wide range of 2.7–3.7 Å and that the Na Cl distance at the transition state did not correlate with the commonly used solvation coordinates. This suggests that the definition of the transition states with specific structures as well as good reaction coordinate is very difficult for the ionic dissociation process even in a small water cluster. © 2018 Wiley Periodicals, Inc.     

Se和SeO2在O2/CaO (001)表面吸附反应的第一性原理研究

基于密度泛函理论的第一性原理和平板模型构造了最稳定的O₂/CaO（001）表面,通过优化Se和SeO₂在此表面可能的初始吸附结构得到最佳吸附构型,分析了Se原子在O₂/CaO（001）表面向SeO₂的转化。结果表明,Se原子在O₂/CaO（001）表面的稳定吸附构型主要有两种,即O-Se-O和O-O-Se基团,其中,O-O-Se基团的Se终端具有一定化学活性;Se在O₂/CaO（001）表面向SeO₂转化所需反应能垒小于均相条件下生成SeO₂所需反应能垒,表明CaO不仅作为吸附剂,也能促进Se向SeO₂的转化;SeO₂分子在O₂/CaO（001）表面发生化学吸附时,吸附基底的部分价电子转移至SeO₂分子轨道中。