Electrostatic potentials and fields from density expansions of deformed atoms in molecules

The exact representation of the molecular density by means of atomic expansions, consisting in spherical harmonics times analytical radial factors, is employed for the calculation of electrostatic potentials, fields, and forces. The resulting procedure is equivalent to an atomic multipolar expansion in the long-range regions, but works with similar efficiency and accuracy in the short-range region, where multipolar expansions are not valid. The performances of this procedure are tested on the calculation of the electrostatic potential contour maps and electrostatic field flux lines of water and nitrobenzene, computed from high-quality molecular electron densities obtained with Slater basis sets.     

离子膜电槽电流密度的研究及应用

前言氯碱是基础化工原料,至今需用烧碱与氯的产品已达数千种,在国民经济中占有颇为重要的地位。近年来,我国氯碱工业发展十分迅猛,原有氯碱企业纷纷扩大生产能力,同时新的企业也相继诞生,烧碱产能快速提升,已从1998年的745万t/a增加到2005年的1470万t/a,从而使我国在烧碱产能上     

CO Oxidation Promoted by the Gold Dimer in Au2VO3− and Au2VO4− Clusters

Investigations on the reactivity of atomic clusters have led to the identification of the elementary steps involved in catalytic CO oxidation, a prototypical reaction in heterogeneous catalysis. The atomic oxygen species O^.? and O^2? bonded to early‐transition‐metal oxide clusters have been shown to oxidize CO. This study reports that when an Au₂ dimer is incorporated within the cluster, the molecular oxygen species O₂^2? bonded to vanadium can be activated to oxidize CO under thermal collision conditions. The gold dimer was doped into Au₂VO₄^? cluster ions which then reacted with CO in an ion‐trap reactor to produce Au₂VO₃^? and then Au₂VO₂^?. The dynamic nature of gold in terms of electron storage and release promotes CO oxidation and O? O bond reduction. The oxidation of CO by atomic clusters in this study parallels similar behavior reported for the oxidation of CO by supported gold catalysts.     

激光光解NO2产物——氧原子O(3PJ″)的REMPI离子谱

由Nd:YAG激光器三倍频, 输出波长为λ=355 nm（28 169 cm－1）的激光光解NO2分子产生的氧原子, 通过共振增强多光子电离（REMPI, resonance enhanced multiphoto ionization）及飞行时间（TOF, time of flight）质谱技术, 获得了自旋-轨道精细能级分辨的氧原子O(2p 3PJ″=2, 1, 0)离子谱.氧离子信号强度与UV电离激光能量（λ≈226 nm）之间的关系能用三次方曲线很好拟合, 它表明光解产物氧原子是通过（2＋1）多光子吸收过程而被电离的.由离子信号得到的氧原子基态三个自旋-轨道支能级布居比f1=I(3P1)/I(3P2)与f0=I(3P0)/I(3P2)分别为0.54±0.09和0.20±0.04, 并且在不同的光解激光能量下其布居比保持不变.这一比值与统计分布计算的值为0.6和0.2一致（即统计分布3P2∶3P1∶3P0=1:0.6:0.2）.这是由于样品(NO2)在较低的压力下（1.33×10－4 Pa）和极短的光解-电离时间范围内（10－8 s）, 产物O（3PJ″）支能级间几乎不可能发生碰撞能量转移, 因此, 氧原子三个自旋-轨道角动量分裂能级布居O（3PJ″=2, 1, 0）是统计分布的.     

Atomic transferability within the exchange‐correlation density

Starting from either the exchange or the exchange‐correlation density together with Bader's definition of an atom in a molecule, an atomic hole density function can be defined. Contour maps of atomic hole density functions are able to show how the electron density of each atom in a molecule is partially delocalized into the rest of atoms in the molecule. The degree of delocalization of the atomic density ultimately depends on the nature of the atom studied and its environment. Atomic hole density functions are also used to define an atomic similarity measure, which allows for the quantitative assessment of the degree of atomic transferability in different molecular environments. In this article, contour maps for the N atom in the (N₂, CN⁻, NO⁺) series and the O atom in the (CO, H₂CO, and HCOOH) series are presented at the Hartree–Fock and CISD levels of theory. Moreover, the transferability of N and O within the two series is studied by means of atomic similarity measures. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1361–1374, 2000     

镧系水合离子的密度泛函理论研究

用密度泛函理论(DFT)方法研究了镧系水合离子[Ln(H2O9)]^3+(Ln=Ce,Pr,Nd,Pm,Ho,Er,Tm,Yb)的几何构型、电荷分布和Ln^3+与水的结合能,计算结果与实验基本符合,表明DFT方法也适用于计算镧系离子与中性配体形成的化合物,对计算结果的分析表明,Ln^3+与H2O之间主要通过Ln5d轨道与氧孤对电子相互作用成键而结合,其余轨道起的作用比较小,用镧系化合物成键模型解释了镧系离子与水的结合能从La到Lu逐渐增加的事实。     

A note on atomic density

In atomic systems, electron density has a simple finite expansion in spherical harmonics times radial factors. The difficulties in the calculation of some radial factors are illustrated in the low‐lying states of the carbon atom. Single‐particle methods such as Hartree–Fock and approximate density functional theory cannot ensure the correct expansion of the density in spherical harmonics. Wave‐function methods are appropriate but, as some expansion terms are entirely due to correlation, these methods only will give correct results for high‐quality variational functions. Using full‐configuration integration (CI), all the terms predicted by the theory appear and are not negligible but the convergence of the term due to correlation toward its correct value is uncertain even for very large CI spaces. © 2012 Wiley Periodicals, Inc.     

Efficient gaussian density formulation of volume and surface areas of macromolecules on graphical processing units

We present an algorithm to efficiently compute accurate volumes and surface areas of macromolecules on graphical processing unit (GPU) devices using an analytic model which represents atomic volumes by continuous Gaussian densities. The volume of the molecule is expressed by means of the inclusion–exclusion formula, which is based on the summation of overlap integrals among multiple atomic densities. The surface area of the molecule is obtained by differentiation of the molecular volume with respect to atomic radii. The many‐body nature of the model makes a port to GPU devices challenging. To our knowledge, this is the first reported full implementation of this model on GPU hardware. To accomplish this, we have used recursive strategies to construct the tree of overlaps and to accumulate volumes and their gradients on the tree data structures so as to minimize memory contention. The algorithm is used in the formulation of a surface area‐based non‐polar implicit solvent model implemented as an open source plug‐in (named GaussVol) for the popular OpenMM library for molecular mechanics modeling. GaussVol is 50 to 100 times faster than our best optimized implementation for the CPUs, achieving speeds in excess of 100 ns/day with 1 fs time‐step for protein‐sized systems on commodity GPUs. © 2017 Wiley Periodicals, Inc.     

Selective oxidation of styrene on an oxygen-adsorbed Au(111): A density functional theory study

The reaction mechanism for the styrene selective oxidation on the oxygen preadsorbed Au(111) surface has been studied by the density functional theory calculation with the periodic slab model. The calculated results showed that the process of reaction includes two steps: forming the oxametallacycle intermediate (OMME) and then producing the products. It was found that the second step, from OMME to product is the rate-controlling step, which is similar to ethylene selective oxidation on Ag. Importantly, the present density-functional-theory calculation results suggested that the mechanism via the OMME (2) (i.e. the preadsorbed atomic oxygen bound to the CH2 group involved in C6H5--CH=CH2) to produce styrene epoxide is kinetically favored than that of OMME (1).     

Atomic properties of selected biomolecules: quantum topological atom types of hydrogen,oxygen, nitrogen and sulfur occurring in natural amino acids and their derivatives

Molecular electron densities are generated at B3LYP/6-311+G(2d,p)//HF/6-31G(d) level for 57 molecules, including one conformation of each naturally occurring amino acid and smaller derived molecules. The electron densities are partitioned into atomic fragments according to the approach of quantum chemical topology (QCT). A set of 547 unique topological atoms is obtained, containing 421 hydrogens, 63 oxygens, 57 nitrogens and 6 sulfurs. Each atom is described by seven properties: volume, kinetic energy, monopole, dipole, quadrupole, octupole and hexadecapole moment. Cluster analysis groups atoms into atom types based on their similarity expressed in the discrete 7D space of atomic properties. Using a separation criterion we distinguish seven hydrogen, six oxygen, two nitrogen and six sulfur atom types.     

Alkali Metal Complexes of the Dipeptides PheAla and AlaPhe: IRMPD Spectroscopy

Complexes of PheAla and AlaPhe with alkali metal ions Na⁺ and K⁺ are generated by electrospray ionization, isolated in the Fourier‐transform ion cyclotron resonance (FT–ICR) ion trapping mass spectrometer, and investigated by infrared multiple‐photon dissociation (IRMPD) using light from the FELIX free electron laser over the mid‐infrared range from 500 to 1900 cm^?1. Insight into structural features of the complexes is gained by comparing the obtained spectra with predicted spectra and relative free energies obtained from DFT calculations for candidate conformers. Combining spectroscopic and energetic results establishes that the metal ion is always chelated by the amide carbonyl oxygen, whilst the C‐terminal hydroxyl does not complex the metal ion and is in the endo conformation. It is also likely that the aromatic ring of Phe always chelates the metal ion in a cation‐π binding configuration. Along with the amide CO and ring chelation sites, a third Lewis‐basic group almost certainly chelates the metal ion, giving a threefold chelation geometry. This third site may be either the C‐terminal carbonyl oxygen, or the N‐terminal amino nitrogen. From the spectroscopic and computational evidence, a slight preference is given to the carbonyl group, in an RO_aO_t chelation pattern, but coordination by the amino group is almost equally likely (particularly for K⁺PheAla) in an RO_aN_t chelation pattern, and either of these conformations, or a mixture of them, would be consistent with the present evidence. (R represents the π ring site, O_a the amide oxygen, O_t the terminal carbonyl oxygen, and N_t the terminal nitrogen.) The spectroscopic findings are in better agreement with the MPW1PW91 DFT functional calculations of the thermochemistry compared with the B3LYP functional, which seems to underestimate the importance of the cation–π interaction.     

Systematic formulations for electronegativity and hardness and their atomic scales within density functional softness theory

A unified Mulliken valence with Parr ground‐state electronegativity picture is presented. It provides a useful analytical tool on which the absolute hardness as well ionization potential and electron affinity functionals are based. For all these chemical reactivity indices, systematic approximate density functionals are formulated within density functional softness theory and are applied to atomic systems. For the absolute hardness, a special relationship with the new electronegativity ansatz and a particular atomic trend paralleling the absolute electron affinity are established that should complement and augment the earlier finite‐difference energetic approach. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Investigation of the metal binding site in methionine aminopeptidase by density functional theory

All methionine aminopeptidases exhibit the same conserved metal binding site. The structure of this site with either Co²⁺ions or Zn²⁺ions was investigated using density functional theory. The calculations showed that the structure of the site was not influenced by the identity of the metal ions. This was the case for both of the systems studied; one based on the X-ray structure of the human methionine aminopeptidase type 2 (hMetAP-2) and the other based on the X-ray structure of the E. colimethionine aminopeptidase type 1 (eMetAP-1). Another important structural issue is the identity of the bridging oxygen, which is part of either a water molecule or a hydroxide ion. Within the site of hMetAP-2 the results strongly indicate that a hydroxide ion bridges the metal ions. By contrast, the nature of the oxygen bridging the metal ions within the metal binding site of eMetAP-1 cannot be determined based on the results here, due to the similar structural results obtained with a bridging water molecule and a bridging hydroxide ion.     

Time-dependent density functional theory Ehrenfest dynamics: collisions between atomic oxygen and graphite clusters

An ab initio direct Ehrenfest dynamics method with time-dependent density functional theory is introduced and applied to collisions of 5 eV oxygen atoms and ions with graphite clusters. Collisions at three different sites are simulated. Kinetic energy transfer from the atomic oxygen to graphite local vibrations is observed and electron-nuclear coupling resulting in electronic excitation within the graphite surface as well as alteration of the atomic charge is first reported in this paper. The three oxygen species studied, O(3P), O-(2P), and O+(4S), deposit different amounts of energy to the surface, with the highest degree of damage to the pi conjugation of the cluster produced by the atomic oxygen cation. Memory of the initial charge state is not lost as the atom approaches, in contrast to the usual assumption.     

Functional groups expressed as graphs extracted from the Laplacian of the electron density

The valence charge concentration shell, as determined by the Laplacian of the electron density, is used as a source of quantum topological graphs, called L‐graphs. A considerable number of such graphs are extracted from the ab initio wave functions of 31 molecules calculated at the B3LYP/6‐311+G(2d,p)//B3LYP/6‐311+G(2d,p) level, covering common functional groups in organic chemistry. We show how L‐graphs can be constructed from a largely transferable subgraph called atomic L‐graph. We investigate the topological stability of the L‐graphs as a function of the basis set. Reliable and consistent atomic L‐graphs are only obtained with basis sets of triple‐zeta quality or higher. The recurrence of invariant motifs or subgraphs in the L‐graphs enables the isolation of 16 atomic L‐graphs. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

The role of induced current density in Steroelectronic effects: Perlin effect

The normal and reverse Perlin effect is usually explained by the redistribution of electron density produced by hyperconjugative mechanisms, which increases the electron population within axial or equatorial proton in normal or reverse effect, respectively. Here an alternative explanation for the Perlin effect is presented on the basis of the topology of the induced current density, which directly determines the nuclear magnetic shielding. Current densities around the C? H bond critical point and intra‐atomic and interatomic contributions to the magnetic shielding explain the observed Perlin effect. The balance between intra‐atomic and interatomic contributions determines the difference in the total atomic shielding. Normal Perlin effect is dominated by intra‐atomic part, whereas reverse effect is dominated by interatomic contribution. © 2015 Wiley Periodicals, Inc.     

Theoretical study of atoms by the electronic kinetic energy density and stress tensor density

The electronic structure of atoms in the first, second, and third periods were analyzed using the electronic kinetic energy density and stress tensor density, which are local quantities motivated by quantum field theoretic consideration, specifically the rigged quantum electrodynamics. The zero surfaces of the electronic kinetic energy density, which are called as the electronic interfaces, of the atoms were computed. It was found that their sizes exhibited clear periodicity and were comparable to the conventional atomic and ionic radii. The electronic stress tensor density and its divergence, tension density, of the atoms, were also computed and how their electronic structures were characterized by them was discussed. © 2016 Wiley Periodicals, Inc.     

A density functional theory study of atomic oxygen and nitrogen adsorption over alpha-alumina (0001)

The interaction of atomic oxygen and nitrogen on the (0001) surface of corundum (alpha-alumina) is investigated from first-principles by means of periodic density functional calculations within the generalized gradient approximation. A large Al(2)O(3) slab model (18 layers relaxing 10) ended with the most stable aluminium layer is used throughout the study. Geometries, adsorption energies and vibrational frequencies are calculated for several stationary points for two spin states at different sites over an 1 x 1 unit cell. Two stable adsorption minima over Al or in a bridge between Al and O surface atoms are found for oxygen and nitrogen, without activation energies. The oxygen adsorption (e.g., E(ad) = 2.30 eV) seems to be much more important than for nitrogen (e.g., E(ad) = 1.23 eV). Transition states for oxygen surface diffusion are characterized and present not very high-energy barriers. The computed geometries and adsorption energies are consistent with similar adsorption theoretical studies and related experimental data for O, N or alpha-alumina. The present results along with our previous results for beta-cristobalite do not support the assumption of an equal E(ad) for O and N over similar oxides, which is commonly used in some kinetic models to derive catalytic atomic recombination coefficients for atomic oxygen and nitrogen. The magnitude of O and N adsorption energies imply that Eley-Rideal and Langmuir-Hinshelwood reactions with these species will be exothermic, contrary to what happens for beta-cristobalite.     

Multiplet splitting of core level binding energies in paramagnetic species and the unpaired orbital spin density distribution

The relationship between the multiplet splitting in core electron binding energies of radicals and the unpaired orbital spin density distribution is developed and an explicit formula derived. The atomic intershell exchange interaction is shown to be important to determining magnitudes and trends in the multiplet splitting. The information obtained from an electron spin resonance spectroscopy experiment through the isotropic electron-nuclear hyperfine interaction and an X-ray photoelectron spectroscopy experiment is shown to be complementary.