Bayesian error estimation in density-functional theory

We present a practical scheme for performing error estimates for density-functional theory calculations. The approach, which is based on ideas from Bayesian statistics, involves creating an ensemble of exchange-correlation functionals by comparing with an experimental database of binding energies for molecules and solids. Fluctuations within the ensemble can then be used to estimate errors relative to experiment on calculated quantities such as binding energies, bond lengths, and vibrational frequencies. It is demonstrated that the error bars on energy differences may vary by orders of magnitude for different systems in good agreement with existing experience.     

Density functional study of the molecular structures,infrared and Raman spectra of carbon suboxide,its sulfur and selenium analogues

Carbon suboxide, and its sulfur and selenium analogues in D _∞h symmetry have been studied in the gas phase by a density functional method using B3LYP as the functional. The basis sets employed are 6-31++G(d,p), 6-311++G(d,p), cc-pVDZ and all calculations have been carried out using Gaussian 03W. Molecular parameters, namely bond lengths, rotational constants, quadrupole moments, and infrared and Raman frequencies are predicted for these molecules. Atomization energies have also been predicted. The calculated molecular parameters and vibrational spectra of the parent molecule, namely carbon suboxide, are in good agreement with literature data. Therefore, data from the present theoretical gas phase study are expected to be valid for the molecular structures and vibrational spectra of carbon subsulfide and carbon subselenide. The results from this study could be used as a reference for these molecules.     

The Influence of Hydrogen Adsorption on Magnetic Properties of Ni/Cu(001) Surface

Ni/Cu(001) is known as a unique system showing the spin-reorientation transition from an in-plane to out-of-plane magnetization direction when the Ni-overlayer thickness is increased. We investigate different relaxed multilayer structures with a hydrogen adlayer using the full-potential linearized augmented plane-wave method. The relaxed geometries, determined by total energy and atomic force calculations, show that H-monolayer strongly influences the interlayer distance between the Ni-surface and sub-surface layers yielding the outward relaxation of Ni-layer at H/Ni interface. Furthermore, large decrease of local magnetic moments at the top surface area is found for the surface covered by H. The magneto-crystalline anisotropy energies are calculated for fully relaxed H/Ni-films. The spin-reorientation transition critical thickness of 4 ML is found in good quantitative agreement with the experiment.     

The interaction of ultrathin films of Ni and Pd with W(110): an XPS study

The interaction of ultrathin films of Ni and Pd with W(110) has been examined using X-ray photoelectron spectroscopy (XPS) and the effects of annealing temperature and adsorbate coverage (film thickness) are investigated. The XPS data show that the atoms in a monolayer of Pd or Ni supported on W(110) are electronically perturbed with respect to the surface atoms of Pd(100) and Ni(100). The magnitude of the electronic perturbations is larger for Pd than for Ni adatoms. Our results indicate that the difference in Pd(3d_5/2) XPS binding energies between a pseudomorphic monolayer of Pd on W(110) and the surface atoms of Pd(100) correlates with the variations observed for the desorption temperature of CO (i.e., the strength of the Pd---CO bond) on these surfaces. A similar correlation is seen for the Ni(2p_3/2) XPS binding energies of Ni/W(110) and Ni(100) and the CO desorption temperatures from the surfaces. The shifts in XPS binding energies and CO desorption temperatures can be explained in terms of: (1) variations that occur in the Ni---Ni and Pd---Pd interactions when Ni and Pd adopt the lattice parameters of W(110) in a pseudomorphic adlayer; and (2) transfer of electron density from the metal overlayer to the W(110) substrate upon adsorption. Measurements of the Pd(3d_5/2) XP binding energy of Pd/W(110) as a function of film thickness indicate that the Pd---W interaction affects the electronic properties of several layers of Pd atoms.     

H_2在Ni,Pd与Cu表面的解离吸附

用EAM方法(embeded-atommethod)研究H_2在Ni,Pd与Cu的(100),(110)与(111)面上的解离吸附.首先通过拟合单个H原子在Ni,Pd与Cu不同表面上的吸附能和吸附键长,得到H与这些金属表面相互作用的EAM势,然后计算H_2在这些表面上以不同方式进行解离吸附时的活化势垒E_a,吸附热q_(ad)与吸附键长R.并给出H_2在(110)面上解离吸附的势能曲线.计算结果表明H_2的解离吸附与衬底种类、衬底表面取向及解离方式有关.H_2在Ni表面上解离时活化势垒很低,而在Cu表面解 关键词：     

The role of HH interactions in the formation of ordered structures on Ni and Pd single crystals

The interaction between H adatoms on a surface is calculated within the embedded cluster model of chemisorption. The model is first applied to the case of two H atoms on a free electron surface. The interaction energy is found to be an oscillatory function of the H-H separation R_ab. Application of the free electron model to the problem of chemisorption on transition metal surfaces leads to unphysical results with the prediction of formation of ordered H overlayers which are not observed in LEED experiments. We next include the l = 2 TM muffin tins. Results for H adsorption on the low index faces of Ni and Pd substrates are presented. Graphitic structures are predicted for the (111) faces of both Ni and Pd with the H atoms occupying both types of three-fold hollow sites on the surface. This agrees with the results of LEED experiments for H/Ni(111). Comparison with experiment is not possible in the case of H/Pd(111) owing to the lack of low temperature studies for that system. Zig-zag chains with the H atoms adsorbed in sites of three-fold coordination on alternate sides of the TM(110) rows are predicted for both Ni and Pd. This is in agreement with the results of He diffraction experiments for H/Ni(110). No structure determination has been done for H/Pd(110). Adsorption in the four-fold centre sites for H on the (100) faces of Ni and Pd is found to be unfavourable. The H atoms are expected to adsorb in sites of three-fold symmetry below the (100) surface for H on Pd with formation of a c(2 × 2) structure in agreement with the LEED observations. For H/Ni(100) the H atoms are believed to adsorb above the surface, away from the centre site and to bond to two surface Ni atoms. No short-range ordered structures are predicted in this case.     

Theory of molecule-surface scattering at thermal and hyperthermal energies

A theoretical model of molecule-surface scattering is developed which includes energy and momentum transfers between the surface and projectile for both translational and rotational motions and internal mode excitation for the projectile molecule. The translation and rotation motions are treated in the classical limit, while a quantum treatment for internal vibrational mode excitation is used. The results of calculations are compared with recent high-precision measurements of the scattering of a beam of C(2)H(2) molecules from a clean, ordered LiF(001) surface at energies of up to nearly 1 eV. The calculated results for angular distributions and rotational excitations are in good agreement with experiment.     

组氨酸电离能与红外光谱的密度泛涵理论计算研究

采用混合密度泛涵理论中的B3LYP方法,结合4种基组6-31G(d),6-31G(df, p),6-31+G(d)和6-311+G(2d, 2p),系统计算了光合反应中心叶绿素的配位体-组氨酸在空气、四碌化碳、四氢呋喃、水和蛋白质模拟环境中的几何结构、电离能、红外光谱及同位素标记谱。计算及分析结果表明：组氨酸分子的几何参数在不同计算基组和介质中略有不同,且C₂—N₃,N₃—C₄的键长在空气中最大;同一介质中,增大计算基组和采用扩散函数,均使计算的单点势能和振动频率降低,电离能增加,对应光谱强度增高;而同一计算方法下,介质的电介常数越高,分子的单点势能越低,电离能越小,对应的振动频率减小强度增加;另外,电离能和主要特征峰位及其15N和13C标记谱的计算结果与文献中的实验结果相吻合。所有计算均显示,高基组和施加扩散函数的计算结果与实验更接近。该研究为深入探索叶绿素与组氨酸配位后在光合反应中心的功能与振动光谱特性提供理论参考依据。     

Molecular cluster calculations for the interpretation of CO chemisorption on a Ni(100) surface

Self-consistent Hartree-Fock-Slater molecular cluster calculations for the chemisorption of carbon monoxide on a Ni(100) surface are presented. In earlier calculations of this type the CO molecule has been assumed to be chemisorbed in a hollow position of C_4v symmetry. A recent EELS experiment shows however that in the most stable configuration CO is linearly bonded to the Ni atoms, i.e. a top position of the CO-molecule. This experiment indicates also that there exists an additional bridge bonding of the CO molecule to the two nearest neighbour Ni atoms. The variation of the energy levels, binding energies and charge distribution with the height of the CO molecule above the nickel surface is calculated for the top position using the NiCO and Ni₅CO clusters and for the bridge bonding configuration using the Ni₂CO cluster. The CO 1π level is found to be split by about 0.8 eV in bridge bonding geometry. For both hollow and top positions the 1π and 5σ levels are separated by about 0.5 eV. The energy separation to the 4σ level is about 3 eV, which is in good agreement with experimental data. Theoretical ionization energies relative to the Fermi energy for top position geometry at a bond distance of 3.5 au between the carbon atom and nickel surface were found to be 25.7, 11.7, 8.7 and 8.2 eV for the 3σ, 4σ, 5σ and 1π levels which should be compared with the experimental data of 29.0, 10.8, 8.4 and 7.8 eV, respectively. The corresponding ionization energies for a bond angle of 99° in bridge bonding were 23.7, 12.1, 7.3, 7.0 and 7.9 eV. The two last values represent the 1π level which is split into two levels in this geometry. The variation of the C-O stretch vibrational frequencies with the height of the CO molecule above the surface for the top-position geometry is estimated from the 5σ and 2π gross orbital populations and from the CO σ and π overlap populations.     

Ultrasoft pseudopotentials and projector augmented-wave data sets: application to diatomic molecules

We test several ultrasoft pseudopotentials (US-PPs) and projector augmented-wave (PAW) data sets, calculating the bond lengths, the atomization energies and the frequencies of the vibrational stretch modes of various diatomic molecules. The US-PPs and the PAW data sets are constructed with the same recipe and using the local density approximation or the Perdew, Burke and Ernzerhof generalized gradient approximation for the exchange and correlation energies. We study the dimers H(2), N(2), O(2), F(2), Al(2), Si(2), P(2), S(2) and Cl(2) and several monohydrides, carbides, nitrides and oxides of boron, carbon, nitrogen, oxygen, fluorine, aluminum, silicon, phosphorus, sulfur, chlorine, iron and nickel. We find that US-PPs and PAW data sets constructed with the same parameters provide almost equivalent results for the bond lengths and the vibrational stretch frequencies while, for some molecules, the PAW method is superior to the US-PP method for the calculation of the atomization energies. Our geometries and vibrational frequencies are compared with the results present in the literature and obtained by localized basis sets. It is found that the agreement is very good, with discrepancies comparable to those due to the use of different localized basis sets.     

Rh超薄膜在Mo(111)及W(111)上引起{110}小面再构的可能性

用第一性原理总能计算方法,计算了Mo和W表面吸附金属Rh薄膜前后[111],[110]方向的表面能.计算结果表明,清洁Mo和W的（111）面不会发生{111}小面再构,与实验观察一致,当Rh的覆盖厚度达到一物理单层后,Rh/Mo（111）仍不会形成{110}小面;面Rh/W（111）满足小面再构到{110}的热力学条件,在一定条件下可能形成{110}小面. 关键词：     

Hydrogen vibrations at transition metal surfaces

Chemisorbed hydrogen has been studied on a variety of simple and composite transition metal surfaces using local density functional calculations. The goal of these studies is to elucidate trends and general principles in bond energies, atomic geometries, vibrational frequencies, and dynamic effective charges. The theoretical approach, based on the linear augmented plane wave method, will be reviewed. Results will be discussed for H in 2-, 3-, and 4-fold sites on W(001), Ru(0001), Cu(111), Pt(111), Rh(001), and the metal overlayer systems Cu-Ru(0001) and Ni-W(001). In most cases, all the harmonic vibrational modes were studied. Some anharmonic effects were examined. While good agreement has been obtained with much of the available experimental data, some outstanding disagreements will be discussed. Our results will be compared with the nearest-neighbor harmonic potential model and effective medium approach.     

Ab initio chemisorption studies of H on Fe(110)

Ab initio configuration interaction calculations are performed to study the chemisorption of atomic H on a Fe(110) surface. The lattice is modeled as an embedded three-layer, 40-atom cluster with the Fe atoms fixed at the bulk position. Fe 3d orbitals are explicitly included on five Fe atoms on the surface. Hydrogen strongly binds to the Fe(110) surface at the long-bridge, short-bridge, and quasi three-fold sites. The calculated adsorption energies are 2.76, 2.73, and 2.71 eV, respectively. H-surface bonding at the on-top Fe site is more than 0.4 eV weaker. The calculated H-surface distances are 0.89, 1.03, and 0.87 Å for H at the long-bridge, short-bridge, and quasi three-fold sites, respectively, which agrees well with the LEED value of 0.9 ± 0.1 Å. The H-surface stretching vibrational frequencies are calculated to be 1070, 1066, and 1073 cm⁻¹, at the long-bridge, short-bridge, and quasi three-fold sites, respectively. The work function of Fe(110) decreases on H adsorption. The present calculations indicate that H diffusion into the bulk through the short-bridge site will have a much higher activation barrier than via the long-bridge and quasi three-fold sites.     

A calculation of surface diffusion coefficients of adsorbates on the (110) plane of tungsten

An attempt to calculate the prefactors of the diffusion coefficients of tungsten, xenon and oxygen atoms on the W(110) plane in the zero-coverage limit was made, using a Fokker-Planck formalism. Pairwise substrate-substrate and adsorbate-substrate atom interactions were assumed and expressed by appropriate Morse potentials. The vibrations of the substrate were approximated by an Einstein model of independent oscillators. When Morse potentials were so adjusted as to give good agreement between experimental and calculated activation energies, a prefactor in excellent agreement with experiment was calculated for W/W(110). For Xe/W(110) and O/W(110) the calculated values were ～10^?4 cm²/s, i.e. essentially “normal”, while the experimental values are much lower. Possible reasons for the discrepancies are discussed.     

Chemisorption bonding and bond lengths on transition metal surfaces: Effect of coordination and valency saturation

A smooth correlation between the determined chemisorption bond lengths, for O, S, Se and Te on Ni (001) and for sulphur on Ni (110) and Ni (111) as well, and Pauling's resonating bond ionicity is demonstrated, when the latter are calculated with due regard for the coordination and valency saturation effects. Pauling's bond length-bond number relation is used to provide (i) an independent estimate of the Ni-O bond length on Ni (001), which is found capable of discriminating among the reported values, and (ii) estimates of the bond lengths for O, S, Se and Te on Ni (111) and Ni (110) by using the determined bond lengths on Ni (001). Agreement with the determined values for sulphur is surprisingly good.     

乙烯在Ni（110）表面吸附的几何结构

用理论计算的方法研究了不同覆盖度的乙烯在Ni（110）表面吸附的位置.乙烯的吸附几何结构在团簇计算中进行了局部优化.在低覆盖度下，单个乙烯分子占据了短桥位和顶位之间的中间位置.乙烯分子的C—C轴大致沿衬底的Ni原子链排列（即沿<110>晶向），C—C轴与衬底Ni（110）表面有10°的倾斜角.乙烯分子的C—C键的键长为0151nm.在高覆盖度下(05ML)，乙烯在Ni (110)上形成了有序的c（2×4）相，在一个表面元胞内的两个乙烯分子的吸附位置类似于低覆盖度时的结果，但乙烯分子的C—C 键键长分别为0142和0143nm.     

Helium scattering from metal surfaces: potential determination and crystallography

We describe a method for determining the interaction potential between a helium atom and a metal surface from diffraction data. Results are presented for He/Ni(110) and He/Cu(110). For He/Cu(110) the potential 3s in good agreement with a first principles calculation but this is not true for He/Ni(110). We also show that a surface relaxation of 10% produces measurable changes in intensities.     

Adsorption of SH and OH and coadsorption of S, O and H on Ni(111)

The adsorption of SH and OH radicals on Ni(111) is treated using an ab initio embedding theory. The Ni(111) surface is modeled as a three-layer, 28-atom cluster with the Ni atoms fixed at bulk lattice sites. The Ni(111) energy surface is very flat for SH adsorption if the H tilt angle is allowed to vary. At both atop and bridge sites, the S---H axis is tilted away from the surface normal by 70°, resulting in the sulfur atom being sp³-hybridized and the adsorption energy being 59 kcal mol⁻¹. For SH at the three-fold site, the S---H axis is normal to the surface, the sulfur is sp-hybridized, and the adsorption energy is 58 kcal mol⁻¹. OH is preferentially adsorbed at the three-fold site. The calculated adsorption energy is 90 kcal mol⁻¹ and the O---H axis is perpendicular to the surface. OH adsorption at the atop and bridge sites is 16 and 5 kcal mol⁻¹ less stable than at the three-fold site, respectively. Atomic H, O and S are preferentially adsorbed at the three-fold site. The calculated adsorption energies are 62, 92 and 87 kcal mol⁻¹, for H, O and S, respectively. The calculated adsorbate---Ni bond distances of 1.86 Å for H, 1.86 Å for O and 2.29 Å for S are in good agreement with experimental data. SH and OH bonding to the surface involves a combination of ionic and covalent contributions and substantial mixing with the Ni 3d orbitals. Dipole-moment calculations indicate strong ionic bonding for the atomic O/Ni system and ionic plus covalent character for the atomic S/Ni interactions. Adsorption of S and O at the three-fold site blocks H adsorption at the nearby surface. Moving H away from the S or O adatom reduces the repulsion. The dissociation of SH_ad → S_ad + H_ad is calculated to be exothermic by 5 kcal mol⁻¹ and OH_ad → O_ad + H_ad to be endothermic by 30 kcal mol⁻¹ for infinite separation between S, O and H.     

Ni(111)表面一氧化碳和氢共吸附的密度泛函理论研究

本文用密度泛函理论(DFT)的总能计算研究了一氧化碳和氢原子在Ni(111)表面上p(2×2)共吸附系统的原子结构和电子态，结果表明CO和H原子分别被吸附于两个对角p(1×1)元胞的hcp和fcc位置.以氢分子和CO分子作为能量参考点，总吸附能为2.81 eV，相应的共吸附表面功函数φ为6.28 eV.计算得到的C—O，C—Ni和H—Ni的键长分别是1.19?, 1.96?和 1.71?，并且CO分子以C原子处于hcp的谷位与金属衬底原子结合.衬底Ni(111)的最外两层的晶面间距在吸附后的相对变化分别是 关键词： Fisher-Tropsch反应 催化作用 Ni(111) p(2×2)/(CO+H) 共吸附     

First-principles investigation on diffusion behaviours of H isotopes: From W(110) surface into bulk and in bulk W

The diffusion behaviours of hydrogen (H), deuterium (D), and tritium (T) from W(110) surface into bulk and in bulk W are investigated using a first-principles calculations combined with simplified models. The diffusion energy barrier is shown to be 1.87 eV from W(110) surface to the subsurface, along with a much reduced barrier of 0.06 eV for the reverse diffusion process. After H enters into the bulk, its diffusion energy barrier with quantum correction is 0.19 eV. In terms of the diffusion theory presented by Wert and Zener, the diffusion pre-exponential factor of H is calculated to be 1.57×10^-7 m²·s^-1, and it is quantitatively in agreement with experimental value of 4.1×10^-7 m²·s^-1. Subsequently, according to mass dependence (√1/m ) of H isotope effect, the diffusion pre-exponential factors of D and T are estimated to be 1.11×10^-7 m²·s^-1 and 0.91×10^-7 m²·s^-1, respectively.