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Elements of Bader’s theory of atoms in molecules are combined with density-functional theory to provide an electron-preceding perspective on the deformation of materials. From this perspective, a network of atoms is changed by moving the bonds that connect them; the nuclei then follow. The electronic stress tensor is the key to understanding this process. Eigenvectors of the electronic stress tensor at critical points of the electron density provide insight into the “normal electronic modes” that accompany structural dynamics and rearrangements. Eigenvectors of the second-derivative matrix of the electron density emerge as effective approximations to the eigenvectors of the stress tensor; this makes it possible to apply our results to experimentally and computationally determined electron densities. To demonstrate the usefulness of our analysis, we show that (a) the low-frequency modes of ice Ic can be predicted from the eigenvectors of the second-derivative matrix and (b) the eigenvectors of the second-derivative matrix are associated with the direction of structural change during the pressure-induced phase transition from ice XI to a ferroelectric ice VIII-like structure. We conclude that the eigenvectors of the second-derivative matrix of the electron density are the key ingredient for constructing a dynamical theory of atoms in molecules. [ABSTRACT FROM AUTHOR]

Examines the axiomatic basis for the concept of an atom within a molecule. Difficulty in providing a satisfactory mathematical basis; Definition of transferability; Description of Hirshfeld atom in a molecule.

The atoms in molecules associated with the Hirshfeld partitioning minimize the generalized Hellinger-Bhattacharya distance to the reference pro-atom densities. Moreover, the reference proatoms can be chosen by minimizing the distance between the pro-molecule density and the true molecular density. This provides an alternative to both the heuristic "stockholder" and the mathematical information-theoretic interpretations of the Hirshfeld partitioning. These results extend to any member of the family of f-divergences. [ABSTRACT FROM AUTHOR]

Discusses the alternative definition of exchange-correlation charge in density functional theory (DFT). Numerical evaluation of the exchange-correlation charge by using the Zhao-Morrison-Parr method; Radial distribution of exchange-correlation charge and atomic density for atom neon; Comparison of accurate exchange-correlation charge for atom argon.

Condensed-to-atom Fukui functions which reflect the atomic reactivity like the tendency susceptible to either nucleophilic or electrophilic attack demonstrate the bonding trend of an atom in a molecule. Accordingly, Fukui functions based concepts, that is, bonding reactivity descriptors which reveal the bonding properties of molecules in the reaction were put forward and then applied to pericyclic and cluster reactions to confirm their effectiveness and reliability. In terms of the results from the bonding descriptors, a covalent bond can readily be predicted between two atoms with large Fukui functions (i.e., one governs nucleophilic attack while the other one governs electrophilic attack, or both of them govern radical attacks) for pericyclic reactions. For SinOm clusters' reactions, the clusters with a low O atom ratio readily form a bond between two Si atoms with big values of their Fukui functions in which they respectively govern nucleophilic and electrophilic attacks or both govern radical attacks. Also, our results from bonding descriptors show that Si—Si bonds can be formed via the radical mechanism between two Si atoms, and formations of Si—O and O—O bonds are possible when the O content is high. These results conform with experimental findings and can help experimentalists design appropriate clusters to synthesize Si nanowires with high yields. The approach established in this work could be generalized and applied to study reactivity properties for other systems. [ABSTRACT FROM AUTHOR]

We develop a variational procedure for the iterative Hirshfeld (HI) partitioning scheme. The main practical advantage of having a variational framework is that it provides a formal and straightforward approach for imposing constraints (e.g., fixed charges on certain atoms or molecular fragments) when computing HI atoms and their properties. Unlike many other variants of the Hirshfeld partitioning scheme, HI charges do not arise naturally from the information-theoretic framework, but only as a reverse-engineered construction of the objective function. However, the procedure we use is quite general and could be applied to other problems as well. We also prove that there is always at least one solution to the HI equations, but we could not prove that its self-consistent equations would always converge for any given initial pro-atom charges. Our numerical assessment of the constrained iterative Hirshfeld method shows that it satisfies many desirable traits of atoms in molecules and has the potential to surpass existing approaches for adding constraints when computing atomic properties. [ABSTRACT FROM AUTHOR]

A new numerical integration procedure for exchange-correlation energies and potentials is proposed and “proof of principle” results are presented. The numerical integration grids are built from sparse-tensor product grids (constructed according to Smolyak’s prescription [Dokl. Akad. Nauk. 4, 240 (1963)] ) on the unit cube. The grid on the unit cube is then transformed to a grid over real space with respect to a weight function, which we choose to be the promolecular density. This produces a “whole molecule” grid, in contrast to conventional integration methods in density-functional theory, which use atom-in-molecule grids. The integration scheme was implemented in a modified version of the DEMON2K density-functional theory program, where it is used to evaluate integrals of the exchange-correlation energy density and the exchange-correlation potential. Ground-state energies and molecular geometries are accurately computed. The biggest advantages of the grid are its flexibility (it is easy to change the number and distribution of grid points) and its whole molecule nature. The latter feature is potentially helpful for basis-set-free computational algorithms. [ABSTRACT FROM AUTHOR]

The computational approach to the Hirshfeld [Theor. Chim. Acta 44, 129 (1977)] atom in a molecule is critically investigated, and several difficulties are highlighted. It is shown that these difficulties are mitigated by an alternative, iterative version, of the Hirshfeld partitioning procedure. The iterative scheme ensures that the Hirshfeld definition represents a mathematically proper information entropy, allows the Hirshfeld approach to be used for charged molecules, eliminates arbitrariness in the choice of the promolecule, and increases the magnitudes of the charges. The resulting “Hirshfeld-I charges” correlate well with electrostatic potential derived atomic charges. [ABSTRACT FROM AUTHOR]

A double-index atomic partitioning of the molecular first-order density matrix is proposed. Contributions diagonal in the atomic indices correspond to atomic density matrices, whereas off-diagonal contributions carry information about the bonds. The resulting matrices have good localization properties, in contrast to single-index atomic partitioning schemes of the molecular density matrix. It is shown that the electron density assigned to individual atoms, when derived from the density matrix partitioning, can be made consistent with well-known partitions of the electron density over atom in the molecule basins, either with sharp or with fuzzy boundaries. The method is applied to a test set of about 50 molecules, representative for various types of chemical binding. A close correlation is observed between the trace of the bond matrices and the shared electron density index. [ABSTRACT FROM AUTHOR]