Direct-space analysis of the Si–Si bonding pattern in the π-bonded chain reconstructed Si(111)(2 × 1) surface

Atomic and bond properties of silicon atoms in the buckled π-bonded chain reconstructed Si(111)(2 × 1) system were investigated by applying the quantum theory of atoms in molecules to a number of wavefunctions from periodic ab initio calculations using a slab model for the surface and geometries from experiment. Reconstruction involves much larger surface-cell charge distortions than in the unrelaxed surface and drastic changes in the atomic polarizations of the surface layer atoms. The effect of buckling is to largely differentiate the properties (charge, energy, volume, atomic polarizations) of the two unique atoms of each surface layer. The direction of electronic charge transfer in the topmost chain (from the “up” to the “down” atom) was found to be opposite to what was claimed previously. The π conjugation is not strictly localized along the topmost layer chains (where it is also largely incomplete), but rather it extends over a 2D array of bonds between the topmost and the lower surface layers. Received: 19 July 2000 / Accepted: 2 October 2000 / Published online: 23 January 2001     

噻吩在M(111)(M=Pd,Pt, Au)表面的吸附

采用密度泛函理论(DFT), 选取DMol³程序模块, 对噻吩在M(111) (M=Pd, Pt, Au)表面上的吸附行为进行了探讨. 通过对噻吩在不同底物金属上的吸附能、吸附构型、Mulliken 电荷布居、差分电荷密度以及态密度的分析发现, 噻吩在Pd(111)面上的吸附能最大, Pt(111)面次之, Au(111)面最小. 吸附后, 噻吩在Au(111)面上的构型几乎保持不变, 最终通过S端倾斜吸附于top 位; 噻吩在Pd(111)及Pt(111)面上发生了折叠与变形, 环中氢原子向上翘起, 最终通过环平面平行吸附于hollow 位. 此外, 噻吩环吸附后芳香性遭到了破坏, 环中碳原子发生sp³杂化, 同时电子逐渐由噻吩向M(111)面发生转移, M(111)面上的部分电子也反馈给了噻吩环中的空轨道, 这种协同作用最终导致了噻吩分子稳定吸附于M(111)面.     

Excitation energies, electron affinities and ionization potentials of the transition metals V, Cr and Mn

 Configuration interaction calculations were carried out for neutral ground and excited states and positively and negatively ionized states of the V, Cr and Mn atoms. Energy convergence with respect to systematic expansion of both the one-electron and configuration bases was investigated for valence correlation. Contributions from core electrons to the differential correlation energies and relativistic effects were evaluated separately. Assuming additivity of these contributions, excitation energies, electron affinities and ionization potentials of the atoms were obtained. All calculated values were in excellent agreement with the observed values within a deviation of 0.056 eV except for the electron affinity of the V atom, which had a calculated value 0.110 eV larger than the experimental value. Received: 9 August 2000 / Accepted: 26 October 2000 / Published online: 3 April 2001     

噻吩在M(111)(M=Pd,Pt,Au)表面的吸附(英文)

采用密度泛函理论(DFT),选取DMol3程序模块,对噻吩在M(111)(M=Pd,Pt,Au)表面上的吸附行为进行了探讨.通过对噻吩在不同底物金属上的吸附能、吸附构型、Mulliken电荷布居、差分电荷密度以及态密度的分析发现,噻吩在Pd(111)面上的吸附能最大,Pt(111)面次之,Au(111)面最小.吸附后,噻吩在Au(111)面上的构型几乎保持不变,最终通过S端倾斜吸附于top位;噻吩在Pd(111)及Pt(111)面上发生了折叠与变形,环中氢原子向上翘起,最终通过环平面平行吸附于hollow位.此外,噻吩环吸附后芳香性遭到了破坏,环中碳原子发生sp3杂化,同时电子逐渐由噻吩向M(111)面发生转移,M(111)面上的部分电子也反馈给了噻吩环中的空轨道,这种协同作用最终导致了噻吩分子稳定吸附于M(111)面.     

Electron affinities, excitation energies and ionization potentials of the transition metals (I) Sc and Ti

The electron affinities of the Sc and Ti atoms have been obtained by configuration interaction calculations. Energy convergence with respect to the systematic expansion of both the one-electron basis set and the configuration space was investigated for valence electrons, and the inclusion of correlation contributions from core electrons and relativistic effects gave the electron affinities of 0.181 eV and 0.163 eV for Sc and Ti, respectively. These are in excellent agreement with the observed values of 0.189 ± 0.020 eV and 0.080 eV. The same approach was applied for the first excited states and positive ions of both atoms. Excellent agreement with the experimental results was also obtained for these states. Received: 16 February 1998 / Accepted: 2 April 1998 / Published online: 23 June 1998     

Oxygen Atom Adsorption and Diffusion on Pd Low-index Surfaces and （311） Stepped Surface

Introduction Atom adsorption on transition metal surfaces has attracted special attention as a base for understanding the fundamental processes of oxidative catalysis. Particularly interesting is the adsorption and diffusion of oxygen on well-defined metal surfaces. An oxygen covered palladium surface, for example, plays a central role in several important reactions such as oxidation of carbon monoxide and ammonia. In particular, the (100), (111), (110) surfaces and the interactions with oxyge…     

Auxiliary basis sets for main row atoms and transition metals and their use to approximate Coulomb potentials

We present auxilliary basis sets for the atoms H to At – excluding the Lanthanides – optimized for an efficient treatment of molecular electronic Coulomb interactions. For atoms beyond Kr our approach is based on effective core potentials to describe core electrons. The approximate representation of the electron density in terms of the auxilliary basis has virtually no effect on computed structures and affects the energy by less than 10⁻⁴ a.u. per atom. Efficiency is demonstrated in applications for molecules with up to 300 atoms and 2500 basis functions. Received: 17 December 1996 / Accepted: 8 May 1997     

Contracted Gaussian-type basis functions revisited II. Atoms Na through Ar

We report five minimal-type contracted Gaussian-type function (CGTF) basis sets of the second-row atoms, Na – Ar, for molecular applications. Three of the present CGTF sets are revised versions of those given by Huzinaga and co-workers and the other two are newly developed for more accurate calculations. Practical utility and improved reliability of the present basis sets, augmented by polarization functions, are confirmed by test calculations on the P atom and P₂ molecule both at the self-consistent field (SCF) and configuration interaction (CI) levels. Received: 10 February 1997 / Accepted: 23 April 1997     

DFT studies of oxidation routes for Pd9 clusters supported on γ-alumina

This research is focused on the analysis of adsorbed bare and oxidized Pd(9) nanoparticles supported on γ-alumina. From first-principle density functional theory calculations, several configurations, charge transfer and electronic density of states have been analyzed in order to determine feasible paths for the oxidation process. Studies of Pd/PdO nanoparticles prove that they are stable at γ-alumina supports. It is shown that the Pd(9) nanoparticle favors dissociative adsorption of oxygen molecules. The most energetically preferable sites for adsorption are close to the contact between the cluster and the support, where one oxygen atom interacts with a 5-coordinated aluminium atom, and the remaining oxygen is in contact with the closest palladium atom. After first dissociation, one oxygen atom creates a bridge between the palladium atom and the 5-coordinated aluminium atom and the second oxygen atom moves to the top of the Pd(9) cluster, making a bridge between two palladium atoms. Subsequent dissociations arise analogously, with the difference that oxygen atoms in the second layer of the palladium cluster occupy hollow sides of the cluster. Investigation of the charge distribution in each oxidation step reveals that charge transfer increases towards the Pd/PdO nanoclusters. The electronic density of states indicates that gradual oxygen molecule adsorption and dissociation shift the highest states of the Pd/PdO nanoparticles in different ways. The overall investigation is found to be beneficial for studying methane oxidation.     

Tetrahydrofuran analogues with silicon and sulphur atoms

Quantum-mechanical calculations at the self-consistent-field–M?ller–Plesset level have been performed for various compounds obtained by substituting two or four CH₂ groups of the tetrahydrofuran molecule with SiH₂ groups, as well as the oxygen with a sulphur atom. Cyclic tetrasilane oxide, (SiH₂)₄O, and sulphide, (SiH₂)₄S, are suggested as possible alternatives to the carbon ring of natural sugars for the design of exobiological molecules because of certain similarities with tetrahydrofuran, (CH₂)₄O, especially the relatively small energy differences between different conformers and the subsequent ability to cross the energy barriers between them by puckering on the pseudorotation wheel. Received: 16 September 1999 / Accepted: 3 February 2000 / Published online: 21 June 2000     

Electronic excitation of sulfur-organic compounds – performance of time-dependent density functional theory

 To define the scope and limitations of the time-dependent density functional theory (TDDFT) method, spectral absorption data of a series of about 100 neutral or charged sulfur-organic compounds with up to 24 non-hydrogen atoms and up to four sulfur atoms were calculated in the near-UV, visible and IR regions. Although the theoretical vertical transition energies correspond only approximately to experimental absorption band maxima, the mean absolute deviation was calculated to be 0.21 eV (1600 cm⁻¹). The main absorption features of various compounds with monocoordinated or dicoordinated sulfur atoms are well reproduced. As far as possible TDDFT results were compared with those of semiempirical Zerner's intermediate neglect of differential overlap (ZINDO/S) and of Pariser–Parr–Pople (PPP) calculations. TDDFT also works well in cases where the semiempirical methods fail. Limitations of TDDFT were encountered with calculations of spectral absorptions of dye molecules. The “vinylene shift” of polymethine dyes is not reproduced by TDDFT. Whereas electronic excitation energies delocalized polar and betainic chromophores are reasonably well reproduced, excitation energies of charge-transfer-type and charge-resonance-type transitions of weakly interacting composite chromophores are significantly underestimated. Received: 30 October 2000 / Accepted: 29 November 2000 / Published online: 22 May 2001     

ab initio Calculation of the stereoelectronic structure of 1-(1-trichlorogermylethyl)-pyrrolidin-2-one*

RHF/6-31G(d) and MP2/6-31G(d) calculations were carried out to study the stereoelectronic structure of 1-(1-trichlorogermylethyl)pyrrolidin-2-one with a pentacoordinated germanium atom. These results were compared with the X-ray diffraction structural analysis data. Upon formation of the Ge ← O coordination bond in this molecule, the electron density of all the atoms of the coordination polyhedron of the germanium atom, including the oxygen atom, increases, especially the axial chlorine atom, while the electron density of the germanium, nitrogen, and carbonyl group carbon atoms decreases. Different polarization of all three valence p-orbitals of each Cl atom of this molecule was established. ³⁵Cl nuclear quadrupole resonance spectrum parameters were evaluated. The molecule also has stable form, in which the germanium atom is tetracoordinated. The total energy of this form is 2.7 kcal/mol higher than for the structure with a pentacoordinated germanium atom.     

Ab initio calculations with effective core potentials on trivalent lanthanide–terpyridine complexes

 The electronic structures of complexes of terpyridine (tpy) with trivalent lanthanides (Ln) were calculated using ab initio methods with effective core potentials at Hartree–Fock and post-Hartree–Fock levels of theory. The quasirelativistic large-core (with 4f electrons included in the core) pseudopotentials of the Stuttgart group were chosen for the Ln atoms. The variation of several properties of the Ln(tpy)³⁺ complexes was studied for the whole Ln series. It was shown that there was a monotonous variation for all properties (geometrical and energetic) along the Ln series, except for Mulliken charges on the metal atom. Calculations were performed on three complexes of known solid-state structure. The difference between experimental and calculated geometries is discussed; for all structures, it is found to be lower than 0.2 ?. In all cases, the relative order from one complex to another is conserved. Received: 13 September 1999 / Accepted: 3 February 2000 / Published online: 19 April 2000     

Recognizing a triple bond between main group atoms

The electron pair density, in conjunction with the theory of an atom in a molecule, enables one to unambiguously determine the nature of the bonding between the gallium atoms in bent [HGa-GaH]²⁻. The Ga-Ga bonding in the dianion at the experimental bond length is found to be the result of the sharing of two electron pairs at the Hartree-Fock level of theory, the level consistent with the Lewis model of the electron pair. Received: 27 July 2000 / Accepted: 4 October 2000 / Published online: 19 January 2001     

Gas-phase properties and Fukui indices of sulfine (CH2SO). Potential energy surface and maximum hardness principle for its protonation process. A density functional study

Gas-phase thermochemical properties of sulfine (CH₂SO) and the potential energy surface of its protonation process were studied by the density functional method employing different exchange-correlation potentials. All calculations showed that the most stable protonated isomer is planar with the proton bonded to the oxygen atom in a trans arrangement of the skeleton. Three transition states were located that allow interconversion between the different isomers. Hardnesses and Fukui indices were calculated to follow the reactivity trend along the protonation path and to explain the preference for a particular protonation site on neutral sulfine. Proton affinity, gas-phase basicity and heat of formation values, obtained for the first time fully quantum mechanically, agree well with those derived by a recent mass spectrometry experimental study. Good agreement between density functional theory and previous high-level theoretical and experimental data was also found for the heat of formation of sulfine and its most stable protonated form. Received: 12 October 1998 / Accepted: 24 November 1998 / Published online: 16 March 1999     

How accurate can molecular dynamics/linear response and Poisson–Boltzmann/solvent accessible surface calculations be for predicting relative binding affinities? Acetylcholinesterase huprine inhibitors as a test case

This study examines the accuracy of molecular dynamics-linear response (MD/LR) and Poisson–Boltzmann/solvent accessible surface (PB/SAS) calculations to predict relative binding affinities. A series of acetylcholinesterase (AChE) huprine inhibitors has been chosen as a test system owing to the availability of free-energy (thermodynamic integration) calculations. The results obtained with the MD/LR approach point out a clear relationship between the experimental affinity and the electrostatic interaction energy alone for a subset of huprines, but the suitability of the MD/LR approach to predict the binding affinity of the whole series of compounds is limited. On the other hand, PB/SAS calculations show a marked dependence on both the computational protocol and the nature of the inhibitor–enzyme complex. Received: 2 August 2000 / Accepted: 8 September 2000 / Published online: 21 December 2000     

The three-center-four-electron (3c-4e) bond nature revisited. An atoms-in-molecules theory (AIM) and ELF study

Theoretical calculations (B3LYP/6–311+ +G**) were performed on a series of formally hypervalent compounds showing linear three-center geometries. The bonding nature was analyzed by the electron density, ρ(r), and electron-localization function (ELF) topologies, including calculations of the AIM charges and NMR chemical shifts (GIAO method). In addition, a quantitative analysis was also performed of the localization and delocalization indexes, obtained from the electron-pair density in conjunction with the definition of an atom in a molecule. Furthermore, the populations and fluctuations in the ELF basins were also evaluated. The compounds studied presented linear (1–5), T-shaped (6–9), and bipyramidal structures (10–15). Our results support the 3c-4e model for the linear (1–5) structures, but reveal for the T-shaped (6–9) structures only a small contribution from this model. In addition, there is no evidence to support the 3c-4e bond scheme for the bipyramidal compounds (10–15). Received: 1 June 2000 / Accepted: 4 October 2000 / Published online: 19 January 2001     

Some fundamental problems with zero flux partitioning of electron densities

A number of fundamental problems with the topological analysis of molecular electron densities using the atoms in molecules (AIM) theory developed by Bader and coworkers are highlighted. In particular, contrary to statements made in the literature, we show that the local zero flux condition used in the AIM theory to define an atom in a molecule does not follow from the Schwinger variation principle, nor does it define unambiguously the atomic domains. Serious limitations of the definition of an atom in AIM theory also arise due to vibrational effects. A general definition of the structure of a molecular isomer based on a generalisation of the Born-Oppenheimer potential energy surface allow these limitations to be overcome. Received: 9 March 2000 / Accepted: 13 August 2000 / Published online: 21 December 2000     

Domain-averaged Fermi holes – a new means of visualization of chemical bonds. Bonding in hypervalent molecules

The nature of bonding in several hypervalent molecules was analyzed at the ab initio SCF level using the recently proposed methodology based on the analysis of domain-averaged Fermi holes. The results of the analysis demonstrate that, for sufficiently flexible basis sets, the expansion of the valence shell does indeed take place for second row central atoms in PF₅, SF₄, and SF₆. On the other hand, no such expansion was observed for the first row N atom in NF₅. Received: 1 June 2000 / Accepted: 11 October 2000 / Published online: 23 January 2001     

Hydrogenation of acetylene–ethylene mixtures on Pd catalysts: study of the surface mechanism by computational approaches. Metal dispersion and catalytic activity

The hydrogenation mechanism of acetylene–ethylene mixtures on Pd catalysts under different experimental conditions was studied by employing a time-dependent Monte Carlo approach set to use a fixed series of event probabilities. The dependence of the catalyst activity and selectivity on the sizes of the metal particles was simulated at microscopic level and the results, also refined by fitting procedures, suggested proper explanations for the apparent nonuniformity of the related experimental findings. The use of the steric hindrance parameter of the surface species and the available surface energy on the metallic catalyst sites was decisive for reproducing the experimental results. Received: 16 September 1999 / Accepted: 3 February 2000 / Published online: 2 May 2000