Measuring electron sharing between atoms in first-principle simulations

Calculations of large scale electronic structure within periodic boundary conditions, mostly based on solid state physics, allow the modeling of atomic forces and molecular dynamics for atomic assemblies of 100–1000 atoms, thus providing complementary information in material and macromolecular sciences. Nevertheless, these methods lack connections with the chemistry of simple molecules as isolated entities. In order to contribute to establish a conceptual connection between solid state physics and chemistry, the calculation of the extent of electron sharing between atoms, also known as delocalization index, is performed on simple molecules and on complexes with transition metal atoms, using density functional calculations where the Kohn–Sham molecular orbitals are represented in terms of plane waves and in periodic boundary conditions. These applications show that the useful measure of electron sharing between atomic pairs can be recovered from density functional calculations using the same set-up applied to large atomic assemblies in condensed phases, with no projections of molecular orbitals onto atomic orbitals.     

Construction of basis sets of hybrid atomic orbitals for describing the nonequivalent bonds of an atom with three neighboring atoms (sp 2 andsp 3 hybridization)

The paper describes methods for obtaining basis sets of sp² and sp³ hybrid atomic orbitals to describe nonequivalent chemical bonds in organic molecules with heteroatoms. Being affine, these basis sets present an alternative to the conventional basis sets of Cartesian atomic orbitals. Unlike the latter, the hybrid atomic orbitals are invariant to spatial rotations of molecules, thus providing the rotational invariance of the results of any semiempirical quantum chemical calculations. The construction of the basis sets of hybrid functions for atoms surrounded with three neighboring atoms (planar and nonplanar configurations) is considered in detail. V. I. Vernadskii Institute of Geochemistry and Analytical Chemistry, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 36. No. 6, pp. 963–968, November–December, 1995. Translated by I. Izvekova     

Efficient algorithm for quantitative assessment of similarities among atoms in molecules

A new algorithm for quantitative assessment of similarity between two atoms in molecules is presented. Both the atomic similarity index and its derivatives with respect to the three Euler angles that describe the mutual orientation of the atoms under comparison are computed efficiently by taking advantage of the recently developed analytical representations for atomic zero-flux surfaces. The use of such representations makes it possible to substantially enhance the accuracy of the computed similarity indices without increasing the cost of their evaluation. Numerical tests involving oxygen atoms in several carbonyl compounds demonstrate the ability of the new algorithm to discern small changes in atomic similarity that are brought about by second-neighbor effects. Comparisons among hydrogen atoms in the acrolein molecule reveal the usefulness of the similarity index in detection and quantification of the effects of steric interactions on atomic shapes. © 1996 by John Wiley & Sons, Inc.     

A quantum‐chemical study of phosphor impurity in BaTiO3 crystal

Structural and electronic effects produced by a P impurity in the cubic and tetragonal BaTiO₃ lattices are investigated using a simple quantum chemical computer code based on the Hartree–Fock methodology. The obtained atomic displacements due to the defect present in otherwise pure crystal are mainly toward the impurity atom, thus reducing the interatomic distances within the defective region. It is also found that the phosphor produces some redistribution of electron density from the defect‐neighboring atoms toward the chemical bonds thus diminishing the charges on atoms. We also observe a local energy level in the band‐gap of material being composed mainly of P 3s atomic orbital. The level finds itself close to the top of the upper valence band, in no case contributing into the n‐type conductivity in BaTiO₃. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

On the equivalence of conformational and enantiomeric changes of atomic configuration for vibrational circular dichroism signs

We study systematically the vibrational circular dichroism (VCD) spectra of the conformers of a simple chiral molecule, with one chiral carbon and an "achiral" alkyl substituent of varying length. The vibrational modes can be divided into a group involving the chiral center and its direct neighbors and the modes of the achiral substituent. Conformational changes that consist of rotations around the bond from the next-nearest neighbor to the following carbon, and bond rotations further in the chain, do not affect the modes around the chiral center. However, conformational changes within the chiral fragment have dramatic effects, often reversing the sign of the rotational strength. The equivalence of the effect of enantiomeric change of the atomic configuration and conformational change on the VCD sign (rotational strength) is studied. It is explained as an effect of atomic characteristics, such as the nuclear amplitudes in some vibrational modes as well as the atomic polar and axial tensors, being to a high degree determined by the local topology of the atomic configuration. They reflect the local physics of the electron motions that generate the chemical bonds rather than the overall shape of the molecule.     

MD Simulation of Effect of Crystal Orientation and Cutting Direction on Nanometric Cutting Using AFM Pin Tool

"Three-dimensional molecular dynamics simulations of nanometric cutting monocrystalline copper using atomic force microscopy pin tool are conducted to investigate the effect of crystal orientation and corresponding cutting direction on the deformation characteristics. EAM potential and Morse potential are utilized respectively to compute the interactions between workpiece atoms, interactions between workpiece atoms and tool atoms. The results reveal that the nanometric cutting processes are significantly affected by crystal orientation and cutting direction. Along the 110 cutting direction, better quality of chip pattern and smaller workpiece material deformation region can be obtained than along the 100 cutting direction. Cutting the workpiece material (110) crystal orientation, samaller chip volume and smaller subsurface deformed region can be obtained than cutting the workpiece material (100) crystal orientation. The variations of workpiece atoms potential energy in different cutting processes are investigated."     

Quantum similarity measures under atomic shell approximation: First order density fitting using elementary Jacobi rotations

The elementary Jacobi rotations technique is proposed as a useful tool to obtain fitted electronic density functions expressed as linear combinations of atomic spherical shells, with the additional constraint that all coefficients are kept positive. Moreover, a Newton algorithm has been implemented to optimize atomic shell exponents, minimizing the quadratic error integral function between ab initio and fitted electronic density functions. Although the procedure is completely general, as an application example both techniques have been used to compute a 1S-type Gaussian basis for atoms H through Kr, fitted from a 3-21G basis set. Subsequently, molecular electronic densities are modeled in a promolecular approximation, as a simple sum of parameterized atomic contributions. This simple molecular approximation has been employed to show, in practice, its usefulness to some computational examples in the field of molecular quantum similarity measures. © 1997 John Wiley & Sons, Inc. J Comput Chem 18 : 2023–2039, 1997     

Atomic Ensemble Effects in Electrocatalysis: The Site‐Knockout Strategy

During an electrocatalytic reaction bonds are broken and formed, and this requires that the reactants, the intermediates formed at the elementary reaction steps, and the products interact with a given number of surface atoms of the catalyst. Modifying the number of groups with an adequate number of surface atoms in a suitable geometric arrangement for a determined reaction step to proceed may affect the activity and/or selectivity of the catalyst. Although separating purely geometric atomic ensemble effects from electronic effects is not straightforward, the insights extracted from a detailed investigation of atomic ensemble effects can have a profound impact in the determination of electrocatalytic reaction mechanisms and in the design of more active and more selective electrocatalysts. This Minireview illustrates, using cyanide‐modified Pt(111) electrodes as an archetype, how eliminating only one kind of site from the surface (the site‐knockout strategy) by means of a regular array of inert adsorbates can be used to successfully study atomic ensemble effects in electrocatalysis. The possible consequences for the design of more efficient and more selective electrocatalysts are also commented on.     

Molecular Dynamics Simulation of Sub‐Transition for Polyethersulfone

Molecular dynamics (MD) simulations of a polyethersulfone (PES) chain are carried out in the amorphous state by using the Dreiding 2.21 force field at four temperatures. Two types of molecular motion, i.e. rotations of phenylene rings and torsions of large segments containing two oxygen atoms, two sulfur atoms, and five phenylene rings on the backbone, are simulated. The modeling results show that the successive phenylene rings should be in‐phase cooperative rotations, whereas the successive large segments should be out‐of‐phase cooperative torsions. By calculating the diffusion coefficient for the phenylene ring rotations, it is found that this rotation contributes to the β‐transition of PES.     

Approaches to charge calculations in molecular mechanics

Alternative methods of estimating atomic charges in haloalkanes are presented, derived from quantum mechanical and classical treatments. A scheme based on a breakdown of the transmission of charge by polar atoms into one-bond, two-bond, and three-bond additive contributions is given, in which the one-bond effect is proportional to the difference in the electronegativities of the bonded atoms, and the two- and three-bond effects functions of the atomic electronegativity and polarizability. Suitable developments of the basic scheme, including an iterative self-consistent process, give calculated dipole moments for a variety of haloalkanes in good agreement with the observed values. The atomic charges obtained by this scheme are compared with other estimates of these charges. They are similar to those derived from a simple LCAO –MO scheme but differ from those obtained by population analysis of more refined quantum mechanical calculations.     

Comparison of time-dependent density-functional theory and coupled cluster theory for the calculation of the optical rotations of chiral molecules

A comparison of the abilities of time-dependent density-functional theory (TDDFT) and coupled cluster (CC) theory to reproduce experimental sodium D-line specific rotations for 13 conformationally rigid organic molecules is reported. The test set includes alkanes, alkenes, and ketones with known absolute configurations. TDDFT calculations make use of gauge-including atomic orbitals and give origin-independent specific rotations. CC rotations are computed using both the origin-independent dipole-velocity and origin-dependent dipole-length representations. The mean absolute deviations of calculated and experimental rotations are of comparable magnitudes for all three methods. The origin-independent DFT and CC methods give the same sign of [alpha]D for every molecule except norbornanone. For every large-rotation ketone and alkene for which DFT and CC yield the incorrect sign as compared to liquid-phase experimental data, the corresponding optical rotatory dispersion (ORD) curve is bisignate, suggesting that the two models cannot reliably reproduce the relative excitation energies and antagonistic rotational strengths of multiple competing electronic states that contribute to the total long-wavelength rotation. Several potential sources of error in the theoretical treatments are considered, including basis set incompleteness, vibrational and temperature effects, electron correlation, and solvent effects.     

Atomic absorption with ultracold atoms

Recent advances in laser-atom cooling techniques and diode-laser technology now allow one to conduct an idealised atomic absorption experiment comprising a sample of ultracold, quasi-stationary absorbing atoms and a source of near-monochromatic resonant light. Under such conditions, the atomic absorption coefficient at line centre is independent of the oscillator strength of the atomic resonance line. This offers the prospect of ‘oscillator-strength-free’ atomic absorption spectroscopy in which the absorption signal is equally large for both strong and weak (closed) transitions of the same wavelength and in which absolute atomic absorption could be performed without knowledge of the oscillator strength. Moreover, the resolution and sensitivity for a given atom density are greatly enhanced, typically by approximately three orders of magnitude (and even more for weak transitions), compared with conventional flame or graphite-furnace atomic absorption. We describe an atomic absorption experiment based on samples of ultracold, laser-cooled caesium atoms and a narrow-bandwidth diode laser source that approximates the idealised conditions for oscillator-strength-free atomic absorption. The absorption measurements are used to determine the number density and temperature (approx. 6 μK) of the sample of ultracold atoms. Some of the technical obstacles that would have to be overcome before samples of ultracold atoms and diode laser sources could be used in analytical atomic absorption spectroscopy are discussed.     

Second-order atomic Fukui indices from the electron-pair density in the framework of the atoms in molecules theory

Atomic Fukui indices, which are obtained from the electron density, have been previously shown to be useful in predicting which atoms in a molecule are most likely to suffer nucleophilic, electrophilic, or radicalary attacks. Here, we present a second-order generalization of these indices based on the electron pair density. We show how second-order atomic Fukui indices can be used to analyze the effects of electron loss or gain in several molecules from an electron pair point of view. Further, these indices also highlight which atoms or pairs of atoms are more likely to suffer nucleophilic, electrophilic, or radical attacks. In conclusion, second-order indices can complement first-order ones by affording relevant information on molecular reactivity from an electron pair perspective.     

XRD Analysis on the Fluorescence Material of Sm Doped Si-Ca-Mg System

Fluorescence material of Sm doped Si-Ca-Mg system was synthesized by using the method of solid phase reaction at high temperature. The phase composition and crystal structure of this material were analyzed with XRD method for its composition and the existence form of Sm atom. We aimed to exactly determine the phase composition of this fluorescence material and the doping position and environment of rare-earth Sm atom in the system because these factors have significant effects on the properties. The analytical results show that the Sm atoms dope in Ca2O26Si6Sm8 lattice in the form of atomic site-occupation in three different space positions with different occupancy rates. Therefore, based on the XRD analytical results, the fluorescence material of Sm doped Si-Ca-Mg system with high performance can be synthesized.     

Covalent bond orders and atomic anisotropies from iterated stockholder atoms

Iterated stockholder atoms are produced by dividing molecular electron densities into sums of overlapping, near-spherical atomic densities. It is shown that there exists a good correlation between the overlap of the densities of two atoms and the order of the covalent bond between the atoms (as given by simple valence rules). Furthermore, iterated stockholder atoms minimise a functional of the charge density, and this functional can be expressed as a sum of atomic contributions, which are related to the deviation of the atomic densities from spherical symmetry. Since iterated stockholder atoms can be obtained uniquely from the electron density, this work gives an orbital-free method for predicting bond orders and atomic anisotropies from experimental or theoretical charge density data.     

From Electronegativity towards Reactivity—Searching for a Measure of Atomic Reactivity

Pauling introduced the concept of electronegativity of an atom which has played an important role in understanding the polarity and ionic character of bonds between atoms. We set out to define a related concept of atomic reactivity in such a way that it can be quantified and used to predict the stability of covalent bonds in molecules. Guided by the early definition of electronegativity by Mulliken in terms of first ionization energies and Pauling in terms of bond energies, we propose corresponding definitions of atomic reactivity. The main goal of clearly distinguishing the inert gas atoms as nonreactive is fulfilled by three different proposed measures of atomic reactivity. The measure likely to be found most useful is based on the bond energies in atomic hydrides, which are related to atomic reactivities by a geometric average. The origin of the atomic reactivity is found in the symmetry of the atomic environment and related conservation laws which are also the origin of the shell structure of atoms and the periodic table. The reactive atoms are characterized by degenerate or nearly degenerate (several states of the same or nearly the same energy) ground states, while the inert atoms have nondegenerate ground states and no near-degeneracies. We show how to extend the use of the Aufbau model of atomic structure to qualitatively describe atomic reactivity in terms of ground state degeneracy. The symmetry and related conservation laws of atomic electron structures produce a strain (energy increase) in the structure, which we estimate by use of the Thomas-Fermi form of DFT implemented approximately with and without the symmetry and conservation constraints. This simplified and approximate analysis indicates that the total strain energy of an atom correlates strongly with the corresponding atomic reactivity measures but antibonding mechanisms prevent full conversion of strain relaxation to bonding.     

Laser-excited fluorescence of diatomic lead in a glow discharge source

Glow discharge sources provide simple and convenient means for laser-excited atomic spectroscopic studies of atoms sputtered from the cathode material. Presence of molecular species was observed in the course of investigation on this source as an atom cell for the laser-excited atomic fluorescence spectroscopic studies of lead. Spectral studies revealed characteristic band spectra, indicating the presence of molecular species in the discharge. The spectra were identified as belonging to the lead dimer species (diatomic lead molecule). It is, therefore, essential to examine the presence and possibility of interferences from molecular species while using glow discharge sources as atomization cells in atomic spectroscopic applications.     

Structural and Chemical Analysis of Materials with High Spatial Resolution

 An understanding of the correlation between microstructures and properties of materials require the characterization of the material on many different length scales. Often the properties depend primarily on the atomistics of defects, such as dislocations and interfaces. The different techniques of transmission electron microscopy allow the characterization of the structure and of the chemical composition of materials with high spatial resolution to the atomic level: high resolution transmission electron microscopy allows the determination of the position of the columns of atoms (ions) with high accuracy. The accuracy which can be achieved in these measurements depends not only on the instrumentation but also on the quality of the transmitted specimen and on the scattering power of the atoms (ions) present in the analyzed column. The chemical composition can be revealed from investigations by analytical microscopy which includes energy dispersive X-ray spectroscopy, mainly quantitatively applied for heavy elements, and electron energy-loss spectroscopy. Furthermore, the energy-loss near-edge structure of EELS data results in information on the local band structure of unoccupied states of the excited atoms and, therefore, on bonding. A quantitative evaluation of convergent beam electron diffraction results in information on the electron charge density distribution of the bulk (defect-free) material. The different techniques are described and applied to different problems in materials science. It will be shown that nearly atomic resolution can be achieved in high resolution electron microscopy and in analytical electron microscopy. Recent developments in electron microscopy instrumentation will result in atomic resolution in the foreseeable future.