Atoms-in-molecules theory

Cioslowski et al. used fragment similarity indices to compute the degree of similarity between atoms of the same element in different molecules, where the atoms were those derived from Bader s atoms in molecules theory [68,69]. They introduced a novel atomic similarity index for atom A in molecule X and atom B in molecule Y defined as [70]... 

M. Alcami, O. Mo and M. Yanez, Modeling Intrinsic Basicities The Use of Electrostatic Potentials and the Atoms-in-Molecules Theory, in Molecular Electrostatic Potentials Concepts and Applications (J. S. Murray and K. Sen, Eds.). Elsevier, Amsterdam 1996. Page 407. 

Thus pure MM (MM by itself) can t calculate UV spectra, the shapes and energies of molecular orbitals, and electron distribution and derivative properties of this, like atomic charges, dipole moments, and more arcane molecular features like bond paths (associated with atoms-in-molecules theory, AIM [1]). 

In this section, we discuss briefly two of the important developments of VB theory that have occurred over the past 10 or 15 years, namely the theory of separated pair functions, and the atoms-in-molecules theory. 

An analysis of the topological characteristics of electron density was performed for the studied Sarin-magnesium oxide complexes following Bader s Atoms in Molecules Theory (AIM).82 This analysis can be used to characterize hydrogen bonding solely from the charge density. There have been formulated several effects... 

Occasionally, he has approached an experimentalist with a computationally inspired problem. In working with Bader s Atoms-In-Molecules theory, Grimme was interested in whether bond paths really correlate with bonds. Grimme proposed to Erker to synthesize 4,5-dideuterated phenanthrene and we got spectroscopists to measure this ... 

J. Poater, X. Fradera, M. Sola, M. Duran, and S. Simon, On the electron-pair nature of the hydrogen bond in the framework of the atoms in molecules theory, Chem. Phys. Lett. 369, 248-255 (2003). 

Abstract The different C-H- X interactions are analyzed in this chapter. They are compared with the other types of hydrogen bonds, especially O-H- O ones. Theoretical tools are presented, among them the atoms in molecules theory (AIM). The H-bond motifs existing in crystals are presented. The evidences that C-H- -X interactions may be often classified as H-bonds are discussed. Etter s graph set analysis is also used to describe the structure of complex aggregates. 

One can ask another important question what is the current situation on investigations on H-bond Recently, different kinds of interactions are analyzed which may be classified as hydrogen bonds one can mention dihydrogen bonds or blue-shifting hydrogen bonds. There are new various theoretical methods. One of the most important tools often recently applied in studies on H-bonds is the atoms in molecules theory (AIM). It is worth mentioning the studies on the nature of H-bond interaction since the following questions arise... 

Bader s theory, based upon the topological analysis of the electron density, is now nsed to describe many different types of compounds [37-39]. The phosphonic acid derivatives [40,41] are among these, hi our group the Atoms in Molecules Theory has also been used in the field of intermolecular interactions [42,43] and transition metal complexes [44,45],... 

Avogadro (1811) further developed the (atomic) proportion theory into molecules (so anticipating a kind of atoms-in-molecules theory) by the following considerations. 

In fact, this feature of Laplacian was extensively employed by Bader s atoms in molecules theory at the purely electronic density level in order to quantum rationalize the previous Gillespie s geometrical VSEPR (Valence Shell Electron Pair Repulsion) description of the molecular bonds (Gillespie, 1972 Bader etal., 1988). 

The complexes of metal cations Fe, Co, NF+, and with guanine tetrads (G ) of C, and symmetry) were studied in [100]. The system contained two water molecules above and under the G -cation plane, with six-coordinated metal ion. G -Co and G -Cu being open shell species were treated using unrestricted method UB3LYP and 6-3 lG(d) basis set. BSSE (Basis Set Superposition Error) correction was evaluated according to the counterpoise method of Boys and Bemardi [101]. Bader s AIM (atoms in molecules) theory [102] was applied to determine a strong hydrogen bond [103]. The main conclusiorrs were as follows ... 

Poater J, Sola M, Bickelhaupt FM (2006) Hydrogen-hydrogen bonding in planar biphenyl, predicted by atoms-in-molecules theory, does not exist. Chem Eur J 12 2889... 

As Silvi et al. [131] stated ... the ELF topological analysis provides a mathematical bridge between quantum mechanics and chemistry which relies on the one hand on the statistical interpretation and on the other hand on the theory of dynamical system. This approach shares the dynamical system theory as common mathematical method with the Atoms in Molecules theory, the difference being the nature of the potential function and therefore the namre of the investigated properties. The QTAIM theory is rightly claimed to be rooted in physics rather than in chemistry and its partition scheme aims accordingly to define open quanmm systems within which the virial theorem holds. ... 

Following Halogen Bonds Formation with Bader s Atoms-in-Molecules Theory... 

Keywords Halogen bonds Bader s atoms-in-molecules theory Energy decomposition Interacting quantum atoms scheme Electrostatic interactions Electronic quantum exchange... 

Bader s atoms-in-molecules theory [69, 70] is based on the topology of the electron density p(r) and enables to partition the three-dimensional real space into non-overlapping domains called basins . To achieve such separation, one looks at the so-called gradient paths (GPs), which are the equivalent of field lines in classical electromagnetism. A GP is defined as a curve C such that the electron density gradient pif) (which can stem from theoretical calculations as well as from X-ray diffraction experiments) is tangent to C at every C point. In general (non-nuclear... 

Tognetti V, Joubeit L (2014) Density functional theory and Bader s atoms-in-molecules theory towards a vivid dialogue. Phys Chem Chem Phys 16 14539-14550... 

Of extreme elegance and rigor, the Atoms in Molecules theory explains in clear quantitative terms a wide range of facts about chemical bonding within molecules, and hardly needs further praise here. In some instances, however, like the above mentioned biphenyl and NaCl cases, it remains for many practicing chemists a sour mouthful to swallow. 

---